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Sample records for 1h chemical shifts

  1. (1)H chemical shift differences of Prelog-Djerassi lactone derivatives: DFT and NMR conformational studies.

    PubMed

    Aímola, Túlio J; Lima, Dimas J P; Dias, Luiz C; Tormena, Cláudio F; Ferreira, Marco A B

    2015-02-21

    This work reports an experimental and theoretical study of the conformational preferences of several Prelog-Djerassi lactone derivatives, to elucidate the (1)H NMR chemical shift differences in the lactonic core that are associated with the relative stereochemistry of these derivatives. The boat-like conformation of explains the anomalous (1)H chemical shift between H-5a and H-5b, in which the two methyl groups (C-8 and C-9) face H-5b, leading to its higher shielding effect.

  2. Structure determination of noncanonical RNA motifs guided by 1H NMR chemical shifts

    PubMed Central

    Sripakdeevong, Parin; Cevec, Mirko; Chang, Andrew T.; Erat, Michèle C.; Ziegeler, Melanie; Zhao, Qin; Fox, George E.; Gao, Xiaolian; Kennedy, Scott D.; Kierzek, Ryszard; Nikonowicz, Edward P.; Schwalbe, Harald; Sigel, Roland K. O.; Turner, Douglas H.; Das, Rhiju

    2014-01-01

    Structured non-coding RNAs underline fundamental cellular processes, but determining their 3D structures remains challenging. We demonstrate herein that integrating NMR 1H chemical shift data with Rosetta de novo modeling can consistently return high-resolution RNA structures. On a benchmark set of 23 noncanonical RNA motifs, including 11 blind targets, Chemical-Shift-ROSETTA for RNA (CS-ROSETTA-RNA) recovered the experimental structures with high accuracy (0.6 to 2.0 Å all-heavy-atom rmsd) in 18 cases. PMID:24584194

  3. 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

    2011-04-07

    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.

  4. Sequential acquisition of multi-dimensional heteronuclear chemical shift correlation spectra with 1H detection

    NASA Astrophysics Data System (ADS)

    Bellstedt, Peter; Ihle, Yvonne; Wiedemann, Christoph; Kirschstein, Anika; Herbst, Christian; Görlach, Matthias; Ramachandran, Ramadurai

    2014-03-01

    RF pulse schemes for the simultaneous acquisition of heteronuclear multi-dimensional chemical shift correlation spectra, such as {HA(CA)NH & HA(CACO)NH}, {HA(CA)NH & H(N)CAHA} and {H(N)CAHA & H(CC)NH}, that are commonly employed in the study of moderately-sized protein molecules, have been implemented using dual sequential 1H acquisitions in the direct dimension. Such an approach is not only beneficial in terms of the reduction of experimental time as compared to data collection via two separate experiments but also facilitates the unambiguous sequential linking of the backbone amino acid residues. The potential of sequential 1H data acquisition procedure in the study of RNA is also demonstrated here.

  5. Sequential acquisition of multi-dimensional heteronuclear chemical shift correlation spectra with 1H detection

    PubMed Central

    Bellstedt, Peter; Ihle, Yvonne; Wiedemann, Christoph; Kirschstein, Anika; Herbst, Christian; Görlach, Matthias; Ramachandran, Ramadurai

    2014-01-01

    RF pulse schemes for the simultaneous acquisition of heteronuclear multi-dimensional chemical shift correlation spectra, such as {HA(CA)NH & HA(CACO)NH}, {HA(CA)NH & H(N)CAHA} and {H(N)CAHA & H(CC)NH}, that are commonly employed in the study of moderately-sized protein molecules, have been implemented using dual sequential 1H acquisitions in the direct dimension. Such an approach is not only beneficial in terms of the reduction of experimental time as compared to data collection via two separate experiments but also facilitates the unambiguous sequential linking of the backbone amino acid residues. The potential of sequential 1H data acquisition procedure in the study of RNA is also demonstrated here. PMID:24671105

  6. 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

  7. 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).

  8. The influence of sulfur configuration in (1) H NMR chemical shifts of diasteromeric five-membered cyclic sulfites.

    PubMed

    Obregón-Mendoza, Marco A; Sánchez-Castellanos, Mariano; Cuevas, Gabriel; Gnecco, Dino; Cassani, Julia; Poveda-Jaramillo, Juan C; Reynolds, William F; Enríquez, Raúl G

    2017-03-01

    The effect of the stereochemistry of the sulfur atom on (1) H chemical shifts of the diasteromeric pair of cyclic sulfites of 4-[methoxy(4-nitrophenyl)methyl]-5-phenyl-1,3,2-dioxathiolan-2-oxide was investigated. The complete (1) H and (13) C NMR spectral assignment was achieved by the use of one-dimensional and two-dimensional NMR techniques in combination with X-ray data. A correlation of experimental data with theoretical calculations of chemical shift tensors using density functional theory and topological theory of atoms in molecules was made. Copyright © 2016 John Wiley & Sons, Ltd.

  9. Syntheses, structures, and 1H, 13C{1H} and 119Sn{1H} NMR chemical shifts of a family of trimethyltin alkoxide, amide, halide and cyclopentadienyl compounds

    DOE PAGES

    Lichtscheidl, Alejandro G.; Janicke, Michael T.; Scott, Brian L.; ...

    2015-08-21

    The synthesis and full characterization, including Nuclear Magnetic Resonance (NMR) data (1H, 13C{1H} and 119Sn{1H}), for a series of Me3SnX (X = O-2,6-tBu2C6H3 (1), (Me3Sn)N(2,6-iPr2C6H3) (3), NH-2,4,6-tBu3C6H2 (4), N(SiMe3)2 (5), NEt2, C5Me5 (6), Cl, Br, I, and SnMe3) compounds in benzene-d6, toluene-d8, dichloromethane-d2, chloroform-d1, acetonitrile-d3, and tetrahydrofuran-d8 are reported. The X-ray crystal structures of Me3Sn(O-2,6-tBu2C6H3) (1), Me3Sn(O-2,6-iPr2C6H3) (2), and (Me3Sn)(NH-2,4,6-tBu3C6H2) (4) are also presented. As a result, these compiled data complement existing literature data and ease the characterization of these compounds by routine NMR experiments.

  10. Dynamics-based selective 2D {sup 1}H/{sup 1}H chemical shift correlation spectroscopy under ultrafast MAS conditions

    SciTech Connect

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy

    2015-05-28

    Dynamics plays important roles in determining the physical, chemical, and functional properties of a variety of chemical and biological materials. However, a material (such as a polymer) generally has mobile and rigid regions in order to have high strength and toughness at the same time. Therefore, it is difficult to measure the role of mobile phase without being affected by the rigid components. Herein, we propose a highly sensitive solid-state NMR approach that utilizes a dipolar-coupling based filter (composed of 12 equally spaced 90° RF pulses) to selectively measure the correlation of {sup 1}H chemical shifts from the mobile regions of a material. It is interesting to find that the rotor-synchronized dipolar filter strength decreases with increasing inter-pulse delay between the 90° pulses, whereas the dipolar filter strength increases with increasing inter-pulse delay under static conditions. In this study, we also demonstrate the unique advantages of proton-detection under ultrafast magic-angle-spinning conditions to enhance the spectral resolution and sensitivity for studies on small molecules as well as multi-phase polymers. Our results further demonstrate the use of finite-pulse radio-frequency driven recoupling pulse sequence to efficiently recouple weak proton-proton dipolar couplings in the dynamic regions of a molecule and to facilitate the fast acquisition of {sup 1}H/{sup 1}H correlation spectrum compared to the traditional 2D NOESY (Nuclear Overhauser effect spectroscopy) experiment. We believe that the proposed approach is beneficial to study mobile components in multi-phase systems, such as block copolymers, polymer blends, nanocomposites, heterogeneous amyloid mixture of oligomers and fibers, and other materials.

  11. Regression formulas for density functional theory calculated 1H and 13C NMR chemical shifts in toluene-d8.

    PubMed

    Konstantinov, Ivan A; Broadbelt, Linda J

    2011-11-10

    This study aimed at investigating the performance of a series of basis sets, density functional theory (DFT) functionals, and the IEF-PCM solvation model in the accurate calculation of (1)H and (13)C NMR chemical shifts in toluene-d(8). We demonstrated that, on a test set of 37 organic species with various functional moieties, linear scaling significantly improved the calculated shifts and was necessary to obtain more accurate results. Inclusion of a solvation model produced larger deviations from the experimental data as compared to the gas-phase calculations. Moreover, we did not find any evidence that very large basis sets were necessary to reproduce the experimental NMR data. Ultimately, we recommend the use of the BMK functional. For the (1)H shifts the use of the 6-311G(d) basis set gave linearly scaled mean unsigned (MU) and root-mean-square (rms) errors of 0.15 ppm and 0.21 ppm, respectively. For the calculation of the (13)C chemical shifts the 6-31G(d) basis set produced MUE of 1.82 ppm and RMSE of 3.29 ppm.

  12. (1)H and (13)C NMR chemical shifts of methacrylate molecules associated with DMPC and/or DPPC liposomes.

    PubMed

    Fujisawa, Seiichiro; Ishihara, Mariko; Kadoma, Yoshinori

    2005-01-01

    In the light of recent developments, changes in (1)H and (13)C NMR chemical shifts of methacrylate molecule associated with DMPC (L-alpha dimyristoylphosphatidylcholine) or DPPC (L-alpha-dipalmitoylphosphatidylcholine) liposomes as a model for mimic native lipid bilayers were studied at 30, 37, and 52 degrees C. The chemical shifts of 3Ha, 3C, and 4C resonances in methacrylates (see Fig. 2) were greatly shifted higher field, suggesting the methacrylate molecule-lipid bilayer interaction. Comparison of the findings with methyl methacrylate (MMA), ethylene dimethacrylate (EDMA), and triethyleneglycol dimethacrylate (TEGDMA) revealed that the interaction of dimethacrylates (EDMA, TEGDMA) was greater than monomethacrylate, MMA. Their interaction with DMPC liposomes was also judged by a differential scanning calorimetry (DSC), indicating that the interaction was characterized by decreasing the enthalpy, entropy, and transition co-operativity. The evidence of the upfield NMR-shifts for methacrylate molecules was also judged by the descriptors such as the reactivity (HOMO-LUMO energy) and the electrostatic function (partial charges) between methacrylate molecules and DPPC, calculated by a PM 3 semiempirical MO method. The upfield NMR shifts were considerably well interpreted from the descriptors. NMR screening technique in methacrylates to phospholipid targets would be highly valuable in biomaterial developments. Figure 2 Changes in (1)H and (13)C NMR chemical shifts of methacrylate molecule associated with DMPC or DPPC liposomes. DMPC liposomes/MMA (1:1, molar ratio) and DMPC/TEGDMA (1:1) liposomes were measured at 30 degrees C. In DPPC liposome system, the rippled gel phase was measured at 30 degrees C, whereas the liquid crystalline phase for MMA and for both EDMA and TEGDMA were measured at 52 degrees C and 37 degrees C, respectively.

  13. Stereospecific assignment of 1H resonances through chemical shift calculation and their use in structure determination by NMR

    NASA Astrophysics Data System (ADS)

    Harvey, Timothy S.; van Gunsteren, Wilfred F.; Ikura, Mitsuhiko

    1995-04-01

    Understanding of the factors which influence proton chemical shifts in nuclear magnetic resonance (NMR) spectra of proteins has advanced steadily as the number of proteins, for which assignments in conjunction with high resolution structures have been obtained, has increased. Progress has been made in both the calculation of chemical shifts from given coordinates, both empirically for 1H (Williamson & Asakura J. Magn. Reson. (1991) 94, 557) and using ab initio approaches for calculation of 13C (De Dios et al. Science (1993) 260, 1491). Concomitantly Wishart et al. (J. Mol. Biol. (1992) 222, 311), using statistical methods have clarified the relationship between Hα chemical shift and regular secondary structure in proteins to a high degree of accuracy. We recently demonstrated the significant amount of structural information present in the Hα chemical shift through the use of chemical shift restrained molecular dynamics simulations (Harvey & van Gunsteren Techniques in Protein Chemistry IV (1993) 615, Academic Press). Here we apply a similar methodology to the stereospecific assignment of methylene and methyl proton resonances in proteins. Stereospecific assignment of such 1H resonances dramatically increases the degree of precision of ensembles of structures derived from NMR data. However, this is often a cumbersome process, requiring detailed analysis of large amounts of data. Furthermore, experimental considerations such as poor signal-to-noise ratios, spectral overlap and spin diffusion combine to make this process somewhat unreliable. We present calculations of the chemical shifts for the known structures of bovine pancreatic trypsin inhibitor (Mw 6.5 kDa) and the α-amylase inhibitor tendamistat (Mw 8 kDa), for which stereospecific assignments and high resolution structures from both NMR and crystallographic studies are available. The methods described are also applied to the ensemble of structures obtained for protein S (Mw 19 kDa) for both structure

  14. Robust algorithms for automated chemical shift calibration of 1D 1H NMR spectra of blood serum.

    PubMed

    Pearce, Jake T M; Athersuch, Toby J; Ebbels, Timothy M D; Lindon, John C; Nicholson, Jeremy K; Keun, Hector C

    2008-09-15

    In biofluid NMR spectroscopy, the frequency of each resonance is typically calibrated by addition of a reference compound such as 3-(trimethylsilyl)-propionic acid- d 4 (TSP) to the sample. However biofluids such as serum cannot be referenced to TSP, due to shifts resonance caused by binding to macromolecules in solution. In order to overcome this limitation we have developed algorithms, based on analysis of derivative spectra, to locate and calibrate (1)H NMR spectra to the alpha-glucose anomeric doublet. We successfully used these algorithms to calibrate 77 serum (1)H NMR spectra and demonstrate the greater reproducibility of the calculated chemical-shift corrections ( r = 0.97) than those generated by manual alignment ( r = 0.8-0.88). Hence we show that these algorithms provide robust and reproducible methods of calibrating (1)H NMR of serum, plasma, or any biofluid in which glucose is abundant. Precise automated calibration of complex biofluid NMR spectra is an important tool in large-scale metabonomic or metabolomic studies, where hundreds or even thousands of spectra may be analyzed in high-resolution by pattern recognition analysis.

  15. Water Solvent Effect on Theoretical Evaluation of (1)H NMR Chemical Shifts: o-Methyl-Inositol Isomer.

    PubMed

    Dos Santos, Hélio F; Chagas, Marcelo A; De Souza, Leonardo A; Rocha, Willian R; De Almeida, Mauro V; Anconi, Cleber P A; De Almeida, Wagner B

    2017-04-13

    In this paper, density functional theory calculations of nuclear magnetic resonance (NMR) chemical shifts for l-quebrachitol isomer, previously studied in our group, are reported with the aim of investigating in more detail the water solvent effect on the prediction of (1)H NMR spectra. In order to include explicit water molecules, 20 water-l-quebrachitol configurations obtained from Monte Carlo simulation were selected to perform geometry optimizations using the effective fragment potential method encompassing 60 water molecules around the solute. The solvated solute optimized geometries were then used in B3LYP/6-311+G(2d,p) NMR calculations with PCM-water. The inclusion of explicit solvent in the B3LYP NMR calculations resulted in large changes in the (1)H NMR profiles. We found a remarkable improvement in the agreement with experimental NMR profiles when the explicit hydrated l-quebrachitol structure is used in B3LYP (1)H NMR calculations, yielding a mean absolute error (MAE) of only 0.07 ppm, much lower than reported previously for the gas phase optimized structure (MAE = 0.11 ppm). In addition, a very improved match between theoretical and experimental (1)H NMR spectrum measured in D2O was achieved with the new hydrated optimized l-quebrachitol structure, showing that a fine-tuning of the theoretical NMR spectra can be accomplished once solvent effects are properly considered.

  16. 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.

  17. 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.

  18. High-Frequency (1)H NMR Chemical Shifts of Sn(II) and Pb(II) Hydrides Induced by Relativistic Effects: Quest for Pb(II) Hydrides.

    PubMed

    Vícha, Jan; Marek, Radek; Straka, Michal

    2016-10-17

    The role of relativistic effects on (1)H NMR chemical shifts of Sn(II) and Pb(II) hydrides is investigated by using fully relativistic DFT calculations. The stability of possible Pb(II) hydride isomers is studied together with their (1)H NMR chemical shifts, which are predicted in the high-frequency region, up to 90 ppm. These (1)H signals are dictated by sizable relativistic contributions due to spin-orbit coupling at the heavy atom and can be as large as 80 ppm for a hydrogen atom bound to Pb(II). Such high-frequency (1)H NMR chemical shifts of Pb(II) hydride resonances cannot be detected in the (1)H NMR spectra with standard experimental setup. Extended (1)H NMR spectral ranges are thus suggested for studies of Pb(II) compounds. Modulation of spin-orbit relativistic contribution to (1)H NMR chemical shift is found to be important also in the experimentally known Sn(II) hydrides. Because the (1)H NMR chemical shifts were found to be rather sensitive to the changes in the coordination sphere of the central metal in both Sn(II) and Pb(II) hydrides, their application for structural investigation is suggested.

  19. 1H, 13C and 15N chemical shift assignments of the thioredoxin from the obligate anaerobe Desulfovibrio vulgaris Hildenborough.

    PubMed

    Garcin, Edwige B; Bornet, Olivier; Pieulle, Laetitia; Guerlesquin, Françoise; Sebban-Kreuzer, Corinne

    2011-10-01

    Thioredoxins are ubiquitous key antioxidant enzymes which play an essential role in cell defense against oxidative stress. They maintain the redox homeostasis owing to the regulation of thiol-disulfide exchange. In the present paper, we report the full resonance assignments of (1)H, (13)C and (15)N atoms for the reduced and oxidized forms of Desulfovibrio vulgaris Hildenborough thioredoxin 1 (Trx1). 2D and 3D heteronuclear NMR experiments were performed using uniformly (15)N-, (13)C-labelled Trx1. Chemical shifts of 97% of the backbone and 90% of the side chain atoms were obtained for the oxidized and reduced form (BMRB deposits with accession number 17299 and 17300, respectively).

  20. A Simple and Fast Approach for Predicting 1H and 13C Chemical Shifts: Toward Chemical Shift-Guided Simulations of RNA

    PubMed Central

    2014-01-01

    We introduce a simple and fast approach for predicting RNA chemical shifts from interatomic distances that performs with an accuracy similar to existing predictors and enables the first chemical shift-restrained simulations of RNA to be carried out. Our analysis demonstrates that the applied restraints can effectively guide conformational sampling toward regions of space that are more consistent with chemical shifts than the initial coordinates used for the simulations. As such, our approach should be widely applicable in mapping the conformational landscape of RNAs via chemical shift-guided molecular dynamics simulations. The simplicity and demonstrated sensitivity to three-dimensional structure should also allow our method to be used in chemical shift-based RNA structure prediction, validation, and refinement. PMID:25255209

  1. Brain temperature and pH measured by (1)H chemical shift imaging of a thulium agent.

    PubMed

    Coman, Daniel; Trubel, Hubert K; Rycyna, Robert E; Hyder, Fahmeed

    2009-02-01

    Temperature and pH are two of the most important physiological parameters and are believed to be tightly regulated because they are intricately related to energy metabolism in living organisms. Temperature and/or pH data in mammalian brain are scarce, however, mainly because of lack of precise and non-invasive methods. At 11.7 T, we demonstrate that a thulium-based macrocyclic complex infused through the bloodstream can be used to obtain temperature and pH maps of rat brain in vivo by (1)H chemical shift imaging (CSI) of the sensor itself in conjunction with a multi-parametric model that depends on several proton resonances of the sensor. Accuracies of temperature and pH determination with the thulium sensor - which has a predominantly extracellular presence - depend on stable signals during the course of the CSI experiment as well as redundancy for temperature and pH sensitivities contained within the observed signals. The thulium-based method compared well with other methods for temperature ((1)H MRS of N-acetylaspartate and water; copper-constantan thermocouple wire) and pH ((31)P MRS of inorganic phosphate and phosphocreatine) assessment, as established by in vitro and in vivo studies. In vitro studies in phantoms with two compartments of different pH value observed under different ambient temperature conditions generated precise temperature and pH distribution maps. In vivo studies in alpha-chloralose-anesthetized and renal-ligated rats revealed temperature (33-34 degrees C) and pH (7.3-7.4) distributions in the cerebral cortex that are in agreement with observations by other methods. These results show that the thulium sensor can be used to measure temperature and pH distributions in rat brain in vivo simultaneously and accurately using Biosensor Imaging of Redundant Deviation in Shifts (BIRDS).

  2. Elucidation of the resting state of a rhodium NNN-pincer hydrogenation catalyst that features a remarkably upfield hydride (1)H NMR chemical shift.

    PubMed

    Hänninen, Mikko M; Zamora, Matthew T; MacNeil, Connor S; Knott, Jackson P; Hayes, Paul G

    2016-01-11

    Rhodium(I) alkene complexes of an NNN-pincer ligand catalyze the hydrogenation of alkenes, including ethylene. The terminal or resting state of the catalyst, which exhibits an unprecedentedly upfield Rh-hydride (1)H NMR chemical shift, has been isolated and a synthetic cycle for regenerating the catalytically active species has been established.

  3. 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.

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

    PubMed

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

    2016-04-14

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

  5. 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.

  6. 1H and 13C NMR chemical shift assignments of spiro-cycloalkylidenehomo- and methanofullerenes by the DFT-GIAO method.

    PubMed

    Khalilov, L M; Tulyabaev, A R; Yanybin, V M; Tuktarov, A R

    2011-06-01

    The (1)H and (13)C NMR chemical shifts of spiro-cycloalkylidene[60]fullerenes were assigned using experimental NMR data and the Density Functional Theory (DFT)-Gauge Independence Of Atomic Orbitals method (GAIO) calculation method in the Perdew Burke Ernzerhof (PBE)/3z approach. The calculated values of the (13)C NMR chemical shifts adequately reproduce the experimental values at this quantum chemistry approach. Similar assignments will be helpful for (13)C NMR spectral analysis of homo- and methano[60]fullerene derivatives for structure elucidation and to determine the influence of fullerene frames on substituents and the influence of substituents on fullerene cores.

  7. 1H NMR spectra of alcohols and diols in chloroform: DFT/GIAO calculation of chemical shifts.

    PubMed

    Lomas, John S

    2014-12-01

    Proton nuclear magnetic resonance (NMR) shifts of aliphatic alcohols in chloroform have been computed on the basis of density functional theory, the solvent being included by the integral-equation-formalism polarisable continuum model of Gaussian 09. Relative energies of all conformers are calculated at the Perdew, Burke and Ernzerhof (PBE)0/6-311+G(d,p) level, and NMR shifts by the gauge-including atomic orbital method with the PBE0/6-311+G(d,p) geometry and the cc-pVTZ basis set. The 208 computed CH proton NMR shifts for 34 alcohols correlate very well with the experimental values, with a gradient of 1.00 ± 0.01 and intercept close to zero; the overall root mean square difference (RMSD) is 0.08 ppm. Shifts for CH protons of diols in chloroform are well correlated with the theoretical values for (isotropic) benzene, with similar gradient and intercept (1.02 ± 0.01, -0.13 ppm), but the overall RMSD is slightly higher, 0.12 ppm. This approach generally gives slightly better results than the CHARGE model of Abraham et al. The shifts of unsaturated alcohols in benzene have been re-examined with Gaussian 09, but the overall fit for CH protons is not improved, and OH proton shifts are worse. Shifts of vinyl protons in alkenols are systematically overestimated, and the correlation of computed shifts against the experimental data for unsaturated alcohols follows a quadratic equation. Splitting the 20 compounds studied into two sets, and applying empirical scaling based on the quadratic for the first set to the second set, gives an RMSD of 0.10 ppm. A multi-standard approach gives a similar result.

  8. (1)H NMR spectra of alcohols in hydrogen bonding solvents: DFT/GIAO calculations of chemical shifts.

    PubMed

    Lomas, John S

    2016-01-01

    Proton nuclear magnetic resonance (NMR) shifts of aliphatic alcohols in hydrogen bonding solvents have been computed on the basis of density functional theory by applying the gauge-including atomic orbital method to geometry-optimized alcohol/solvent complexes. The OH proton shifts and hydrogen bond distances for methanol or ethanol complexed with pyridine depend very much on the functional employed and very little on the basis set, provided it is sufficiently large to give the correct quasi-linear hydrogen bond geometry. The CH proton shifts are insensitive to both the functional and the basis set. NMR shifts for all protons in several alcohol/pyridine complexes are calculated at the Perdew, Burke and Ernzerhof PBE0/cc-pVTZ//PBE0/6-311 + G(d,p) level in the gas phase. The results correlate with the shifts for the pyridine-complexed alcohols, determined by analysing data from the NMR titration of alcohols against pyridine. More pragmatically, computed shifts for a wider range of alcohols correlate with experimental shifts in neat pyridine. Shifts for alcohols in dimethylsulfoxide, based on the corresponding complexes in the gas phase, correlate well with the experimental values, but the overall root mean square difference is high (0.23 ppm), shifts for the OH, CHOH and other CH protons being systematically overestimated, by averages of 0.42, 0.21 and 0.06 ppm, respectively. If the computed shifts are corrected accordingly, a very good correlation is obtained with a gradient of 1.00 ± 0.01, an intercept of 0.00 ± 0.02 ppm and a root mean square difference of 0.09 ppm. This is a modest improvement on the result of applying the CHARGE programme to a slightly different set of alcohols. Some alcohol complexes with acetone and acetonitrile were investigated both in the gas phase and in a continuum of the relevant solvent.

  9. A Relativistic Quantum-Chemical Analysis of the trans Influence on (1)H NMR Hydride Shifts in Square-Planar Platinum(II) Complexes.

    PubMed

    Greif, Anja H; Hrobárik, Peter; Hrobáriková, Veronika; Arbuznikov, Alexei V; Autschbach, Jochen; Kaupp, Martin

    2015-08-03

    Empirical correlations between characteristic (1)H NMR shifts in Pt(II) hydrides with trans ligand influence series, Pt-H distances, and (195)Pt shifts are analyzed at various levels of including relativistic effects into density-functional calculations. A close examination of the trans ligand effects on hydride NMR shifts is shown to be dominated by spin-orbit shielding σ(SO). A rather complete understanding of the trends has been obtained by detailed molecular orbital (MO)-by-MO and localized MO analyses of the paramagnetic and spin-orbit (SO) contributions to the chemical shifts, noting that it is the perpendicular shift-tensor components that determine the trend of the (1)H hydride shifts. In contrast to previous assumptions, the change of the Pt-H distance in given complexes does not allow correlations between hydride shifts and metal-hydrogen bond length to be understood. Instead, variations in the polarization of metal 5d orbitals by the trans ligand affects the SO (and partly paramagnetic) shift contributions, as well as the Pt-H distances and the covalency of the metal-hydrogen bond (quantified, e.g., by natural atomic charges and delocalization indices from quantum theory atoms-in-molecules), resulting in a reasonable correlation of these structural/electronic quantities with hydride σ(SO) shieldings. Our analysis also shows that specific σ(p)- and σ(SO)-active MOs are not equally important across the entire series. This explains some outliers in the correlation for limited ranges of trans-influence ligands. Additionally, SO effects from heavy-halide ligands may further complicate trends, indicating some limitations of the simple one-parameter correlations. Strikingly, σ-donating/π-accepting ligands with a very strong trans influence are shown to invert the sign of the usually shielding σ(SO) contribution to the (1)H shifts, by a substantial reduction of the metal 5d orbital involvement in Pt-H bonding, and by involvement of metal 6p-type orbitals

  10. Determination of NH proton chemical shift anisotropy with 14N-1H heteronuclear decoupling using ultrafast magic angle spinning solid-state NMR

    NASA Astrophysics Data System (ADS)

    Pandey, Manoj Kumar; Nishiyama, Yusuke

    2015-12-01

    The extraction of chemical shift anisotropy (CSA) tensors of protons either directly bonded to 14N nuclei (I = 1) or lying in their vicinity using rotor-synchronous recoupling pulse sequence is always fraught with difficulty due to simultaneous recoupling of 14N-1H heteronuclear dipolar couplings and the lack of methods to efficiently decouple these interactions. This difficulty mainly arises from the presence of large 14N quadrupolar interactions in comparison to the rf field that can practically be achieved. In the present work it is demonstrated that the application of on-resonance 14N-1H decoupling with rf field strength ∼30 times weaker than the 14N quadrupolar coupling during 1H CSA recoupling under ultrafast MAS (90 kHz) results in CSA lineshapes that are free from any distortions from recoupled 14N-1H interactions. With the use of extensive numerical simulations we have shown the applicability of our proposed method on a naturally abundant L-Histidine HCl·H2O sample.

  11. 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.

  12. Ethanol-induced fatty liver in the rat examined by in vivo 1H chemical shift selective magnetic resonance imaging and localized spectroscopic methods.

    PubMed

    Ling, M; Brauer, M

    1992-01-01

    In vivo 1H magnetic resonance imaging (MRI), chemical shift selective imaging (CSI), and localized (VOSY) 1H magnetic resonance spectroscopy (MRS) were used to study fatty infiltration in the livers of rats chronically fed an ethanol-containing all-liquid DeCarli-Lieber diet. Conventional total proton MRI showed a somewhat hyperintense liver for ethanol-fed rats, compared with pair-fed controls. CSI showed a dramatic increase in the fat signal intensity for ethanol-treated rats that was fairly homogeneous throughout the liver. However, CSI also showed a substantial decrease in the water signal intensity for the ethanol-treated rats compared to pair-fed control rats. 1H VOSY MR spectra also showed a 5.5-fold increase in the methylene resonance (1.3 ppm) of fat and a 50-70% decrease in the water resonance (4.8 ppm). Relative in vivo proton T1 and T2 relaxation times for the water resonance separate from the fat resonance, determined from modified VOSY experiments, were found to tend to increase and decrease, respectively, for ethanol-treated rat livers compared with controls. The decrease in hepatic water signal intensity could be accounted for by the decrease in T2 and decrease in water density due to the presence of accumulated hepatic fat (approximately 25 mg/g wet weight of liver). When ethanol was withdrawn from the chronically treated rats, fatty infiltration was observed by both CSI and VOSY spectra to revert toward control values with a half-life of 2-4 days. By day 16, however, the signal intensity for hepatic fat was still significantly higher than control levels. In vitro 1H MRS studies of chloroform-methanol extracts confirmed the 5.5-fold increase in total hepatic fat induced by the chronic ethanol treatment, and showed further that triacylglycerols were increased 7.7-fold, cholesterol was increased fourfold, and phospholipids were increased 3.3-fold, compared with liver extracts from pair-fed control rats.

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

    PubMed

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

    2015-09-21

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

  14. Relativistic four-component DFT calculations of 1H NMR chemical shifts in transition-metal hydride complexes: unusual high-field shifts beyond the Buckingham-Stephens model.

    PubMed

    Hrobárik, Peter; Hrobáriková, Veronika; Meier, Florian; Repiský, Michal; Komorovský, Stanislav; Kaupp, Martin

    2011-06-09

    State-of-the-art relativistic four-component DFT-GIAO-based calculations of (1)H NMR chemical shifts of a series of 3d, 4d, and 5d transition-metal hydrides have revealed significant spin-orbit-induced heavy atom effects on the hydride shifts, in particular for several 4d and 5d complexes. The spin-orbit (SO) effects provide substantial, in some cases even the dominant, contributions to the well-known characteristic high-field hydride shifts of complexes with a partially filled d-shell, and thereby augment the Buckingham-Stephens model of off-center paramagnetic ring currents. In contrast, complexes with a 4d(10) and 5d(10) configuration exhibit large deshielding SO effects on their hydride (1)H NMR shifts. The differences between the two classes of complexes are attributed to the dominance of π-type d-orbitals for the true transition-metal systems compared to σ-type orbitals for the d(10) systems.

  15. 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).

  16. 1H chemical shift imaging of the brain in guanidino methyltransferase deficiency, a creatine deficiency syndrome; guanidinoacetate accumulation in the gray matter.

    PubMed

    Sijens, P E; Verbruggen, K T; Meiners, L C; Soorani-Lunsing, R J; Rake, J P; Oudkerk, M

    2005-09-01

    MR spectroscopy results in a mild case of guanidinoacetate methyltransferase (GAMT) deficiency are presented. The approach differs from previous MRS studies in the acquisition of a chemical shift imaging spectral map showing gray and white matter with the corresponding spectra in one overview. MR spectroscopy revealed guanidinoacetate (GAA) in the absence of creatine. New is that GAA signals are more prominent in gray matter than in white. In the prevailing view, that enzyme deficiency is localized in liver and pancreas and that all GAA is transported into the brain from the blood and the cerebrospinal fluid, this would be compatible with a more limited uptake and/or better clearance of GAA from the white matter compared to the grey matter.

  17. (1) H NMR Spectra. Part 28: Proton chemical shifts and couplings in three-membered rings. A ring current model for cyclopropane and a novel dihedral angle dependence for (3) J(HH) couplings involving the epoxy proton.

    PubMed

    Abraham, Raymond J; Leonard, Paul; Tormena, Cláudio F

    2012-04-01

    The (1) H chemical shifts of selected three-membered ring compounds in CDCl(3) solvent were obtained. This allowed the determination of the substituent chemical shifts of the substituents in the three-membered rings and the long-range effect of these rings on the distant protons. The substituent chemical shifts of common substituents in the cyclopropane ring differ considerably from the same substituents in acyclic fragments and in cyclohexane and were modelled in terms of a three-bond (γ)-effect. For long-range protons (more than three bonds removed), the substituent effects of the cyclopropane ring were analysed in terms of the cyclopropane magnetic anisotropy and steric effect. The cyclopropane magnetic anisotropy (ring current) shift was modelled by (a) a single equivalent dipole perpendicular to and at the centre of the cyclopropane ring and (b) by three identical equivalent dipoles perpendicular to the ring placed at each carbon atom. Model (b) gave a more accurate description of the (1) H chemical shifts and was the selected model. After parameterization, the overall root mean square error for the dataset of 289 entries was 0.068 ppm. The anisotropic effects are significant for the cyclopropane protons (ca 1 ppm) but decrease rapidly with distance. The heterocyclic rings of oxirane, thiirane and aziridine do not possess a ring current. (3) J(HH) couplings of the epoxy ring proton with side-chain protons were obtained and shown to be dependent on both the H-C-C-H and H-C-C-O orientations. Both density functional theory calculations and a simple Karplus-type equation gave general agreement with the observed couplings (root mean square error 0.5 Hz over a 10-Hz range).

  18. pH-dependent random coil (1)H, (13)C, and (15)N chemical shifts of the ionizable amino acids: a guide for protein pK a measurements.

    PubMed

    Platzer, Gerald; Okon, Mark; McIntosh, Lawrence P

    2014-11-01

    The pK a values and charge states of ionizable residues in polypeptides and proteins are frequently determined via NMR-monitored pH titrations. To aid the interpretation of the resulting titration data, we have measured the pH-dependent chemical shifts of nearly all the (1)H, (13)C, and (15)N nuclei in the seven common ionizable amino acids (X = Asp, Glu, His, Cys, Tyr, Lys, and Arg) within the context of a blocked tripeptide, acetyl-Gly-X-Gly-amide. Alanine amide and N-acetyl alanine were used as models of the N- and C-termini, respectively. Together, this study provides an essentially complete set of pH-dependent intra-residue and nearest-neighbor reference chemical shifts to help guide protein pK a measurements. These data should also facilitate pH-dependent corrections in algorithms used to predict the chemical shifts of random coil polypeptides. In parallel, deuterium isotope shifts for the side chain (15)N nuclei of His, Lys, and Arg in their positively-charged and neutral states were also measured. Along with previously published results for Asp, Glu, Cys, and Tyr, these deuterium isotope shifts can provide complementary experimental evidence for defining the ionization states of protein residues.

  19. Determination of pKa values of tenoxicam from 1H NMR chemical shifts and of oxicams from electrophoretic mobilities (CZE) with the aid of programs SQUAD and HYPNMR.

    PubMed

    Rodríguez-Barrientos, Damaris; Rojas-Hernández, Alberto; Gutiérrez, Atilano; Moya-Hernández, Rosario; Gómez-Balderas, Rodolfo; Ramírez-Silva, María Teresa

    2009-12-15

    In this work it is explained, by the first time, the application of programs SQUAD and HYPNMR to refine equilibrium constant values through the fit of electrophoretic mobilities determined by capillary zone electrophoresis experiments, due to the mathematical isomorphism of UV-vis absorptivity coefficients, NMR chemical shifts and electrophoretic mobilities as a function of pH. Then, the pK(a) values of tenoxicam in H(2)O/DMSO 1:4 (v/v) have been obtained from (1)H NMR chemical shifts, as well as of oxicams in aqueous solution from electrophoretic mobilities determined by CZE, at 25 degrees C. These values are in very good agreement with those reported by spectrophotometric and potentiometric measurements.

  20. 1H, 13C NMR spectral and single crystal structural studies of toxaphene congeners. Quantum chemical calculations for preferred conformers of 2,5- endo,6- exo,8,9,9,10,10-octachloro-2-bornene and their DFT/GIAO 13C chemical shifts

    NASA Astrophysics Data System (ADS)

    Laihia, K.; Valkonen, A.; Kolehmainen, E.; Suontamo, R.; Nissinen, M.; Nikiforov, V.; Selivanov, S.

    2005-11-01

    The 1H and 13C NMR chemical shifts for six toxaphene congeners: 2- exo,3- endo,6- exo,8,9,10-hexachloro- ( 1), 2- exo,3- endo,5- exo,9,9,10,10-heptachloro- ( 2), 2- exo,3- endo,6- exo,8,9,10,10-heptachloro- ( 3), 2- exo,3- endo,5- exo,6- endo,8,9,10-heptachloro- ( 4), 2- exo,3- endo,5- exo,6- endo,8,9,9,10-octachlorobornane ( 5) and 2,5- endo,6- exo,8,9,9,10,10-octachloro-2-bornene ( 6) are reported. Their chemical shift assignments have been obtained by means of Pulsed Field Gradient (PFG) Double Quantum Filtered (DQF) 1H, 1H correlation spectroscopy (COSY), PFG 1H, 13C Heteronuclear Multiple Quantum Coherence (HMQC) and PFG 1H, 13C Heteronuclear Multiple Bond Correlation (HMBC) experiments. A single crystal X-ray structural analysis was made for compounds 1, 3, 4 and 6. The prevalences of two octachlorobornene rotamers ( 6 a, 6 b) were elucidated by ab initio MO method and single point DFT/GIAO calculations for 13C chemical shifts. Theoretical calculations proved that the single crystal structure of 6 corresponds its most stable conformer in solution.

  1. Pressure and temperature effects on 2H spin-lattice relaxation times and 1H chemical shifts in tert-butyl alcohol- and urea-D2O solutions

    NASA Astrophysics Data System (ADS)

    Yoshida, Koji; Ibuki, Kazuyasu; Ueno, Masakatsu

    1998-01-01

    The pressure and temperature effects of hydrophobic hydration were studied by NMR spectroscopy. The 1H chemical shifts (δ) were measured at 7.7, 29.9, and 48.4 °C under high pressure up to 294 MPa for HDO contained as impurity in neat D2O, 1 mol kg-1 tert-butyl alcohol (TBA)-D2O, and 1 mol kg-1 urea-D2O solutions, for the methyl group of TBA in the TBA-D2O solution, and for the amino group of urea in the urea-D2O solution. The 2H spin-lattice relaxation times (T1) were measured under the same conditions as the chemical shift measurements for D2O in neat D2O, TBA-D2O and urea-D2O solutions with organic contents up to 8 mol%. The following features are observed for the pressure effect on δ (HDO) and 2H-T1 in TBA-D2O solutions: (1) The δ (HDO) exhibits a downfield shift relative to that in neat D2O, and the difference of δ (HDO) between TBA solution and neat D2O becomes larger with increasing pressure at lower temperature. (2) The decrement of the rotational correlation time of water in the hydration shell of TBA (τcs) relative to the value at atmospheric pressure is smaller than that in the bulk (τc0). (3) The pressure coefficients of T1 are positive in dilute solutions but are negative in more than 4 to 5 mol% solutions. These results suggest that the hydrophobic hydration shell of TBA is different than the open structure of water present in bulk, and resists pressure more strongly than the open structure of water in the bulk. In solutions of 4 to 5 mol%, the hydration shell collapses. On the other hand, the τcs in the hydration shell of urea is slightly larger than that in bulk water at lower pressure, but is obviously larger at higher pressure. In view of the rotational motion of water molecules, urea seems to strengthen the water structure slightly rather than weaken it, although δ (HDO) approaches that in the bulk with pressure. It is difficult to classify urea into a structure maker or a breaker.

  2. 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.

  3. Understanding NMR Chemical Shifts

    NASA Astrophysics Data System (ADS)

    Jameson, Cynthia J.

    1996-10-01

    The NMR chemical shift serves as a paradigm for molecular electronic properties. We consider the factors that determine the general magnitudes of the shifts, the state of the art in theoretical calculations, the nature of the shielding tensor, and the multidimensional shielding surface that describes the variation of the shielding with nuclear positions. We also examine the nature of the intermolecular shielding surface as a general example of a supermolecule property surface. The observed chemical shift in the zero-pressure limit is determined not only by the value of the shielding at the equilibrium geometry, but the dynamic average over the multidimensional shielding surface during rotation and vibration of the molecule. In the gas, solution, or adsorbed phase it is an average of the intermolecular shielding surface over all the configurations of the molecule with its neighbors. The temperature dependence of the chemical shift in the isolated molecule, the changes upon isotopic substitution, the changes with environment, are well characterized experimentally so that quantum mechanical descriptions of electronic structure and theories related to dynamics averaging of any electronic property can be subjected to stringent test.

  4. Chemical shift prediction for denatured proteins.

    PubMed

    Prestegard, James H; Sahu, Sarata C; Nkari, Wendy K; Morris, Laura C; Live, David; Gruta, Christian

    2013-02-01

    While chemical shift prediction has played an important role in aspects of protein NMR that include identification of secondary structure, generation of torsion angle constraints for structure determination, and assignment of resonances in spectra of intrinsically disordered proteins, interest has arisen more recently in using it in alternate assignment strategies for crosspeaks in (1)H-(15)N HSQC spectra of sparsely labeled proteins. One such approach involves correlation of crosspeaks in the spectrum of the native protein with those observed in the spectrum of the denatured protein, followed by assignment of the peaks in the latter spectrum. As in the case of disordered proteins, predicted chemical shifts can aid in these assignments. Some previously developed empirical formulas for chemical shift prediction have depended on basis data sets of 20 pentapeptides. In each case the central residue was varied among the 20 amino common acids, with the flanking residues held constant throughout the given series. However, previous choices of solvent conditions and flanking residues make the parameters in these formulas less than ideal for general application to denatured proteins. Here, we report (1)H and (15)N shifts for a set of alanine based pentapeptides under the low pH urea denaturing conditions that are more appropriate for sparse label assignments. New parameters have been derived and a Perl script was created to facilitate comparison with other parameter sets. A small, but significant, improvement in shift predictions for denatured ubiquitin is demonstrated.

  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. 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...

  7. Proton-detected 3D 14N/14N/1H isotropic shift correlation experiment mediated through 1H-1H RFDR mixing on a natural abundant sample under ultrafast MAS

    NASA Astrophysics Data System (ADS)

    Pandey, Manoj Kumar; Nishiyama, Yusuke

    2015-09-01

    In this contribution, we have demonstrated a proton detection-based approach on a natural abundant powdered L-Histidine HCl-H2O sample at ultrafast magic angle spinning (MAS) to accomplish 14N/14N correlation from a 3D 14N/14N/1H isotropic shift correlation experiment mediated through 1H finite-pulse radio frequency-driven recoupling (fp-RFDR). Herein the heteronuclear magnetization transfer between 14N and 1H has been achieved by HMQC experiment, whereas 14N/14N correlation is attained through enhanced 1H-1H spin diffusion process due to 1H-1H dipolar recoupling during the RFDR mixing. While the use of ultrafast MAS (90 kHz) provides sensitivity enhancement through increased 1H transverse relaxation time (T2), the use of micro-coil probe which can withstand strong 14N radio frequency (RF) fields further improves the sensitivity per unit sample volume.

  8. 1H, 13C, and 15N backbone, side-chain, and heme chemical shift assignments for oxidized and reduced forms of the monoheme c-type cytochrome ApcA isolated from the acidophilic metal-reducing bacterium Acidiphilium cryptum.

    SciTech Connect

    Cort, John R.; Swenson, Michael; Magnuson, Timothy S.

    2011-03-04

    We report the 1H, 13C, and 15N chemical shift assignments of both oxidized and reduced forms of an abundant periplasmic c-type cytochrome, designated ApcA, from the acidophilic gram-negative facultatively anaerobic metal-reducing alpha-proteobacterium Acidiphilium cryptum. These resonance assignments prove that ApcA is a monoheme cytochrome c2 and the product of the Acry_2099 gene. An absence of resonance peaks in the NMR spectra for the 21 N-terminal residues suggests that a predicted N-terminal signal sequence is cleaved. We also describe the preparation and purification of the protein in labeled form from laboratory cultures of A. cryptum growing on 13C- and 15N- labeled substrates.

  9. Using chemical shift perturbation to characterise ligand binding.

    PubMed

    Williamson, Mike P

    2013-08-01

    Chemical shift perturbation (CSP, chemical shift mapping or complexation-induced changes in chemical shift, CIS) follows changes in the chemical shifts of a protein when a ligand is added, and uses these to determine the location of the binding site, the affinity of the ligand, and/or possibly the structure of the complex. A key factor in determining the appearance of spectra during a titration is the exchange rate between free and bound, or more specifically the off-rate koff. When koff is greater than the chemical shift difference between free and bound, which typically equates to an affinity Kd weaker than about 3μM, then exchange is fast on the chemical shift timescale. Under these circumstances, the observed shift is the population-weighted average of free and bound, which allows Kd to be determined from measurement of peak positions, provided the measurements are made appropriately. (1)H shifts are influenced to a large extent by through-space interactions, whereas (13)Cα and (13)Cβ shifts are influenced more by through-bond effects. (15)N and (13)C' shifts are influenced both by through-bond and by through-space (hydrogen bonding) interactions. For determining the location of a bound ligand on the basis of shift change, the most appropriate method is therefore usually to measure (15)N HSQC spectra, calculate the geometrical distance moved by the peak, weighting (15)N shifts by a factor of about 0.14 compared to (1)H shifts, and select those residues for which the weighted shift change is larger than the standard deviation of the shift for all residues. Other methods are discussed, in particular the measurement of (13)CH3 signals. Slow to intermediate exchange rates lead to line broadening, and make Kd values very difficult to obtain. There is no good way to distinguish changes in chemical shift due to direct binding of the ligand from changes in chemical shift due to allosteric change. Ligand binding at multiple sites can often be characterised, by

  10. Chemical Shift Anisotropy Selective Inversion*

    PubMed Central

    Caporini, Marc. A.; Turner, Christopher. J.; Bielecki, Anthony; Griffin, Robert G.

    2009-01-01

    Magic Angle Spinning (MAS) is used in solid-state NMR to remove the broadening effects of the chemical shift anisotropy (CSA). In this work we investigate a technique that can reintroduce the CSA in order to selectively invert transverse magnetization. The technique involves an amplitude sweep of the radio frequency field through a multiple of the spinning frequency. The selectivity of this inversion mechanism is determined by the size of the CSA. We develop a theoretical framework to describe this process and demonstrate the CSA selective inversion with numerical simulations and experimental data. We combine this approach with cross polarization (CP) for potential applications in multi-dimensional MAS NMR. PMID:19648036

  11. A Short History of Three Chemical Shifts

    ERIC Educational Resources Information Center

    Nagaoka, Shin-ichi

    2007-01-01

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

  12. Chemical shift and coupling constant analysis of dibenzyloxy disulfides

    NASA Astrophysics Data System (ADS)

    Stoutenburg, Eric G.; Gryn'ova, Ganna; Coote, Michelle L.; Priefer, Ronny

    2015-02-01

    Dialkoxy disulfides have found applications in the realm of organic synthesis as an S2 or alkoxy donor, under thermal and photolytic decompositions conditions, respectively. Spectrally, dibenzyloxy disulfides possess an ABq in the 1H NMR, which can shift by over 1.1 ppm depending on the substituents present on the aromatic ring, as well as the solvent employed. The effect of the said substituents and solvent were analyzed and compared to the center of the ABq, geminal coupling, and the differences in chemical shifts of the individual doublets. Additionally, quantum-chemical calculations demonstrated the intramolecular H-bonding arrangement, found within the dibenzyloxy disulfides.

  13. Counterion influence on chemical shifts in strychnine salts

    SciTech Connect

    Metaxas, Athena E.; Cort, John R.

    2013-05-01

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

  14. Solution structure of Ln(III) complexes with macrocyclic ligands through theoretical evaluation of 1H NMR contact shifts.

    PubMed

    Rodríguez-Rodríguez, Aurora; Esteban-Gómez, David; de Blas, Andrés; Rodríguez-Blas, Teresa; Botta, Mauro; Tripier, Raphaël; Platas-Iglesias, Carlos

    2012-12-17

    Herein, we present a new approach that combines DFT calculations and the analysis of Tb(III)-induced (1)H NMR shifts to quantitatively and accurately account for the contact contribution to the paramagnetic shift in Ln(III) complexes. Geometry optimizations of different Gd(III) complexes with macrocyclic ligands were carried out using the hybrid meta-GGA TPSSh functional and a 46 + 4f(7) effective core potential (ECP) for Gd. The complexes investigated include [Ln(Me-DODPA)](+) (H(2)Me-DODPA = 6,6'-((4,10-dimethyl-1,4,7,10-tetraazacyclododecane-1,7-diyl)bis(methylene))dipicolinic acid, [Ln(DOTA)(H(2)O)](-) (H(4)DOTA = 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetate), [Ln(DOTAM)(H(2)O)](3+) (DOTAM = 1,4,7,10- tetrakis[(carbamoyl)methyl]-1,4,7,10-tetraazacyclododecane), and related systems containing pyridyl units (Ln = Gd, Tb). Subsequent all-electron relativistic calculations based on the DKH2 approximation, or small-core ECP calculations, were used to compute the (1)H hyperfine coupling constants (HFCCs) at the ligand nuclei (A(iso) values). The calculated A(iso) values provided direct access to contact contributions to the (1)H NMR shifts of the corresponding Tb(III) complexes under the assumption that Gd and Tb complexes with a given ligand present similar HFCCs. These contact shifts were used to obtain the pseudocontact shifts, which encode structural information as they depend on the position of the nucleus with respect to the lanthanide ion. An excellent agreement was observed between the experimental and calculated pseudocontact shifts using the DFT-optimized geometries as structural models of the complexes in solution, which demonstrates that the computational approach used provides (i) good structural models for the complexes, (ii) accurate HFCCs at the ligand nuclei. The methodology presented in this work can be classified in the context of model-dependent methods, as it relies on the use of a specific molecular structure obtained from DFT

  15. 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

  16. Protein structure determination from NMR chemical shifts.

    PubMed

    Cavalli, Andrea; Salvatella, Xavier; Dobson, Christopher M; Vendruscolo, Michele

    2007-06-05

    NMR spectroscopy plays a major role in the determination of the structures and dynamics of proteins and other biological macromolecules. Chemical shifts are the most readily and accurately measurable NMR parameters, and they reflect with great specificity the conformations of native and nonnative states of proteins. We show, using 11 examples of proteins representative of the major structural classes and containing up to 123 residues, that it is possible to use chemical shifts as structural restraints in combination with a conventional molecular mechanics force field to determine the conformations of proteins at a resolution of 2 angstroms or better. This strategy should be widely applicable and, subject to further development, will enable quantitative structural analysis to be carried out to address a range of complex biological problems not accessible to current structural techniques.

  17. 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

  18. The Effects of Dissolved Oxygen upon Amide Proton Relaxation and Chemical Shift in a Perdeuterated Protein

    NASA Astrophysics Data System (ADS)

    Ulmer, Tobias S.; Campbell, Iain D.; Boyd, Jonathan

    2002-08-01

    The effects of dissolved molecular oxygen upon amide proton ( 1H N) longitudinal and transverse relaxation rates and chemical shifts were studied for a small protein domain, the second type 2 module of fibronectin ( 2F2)—isotopically enriched to 99% 2H, 98% 15N. Longitudinal relaxation rate enhancements, R O 2( 1H N), of individual backbone 1H N nuclei varied up to 14 fold between a degassed and oxygenated (1 bar) solution, indicating that the oxygen distribution within the protein is inhomogeneous. On average, smaller relaxation rate enhancements were observed for 1H N nuclei associated with the core of the protein compared to 1H N nuclei closer to the surface, suggesting restricted oxygen accessibility to some regions. In agreement with an O 2- 1H N hyperfine interaction in the extreme narrowing limit, the 1H N transverse relaxation rates showed no significant change, up to an oxygen pressure of 9.5 bar (the maximum pressure used in this study). For most 1H N resonances, small Δδ O 2( 1H N) hyperfine chemical shifts could be detected between oxygen pressures of 1 bar and 9.5 bar.

  19. Detection and classification of hyperfine-shifted 1H, 2H, and 15N resonances of the Rieske ferredoxin component of toluene 4-monooxygenase.

    PubMed

    Xia, B; Pikus, J D; Xia, W; McClay, K; Steffan, R J; Chae, Y K; Westler, W M; Markley, J L; Fox, B G

    1999-01-12

    T4MOC is a 12.3 kDa soluble Rieske ferredoxin that is obligately required for electron transfer between the oxidoreductase and diiron hydroxylase components of toluene 4-monooxygenase from Pseudomonas mendocina KR1. Our preliminary 1H NMR studies of oxidized and reduced T4MOC [Markley, J. L., Xia, B., Chae, Y. K., Cheng, H., Westler, W. M., Pikus, J. D., and Fox, B. G. (1996) in Protein Structure Function Relationships (Zaidi, Z., and Smith, D., Eds.) pp 135-146, Plenum Press, London] revealed the presence of hyperfine-shifted 1H resonances whose short relaxation times made it impractical to use nuclear Overhauser effect (NOE) measurements for assignment purposes. We report here the use of selective isotopic labeling to analyze the hyperfine-shifted 1H, 2H, and 15N signals from T4MOC. Selective deuteration led to identification of signals from the four Hbeta atoms of cluster ligands C45 and C64 in the oxidized and reduced forms of T4MOC. In the reduced state, the Curie temperature dependence of the Hbeta protons corresponded to that predicted from the simple vector spin-coupling model for nuclei associated with the localized ferric site. The signal at 25.5 ppm in the 1H spectrum of reduced T4MOC was assigned on the basis of selective 2H labeling to the His Hepsilon1 atom of one of the cluster ligands (H47 or H67). This assignment was corroborated by a one bond 1H-13C correlation (at 25.39 ppm 1H and 136.11 ppm 13C) observed in spectra of [U-13C]T4MOC with a 1H-13C coupling constant of approximately 192 Hz. The carbon chemical shift and one bond coupling constant are those expected for 1Hepsilon1-13Cepsilon1 in the imidazolium ring of histidine and are inconsistent with values expected for cysteine 1Halpha-13Calpha. The His Hepsilon1 proton exhibited weak Curie temperature dependence from 283 to 303 K, contrary to the anti-Curie temperature dependence predicted from the spin coupling model for nuclei associated with the localized ferrous site. A 1H peak at -12.3 ppm

  20. 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

  1. 1H-n.m.r. investigation of naturally occurring and chemically oversulphated dermatan sulphates. Identification of minor monosaccharide residues.

    PubMed Central

    Bossennec, V; Petitou, M; Perly, B

    1990-01-01

    The 1H-n.m.r. spectra of various dermatan sulphate preparations present, besides the major signals of the basic disaccharide unit, several other minor signals. We have assigned most of them by n.m.r., using two-dimensional proton-proton double-quantum-correlation and nuclear-Overhauser-effect spectroscopy experiments. This allowed us to identify 2-O-sulphated L-iduronic acid and D-glucuronic acid residues as well as 6-sulphated N-acetylgalactosamine (presumably 4-O-sulphated as well). 2-O-Sulphated iduronic acid was present to similar extents (6-10% of total uronic acids) in pig skin dermatan sulphate and pig intestine dermatan sulphate, whereas glucuronic acid represented 17% of the uronic acid of pig skin dermatan sulphate and was virtually absent (1%) from the other preparation. 6-O-Sulphated N-acetylgalactosamine was present in minor amounts in pig intestine dermatan sulphate only. The influence of sulphation of iduronic acid units on their conformation was assessed by using chemically oversulphated pig intestine dermatan sulphate. Introduction of sulphate groups in this unit in dermatan sulphate tends to shift the conformational equilibrium towards the 1C4 conformer. PMID:2339978

  2. Computation of Chemical Shifts for Paramagnetic Molecules: A Laboratory Experiment for the Undergraduate Curriculum

    ERIC Educational Resources Information Center

    Pritchard, Benjamin P.; Simpson, Scott; Zurek, Eva; Autschbach, Jochen

    2014-01-01

    A computational experiment investigating the [superscript 1]H and [superscript 13]C nuclear magnetic resonance (NMR) chemical shifts of molecules with unpaired electrons has been developed and implemented. This experiment is appropriate for an upper-level undergraduate laboratory course in computational, physical, or inorganic chemistry. The…

  3. Chemical characterization of a prominent phosphomonoester resonance from mammalian brain. 31P and 1H NMR analysis at 4.7 and 14.1 tesla

    NASA Astrophysics Data System (ADS)

    Pettegrew, J. W.; Kopp, S. J.; Dadok, J.; Minshew, N. J.; Feliksik, J. M.; Glonek, T.; Cohen, M. M.

    A prominent 31P NMR resonance at 3.84 ppm in mammalian brain has been identified as ethanolamine phosphate. The identification was based on 1H and 31P NMR findings (including pH titrations) at 4.7 and 14.1 T, as well as thin-layer chromatography studies. We previously incorrectly assigned the 3.84 ppm resonance to ribose-5-phosphate. The incorrect assignment occurred because the two compounds have very similar 31P chemical shifts, and because we did not carefully consider the effects of counter ions and ionic strengths when interpreting the 31P chemical shifts. In separate preliminary studies we have demonstrated ethanolamine phosphate to be high in immature developing brain and in the degenerating brain of Alzheimer's and Huntington's disease patients. Ethanolamine phosphate may therefore serve as a sensitive marker of membrane phospholipid turnover for both in vitro and in vivo31P NMR studies.

  4. Mapping of protein structural ensembles by chemical shifts.

    PubMed

    Baskaran, Kumaran; Brunner, Konrad; Munte, Claudia E; Kalbitzer, Hans Robert

    2010-10-01

    Applying the chemical shift prediction programs SHIFTX and SHIFTS to a data base of protein structures with known chemical shifts we show that the averaged chemical shifts predicted from the structural ensembles explain better the experimental data than the lowest energy structures. This is in agreement with the fact that proteins in solution occur in multiple conformational states in fast exchange on the chemical shift time scale. However, in contrast to the real conditions in solution at ambient temperatures, the standard NMR structural calculation methods as well chemical shift prediction methods are optimized to predict the lowest energy ground state structure that is only weakly populated at physiological temperatures. An analysis of the data shows that a chemical shift prediction can be used as measure to define the minimum size of the structural bundle required for a faithful description of the structural ensemble.

  5. Chemical shift assignments of the connexin37 carboxyl terminal domain.

    PubMed

    Li, Hanjun; Spagnol, Gaelle; Pontifex, Tasha K; Burt, Janis M; Sorgen, Paul L

    2017-03-01

    Connexin37 (Cx37) is a gap junction protein involved in cell-to-cell communication in the vasculature and other tissues. Cx37 suppresses proliferation of vascular cells involved in tissue development and repair in vivo, as well as tumor cells. Global deletion of Cx37 in mice leads to enhanced vasculogenesis in development, as well as collateralgenesis and angiogenesis in response to injury, which together support improved tissue remodeling and recovery following ischemic injury. Here we report the (1)H, (15)N, and (13)C resonance assignments for an important regulatory domain of Cx37, the carboxyl terminus (CT; C233-V333). The predicted secondary structure of the Cx37CT domain based on the chemical shifts is that of an intrinsically disordered protein. In the (1)H-(15)N HSQC, N-terminal residues S254-Y259 displayed a second weaker peak and residues E261-Y266 had significant line broadening. These residues are flanked by prolines (P250, P258, P260, and P268), suggesting proline cis-trans isomerization. Overall, these assignments will be useful for identifying the binding sites for intra- and inter-molecular interactions that affect Cx37 channel activity.

  6. Empirical NMR Chemical Shift Correlations for Methyl and Methylene Protons.

    ERIC Educational Resources Information Center

    Friedrich, Edwin C.; Runkle, Katherine Gates

    1984-01-01

    Presents an internally consistent set of 63 substituent constants developed for use with the Schoolery Relationship to predict the chemical shifts of methylene protons of acyclic compounds. Chemical shift data used in deriving the constants were taken mainly from primary sources of HNMR (nuclear magnetic resonance) spectra. (JN)

  7. An isotropic chemical shift-chemical shift anisotropic correlation experiment using discrete magic angle turning.

    PubMed

    Hu, Jian Zhi; Sears, Jesse A; Kwak, Ja Hun; Hoyt, David W; Wang, Yong; Peden, Charles H F

    2009-05-01

    An isotropic-anisotropic shift 2D correlation spectroscopy is introduced that combines the advantages of both magic angle turning (MAT) and magic angle hopping (MAH) technologies. In this new approach, denoted DMAT for "discrete magic angle turning", the sample rotates clockwise followed by an anticlockwise rotation of exactly the same amount with each rotation less or equal than 360 degrees but greater than 240 degrees , with the rotation speed being constant only for times related to the evolution dimension. This back and forth rotation is repeated and synchronized with a special radio frequency (RF) pulse sequence to produce an isotropic-anisotropic shift 2D correlation spectrum. For any spin-interaction of rank-2 such as chemical shift anisotropy, isotropic magnetic susceptibility interaction, and residual homo-nuclear dipolar interaction in biological fluid samples, the projection along the isotropic dimension is a high resolution spectrum. Since a less than 360 degrees sample rotation is involved, the design potentially allows for in situ control over physical parameters such as pressure, flow conditions, feed compositions, and temperature so that true in situ NMR investigations can be carried out.

  8. Magnetic susceptibility shift selected imaging (MESSI) and localized (1)H(2)O spectroscopy in living plant tissues.

    PubMed

    Zhong, K; Li, X; Shachar-Hill, Y; Picart, F; Wishnia, A; Springer, C S

    2000-11-01

    Maize root segments permeated with aqueous solutions of the paramagnetic agents GdDTPA(2-) or DyDTPA-BMA display two well-resolved NMR peaks corresponding to the signals from intracellular and extracellular (1)H(2)O, which arise from well-understood bulk magnetic susceptibility effects. This allows each component to be studied separately. Images obtained at each frequency with MESSI editing, and single- and multiple-voxel ('spectroscopic imaging') localized spectra, clearly indicate that the agents permeate into the interstitial spaces, and into the longitudinal (xylem/phloem) channels in the stele (core) of the root, confirming earlier assessments. We believe these are the first images of a multicellular tissue acquired in vivo exclusively from the intracellular water proton resonance. This method can be further exploited to study water transport in similar systems.

  9. Giant spin-orbit effects on (1)H and (13)C NMR shifts for uranium(vi) complexes revisited: role of the exchange-correlation response kernel, bonding analyses, and new predictions.

    PubMed

    Greif, Anja H; Hrobárik, Peter; Autschbach, Jochen; Kaupp, Martin

    2016-11-09

    Previous relativistic quantum-chemical predictions of unusually large (1)H and (13)C NMR chemical shifts for ligand atoms directly bonded to a diamagnetic uranium(vi) center (P. Hrobárik, V. Hrobáriková, A. H. Greif and M. Kaupp, Angew. Chem., Int. Ed., 2012, 51, 10884) have been revisited by two- and four-component relativistic density functional methods. In particular, the effect of the exchange-correlation response kernel, which had been missing in the previously used two-component version of the Amsterdam Density Functional program, has been examined. Kernel contributions are large for cases with large spin-orbit (SO) contributions to the NMR shifts and may amount to up to ∼30% of the total shifts, which means more than a 50 ppm difference for the metal-bonded carbon shifts in some extreme cases. Previous calculations with a PBE-40HF functional had provided overall reasonable predictions, due to cancellation of errors between the missing kernel contributions and the enhanced exact-exchange (EXX) admixture of 40%. In the presence of an exchange-correlation kernel, functionals with lower EXX admixtures give already good agreement with experiments, and the PBE0 functional provides reasonable predictive quality. Most importantly, the revised approach still predicts unprecedented giant (1)H NMR shifts between +30 ppm and more than +200 ppm for uranium(vi) hydride species. We also predict uranium-bonded (13)C NMR shifts for some synthetically known organometallic U(vi) complexes, for which no corresponding signals have been detected to date. In several cases, the experimental lack of these signals may be attributed to unexpected spectral regions in which some of the (13)C NMR shifts can appear, sometimes beyond the usual measurement area. An extremely large uranium-bonded (13)C shift above 550 ppm, near the upper end of the diamagnetic (13)C shift range, is predicted for a known pincer carbene complex. Bonding analyses allow in particular the magnitude of the SO

  10. Applications of Chemical Shift Imaging to Marine Sciences

    PubMed Central

    Lee, Haakil; Tikunov, Andrey; Stoskopf, Michael K.; Macdonald, Jeffrey M.

    2010-01-01

    The successful applications of magnetic resonance imaging (MRI) in medicine are mostly due to the non-invasive and non-destructive nature of MRI techniques. Longitudinal studies of humans and animals are easily accomplished, taking advantage of the fact that MRI does not use harmful radiation that would be needed for plain film radiographic, computerized tomography (CT) or positron emission (PET) scans. Routine anatomic and functional studies using the strong signal from the most abundant magnetic nucleus, the proton, can also provide metabolic information when combined with in vivo magnetic resonance spectroscopy (MRS). MRS can be performed using either protons or hetero-nuclei (meaning any magnetic nuclei other than protons or 1H) including carbon (13C) or phosphorus (31P). In vivo MR spectra can be obtained from single region of interest (ROI or voxel) or multiple ROIs simultaneously using the technique typically called chemical shift imaging (CSI). Here we report applications of CSI to marine samples and describe a technique to study in vivo glycine metabolism in oysters using 13C MRS 12 h after immersion in a sea water chamber dosed with [2-13C]-glycine. This is the first report of 13C CSI in a marine organism. PMID:20948912

  11. Is the Lamb shift chemically significant?

    NASA Technical Reports Server (NTRS)

    Dyall, Kenneth G.; Bauschlicher, Charles W., Jr.; Schwenke, David W.; Pyykko, Pekka; Arnold, James (Technical Monitor)

    2001-01-01

    The contribution of the Lamb shift to the atomization energies of some prototype molecules, BF3, AlF3, and GaF3, is estimated by a perturbation procedure. It is found to be in the range of 3-5% of the one-electron scalar relativistic contribution to the atomization energy. The maximum absolute value is 0.2 kcal/mol for GaF3. These sample calculations indicate that the Lamb shift is probably small enough to be neglected for energetics of molecules containing light atoms if the target accuracy is 1 kcal/mol, but for higher accuracy calculations and for molecules containing heavy elements it must be considered.

  12. Synthesis, spectral analysis and quantum chemical studies on molecular geometry, chemical reactivity of 7-chloro-9-(2‧-chlorophenyl)-2,3-dihydroacridin-4(1H)-one and 7-chloro-9-(2‧-fluorophenyl)-2,3-dihydroacridin-4(1H)-one

    NASA Astrophysics Data System (ADS)

    Satheeshkumar, Rajendran; Sayin, Koray; Kaminsky, Werner; Rajendra Prasad, Karnam Jayarampillai

    2017-01-01

    7-Chloro-9-(2'-chlorophenyl)-2,3-dihydroacridin-4(1H)-one (3a) and 7-chloro-9-(2'-fluorophenyl)-2,3-dihydroacridin-4-(1H)-one (3b) were synthesized from 2-amino-2‧,5-dichlorobenzophenone (1a) and 2-amino-5-chloro-2'-fluorobenzophenone (1b) respectively with 1,2-cyclohexanedione (2) in the presence of 1-butyl-3-methylimidazolium tetrafluoroborate and InCl3 condition. The synthesized compounds have been recorded of FT-IR, NMR spectra and the structure was further confirmed by using single crystal X-ray diffraction. The synthesized compounds have been further checked the photo physical properties like UV, emission and fluorescent quantum yields were calculated. FT-NMR spectra and 1H and 13C NMR chemical shifts have been measured and computational calculations of compounds 3 are done by using B3LYP method with 6-311G basis set in gas phase. Similarly calculated vibrational frequencies were found in good agreement with experimental findings. The optimized geometry of molecules 3 was compared with experimental XRD values. DFT calculations of the molecular electrostatic potential (MEP) and HOMO - LUMO frontier orbitals identified chemically active sites of compounds 3 responsible for its chemical reactivity.

  13. Can Holo NMR Chemical Shifts be Directly Used to Resolve RNA-Ligand Poses?

    PubMed

    Frank, Aaron T

    2016-02-22

    Using a set of machine learning based predictors that are capable of predicting ligand-induced shielding effects on (1)H and (13)C nonexchangeable nuclei, it was discovered that holo NMR chemical shifts can be used to resolve RNA-ligand poses. This was accomplished by quantitatively comparing measured and predicted holo chemical shifts in conformationally diverse "decoy" pools for three test cases and then, for each, comparing the native pose to the pose in the decoy pool that exhibited the lowest error. For three test cases, the poses in the decoy pools that exhibited the best agreement between measured and predicted holo chemical shifts were within 0.28, 1.12, and 2.38 Å of the native poses. Interestingly, the predictors used in this study were trained on a database containing, only, apo RNA data. The agreement between the chemical shift-selected poses and the native NMR poses suggests that the predictors used in this study were able to "learn" general chemical shift-structure relationships from apo RNA data that could be used to account for ligand-induced shielding effects on RNA nuclei for the test cases studied.

  14. Quantum Chemical Study of the Solvent Effect on the Anticancer Active Molecule of Iproplatin: Structural, Electronic, and Spectroscopic Properties (IR, 1H NMR, UV)

    NASA Astrophysics Data System (ADS)

    Sadeghi, N.; Ghiasi, R.; Fazaeli, R.; Jamehbozorgi, S.

    2017-01-01

    The structural, electronic, and spectroscopic properties of the anticancer active molecule of iproplatin were investigated in the gas and liquid phases. Based on the polarizable continuum model (PCM), the solvent effect on the structural parameters, frontier orbitals, and spectroscopic parameters of the complex was investigated. The results indicate that the polarity of solvents plays a significant role in the structure and pro perties of the complex. 1H and 13C NMR chemical shifts were calculated using the Gauge-invariant atomic orbital (GIAO) method. Pt-Cl and Pt-OH bonds were investigated through a vibrational analysis. Moreover, time dependent density functional theory (TD-DFT) was used to calculate the energy, oscillatory strength, and wavelength absorption maximum (λmax) of electronic transitions and its nature within the complex.

  15. 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

    2010-11-04

    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.

  16. Photoluminescence of 1,3-Diphenyl-1 H-pyrazolo[3,4- b]quinoline and its derivatives: Experiment and quantum chemical simulations

    NASA Astrophysics Data System (ADS)

    Całus, S.; Gondek, E.; Danel, A.; Jarosz, B.; Kityk, A. V.

    2007-03-01

    The optical absorption and photoluminescent spectra are studied in recently synthesized diphenyl pyrazoloquinolines (DPPQ): 1,3-diphenyl-1H-pyrazolo[3,4-b] quinoline and its 6-vinyl, 6-N,N-diphenyl, 6-methyl, 6-fluoro, 6-bromo and 6-chloro derivatives. The photoemission spectra are recorded in organic solvents of different polarity and found to be highly solvatochromic. The measured spectra are compared with the quantum chemical calculations performed by means of the semiempirical methods (AM1 or PM3) in combination with the equilibrium molecular conformation (EMC) in vacuo (T = 0 K, Γ = 0.12 eV) or MD simulations (T = 300 K). The broadening of absorption and emission bands and their red-shift with increasing of temperature may be well reproduced by MD simulations. The Stokes shift of the photoluminescent spectra is obtained by including vibrational modes into the emission equation. The quantum chemical method AM1 in combination with MD simulations gives in most cases the best agreement with the experimental data. By comparing the emission spectra of 6-N,N-diphenyl-DPPQ with other DPPQ-derivatives one concludes that the molecular fragment diphenyl-amin [(C6H5)2N-] is likely subjected to strong conformational changes in solvents. The large difference between the excited- and state-dipole moments indicates on a strong electron transfer effect being common for all DPPQ derivatives.

  17. Bayesian inference of protein structure from chemical shift data.

    PubMed

    Bratholm, Lars A; Christensen, Anders S; Hamelryck, Thomas; Jensen, Jan H

    2015-01-01

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

  18. 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.

  19. A Magic-Angle Spinning NMR Method for the Site-Specific Measurement of Proton Chemical-Shift Anisotropy in Biological and Organic Solids

    PubMed Central

    Hou, Guangjin; Gupta, Rupal; Polenova, Tatyana; Vega, Alexander J.

    2014-01-01

    Proton chemical shifts are a rich probe of structure and hydrogen bonding environments in organic and biological molecules. Until recently, measurements of 1H chemical shift tensors have been restricted to either solid systems with sparse proton sites or were based on the indirect determination of anisotropic tensor components from cross-relaxation and liquid-crystal experiments. We have introduced an MAS approach that permits site-resolved determination of CSA tensors of protons forming chemical bonds with labeled spin-1/2 nuclei in fully protonated solids with multiple sites, including organic molecules and proteins. This approach, originally introduced for the measurements of chemical shift tensors of amide protons, is based on three RN-symmetry based experiments, from which the principal components of the 1H CS tensor can be reliably extracted by simultaneous triple fit of the data. In this article, we expand our approach to a much more challenging system involving aliphatic and aromatic protons. We start with a review of the prior work on experimental-NMR and computational-quantum-chemical approaches for the measurements of 1H chemical shift tensors and for relating these to the electronic structures. We then present our experimental results on U-13C,15N-labeled histdine demonstrating that 1H chemical shift tensors can be reliably determined for the 1H15N and 1H13C spin pairs in cationic and neutral forms of histidine. Finally, we demonstrate that the experimental 1H(C) and 1H(N) chemical shift tensors are in agreement with Density Functional Theory calculations, therefore establishing the usefulness of our method for characterization of structure and hydrogen bonding environment in organic and biological solids. PMID:25484446

  20. NMR Chemical Shifts in Hard Carbon Nitride Compounds

    SciTech Connect

    Yoon, Y.; Yoon, Y.; Pfrommer, B.G.; Pfrommer, B.G.; Louie, S.G.; Louie, S.G.; Mauri, F.

    1998-04-01

    We show that NMR chemical shift spectroscopy could help to identify the crystalline phases of hard carbon nitride compounds. To this purpose we compute the NMR chemical shifts of defect zinc-blende, cubic, {alpha}{minus} , {beta}{minus} , and graphitic C{sub 3}N{sub 4} with a newly developed {ital ab initio} method. The C shifts can be used to identify the CN bonds and to characterize C hybridization. The N shifts distinguish the {alpha}-C{sub 3}N{sub 4} from the {beta}-C{sub 3}N{sub 4} phases, and indicate the presence of the graphitic phase. {copyright} {ital 1998} {ital The American Physical Society}

  1. Protein Structure Refinement Using 13Cα Chemical Shift Tensors

    PubMed Central

    Wylie, Benjamin J.; Schwieters, Charles D.; Oldfield, Eric; Rienstra, Chad M.

    2009-01-01

    We have obtained the 13Cα chemical shift tensors for each amino acid in the protein GB1. We then developed a CST force field and incorporated this into the Xplor-NIH structure determination program. GB1 structures obtained by using CST restraints had improved precision over those obtained in the absence of CST restraints, and were also more accurate. When combined with isotropic chemical shifts, distance and vector angle restraints, the root-mean squared error with respect to existing x-ray structures was better than ~1.0 Å. These results are of broad general interest since they show that chemical shift tensors can be used in protein structure refinement, improving both structural accuracy and precision, opening up the way to accurate de novo structure determination. PMID:19123862

  2. Chemical purity using quantitative 1H-nuclear magnetic resonance: a hierarchical Bayesian approach for traceable calibrations

    NASA Astrophysics Data System (ADS)

    Toman, Blaza; Nelson, Michael A.; Lippa, Katrice A.

    2016-10-01

    Chemical purity assessment using quantitative 1H-nuclear magnetic resonance spectroscopy is a method based on ratio references of mass and signal intensity of the analyte species to that of chemical standards of known purity. As such, it is an example of a calculation using a known measurement equation with multiple inputs. Though multiple samples are often analyzed during purity evaluations in order to assess measurement repeatability, the uncertainty evaluation must also account for contributions from inputs to the measurement equation. Furthermore, there may be other uncertainty components inherent in the experimental design, such as independent implementation of multiple calibration standards. As such, the uncertainty evaluation is not purely bottom up (based on the measurement equation) or top down (based on the experimental design), but inherently contains elements of both. This hybrid form of uncertainty analysis is readily implemented with Bayesian statistical analysis. In this article we describe this type of analysis in detail and illustrate it using data from an evaluation of chemical purity and its uncertainty for a folic acid material.

  3. Molecular dynamics averaging of Xe chemical shifts in liquids

    NASA Astrophysics Data System (ADS)

    Jameson, Cynthia J.; Sears, Devin N.; Murad, Sohail

    2004-11-01

    The Xe nuclear magnetic resonance chemical shift differences that afford the discrimination between various biological environments are of current interest for biosensor applications and medical diagnostic purposes. In many such environments the Xe signal appears close to that in water. We calculate average Xe chemical shifts (relative to the free Xe atom) in solution in eleven liquids: water, isobutane, perfluoro-isobutane, n-butane, n-pentane, neopentane, perfluoroneopentane, n-hexane, n-octane, n-perfluorooctane, and perfluorooctyl bromide. The latter is a liquid used for intravenous Xe delivery. We calculate quantum mechanically the Xe shielding response in Xe-molecule van der Waals complexes, from which calculations we develop Xe (atomic site) interpolating functions that reproduce the ab initio Xe shielding response in the complex. By assuming additivity, these Xe-site shielding functions can be used to calculate the shielding for any configuration of such molecules around Xe. The averaging over configurations is done via molecular dynamics (MD). The simulations were carried out using a MD technique that one of us had developed previously for the simulation of Henry's constants of gases dissolved in liquids. It is based on separating a gaseous compartment in the MD system from the solvent using a semipermeable membrane that is permeable only to the gas molecules. We reproduce the experimental trends in the Xe chemical shifts in n-alkanes with increasing number of carbons and the large chemical shift difference between Xe in water and in perfluorooctyl bromide. We also reproduce the trend for a given solvent of decreasing Xe chemical shift with increasing temperature. We predict chemical shift differences between Xe in alkanes vs their perfluoro counterparts.

  4. Two-Dimensional Proton Chemical-Shift Imaging of Human Muscle Metabolites

    NASA Astrophysics Data System (ADS)

    Hu, Jiani; Willcott, M. Robert; Moore, Gregory J.

    1997-06-01

    Large lipid signals and strong susceptibility gradients introduced by muscle-bone interfaces represent major technical challenges forin vivoproton MRS of human muscle. Here, the demonstration of two-dimensional proton chemical-shift imaging of human muscle metabolites is presented. This technique utilizes a chemical-shift-selective method for water and lipid suppression and automatic shimming for optimal homogeneity of the magnetic field. The 2D1H CSI technique described facilitates the acquisition of high-spatial-resolution spectra, and allows one to acquire data from multiple muscle groups in a single experiment. A preliminary investigation utilizing this technique in healthy adult males (n= 4) revealed a highly significant difference in the ratio of the creatine to trimethylamine resonance between the fast and slow twitch muscle groups examined. The technique is robust, can be implemented on a commercial scanner with relative ease, and should prove to be a useful tool for both clinical and basic investigators.

  5. Spinning sidebands from chemical shift anisotropy in 13C MAS imaging.

    PubMed

    Scheler, U; Blümich, B; Spiess, H W

    1993-07-01

    Solid state imaging by 13C MAS imaging is described. The spinning sidebands occurring at moderate spinning speeds, which disturb the images, can be suppressed by TOSS. For rigid solids the spatial resolution that can be achieved in this way is better than that of 1H images at the same spinning speed. Spatially resolved spectra with or without spinning sidebands can likewise be recorded providing information about the isotropic and the anisotropic chemical shifts which can be exploited for the study of structure, order and dynamics. The techniques are demonstrated on a phantom made with 13C-labelled glycine.

  6. 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.

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

    NASA Astrophysics Data System (ADS)

    Chen, Fang; Yao, Guo-hua; He, Tian-jing; Chen, Dong-ming; Liu, Fan-chen

    2014-05-01

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

  8. Complete assignment of NMR data of 22 phenyl-1H-pyrazoles' derivatives.

    PubMed

    de Oliveira, Aline Lima; Alves de Oliveira, Carlos Henrique; Mairink, Laura Maia; Pazini, Francine; Menegatti, Ricardo; Lião, Luciano Morais

    2011-08-01

    Complete assignment of (1)H and (13)C NMR chemical shifts and J((1)H/(1)H and (1)H/(19)F) coupling constants for 22 1-phenyl-1H-pyrazoles' derivates were performed using the concerted application of (1)H 1D and (1)H, (13)C 2D gs-HSQC and gs-HMBC experiments. All 1-phenyl-1H-pyrazoles' derivatives were synthesized as described by Finar and co-workers. The formylated 1-phenyl-1H-pyrazoles' derivatives were performed under Duff's conditions.

  9. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  11. Ligand binding analysis and screening by chemical denaturation shift.

    PubMed

    Schön, Arne; Brown, Richard K; Hutchins, Burleigh M; Freire, Ernesto

    2013-12-01

    The identification of small molecule ligands is an important first step in drug development, especially drugs that target proteins with no intrinsic activity. Toward this goal, it is important to have access to technologies that are able to measure binding affinities for a large number of potential ligands in a fast and accurate way. Because ligand binding stabilizes the protein structure in a manner dependent on concentration and binding affinity, the magnitude of the protein stabilization effect elicited by binding can be used to identify and characterize ligands. For example, the shift in protein denaturation temperature (Tm shift) has become a popular approach to identify potential ligands. However, Tm shifts cannot be readily transformed into binding affinities, and the ligand rank order obtained at denaturation temperatures (≥60°C) does not necessarily coincide with the rank order at physiological temperature. An alternative approach is the use of chemical denaturation, which can be implemented at any temperature. Chemical denaturation shifts allow accurate determination of binding affinities with a surprisingly wide dynamic range (high micromolar to sub nanomolar) and in situations where binding changes the cooperativity of the unfolding transition. In this article, we develop the basic analytical equations and provide several experimental examples.

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

    PubMed

    Zhang, Rongchun; Nishiyama, Yusuke; Ramamoorthy, Ayyalusamy

    2015-10-28

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

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

    NASA Astrophysics Data System (ADS)

    Zhang, Rongchun; Nishiyama, Yusuke; Ramamoorthy, Ayyalusamy

    2015-10-01

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

  14. Chemical-shift MRI of exogenous lipoid pneumonia

    SciTech Connect

    Cox, J.E.; Choplin, R.H.; Chiles, C.

    1996-05-01

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

  15. Heteronuclear three-dimensional NMR spectroscopy. Natural abundance sup 13 C chemical shift editing of sup 1 H- sup 1 H COSY spectra

    SciTech Connect

    Fesik, S.W.; Gampe, R.T. Jr.; Zuiderweg, E.R.P. )

    1989-01-18

    It has been demonstrated that heteronuclear 3D NMR spectroscopy can be effectively applied to small molecules with {sup 13}C at natural abundance. A 78mM solution of the aminoglycoside, kanamycin A was used for this experiment. The heteronuclear 3D NMR spectroscopy is shown to be a useful method for resolving spectral overlap in all frequency domains. 10 refs., 2 figs.

  16. Heuristic overlap-exchange model of noble gas chemical shifts

    NASA Astrophysics Data System (ADS)

    Adrian, Frank J.

    2004-05-01

    It is now generally recognized that overlap-exchange interactions are the primary cause of the medium-dependent magnetic shielding (chemical shift) in all noble gases except helium, although the attractive electrostatic-dispersion (van der Waals) interactions play an indirect role in determining the penetration of the interacting species into the repulsive overlap-exchange region. The short-range nature of these overlap-exchange interactions, combined with the fact that they often can be approximated by simple functions of the overlap of the wave functions of the interacting species, suggests a useful semiempirical model of these chemical shifts. In it the total shielding is the sum of shieldings due to pairwise interactions of the noble gas atom with the individual atoms of the medium, with the "atomic" shielding terms either estimated by simple functions of the atomic overlap integrals averaged over their Boltzmann-weighted separations, or determined by fits to experimental data in systems whose complexity makes the former procedure impractical. Results for 129Xe chemical shifts in the noble gases and in a variety of molecular and condensed systems, including families of n-alkanes, straight-chain alcohols, and the endohedral compounds Xe@C60 and Xe@C70 are encouraging for the applicability of the model to systems of technical and biomedical interest.

  17. A predictive tool for assessing (13)C NMR chemical shifts of flavonoids.

    PubMed

    Burns, Darcy C; Ellis, David A; March, Raymond E

    2007-10-01

    Herein are presented the (1)H and (13)C NMR data for seven monohydroxyflavones (3-, 5-, 6-, 7-, 2'-, 3'-, and 4'-hydroxyflavone), five dihydroxyflavones (3,2'-, 3,3'-, 3,4'-, 3,6-, 2',3'-dihydroxyflavone), a trihydroxyflavone (apigenin; 5,7,4'-trihydroxyflavone), a tetrahydroxyflavone (luteolin; 5,7,3',4'-tetrahydroxyflavone), and three glycosylated hydroxyflavones (orientin; luteolin-6C-beta-D-glucoside, homoorientin; luteolin-8C-beta-D-glucoside, vitexin; apigenin-8C-beta-D-glucoside). When these NMR spectra are compared, it is possible to assess the impact of flavone modification and to elucidate detailed structural and electronic information for these flavonoids. A simple predictive tool for assigning flavonoid (13)C chemical shifts, which is based on the cumulative differences between the monohydroxyflavones and flavone (13)C chemical shifts, is demonstrated. The tool can be used to accurately predict (13)C flavonoid chemical shifts and it is expected to be useful for rapid assessment of flavonoid (13)C NMR spectra and for assigning substitution patterns in newly isolated flavonoids.

  18. 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.

  19. 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

  20. Solvent Effects on Oxygen-17 Chemical Shifts in Amides. Quantitative Linear Solvation Shift Relationships

    NASA Astrophysics Data System (ADS)

    Díez, Ernesto; Fabián, Jesús San; Gerothanassis, Ioannis P.; Esteban, Angel L.; Abboud, José-Luis M.; Contreras, Ruben H.; de Kowalewski, Dora G.

    1997-01-01

    A multiple-linear-regression analysis (MLRA) has been carried out using the Kamlet-Abboud-Taft (KAT) solvatochromic parameters in order to elucidate and quantify the solvent effects on the17O chemical shifts ofN-methylformamide (NMF),N,N-dimethylformamide (DMF),N-methylacetamide (NMA), andN,N-dimethylacetamide (DMA). The chemical shifts of the four molecules show the same dependence (in ppm) on the solvent polarity-polarizability, i.e., -22π*. The influence of the solvent hydrogen-bond-donor (HBD) acidities is slightly larger for the acetamides NMA and DMA, i.e., -48α, than for the formamides NMF and DMF, i.e., -42α. The influence of the solvent hydrogen-bond-acceptor (HBA) basicities is negligible for the nonprotic molecules DMF and DMA but significant for the protic molecules NMF and NMA, i.e., -9β. The effect of substituting the N-H hydrogen by a methyl group amounts to -5.9 ppm in NMF and 5.4 ppm in NMA. The effect of substituting the O=C-H hydrogen amounts to 5.5 ppm in NMF and 16.8 ppm in DMF. The model of specific hydration sites of amides by I. P. Gerothanassis and C. Vakka [J. Org. Chem.59,2341 (1994)] is settled in a more quantitative basis and the model by M. I. Burgar, T. E. St. Amour, and D. Fiat [J. Phys. Chem.85,502 (1981)] is critically evaluated.17O hydration shifts have been calculated for formamide (FOR) by the ab initio LORG method at the 6-31G* level. For a formamide surrounded by the four in-plane molecules of water in the first hydration shell, the calculated17O shift change due to the four hydrogen bonds, -83.2 ppm, is smaller than the empirical hydration shift, -100 ppm. The17O shift change from each out-of-plane water molecule hydrogen-bonded to the amide oxygen is -18.0 ppm. These LORG results support the conclusion that no more than four water molecules are hydrogen-bonded to the amide oxygen in formamide.

  1. Exploring new 129Xe chemical shift ranges in HXeY compounds: hydrogen more relativistic than xenon.

    PubMed

    Lantto, Perttu; Standara, Stanislav; Riedel, Sebastian; Vaara, Juha; Straka, Michal

    2012-08-21

    Among rare gases, xenon features an unusually broad nuclear magnetic resonance (NMR) chemical shift range in its compounds and as a non-bonded Xe atom introduced into different environments. In this work we show that (129)Xe NMR chemical shifts in the recently prepared, matrix-isolated xenon compounds appear in new, so far unexplored (129)Xe chemical shift ranges. State-of-the-art theoretical predictions of NMR chemical shifts in compounds of general formula HXeY (Y = H, F, Cl, Br, I, -CN, -NC, -CCH, -CCCCH, -CCCN, -CCXeH, -OXeH, -OH, -SH) as well as in the recently prepared ClXeCN and ClXeNC species are reported. The bonding situation of Xe in the studied compounds is rather different from the previously characterized cases as Xe appears in the electronic state corresponding to a situation with a low formal oxidation state, between I and II in these compounds. Accordingly, the predicted (129)Xe chemical shifts occur in new NMR ranges for this nucleus: ca. 500-1000 ppm (wrt Xe gas) for HXeY species and ca. 1100-1600 ppm for ClXeCN and ClXeNC. These new ranges fall between those corresponding to the weakly-bonded Xe(0) atom in guest-host systems (δ < 300 ppm) and in the hitherto characterized Xe molecules (δ > 2000 ppm). The importance of relativistic effects is discussed. Relativistic effects only slightly modulate the (129)Xe chemical shift that is obtained already at the nonrelativistic CCSD(T) level. In contrast, spin-orbit-induced shielding effects on the (1)H chemical shifts of the H1 atom directly bonded to the Xe center largely overwhelm the nonrelativistic deshielding effects. This leads to an overall negative (1)H chemical shift in the range between -5 and -25 ppm (wrt CH(4)). Thus, the relativistic effects induced by the heavy Xe atom appear considerably more important for the chemical shift of the neighbouring, light hydrogen atom than that of the Xe nucleus itself. The predicted NMR parameters facilitate an unambiguous experimental identification of

  2. Systemic bone marrow disorders: Characterization with proton chemical shift imaging

    SciTech Connect

    Gueckel, F.B.; Brix, G.; Semmler, W.; Zuna, I.; Knauf, W.; Ho, A.D.; van Kaick, G. )

    1990-07-01

    In a prospective clinical study, 26 patients (22 with malignant lymphoma and 4 with myelofibrosis) and 9 healthy volunteers were examined by conventional magnetic resonance and proton chemical shift imaging (CSI; modified Dixon method). On the basis of the CSI data, a quantitative evaluation of the relative fat and water signal fractions in regions of interest of the femur, pelvis, and spine was performed. In 16 of 17 patients with biopsy-proven bone marrow disorders, CSI revealed a significant reduction in the fat fraction of the bone marrow relative to that of normal volunteers. The visual assessment could detect only 14 of the 17 pathological cases.

  3. 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.

  4. 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.

  5. Chemical shift-based water/fat separation in the presence of susceptibility-induced fat resonance shift

    PubMed Central

    Karampinos, Dimitrios C.; Yu, Huanzhou; Shimakawa, Ann; Link, Thomas M.; Majumdar, Sharmila

    2011-01-01

    Chemical shift-based water/fat separation methods have been emerging due to the growing clinical need for fat quantification in different body organs. Accurate quantification of proton-density fat fraction requires the assessment of many confounding factors, including the need of modeling the presence of multiple peaks in the fat spectrum. Most recent quantitative chemical shift-based water/fat separation approaches rely on a multi-peak fat spectrum with pre-calibrated peak locations and pre-calibrated or self-calibrated peak relative amplitudes. However, water/fat susceptibility differences can induce fat spectrum resonance shifts depending on the shape and orientation of the fatty inclusions. The effect is of particular interest in the skeletal muscle due to the anisotropic arrangement of extracellular lipids. In the present work, the effect of susceptibility-induced fat resonance shift on the fat fraction is characterized in a conventional complex-based chemical shift-based water/fat separation approach that does not model the susceptibility-induced fat resonance shift. A novel algorithm is then proposed in order to quantify the resonance shift in a complex-based chemical shift-based water/fat separation approach that considers the fat resonance shift in the signal model, aiming to extract information about the orientation/geometry of lipids. The technique is validated in a phantom and preliminary in vivo results are shown in the calf musculature of healthy and diabetic subjects. PMID:22247024

  6. Backbone and side chain chemical shift assignments of apolipophorin III from Galleria mellonella.

    PubMed

    Crowhurst, Karin A; Horn, James V C; Weers, Paul M M

    2016-04-01

    Apolipophorin III, a 163 residue monomeric protein from the greater wax moth Galleria mellonella (abbreviated as apoLp-IIIGM), has roles in upregulating expression of antimicrobial proteins as well as binding and deforming bacterial membranes. Due to its similarity to vertebrate apolipoproteins there is interest in performing atomic resolution analysis of apoLp-IIIGM as part of an effort to better understand its mechanism of action in innate immunity. In the first step towards structural characterization of apoLp-IIIGM, 99 % of backbone and 88 % of side chain (1)H, (13)C and (15)N chemical shifts were assigned. TALOS+ analysis of the backbone resonances has predicted that the protein is composed of five long helices, which is consistent with the reported structures of apolipophorins from other insect species. The next stage in the characterization of apoLp-III from G. mellonella will be to utilize these resonance assignments in solving the solution structure of this protein.

  7. The Relationship between NMR Chemical Shifts of Thermally Polarized and Hyperpolarized (89) Y Complexes and Their Solution Structures.

    PubMed

    Xing, Yixun; Jindal, Ashish K; Regueiro-Figueroa, Martín; Le Fur, Mariane; Kervarec, Nelly; Zhao, Piyu; Kovacs, Zoltan; Valencia, Laura; Pérez-Lourido, Paulo; Tripier, Raphaël; Esteban-Gómez, David; Platas-Iglesias, Carlos; Sherry, A Dean

    2016-11-07

    Recently developed dynamic nuclear polarization (DNP) technology offers the potential of increasing the NMR sensitivity of even rare nuclei for biological imaging applications. Hyperpolarized (89) Y is an ideal candidate because of its narrow NMR linewidth, favorable spin quantum number (I=1/2 ), and long longitudinal relaxation times (T1 ). Strong NMR signals were detected in hyperpolarized (89) Y samples of a variety of yttrium complexes. A dataset of (89) Y NMR data composed of 23 complexes with polyaminocarboxylate ligands was obtained using hyperpolarized (89) Y measurements or (1) H,(89) Y-HMQC spectroscopy. These data were used to derive an empirical equation that describes the correlation between the (89) Y chemical shift and the chemical structure of the complexes. This empirical correlation serves as a guide for the design of (89) Y sensors. Relativistic (DKH2) DFT calculations were found to predict the experimental (89) Y chemical shifts to a rather good accuracy.

  8. Using chemical shifts to determine structural changes in proteins upon complex formation.

    PubMed

    Cavalli, Andrea; Montalvao, Rinaldo W; Vendruscolo, Michele

    2011-08-04

    Methods for determining protein structures using only chemical shift information are progressively becoming more accurate and reliable. A major problem, however, in the use of chemical shifts for the determination of the structures of protein complexes is that the changes in the chemical shifts upon binding tend to be rather limited and indeed often smaller than the standard errors made in the predictions of chemical shifts corresponding to given structures. We present a procedure that, despite this problem, enables one to use of chemical shifts to determine accurately the conformational changes that take place upon complex formation.

  9. Determination of amyloid core structure using chemical shifts.

    PubMed

    Skora, Lukasz; Zweckstetter, Markus

    2012-12-01

    Amyloid fibrils are the pathological hallmark of a large variety of neurodegenerative disorders. The structural characterization of amyloid fibrils, however, is challenging due to their non-crystalline, heterogeneous, and often dynamic nature. Thus, the structure of amyloid fibrils of many proteins is still unknown. We here show that the structure calculation program CS-Rosetta can be used to obtain insight into the core structure of amyloid fibrils. Driven by experimental solid-state NMR chemical shifts and taking into account the polymeric nature of fibrils CS-Rosetta allows modeling of the core of amyloid fibrils. Application to the Y145X stop mutant of the human prion protein reveals a left-handed β-helix.

  10. 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.

  11. Theoretical Modeling of 99 Tc NMR Chemical Shifts

    SciTech Connect

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

    2016-09-06

    Technetium (Tc) displays a rich chemistry due to the wide range of oxidation states (from -I to +VII) and ability to form coordination compounds. Determination of Tc speciation in complex mixtures is a major challenge, and 99Tc NMR spec-troscopy is widely used to probe chemical environments of Tc in odd oxidation states. However interpretation of the 99Tc NMR data is hindered by the lack of reference compounds. DFT computations can help fill this gap, but to date few com-putational studies have focused on 99Tc NMR of compounds and complexes. This work systematically evaluates the inclu-sion small percentages of Hartree-Fock exchange correlation and relativistic effects in DFT computations to support in-terpretation of the 99Tc NMR spectra. Hybrid functionals are found to perform better than their pure GGA counterparts, and non-relativistic calculations have been found to generally show a lower mean absolute deviation from experiment. Overall non-relativistic PBE0 and B3PW91 calculations are found to most accurately predict 99Tc NMR chemical shifts.

  12. 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

  13. NMR chemical shifts as a tool to analyze first principles molecular dynamics simulations in condensed phases: the case of liquid water.

    PubMed

    Banyai, Douglas R; Murakhtina, Tatiana; Sebastiani, Daniel

    2010-12-01

    We present (1)H NMR chemical shift calculations of liquid water based on first principles molecular dynamics simulations under periodic boundary conditions. We focus on the impact of computational parameters on the structural and spectroscopic data, which is an important question for understanding how sensitive the computed (1)H NMR resonances are upon variation of the simulation setup. In particular, we discuss the influence of the exchange-correlation functional and the size of the basis set, the choice for the fictitious electronic mass and the use of pseudopotentials for the nuclear magnetic resonance (NMR) calculation on one hand and the underlying Car-Parrinello-type molecular dynamics simulations on the other hand. Our findings show that the direct effect of these parameters on (1)H shifts is not big, whereas the indirect dependence via the structural data is more important. The (1)H NMR chemical shifts clearly reflect the induced structural changes, illustrating once again the sensitivity of (1)H NMR observables on small changes in the local chemical structure of complex hydrogen-bonded liquids.

  14. Natural Linewidth Chemical Shift Imaging (NL-CSI)

    PubMed Central

    Bashir, Adil; Yablonskiy, Dmitriy A.

    2007-01-01

    The discrete Fourier transform (FT) is a conventional method for spatial reconstruction of chemical shifting imaging (CSI) data. Due to point spread function (PSF) effects, FT reconstruction leads to intervoxel signal leakage (Gibbs ringing). Spectral localization by imaging (SLIM) reconstruction was previously proposed to overcome this intervoxel signal contamination. However, the existence of magnetic field inhomogeneities creates an additional source of intervoxel signal leakage. It is demonstrated herein that even small field inhomogeneities substantially amplify intervoxel signal leakage in both FT and SLIM reconstruction approaches. A new CSI data acquisition strategy and reconstruction algorithm (natural linewidth (NL) CSI) is presented that eliminates effects of magnetic field inhomogeneity-induced intervoxel signal leakage and intravoxel phase dispersion on acquired data. The approach is based on acquired CSI data, high-resolution images, and magnetic field maps. The data are reconstructed based on the imaged object structure (as in the SLIM approach) and a reconstruction matrix that takes into account the inhomogeneous field distribution inside anatomically homogeneous compartments. Phantom and in vivo results show that the new method allows field inhomogeneity effects from the acquired MR signal to be removed so that the signal decay is determined only by the “natural”R2 relaxation rate constant (hence the term “natural linewidth” CSI). PMID:16721752

  15. Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps

    NASA Astrophysics Data System (ADS)

    Kumari, Amrita; Dorai, Kavita

    2013-06-01

    NMR chemical shifts are accurate indicators of molecular environment and have been extensively used as aids in protein structure determination. This work focuses on creating empirical 3D correlation maps of backbone chemical shift nuclei for use as identifiers of secondary structure elements in proteins. A correlated database of backbone nuclei chemical shifts was constructed from experimental structural data gathered from entries in the Protein Data Bank (PDB) as well as isotropic chemical shift values from the RefDB database. Rigorous statistical analysis of the maps led to the conclusion that specific correlations between triplets of backbone chemical shifts are best able to differentiate between different secondary structures such as α-helices, β-strands and turns. The method is compared with similar techniques that use NMR chemical shift information as aids in biomolecular structure determination and performs well in tests done on experimental data determined for different types of proteins, including large multi-domain proteins and membrane proteins.

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

    PubMed Central

    Lebedev, A V; Rezvukhin, A I

    1984-01-01

    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

  17. Molecular orbital studies (hardness, chemical potential and electrophilicity), vibrational investigation and theoretical NBO analysis of 4-4'-(1H-1,2,4-triazol-1-yl methylene) dibenzonitrile based on abinitio and DFT methods.

    PubMed

    Sheela, N R; Muthu, S; Sampathkrishnan, S

    2014-01-01

    The Fourier transform infrared (FTIR) and FT Raman (FTR) of 4-4'-(1H-1, 2, 4-triazol-1-yl methylene) dibenzonitrile (4-HTMDBN) have been recorded and analyzed. The equilibrium geometry harmonic vibrational frequencies have been investigated with the help of standard HF and DFT methods with 6-31G(d,p) as basis set. The assignments of the vibrational spectra have been carried out with the help of normal co-ordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). Theoretical simulations of the FTIR and FTR spectra of the title compound have been calculated. The (1)H and (13)C Nuclear Magnetic Resonance (NMR) chemical shifts of the molecule were calculated by the Gauge including atomic orbital (GIAO) method. The stability of the molecule has been analyzed using natural bond orbital (NBO) analysis. The linear polarizability (α) and the first order hyperpolarizability (β) values of the investigated molecule have been computed using HF/DFT/6-31G(d,p) methods on the finite field approach. UV-Vis spectrum of the compound is recorded and the electronic properties such as HOMO and LUMO energies, are performed. The directly calculated ionization potential (IP), electron affinity (EA), electronegativity (χ), electrophilicity index (ω), hardness (η) and chemical potential (ρ) are all correlated with the HOMO and LUMO energies with their molecular properties. Mulliken population analysis on atomic charges, molecular electrostatic potential maps (MEP) and thermodynamical properties of title compound at different temperature have been calculated.

  18. Derivatives of pyrazinecarboxylic acid: 1H, 13C and 15N NMR spectroscopic investigations.

    PubMed

    Holzer, Wolfgang; Eller, Gernot A; Datterl, Barbara; Habicht, Daniela

    2009-07-01

    NMR spectroscopic studies are undertaken with derivatives of 2-pyrazinecarboxylic acid. Complete and unambiguous assignment of chemical shifts ((1)H, (13)C, (15)N) and coupling constants ((1)H,(1)H; (13)C,(1)H; (15)N,(1)H) is achieved by combined application of various 1D and 2D NMR spectroscopic techniques. Unequivocal mapping of (13)C,(1)H spin coupling constants is accomplished by 2D (delta,J) long-range INEPT spectra with selective excitation. Phenomena such as the tautomerism of 3-hydroxy-2-pyrazinecarboxylic acid are discussed.

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

    SciTech Connect

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy; Nishiyama, Yusuke

    2015-10-28

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

  20. 1H NMR spectroscopic and quantum chemical studies on a poly(ester amide) model compound: Nalpha-benzoyl-L-argininate ethyl ester chloride. Structural preferences for the isolated molecule and in solution.

    PubMed

    Fonseca, A C; Jarmelo, S; Carvalho, R A; Fausto, R; Gil, M H; Simões, P N

    2010-05-13

    The molecular structure of the L-arginine derivative, N(alpha)-benzoyl-L-argininate ethyl ester chloride (BAEEH(+).Cl(-)), was characterized by combining quantum chemical methods and (1)H NMR spectroscopy. A conformational search on the potential energy surfaces of the three lowest-energy tautomers of BAEEH(+) [A: R-N(+)H=(NH(2))(2); B: R-NH-C(=NH)N(+)H(3); C: R-N(+)H(2)-C(=NH)NH(2); R = C(6)H(5)C(=O)NH-CH(COOCH(2)CH(3))CH(2)CH(2)CH(2)-] was carried out using the semiempirical PM3 method. The lowest-energy conformations obtained using this method were then optimized at the DFT(B3LYP)/6-31++G(d,p) level of theory. For all tautomers, it was found that all low-energy conformers present folded structures, in which a H-bond interaction between the guanidinium group and the amide carbonyl oxygen atom appears to be the most relevant stabilizing factor. (1)H NMR spectra of BAEEH(+).Cl(-) in DMF-D(7) were acquired in the temperature range [-55 to 75 degrees C], providing information about the rotational motions in the guanidinium group and showing that the tautomeric form of BAEEH(+) that exists in solution is tautomer A. The interpretation of the experimental findings was supported by (1)H NMR chemical shifts obtained theoretically at the DFT(B3LYP)/6-31++G(d,p) level of approximation, using both the polarized continuum model and a BAEEH(+)-water complex model.

  1. Hydrophobic clustering in nonnative states of a protein: Interpretation of chemical shifts in NMR spectra of denatured states of lysozyme

    SciTech Connect

    Evans, P.A.; Topping, K.D.; Woolfson, D.N.; Dobson, C.M. )

    1991-01-01

    Chemical shifts of resonances of specific protons in the 1H NMR spectrum of thermally denatured hen lysozyme have been determined by exchange correlation with assigned native state resonances in 2D NOESY spectra obtained under conditions where the two states are interconverting. There are subtle but widespread deviations of the measured shifts from the values which would be anticipated for a random coil; in the case of side chain protons these are virtually all net upfield shifts and it is shown that this may be the averaged effect of interactions with aromatic rings in a partially collapsed denatured state. In a very few cases, notably that of two sequential tryptophan residues, it is possible to interpret these effects in terms of specific, local interresidue interactions. Generally, however, there is no correlation with either native state shift perturbations or with sequence proximity to aromatic groups. Diminution of most of the residual shift perturbations on reduction of the disulfide cross-links confirms that they are not simply effects of residues adjacent in the sequence. Similar effects of chemical denaturants, with the disulfides intact, demonstrate that the shift perturbations reflect an enhanced tendency to side chain clustering in the thermally denatured state. The temperature dependences of the shift perturbations suggest that this clustering is noncooperative and is driven by small, favorable enthalpy changes. While the extent of conformational averaging is clearly much greater than that observed for a homologous protein, alpha-lactalbumin, in its partially folded molten globule state, the results clearly show that thermally denatured lysozyme differs substantially from a random coil, principally in that it is partially hydrophobically collapsed.

  2. Fragment-Based Approach for the Evaluation of NMR Chemical Shifts for Large Biomolecules Incorporating the Effects of the Solvent Environment.

    PubMed

    Jose, K V Jovan; Raghavachari, Krishnan

    2017-03-14

    We present an efficient implementation of the molecules-in-molecules (MIM) fragment-based quantum chemical method for the evaluation of NMR chemical shifts of large biomolecules. Density functional techniques have been employed in conjunction with large basis sets and including the effects of the solvent environment in these calculations. The MIM-NMR method is initially benchmarked on a set of (alanine)10 conformers containing strong intramolecular interactions. The incorporation of a second low level of theory to recover the missing long-range interactions in the primary fragmentation scheme is critical to yield reliable chemical shifts, with a mean absolute deviation (MAD) from direct unfragmented calculations of 0.01 ppm for (1)H chemical shifts and 0.07 ppm for (13)C chemical shifts. In addition, the performance of MIM-NMR has been assessed on two large peptides: the helical portion of ubiquitin ( 1UBQ ) containing 12 residues where the X-ray structure is known, and E6-binding protein of papilloma virus ( 1RIJ ) containing 23 residues where the structure has been derived from solution-phase NMR analysis. The solvation environment is incorporated in these MIM-NMR calculations, either through an explicit, implicit, or a combination of both solvation models. Using an explicit treatment of the solvent molecules within the first solvation sphere (3 Å) and an implicit solvation model for the rest of the interactions, the (1)H and (13)C chemical shifts of ubiquitin show excellent agreement with experiment (mean absolute deviation of 0.31 ppm for (1)H and 1.72 ppm for (13)C), while the larger E6-binding protein yields a mean absolute deviation of 0.34 ppm for (1)H chemical shifts. The proposed MIM-NMR method is computationally cost-effective and provides a substantial speedup relative to conventional full calculations, the largest density functional NMR calculation included in this work involving more than 600 atoms and over 10,000 basis functions. The MIM

  3. Complete (1) H NMR assignment of cedranolides.

    PubMed

    Perez-Hernandez, Nury; Gordillo-Roman, Barbara; Arrieta-Baez, Daniel; Cerda-Garcia-Rojas, Carlos M; Joseph-Nathan, Pedro

    2017-03-01

    Complete and unambiguous (1) H NMR chemical shift assignment of α-cedrene (2) and cedrol (9), as well as for α-pipitzol (1), isocedrol (10), and the six related compounds 3-8 has been established by iterative full spin analysis using the PERCH NMR software (PERCH Solutions Ltd., Kuopio, Finland). The total sets of coupling constants are described and correlated with the conformational equilibria of the five-membered ring of 1-10, which were calculated using the complete basis set method. Copyright © 2015 John Wiley & Sons, Ltd.

  4. Carbon-13 chemical shift anisotropy in DNA bases from field dependence of solution NMR relaxation rates.

    PubMed

    Ying, Jinfa; Grishaev, Alexander; Bax, Ad

    2006-03-01

    Knowledge of (13)C chemical shift anisotropy (CSA) in nucleotide bases is important for the interpretation of solution-state NMR relaxation data in terms of local dynamic properties of DNA and RNA. Accurate knowledge of the CSA becomes particularly important at high magnetic fields, prerequisite for adequate spectral resolution in larger oligonucleotides. Measurement of (13)C relaxation rates of protonated carbons in the bases of the so-called Dickerson dodecamer, d(CGCGAATTCGCG)(2), at 500 and 800 MHz (1)H frequency, together with the previously characterized structure and diffusion tensor yields CSA values for C5 in C, C6 in C and T, C8 in A and G, and C2 in A that are closest to values previously reported on the basis of solid-state FIREMAT NMR measurements, and mostly larger than values obtained by in vacuo DFT calculations. Owing to the noncollinearity of dipolar and CSA interactions, interpretation of the NMR relaxation rates is particularly sensitive to anisotropy of rotational diffusion, and use of isotropic diffusion models can result in considerable errors.

  5. 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.

  6. Stereospecific assignment of the asparagine and glutamine sidechain amide protons in proteins from chemical shift analysis.

    PubMed

    Harsch, Tobias; Schneider, Philipp; Kieninger, Bärbel; Donaubauer, Harald; Kalbitzer, Hans Robert

    2017-02-01

    Side chain amide protons of asparagine and glutamine residues in random-coil peptides are characterized by large chemical shift differences and can be stereospecifically assigned on the basis of their chemical shift values only. The bimodal chemical shift distributions stored in the biological magnetic resonance data bank (BMRB) do not allow such an assignment. However, an analysis of the BMRB shows, that a substantial part of all stored stereospecific assignments is not correct. We show here that in most cases stereospecific assignment can also be done for folded proteins using an unbiased artificial chemical shift data base (UACSB). For a separation of the chemical shifts of the two amide resonance lines with differences ≥0.40 ppm for asparagine and differences ≥0.42 ppm for glutamine, the downfield shifted resonance lines can be assigned to H(δ21) and H(ε21), respectively, at a confidence level >95%. A classifier derived from UASCB can also be used to correct the BMRB data. The program tool AssignmentChecker implemented in AUREMOL calculates the Bayesian probability for a given stereospecific assignment and automatically corrects the assignments for a given list of chemical shifts.

  7. An Improved Experiment to Illustrate the Effect of Electronegativity on Chemical Shift.

    ERIC Educational Resources Information Center

    Boggess, Robert K.

    1988-01-01

    Describes a method for using nuclear magnetic resonance to observe the effect of electronegativity on the chemical shift of protons in similar compounds. Suggests the use of 1,3-dihalopropanes as samples. Includes sample questions. (MVL)

  8. 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.

  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. 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.

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

    PubMed

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

    2016-06-01

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

  12. Density functional theory study of (13)C NMR chemical shift of chlorinated compounds.

    PubMed

    Li, Songqing; Zhou, Wenfeng; Gao, Haixiang; Zhou, Zhiqiang

    2012-02-01

    The use of the standard density functional theory (DFT) leads to an overestimation of the paramagnetic contribution and underestimation of the shielding constants, especially for chlorinated carbon nuclei. For that reason, the predictions of chlorinated compounds often yield too high chemical shift values. In this study, the WC04 functional is shown to be capable of reducing the overestimation of the chemical shift of Cl-bonded carbons in standard DFT functionals and to show a good performance in the prediction of (13)C NMR chemical shifts of chlorinated organic compounds. The capability is attributed to the minimization of the contributions that intensively increase the chemical shift in the WC04. Extensive computations and analyses were performed to search for the optimal procedure for WC04. The B3LYP and mPW1PW91 standard functionals were also used to evaluate the performance. Through detailed comparisons between the basis set effects and the solvent effects on the results, the gas-phase GIAO/WC04/6-311+G(2d,p)//B3LYP/6-31+G(d,p) was found to be specifically suitable for the prediction of (13)C NMR chemical shifts of chlorides in both chlorinated and non-chlorinated carbons. Further tests with eight molecules in the probe set sufficiently confirmed that WC04 was undoubtedly effective for accurately predicting (13) C NMR chemical shifts of chlorinated organic compounds.

  13. Errors in the Calculation of 27Al Nuclear Magnetic Resonance Chemical Shifts

    PubMed Central

    Wang, Xianlong; Wang, Chengfei; Zhao, Hui

    2012-01-01

    Computational chemistry is an important tool for signal assignment of 27Al nuclear magnetic resonance spectra in order to elucidate the species of aluminum(III) in aqueous solutions. The accuracy of the popular theoretical models for computing the 27Al chemical shifts was evaluated by comparing the calculated and experimental chemical shifts in more than one hundred aluminum(III) complexes. In order to differentiate the error due to the chemical shielding tensor calculation from that due to the inadequacy of the molecular geometry prediction, single-crystal X-ray diffraction determined structures were used to build the isolated molecule models for calculating the chemical shifts. The results were compared with those obtained using the calculated geometries at the B3LYP/6-31G(d) level. The isotropic chemical shielding constants computed at different levels have strong linear correlations even though the absolute values differ in tens of ppm. The root-mean-square difference between the experimental chemical shifts and the calculated values is approximately 5 ppm for the calculations based on the X-ray structures, but more than 10 ppm for the calculations based on the computed geometries. The result indicates that the popular theoretical models are adequate in calculating the chemical shifts while an accurate molecular geometry is more critical. PMID:23203134

  14. Computed and experimental chemical shift parameters for rigid and flexible YAF peptides in the solid state.

    PubMed

    Pawlak, Tomasz; Trzeciak-Karlikowska, Katarzyna; Czernek, Jiri; Ciesielski, Wlodzimierz; Potrzebowski, Marek J

    2012-02-16

    DFT methods were employed to compute the (13)C NMR chemical shift tensor (CST) parameters for crystals of YAF peptides (Tyr-Ala-Phe) with different stereochemistry for the Ala residue. Tyr-D-Ala-Phe 1 crystallizes in the C2 space group while Tyr-L-Ala-Phe crystallizes in either the P2(1)2(1)2 space group (2a) or the P6(5) space group (2b). PISEMA MAS measurements for samples with a natural abundance of (1)H and (13)C nuclei and (2)H QUADECHO experiments for samples with deuterium labeled aromatic rings were used to analyze the geometry and time scale of the molecular motion. At ambient temperature, the tyrosine ring of sample 1 is rigid and the phenylalanine ring undergoes a π-jump, both rings in sample 2a are static, and both rings in sample 2b undergo a fast regime exchange. The theoretical values of the CST were obtained for isolated molecules (IM) and clusters employing the ONIOM approach. The experimental (13)C δ(ii) parameters for all of the samples were measured via a 2D PASS sequence. Significant scatter of the computed versus the experimental (13)C CST parameters was observed for 1 and 2b, while the observed correlation was very good for 2a. In this report, we show that the quality of the (13)C σ(ii)/(13)C δ(ii) correlations, when properly interpreted, can be a source of important information about local molecular motions.

  15. Determination of 15N chemical shift anisotropy from a membrane-bound protein by NMR spectroscopy.

    PubMed

    Pandey, Manoj Kumar; Vivekanandan, Subramanian; Ahuja, Shivani; Pichumani, Kumar; Im, Sang-Choul; Waskell, Lucy; Ramamoorthy, Ayyalusamy

    2012-06-21

    Chemical shift anisotropy (CSA) tensors are essential in the structural and dynamic studies of proteins using NMR spectroscopy. Results from relaxation studies in biomolecular solution and solid-state NMR experiments on aligned samples are routinely interpreted using well-characterized CSA tensors determined from model compounds. Since CSA tensors, particularly the (15)N CSA, highly depend on a number of parameters including secondary structure, electrostatic interaction, and the amino acid sequence, there is a need for accurately determined CSA tensors from proteins. In this study, we report the backbone amide-(15)N CSA tensors for a 16.7-kDa membrane-bound and paramagnetic-heme containing protein, rabbit Cytochrome b(5) (cytb(5)), determined using the (15)N CSA/(15)N-(1)H dipolar transverse cross-correlation rates. The mean values of (15)N CSA determined for residues in helical, sheet, and turn regions are -187.9, -166.0, and -161.1 ppm, respectively, with an overall average value of -171.7 ppm. While the average CSA value determined from this study is in good agreement with previous solution NMR experiments on small globular proteins, the CSA value determined for residues in helical conformation is slightly larger, which may be attributed to the paramagnetic effect from Fe(III) of the heme unit in cytb(5). However, like in previous solution NMR studies, the CSA values reported in this study are larger than the values measured from solid-state NMR experiments. We believe that the CSA parameters reported in this study will be useful in determining the structure, dynamics, and orientation of proteins, including membrane proteins, using NMR spectroscopy.

  16. Measurement of large /sup 19/F chemical shifts with the RYa-2305 spectrometer

    SciTech Connect

    Iorga, E.V.; Kucheryaev, A.G.; Lebedev, V.A.; Leont'eva, I.N.

    1985-06-01

    In order to extend the range of F-19 resonant frequencies in the RYa-2305 high-resolution NMR spectrometer, the authors have replaced the generator 9 by a tunable generator. This allows recording of the spectra together or to measure the chemical shifts exactly. The chemical shifts for MeF/sub 6/ in solutions of the hexafluorides of Mo, W, and U in organic solvents are shown, as measured at +20 degrees C. The upgrades in the RYa-2305 not only extend the range of measurable F-19 chemical shifts, but also enable one to measure large shifts with high accuracy. This principle for recording and measuring can be applied to other nuclides with the RYa2305 spectrometer.

  17. 29Si NMR Chemical Shift Calculation for Silicate Species by Gaussian Software

    NASA Astrophysics Data System (ADS)

    Azizi, S. N.; Rostami, A. A.; Godarzian, A.

    2005-05-01

    Hartree-Fock self-consistent-field (HF-SCF) theory and the Gauge-including atomic orbital (GIAO) methods are used in the calculation of 29Si NMR chemical shifts for ABOUT 90 units of 19 compounds of various silicate species of precursors for zeolites. Calculations have been performed at geometries optimized at the AM1 semi-empirical method. The GIAO-HF-SCF calculations were carried out with using three different basis sets: 6-31G*, 6-31+G** and 6-311+G(2d,p). To demonstrate the quality of the calculations the calculated chemical shifts, δ, were compared with the corresponding experimental values for the compounds in study. The results, especially with 6-31+g** are in excellent agreement with experimental values. The calculated chemical shifts, in practical point of view, appear to be accurate enough to aid in experimental peak assignments. The difference between the experimental and calculated 29Si chemical shift values not only depends on the Qn units but also it seems that basis set effects and the level of theory is more important. For the series of molecules studied here, the standard deviations and mean absolute errors for 29Si chemical shifts relative to TMS determined using Hartree--Fock 6-31+G** basis is nearly in all cases smaller than the errors for shifts determined using HF/6-311+G(2d,p).

  18. Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field.

    PubMed

    Nielsen, Jakob T; Eghbalnia, Hamid R; Nielsen, Niels Chr

    2012-01-01

    The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we present a new and highly accurate, precise, and robust formulation for the prediction of NMR chemical shifts from protein structures. Our approach, shAIC (shift prediction guided by Akaikes Information Criterion), capitalizes on mathematical ideas and an information-theoretic principle, to represent the functional form of the relationship between structure and chemical shift as a parsimonious sum of smooth analytical potentials which optimally takes into account short-, medium-, and long-range parameters in a nuclei-specific manner to capture potential chemical shift perturbations caused by distant nuclei. shAIC outperforms the state-of-the-art methods that use analytical formulations. Moreover, for structures derived by NMR or structures with novel folds, shAIC delivers better overall results; even when it is compared to sophisticated machine learning approaches. shAIC provides for a computationally lightweight implementation that is unimpeded by molecular size, making it an ideal for use as a force field.

  19. 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.

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

    PubMed

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

    2015-01-25

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  2. Correlation between the covalency and the thallium-205 nuclear magnetic resonance chemical shift in oxides and halides

    NASA Astrophysics Data System (ADS)

    Jouini, N.

    1986-07-01

    205Tl chemical shift measurements were carried out on thallium(I) oxides and halides. A correlation between the chemical shift and the stereochemical activity of the 6 s2 lone pair of Tl I was established; the greater this activity, the greater the absolute value of the chemical shift. For the halides, optical and chemical shift measurements gave access to the Tl- X bond ionicity via Ramsey's equation. In thallium(I) halides the absolute value of the chemical shift increases with the covalency. The work of Glaser on thallium(III) halides showed the chemical shift to decrease with increasing covalency. An explication of this difference is proposed. The hyperfine coupling constant A of the paramagnetic compound Tl 4MnI 6 was determined by the study of the chemical shift as a function of the susceptibility. This constant A is seen to be weak (-7 KG/μ B).

  3. Correlation between the covalency and the thallium-205 nuclear magnetic resonance chemical shift in oxides and halides

    SciTech Connect

    Jouini, N.

    1986-07-15

    /sup 205/Tl chemical shift measurements were carried out on thallium(I) oxides and halides. A correlation between the chemical shift and the stereochemical activity of the 6s/sup 2/ lone pair of Tl/sup I/ was established; the greater this activity, the greater the absolute value of the chemical shift. For the halides, optical and chemical shift measurements gave access to the Tl-X bond ionicity via Ramsey's equation. In thallium(I) halides the absolute value of the chemical shift increases with the covalency. The work of Glaser on thallium(III) halides showed the chemical shift to decrease with increasing covalency. An explication of this difference is proposed. The hyperfine coupling constant A of the paramagnetic compound Tl/sub 4/MnI/sub 6/ was determined by the study of the chemical shift as a function of the susceptibility. This constant A is seen to be weak (-7 KG/..mu../sub B/).

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

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

    PubMed

    Labudde, D; Leitner, D; Krüger, M; Oschkinat, H

    2003-01-01

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

  6. 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.

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

    PubMed

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

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts--sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond ((h3)J(NC')) spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding.

  8. Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics

    PubMed Central

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

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding. PMID:24391900

  9. 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.

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

    PubMed

    Hansen, Poul Erik

    2015-01-30

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

  11. 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.

  12. Synthesis, NMR spectroscopic characterization and structure of a divinyldisilazane-(triphenylphosphine)platinum(0) complex: observation of isotope-induced chemical shifts (1)Δ(12/13)C((195)Pt).

    PubMed

    Wrackmeyer, Bernd; Klimkina, Elena V; Schmalz, Thomas; Milius, Wolfgang

    2013-05-01

    Tetramethyldivinyldisilazane-(triphenylphosphine)platinum(0) was prepared, characterized in solid state by X-ray crystallography and in solution by multinuclear magnetic resonance spectroscopy ((1)H, (13)C, (15)N, (29)Si, (31)P and (195)Pt NMR). Numerous signs of spin-spin coupling constants were determined by two-dimensional heteronuclear shift correlations (HETCOR) and two-dimensional (1)H/(1)H COSY experiments. Isotope-induced chemical shifts (1)Δ(12/13)C((195)Pt) were measured from (195)Pt NMR spectra of the title compound as well as of other Pt(0), Pt(II) and Pt(IV) compounds for comparison. In contrast to other heavy nuclei such as (199)Hg or (207)Pb, the "normal" shifts of the heavy isotopomers to low frequencies are found, covering a range of >500 ppb.

  13. Simultaneous quantification and identification of individual chemicals in metabolite mixtures by two-dimensional extrapolated time-zero (1)H-(13)C HSQC (HSQC(0)).

    PubMed

    Hu, Kaifeng; Westler, William M; Markley, John L

    2011-02-16

    Quantitative one-dimensional (1D) (1)H NMR spectroscopy is a useful tool for determining metabolite concentrations because of the direct proportionality of signal intensity to the quantity of analyte. However, severe signal overlap in 1D (1)H NMR spectra of complex metabolite mixtures hinders accurate quantification. Extension of 1D (1)H to 2D (1)H-(13)C HSQC leads to the dispersion of peaks along the (13)C dimension and greatly alleviates peak overlapping. Although peaks are better resolved in 2D (1)H-(13)C HSQC than in 1D (1)H NMR spectra, the simple proportionality of cross peaks to the quantity of individual metabolites is lost by resonance-specific signal attenuation during the coherence transfer periods. As a result, peaks for individual metabolites usually are quantified by reference to calibration data collected from samples of known concentration. We show here that data from a series of HSQC spectra acquired with incremented repetition times (the time between the end of the first (1)H excitation pulse to the beginning of data acquisition) can be extrapolated back to zero time to yield a time-zero 2D (1)H-(13)C HSQC spectrum (HSQC(0)) in which signal intensities are proportional to concentrations of individual metabolites. Relative concentrations determined from cross peak intensities can be converted to absolute concentrations by reference to an internal standard of known concentration. Clustering of the HSQC(0) cross peaks by their normalized intensities identifies those corresponding to metabolites present at a given concentration, and this information can assist in assigning these peaks to specific compounds. The concentration measurement for an individual metabolite can be improved by averaging the intensities of multiple, nonoverlapping cross peaks assigned to that metabolite.

  14. Work function shifts of catalytic metals under hydrogen gas visualized by terahertz chemical microscopy.

    PubMed

    Kiwa, Toshihiko; Hagiwara, Takafumi; Shinomiya, Mitsuhiro; Sakai, Kenji; Tsukada, Keiji

    2012-05-21

    Terahertz chemical microscopy (TCM) was applied to visualize the distribution of the work function shift of catalytic metals under hydrogen gas. TCM measures the chemical potential on the surface of a SiO(2)/Si/sapphire sensing plate without any contact with the plate. By controlling the bias voltage between an electrode on the SiO(2)/ surface and the Si layer, the relationship between the voltage and the THz amplitude from the sensing plate can be obtained. As a demonstration, two types of structures were fabricated on the sensing plate, and the work function shifts due to catalytic reactions were visualized.

  15. Grand canonical Monte Carlo simulations of the distribution and chemical shifts of xenon in the cages of zeolite NaA. I. Distribution and 129Xe chemical shifts

    NASA Astrophysics Data System (ADS)

    Jameson, Cynthia J.; Jameson, A. Keith; Baello, Bernoli I.; Lim, Hyung-Mi

    1994-04-01

    The equilibrium distribution of the Xe atoms among the alpha cages of the zeolite NaA have been measured directly by nuclear magnetic resonance (NMR) in ten samples ranging from very low xenon loading up to saturation. These distributions are simulated by a grand canonical Monte Carlo (GCMC) method which reproduces the experimental data quantitatively for all ten samples at 296 K and also at 360 K. The adsorption isotherm of the high loading samples has been determined directly from the chemical shift of the gas in equilibrium with the adsorbed xenon. The data compare favorably with the adsorption isotherms resulting from the simulations. The previously reported 129Xe chemical shifts of the individual Xen clusters and their temperature dependences in the range 188-420 K are reproduced quantitatively by the GCMC simulation which makes use of pairwise additive ab initio intermolecular shielding functions. These cluster shifts and their temperature dependence encode the distribution of configurations for a given Xen cluster in an alpha cage. Quantitative agreement with the three experimental measures of the distribution of Xe atoms in NaA (partitioning between the adsorbed phase and the gas phase, distribution of the intrazeolitic atoms among the alpha cages, and the distribution of Xe atoms within an alpha cage containing Xen) as a function of temperature has been achieved for the first time.

  16. Sequential nearest-neighbor effects on computed 13Calpha chemical shifts.

    PubMed

    Vila, Jorge A; Serrano, Pedro; Wüthrich, Kurt; Scheraga, Harold A

    2010-09-01

    To evaluate sequential nearest-neighbor effects on quantum-chemical calculations of (13)C(alpha) chemical shifts, we selected the structure of the nucleic acid binding (NAB) protein from the SARS coronavirus determined by NMR in solution (PDB id 2K87). NAB is a 116-residue alpha/beta protein, which contains 9 prolines and has 50% of its residues located in loops and turns. Overall, the results presented here show that sizeable nearest-neighbor effects are seen only for residues preceding proline, where Pro introduces an overestimation, on average, of 1.73 ppm in the computed (13)C(alpha) chemical shifts. A new ensemble of 20 conformers representing the NMR structure of the NAB, which was calculated with an input containing backbone torsion angle constraints derived from the theoretical (13)C(alpha) chemical shifts as supplementary data to the NOE distance constraints, exhibits very similar topology and comparable agreement with the NOE constraints as the published NMR structure. However, the two structures differ in the patterns of differences between observed and computed (13)C(alpha) chemical shifts, Delta(ca,i), for the individual residues along the sequence. This indicates that the Delta(ca,i)-values for the NAB protein are primarily a consequence of the limited sampling by the bundles of 20 conformers used, as in common practice, to represent the two NMR structures, rather than of local flaws in the structures.

  17. Exploiting the phase of NMR signals to carry useful information. Application to the measurement of chemical shifts in aliased 2D spectra.

    PubMed

    Ramírez-Gualito, Karla; Jeannerat, Damien

    2015-11-01

    Taking advantage of the phase of nuclear magnetic resonance (NMR) signals to encode NMR information is not easy because of their low precision and their sensitivity to nearby signals. We nevertheless demonstrated that the phase in indirect dimension of (1) H-(13) C heteronuclear single quantum coherence (HSQC) signals could provide carbon chemical shifts at low, but sufficient precision to resolve the ambiguities of the chemical shifts in aliased spectra. This approach, we called phase-encoding of the aliasing order Na (PHANA), only requires inserting a constant delay during the t1 evolution time to obtain spectra where signals with mixed phases can be decoded at the processing to reconstruct full spectra with a 15-fold increase in resolution.

  18. Hydrogen bonding between acetate-based ionic liquids and water: Three types of IR absorption peaks and NMR chemical shifts change upon dilution

    NASA Astrophysics Data System (ADS)

    Chen, Yu; Cao, Yuanyuan; Zhang, Yuwei; Mu, Tiancheng

    2014-01-01

    The hydrogen-bonding interaction between acetate-based ionic liquids (AcIL) and water was investigated by attenuated total reflection infrared (ATR-IR) and 1H NMR. Interestingly, the relative change of chemical shift δ of 1H NMR upon dilution could be divided into three regions. All the H show an upfield shift in Regions 1 and 2 while a different tendency in Region 3 (upfield, no, and downfield shift classified as Types 1, 2, 3, respectively). For ATR-IR, the red, no, or blue shift of νOD (IR absorption peak of OD in D2O) and ν± (IR absorption peak of AcILs) also have three types, respectively. Two-Times Explosion Mechanism (TTEM) was proposed to interpret the dynamic processes of AcILs upon dilution macroscopically, meanwhile an Inferior Spring Model (ISM) was proposed to help to understand the TTEM microscopically, All those indicate that AcILs present the state of network, sub-network, cluster, sub-cluster, ion pairs and sub-ion pairs in sequence upon dilution by water and the elongation of hydrogen bonding between AcILs-water, between cation-anion of AcILs is plastic deformation rather than elastic deformation.

  19. Magnetic Shift of the Chemical Freeze-out and Electric Charge Fluctuations

    NASA Astrophysics Data System (ADS)

    Fukushima, Kenji; Hidaka, Yoshimasa

    2016-09-01

    We discuss the effect of a strong magnetic field on the chemical freeze-out points in ultrarelativistic heavy-ion collisions. As a result of inverse magnetic catalysis or magnetic inhibition, the crossover onset to hot and dense matter out of quarks and gluons should be shifted to a lower temperature. To quantify this shift we employ the hadron resonance gas model and an empirical condition for the chemical freeze-out. We point out that the charged particle abundances are significantly affected by the magnetic field so that the electric charge fluctuation is largely enhanced, especially at high baryon density. The charge conservation partially cancels the enhancement, but our calculation shows that the electric charge fluctuation could serve as a magnetometer. We find that the fluctuation exhibits a crossover behavior rapidly increased for e B ≳(0.4 GeV )2, while the charge chemical potential has smoother behavior with an increasing magnetic field.

  20. 13C NMR chemical shifts of the triclinic and monoclinic crystal forms of valinomycin.

    PubMed

    Kameda, Tsunenori; McGeorge, Gary; Orendt, Anita M; Grant, David M

    2004-07-01

    Two different crystalline polymorphs of valinomycin, the triclinic and monoclinic forms, have been studied by high resolution, solid state (13)C CP-MAS NMR spectroscopy. Although the two polymorphs of the crystal are remarkably similar, there are distinct differences in the isotropic chemical shifts between the two spectra. For the triclinic form, the carbon chemical shift tensor components for the alpha carbons adjacent to oxygen in the lactic acid and hydroxyisovaleric acid residues and the ester carbonyls of the valine residue were obtained using the FIREMAT experiment. From the measured components, it was found that the behavior of the isotropic chemical shift, delta(iso), for valine residue ester carbonyl carbons is predominately influenced by the intermediate component, delta(22). Additionally it was found that the smallest shift component, delta(33), for the L -lactic acid ( L -Lac) and D -alpha-hydroxyisovaleric acid ( D -Hyi) C(alpha)-O carbon was significantly displaced depending upon the nature of individual amino acid residues, and it is the delta(33) component that governs the behavior of delta(iso) in these alpha carbons.

  1. Characteristic chemical shifts of quasicrystalline Zn-Mg-Zr alloys studied by EELS and SXES

    NASA Astrophysics Data System (ADS)

    Koshiya, S.; Terauchi, M.; Ohhashi, S.; Tsai, A. P.

    2013-06-01

    Chemical shifts of the constituent atoms of primitive icosahedral quasicrystal (P-QC), face-centred icosahedral quasicrystal (F-QC) and 1/1-approximant (1/1-AP) of F-QC Zn-Mg-Zr alloys were investigated for the first time using high energy-resolution electron energy-loss spectroscopy (EELS) and soft-X-ray emission spectroscopy (SXES). Among Zn M-shell and Mg L-shell excitation EELS spectra of P-QC, F-QC and 1/1-AP alloys, only the quasicrystalline alloys showed a chemical shift towards the larger binding energy side. In Zn-L and Zr-L emission SXES spectra, the P-QC and F-QC alloys showed a chemical shift towards larger binding energy side. The magnitudes of the shifts in the Zn-L emission spectra of the quasicrystalline alloys were almost the same as for ZnO. These results strongly suggest a decrease in valence charge in quasicrystalline states. Therefore, it should be concluded that bonding in quasicrystalline states involves a characteristic increase in covalency compared with bonding in corresponding approximant and standard metal crystals.

  2. Carbon 13 chemical shift tensors in aromatic compounds. 3. Phenanthrene and triphenylene

    SciTech Connect

    Soderquist, A.; Hughes, C.D.; Horton, W.J.; Facelli, J.C.; Grant, D.M.

    1992-04-08

    Measurements of the principal values of the {sup 13}C chemical shift tensor are presented for the three carbons in triphenylene and for three different {alpha} carbons in phenanthrene. The measurements in triphenylene were made in natural abundance samples at room temperature, while the phenanthrene tensors were obtained from selectively labeled compounds (99% {sup 13}C) at low temperatures ({approx} 25 K). The principal values of the shift tensors were oriented in the molecular frame using ab initio LORG calculations. The steric compression at C{sub 4} in phenanthrene and in corresponding positions in triphenylene is manifested in sizable upfield shift in the {sigma} 33 component relative to the corresponding {sigma} 33 values at C{sub 1} and C{sub 9} in phenanthrene. The upfield shift in {sigma} 33 is mainly responsible for the well-known upfield shift of the isotropic chemical shifts of such sterically perturbed carbons. In phenanthrene c{sub 9} exhibits a unique {sigma} 22 value reflecting the greater localization of {pi}-electrons in the c{sub 9}-C{sub 10} bond. This localization of the {pi}-electrons at the C{sub 9}-C{sub 10} bond in the central ring of phenanthrene also corresponds with the most likely ordering of electrons described by the various Kekule structures in phenanthrene. The analysis of the {sup 13}C chemical shieldings of the bridgehead carbons in the triphenylene provides significant experimental information on bonding between rings in polycyclic aromatic compounds. 39 refs., 8 fig., 3 tab.

  3. Density Functional Studies of the 13C NMR Chemical Shifts in Single-Walled Carbon Nanotubes

    NASA Astrophysics Data System (ADS)

    Zurek, Eva; Autschbach, Jochen

    2007-12-01

    Density functional theory has been used to compute the electronic structure and 13C NMR chemical shifts of finite (9,0) single-walled carbon nanotubes (SWNTs) capped with fullerene hemispheres and with hydrogen atoms. The chemical shifts and HOMO-LUMO gaps were found to be dependent upon the mode of capping. The shifts of semiconducting and metallic tubes were estimated as being around 130 ppm and 141 ppm, respectively. Periodic boundary calculations on infinite zigzag (n,0) SWNTs with 7⩽n⩽17 were performed. These entities can be characterized by a family index, λ = mod(n,3), and the chemical shifts can be fitted well by a function inversely proportional to the diameter of the tube and proportional to a constant which depends on the nanotube family. Direct comparison of the molecular and periodic approaches can be made if benzene is used as the internal reference. Such a comparison indicates that capping may have a strong effect on the computed properties. Calculations on infinite zigzag (7⩽n⩽10) amine functionalized SWNTs have been performed. The functional group may react with a C-C bond which is parallel or diagonal to the tube axis and both sites have been considered. The shifts of the carbons directly attached to the group are sensitive to the bond which has been functionalized and may therefore be used to discriminate between the two products. Functionalization induces a significant line broadening of the NMR signals but it does not dramatically change the average shift of the unfunctionalized SWNT carbons.

  4. A sensitive, high resolution magic angle turning experiment for measuring chemical shift tensor principal values

    NASA Astrophysics Data System (ADS)

    Alderman, D. W.

    1998-12-01

    A sensitive, high-resolution 'FIREMAT' two-dimensional (2D) magic-angle-turning experiment is described that measures chemical shift tensor principal values in powdered solids. The spectra display spinning-sideband patterns separated by their isotropic shifts. The new method's sensitivity and high resolution in the isotropic-shift dimension result from combining the 5pi magic-angle-turning pulse sequence, an extension of the pseudo-2D sideband-suppression data rearrangement, and the TIGER protocol for processing 2D data. TPPM decoupling is used to enhance resolution. The method requires precise synchronization of the pulses and sampling to the rotor position. It is shown that the technique obtains 35 natural-abundance 13C tensors from erythromycin in 19 hours, and high quality naturalabundance 15N tensors from eight sites in potassium penicillin V in three days on a 400MHz spectrometer.

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

    PubMed

    Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L

    2012-10-01

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

  6. Nonlinear detection of secondary isotopic chemical shifts in NMR through spin noise

    NASA Astrophysics Data System (ADS)

    Pöschko, Maria Theresia; Rodin, Victor V.; Schlagnitweit, Judith; Müller, Norbert; Desvaux, Hervé

    2017-01-01

    The detection of minor species in the presence of large amounts of similar main components remains a key challenge in analytical chemistry, for instance, to obtain isotopic fingerprints. As an alternative to the classical NMR scheme based on coherent excitation and detection, here we introduce an approach based on spin-noise detection. Chemical shifts and transverse relaxation rates are determined using only the detection circuit. Thanks to a nonlinear effect in mixtures with small chemical shift dispersion, small signals on top of a larger one can be observed with increased sensitivity as bumps on a dip; the latter being the signature of the main magnetization. Experimental observations are underpinned by an analytical theory: the coupling between the magnetization and the coil provides an amplified detection capability of both small static magnetic field inhomogeneities and small NMR signals. This is illustrated by two-bond 12C/13C isotopic measurements.

  7. Nonlinear detection of secondary isotopic chemical shifts in NMR through spin noise

    PubMed Central

    Pöschko, Maria Theresia; Rodin, Victor V.; Schlagnitweit, Judith; Müller, Norbert; Desvaux, Hervé

    2017-01-01

    The detection of minor species in the presence of large amounts of similar main components remains a key challenge in analytical chemistry, for instance, to obtain isotopic fingerprints. As an alternative to the classical NMR scheme based on coherent excitation and detection, here we introduce an approach based on spin-noise detection. Chemical shifts and transverse relaxation rates are determined using only the detection circuit. Thanks to a nonlinear effect in mixtures with small chemical shift dispersion, small signals on top of a larger one can be observed with increased sensitivity as bumps on a dip; the latter being the signature of the main magnetization. Experimental observations are underpinned by an analytical theory: the coupling between the magnetization and the coil provides an amplified detection capability of both small static magnetic field inhomogeneities and small NMR signals. This is illustrated by two-bond 12C/13C isotopic measurements. PMID:28067218

  8. Modeling proteins using a super-secondary structure library and NMR chemical shift information.

    PubMed

    Menon, Vilas; Vallat, Brinda K; Dybas, Joseph M; Fiser, Andras

    2013-06-04

    A remaining challenge in protein modeling is to predict structures for sequences with no sequence similarity to any experimentally solved structure. Based on earlier observations, the library of protein backbone supersecondary structure motifs (Smotifs) saturated about a decade ago. Therefore, it should be possible to build any structure from a combination of existing Smotifs with the help of limited experimental data that are sufficient to relate the backbone conformations of Smotifs between target proteins and known structures. Here, we present a hybrid modeling algorithm that relies on an exhaustive Smotif library and on nuclear magnetic resonance chemical shift patterns without any input of primary sequence information. In a test of 102 proteins, the algorithm delivered 90 homology-model-quality models, among them 24 high-quality ones, and a topologically correct solution for almost all cases. The current approach opens a venue to address the modeling of larger protein structures for which chemical shifts are available.

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

    PubMed Central

    Shen, Yang; Bax, Ad

    2013-01-01

    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 12°. TALOS-N also reports sidechain χ1 rotameric states for about 50% of the residues, and a consistency with reference structures of 89%. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts. PMID:23728592

  10. 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.

  11. Evaluation of cerebral 31-P chemical shift images utilizing statistical parametric mapping

    NASA Astrophysics Data System (ADS)

    Riehemann, Stefan; Gaser, Christian; Volz, Hans-Peter; Sauer, Heinrich

    1999-05-01

    We present an evaluation technique of two dimensional (2D) nuclear magnetic resonance (NMR) chemical shift images (CSI) to analyze spatial differences of metabolite distributions and/or concentrations between groups of probands. Thus, chemical shift imaging is not only used as localization technique for NMR-spectroscopy, but the information of the complete spectroscopic image is used for the evaluation process. 31P CSI of the human brain were acquired with a Philips Gyroscan ACSII whole-body scanner at 1.5 T. CSI for different phosphorus metabolites were generated, all representing the same anatomical location. For each metabolite the CSI of two groups of subjects were compared with each other using the general linear model implemented in the widely distributed SPM96 software package. With this approach, even covariates or confounding variables like age or medication can be considered. As an example for the application of this technique, variations in the distribution of the 31P metabolite phosphocreatin between unmedicated schizophrenic patients and healthy controls were visualized. To our knowledge, this is the first approach to analyze spatial variations in metabolite concentrations between groups of subjects on the basis of chemical shift images. The presented technique opens a new perspective in the evaluation of 2D NMR spectroscopic data.

  12. Quantitative analysis of deuterium using the isotopic effect on quaternary (13)C NMR chemical shifts.

    PubMed

    Darwish, Tamim A; Yepuri, Nageshwar Rao; Holden, Peter J; James, Michael

    2016-07-13

    Quantitative analysis of specifically deuterated compounds can be achieved by a number of conventional methods, such as mass spectroscopy, or by quantifying the residual (1)H NMR signals compared to signals from internal standards. However, site specific quantification using these methods becomes challenging when dealing with non-specifically or randomly deuterated compounds that are produced by metal catalyzed hydrothermal reactions in D2O, one of the most convenient deuteration methods. In this study, deuterium-induced NMR isotope shifts of quaternary (13)C resonances neighboring deuterated sites have been utilized to quantify the degree of isotope labeling of molecular sites in non-specifically deuterated molecules. By probing (13)C NMR signals while decoupling both proton and deuterium nuclei, it is possible to resolve (13)C resonances of the different isotopologues based on the isotopic shifts and the degree of deuteration of the carbon atoms. We demonstrate that in different isotopologues, the same quaternary carbon, neighboring partially deuterated carbon atoms, are affected to an equal extent by relaxation. Decoupling both nuclei ((1)H, (2)H) resolves closely separated quaternary (13)C signals of the different isotopologues, and allows their accurate integration and quantification under short relaxation delays (D1 = 1 s) and hence fast accumulative spectral acquisition. We have performed a number of approaches to quantify the deuterium content at different specific sites to demonstrate a convenient and generic analysis method for use in randomly deuterated molecules, or in cases of specifically deuterated molecules where back-exchange processes may take place during work up.

  13. 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.

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

    PubMed

    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(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(n) with n = 2 and higher.

  15. Molecular structure and vibrational and chemical shift assignments of 3'-chloro-4-dimethylamino azobenzene by DFT calculations.

    PubMed

    Toy, Mehmet; Tanak, Hasan

    2016-01-05

    In the present work, a combined experimental and theoretical study on ground state molecular structure, spectroscopic and nonlinear optical properties of azo compound 3'-chloro-4-dimethlamino azobenzene are reported. The molecular geometry, vibrational wavenumbers and the first order hyperpolarizability of the title compound were calculated with the help of density functional theory computations. The optimized geometric parameters obtained by using DFT (B3LYP/6-311++G(d,p)) show good agreement with the experimental data. The vibrational transitions were identified based on the recorded FT-IR spectra in the range of 4000-400cm(-1) for solid state. The (1)H isotropic chemical shifts with respect to TMS were also calculated using the gauge independent atomic orbital (GIAO) method and compared with the experimental data. Using the TD-DFT method, electronic absorption spectra of the title compound have been predicted, and good agreement is determined with the experimental ones. To investigate the NLO properties of the title compound, the polarizability and the first hyperpolarizability were calculated using the density functional B3LYP method with the 6-311++G(d,p) basis set. According to results, the title compound exhibits non-zero first hyperpolarizability value revealing second order NLO behavior. In addition, DFT calculations of the title compound, molecular electrostatic potential and frontier molecular orbitals were also performed at 6-311++G(d,p) level of theory.

  16. 1H and 13C resonance designation of antimycin A1 by two-dimensional NMR spectroscopy

    USGS Publications Warehouse

    Abidi, S.L.; Adams, B.R.

    1987-01-01

    Complete 1H and 13C resonance assignments of antimycin A1 were accomplished by two-dimensional NMR techniques, viz. 1H homonuclear COSY correlation, heteronuclear 13C-1H chemical shift correlation and long-range heteronuclear 13C-1H COLOC correlation. Antimycin A1 was found to consist of two isomeric components in a 2:1 ratio based on NMR spectroscopic evidence. The structure of the major component was newly assigned as the 8-isopentanoic acid ester. The spectra of the minor component were consistent with the known structure of antimycin A1.

  17. Ring current effects in crystals. Evidence from 13C chemical shift tensors for intermolecular shielding in 4,7-di-t-butylacenaphthene versus 4,7-di-t-butylacenaphthylene.

    PubMed

    Ma, Zhiru; Halling, Merrill D; Solum, Mark S; Harper, James K; Orendt, Anita M; Facelli, Julio C; Pugmire, Ronald J; Grant, David M; Amick, Aaron W; Scott, Lawrence T

    2007-03-15

    13C chemical shift tensor data from 2D FIREMAT spectra are reported for 4,7-di-t-butylacenaphthene and 4,7-di-t-butylacenaphthylene. In addition, calculations of the chemical shielding tensors were completed at the B3LYP/6-311G** level of theory. While the experimental tensor data on 4,7-di-t-butylacenaphthylene are in agreement with theory and with previous data on polycyclic aromatic hydrocarbons, the experimental and theoretical data on 4,7-di-t-butylacenaphthene lack agreement. Instead, larger than usual differences are observed between the experimental chemical shift components and the chemical shielding tensor components calculated on a single molecule of 4,7-di-t-butylacenaphthene, with a root mean square (rms) error of +/-7.0 ppm. The greatest deviation is concentrated in the component perpendicular to the aromatic plane, with the largest value being a 23 ppm difference between experiment and theory for the 13CH2 carbon delta11 component. These differences are attributed to an intermolecular chemical shift that arises from the graphitelike, stacked arrangement of molecules found in the crystal structure of 4,7-di-t-butylacenaphthene. This conclusion is supported by a calculation on a trimer of molecules, which improves the agreement between experiment and theory for this component by 14 ppm and reduces the overall rms error between experiment and theory to 4.0 ppm. This intermolecular effect may be modeled with the use of nuclei independent chemical shieldings (NICS) calculations and is also observed in the isotropic 1H chemical shift of the CH2 protons as a 4.2 ppm difference between the solution value and the solid-state chemical shift measured via a 13C-1H heteronuclear correlation experiment.

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

    PubMed

    Kjaergaard, Magnus; Poulsen, Flemming M

    2011-06-01

    Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues. The contributions from the neighboring residues are typically removed by using neighbor correction factors determined based on each residue's effect on glycine chemical shifts. Due to its unusual conformational freedom, glycine may be particularly unrepresentative for the remaining residue types. In this study, we use random coil peptides containing glutamine instead of glycine to determine the random coil chemical shifts and the neighbor correction factors. The resulting correction factors correlate to changes in the populations of the major wells in the Ramachandran plot, which demonstrates that changes in the conformational ensemble are an important source of neighbor effects in disordered proteins. Glutamine derived random coil chemical shifts and correction factors modestly improve our ability to predict (13)C chemical shifts of intrinsically disordered proteins compared to existing datasets, and may thus improve the identification of small populations of transient structure in disordered proteins.

  19. Complete assignment of the (1)H and (13)C NMR spectra of cis and trans isonucleoside derivatives of purine with a tetrahydropyran ring.

    PubMed

    Besada, Pedro; Costas, Tamara; Terán, Carmen

    2010-06-01

    (1)H and (13)C NMR chemical shifts of cis and trans isonucleoside analogues of purine in which the furanose moiety is substituted by a tetrahydropyran ring were completely assigned using one- and two-dimensional NMR experiments that include NOE, DEPT, COSY and HSQC. The significant (1)H and (13)C NMR signals differentiating between the cis and trans stereoisomers were compared.

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

    PubMed

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

    2016-02-01

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

  1. Study the chemical composition and biological outcomes resulting from the interaction of the hormone adrenaline with heavy elements: Infrared, Raman, electronic, 1H NMR, XRD and SEM studies

    NASA Astrophysics Data System (ADS)

    Ibrahim, Omar B.; Mohamed, Mahmoud A.; Refat, Moamen S.

    2014-01-01

    Heavy metal adrenaline complexes formed from the reaction of adrenaline with Al3+, Zn2+, Sn2+, Sb3+, Pb2+and Bi3+ ions in methanolic solvent at 60 °C. The final reaction products have been isolated and characterization using elemental analyses (% of carbon, hydrogen and nitrogen), conductivity measurements, mid infrared, Raman laser, UV-Vis, 1H NMR spectra, X-ray powder diffraction, scanning electron microscopy and energy-dispersive X-ray spectroscopy (EDX). Upon the spectroscopic, conductivity and elemental analyses, the stoichiometric reactions indicated that the data obtained refer to 1:2 (M:L) for Zn2+, Sn2+, Pb2+and Bi3+ complexes [Zn(Adr)2(Cl)2], [Sn(Adr)2]Cl2, [Pb(Adr)2](NO3)2 and [Bi(Adr)2(Cl)2]Cl, while the molar ratio 1:3 (M:L) for Al3+ and Sb3+ with formulas [Al(Adr)3](NO3)3 and [Sb(Adr)3]Cl3. The infrared and Raman laser spectra interpreted the mode of interactions which associated through the two phenolic groups of catechol moiety. The adrenaline chelates have been screened for their in vitro antibacterial activity against four bacteria, Gram-positive (Bacillus subtilis and Staphylococcus aureus) and Gram-negative (Escherichia coli and Pseudomonas aeruginosa) and two strains of fungus (Aspergillus flavus and Candida albicans). The metal chelates were shown to possess more antibacterial and antifungal activities than the free adrenaline chelate.

  2. FT-IR, Laser-Raman spectra and quantum chemical calculations of methyl 4-(trifluoromethyl)-1H-pyrrole-3-carboxylate-A DFT approach

    NASA Astrophysics Data System (ADS)

    Sert, Yusuf; Sreenivasa, S.; Doğan, H.; Manojkumar, K. E.; Suchetan, P. A.; Ucun, Fatih

    2014-06-01

    In this study the experimental and theoretical vibrational frequencies of a newly synthesized anti-tumor and anti-inflammatory agent namely, methyl 4-(trifluoromethyl)-1H-pyrrole-3-carboxylate have been investigated. The experimental FT-IR (4000-400 cm-1) and Laser-Raman spectra (4000-100 cm-1) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths, bond angles and torsion angles) have been calculated using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr and DFT/M06-2X: highly parameterized, empirical exchange correlation function) with 6-311++G(d,p) basis set by Gaussian 03 software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data and results in the literature. In addition, the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy and the other related molecular energy values of the compound have been investigated using the same theoretical calculations.

  3. FT-IR, Laser-Raman spectra and quantum chemical calculations of methyl 4-(trifluoromethyl)-1H-pyrrole-3-carboxylate-A DFT approach.

    PubMed

    Sert, Yusuf; Sreenivasa, S; Doğan, H; Manojkumar, K E; Suchetan, P A; Ucun, Fatih

    2014-06-05

    In this study the experimental and theoretical vibrational frequencies of a newly synthesized anti-tumor and anti-inflammatory agent namely, methyl 4-(trifluoromethyl)-1H-pyrrole-3-carboxylate have been investigated. The experimental FT-IR (4000-400cm(-1)) and Laser-Raman spectra (4000-100cm(-1)) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths, bond angles and torsion angles) have been calculated using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr and DFT/M06-2X: highly parameterized, empirical exchange correlation function) with 6-311++G(d,p) basis set by Gaussian 03 software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data and results in the literature. In addition, the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy and the other related molecular energy values of the compound have been investigated using the same theoretical calculations.

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

    NASA Technical Reports Server (NTRS)

    Grodzka, P.; Facemire, B.

    1977-01-01

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

  5. 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

  6. Sclerosing liposarcoma of epididymis: Role of chemical shift magnetic resonance imaging

    PubMed Central

    Ramanathan, Subramaniyan; Raghu, Vineetha; Kumar, Devendra; Sempiege, Venkata R P

    2016-01-01

    Sclerosing liposarcoma of epididymis is a rare extratesticular scrotal tumor with variable prognosis. Ultrasonography is the initial imaging modality of choice for the evaluation of scrotal mass and helps to differentiate testicular and extratesticular masses, thereby narrowing down the differential diagnosis. Magnetic resonance imaging with its excellent soft tissue resolution can help in the further characterization of the nature of the tumor. In this case report, we highlight the role of chemical shift imaging in making a confident preoperative diagnosis of liposarcoma thereby guiding optimal and timely management. PMID:27857462

  7. 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.

  8. Deuterium isotope effect on 13C chemical shifts of tetrabutylammonium salts of Schiff bases amino acids.

    PubMed

    Rozwadowski, Z

    2006-09-01

    Deuterium isotope effects on 13C chemical shift of tetrabutylammonium salts of Schiff bases, derivatives of amino acids (glycine, L-alanine, L-phenylalanine, L-valine, L-leucine, L-isoleucine and L-methionine) and various ortho-hydroxyaldehydes in CDCl3 have been measured. The results have shown that the tetrabutylammonium salts of the Schiff bases amino acids, being derivatives of 2-hydroxynaphthaldehyde and 3,5-dibromosalicylaldehyde, exist in the NH-form, while in the derivatives of salicylaldehyde and 5-bromosalicylaldehyde a proton transfer takes place. The interactions between COO- and NH groups stabilize the proton-transferred form through a bifurcated intramolecular hydrogen bond.

  9. Autoregressive moving average modeling for spectral parameter estimation from a multigradient echo chemical shift acquisition.

    PubMed

    Taylor, Brian A; Hwang, Ken-Pin; Hazle, John D; Stafford, R Jason

    2009-03-01

    The authors investigated the performance of the iterative Steiglitz-McBride (SM) algorithm on an autoregressive moving average (ARMA) model of signals from a fast, sparsely sampled, multiecho, chemical shift imaging (CSI) acquisition using simulation, phantom, ex vivo, and in vivo experiments with a focus on its potential usage in magnetic resonance (MR)-guided interventions. The ARMA signal model facilitated a rapid calculation of the chemical shift, apparent spin-spin relaxation time (T2*), and complex amplitudes of a multipeak system from a limited number of echoes (< or equal 16). Numerical simulations of one- and two-peak systems were used to assess the accuracy and uncertainty in the calculated spectral parameters as a function of acquisition and tissue parameters. The measured uncertainties from simulation were compared to the theoretical Cramer-Rao lower bound (CRLB) for the acquisition. Measurements made in phantoms were used to validate the T2* estimates and to validate uncertainty estimates made from the CRLB. We demonstrated application to real-time MR-guided interventions ex vivo by using the technique to monitor a percutaneous ethanol injection into a bovine liver and in vivo to monitor a laser-induced thermal therapy treatment in a canine brain. Simulation results showed that the chemical shift and amplitude uncertainties reached their respective CRLB at a signal-to-noise ratio (SNR) > or =5 for echo train lengths (ETLs) > or =4 using a fixed echo spacing of 3.3 ms. T2* estimates from the signal model possessed higher uncertainties but reached the CRLB at larger SNRs and/or ETLs. Highly accurate estimates for the chemical shift (<0.01 ppm) and amplitude (<1.0%) were obtained with > or =4 echoes and for T2*(<1.0%) with > or =7 echoes. We conclude that, over a reasonable range of SNR, the SM algorithm is a robust estimator of spectral parameters from fast CSI acquisitions that acquire < or =16 echoes for one- and two-peak systems. Preliminary ex vivo

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

    NASA Astrophysics Data System (ADS)

    Özdemir, Namık; Dayan, Osman; Demirmen, Selin

    2016-05-01

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

  11. Backbone chemical shift assignments for Xanthomonas campestris peroxiredoxin Q in the reduced and oxidized states: a dramatic change in backbone dynamics.

    PubMed

    Buchko, Garry W; Perkins, Arden; Parsonage, Derek; Poole, Leslie B; Karplus, P Andrew

    2016-04-01

    Peroxiredoxins (Prx) are ubiquitous enzymes that reduce peroxides as part of antioxidant defenses and redox signaling. While Prx catalytic activity and sensitivity to hyperoxidative inactivation depend on their dynamic properties, there are few examples where their dynamics has been characterized by NMR spectroscopy. Here, we provide a foundation for studies of the solution properties of peroxiredoxin Q from the plant pathogen Xanthomonas campestris (XcPrxQ) by assigning the observable (1)H(N), (15)N, (13)C(α), (13)C(β), and (13)C' chemical shifts for both the reduced (dithiol) and oxidized (disulfide) states. In the reduced state, most of the backbone amide resonances (149/152, 98 %) can be assigned in the XcPrxQ (1)H-(15)N HSQC spectrum. In contrast, a remarkable 51 % (77) of these amide resonances are not visible in the (1)H-(15)N HSQC spectrum of the disulfide state of the enzyme, indicating a substantial change in backbone dynamics associated with the formation of an intramolecular C48-C84 disulfide bond.

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

    NASA Astrophysics Data System (ADS)

    Ota, Yukihiro; Mikami, Shuji; Yoshida, Motoyuki; Ohba, Ichiro

    2007-11-01

    Yu, Brown and Chuang investigated the entanglement attainable from unitary transformed thermal states in liquid-state nuclear magnetic resonance (NMR). Their research gave insight into the role of entanglement in a liquid-state NMR quantum computer. However, they assumed that the Zeeman energy of each nuclear spin which corresponds to a qubit takes a common value for all; there is no chemical shift. In this paper, we research a model with chemical shifts and analytically derive the physical parameter region where unitary transformed thermal states are entangled, by employing the positive partial transposition (PPT) criterion with respect to any bipartition. The analysis taking account of the chemical shift reveals how the difference between quantum gates reflects on the physical parameter region where unitary transformed thermal states are entangled. In addition, we examine the distillability of unitary transformed thermal states and the effect of the chemical shifts on the boundary between the separability and the nonseparability.

  13. 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

    2012-03-07

    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.

  14. Noninvasive temperature mapping with MRI using chemical shift water-fat separation.

    PubMed

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

    2010-05-01

    Tissues containing both water and lipids, e.g., breast, confound standard MR proton reference frequency-shift methods for mapping temperatures due to the lack of temperature-induced frequency shift in lipid protons. Generalized Dixon chemical shift-based water-fat separation methods, such as GE's iterative decomposition of water and fat with echo asymmetry and least-squares estimation method, can result in complex water and fat images. Once separated, the phase change over time of the water signal can be used to map temperature. Phase change of the lipid signal can be used to correct for non-temperature-dependent phase changes, such as amplitude of static field drift. In this work, an image acquisition and postprocessing method, called water and fat thermal MRI, is demonstrated in phantoms containing 30:70, 50:50, and 70:30 water-to-fat by volume. Noninvasive heating was applied in an Off1-On-Off2 pattern over 50 min, using a miniannular phased radiofrequency array. Temperature changes were referenced to the first image acquisition. Four fiber optic temperature probes were placed inside the phantoms for temperature comparison. Region of interest (ROI) temperature values colocated with the probes showed excellent agreement (global mean +/- standard deviation: -0.09 +/- 0.34 degrees C) despite significant amplitude of static field drift during the experiments.

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

    PubMed

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

    2009-09-10

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

  16. 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

    2016-10-05

    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.

  17. Determination of secondary structure populations in disordered states of proteins using nuclear magnetic resonance chemical shifts.

    PubMed

    Camilloni, Carlo; De Simone, Alfonso; Vranken, Wim F; Vendruscolo, Michele

    2012-03-20

    One of the major open challenges in structural biology is to achieve effective descriptions of disordered states of proteins. This problem is difficult because these states are conformationally highly heterogeneous and cannot be represented as single structures, and therefore it is necessary to characterize their conformational properties in terms of probability distributions. Here we show that it is possible to obtain highly quantitative information about particularly important types of probability distributions, the populations of secondary structure elements (α-helix, β-strand, random coil, and polyproline II), by using the information provided by backbone chemical shifts. The application of this approach to mammalian prions indicates that for these proteins a key role in molecular recognition is played by disordered regions characterized by highly conserved polyproline II populations. We also determine the secondary structure populations of a range of other disordered proteins that are medically relevant, including p53, α-synuclein, and the Aβ peptide, as well as an oligomeric form of αB-crystallin. Because chemical shifts are the nuclear magnetic resonance parameters that can be measured under the widest variety of conditions, our approach can be used to obtain detailed information about secondary structure populations for a vast range of different protein states.

  18. Contribution of high-energy conformations to NMR chemical shifts, a DFT-BOMD study.

    PubMed

    Goursot, A; Mineva, T; Vásquez-Pérez, J M; Calaminici, P; Köster, A M; Salahub, D R

    2013-01-21

    This paper highlights the relevance of including the high-energy conformational states sampled by Born-Oppenheimer molecular dynamics (BOMD) in the calculation of time-averaged NMR chemical shifts. Our case study is the very flexible glycerol molecule that undergoes interconversion between conformers in a nonrandom way. Along the sequence of structures from one backbone conformer to another, transition states have been identified. The three (13)C NMR chemical shifts of the molecule were estimated by averaging their calculated values over a large set of BOMD snapshots. The simulation time needed to obtain a good agreement with the two signals present in the experimental spectrum is shown to be dependent on the atomic orbital basis set used for the dynamics, with a necessary longer trajectory for the most extended basis sets. The large structural deformations with respect to the optimized conformer geometries that occur along the dynamics are related to a kinetically driven conformer distribution. Calculated conformer type populations are in good agreement with experimental gas phase microwave results.

  19. Solvation effects on chemical shifts by embedded cluster integral equation theory.

    PubMed

    Frach, Roland; Kast, Stefan M

    2014-12-11

    The accurate computational prediction of nuclear magnetic resonance (NMR) parameters like chemical shifts represents a challenge if the species studied is immersed in strongly polarizing environments such as water. Common approaches to treating a solvent in the form of, e.g., the polarizable continuum model (PCM) ignore strong directional interactions such as H-bonds to the solvent which can have substantial impact on magnetic shieldings. We here present a computational methodology that accounts for atomic-level solvent effects on NMR parameters by extending the embedded cluster reference interaction site model (EC-RISM) integral equation theory to the prediction of chemical shifts of N-methylacetamide (NMA) in aqueous solution. We examine the influence of various so-called closure approximations of the underlying three-dimensional RISM theory as well as the impact of basis set size and different treatment of electrostatic solute-solvent interactions. We find considerable and systematic improvement over reference PCM and gas phase calculations. A smaller basis set in combination with a simple point charge model already yields good performance which can be further improved by employing exact electrostatic quantum-mechanical solute-solvent interaction energies. A larger basis set benefits more significantly from exact over point charge electrostatics, which can be related to differences of the solvent's charge distribution.

  20. Molecular structure, spectral investigation (1H NMR, 13C NMR, UV-Visible, FT-IR, FT-Raman), NBO, intramolecular hydrogen bonding, chemical reactivity and first hyperpolarizability analysis of formononetin [7-hydroxy-3(4-methoxyphenyl)chromone]: A quantum chemical study

    NASA Astrophysics Data System (ADS)

    Srivastava, Anubha; Mishra, Rashmi; Kumar, Sudhir; Dev, Kapil; Tandon, Poonam; Maurya, Rakesh

    2015-03-01

    Formononetin [7-hydroxy-3(4-methoxyphenyl)chromone or 4‧-methoxy daidzein] is a soy isoflavonoid that is found abundantly in traditional Chinese medicine Astragalus mongholicus (Bunge) and Trifolium pretense L. (red clover), and in an Indian medicinal plant, Butea (B.) monosperma. Crude extract of B.monosperma is used for rapid healing of fracture in Indian traditional medicine. In this study, a combined theoretical and experimental approach is used to study the properties of formononetin. The optimized geometry was calculated by B3LYP method using 6-311++G(d,p) as a large basis set. The FT-Raman and FT-IR spectra were recorded in the solid phase, and interpreted in terms of potential energy distribution (PED) analysis. Density functional theory (DFT) is applied to explore the nonlinear optical properties of the molecule. Good consistency is found between the calculated results and observed data for the electronic absorption, IR and Raman spectra. The solvent effects have been calculated using time-dependent density functional theory in combination with the integral equation formalism polarized continuum model, and the results are in good agreement with observed measurements. The double well potential energy curve of the molecule about the respective bonds, have been plotted, as obtained from DFT/6-31G basis set. The computational results diagnose the most stable conformer of formononetin. The HOMO-LUMO energy gap of possible conformers has been calculated for comparing their chemical activity. Chemical reactivity has been measured by reactivity descriptors and molecular electrostatic potential surface (MEP). The 1H and 13C NMR chemical shifts of the molecule were calculated by the Gauge including atomic orbital (GIAO) method. Furthermore, the role of CHsbnd O intramolecular hydrogen bond in the stability of molecule is investigated on the basis of the results of topological properties of AIM theory and NBO analysis. The calculated first hyperpolarizability shows

  1. Cuticular hydrocarbon divergence in the jewel wasp Nasonia: Evolutionary shifts in chemical communication channels?

    PubMed Central

    Buellesbach, Jan; Gadau, Jürgen; Beukeboom, Leo W.; Echinger, Felix; Raychoudhury, Rhitoban; Werren, John H.; Schmitt, Thomas

    2013-01-01

    The evolution and maintenance of intraspecific communication channels constitutes a key feature of chemical signaling and sexual communication. However, how divergent chemical communication channels evolve while maintaining their integrity for both sender and receiver is poorly understood. In the present study, we compare male and female cuticular hydrocarbon (CHC) profiles in the jewel wasp genus Nasonia, analyze their chemical divergence, and investigate their role as species-specific sexual signaling cues. Males and females of all four Nasonia species showed unique, non-overlapping CHC profiles unambiguously separating them. Surprisingly, male and female phylogenies based on the chemical distances between their CHC profiles differed dramatically, where only male CHC divergence parallels the molecular phylogeny of Nasonia. In particular, N. giraulti female CHC profiles were the most divergent from all other species and very different from its most closely related sibling species N. oneida. Furthermore, although our behavioural assays indicate that female CHC can generally be perceived as sexual cues attracting males in Nasonia, this function has apparently been lost in the highly divergent female N. giraulti CHC profiles. Curiously, N. giraulti males are still attracted to heterospecific, but not to conspecific female CHC profiles. We suggest that this striking discrepancy has been caused by an extensive evolutionary shift in female N. giraulti CHC profiles, which are no longer used as conspecific recognition cues. Our study constitutes the first report of an apparent abandonment of a sexual recognition cue that the receiver did not adapt to. PMID:24118588

  2. U1h Superstructure

    SciTech Connect

    Glen Sykes

    2000-11-01

    The U1H Shaft Project is a design build subcontract to supply the U. S. Department of Energy (DOE) a 1,045 ft. deep, 20 ft. diameter, concrete lined shaft for unspecified purposes. The subcontract awarded to Atkinson Construction by Bechtel Nevada to design and construct the shaft for the DOE has been split into phases with portions of the work being released as dictated by available funding. The first portion released included the design for the shaft, permanent hoist, headframe, and collar arrangement. The second release consisted of constructing the shaft collar to a depth of 110 ft., the service entry, utility trenches, and installation of the temporary sinking plant. The temporary sinking plant included the installation of the sinking headframe, the sinking hoist, two deck winches, the shaft form, the sinking work deck, and temporary utilities required to sink the shaft. Both the design and collar construction were completed on schedule. The third release consisted of excavating and lining the shaft to the station depth of approximately 950 feet. Work is currently proceeding on this production sinking phase. At a depth of approximately 600 feet, Atkinson has surpassed production expectation and is more than 3 months ahead of schedule. Atkinson has employed the use of a Bobcat 331 excavator as the primary means of excavation. the shaft is being excavated entirely in an alluvial deposit with varying degrees of calcium carbonate cementation. Several more work packages are expected to be released in the near future. The remaining work packages include, construction of the shaft station a depth of 975 ft. and construction of the shaft sump to a depth of 1,045 ft., installation of the loading pocket and station steel and equipment, installation of the shaft steel and guides, installation of the shaft utilities, and installation of the permanent headframe, hoist, collar utilities, and facilities.

  3. Monitoring the on-line titration of enantiomeric omeprazole employing continuous-flow capillary microcoil 1H NMR spectroscopy.

    PubMed

    Hentschel, Petra; Holtin, Karsten; Steinhauser, Lisa; Albert, Klaus

    2012-12-01

    The titration of the (S)-enantiomer of omeprazole with the (R)-enantiomer in chloroform-d(1) is monitored by continuous-flow capillary microcoil (1)H NMR spectroscopy employing a microcoil with a detection volume of 1.5 µl. The observed changes of the (1)H NMR chemical shifts indicate the formation of a heterochiral (R,S) dimer of omeprazole via its sulfinyl group and the NH group of the benzimidazole ring.

  4. 1H NMR investigation of self-association of vanillin in aqueous solution

    NASA Astrophysics Data System (ADS)

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

    2009-08-01

    A self-association of vanillin have been studied by 1H NMR spectroscopy using the analysis of proton chemical shifts changes in aqueous solution as a function of concentration. The experimental results have been analysed using indefinite non-cooperative and cooperative models of molecular self-association, enabling the determination of equilibrium constants, parameters of cooperativity and the limiting values of vanillin proton chemical shifts in the complex. It was found that the dimer formation creates energetically favourable conditions for subsequent molecular association.

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

    SciTech Connect

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

    2015-06-22

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

  6. 125Te NMR chemical-shift trends in PbTe-GeTe and PbTe-SnTe alloys.

    PubMed

    Njegic, B; Levin, E M; Schmidt-Rohr, K

    2013-01-01

    Complex tellurides, such as doped PbTe, GeTe, and their alloys, are among the best thermoelectric materials. Knowledge of the change in (125)Te NMR chemical shift due to bonding to dopant or "solute" atoms is useful for determination of phase composition, peak assignment, and analysis of local bonding. We have measured the (125)Te NMR chemical shifts in PbTe-based alloys, Pb1-xGexTe and Pb1-xSnxTe, which have a rocksalt-like structure, and analyzed their trends. For low x, several peaks are resolved in the 22-kHz MAS (125)Te NMR spectra. A simple linear trend in chemical shifts with the number of Pb neighbors is observed. No evidence of a proposed ferroelectric displacement of Ge atoms in a cubic PbTe matrix is detected at low Ge concentrations. The observed chemical shift trends are compared with the results of DFT calculations, which confirm the linear dependence on the composition of the first-neighbor shell. The data enable determination of the composition of various phases in multiphase telluride materials. They also provide estimates of the (125)Te chemical shifts of GeTe and SnTe (+970 and +400±150 ppm, respectively, from PbTe), which are otherwise difficult to access due to Knight shifts of many hundreds of ppm in neat GeTe and SnTe.

  7. Relationship between nonlinear pressure-induced chemical shift changes and thermodynamic parameters.

    PubMed

    Beck Erlach, Markus; Koehler, Joerg; Moeser, Beate; Horinek, Dominik; Kremer, Werner; Kalbitzer, Hans Robert

    2014-05-29

    NMR chemical shift analysis is a powerful method to investigate local changes in the environment of the observed nuclear spin of a polypeptide that are induced by application of high hydrostatic pressure. Usually, in the fast exchange regime, the pressure dependence of chemical shifts is analyzed by a second order Taylor expansion providing the first- and second-order pressure coefficient B1 and B2. The coefficients then are interpreted in a qualitative manner. We show here that in a two-state model, the ratio of B2/B1 is related to thermodynamic parameters, namely the ratio of the difference of compressibility factors Δβ' and partial molar volumes ΔV. The analysis is applied to the random-coil model peptides Ac-Gly-Gly-Xxx-Ala-NH2, with Xxx being one of the 20 proteinogenic amino acids. The analysis gives an average Δβ'/ΔV ratio of 1.6 GPa(-1) provided the condition |ΔG(0)| ≪ 2RT holds for the difference of the Gibbs free energies (ΔG(0)) of the two states at the temperature (T0) and the pressure (p0). The amide proton and nitrogen B2/B1 of a given amino acid Xxx are strongly correlated, indicating that their pressure-dependent chemical shift changes are due to the same thermodynamic process. As a possible physical mechanism providing a two-state model, the hydrogen bonding of water with the corresponding amide protein was simulated for isoleucine in position Xxx. The obtained free energy could satisfy the relation |ΔG(0)| ≪ 2RT. The derived relation was applied to the β-amyloid peptide Aβ and the phosphocarrier protein HPr from S. carnosus. For the transition of state 1 to state 2' of Aβ, the derived relation of B2/B1 to Δβ'/ΔV can be confirmed experimentally. The HPr protein is characterized by substantially higher negative B2/B1 values than those found in the tetrapeptides with an average value of approximately -5.1 GPa(-1) (Δβ'/ΔV of 5.1 GPa(-1) provided |ΔG(0)| ≪ 2RT holds). Qualitatively, the B2/B1 ratio can be used to predict

  8. 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…

  9. Identify five kinds of simple super-secondary structures with quadratic discriminant algorithm based on the chemical shifts.

    PubMed

    Kou, Gaoshan; Feng, Yonge

    2015-09-07

    The biological function of protein is largely determined by its spatial structure. The research on the relationship between structure and function is the basis of protein structure prediction. However, the prediction of super secondary structure is an important step in the prediction of protein spatial structure. Many algorithms have been proposed for the prediction of protein super secondary structure. However, the parameters used by these methods were primarily based on amino acid sequences. In this paper, we proposed a novel model for predicting five kinds of protein super secondary structures based on the chemical shifts (CSs). Firstly, we analyzed the statistical distribution of chemical shifts of six nuclei in five kinds of protein super secondary structures by using the analysis of variance (ANOVA). Secondly, we used chemical shifts of six nuclei as features, and combined with quadratic discriminant analysis (QDA) to predict five kinds of protein super secondary structures. Finally, we achieved the averaged sensitivity, specificity and the overall accuracy of 81.8%, 95.19%, 82.91%, respectively in seven-fold cross-validation. Moreover, we have performed the prediction by combining the five different chemical shifts as features, the maximum overall accuracy up to 89.87% by using the C,Cα,Cβ,N,Hα of Hα chemical shifts, which are clearly superior to that of the quadratic discriminant analysis (QDA) algorithm by using 20 amino acid compositions (AAC) as feature in the seven-fold cross-validation. These results demonstrated that chemical shifts (CSs) are indeed an outstanding parameter for the prediction of five kinds of super secondary structures. In addition, we compared the prediction of the quadratic discriminant analysis (QDA) with that of support vector machine (SVM) by using the same six CSs as features. The result suggested that the quadratic discriminant analysis method by using chemical shifts as features is a good predictor for protein super

  10. 129Xe chemical shift in human blood and pulmonary blood oxygenation measurement in humans using hyperpolarized 129Xe NMR

    PubMed Central

    Norquay, Graham; Leung, General; Stewart, Neil J.; Wolber, Jan

    2016-01-01

    Purpose To evaluate the dependency of the 129Xe‐red blood cell (RBC) chemical shift on blood oxygenation, and to use this relation for noninvasive measurement of pulmonary blood oxygenation in vivo with hyperpolarized 129Xe NMR. Methods Hyperpolarized 129Xe was equilibrated with blood samples of varying oxygenation in vitro, and NMR was performed at 1.5 T and 3 T. Dynamic in vivo NMR during breath hold apnea was performed at 3 T on two healthy volunteers following inhalation of hyperpolarized 129Xe. Results The 129Xe chemical shift in RBCs was found to increase nonlinearly with blood oxygenation at 1.5 T and 3 T. During breath hold apnea, the 129Xe chemical shift in RBCs exhibited a periodic time modulation and showed a net decrease in chemical shift of ∼1 ppm over a 35 s breath hold, corresponding to a decrease of 7–10 % in RBC oxygenation. The 129Xe‐RBC signal amplitude showed a modulation with the same frequency as the 129Xe‐RBC chemical shift. Conclusion The feasibility of using the 129Xe‐RBC chemical shift to measure pulmonary blood oxygenation in vivo has been demonstrated. Correlation between 129Xe‐RBC signal and 129Xe‐RBC chemical shift modulations in the lung warrants further investigation, with the aim to better quantify temporal blood oxygenation changes in the cardiopulmonary vascular circuit. Magn Reson Med 77:1399–1408, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. PMID:27062652

  11. 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.

  12. Earth field NMR with chemical shift spectral resolution: theory and proof of concept.

    PubMed

    Katz, Itai; Shtirberg, Lazar; Shakour, Gubrail; Blank, Aharon

    2012-06-01

    A new method for obtaining an NMR signal in the Earth's magnetic field (EF) is presented. The method makes use of a simple pulse sequence with only DC fields which is much less demanding than previous approaches in terms of the pulses' rise and fall times. Furthermore, it offers the possibility of obtaining NMR data with enough spectral resolution to allow retrieving high resolution molecular chemical shift (CS) information - a capability that was not considered possible in EF NMR until now. Details of the pulse sequence, the experimental system, and our specially tailored EF NMR probe are provided. The experimental results demonstrate the capability to differentiate between three types of samples made of common fluorine compounds, based on their CS data.

  13. Protein dynamics from chemical shift and dipolar rotational spin-echo sup 15 N NMR

    SciTech Connect

    Garbow, J.R.; Jacob, G.S.; Stejskal, E.O.; Schaefer, J. )

    1989-02-07

    The partial collapse of dipolar and chemical shift tensors for peptide NH and for the amide NH at cross-link sites in cell wall peptidoglycan, of intact lyophilized cells of Aerococcus viridans, indicates NH vector root-mean-square fluctuations of 23{degree}. This result is consistent with the local mobility calculated in typical picosecond regime computer simulations of protein dynamics in the solid state. The experimental root-mean-square angular fluctuations for both types of NH vectors increase to 37{degree} for viable wet cells at 10{degree}C. The similarity in mobilities for both general protein and cell wall peptidoglycan suggests that one additional motion in wet cells involves cooperative fluctuations of segments of cell walls, attached proteins, and associated cytoplasmic proteins.

  14. A critical evaluation of heteronuclear TOCSY (HEHAHA) experiments for 1H,6Li spin pairs.

    PubMed

    Bergander, Klaus; Hüls, Dietmar; Glaser, Steffen J; Günther, Harald; Luy, Burkhard

    2014-12-01

    Heteronuclear TOCSY (HEHAHA) experiments for (1) H,(6) Li spin pairs in organolithium compounds with adjacent strongly coupled (1) H,(1) H spin systems showed unexpected cross peak behaviour: for n-butyllithium (1) H,(6) Li cross peaks were completely missing, whereas for the dimer of (Z)-2-lithio-1-(o-lithiophenyl)ethane, a cross peak for remote protons was observed even at very short mixing times. It was assumed that strong magnetization transfer within the proton spin systems was responsible for these results, which prevented unambiguous chemical shift assignments. Selective experiments with the (6) Li,(1) H-HET-PLUSH-TACSY sequence then showed the expected (6) Li,(1) H cross peaks for the transfer via the directly coupled (1) H and (6) Li nuclei. For n-butyllithium transfer to H(Cα) via an unresolved heteronuclear coupling constant below 0.1 Hz is unambiguously observed. Cross peaks in the 2D (6) Li,(1) H-HET-PLUSH-TACSY spectra for the dimer of (Z)-2-lithio-1-(o-lithiophenyl)ethane are readily explained by the measured coupling network and the corresponding active mixing conditions.

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

    SciTech Connect

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

    2011-09-21

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

  16. 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.

  17. Characteristic chemical shift of quasicrystalline alloy Al53Si27Mn20 studied by EELS and SXES

    NASA Astrophysics Data System (ADS)

    Koshiya, S.; Terauchi, M.; Tsai, A. P.

    2011-06-01

    Chemical shifts of all constituent atoms for amorphous (Am), quasicrystalline (QC) and crystalline (Cryst) alloys of Al53Si27Mn20 were investigated for the first time by high energy-resolution electron energy-loss spectroscopy (EELS) and soft-X-ray emission spectroscopy (SXES). Among Al L-shell excitation EELS spectra of Am, QC and Cryst alloys, only QC alloy showed an apparent chemical shift to the larger binding energy side by 0.4 eV. In Al-Kα and Si-Kα emission SXES spectra of these alloys, only QC alloy showed a chemical shift to the larger binding energy side by 4 eV for Al-Kα and 6 eV for Si-Kα. These chemical shift values are comparable to those of corresponding metal oxides. This indicates a smaller amount of valence charge at Al and Si atomic sites in QC alloy. On the other hand, Mn-L SXES spectra did not show any chemical shift. Therefore, the decreased charge from Al and Si sites should be distributed between atomic sites, indicating the presence of covalent bonding nature for QC ordered alloy.

  18. Chemical amplification--cavity attenuated phase shift spectroscopy measurements of atmospheric peroxy radicals.

    PubMed

    Wood, Ezra C; Charest, John R

    2014-10-21

    We describe a new instrument for the quantification of atmospheric peroxy radicals (HO2, CH3O2, C2H5O2, etc.) using the chemical amplification method. Peroxy radicals are mixed with high concentrations of NO and CO, causing a chain reaction that produces a measurable increase in NO2 which is quantified by cavity attenuated phase shift (CAPS) spectroscopy, a highly sensitive spectroscopic detection technique. The instrument utilizes two identical reaction chambers, each with a dedicated CAPS NO2 sensor. Similar to all dual-channel chemical amplifiers, one reaction chamber operates in amplification or "ROx" mode and the other in background or "Ox" mode. The peroxy radical mixing ratio is determined by the difference between the two channels' NO2 readings divided by a laboratory-determined chain length. Each reaction chamber alternates between ROx and Ox mode on an anti-synchronized schedule, eliminating the effect of CAPS baseline offsets on the calculated peroxy radical concentrations. The chain length is determined by a new calibration method: peroxyacetyl and methyl peroxy radicals are produced by the photolysis of acetone and quantified as NO2 following reaction with excess NO. We demonstrate the performance of the instrument with results from ambient sampling in Amherst and several diagnostics of its precision. The detection limit while sampling ambient air at a relative humidity (RH) of 40% is 0.6 ppt (1 min average, signal-to-noise ratio =2), with an estimated accuracy of 25% (2σ).

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

    SciTech Connect

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

    2015-09-14

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

  20. Chemical shift tensor determination using magnetically oriented microcrystal array (MOMA): 13C solid-state CP NMR without MAS

    NASA Astrophysics Data System (ADS)

    Kusumi, R.; Kimura, F.; Song, G.; Kimura, T.

    2012-10-01

    Chemical shift tensors for the carboxyl and methyl carbons of L-alanine crystals were determined using a magnetically oriented microcrystal array (MOMA) prepared from a microcrystalline powder sample of L-alanine. A MOMA is a single-crystal-like composite in which microcrystals are aligned three-dimensionally in a matrix resin. The single-crystal rotation method was applied to the MOMA to determine the principal values and axes of the chemical shift tensors. The result showed good agreement with the literature data for the single crystal of L-alanine. This demonstrates that the present technique is a powerful tool for determining the chemical shift tensor of a crystal from a microcrystal powder sample.

  1. Quantitative produced water analysis using mobile 1H NMR

    NASA Astrophysics Data System (ADS)

    Wagner, Lisabeth; Kalli, Chris; Fridjonsson, Einar O.; May, Eric F.; Stanwix, Paul L.; Graham, Brendan F.; Carroll, Matthew R. J.; Johns, Michael L.

    2016-10-01

    Measurement of oil contamination of produced water is required in the oil and gas industry to the (ppm) level prior to discharge in order to meet typical environmental legislative requirements. Here we present the use of compact, mobile 1H nuclear magnetic resonance (NMR) spectroscopy, in combination with solid phase extraction (SPE), to meet this metrology need. The NMR hardware employed featured a sufficiently homogeneous magnetic field, such that chemical shift differences could be used to unambiguously differentiate, and hence quantitatively detect, the required oil and solvent NMR signals. A solvent system consisting of 1% v/v chloroform in tetrachloroethylene was deployed, this provided a comparable 1H NMR signal intensity for the oil and the solvent (chloroform) and hence an internal reference 1H signal from the chloroform resulting in the measurement being effectively self-calibrating. The measurement process was applied to water contaminated with hexane or crude oil over the range 1-30 ppm. The results were validated against known solubility limits as well as infrared analysis and gas chromatography.

  2. 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.

  3. Correlation of Electronic Effects in N-Alkylnicotinamides with NMR Chemical Shifts and Hydride Transfer Reactivity.

    PubMed

    Burke, James R.; Frey, Perry A.

    1996-01-26

    The (13)C and (15)N NMR chemical shifts for ring atoms of a series of N-alkylnicotinamides are shown to be correlated with their reduction potentials and reactivities toward NaBH(3)CN. The nicotinamide compounds include N-ethyl-N-benzyl-N-[p-(trifluoromethyl)benzyl]-, N-(p-cyanobenzyl)-, N-(carbomethoxymethyl)-, and N-(cyanomethyl)nicotinamides. The values of delta()13(C) for all the ring carbons increase with increasing electron-withdrawing power of the N-alkyl substituent. The value for C-4 increases the most, a range of 2.4 ppm in this series, whereas those for other atoms increase on the order of 1 ppm. The value of delta()15(N) for N-1 decreases with increasing electron-withdrawing power over a range of 20 ppm. The NMR data indicate that inductive electron withdrawal by N-alkyl substituents polarizes the pi-electron system to decrease electron density on ring carbons and increase electron density on the ring nitrogen. The values of log k (second order) for reduction of these compounds by NaBH(3)CN are proportional to the values of delta()13(C) for C-4 and inversely proportional to delta()15(N) for N-1. The reduction potentials are proportional to delta()13(C). The substituent effects are qualitatively similar to the substrate-induced electrostatic effects on the nicotinamide ring of NAD(+) at the active site of UDP-galactose 4-epimerase (Burke, J. R.; Frey, P. A. Biochemistry 1993, 32, 13220-13230). However, they differ quantitatively in that the upfield perturbation at N-1 is smaller in the enzyme and the signal for C-6 is also shifted upfield. The substrate-induced enzymatic perturbation of electron density at C-4 of NAD(+) quantitatively accounts for its increase in reactivity at the active site, but the perturbation at N-1 is less closely correlated with reactivity.

  4. Multiparametric fat–water separation method for fast chemical-shift imaging guidance of thermal therapies

    PubMed Central

    Lin, Jonathan S.; Hwang, Ken-Pin; Jackson, Edward F.; Hazle, John D.; Jason Stafford, R.; Taylor, Brian A.

    2013-01-01

    Purpose: A k-means-based classification algorithm is investigated to assess suitability for rapidly separating and classifying fat/water spectral peaks from a fast chemical shift imaging technique for magnetic resonance temperature imaging. Algorithm testing is performed in simulated mathematical phantoms and agar gel phantoms containing mixed fat/water regions. Methods: Proton resonance frequencies (PRFs), apparent spin-spin relaxation (T2*) times, and T1-weighted (T1-W) amplitude values were calculated for each voxel using a single-peak autoregressive moving average (ARMA) signal model. These parameters were then used as criteria for k-means sorting, with the results used to determine PRF ranges of each chemical species cluster for further classification. To detect the presence of secondary chemical species, spectral parameters were recalculated when needed using a two-peak ARMA signal model during the subsequent classification steps. Mathematical phantom simulations involved the modulation of signal-to-noise ratios (SNR), maximum PRF shift (MPS) values, analysis window sizes, and frequency expansion factor sizes in order to characterize the algorithm performance across a variety of conditions. In agar, images were collected on a 1.5T clinical MR scanner using acquisition parameters close to simulation, and algorithm performance was assessed by comparing classification results to manually segmented maps of the fat/water regions. Results: Performance was characterized quantitatively using the Dice Similarity Coefficient (DSC), sensitivity, and specificity. The simulated mathematical phantom experiments demonstrated good fat/water separation depending on conditions, specifically high SNR, moderate MPS value, small analysis window size, and low but nonzero frequency expansion factor size. Physical phantom results demonstrated good identification for both water (0.997 ± 0.001, 0.999 ± 0.001, and 0.986 ± 0.001 for DSC, sensitivity, and specificity, respectively

  5. Chemical-shift-selective filter for the in vivo detection of J-coupled metabolites at 3T.

    PubMed

    Schulte, Rolf F; Trabesinger, Andreas H; Boesiger, Peter

    2005-02-01

    A chemical-shift-selective filter (CSSF) was applied to the detection of J-coupled metabolites in the human brain. This filter is an acquisition-based technique that requires the chemical shifts (CS's) of different metabolites, but not their whole multiplet structures, to be resolved. The sequence is based on the 2D constant-time spin-echo experiment, which yields pure CS spectra in the indirect dimension. Localization is achieved through point-resolved spectroscopy (PRESS). The method enables unequivocal detection of glutamate and myo-inositol, both in vitro and in vivo in the human brain, at 3T.

  6. 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

  7. Regional Differences in Muscle Energy Metabolism in Human Muscle by 31P-Chemical Shift Imaging.

    PubMed

    Kime, Ryotaro; Kaneko, Yasuhisa; Hongo, Yoshinori; Ohno, Yusuke; Sakamoto, Ayumi; Katsumura, Toshihito

    2016-01-01

    Previous studies have reported significant region-dependent differences in the fiber-type composition of human skeletal muscle. It is therefore hypothesized that there is a difference between the deep and superficial parts of muscle energy metabolism during exercise. We hypothesized that the inorganic phosphate (Pi)/phosphocreatine (PCr) ratio of the superficial parts would be higher, compared with the deep parts, as the work rate increases, because the muscle fiber-type composition of the fast-type may be greater in the superficial parts compared with the deep parts. This study used two-dimensional 31Phosphorus Chemical Shift Imaging (31P-CSI) to detect differences between the deep and superficial parts of the human leg muscles during dynamic knee extension exercise. Six healthy men participated in this study (age 27±1 year, height 169.4±4.1 cm, weight 65.9±8.4 kg). The experiments were carried out with a 1.5-T superconducting magnet with a 5-in. diameter circular surface coil. The subjects performed dynamic one-legged knee extension exercise in the prone position, with the transmit-receive coil placed under the right quadriceps muscles in the magnet. The subjects pulled down an elastic rubber band attached to the ankle at a frequency of 0.25, 0.5 and 1 Hz for 320 s each. The intracellular pH (pHi) was calculated from the median chemical shift of the Pi peak relative to PCr. No significant difference in Pi/PCr was observed between the deep and the superficial parts of the quadriceps muscles at rest. The Pi/PCr of the superficial parts was not significantly increased with increasing work rate. Compared with the superficial areas, the Pi/PCr of the deep parts was significantly higher (p<0.05) at 1 Hz. The pHi showed no significant difference between the two parts. These results suggest that muscle oxidative metabolism is different between deep and superficial parts of quadriceps muscles during dynamic exercise.

  8. 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

  9. Insight into hydrogen bonding of uranyl hydroxide layers and capsules by use of 1H magic-angle spinning NMR spectroscopy [Insight into the hydrogen bonding for uranyl hydroxides using 1H MAS NMR spectroscopy

    DOE PAGES

    Alam, Todd M.; Liao, Zuolei; Nyman, May; ...

    2016-04-27

    Solid-state 1H magic-angle spinning (MAS) NMR was used to investigate local proton environments in anhydrous [UO2(OH)2] (α-UOH) and hydrated uranyl hydroxide [(UO2)4O(OH)6·5H2O (metaschoepite). For the metaschoepite material, proton resonances of the μ2-OH hydroxyl and interlayer waters were resolved, with two-dimensional (2D) double-quantum (DQ) 1H–1H NMR correlation experiments revealing strong dipolar interactions between these different proton species. The experimental NMR results were combined with first-principles CASTEP GIPAW (gauge including projector-augmented wave) chemical shift calculations to develop correlations between hydrogen-bond strength and observed 1H NMR chemical shifts. Furthermore, these NMR correlations allowed characterization of local hydrogen-bond environments in uranyl U24 capsules andmore » of changes in hydrogen bonding that occurred during thermal dehydration of metaschoepite.« less

  10. Atmospheric Peroxy Radical Measurements by Chemical Amplification - Cavity Attenuated Phase Shift Spectroscopy

    NASA Astrophysics Data System (ADS)

    Wood, E. C.; Charest, J. R.

    2013-12-01

    We present a new chemical amplifier for the detection of peroxy radicals using Cavity Attenuated Phase Shift spectroscopy (CAPS) detection of NO2. The amplification scheme is similar to other chemical amplifiers and involves addition of CO (8%) and NO (3 ppm) to air sampled in a PFA tube. The chain length is quantified by amplification of a known concentration of methyl peroxy radicals (CH3O2) and peroxyacetyl radicals (CH3COO2) sampled by the instrument's reactor. The CH3O2 and CH3COO2 radicals are produced by photolysis of acetone at 254 nm and quantified by conversion to NO2 by reaction with excess NO. The chain length (CL) in dry air is over 200 and constant at RO2 concentrations under 500 ppt. The CL decreases by 55% at a relative humidity of 50%. A 0.95 cm (3/8') ID PFA tube, a 0.32 cm (1/8' ID) PFA tube, and a 0.48 cm ID quartz reactor give near-identical chain lengths and RH dependence, demonstrating the small importance of wall reactions (for clean tubing) as radical termination steps. The instrument comprises two independent inlets and CAPS detectors, allowing for simultaneous measurements in ROx mode (= NO2 + O3 + RO2 + HO2) and Ox mode (= NO2 + O3) thereby greatly reducing the effect of variations in background [Ox]. The 1σ precision of the instrument at constant background [Ox] and 0% relative humidity is 0.2 ppt ROx with 100 second averaging and increases to 0.3 ppt at an RH of 50%. The absolute uncertainty of the measurements is estimated as 20% and is affected by the accuracy of the NO2 calibration, the precision of the CAPS when calibrating at low RO2 concentrations, and the uncertainty in the photolysis quantum yield for the CH3CO + CH3 channel of acetone photolysis.

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

    NASA Astrophysics Data System (ADS)

    Badawi, Hassan M.; Khan, Ibrahim

    2016-08-01

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

  12. Effects of Irritant Chemicals on Aedes aegypti Resting Behavior: Is There a Simple Shift to Untreated "Safe Sites"?

    DTIC Science & Technology

    2011-07-26

    Effects of Irritant Chemicals on Aedes aegypti Resting Behavior: Is There a Simple Shift to Untreated ‘‘Safe Sites’’? Hortance Manda*, Luana M. Arce... aegypti to irritant and repellent chemicals that can be exploited to reduce man-vector contact. Maximum efficacy of interventions based on irritant...overall impact. Methods: Using a laboratory box assay, resting patterns of two population strains of female Ae. aegypti (THAI and PERU) were evaluated

  13. C-13 NMR chemical shifts and visible absorption spectra of unsymmetrical fluoran dye by MO calculations

    NASA Astrophysics Data System (ADS)

    Hoshiba, T.; Ida, T.; Mizuno, M.; Otsuka, T.; Takaoka, K.; Endo, K.

    2002-01-01

    An unsymmetrical fluoran dye, 3-diethylamino-6-methyl-7-chlorofluoran (DEAMCF) is one of the leuco dyes which shows the coloring-to-decoloring reversible reaction with acidity. We calculated the 13C chemical shieldings of the DEAMCF with the frame model compounds using ab initio gauge invariant atomic orbital methods, and compared it with the experimental shifts. The calculated values of the frame compounds are in good agreement with the experimental ones in the error range of -4.9-16.7 ppm. The calculated ones for the decolored-form of the DEAMCF reflected the observed ones, although the errors range from -13.4 to 23.1 ppm. Furthermore, we analyzed the UV-Visible absorption spectra of the decolored and colored forms of DEAMCF by a semiempirical ZINDO MO method. For the colored form, the observed absorption peaks at 550 and 510 nm correspond to the excitation from π-bonding HOMO (π-electrons which conjugated in xanthene ring) and π-bonding nearest HOMO (π-electrons concentrated in benzene-ring with methyl and Cl groups of xanthene) to π ∗-antibonding LUMO (π ∗-electrons of xanthene), respectively.

  14. Solid-state NMR chemical shift assignments for AL-09 VL immunoglobulin light chain fibrils.

    PubMed

    Piehl, Dennis W; Blancas-Mejía, Luis M; Ramirez-Alvarado, Marina; Rienstra, Chad M

    2017-04-01

    Light chain (AL) amyloidosis is a systemic disease characterized by the formation of immunoglobulin light-chain fibrils in critical organs of the body. The light-chain protein AL-09 presents one severe case of cardiac AL amyloidosis, which contains seven mutations in the variable domain (VL) relative to its germline counterpart, κI O18/O8 VL. Three of these mutations are non-conservative-Y87H, N34I, and K42Q-and previous work has shown that they are responsible for significantly reducing the protein's thermodynamic stability, allowing fibril formation to occur with fast kinetics and across a wide-range of pH conditions. Currently, however, there is extremely limited structural information available which explicitly describes the residues that are involved in supporting the misfolded fibril structure. Here, we assign the site-specific (15)N and (13)C chemical shifts of the rigid residues of AL-09 VL fibrils by solid-state NMR, reporting on the regions of the protein involved in the fibril as well as the extent of secondary structure.

  15. Chemical shift anisotropy and offset effects in cross polarization solid-state NMR spectroscopy.

    PubMed

    Shekar, Srinivasan C; Lee, Dong-Kuk; Ramamoorthy, A

    2002-08-01

    The effect of an offset term in the cross-polarization (CP) Hamiltonian of a heteronuclear spin-12 pair due to off-resonant radio frequency (rf) irradiation and/or chemical shift anisotropy on one of the rf channels is investigated. Analytical solutions, simulations, and experimental results are presented. Formulating the CP spin dynamics in terms of an explicit unitary evolution operator enables the CP period to be inserted as a module in a given pulse scheme regardless of the initial density matrix present. The outcome of post-CP manipulation via pulses can be calculated on the resulting density matrix as the phases and amplitudes of all coherence modes are available. Using these tools it is shown that the offset can be used to reduce the rf power on that channel and the performance is further improved by a post-CP pulse whose flip angle matches and compensates the tilt of the effective field on the offset channel. Experimental investigations on single crystalline and polycrystalline samples of peptides confirm the oscillatory nature of CP dynamics and prove the slowing down of the dynamics under offset and/or mismatch conditions.

  16. Effects of side-chain orientation on the 13C chemical shifts of antiparallel beta-sheet model peptides.

    PubMed

    Villegas, Myriam E; Vila, Jorge A; Scheraga, Harold A

    2007-02-01

    The dependence of the (13)C chemical shift on side-chain orientation was investigated at the density functional level for a two-strand antiparallel beta-sheet model peptide represented by the amino acid sequence Ac-(Ala)(3)-X-(Ala)(12)-NH(2) where X represents any of the 17 naturally occurring amino acids, i.e., not including alanine, glycine and proline. The dihedral angles adopted for the backbone were taken from, and fixed at, observed experimental values of an antiparallel beta-sheet. We carried out a cluster analysis of the ensembles of conformations generated by considering the side-chain dihedral angles for each residue X as variables, and use them to compute the (13)C chemical shifts at the density functional theory level. It is shown that the adoption of the locally-dense basis set approach for the quantum chemical calculations enabled us to reduce the length of the chemical-shift calculations while maintaining good accuracy of the results. For the 17 naturally occurring amino acids in an antiparallel beta-sheet, there is (i) good agreement between computed and observed (13)C(alpha) and (13)C(beta) chemical shifts, with correlation coefficients of 0.95 and 0.99, respectively; (ii) significant variability of the computed (13)C(alpha) and (13)C(beta) chemical shifts as a function of chi(1) for all amino acid residues except Ser; and (iii) a smaller, although significant, dependence of the computed (13)C(alpha) chemical shifts on chi(xi) (with xi > or = 2) compared to chi(1) for eleven out of seventeen residues. Our results suggest that predicted (13)C(alpha) and (13)C(beta) chemical shifts, based only on backbone (phi,psi) dihedral angles from high-resolution X-ray structure data or from NMR-derived models, may differ significantly from those observed in solution if the dihedral-angle preferences for the side chains are not taken into account.

  17. Analysis of the contributions of ring current and electric field effects to the chemical shifts of RNA bases.

    PubMed

    Sahakyan, Aleksandr B; Vendruscolo, Michele

    2013-02-21

    Ring current and electric field effects can considerably influence NMR chemical shifts in biomolecules. Understanding such effects is particularly important for the development of accurate mappings between chemical shifts and the structures of nucleic acids. In this work, we first analyzed the Pople and the Haigh-Mallion models in terms of their ability to describe nitrogen base conjugated ring effects. We then created a database (DiBaseRNA) of three-dimensional arrangements of RNA base pairs from X-ray structures, calculated the corresponding chemical shifts via a hybrid density functional theory approach and used the results to parametrize the ring current and electric field effects in RNA bases. Next, we studied the coupling of the electric field and ring current effects for different inter-ring arrangements found in RNA bases using linear model fitting, with joint electric field and ring current, as well as only electric field and only ring current approximations. Taken together, our results provide a characterization of the interdependence of ring current and electric field geometric factors, which is shown to be especially important for the chemical shifts of non-hydrogen atoms in RNA bases.

  18. Generalized k-space decomposition with chemical shift correction for non-Cartesian water-fat imaging.

    PubMed

    Brodsky, Ethan K; Holmes, James H; Yu, Huanzhou; Reeder, Scott B

    2008-05-01

    Chemical-shift artifacts associated with non-Cartesian imaging are more complex to model and less clinically acceptable than the bulk fat shift that occurs with conventional spin-warp Cartesian imaging. A novel k-space based iterative decomposition of water and fat with echo asymmetry and least-squares estimation (IDEAL) approach is introduced that decomposes multiple species while simultaneously correcting distortion of off-resonant species. The new signal model accounts for the additional phase accumulated by off-resonant spins at each point in the k-space acquisition trajectory. This phase can then be corrected by adjusting the decomposition matrix for each k-space point during the final IDEAL processing step with little increase in reconstruction time. The technique is demonstrated with water-fat decomposition using projection reconstruction (PR)/radial, spiral, and Cartesian spin-warp imaging of phantoms and human subjects, in each case achieving substantial correction of chemical-shift artifacts. Simulations of the point-spread-function (PSF) for off-resonant spins are examined to show the nature of the chemical-shift distortion for each acquisition. Also introduced is an approach to improve the signal model for species which have multiple resonant peaks. Many chemical species, including fat, have multiple resonant peaks, although such species are often approximated as a single peak. The improved multipeak decomposition is demonstrated with water-fat imaging, showing a substantial improvement in water-fat separation.

  19. {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.

  20. Detection of methylation, acetylation and glycosylation of protein residues by monitoring (13)C chemical-shift changes: A quantum-chemical study.

    PubMed

    Garay, Pablo G; Martin, Osvaldo A; Scheraga, Harold A; Vila, Jorge A

    2016-01-01

    Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several biological processes. Their detection by experimental methods is not free of limitations such as the amount of sample needed or the use of destructive procedures to obtain the sample. Certainly, new approaches are needed and, therefore, we explore here the feasibility of using (13)C chemical shifts of different nuclei to detect methylation, acetylation and glycosylation of protein residues by monitoring the deviation of the (13)C chemical shifts from the expected (mean) experimental value of the non-modified residue. As a proof-of-concept, we used (13)C chemical shifts, computed at the DFT-level of theory, to test this hypothesis. Moreover, as a validation test of this approach, we compare our theoretical computations of the (13)Cε chemical-shift values against existing experimental data, obtained from NMR spectroscopy, for methylated and acetylated lysine residues with good agreement within ∼1 ppm. Then, further use of this approach to select the most suitable (13)C-nucleus, with which to determine other modifications commonly seen, such as methylation of arginine and glycosylation of serine, asparagine and threonine, shows encouraging results.

  1. Ab initio calculations of the intermolecular chemical shift in nuclear magnetic resonance in the gas phase and for adsorbed species

    NASA Astrophysics Data System (ADS)

    Jameson, Cynthia J.; de Dios, Angel C.

    1992-07-01

    The chemical shifts observed in nuclear magnetic resonance experiments are the differences in shielding of the nuclear spin in different electronic environments. These are known to depend on intermolecular interactions as evidenced by density-dependent chemical shifts in the gas phase, gas-to-liquid shifts, and adsorption shifts on surfaces. We present the results of the first ab initio intermolecular chemical shielding function calculated for a pair of interacting atoms for a wide range of internuclear separations. We used the localized orbital local origin (LORG) approach of Hansen and Bouman and also investigated the second-order electron correlation contributions using second-order LORG (SOLO). The 39Ar shielding in Ar2 passes through zero at some very short distance, going through a minimum, and asymptotically approaches zero at larger separations. The 21Ne shielding function in Ne2 has a similar shape. The Drude model suggests a method of scaling that portion of the shielding function that is weighted most heavily by exp[-V(R)/kT]. The scaling factors, which have been verified in the comparison of 21Ne in Ne2 against 39Ar in Ar2 ab initio results, allows us to project out from the same 39Ar in Ar2 ab initio values the appropriate 129Xe shielding functions in the Xe-Ar, Xe-Kr, and Xe-Xe interacting pairs. These functions lead to temperature-dependent second virial coefficients of chemical shielding which agree with experiments in the gas phase. Ab initio calculations of 39Ar shielding in clusters of argon are used to model the observed 129Xe chemical shifts of Xe, Xe2,...,Xe8 trapped in the cages of zeolite NaA.

  2. Ab initio studies of the nuclear magnetic resonance chemical shifts of a rare gas atom in a zeolite

    NASA Astrophysics Data System (ADS)

    Jameson, Cynthia J.; Lim, Hyung-Mi

    1995-09-01

    The intermolecular chemical shift of a rare gas atom inside a zeolite cavity is calculated by ab initio analytical derivative theory using gauge-including atomic orbitals (GIAO) at the Ar atom and the atoms of selected neutral clusters each of which is a 4-, 6-, or 8-ring fragment of the zeolite cage. The Si, Al, O atoms and the charge-balancing counterions (Na+, K+, Ca2+) of the clusters (from 24 to 52 atoms) are at coordinates taken from the refined single crystal x-ray structure of the NaA, KA, and CaA zeolites. Terminating OH groups place the H atom at an appropriate O-H distance along the bond to the next Si or Al atom in the crystal. The chemical shift of the Ar atom located at various positions relative to the cluster is calculated using Boys-Bernardi counterpoise correction at each position. The dependence of the rare gas atom chemical shift on the Al/Si ratio of the clusters is investigated. The resulting shielding values are fitted to a pairwise additive form to elicit effective individual Ar-O, Ar-Na, Ar-K, Ar-Ca intermolecular shielding functions of the form σ(39Ar, Ar...Ozeol)= a6r-6+a8r-8+a10r-10+a12r -12, where r is the distance between the Ar and the O atom. A similar form is used for the counterions. The dependence of the Ar shielding on the Al/Si ratio is established (the greater the Al content, the higher the Ar chemical shift), which is in agreement with the few experimental cases where the dependence of the 129Xe chemical shift on the Al/Si ratio of the zeolite has been observed.

  3. 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

    2015-09-03

    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.

  4. Female sea lamprey shift orientation toward a conspecific chemical cue to escape a sensory trap

    USGS Publications Warehouse

    Brant, Cory O.; Johnson, Nicholas; Li, Ke; Buchinger, Tyler J.; Li, Weiming

    2016-01-01

    The sensory trap model of signal evolution hypothesizes that signalers adapt to exploit a cue used by the receiver in another context. Although exploitation of receiver biases can result in conflict between the sexes, deceptive signaling systems that are mutually beneficial drive the evolution of stable communication systems. However, female responses in the nonsexual and sexual contexts may become uncoupled if costs are associated with exhibiting a similar response to a trait in both contexts. Male sea lamprey (Petromyzon marinus) signal with a mating pheromone, 3-keto petromyzonol sulfate (3kPZS), which may be a match to a juvenile cue used by females during migration. Upstream movement of migratory lampreys is partially guided by 3kPZS, but females only move toward 3kPZS with proximal accuracy during spawning. Here, we use in-stream behavioral assays paired with gonad histology to document the transition of female preference for juvenile- and male-released 3kPZS that coincides with the functional shift of 3kPZS as a migratory cue to a mating pheromone. Females became increasingly biased toward the source of synthesized 3kPZS as their maturation progressed into the reproductive phase, at which point, a preference for juvenile odor (also containing 3kPZS naturally) ceased to exist. Uncoupling of female responses during migration and spawning makes the 3kPZS communication system a reliable means of synchronizing mate search. The present study offers a rare example of a transition in female responses to a chemical cue between nonsexual and sexual contexts, provides insights into the origins of stable communication signaling systems.

  5. A theoretical interpretation of the chemical shift of 29Si NMR peaks in alkali borosilicate glasses

    NASA Astrophysics Data System (ADS)

    Nanba, Tokuro; Nishimura, Mitsunori; Miura, Yoshinari

    2004-12-01

    In 29Si-NMR, it has so far been accepted that the chemical shifts of Q n species (SiO 4 units containing n bridging oxygens) were equivalent between alkali borosilicate and boron-free alkali silicate glasses. In the sodium borosilicate glasses with low sodium content, however, a contradiction was confirmed in the estimation of alkali distribution; 11B NMR suggested that Na ions were entirely distributed to borate groups to form BO 4 units, whereas a -90 ppm component was also observed in 29Si-NMR spectra, which has been attributed to Q 3 species associated with a nonbridging oxygen (NBO). Then, cluster molecular orbital calculations were performed to interpret the -90 ppm component in the borosilicate glasses. It was found that a silicon atom which had two tetrahedral borons (B4) as its second nearest neighbors was similar in atomic charge and Si2p energy to the Q 3 species in boron-free alkali silicates. Unequal distribution of electrons in Si-O-B4 bridging bonds was also found, where much electrons were localized on the Si-O bonds. It was finally concluded that the Si-O-B4 bridges with narrow bond angle were responsible for the -90 ppm 29Si component in the borosilicate glasses. There still remained another interpretation; the Q 3 species were actually present in the glasses, and NBOs in the Q 3 species were derived from the tricluster groups, such as (O 3Si)O(BO 3) 2. In the glasses with low sodium content, however, it was concluded that the tricluster groups were not so abundant to contribute to the -90 ppm component.

  6. Protein-Observed Fluorine NMR Is a Complementary Ligand Discovery Method to (1)H CPMG Ligand-Observed NMR.

    PubMed

    Urick, Andrew K; Calle, Luis Pablo; Espinosa, Juan F; Hu, Haitao; Pomerantz, William C K

    2016-11-18

    To evaluate its potential as a ligand discovery tool, we compare a newly developed 1D protein-observed fluorine NMR (PrOF NMR) screening method with the well-characterized ligand-observed (1)H CPMG NMR screen. We selected the first bromodomain of Brd4 as a model system to benchmark PrOF NMR because of the high ligandability of Brd4 and the need for small molecule inhibitors of related epigenetic regulatory proteins. We compare the two methods' hit sensitivity, triaging ability, experiment speed, material consumption, and the potential for false positives and negatives. To this end, we screened 930 fragment molecules against Brd4 in mixtures of five and followed up these studies with mixture deconvolution and affinity characterization of the top hits. In selected examples, we also compare the environmental responsiveness of the (19)F chemical shift to (1)H in 1D-protein observed (1)H NMR experiments. To address concerns of perturbations from fluorine incorporation, ligand binding trends and affinities were verified via thermal shift assays and isothermal titration calorimetry. We conclude that for the protein understudy here, PrOF NMR and (1)H CPMG have similar sensitivity, with both being effective tools for ligand discovery. In cases where an unlabeled protein can be used, 1D protein-observed (1)H NMR may also be effective; however, the (19)F chemical shift remains significantly more responsive.

  7. Distribution and Xe129 NMR chemical shifts of Xen clusters in the alpha cages of zeolite AgA

    NASA Astrophysics Data System (ADS)

    Jameson, Cynthia J.; Lim, Hyung-Mi

    1997-09-01

    The distributions and 129Xe NMR chemical shifts of xenon in zeolite AgA have been measured in a series of experiments by Moudrakovski, Ratcliffe, and Ripmeester [Proc. Internat. Zeolite Conference, Quebec, 1995; unpublished]. We carry out grand canonical Monte Carlo (GCMC) simulations of xenon in a rigid zeolite AgA lattice to provide the average Xen cluster shifts, and the distributions Pn for comparison with their experiments. The GCMC results for the distributions, the fraction Pn of the alpha cages containing n Xe atoms, are compared with the experimental distributions in 12 samples and the agreement is excellent. The distributions in NaA and in AgA are very similar, as can be established from the comparison of the dispersion of the distributions, {-2}, and both are different from the idealized hypergeometric distribution, in which the component atoms occupy eight lattice sites per cage under mutual exclusion. The calculated chemical shift increments [σ(Xen)-σ(Xen-1)]AgA are in good agreement with experiment. The differences between these and the increments in zeolite NaA, {[σ(Xen)-σ(Xen-1)]AgA-[σ(Xen)-σ(Xen-1)]NaA}, are fairly small and are in good agreement with experiment. The absolute 129Xe chemical shifts of Xen in the alpha cages of AgA are nearly uniformly shifted by about 40 ppm compared to the Xen clusters in NaA. This is attributed to the Fermi contact shifts arising from the Ag0 metal atoms that form the linear Ag32+ complexes that are found within the beta cages of AgA.

  8. Experimental and theoretical study of substituent effect on 13C NMR chemical shifts of 5-arylidene-2,4-thiazolidinediones

    NASA Astrophysics Data System (ADS)

    Rančić, Milica P.; Trišović, Nemanja P.; Milčić, Miloš K.; Ajaj, Ismail A.; Marinković, Aleksandar D.

    2013-10-01

    The electronic structure of 5-arylidene-2,4-thiazolidinediones has been studied by using experimental and theoretical methodology. The theoretical calculations of the investigated 5-arylidene-2,4-thiazolidinediones have been performed by the use of quantum chemical methods. The calculated 13C NMR chemical shifts and NBO atomic charges provide an insight into the influence of such a structure on the transmission of electronic substituent effects. Linear free energy relationships (LFERs) have been further applied to their 13C NMR chemical shifts. The correlation analyses for the substituent-induced chemical shifts (SCS) have been performed with σ using SSP (single substituent parameter), field (σF) and resonance (σR) parameters using DSP (dual substituent parameter), as well as the Yukawa-Tsuno model. The presented correlations account satisfactorily for the polar and resonance substituent effects operative at Cβ, and C7 carbons, while reverse substituent effect was found for Cα. The comparison of correlation results for the investigated molecules with those obtained for seven structurally related styrene series has indicated that specific cross-interaction of phenyl substituent and groups attached at Cβ carbon causes increased sensitivity of SCS Cβ to the resonance effect with increasing of electron-accepting capabilities of the group present at Cβ.

  9. Assessing the accuracy of protein structures by quantum mechanical computations of 13C(alpha) chemical shifts.

    PubMed

    Vila, Jorge A; Scheraga, Harold A

    2009-10-20

    Two major techniques have been used to determine the three-dimensional structures of proteins: X-ray diffraction and NMR spectroscopy. In particular, the validation of NMR-derived protein structures is one of the most challenging problems in NMR spectroscopy. Therefore, researchers have proposed a plethora of methods to determine the accuracy and reliability of protein structures. Despite these proposals, there is a growing need for more sophisticated, physics-based structure validation methods. This approach will enable us to (a) characterize the "quality" of the NMR-derived ensemble as a whole by a single parameter, (b) unambiguously identify flaws in the sequence at a residue level, and (c) provide precise information, such as sets of backbone and side-chain torsional angles, that we can use to detect local flaws. Rather than reviewing all of the existing validation methods, this Account describes the contributions of our research group toward a solution of the long-standing problem of both global and local structure validation of NMR-derived protein structures. We emphasize a recently introduced physics-based methodology that makes use of observed and computed (13)C(alpha) chemical shifts (at the density functional theory (DFT) level of theory) for an accurate validation of protein structures in solution and in crystals. By assessing the ability of computed (13)C(alpha) chemical shifts to reproduce observed (13)C(alpha) chemical shifts of a single structure or ensemble of structures in solution and in crystals, we accomplish a global validation by using the conformationally averaged root-mean-square deviation, ca-rmsd, as a scoring function. In addition, the method enables us to provide local validation by identifying a set of individual amino acid conformations for which the computed and observed (13)C(alpha) chemical shifts do not agree within a certain error range and may represent a nonreliable fold of the protein model. Although it is computationally

  10. Probing hydrogen bonding in cocrystals and amorphous dispersions using (14)N-(1)H HMQC solid-state NMR.

    PubMed

    Tatton, Andrew S; Pham, Tran N; Vogt, Frederick G; Iuga, Dinu; Edwards, Andrew J; Brown, Steven P

    2013-03-04

    Cocrystals and amorphous solid dispersions have generated interest in the pharmaceutical industry as an alternative to more established solid delivery forms. The identification of intermolecular hydrogen bonding interactions in a nicotinamide palmitic acid cocrystal and a 50% w/w acetaminophen-polyvinylpyrrolidone solid dispersion are reported using advanced solid-state magic-angle spinning (MAS) NMR methods. The application of a novel (14)N-(1)H HMQC experiment, where coherence transfer is achieved via through-space couplings, is shown to identify specific hydrogen bonding motifs. Additionally, (1)H isotropic chemical shifts and (14)N electric field gradient (EFG) parameters, both accessible from (14)N-(1)H HMQC experiments, are shown to be sensitive to changes in hydrogen bonding geometry. Numerous indicators of molecular association are accessible from this experiment, including NH cross-peaks occurring from intermolecular hydrogen bonds and changes in proton chemical shifts or electric field gradient parameters. First-principles calculations using the GIPAW approach that yield accurate estimates of isotropic chemical shifts, and EFG parameters were used to assist in assignment. It is envisaged that (14)N-(1)H HMQC solid state NMR experiments could become a valuable screening technique of solid delivery forms in the pharmaceutical industry.

  11. Prediction of carbon-13 NMR chemical shift of alkanes with rooted path vector.

    PubMed

    Zhou, L P; Sun, L L; Yu, Y; Lu, W; Li, Z L

    2006-11-01

    Systematic studies were further made on graph theory in quantitative structure-spectrum relationships (QSSR) for various areas of spectroscopies. Chemical shifts (CS) in alkanes for carbon-13 nuclear magnetic resonance (13C NMR) were well correlated with a set of novel molecular graph indices, called the rooted path vector of various lengths, as several multivariate regression equations as following:CS=3.022+5.336P1+7.356P2-1.648P3+0.83859P4+0.210P5-0.138P6-0.506P7+2.486P8-1.669P9; n=402, m=9, R=0.944, RCV=0.9413, S.D.=3.333, F=358.343, U=35833.211, Q=4355.422 for all types (primary, secondly, tertiary, quaternary as well as methane) of carbon atoms CS=0.983+6.811P1+7.584P2-2.029P3+0.809P4+0.106P5+0.043P6-0.124P7+1.715P8-1.101P9; n=374, m=9, R=0.975, RCV=0.9737, S.D.=2.303, F=773.372, U=36912.109, Q=1930.363 for primary, secondly, tertiary (including methane) carbon atoms; and CS=27.819+2.351P2+0.549P3-0.440P4+0.170P5-0.050P6; n=27, m=5, R=0.992, RCV=0.9674, S.D.=0.324, F=265.418, U=138.891, Q=2.198 for quaternary carbon atoms, respectively. Quite good estimation and prediction results were obtained from the quantitative molecular modeling and the performance of multiple linear regression (MLR) equations were tested to work well through cross-validation (CV) with the leave-one-out (LOO) procedure.

  12. 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

  13. Complete assignments of 1H and 13C NMR data for seven arylnaphthalide lignans from Justicia procumbens.

    PubMed

    Yang, Meihua; Wu, Jun; Cheng, Fan; Zhou, Yuan

    2006-07-01

    Three new arylnaphthalide lignans named 6'-hydroxy justicidin A (1), 6'-hydroxy justicidin B (2) and 6'-hydroxy justicidin C (3) have been isolated from the whole plant of Justicia procumbens, together with four known ones, neojusticin A (4), chinensinaphthol methyl ester (5), isodiphyllin (6) and taiwanin C (7). The complete assignments of 1H and 13C NMR chemical shifts for the new lignans and the 13C NMR chemical shifts for the known lignans were obtained for the first time by means of 2D NMR techniques, including HSQC and HMBC.

  14. Backbone chemical shifts assignments, secondary structure, and ligand binding of a family GH-19 chitinase from moss, Bryum coronatum.

    PubMed

    Shinya, Shoko; Nagata, Takuya; Ohnuma, Takayuki; Taira, Toki; Nishimura, Shigenori; Fukamizo, Tamo

    2012-10-01

    Family GH19 chitinases have been recognized as important in the plant defense against fungal pathogens. However, their substrate-recognition mechanism is still unknown. We report here the first resonance assignment of NMR spectrum of a GH19 chitinase from moss, Bryum coronatum (BcChi-A). The backbone signals were nearly completely assigned, and the secondary structure was estimated based on the chemical shift values. The addition of the chitin dimer to the enzyme solution perturbed the chemical shifts of HSQC resonances of the amino acid residues forming the putative substrate-binding cleft. Further NMR analysis of the ligand binding to BcChi-A will improve understanding of the substrate-recognition mechanism of GH-19 enzymes.

  15. NMR chemical shift study of the interaction of selected peptides with liposomal and micellar models of apoptotic cells.

    PubMed

    Van Koninckxloo, Aurore; Henoumont, Céline; Laurent, Sophie; Muller, Robert N; Vander Elst, Luce

    2014-12-01

    The interaction between two peptides previously selected by phage display to target apoptotic cells and phospholipidic models of these cells (liposomes or micelles made of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and/or 1,2-dipalmitoyl-sn-glycero-3-phospho-L-serine (DPPS, phosphatidylserine analog) was studied by the simple analysis of the changes induced on the proton NMR chemical shifts of the peptides. Our approach which does not need healthy and/or apoptotic cells for assessing the affinity of different peptides is fast and efficient and requires small amounts of peptide to determine the association constant, the interacting protons, and the number of interaction sites. The micellar model gave more reliable results than the liposomal one. The preferential interaction of the peptide with DPPS was evidenced by the change of the chemical shifts of specific amino acids of the peptides. Our micellar model is thus well suited to mimic apoptotic cells.

  16. Determination of isoleucine side-chain conformations in ground and excited states of proteins from chemical shifts.

    PubMed

    Hansen, D Flemming; Neudecker, Philipp; Kay, Lewis E

    2010-06-09

    A simple method is presented for quantifying Ile chi(2) rotamer distributions in proteins based on the measurement of Ile (13)C(delta1) chemical shifts. The methodology is well suited for applications involving very high molecular weight protein complexes, where other NMR parameters such as side-chain scalar coupling constants that report on dihedral angles cannot be measured or for studies of invisible, excited protein states, where chemical shifts are obtained from analysis of CPMG relaxation dispersion profiles. The utility of the approach is demonstrated by an application to the folding reaction of a mutant Fyn SH3 domain, where Ile side-chain structure and dynamics of an on-folding pathway intermediate state are studied.

  17. The local order of supercooled water in solution with LiCl studied by NMR proton chemical shift

    NASA Astrophysics Data System (ADS)

    Corsaro, C.; Mallamace, D.; Vasi, S.; Cicero, N.; Dugo, G.; Mallamace, F.

    2016-05-01

    We study by means of Nuclear Magnetic Resonance (NMR) spectroscopy the local order of water molecules in solution with lithium chloride at eutectic concentration. In particular, by measuring the proton chemical shift as a function of the temperature in the interval 203{ K}chemical shift of water solvating lithium and chlorine individually. The thermal behavior of this quantity confirms previous results about the role of the temperature in the solvation mechanisms down to about 225K. This temperature coincides with that of the so-called Widom line for water supporting the liquid-liquid transition hypothesis.

  18. Towards the versatile DFT and MP2 computational schemes for 31P NMR chemical shifts taking into account relativistic corrections.

    PubMed

    Fedorov, Sergey V; Rusakov, Yury Yu; Krivdin, Leonid B

    2014-11-01

    The main factors affecting the accuracy and computational cost of the calculation of (31)P NMR chemical shifts in the representative series of organophosphorous compounds are examined at the density functional theory (DFT) and second-order Møller-Plesset perturbation theory (MP2) levels. At the DFT level, the best functionals for the calculation of (31)P NMR chemical shifts are those of Keal and Tozer, KT2 and KT3. Both at the DFT and MP2 levels, the most reliable basis sets are those of Jensen, pcS-2 or larger, and those of Pople, 6-311G(d,p) or larger. The reliable basis sets of Dunning's family are those of at least penta-zeta quality that precludes their practical consideration. An encouraging finding is that basically, the locally dense basis set approach resulting in a dramatic decrease in computational cost is justified in the calculation of (31)P NMR chemical shifts within the 1-2-ppm error. Relativistic corrections to (31)P NMR absolute shielding constants are of major importance reaching about 20-30 ppm (ca 7%) improving (not worsening!) the agreement of calculation with experiment. Further better agreement with the experiment by 1-2 ppm can be obtained by taking into account solvent effects within the integral equation formalism polarizable continuum model solvation scheme. We recommend the GIAO-DFT-KT2/pcS-3//pcS-2 scheme with relativistic corrections and solvent effects taken into account as the most versatile computational scheme for the calculation of (31)P NMR chemical shifts characterized by a mean absolute error of ca 9 ppm in the range of 550 ppm.

  19. Unraveling the 13C NMR chemical shifts in single-walled carbon nanotubes: dependence on diameter and electronic structure.

    PubMed

    Engtrakul, Chaiwat; Irurzun, Veronica M; Gjersing, Erica L; Holt, Josh M; Larsen, Brian A; Resasco, Daniel E; Blackburn, Jeffrey 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 (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 (13)C labeling and density gradient ultracentrifugation (DGU) to produce an array of (13)C-labeled SWCNT populations with varying diameter, electronic structure, and chiral angle. We find that the SWCNT isotropic (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 (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.

  20. Application of data mining tools for classification of protein structural class from residue based averaged NMR chemical shifts.

    PubMed

    Kumar, Arun V; Ali, Rehana F M; Cao, Yu; Krishnan, V V

    2015-10-01

    The number of protein sequences deriving from genome sequencing projects is outpacing our knowledge about the function of these proteins. With the gap between experimentally characterized and uncharacterized proteins continuing to widen, it is necessary to develop new computational methods and tools for protein structural information that is directly related to function. Nuclear magnetic resonance (NMR) provides powerful means to determine three-dimensional structures of proteins in the solution state. However, translation of the NMR spectral parameters to even low-resolution structural information such as protein class requires multiple time consuming steps. In this paper, we present an unorthodox method to predict the protein structural class directly by using the residue's averaged chemical shifts (ACS) based on machine learning algorithms. Experimental chemical shift information from 1491 proteins obtained from Biological Magnetic Resonance Bank (BMRB) and their respective protein structural classes derived from structural classification of proteins (SCOP) were used to construct a data set with 119 attributes and 5 different classes. Twenty four different classification schemes were evaluated using several performance measures. Overall the residue based ACS values can predict the protein structural classes with 80% accuracy measured by Matthew correlation coefficient. Specifically protein classes defined by mixed αβ or small proteins are classified with >90% correlation. Our results indicate that this NMR-based method can be utilized as a low-resolution tool for protein structural class identification without any prior chemical shift assignments.

  1. Application of Data Mining Tools for Classification of Protein Structural Class from Residue Based Averaged NMR Chemical Shifts

    PubMed Central

    Kumar, Arun. V.; Ali, Rehana F.M.; Cao, Yu; Krishnan, V.V.

    2015-01-01

    The number of protein sequences deriving from genome sequencing projects is outpacing our knowledge about the function of these proteins. With the gap between experimentally characterized and uncharacterized proteins continuing to widen, it is necessary to develop new computational methods and tools for protein structural information that is directly related to function. Nuclear magnetic resonance (NMR) provides powerful means to determine three-dimensional structures of proteins in the solution state. However, translation of the NMR spectral parameters to even low-resolution structural information such as protein class requires multiple time consuming steps. In this paper, we present an unorthodox method to predict the protein structural class directly by using the residue’s averaged chemical shifts (ACS) based on machine learning algorithms. Experimental chemical shift information from 1491 proteins obtained from Biological Magnetic Resonance Bank (BMRB) and their respective protein structural classes derived from structural classification of proteins (SCOP) were used to construct a data set with 119 attributes and 5 different classes. Twenty four different classification schemes were evaluated using several performance measures. Overall the residue based ACS values can predict the protein structural classes with 80 % accuracy measured by Matthew Correlation coefficient. Specifically protein classes defined by mixed αβ or small proteins are classified with > 90% correlation. Our results indicate that this NMR-based method can be utilized as a low-resolution tool for protein structural class identification without any prior chemical shift assignments. PMID:25758094

  2. Vibrational spectra, electronic absorption, nonlinear optical properties, evaluation of bonding, chemical reactivity and thermodynamic properties of ethyl 4-(1-(2-(hydrazinecarbonothioyl)hydrazono)ethyl)-3,5-dimethyl-1H-pyrrole-2-carboxylate molecule by ab initio HF and density functional methods.

    PubMed

    Singh, R N; Rawat, Poonam; Sahu, Sangeeta

    2015-01-25

    In this work, detailed vibrational spectral analysis of ethyl 4-(1-(2-(hydrazinecarbonothioyl)hydrazono)ethyl)-3,5-dimethyl-1H-pyrrole-2-carboxylate (EHCHEDPC) molecule has been carried out using FT-IR spectroscopy and potential energy distribution (PED). Theoretical calculations were performed by ab initio RHF and density functional theory (DFT) method, using 6-31G(d,p) and 6-311+G(d,p) basis sets. The other carried outwork cover: structural, thermodynamic properties, electronic transitions, bonding, multiple interaction, chemical reactivity and hyperpolarizability analysis. The results of the calculation were applied to the simulated spectra of (EHCHEDPC), which show excellent agreement with observed spectra. The vibrational analysis shows red shift in both group, the proton donor (pyrrole N-H) and proton acceptor (C=O of ester) indicating the presence of intermolecular hydrogen bonding. Time dependent density functional theory (TD-DFT) has been used to find electronic excitations and their nature. The results of natural bond orbital (NBOs) analysis show the charges transfer and delocalization in various intra- and intermolecular interactions. The binding energy of intermolecular multiple interactions is calculated to be 12.54 kcal mol(-1) using QTAIM calculation. The electronic descriptors analyses reveal the investigated molecule used as precursor for heterocyclic derivatives synthesis. First hyperpolarizability (β0) has been computed to evaluate non-linear optical (NLO) response.

  3. Chemical synthesis and 1H-NMR 3D structure determination of AgTx2-MTX chimera, a new potential blocker for Kv1.2 channel, derived from MTX and AgTx2 scorpion toxins

    PubMed Central

    Pimentel, Cyril; M'Barek, Sarrah; Visan, Violetta; Grissmer, Stephan; Sampieri, François; Sabatier, Jean-Marc; Darbon, Hervé; Fajloun, Ziad

    2008-01-01

    Agitoxin 2 (AgTx2) is a 38-residue scorpion toxin, cross-linked by three disulfide bridges, which acts on voltage-gated K+ (Kv) channels. Maurotoxin (MTX) is a 34-residue scorpion toxin with an uncommon four-disulfide bridge reticulation, acting on both Ca2+-activated and Kv channels. A 39-mer chimeric peptide, named AgTx2-MTX, was designed from the sequence of the two toxins and chemically synthesized. It encompasses residues 1–5 of AgTx2, followed by the complete sequence of MTX. As established by enzyme cleavage, the new AgTx2-MTX molecule displays half-cystine pairings of the type C1–C5, C2–C6, C3–C7, and C4–C8, which is different from that of MTX. The 3D structure of AgTx2-MTX solved by 1H-NMR, revealed both α-helical and β-sheet structures, consistent with a common α/β scaffold of scorpion toxins. Pharmacological assays of AgTx2-MTX revealed that this new molecule is more potent than both original toxins in blocking rat Kv1.2 channel. Docking simulations, performed with the 3D structure of AgTx2-MTX, confirmed this result and demonstrated the participation of the N-terminal domain of AgTx2 in its increased affinity for Kv1.2 through additional molecular contacts. Altogether, the data indicated that replacement of the N-terminal domain of MTX by the one of AgTx2 in the AgTx2-MTX chimera results in a reorganization of the disulfide bridge arrangement and an increase of affinity to the Kv1.2 channel. PMID:18042681

  4. Chemical synthesis and 1H-NMR 3D structure determination of AgTx2-MTX chimera, a new potential blocker for Kv1.2 channel, derived from MTX and AgTx2 scorpion toxins.

    PubMed

    Pimentel, Cyril; M'Barek, Sarrah; Visan, Violetta; Grissmer, Stephan; Sampieri, François; Sabatier, Jean-Marc; Darbon, Hervé; Fajloun, Ziad

    2008-01-01

    Agitoxin 2 (AgTx2) is a 38-residue scorpion toxin, cross-linked by three disulfide bridges, which acts on voltage-gated K(+) (Kv) channels. Maurotoxin (MTX) is a 34-residue scorpion toxin with an uncommon four-disulfide bridge reticulation, acting on both Ca(2+)-activated and Kv channels. A 39-mer chimeric peptide, named AgTx2-MTX, was designed from the sequence of the two toxins and chemically synthesized. It encompasses residues 1-5 of AgTx2, followed by the complete sequence of MTX. As established by enzyme cleavage, the new AgTx2-MTX molecule displays half-cystine pairings of the type C1-C5, C2-C6, C3-C7, and C4-C8, which is different from that of MTX. The 3D structure of AgTx2-MTX solved by (1)H-NMR, revealed both alpha-helical and beta-sheet structures, consistent with a common alpha/beta scaffold of scorpion toxins. Pharmacological assays of AgTx2-MTX revealed that this new molecule is more potent than both original toxins in blocking rat Kv1.2 channel. Docking simulations, performed with the 3D structure of AgTx2-MTX, confirmed this result and demonstrated the participation of the N-terminal domain of AgTx2 in its increased affinity for Kv1.2 through additional molecular contacts. Altogether, the data indicated that replacement of the N-terminal domain of MTX by the one of AgTx2 in the AgTx2-MTX chimera results in a reorganization of the disulfide bridge arrangement and an increase of affinity to the Kv1.2 channel.

  5. Toward calculations of the 129Xe chemical shift in Xe@C60 at experimental conditions: relativity, correlation, and dynamics.

    PubMed

    Straka, Michal; Lantto, Perttu; Vaara, Juha

    2008-03-27

    We calculate the 129Xe chemical shift in endohedral Xe@C60 with systematic inclusion of the contributing physical effects to model the real experimental conditions. These are relativistic effects, electron correlation, the temperature-dependent dynamics, and solvent effects. The ultimate task is to obtain the right result for the right reason and to develop a physically justified methodological model for calculations and simulations of endohedral Xe fullerenes and other confined Xe systems. We use the smaller Xe...C6H6 model to calibrate density functional theory approaches against accurate correlated wave function methods. Relativistic effects as well as the coupling of relativity and electron correlation are evaluated using the leading-order Breit-Pauli perturbation theory. The dynamic effects are treated in two ways. In the first approximation, quantum dynamics of the Xe atom in a rigid cage takes advantage of the centrosymmetric potential for Xe within the thermally accessible distance range from the center of the cage. This reduces the problem of obtaining the solution of a diatomic rovibrational problem. In the second approach, first-principles classical molecular dynamics on the density functional potential energy hypersurface is used to produce the dynamical trajectory for the whole system, including the dynamic cage. Snapshots from the trajectory are used for calculations of the dynamic contribution to the absorption 129Xe chemical shift. The calculated nonrelativistic Xe shift is found to be highly sensitive to the optimized molecular structure and to the choice of the exchange-correlation functional. Relativistic and dynamic effects are significant and represent each about 10% of the nonrelativistic static shift at the minimum structure. While the role of the Xe dynamics inside of the rigid cage is negligible, the cage dynamics turns out to be responsible for most of the dynamical correction to the 129Xe shift. Solvent effects evaluated with a polarized

  6. Chemical shift assignments of the first and second RRMs of Nrd1, a fission yeast MAPK-target RNA binding protein.

    PubMed

    Kobayashi, Ayaho; Kanaba, Teppei; Satoh, Ryosuke; Ito, Yutaka; Sugiura, Reiko; Mishima, Masaki

    2017-03-11

    Negative regulator differentiation 1 (Nrd1), a fission yeast RNA binding protein, modulates cytokinesis and sexual development and contributes to stress granule formation in response to environmental stresses. Nrd1 comprises four RRM domains and binds and stabilizes Cdc4 mRNA that encodes the myosin II light chain. Nrd1 binds the Cpc2 fission-yeast RACK1 homolog, and the interaction promotes Nrd1 localization to stress granules. Interestingly, Pmk1 mitogen-activated protein kinase phosphorylates Thr40 in the unstructured N-terminal region and Thr126 in the first RRM domain of Nrd1. Phosphorylation significantly reduces RNA-binding activity and likely modulates Nrd1 function. To reveal the relationship between the structure and function of Nrd1 and how phosphorylation affects structure, we used heteronuclear NMR techniques to investigate the three-dimensional structure of Nrd1. Here we report the (1)H, (13)C, and (15)N resonance assignments of RRM1-RRM2 (residues 108-284) comprising the first and second RRMs obtained using heteronuclear NMR techniques. Secondary structures derived from the chemical shifts are reported. These data should contribute to the understanding of the three-dimensional structure of the RRM1-RRM2 region of Nrd1 and the perturbation caused by phosphorylation.

  7. Hydrogen bond geometries and proton tautomerism of homoconjugated anions of carboxylic acids studied via H/D isotope effects on 13C NMR chemical shifts.

    PubMed

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

    2012-11-26

    Ten formally symmetric anionic OHO hydrogen bonded complexes, modeling Asp/Glu amino acid side chain interactions in nonaqueous environment (CDF(3)/CDF(2)Cl solution, 200-110 K) have been studied by (1)H, (2)H, and (13)C NMR spectroscopy, i.e. intermolecularly H-bonded homoconjugated anions of acetic, chloroacetic, dichloroacetic, trifluoroacetic, trimethylacetic, and isobutyric acids, and intramolecularly H-bonded hydrogen succinate, hydrogen rac-dimethylsuccinate, hydrogen maleate, and hydrogen phthalate. In particular, primary H/D isotope effects on the hydrogen bond proton signals as well as secondary H/D isotope effects on the (13)C signals of the carboxylic groups are reported and analyzed. We demonstrate that in most of the studied systems there is a degenerate proton tautomerism between O-H···O(-) and O(-)···H-O structures which is fast in the NMR time scale. The stronger is the proton donating ability of the acid, the shorter and more symmetric are the H-bonds in each tautomer of the homoconjugate. For the maleate and phthalate anions exhibiting intramolecular hydrogen bonds, evidence for symmetric single well potentials is obtained. We propose a correlation between H/D isotope effects on carboxylic carbon chemical shifts and the proton transfer coordinate, q(1) = ½(r(OH) - r(HO)), which allows us to estimate the desired OHO hydrogen bond geometries from the observed (13)C NMR parameters, taking into account the degenerate proton tautomerism.

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

    PubMed Central

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

    2005-01-01

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

  9. ProCS15: a DFT-based chemical shift predictor for backbone and Cβ atoms in proteins

    PubMed Central

    Larsen, Anders S.; Bratholm, Lars A.; Christensen, Anders S.; Channir, Maher

    2015-01-01

    We present ProCS15: a program that computes the isotropic chemical shielding values of backbone and Cβ atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shifts for Ubiquitin and the third IgG-binding domain of Protein G through linear regression and yield RMSD values of up to 2.2, 0.7, and 4.8 ppm for carbon, hydrogen, and nitrogen atoms. These RMSD values are very similar to corresponding RMSD values computed using OPBE/6-31G(d,p) for the entire structure for each proteins. These maximum RMSD values can be reduced by using NMR-derived structural ensembles of Ubiquitin. For example, for the largest ensemble the largest RMSD values are 1.7, 0.5, and 3.5 ppm for carbon, hydrogen, and nitrogen. The corresponding RMSD values predicted by several empirical chemical shift predictors range between 0.7–1.1, 0.2–0.4, and 1.8–2.8 ppm for carbon, hydrogen, and nitrogen atoms, respectively. PMID:26623185

  10. Crystal structure and anomalous chemical shift of 10-(prop-1-yn-1-yl)-10H-phenothiazine 5,5-dioxide: Intramolecular S⋯N transannular effect

    NASA Astrophysics Data System (ADS)

    Umezono, Satoru; Okuno, Tsunehisa

    2013-10-01

    The novel ynamine compounds, 10-(prop-1-yn-1-yl)-10H-phenothiazine 5-oxide (2) and 10-(prop-1-yn-1-yl)-10H-phenothiazine 5,5-dioxide (3), were prepared by MCPBA oxidation of 10-(prop-1-yn-1-yl)-10H-phenothiazine (1). These compounds were characterized successfully by crystallographical analyses, 1H and 13C NMR. The 1H NMR signals of 2 showed downfield shifts compared with 1 as expected. However two kinds of signals, methyl and 1,9-position of 3, indicated upfield shifts compared with 2. These anomalous upfield shifts were reasonably explained by trans-annular S⋯N interaction and by increase of electron density on the nitrogen atom.

  11. The effects of librations on the 13C chemical shift and 2H electric field gradient tensors in β-calcium formate

    NASA Astrophysics Data System (ADS)

    Hallock, Kevin J.; Lee, Dong Kuk; Ramamoorthy, A.

    2000-12-01

    The magnitudes and orientations of the principal elements of the 13C chemical shift anisotropy (CSA) tensor in the molecular frame of the formate ion in β-calcium formate is determined using one-dimensional dipolar-shift spectroscopy. The magnitudes of the principal elements of the 13C CSA tensor are σ11C=104 ppm, σ22C=179 ppm, and σ33C=233 ppm. The least shielding element of the 13C CSA tensor, σ33C, is found to be collinear with the C-H bond. The temperature dependence of the 13C CSA and the 2H quadrupole coupling tensors in β-calcium formate are analyzed for a wide range of temperature (173-373 K). It was found that the span of the 13C CSA and the magnitude of the 2H quadrupole coupling interactions are averaged with the increasing temperature. The experimental results also show that the 2H quadrupole coupling tensor becomes more asymmetric with increasing temperature. A librational motion about the σ22C axis of the 13C CSA tensor is used to model the temperature dependence of the 13C CSA tensor. The temperature dependence of the mean-square amplitude of the librational motion is found to be <α2>=2.6×10-4(T) rad2 K-1. The same librational motion also accounts for the temperature-dependence of the 2H quadrupole coupling tensor after the relative orientation of the 13C CSA and 2H electric field gradient tensors are taken into account. Reconsideration of the results of a previous study found that the librational motion, not the vibrational motion, accounts for an asymmetry in the 1H-13C dipolar coupling tensor of α-calcium formate at room temperature.

  12. 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.

  13. Phenylboronic acid-based (19)F MRI probe for the detection and imaging of hydrogen peroxide utilizing its large chemical-shift change.

    PubMed

    Nonaka, Hiroshi; An, Qi; Sugihara, Fuminori; Doura, Tomohiro; Tsuchiya, Akira; Yoshioka, Yoshichika; Sando, Shinsuke

    2015-01-01

    Herein, we report on a new (19)F MRI probe for the detection and imaging of H2O2. Our designed 2-fluorophenylboronic acid-based (19)F probe promptly reacted with H2O2 to produce 2-fluorophenol via boronic acid oxidation. The accompanying (19)F chemical-shift change reached 31 ppm under our experimental conditions. Such a large chemical-shift change allowed for the imaging of H2O2 by (19)F chemical-shift-selective MRI.

  14. Measurement of T1/T2 relaxation times in overlapped regions from homodecoupled 1H singlet signals

    NASA Astrophysics Data System (ADS)

    Castañar, Laura; Nolis, Pau; Virgili, Albert; Parella, Teodor

    2014-07-01

    The implementation of the HOmodecoupled Band-Selective (HOBS) technique in the conventional Inversion-Recovery and CPMG-based PROJECT experiments is described. The achievement of fully homodecoupled signals allows the distinction of overlapped 1H resonances with small chemical shift differences. It is shown that the corresponding T1 and T2 relaxation times can be individually measured from the resulting singlet lines using conventional exponential curve-fitting methods.

  15. Influence of the chemical shift artifact on measurements of compact bone thickness in equine distal limb MR images.

    PubMed

    Dimock, Abigail N; Spriet, Mathieu

    2010-01-01

    The effect of the chemical shift artifact, resulting from misregistration or phase cancellation at the interface between compact and trabecular bone, on apparent bone thickness was quantified in six isolated equine limbs. Sagittal T1-weighted spin echo (SE) and in-phase three-dimensional spoiled gradient echo (SPGR) images were acquired twice with a 1.5 T magnetic resonance (MR) unit, switching the frequency encoding direction between acquisitions. Out-of-phase SPGR images were also obtained. MR images with different frequency encoding directions were compared with each other and to radiographs made from corresponding 3-mm-bone sections. Compact bone thickness was significantly different when comparing images acquired with different frequency encoding directions for both SE and SPGR sequences. Significant differences were identified in the frequency but not the phase encoding direction when measurements of compact bone in MR images were compared with measurements obtained from thin section radiographs for the majority of surfaces studied (P < 0.05). Correction of MR measurements with the calculated chemical shift abolished these differences (P > 0.05). Measurements of compact bone from out-of-phase SPGR sequences were significantly different than from in-phase sequences (P < 0.001) with out-of-phase measurements greater than in-phase measurements by an average of 0.38mm. These results indicate that the chemical shift artifact results in errors in MR evaluation of compact bone thickness when measurements are performed in the frequency encoding direction or in out-of-phase images. For better accuracy, measurements should be performed parallel to the phase encoding direction and avoiding out-of-phase gradient echo sequences.

  16. Effects of hydrogen bonding on amide-proton chemical shift anisotropy in a proline-containing model peptide

    NASA Astrophysics Data System (ADS)

    Pichumani, Kumar; George, Gijo; Hebbar, Sankeerth; Chatterjee, Bhaswati; Raghothama, Srinivasarao

    2015-05-01

    Longitudinal relaxation due to cross-correlation between dipolar (1HN-1Hα) and amide-proton chemical shift anisotropy (1HN CSA) has been measured in a model tripeptide Piv-LPro-LPro-LPhe-OMe. The peptide bond across diproline segment is known to undergo cis/trans isomerization and only in the cis form does the lone Phe amide-proton become involved in intramolecular hydrogen bonding. The strength of the cross correlated relaxation interference is found to be significantly different between cis and trans forms, and this difference is shown as an influence of intramolecular hydrogen bonding on the amide-proton CSA.

  17. The Effective Synthesis of N-(Arylalkyl)-1-R-4-hydroxy-2,2-dioxo- 1H-2λ6,1-benzothiazine-3-carboxamides as Promising Analgesics of a New Chemical Class

    PubMed Central

    Ukrainets, Igor V.; Petrushova, Lidiya A.; Dzyubenko, Sergiy P.; Sim, Galina; Grinevich, Lina A.

    2015-01-01

    A new, effective preparative method has been proposed and the synthesis of a series of N-(arylalkyl)-1-R-4-hydroxy-2,2-dioxo-1H-2λ6,1-benzothiazine-3-car-boxamides has been carried out. It has been shown that amidation of alkyl 1-R-4-hydroxy-2,2-dioxo-1H-2λ6,1-benzothiazine-3-carboxylates with arylalkyl-amines in boiling xylene proceeds with good yield and purity to the corresponding N-(arylalkyl)-amides. However, the presence of water in the reaction mixture has been shown to cause the formation of specific impurities: N-(arylalkyl)-1-R-2,2-dioxo-1H-2λ6,1-benzothiazin-4-amines. According to the results of the pharmacological studies, powerful analgesics have been found among the substances synthesized. PMID:26839838

  18. Backbone (1)H, (13)C, and (15)N NMR resonance assignments of the Krüppel-like factor 4 activation domain.

    PubMed

    Conroy, Brigid S; Weiss, Emma R; Smith, Steven P; Langelaan, David N

    2017-04-01

    Krüppel-like factor 4 (KLF4) is a transcription factor involved in diverse biological processes, including development, cellular differentiation and proliferation, and maintenance of tissue homeostasis. KLF4 has also been associated with disease states, such as cardiovascular disease and several cancers. KLF4 contains an activation domain, repression domain, and a structurally characterized C-terminal zinc finger domain that mediates its binding to DNA. The structurally uncharacterized KLF4 activation domain is critical for transactivation by KLF4 and mediates its binding to the transcriptional coactivator CBP/p300. Here, we report the (1)H, (15)N, (13)CO, (13)Cα and (13)Cβ NMR chemical shift assignments of KLF41-130, which contains the KLF4 activation domain. Narrow chemical shift dispersion in the (1)H dimension of the (1)H-(15)N HSQC spectrum suggests that the KLF41-130 fragment is intrinsically disordered.

  19. NMR chemical shift as analytical derivative of the Helmholtz free energy.

    PubMed

    Van den Heuvel, Willem; Soncini, Alessandro

    2013-02-07

    We present a theory for the temperature-dependent nuclear magnetic shielding tensor of molecules with arbitrary electronic structure. The theory is a generalization of Ramsey's theory for closed-shell molecules. The shielding tensor is defined as a second derivative of the Helmholtz free energy of the electron system in equilibrium with the applied magnetic field and the nuclear magnetic moments. This derivative is analytically evaluated and expressed as a sum over states formula. Special consideration is given to a system with an isolated degenerate ground state for which the size of the degeneracy and the composition of the wave functions are arbitrary. In this case, the paramagnetic part of the shielding tensor is expressed in terms of the g and A tensors of the electron paramagnetic resonance spin Hamiltonian of the degenerate state. As an illustration of the proposed theory, we provide an explicit formula for the paramagnetic shift of the central lanthanide ion in endofullerenes Ln@C(60), with Ln = Ce(3+), Nd(3+), Sm(3+), Dy(3+), Er(3+), and Yb(3+), where the ground state can be a strongly spin-orbit coupled icosahedral sextet for which the paramagnetic shift cannot be described by previous theories.

  20. Internucleotide J-couplings and chemical shifts of the N-H···N hydrogen-bonds in the radiation-damaged guanine-cytosine base pairs.

    PubMed

    Li, Huifang; Zhang, Laibin; Han, Li; Sun, Wenming; Bu, Yuxiang

    2011-04-30

    Internucleotide (2h)J(NN) spin-spin couplings and chemical shifts (δ((1)H) and Δδ((15)N)) of N-H···N H-bond units in the natural and radiation-damaged G-C base pairs were predicted using the appropriate density functional theory calculations with a large basis set. Four possible series of the damaged G-C pairs (viz., dehydrogenated and deprotonated G-C pairs, GC(•-) and GC(•+) radicals) were discussed carefully in this work. Computational NMR results show that radicalization and anionization of the base pairs can yield strong effect on their (2h)J(NN) spin scalar coupling constants and the corresponding chemical shifts. Thus, variations of the NMR parameters associated with the N-H···N H-bonds may be taken as an important criterion for prejudging whether the natural G-C pair is radiation-damaged or not. Analysis shows that (2h)J(NN) couplings are strongly interrelated with the energy gaps (ΔE(LP→σ*)) and the second-order interaction energies (E(2)) between the donor N lone-pair (LP(N)) and the acceptor σ*(N-H) localized NBO orbitals, and also are sensitive to the electron density distributions over the σ*(N-H) orbital, indicating that (2h)J(NN) couplings across the N-H···N H-bonds are charge-transfer-controlled. This is well supported by variation of the electrostatic potential surfaces and corresponding charge transfer amount between G and C moieties. It should be noted that although the NMR spectra for the damaged G-C pair radicals are unavailable now and the states of the radicals are usually detected by the electron spin resonance, this study provides a correlation of the properties of the damaged DNA species with some of the electronic parameters associated with the NMR spectra for the understanding of the different state character of the damaged DNA bases.

  1. Identification of Gastric Cancer Biomarkers Using 1H Nuclear Magnetic Resonance Spectrometry

    PubMed Central

    Yong, Wei Peng; Yeow, Chen Hua

    2016-01-01

    Existing gastric cancer diagnosing methods were invasive, hence, a reliable non-invasive gastric cancer diagnosing method is needed. As a starting point, we used 1H NMR for identifying gastric cancer biomarkers using a panel of gastric cancer spheroids and normal gastric spheroids. We were able to identify 8 chemical shift biomarkers for gastric cancer spheroids. Our data suggests that the cancerous and non-cancerous spheroids significantly differ in the lipid composition and energy metabolism. These results encourage the translation of these biomarkers into in-vivo gastric cancer detection methodology using MRI-MS. PMID:27611679

  2. 1H NMR spectral studies on the polymerization mechanism of indole and its derivatives

    NASA Astrophysics Data System (ADS)

    Xu, Jingkun; Hou, Jian; Zhou, Weiqiang; Nie, Guangming; Pu, Shouzhi; Zhang, Shusheng

    2006-03-01

    The existence of N sbnd H bond according to the hydrogen nuclear magnetic resonance ( 1H NMR) spectra of polyindole and its derivatives, such as poly(5-bromoindole), poly(5-cyanoindole), poly(5-nitroindole), poly(5-methylindole), proved polymerization of high-quality polyindoles, which were electrosynthesized from middle strong Lewis acid boron trifluoride diethyl etherate (BFEE) and its mixed electrolytes with additional diethyl ether, occurred at 2,3-position. The elongation of the conjugation length made the chemical shift of all the protons of polyindoles to lower field in comparison with those of monomers.

  3. (1)H NMR spectra dataset and solid-state NMR data of cowpea (Vigna unguiculata).

    PubMed

    Alves Filho, Elenilson G; Silva, Lorena M A; Teofilo, Elizita M; Larsen, Flemming H; de Brito, Edy S

    2017-04-01

    In this article the NMR data from chemical shifts, coupling constants, and structures of all the characterized compounds were provided, beyond a complementary PCA evaluation for the corresponding manuscript (E.G. Alves Filho, L.M.A. Silva, E.M. Teofilo, F.H. Larsen, E.S. de Brito, 2017) [3]. In addition, a complementary assessment from solid-state NMR data was provided. For further chemometric analysis, numerical matrices from the raw (1)H NMR data were made available in Microsoft Excel workbook format (.xls).

  4. Using chemical shifts to generate structural ensembles for intrinsically disordered proteins with converged distributions of secondary structure

    PubMed Central

    Ytreberg, F Marty; Borcherds, Wade; Wu, Hongwei; Daughdrill, Gary W

    2015-01-01

    A short segment of the disordered p53 transactivation domain (p53TAD) forms an amphipathic helix when bound to the E3 ubiquitin ligase, MDM2. In the unbound p53TAD, this short segment has transient helical secondary structure. Using a method that combines broad sampling of conformational space with re-weighting, it is shown that it is possible to generate multiple, independent structural ensembles that have highly similar secondary structure distributions for both p53TAD and a P27A mutant. Fractional amounts of transient helical secondary structure were found at the MDM2 binding site that are very similar to estimates based directly on experimental observations. Structures were identified in these ensembles containing segments that are highly similar to short p53 peptides bound to MDM2, even though the ensembles were re-weighted using unbound experimental data. Ensembles were generated using chemical shift data (alpha carbon only, or in combination with other chemical shifts) and cross-validated by predicting residual dipolar couplings. We think this ensemble generator could be used to predict the bound state structure of protein interaction sites in IDPs if there are detectable amounts of matching transient secondary structure in the unbound state.

  5. Ab initio and DFT study of 31P-NMR chemical shifts of sphingomyelin and dihydrosphingomyelin lipid molecule

    NASA Astrophysics Data System (ADS)

    Sugimori, K.; Kawabe, H.; Nagao, H.; Nishikawa, K.

    One of the phospholipids, sphingomyelin (SM, N-acyl-sphingosine-1-phosphorylcholine) is the most abundant component of mammalian membranes in brain, nervous tissues, and human ocular lens. It plays an important role for apoptosis, aging, and signal transduction. Recently, Yappert and coworkers have shown that human lens sphingomyelin and its hydrogenated derivative, dihydrosphingomyelin (DHSM) are interacted with Ca2+ ions to develop human cataracts. Previously, we have investigated conformational differences between an isolated SM/DHSM molecule and Ca2+-coordinated form by using density functional theory (DFT) for geometry optimization and normal mode analysis. As a result, one of stable conformers of SMs has a hydrogen bonding between hydroxyl group and phosphate group, whereas another conformer has a hydrogen bonding between hydroxyl and phosphate amide group. In this study, 31P-Nuclear Magnetic Resonance (NMR) shielding constants of the obtained conformers are investigated by using ab initio and DFT with NMR-gauge invariant atomic orbitals (NMR-GIAO) calculations. The experimental 31P-NMR chemical shifts of SMs and DHSMs have significant small value around 0.1 ppm. We consider the relative conformational changes between SMs and DHSMs affect the slight deviations of 31P-NMR chemical shifts, and discuss intramolecular hydrogen bondings and the solvent effect in relation to NMR experimental reference.

  6. Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints.

    PubMed

    Chen, Jonathan L; Bellaousov, Stanislav; Tubbs, Jason D; Kennedy, Scott D; Lopez, Michael J; Mathews, David H; Turner, Douglas H

    2015-11-17

    Knowledge of RNA structure is necessary to determine structure-function relationships and to facilitate design of potential therapeutics. RNA secondary structure prediction can be improved by applying constraints from nuclear magnetic resonance (NMR) experiments to a dynamic programming algorithm. Imino proton walks from NOESY spectra reveal double-stranded regions. Chemical shifts of protons in GH1, UH3, and UH5 of GU pairs, UH3, UH5, and AH2 of AU pairs, and GH1 of GC pairs were analyzed to identify constraints for the 5' to 3' directionality of base pairs in helices. The 5' to 3' directionality constraints were incorporated into an NMR-assisted prediction of secondary structure (NAPSS-CS) program. When it was tested on 18 structures, including nine pseudoknots, the sensitivity and positive predictive value were improved relative to those of three unrestrained programs. The prediction accuracy for the pseudoknots improved the most. The program also facilitates assignment of chemical shifts to individual nucleotides, a necessary step for determining three-dimensional structure.

  7. Heat Integration of the Water-Gas Shift Reaction System for Carbon Sequestration Ready IGCC Process with Chemical Looping

    SciTech Connect

    Juan M. Salazara; Stephen E. Zitney; Urmila M. Diwekara

    2010-01-01

    Integrated gasification combined cycle (IGCC) technology has been considered as an important alternative for efficient power systems that can reduce fuel consumption and CO2 emissions. One of the technological schemes combines water-gas shift reaction and chemical-looping combustion as post gasification techniques in order to produce sequestration-ready CO2 and potentially reduce the size of the gas turbine. However, these schemes have not been energetically integrated and process synthesis techniques can be applied to obtain an optimal flowsheet. This work studies the heat exchange network synthesis (HENS) for the water-gas shift reaction train employing a set of alternative designs provided by Aspen energy analyzer (AEA) and combined in a process superstructure that was simulated in Aspen Plus (AP). This approach allows a rigorous evaluation of the alternative designs and their combinations avoiding all the AEA simplifications (linearized models of heat exchangers). A CAPE-OPEN compliant capability which makes use of a MINLP algorithm for sequential modular simulators was employed to obtain a heat exchange network that provided a cost of energy that was 27% lower than the base case. Highly influential parameters for the pos gasification technologies (i.e. CO/steam ratio, gasifier temperature and pressure) were calculated to obtain the minimum cost of energy while chemical looping parameters (oxidation and reduction temperature) were ensured to be satisfied.

  8. Suppression of sodium nuclear magnetic resonance double-quantum coherence by chemical shift and relaxation reagents

    NASA Astrophysics Data System (ADS)

    Hutchison, Robert B.; Huntley, James J. A.; Jin, Haoran; Shapiro, Joseph I.

    1992-12-01

    An investigation into the signal suppression behavior of the paramagnetic shift and relaxation reagents, Dy(P3O10)27- and Gd(P3O10)27-, with regard to their use in the nuclear magnetic resonance spectroscopic study of sodium has been performed. Measurements of T1 and T2 relaxation time constants of sodium in normal saline, Krebs-Henseleit buffer, and human blood serum, as a function of concentration of these reagents showed that, although closely coupled in the saline and K-H buffer environments, in plasma T1 and T2 become decoupled, transverse relaxation dominating in comparison to longitudinal relaxation. Linewidth measurements further suggest that relaxation in the plasma milieu is controlled primarily by inherent T2 relaxation, rather than by field inhomogeneity or diffusion effects. Quantitative single-quantum (1Q) and double-quantum (2Q) intensity measurements, biexponential T2 relaxation measurements, and parametric studies of the preparation time of the 2Q pulse sequence, were obtained in suspensions of bovine serum albumin and human erythrocytes. The observed suppression of sodium 2Q coherence by paramagnetic shift and relaxation reagents was found to exhibit a complex behavior in albumin solutions, involving the biexponential T2 decay to be expected during the preparation time of the 2Q filter pulse sequence, as well as the optimum preparation time for production of the double-quantum coherence itself. The controlling factor for both of these effects is the biexponential amplitude function in the expression for the transverse magnetization observed following application of the 2Q pulse sequence. This in turn is determined entirely by the values for the slow and fast components of biexponential relaxation in sodium, which themselves depend upon the concentration of the macromolecular binding sites for quadrupolar interaction. A similar behavior has been observed in suspensions of human erythrocytes.

  9. 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.

  10. Synthesis, XRD crystal structure, spectroscopic characterization (FT-IR, 1H and 13C NMR), DFT studies, chemical reactivity and bond dissociation energy studies using molecular dynamics simulations and evaluation of antimicrobial and antioxidant activities of a novel chalcone derivative, (E)-1-(4-bromophenyl)-3-(4-iodophenyl)prop-2-en-1-one

    NASA Astrophysics Data System (ADS)

    Zainuri, D. Alwani; Arshad, Suhana; Khalib, N. Che; Razak, I. Abdul; Pillai, Renjith Raveendran; Sulaiman, S. Fariza; Hashim, N. Shafiqah; Ooi, K. Leong; Armaković, Stevan; Armaković, Sanja J.; Panicker, C. Yohannan; Van Alsenoy, C.

    2017-01-01

    In the present study, the title compound named as (E)-1-(4-bromophenyl)-3-(4-iodophenyl)prop-2-en-1-one was synthesized and structurally characterized by single-crystal X-ray diffraction. The compound crystallizes in the monoclinic system with P21/c space group with the unit cell parameters of a = 16.147 (2) Å, b = 14.270 (2) Å, c = 5.9058 (9) Å, β = 92.577 (3)° and Z = 4. The molecular geometry obtained from X-Ray structure determination was optimized by Density Functional Theory (DFT) using B3LYP/6-31G+(d, p)/Lanl2dz(f) method in the ground state. The IR spectrum was recorded and interpreted in details with the aid of Density Functional Theory (DFT) calculations and Potential Energy Distribution (PED) analysis. In order to investigate local reactivity properties of the title molecule, we have conducted DFT calculations of average local ionization energy surface and Fukui functions which were mapped to the electron density surface. In order to predict the open air stability and possible degradation properties, within DFT approach, we have also calculated bond dissociation energies. 1H and 13C NMR spectra were recorded and chemical shifts were calculated theoretically and compared with the experimental values. In addition, in vitro antimicrobial results show that the title compound has great potential of antibacterial activity against Staphylococcus aureus, Staphylococcus epidermidis and Micrococcus luteus bacteria and antifungal activity against Candida albicans in comparison to some reported chalcone derivatives. Antioxidant studies revealed the highest metal chelating activity of this compound.

  11. FT-IR and {sup 1}H NMR characterization of the products of an ethylene inverse diffusion flame

    SciTech Connect

    Santamaria, Alexander; Mondragon, Fanor; Molina, Alejandro; Marsh, Nathan D.; Eddings, Eric G.; Sarofim, Adel F.

    2006-07-15

    Knowledge of the chemical structure of young soot and its precursors is very useful in the understanding of the paths leading to soot particle inception. This paper presents analyses of the chemical functional groups, based on FT-IR and {sup 1}H NMR spectroscopy of the products obtained in an ethylene inverse diffusion flame. The trends in the data indicate that the soluble fraction of the soot becomes progressively more aromatic and less aliphatic as the height above the burner increases. Results from {sup 1}H NMR spectra of the chloroform-soluble soot samples taken at different heights above the burner corroborate the infrared results based on proton chemical shifts (Ha, H{alpha}, H{beta}, and H{gamma}). The results indicate that the aliphatic {beta} and {gamma} hydrogens suffered the most drastic reduction, while the aromatic character increased considerably with height, particularly in the first half of the flame. (author)

  12. Solution behavior and complete sup 1 H and sup 13 C NMR assignments of the coenzyme B sub 12 derivative (5 prime -deoxyadenosyl)cobinamide using modern 2D NMR experiments, including 600-MHz sup 1 H NMR data

    SciTech Connect

    Pagano, T.G.; Yohannes, P.G.; Marzilli, L.G. ); Hay, B.P.; Scott, J.R.; Finke, R.G. )

    1989-02-15

    Two-dimensional (2D) NMR methods have been used to assign completely the {sup 1}H and {sup 13}C NMR spectra of the (5{prime}-deoxyadenosyl)cobinamide cation (AdoCbi{sup +}) in D{sub 2}O. Most of the {sup 1}H spectral assignments were made by using 2D homonuclear shift correlation spectroscopy (COSY), homonuclear Hartmann-Hahn spectroscopy (HOHAHA), absorption-mode (phase sensitive) 2D nuclear Overhauser effect (NOE) spectroscopy, and spin-locked NOE spectroscopy (also called ROESY, for rotating-frame Overhauser enhancement spectroscopy). Most of the protonated carbon resonances were assigned by using {sup 1}H-detected heteronuclear multiple-quantum coherence (HMQC) spectroscopy. The nonprotonated carbon resonances, as well as the remaining unassigned {sup 1}H and {sup 13}C NMR signals, were assigned from long-range {sup 1}H-{sup 13}C connectivities determined from {sup 1}H-detected multiple-bond heteronuclear multiple-quantum coherence spectroscopy (HMBC). Comparison of the {sup 13}C chemical shifts and {sup 1}H NOEs of AdoCbi{sup +} with those of coenzyme B{sup 12} ((5{prime}-deoxyadenosyl)cobalamin) and its benzimidazole-protonated, base-off form indicates that the electronic properties and structure of AdoCbi{sup +} are similar to that of coenzyme B{sup 12} in the protonated, base-off form. The {sup 13}C chemical shifts of most of the carbons of AdoCbi{sup +} do not vary significantly from those of base-off, benzimidazole-protonated coenzyme B{sup 12}, indicating that the electronic environment of the corrin ring is also similar in both compounds. However, significant differences in the chemical shifts of some of the corresponding carbons of the b, d, e, and f corrin side chains in AdoCbi{sup +} and in base-off, benzimidazole-protonated coenzyme B{sub 12} indicate that the positions of these side chains may be different in AdoCbi{sup +} compared to base-off coenzyme B{sup 12}.

  13. Position dependence of the 13C chemical shifts of α-helical model peptides. Fingerprint of the 20 naturally occurring amino acids

    PubMed Central

    Vila, Jorge A.; Baldoni, Héctor A.; Scheraga, Harold A.

    2004-01-01

    The position dependence of the 13C chemical shifts was investigated at the density functional level for α-helical model peptides represented by the sequence Ac-(Ala)i-X-(Ala)j-NH2, where X represents any of the 20 naturally occurring amino acids, with 0 ≤ i ≤ 8 and i + j = 8. Adoption of the locally dense basis approach for the quantum chemical calculations enabled us to reduce the length of the chemical-shift calculations while maintaining good accuracy of the results. For the 20 naturally occurring amino acids in α-helices, there is (1) significant variability of the computed 13C shielding as a function of both the guest residue (X) and the position along the sequence; for example, at the N terminus, the 13Cα and 13Cβ shieldings exhibit a uniform pattern of variation with respect to both the central or the C-terminal positions; (2) good agreement between computed and observed 13Cα and 13Cβ chemical shifts in the interior of the helix, with correlation coefficients of 0.98 and 0.99, respectively; for 13Cα chemical shifts, computed in the middle of the helix, only five residues, namely Asn, Asp, Ser, Thr, and Leu, exhibit chemical shifts beyond the observed standard deviation; and (3) better agreement for four of these residues (Asn, Asp, Ser, and Thr) only for the computed values of the 13Cα chemical shifts at the N terminus. The results indicate that 13Cβ, but not 13Cβ, chemical shifts are sensitive enough to reflect the propensities of some amino acids for specific positions within an α-helix, relative to the N and C termini of peptides and proteins. PMID:15498939

  14. Chemical potential shift and gap-state formation in SrTiO3-δ revealed by photoemission spectroscopy

    NASA Astrophysics Data System (ADS)

    Pal, Prabir; Kumar, Pramod; Aswin, V.; Dogra, Anjana; Joshi, Amish G.

    2014-08-01

    In this study, we report on investigations of the electronic structure of SrTiO3 annealed at temperature ranging between 550 and 840 °C in an ultrahigh vacuum. Annealing induced oxygen vacancies (Ovac) impart considerable changes in the electronic structure of SrTiO3. Using core-level photoemission spectroscopy, we have studied the chemical potential shift (Δμ) as a function of annealing temperature. The result shows that the chemical potential monotonously increases with electron doping in SrTiO3-δ. The monotonous increase of the chemical potential rules out the existence of electronic phase separation in the sample. Using valence band photoemission, we have demonstrated the formation of a low density of states at the near Fermi level electronic spectrum of SrTiO3-δ. The gap-states were observed by spectral weight transfer over a large energy scale of the stoichiometric band gap of SrTiO3 system leading finally to an insulator-metal transition. We have interpreted our results from the point of structural distortions induced by oxygen vacancies.

  15. Chemical structure elucidation from ¹³C NMR chemical shifts: efficient data processing using bipartite matching and maximal clique algorithms.

    PubMed

    Koichi, Shungo; Arisaka, Masaki; Koshino, Hiroyuki; Aoki, Atsushi; Iwata, Satoru; Uno, Takeaki; Satoh, Hiroko

    2014-04-28

    Computer-assisted chemical structure elucidation has been intensively studied since the first use of computers in chemistry in the 1960s. Most of the existing elucidators use a structure-spectrum database to obtain clues about the correct structure. Such a structure-spectrum database is expected to grow on a daily basis. Hence, the necessity to develop an efficient structure elucidation system that can adapt to the growth of a database has been also growing. Therefore, we have developed a new elucidator using practically efficient graph algorithms, including the convex bipartite matching, weighted bipartite matching, and Bron-Kerbosch maximal clique algorithms. The utilization of the two matching algorithms especially is a novel point of our elucidator. Because of these sophisticated algorithms, the elucidator exactly produces a correct structure if all of the fragments are included in the database. Even if not all of the fragments are in the database, the elucidator proposes relevant substructures that can help chemists to identify the actual chemical structures. The elucidator, called the CAST/CNMR Structure Elucidator, plays a complementary role to the CAST/CNMR Chemical Shift Predictor, and together these two functions can be used to analyze the structures of organic compounds.

  16. Chemical shift powder spectra enhanced by multiple-contact cross-polarization under slow magic-angle spinning.

    PubMed

    Raya, Jésus; Perrone, Barbara; Hirschinger, Jérôme

    2013-02-01

    A simple multiple-contact cross-polarization (CP) scheme is applied to a powder sample of ferrocene and β-calcium formate under static and magic-angle spinning (MAS) conditions. The method is described analytically through the density matrix formalism. We show that multiple equilibrations-re-equilibrations with the proton spin bath improves the polarization transfer efficiency at short contact times and provides higher signal enhancements than state-of-the art techniques such as adiabatic passage through the Hartmann-Hahn condition CP (APHH-CP) when MAS is applied. The resulting chemical shift powder spectra then are identical to the ones obtained by using ROtor-Directed Exchange of Orientations CP (APHH-RODEO-CP) with intensity gains of a factor 1.1-1.3.

  17. Chemical shift powder spectra enhanced by multiple-contact cross-polarization under slow magic-angle spinning

    NASA Astrophysics Data System (ADS)

    Raya, Jésus; Perrone, Barbara; Hirschinger, Jérôme

    2013-02-01

    A simple multiple-contact cross-polarization (CP) scheme is applied to a powder sample of ferrocene and β-calcium formate under static and magic-angle spinning (MAS) conditions. The method is described analytically through the density matrix formalism. We show that multiple equilibrations-re-equilibrations with the proton spin bath improves the polarization transfer efficiency at short contact times and provides higher signal enhancements than state-of-the art techniques such as adiabatic passage through the Hartmann-Hahn condition CP (APHH-CP) when MAS is applied. The resulting chemical shift powder spectra then are identical to the ones obtained by using ROtor-Directed Exchange of Orientations CP (APHH-RODEO-CP) with intensity gains of a factor 1.1-1.3.

  18. Non-invasive localization of thymol accumulation in Carum copticum (Apiaceae) fruits by chemical shift selective magnetic resonance imaging.

    PubMed

    Gersbach, P V; Reddy, N

    2002-08-01

    Magnetic resonance imaging was used to localize the site of essential oil accumulation in fruit of Carum copticum L. (Apiaceae). A chemical shift method is described that utilized the spectral properties of the aromatic monoterpene thymol, the major component of the essential oil, to image thymol selectively. The presence of essential oil secretory structures in the fruit and an essential oil containing a high proportion of thymol were confirmed with optical microscopy and gas chromatography-mass spectrometry, respectively. Selective imaging of whole C. copticum fruits showed that thymol accumulation was localized to the secretory structures (canals) situated in the fruit wall. The technique was considered non-invasive as the seeds used in the imaging experiments remained intact and viable.

  19. Classification of iron-sulfur cores in ferredoxins by 1H nuclear magnetic resonance spectroscopy.

    PubMed

    Nagayama, K; Ozaki, Y; Kyogoku, Y; Hase, T; Matsubara, H

    1983-09-01

    A 1H nuclear magnetic resonance (NMR) study was carried out on various ferredoxins which possess one of three types of iron-sulfur clusters, (2Fe-2S), (3Fe-3S), or (4Fe-4S). In the isolated form, (2Fe-2S) ferredoxins from spinach (Spinacea oleracia), pokeweed (Phytolacca americana), a blue-green alga (Spirulina platensis), and a halobacterium (Halobacterium halobium) exhibited two broad resonances common in chemical shift at the region downfield of 10 ppm. In their reduced forms, seven contact-shifted resonances appeared spread over 30 ppm. Although the positions of the contact-shifted resonances in the reduced state differed among the four, a common trend in the temperature dependence of their resonance positions was recognized. Two (4Fe-4S) ferredoxins from Bacillus stearothermophilus and Bacillus thermoproteolyticus exhibited almost indistinguishable spectral patterns in both the oxidized and reduced forms. The ferricyanide-treated ferredoxins of B. stearothermophilus and B. thermoproteolyticus showed characteristic contact-shifted resonances distinct from the spectra of the original (4Fe-4S) ferredoxins. This corresponds to the recent finding of the interconversion of (4Fe-4S) and (3Fe-3S) clusters with ferricyanide in the ferredoxin. Based on our data together with reported NMR data on other ferredoxins, contact-shift resonances of three types of clusters were tabulated. The reliability of NMR classification increases when we compare the NMR spectra of a ferredoxin with the classification standards at the two redox states. Moreover, not only the absolute values of the chemical shifts of contact-shifted resonances but also their temperature dependence give distinctive information applicable to iron core identification.

  20. Differential protonation and dynamic structure of doxylamine succinate in solution using 1H and 13C NMR.

    PubMed

    Somashekar, B S; Nagana Gowda, G A; Ramesha, A R; Khetrapal, C L

    2004-07-01

    A protonation and dynamic structural study of doxylamine succinate, a 1:1 salt of succinic acid with dimethyl-[2-(1-phenyl-1-pyridin-2-yl-ethoxy)ethyl]amine, in solution using one- and two-dimensional 1H and 13C NMR experiments at variable temperature and concentration is presented. The two acidic protons of the salt doxylamine succinate are in 'intermediate' exchange at room temperature, as evidenced by the appearance of a broad signal. This signal evolves into two distinct signals below about -30 degrees C. A two-dimensional 1H-1H double quantum filtered correlation experiment carried out at -55 degrees C shows protonation of one of the acidic protons to the dimethylamine nitrogen. A two-dimensional rotating frame 1H-1H NOE experiment at the same temperature reveals that the other proton remains with the succinate moiety. Comparison of the 1H and 13C chemical shifts and the 13C T1 relaxation times of the salt with those of the free base further substantiate the findings.

  1. Portable Sequentially Shifted Excitation Raman spectroscopy as an innovative tool for in situ chemical interrogation of painted surfaces.

    PubMed

    Conti, Claudia; Botteon, Alessandra; Bertasa, Moira; Colombo, Chiara; Realini, Marco; Sali, Diego

    2016-08-07

    We present the first validation and application of portable Sequentially Shifted Excitation (SSE) Raman spectroscopy for the survey of painted layers in art. The method enables the acquisition of shifted Raman spectra and the recovery of the spectral data through the application of a suitable reconstruction algorithm. The technique has a great potentiality in art where commonly a strong fluorescence obscures the Raman signal of the target, especially when conventional portable Raman spectrometers are used for in situ analyses. Firstly, the analytical capability of portable SSE Raman spectroscopy is critically discussed using reference materials and laboratory specimens, comparing its results with other conventional high performance laboratory instruments (benchtop FT-Raman and dispersive Raman spectrometers with an external fiber optic probe); secondly, it is applied directly in situ to study the complex polychromy of Italian prestigious terracotta sculptures of the 16(th) century. Portable SSE Raman spectroscopy represents a new investigation modality in art, expanding the portfolio of non-invasive, chemically specific analytical tools.

  2. Thickness-Dependent Binding Energy Shift in Few-Layer MoS2 Grown by Chemical Vapor Deposition.

    PubMed

    Lin, Yu-Kai; Chen, Ruei-San; Chou, Tsu-Chin; Lee, Yi-Hsin; Chen, Yang-Fang; Chen, Kuei-Hsien; Chen, Li-Chyong

    2016-08-31

    The thickness-dependent surface states of MoS2 thin films grown by the chemical vapor deposition process on the SiO2-Si substrates are investigated by X-ray photoelectron spectroscopy. Raman and high-resolution transmission electron microscopy suggest the thicknesses of MoS2 films to be ranging from 3 to 10 layers. Both the core levels and valence band edges of MoS2 shift downward ∼0.2 eV as the film thickness increases, which can be ascribed to the Fermi level variations resulting from the surface states and bulk defects. Grainy features observed from the atomic force microscopy topographies, and sulfur-vacancy-induced defect states illustrated at the valence band spectra imply the generation of surface states that causes the downward band bending at the n-type MoS2 surface. Bulk defects in thick MoS2 may also influence the Fermi level oppositely compared to the surface states. When Au contacts with our MoS2 thin films, the Fermi level downshifts and the binding energy reduces due to the hole-doping characteristics of Au and easy charge transfer from the surface defect sites of MoS2. The shift of the onset potentials in hydrogen evolution reaction and the evolution of charge-transfer resistances extracted from the impedance measurement also indicate the Fermi level varies with MoS2 film thickness. The tunable Fermi level and the high chemical stability make our MoS2 a potential catalyst. The observed thickness-dependent properties can also be applied to other transition-metal dichalcogenides (TMDs), and facilitates the development in the low-dimensional electronic devices and catalysts.

  3. A combined DFT - NMR study of cyclic 1,2-diones and methyl ethers of their enols: The power and limitations of the method based on theoretical predictions of 13C NMR chemical shifts

    NASA Astrophysics Data System (ADS)

    Kubicki, Dominik; Gryff-Keller, Adam; Szczeciński, Przemysław

    2012-08-01

    A series of cyclic 1,2-diones and methyl ethers of their enols were investigated by a combined 13C NMR/computational DFT method to establish their preferred solution structures. The optimum molecular geometries and magnetic shielding constants of carbon nuclei were calculated with GIAO DFT [PBE1PBE/6-311++G(2d,p) PCM] method for the investigated molecules allowing for enolization and dynamic conformational equilibriums occurring in the solutions. These compounds served simultaneously as model compounds for testing the effectiveness and limitations of the exploited method of investigating molecular structures based on comparison of the theoretically calculated magnetic shielding constants and experimental 13C NMR chemical shifts. Generally, a very good agreement between experimental and theoretical data was obtained for the investigated group of compounds, which proved the applied level of theory and used methodology to be adequate and should ensure a high accuracy of the 13C NMR chemical shift predictions. Some divergences between the experiment and theory could be interpreted as the results of insufficiencies of the molecular modelling and the effects of neglecting vibrational/librational molecular motions. Furthermore, we report herein an observation of an unexpected 1H NMR spectral pattern for 2,3-dimethoxycyclodeca-1,3-diene (diether of cyclodecadione dienol), which was interpreted to be caused by the slow (in NMR time scale) enantiomerization of this molecule which preferentially assumes a chiral conformation.

  4. V79-hCYP2E1-hSULT1A1, a cell line for the sensitive detection of genotoxic effects induced by carbohydrate pyrolysis products and other food-borne chemicals.

    PubMed

    Glatt, Hansruedi; Schneider, Heiko; Liu, Yungang

    2005-02-07

    We recently constructed a Chinese hamster V79-derived cell line that stably expresses human cytochrome P450 (CYP) 2E1 and human sulphotransferase (SULT) 1A1. These enzymes are involved in the bioactivation of numerous promutagens/procarcinogens, but are not taken into account in standard in vitro mutagenicity assays. Various carbohydrate pyrolysis products and other food contaminants that induce tumours or preneoplastic lesions in laboratory animals are inactive or only weakly active in standard in vitro genotoxicity assays. This is the case for acrylamide, furan, 5-hydroxymethylfurfural, nitrofen and N-nitrosodimethylamine. These compounds were investigated for induction of sister chromatid exchange (SCE) in V79-hCYP2E1-hSULT1A1 cells. All test compounds showed positive results over a wide concentration range, starting at 0.01 microM for N-nitrosodimethylamine, 3 microM for furan, 12.5 microM for nitrofen, 20 microM for 5-hydroxymethylfurfural, and 200 microM for acrylamide. The concentration-response curve of furan was unusual, as this compound induced a statistically significant, but rather constant and weak increase in SCE over an extremely wide concentration range (3-16,000 microM). Furan was slightly less active, whereas the remaining compounds were much less active in the parental V79 cell line than in V79-hCYP2E1-hSULT1A1 cells. Compared to many other genotoxic effects, the study of SCE only requires small numbers of cells (and incubation volumes) and usually is detected even at low concentrations of the genotoxicant. Therefore, induction of SCE in V79-hCYP2E1-hSULT1A1 cells may be useful in the genotoxicity testing of preparations of heated food and in their bioassay-directed fractionation.

  5. Comparison of experimental and DFT-calculated NMR chemical shifts of 2-amino and 2-hydroxyl substituted phenyl benzimidazoles, benzoxazoles and benzothiazoles in four solvents using the IEF-PCM solvation model.

    PubMed

    Pierens, Gregory K; Venkatachalam, T K; Reutens, David C

    2016-04-01

    A comparative study of experimental and calculated NMR chemical shifts of six compounds comprising 2-amino and 2-hydroxy phenyl benzoxazoles/benzothiazoles/benzimidazoles in four solvents is reported. The benzimidazoles showed interesting spectral characteristics, which are discussed. The proton and carbon chemical shifts were similar for all solvents. The largest chemical shift deviations were observed in benzene. The chemical shifts were calculated with density functional theory using a suite of four functionals and basis set combinations. The calculated chemical shifts revealed a good match to the experimentally observed values in most of the solvents. The mean absolute error was used as the primary metric. The use of an additional metric is suggested, which is based on the order of chemical shifts. The DP4 probability measures were also used to compare the experimental and calculated chemical shifts for each compound in the four solvents. Copyright © 2015 John Wiley & Sons, Ltd.

  6. The molecular structure and vibrational, (1)H and (13)C NMR spectra of lidocaine hydrochloride monohydrate.

    PubMed

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

    2016-01-05

    The structure, vibrational and NMR spectra of the local anesthetic drug lidocaine hydrochloride monohydrate salt were investigated by B3LYP/6-311G(∗∗) calculations. The lidocaine·HCl·H2O salt is predicted to have the gauche structure as the predominant form at ambient temperature with NCCN and CNCC torsional angles of 110° and -123° as compared to 10° and -64°, respectively in the base lidocaine. The repulsive interaction between the two N-H bonds destabilized the gauche structure of lidocaine·HCl·H2O salt. The analysis of the observed vibrational spectra is consistent with the presence of the lidocaine salt in only one gauche conformation at room temperature. The (1)H and (13)C NMR spectra of lidocaine·HCl·H2O were interpreted by experimental and DFT calculated chemical shifts of the lidocaine salt. The RMSD between experimental and theoretical (1)H and (13)C chemical shifts for lidocaine·HCl·H2O is 2.32 and 8.21ppm, respectively.

  7. Development of multicomponent hybrid density functional theory with polarizable continuum model for the analysis of nuclear quantum effect and solvent effect on NMR chemical shift

    SciTech Connect

    Kanematsu, Yusuke; Tachikawa, Masanori

    2014-04-28

    We have developed the multicomponent hybrid density functional theory [MC-(HF+DFT)] method with polarizable continuum model (PCM) for the analysis of molecular properties including both nuclear quantum effect and solvent effect. The chemical shifts and H/D isotope shifts of the picolinic acid N-oxide (PANO) molecule in chloroform and acetonitrile solvents are applied by B3LYP electron exchange-correlation functional for our MC-(HF+DFT) method with PCM (MC-B3LYP/PCM). Our MC-B3LYP/PCM results for PANO are in reasonable agreement with the corresponding experimental chemical shifts and isotope shifts. We further investigated the applicability of our method for acetylacetone in several solvents.

  8. Simple quantitative structure-property relationship (QSPR) modeling of 17O carbonyl chemical shifts in substituted benzaldehydes compared to DFT and empirical approaches.

    PubMed

    Kiralj, Rudolf; Ferreira, Márcia M C

    2008-07-10

    The geometry of 50 substituted benzaldehydes was optimized at the semiempirical PM3 level, and various electronic and steric descriptors accounting for properties of the benzene ring, aldehyde group, and their connecting carbon-carbon bond were calculated. Quantitative structure-property relationships (QSPR) between (17)O carbonyl chemical shifts and these descriptors were established using partial least-squares regression and principal component regression. These two parsimonious QSPR models were comparable with the literature empirical model and DFT (density functional theory) and capable of predicting (17)O chemical shifts for 10 benzaldehydes. Principal component analysis, hierarchical cluster analysis, and crystal structure data retrieved from the Cambridge Structural Database were additional methods for chemical verification of the regression models. The QSPR models are recommended as being more reliable than and superior to the empirical and DFT models due to the results of all validations, simplicity, and short time that regressions need for (17)O shift prediction.

  9. Difference in the structures of alanine tri- and tetra-peptides with antiparallel β-sheet assessed by X-ray diffraction, solid-state NMR and chemical shift calculations by GIPAW.

    PubMed

    Asakura, Tetsuo; Yazawa, Koji; Horiguchi, Kumiko; Suzuki, Furitsu; Nishiyama, Yusuke; Nishimura, Katsuyuki; Kaji, Hironori

    2014-01-01

    Alanine oligomers provide a key structure for silk fibers from spider and wild silkworms.We report on structural analysis of L-alanyl-L-alanyl-L-alanyl-L-alanine (Ala)4 with anti-parallel (AP) β-structures using X-ray and solid-state NMR. All of the Ala residues in the (Ala)4 are in equivalent positions, whereas for alanine trimer (Ala)3 there are two alternative locations in a unit cell as reported previously (Fawcett and Camerman, Acta Cryst., 1975, 31, 658-665). (Ala)4 with AP β-structure is more stable than AP-(Ala)3 due to formation of the stronger hydrogen bonds. The intermolecular structure of (Ala)4 is also different from polyalanine fiber structure, indicating that the interchain arrangement of AP β-structure changes with increasing alanine sequencelength. Furthermore the precise (1)H positions, which are usually inaccesible by X-ray diffraction method, are determined by high resolution (1)H solid state NMR combined with the chemical shift calculations by the gauge-including projector augmented wave method.

  10. Dynamic structures of intact chicken erythrocyte chromatins as studied by 1H-31P cross-polarization NMR.

    PubMed Central

    Akutsu, H; Nishimoto, S; Kyogoku, Y

    1994-01-01

    The dynamic properties of DNA in intact chicken erythrocyte cells, nuclei, nondigested chromatins, digested soluble chromatins, H1, H5-depleted soluble chromatins and nucleosome cores were investigated by means of single-pulse and 1H-31P cross-polarization NMR. The temperature dependence of the phosphorus chemical shift anisotropy was identical for the former three in the presence of 3 mM MgCl2, suggesting that the local higher order structure is identical for these chromatins. The intrinsic phosphorus chemical shift anisotropy of the nucleosome cores was -159 ppm. The chemical shift anisotropy of DNA in the chromatins can be further averaged by the motion of the linker DNA. The spin-lattice relaxation time in the rotating frame of the proton spins (T1p) of the nondigested chromatins was measured at various locking fields. The result was analyzed on the assumption of the isotropic motion to get a rough value of the correlation time of the motion efficient for the relaxation, which was eventually ascribed to the segmental motion of the linker DNA with restricted amplitude. The 30 nm filament structure induced by NaCl was shown to be dynamically different from that induced by MgCl2. Side-by-side compaction of 30-nm filaments was suggested to be induced in the MgCl2 concentration range higher than 0.3 mM. Biological significance of the dynamic structure was discussed in connection with the results obtained. PMID:7948693

  11. 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.

  12. Novel use of chemical shift in NMR as molecular descriptor: a first report on modeling carbonic anhydrase inhibitory activity and related parameters.

    PubMed

    Khadikar, Padmakar V; Sharma, Vimukta; Karmarkar, Sneha; Supuran, Claudiu T

    2005-02-15

    A novel use of NMR chemical shift of the SO(2)NH(2) protons (in dioxane as solvent) as a molecular descriptor is described for modeling the inhibition constant for benzene sulfonamides against the zinc enzyme carbonic anhydrase (CA, EC 4.2.1.1). The methodology is extended to model diuretic activity and lipophilicity of benzene sulfonamide derivatives. The regression analysis of the data has shown that the NMR chemical shift is incapable of modeling lipophilicity. However, it is quite useful for modeling the diuretic activity of these derivatives. The results are compared with those obtained using distance-based topological indices: Wiener (W)-, Szeged (Sz)-, and PI (Padmakar-Ivan) indices.

  13. MRI chemical shift imaging of the fat content of the pancreas and liver of patients with type 2 diabetes mellitus.

    PubMed

    Chai, Jun; Liu, Peng; Jin, Erhu; Su, Tianhao; Zhang, Jie; Shi, Kaining; Hong, X U; Yin, Jie; Yu, Hengchi

    2016-02-01

    The present study aimed to investigate the association between the content and distribution of fat in the pancreas and liver in patients with type 2 diabetes mellitus (T2DM). A total of 70 patients newly diagnosed with T2DM (T2DM group) and 30 healthy volunteers (normal control group) were enrolled in the present study. Dual-echo magnetic resonance (MR) chemical shift imaging was used to measure the fat content of the liver and the head, body and tail regions of the pancreas. In addition, the distribution of fat in the various regions of the pancreas, as well as the average fat content of the pancreas versus the liver, were compared. The fat content of the pancreatic head, body and tail regions of the T2DM group were 5.59±4.70, 4.80±3.75 and 4.89±3.86%, respectively. The fat content of these regions in the normal control group were 3.89±2.47, 3.30±2.11 and 3.23±2.23%, respectively. The average fat content of the pancreas was 5.19±3.75% for the T2DM group and 3.47±2.00% for the normal control group. The average fat content of the liver was 9.87±3.19% for the T2DM group and 7.24±2.38% for the normal control group. Therefore, the results from MR chemical shift imaging suggested that there were no significant differences in the distribution of fat between the pancreas of patients newly diagnosed with T2DM and that from the healthy population; however, the average fat content in the pancreas of the T2DM group was significantly higher (F=3.597; P<0.05), as compared with the normal control group. In addition, there was no correlation between the fat contents in the pancreas and liver in patients newly diagnosed with T2DM and the healthy population.

  14. The synthesis and characterization of the 'research chemical' N-(1-amino-3-methyl-1-oxobutan-2-yl)-1-(cyclohexylmethyl)-3-(4-fluorophenyl)-1H-pyrazole-5-carboxamide (3,5-AB-CHMFUPPYCA) and differentiation from its 5,3-regioisomer.

    PubMed

    McLaughlin, Gavin; Morris, Noreen; Kavanagh, Pierce V; Power, John D; Twamley, Brendan; O'Brien, John; Talbot, Brian; Dowling, Geraldine; Brandt, Simon D

    2016-09-01

    This study presents the identification of N-(1-amino-3-methyl-1-oxobutan-2-yl)-1-(cyclohexylmethyl)-3-(4-fluorophenyl)-1H-pyrazole-5-carboxamide that was termed 3,5-AB-CHMFUPPYCA. This compound was obtained from a UK-based Internet vendor, who erroneously advertised this 'research chemical' as AZ-037 and which would have been associated with (S)-N-(1-amino-3-methyl-1-oxobutan-2-yl)-1-(5-fluoropentyl)-5-(4-fluorophenyl)-1H-pyrazole-3-carboxamide. The presence of the pyrazole core indicates a bioisosteric replacement of an indazole ring that is frequently associated with synthetic cannabinoids of the PINACA, FUBINACA, and CHMINACA series. The pyrazole ring system present in 3,5-AB-CHMFUPPYCA gives rise to the regioisomer N-(1-amino-3-methyl-1-oxobutan-2-yl)-1-(cyclohexylmethyl)-5-(4-fluorophenyl)-1H-pyrazole-3-carboxamide (named 5,3-AB-CHMFUPPYCA) and both isomers were synthesized using two specific routes which supported the correct identification of the 'research chemical' as 3,5-AB-CHMFUPPYCA. Both isomers could be conveniently differentiated. Interestingly, a route specific chlorine-containing by-product also was observed during the synthesis of 3,5-AB-CHMFUPPYCA and identified as N-(1-amino-3-methyl-1-oxobutan-2-yl)-4-chloro-1-(cyclohexylmethyl)-3-(4-fluorophenyl)-1H-pyrazole-5-carboxamide. An extensive analytical characterization included chromatographic, spectroscopic, mass spectrometric platforms as well as crystal structure analysis. The syntheses and analytical characterizations of both AB-CHMFUPPYCA isomers are reported for the first time and serves as a reminder that the possibility of mislabeling of 'research chemicals' cannot be excluded. The pharmacological activities of both AB-CHMFUPPYCA isomers remain to be explored. Copyright © 2015 John Wiley & Sons, Ltd.

  15. Shifts in controls on the temporal coherence of throughfall chemical flux in Acadia National Park, Maine, USA

    USGS Publications Warehouse

    Nelson, Sarah J.; Webster, Katherine E.; Loftin, Cynthia S.; Weathers, Kathleen C.

    2013-01-01

    Major ion and mercury (Hg) inputs to terrestrial ecosystems include both wet and dry deposition (total deposition). Estimating total deposition to sensitive receptor sites is hampered by limited information regarding its spatial heterogeneity and seasonality. We used measurements of throughfall flux, which includes atmospheric inputs to forests and the net effects of canopy leaching or uptake, for ten major ions and Hg collected during 35 time periods in 1999–2005 at over 70 sites within Acadia National Park, Maine to (1) quantify coherence in temporal dynamics of seasonal throughfall deposition and (2) examine controls on these patterns at multiple scales. We quantified temporal coherence as the correlation between all possible site pairs for each solute on a seasonal basis. In the summer growing season and autumn, coherence among pairs of sites with similar vegetation was stronger than for site-pairs that differed in vegetation suggesting that interaction with the canopy and leaching of solutes differed in coniferous, deciduous, mixed, and shrub or open canopy sites. The spatial pattern in throughfall hydrologic inputs across Acadia National Park was more variable during the winter snow season, suggesting that snow re-distribution affects net hydrologic input, which consequently affects chemical flux. Sea-salt corrected calcium concentrations identified a shift in air mass sources from maritime in winter to the continental industrial corridor in summer. Our results suggest that the spatial pattern of throughfall hydrologic flux, dominant seasonal air mass source, and relationship with vegetation in winter differ from the spatial pattern of throughfall flux in these solutes in summer and autumn. The coherence approach applied here made clear the strong influence of spatial heterogeneity in throughfall hydrologic inputs and a maritime air mass source on winter patterns of throughfall flux. By contrast, vegetation type was the most important influence on

  16. Determination of the Chemical-Shift Difference between the Lactate Multiplets and Its pH Dependence

    NASA Astrophysics Data System (ADS)

    Bunse, Michael; Jung, Wulf-Ingo; Dietze, Günther; Lutz, Otto

    1996-09-01

    A volume-selective NMR method is presented for very exact determination of the difference of the Larmor frequencies between the coupled resonances of homonuclear AX3spin systems, as, for example, lactate. The frequency difference can be determined with an accuracy of 0.003 ppm even if only the doublet of the spin system can be detected. The method is based on the effects of homonuclear polarization transfer which occurs in localized double-spin-echo spectroscopy. It is used for determination of the chemical-shift difference of the lactate multiplets, which depends on the degree of dissociation and consequently on pH. Measurements were performed with a 1.5 T Siemens Magnetom SP 63 whole-body imager on solutions of lactate and acetic acid in physiological sodium chloride solution with pH from 1 to 11. As a consequence of these measurements, conclusions are possible for the optimum echo time for PRESS measurements which avoid signal losses from polarization transfer. Furthermore, the possibility of localized pH determination by this effect is discussed.

  17. 13C-detected NMR experiments for measuring chemical shifts and coupling constants in nucleic acid bases.

    PubMed

    Fiala, Radovan; Sklenár, Vladimír

    2007-10-01

    The paper presents a set of two-dimensional experiments that utilize direct (13)C detection to provide proton-carbon, carbon-carbon and carbon-nitrogen correlations in the bases of nucleic acids. The set includes a (13)C-detected proton-carbon correlation experiment for the measurement of (13)C-(13)C couplings, the CaCb experiment for correlating two quaternary carbons, the HCaCb experiment for the (13)C-(13)C correlations in cases where one of the carbons has a proton attached, the HCC-TOCSY experiment for correlating a proton with a network of coupled carbons, and a (13)C-detected (13)C-(15)N correlation experiment for detecting the nitrogen nuclei that cannot be detected via protons. The IPAP procedure is used for extracting the carbon-carbon couplings and/or carbon decoupling in the direct dimension, while the S(3)E procedure is preferred in the indirect dimension of the carbon-nitrogen experiment to obtain the value of the coupling constant. The experiments supply accurate values of (13)C and (15)N chemical shifts and carbon-carbon and carbon-nitrogen coupling constants. These values can help to reveal structural features of nucleic acids either directly or via induced changes when the sample is dissolved in oriented media.

  18. An artificially evolved albumin binding module facilitates chemical shift epitope mapping of GA domain interactions with phylogenetically diverse albumins.

    PubMed

    He, Yanan; Chen, Yihong; Rozak, David A; Bryan, Philip N; Orban, John

    2007-07-01

    Protein G-related albumin-binding (GA) modules occur on the surface of numerous Gram-positive bacterial pathogens and their presence may promote bacterial growth and virulence in mammalian hosts. We recently used phage display selection to evolve a GA domain, PSD-1 (phage selected domain-1), which tightly bound phylogenetically diverse albumins. With respect to PSD-1's broad albumin binding specificity, it remained unclear how the evolved binding epitope compared to those of naturally occurring GA domains and whether PSD-1's binding mode was the same for different albumins. We investigate these questions here using chemical shift perturbation measurements of PSD-1 with rabbit serum albumin (RSA) and human serum albumin (HSA) and put the results in the context of previous work on structure and dynamics of GA domains. Combined, these data provide insights into the requirements for broad binding specificity in GA-albumin interactions. Moreover, we note that using the phage-optimized PSD-1 protein significantly diminishes the effects of exchange broadening at the binding interface between GA modules and albumin, presumably through stabilization of a ligand-bound conformation. The employment of artificially evolved domains may be generally useful in NMR structural studies of other protein-protein complexes.

  19. Shifting Phases for Patchy Particles - Effect of mutagenesis and chemical modification on the phase diagram of human gamma D crystallin

    NASA Astrophysics Data System (ADS)

    McManus, Jennifer J.; James, Susan; McNamara, Ruth; Quinn, Michelle

    2014-03-01

    Single mutations in human gamma D crystallin (HGD), a protein found in the eye lens are associated with several childhood cataracts. Phase diagrams for several of these protein mutants have been measured and reveal that phase boundaries are shifted compared with the native protein, leading to condensation of protein in a physiologically relevant regime. Using HGD as a model protein, we have constructed phase diagrams for double mutants of the protein, incorporating two single amino acid substitutions for which phase diagrams are already known. In doing so, the characteristics of each of the single mutations are maintained but both are now present in the same protein particle. While these proteins are not of interest physiologically, this strategy allows the controlled synthesis of nano-scale patchy particles in which features associated with a known phase behavior can be included. It can also provide a strategy for the controlled crystallisation of proteins. Phase boundaries also change after the chemical modification of the protein, through the covalent attachment of fluorescent labels, for example, and this will also be discussed. The authors acknowledge Science Foundation Ireland Stokes Lectureship and Grant 11/RFP.1/PHY/3165. The authors also acknowledge the Irish Research Council and the John and Pat Hume Scholarship.

  20. 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...

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

    SciTech Connect

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

    2014-01-03

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

  2. In vivo 1H MR spectra analysis by means of second derivative method.

    PubMed

    Sokół, M

    2001-05-01

    Short echo time (TE) in vivo PRESS 1H MR spectra (2 T, TE=35 ms) of normal brain were fitted in the frequency domain using the second derivative method. In this approach, local maxima and hidden peaks are found as local minima of spectrum second derivative. The Lorentzian robust minimisation procedure (referred to as maximum likelihood or m-estimate fitting) using Levenburg-Marquardt non-linear fitting engine was applied. Spectral lines were approximated under the assumption of the mixed Lorentzian/Gaussian lineshapes. The same procedure was applied to 18 proton spectra. The number of peaks found within the range of 0.74/4.2 parts per million (ppm) was 52+/-3 and their positions were almost the same. The fitted lines were assigned on the basis of the J-pattern recalculated for the field strength of 2 T and by comparing the chemical shifts with the shifts in the single compound spectra. The ratios of main metabolites, such as NAA/Cr, Cho/Cr, Cho/NAA and mI/Cr, are in accord with those obtained earlier using the software supplied with the MR imager and the absolute concentrations of N-acetylaspartate (NAA), choline containing compounds (Cho), myoInositol (mI), glucose (Glc) and glutamate (Glu) obtained from the fit agree with those reported in literature, which confirms the usefulness of the second derivative method in routine analyses of 1H MR brain spectra.

  3. Quantum-chemical analysis of paramagnetic 13C NMR shifts of iron-bound cyanide ions in heme-protein environments

    NASA Astrophysics Data System (ADS)

    Yamaki, Daisuke; Hada, Masahiko

    2012-12-01

    Paramagnetic 13C NMR chemical shifts of iron-bound cyanide ions located in biological environments such as heme-proteins are significantly sensitive to the environments. These chemical shifts are due to negative spin density at 13C induced by the open-shell iron center. In order to examine the environments effects on the electronic states around heme parts, ab initio calculations were performed for model systems of heme-proteins. The proximal residues in proteinparts of cytochrome c, hemoglobin, myoglobin and horseradish peroxidase were included in the model systems with the common active site (cyanide imidazole porphyrinato iron(III)) to take account of the environments effects. The calculated paramagnetic shifts of model systems reproduce the experimental trend of corresponding heme-proteins. It is found that the effects of proximal residues on the electronic states of the heme-parts are significant for these hemeproteins. In this abstract we focused on the calculations and analysis of cytochrome c.

  4. High accuracy NMR chemical shift corrected for bulk magnetization as a tool for structural elucidation of microemulsions. Part 2 - Anionic and nonionic dilutable microemulsions.

    PubMed

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

    2016-02-01

    In our previous report we suggested a new analytical tool, high accuracy NMR chemical shift corrected for bulk magnetization as a supplementary tool to study structural transitions and droplet size and shape of dilutable microemulsions. The aim of this study was to show the generality of this technique and to demonstrate that in almost any type of microemulsion this technique provides additional valuable structural information. The analysis made by the technique adds to the elucidation of some structural aspects that could not be clearly determined by other classical techniques. Therefore, in this part we are extending the study to three additional systems differing in the type of oil phase (toluene and cyclohexane), the nature of the surfactants (anionic and nonionic), and other microemulsion characteristics. We studied sodium dodecyl sulfate (SDS)-based anionic microemulsions with different oils and a nonionic microemulsion based on Tween 20 as the surfactant and toluene as the oil phase. All the microemulsions were fully dilutable with water. We found that the change in the slope of chemical shift against dilution reflects phase transition points of the microemulsion (O/W, bicontinuous, W/O). Chemical shift changes were clearly observed with the transition between spherical and non-spherical (wormlike, etc.) droplet shapes. We compared the interaction of cyclohexane and toluene and used the anisotropic effect of toluene's ring current to determine its preferred orientation relative to SDS. Chemical shifts of the microemulsion components are therefore a useful addition to the arsenal of techniques for characterizing microemulsions.

  5. 1H-NMR study of diamagnetic cytochrome P450cam: assignment of heme resonances and substrate dependance of one cysteinate beta proton.

    PubMed

    Mouro, C; Bondon, A; Simonneaux, G; Jung, C

    1997-09-08

    The 1H-NMR study of diamagnetic cytochrome P450cam FeII-CO has been performed for the first time. Chemical shifts of the cysteinate fifth ligand protons and of several heme protons have been assigned through 1- and 2-dimensional spectra at 500 MHz. A substrate dependance has been observed for the resonance of the cysteinate proton detected in the high-field region.

  6. Determination of individual side-chain conformations, tertiary conformations, and molecular topography of tyrocidine A from scalar coupling constants and chemical shifts.

    PubMed

    Kuo, M C; Gibbons, W A

    1979-12-25

    We report for the decapeptide tyrocidine A: (a) H alpha and H beta chemical shifts and scalar coupling constants for most residues of tyrocidine A in methanol-d4 and dimethyl-d6 sulfoxide (Me2so-d6) and the H alpha and H beta chemical shifts for other residues; (b) scalar coupling constants 3J alpha beta for nine side chains in methanol-d4 but only seven side chains in Me2SO-d6, due to chemical shift degeneracy; the Gln9 and Tyr10 side chains in methanol-d4 were only approximately analyzed; (c) a total spin-spin analysis of Pro5 in Me2SO-d6 and, partly by comparison, also in methanol-d4; (d) conversion of 3J alpha beta values to side-chain conformations for all residues in methanol-d4; comparisons, where possible, led to the conclusion that side-chain conformations are similar in methanol-d4 and Me2SO-d6; (e) an absolute conformational analysis of Pro5 from 3J values and a method of assigning all pro-R,S protons; Pro5 has a Ramachandran B, C2-Cexo-Cendo conformation; (f) chi 1, chi 2 conformations of several aromatic residues based upon proton-chromophore distance measurement from anomalous chemical shifts and Johnson-Bovey diagrams; (g) pro-R and pro-S assignments of H beta's from anomalous chemical shifts, high-temperature dependence of anomalous chemical shifts, and backbone side-chain nuclear Overhauser effects; (h) most tertiary conformations of the whole tyrocidine A molecule possessing residues 4--8 and 10 in highly preferred (ca. 90%) chi 1 conformations, but residues 1--3 and 9 having at least two chi 1 rotamers; (2) description of three topographical regions of the molecule--a hydrophobic region, a flat hydrophilic surface on the other side of the molecule, and a hydrophilic region consisting of two peptide backbone units and the side chains of Asn8, Gln9, and Tyr10; (j) proposed side chain, beta-turn, and beta-pleated sheet conformations that readily account for all "normal" and anomalous chemical shifts.

  7. Fully adiabatic 31P 2D-CSI with reduced chemical shift displacement error at 7 T--GOIA-1D-ISIS/2D-CSI.

    PubMed

    Chmelík, M; Kukurová, I Just; Gruber, S; Krššák, M; Valkovič, L; Trattnig, S; Bogner, W

    2013-05-01

    A fully adiabatic phosphorus (31P) two-dimensional (2D) chemical shift spectroscopic imaging sequence with reduced chemical shift displacement error for 7 T, based on 1D-image-selected in vivo spectroscopy, combined with 2D-chemical shift spectroscopic imaging selection, was developed. Slice-selective excitation was achieved by a spatially selective broadband GOIA-W(16,4) inversion pulse with an interleaved subtraction scheme before nonselective adiabatic excitation, and followed by 2D phase encoding. The use of GOIA-W(16,4) pulses (bandwidth 4.3-21.6 kHz for 10-50 mm slices) reduced the chemical shift displacement error in the slice direction ∼1.5-7.7 fold, compared to conventional 2D-chemical shift spectroscopic imaging with Sinc3 selective pulses (2.8 kHz). This reduction was experimentally demonstrated with measurements of an MR spectroscopy localization phantom and with experimental evaluation of pulse profiles. In vivo experiments in clinically acceptable measurement times were demonstrated in the calf muscle (nominal voxel volume, 5.65 ml in 6 min 53 s), brain (10 ml, 6 min 32 s), and liver (8.33 ml, 8 min 14 s) of healthy volunteers at 7 T. High reproducibility was found in the calf muscle at 7 T. In combination with adiabatic excitation, this sequence is insensitive to the B1 inhomogeneities associated with surface coils. This sequence, which is termed GOIA-1D-ISIS/2D-CSI (goISICS), has the potential to be applied in both clinical research and in the clinical routine.

  8. Synthesis, physical-chemical characterisation and biological evaluation of novel 2-amido-3-hydroxypyridin-4(1H)-ones: Iron chelators with the potential for treating Alzheimer's disease.

    PubMed

    Gaeta, Alessandra; Molina-Holgado, Francisco; Kong, Xiao L; Salvage, Sarah; Fakih, Sarah; Francis, Paul T; Williams, Robert J; Hider, Robert C

    2011-02-01

    A novel class of 2-amido-3-hydroxypyridin-4-one iron chelators is described. These compounds have been designed to behave as suitable molecular probes which will improve our knowledge of the role of iron in neurodegenerative conditions. Neurodegenerative disorders, such as Alzheimer's disease (AD) and Parkinson disease (PD), can be considered as diverse pathological conditions sharing critical metabolic processes such as protein aggregation and oxidative stress. Interestingly, both these metabolic alterations seem to be associated with the involvement of metal ions, including iron. Iron chelation is therefore a potential therapeutic approach. The physico-chemical (pK(a), pFe(3+) and logP) and biological properties (inhibition of iron-containing enzymes) of these chelators have been investigated in order to obtain a suitable profile for the treatment of neurodegenerative conditions. Studies with neuronal cell cultures confirm that the new iron chelators are neuroprotective against β-amyloid-induced toxicity.

  9. Conformation of some N,N'-arylalkyl thioureas by 1H-NMR and infrared spectral analysis

    NASA Astrophysics Data System (ADS)

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

    Several N,N'-arylalkyl thioureas were examined with 1H-NMR and i.r. spectra in order to study the conformation of the -NHCSNH- group. The influence of temperature and substituents on the chemical shift of the NH protons has been investigated. Formation of a strong intramolecular hydrogen bond stabilizes the trans—cis conformation for most systems, while for the others the prevalence of different rotational isomers can be postulated. The influence of the steric effect on hydrogen bonding and molecular conformation is discussed.

  10. 1H and 13C MAS NMR analysis for the role of chemically inequivalent a-N(CH3)4 and b-N(CH3)4 ions in [N(CH3)4]2CuCl4

    NASA Astrophysics Data System (ADS)

    Lim, Ae Ran

    2014-01-01

    The spin-lattice relaxation times in the laboratory frame, T1, and in the rotating frame, T1ρ, for 1H and 13C in [N(CH3)4]2CuCl4 were measured by static NMR and magic angle spinning (MAS) NMR as functions of temperature. The intensities of the 1H and 13C signals changed near phase transition temperatures TC1 and TC3, which indicated that N(CH3)4 plays an important role in these phase transitions. It was thus apparent that the T1 and T1ρ for 1H are governed by the same molecular motions. Two inequivalent ions, a-N(CH3)4 and b-N(CH3)4, were identified by 13C cross-polarization (CP)/MAS NMR. From these results, the behaviors of these two chemically inequivalent N(CH3)4 groups in the paraelastic and ferroelastic phases are discussed.

  11. Combined NMR analysis of huge residual dipolar couplings and pseudocontact shifts in terbium(III)-phthalocyaninato single molecule magnets.

    PubMed

    Damjanovic, Marko; Katoh, Keiichi; Yamashita, Masahiro; Enders, Markus

    2013-09-25

    Several small paramagnetic complexes combine large hyperfine NMR shifts with large magnetic anisotropies. The latter are a prerequisite for single molecule magnet (SMM) behavior. We choose the SMM tris(octabutoxyphthalocyaninato) diterbium (1) for a high resolution NMR study where we combined for the first time a comprehensive (1)H and (13)C chemical shift analysis of a SMM with the evaluation of large residual dipolar couplings (RDCs). The latter are a consequence of partial alignment of SMM 1 in the strong magnetic field of the NMR spectrometer. To the best of our knowledge RDCs in SMMs have never been reported before. We measured RDCs between -78 and +99 Hz for the (13)C-(1)H vectors of CH bonds and up to -109 Hz for (1)H-(1)H vectors of geminal hydrogen atoms (magnetic field of 14.09 T, temperature 295 K). Considerable negative Fermi contact shifts (up to -60 ppm) were determined for (13)C atoms at the phthalocyaninato core. Paramagnetic (13)C NMR shifts of the butoxy chains as well as all (1)H NMR chemical shifts are a result of pseudocontact shifts (pcs), and therefore it is easily possible to determine the positions of the respective nuclei in solution. Measurements of CH and HH vectors by RDC analysis are in accordance with the geometry as determined by the pseudocontact shifts, but in addition to that, RDCs give information about internal mobility. The axial component of the magnetic susceptibility tensor has been determined independently by pcs and by RDC.

  12. NMR-based structural modeling of graphite oxide using multidimensional 13C solid-state NMR and ab initio chemical shift calculations.

    PubMed

    Casabianca, Leah B; Shaibat, Medhat A; Cai, Weiwei W; Park, Sungjin; Piner, Richard; Ruoff, Rodney S; Ishii, Yoshitaka

    2010-04-28

    Chemically modified graphenes and other graphite-based materials have attracted growing interest for their unique potential as lightweight electronic and structural nanomaterials. It is an important challenge to construct structural models of noncrystalline graphite-based materials on the basis of NMR or other spectroscopic data. To address this challenge, a solid-state NMR (SSNMR)-based structural modeling approach is presented on graphite oxide (GO), which is a prominent precursor and interesting benchmark system of modified graphene. An experimental 2D (13)C double-quantum/single-quantum correlation SSNMR spectrum of (13)C-labeled GO was compared with spectra simulated for different structural models using ab initio geometry optimization and chemical shift calculations. The results show that the spectral features of the GO sample are best reproduced by a geometry-optimized structural model that is based on the Lerf-Klinowski model (Lerf, A. et al. Phys. Chem. B 1998, 102, 4477); this model is composed of interconnected sp(2), 1,2-epoxide, and COH carbons. This study also convincingly excludes the possibility of other previously proposed models, including the highly oxidized structures involving 1,3-epoxide carbons (Szabo, I. et al. Chem. Mater. 2006, 18, 2740). (13)C chemical shift anisotropy (CSA) patterns measured by a 2D (13)C CSA/isotropic shift correlation SSNMR were well reproduced by the chemical shift tensor obtained by the ab initio calculation for the former model. The approach presented here is likely to be applicable to other chemically modified graphenes and graphite-based systems.

  13. Theoretical and experimental investigation of the 1H NMR spectrum of putrescine

    NASA Astrophysics Data System (ADS)

    Allouche, A. R.; Graveron-Demilly, D.; Fauvelle, F.; Aubert-Frécon, M.

    2008-12-01

    Chemical shifts δ and spin-spin coupling constants J have been calculated for the putrescine molecule, a polyamine present in prostate tissue, through a DFT/B3LYP/6-311++G(d,p)/PCM/(GIAO) approach, which has been shown to be accurate in previous work. From δ and J values, calculated for the first time for the isolated and the solvated putrescine, the 1H NMR spectra have been simulated. Comparisons between the calculated and the experimental NMR spectra at 400 MHz show a good agreement and allow to propose reliable values for the NMR spin Hamiltonian parameters of putrescine to be used as good starting values for further quantitation methods of metabolites in prostate tissue.

  14. Cloud point, fluorimetric and 1H NMR studies of ibuprofen-polymer systems

    NASA Astrophysics Data System (ADS)

    Khan, Iqrar Ahmad; Anjum, Kahkashan; Koya, P. Ajmal; Qadeer, Atiytul; Kabir-ud-Din

    2014-01-01

    Influence of six polymers viz. hydroxyethyl cellulose (HEC), hydroxypropyl methyl cellulose (HPMC), polyethylene glycol (PEG), polyvinyl pyrrolidone (PVP), sodium carboxy methyl cellulose (NaCMC) and dextran sulfate (DxS) on solution properties of amphiphilic drug ibuprofen (IBF) has been described in this work. As only HPMC showed the clouding behavior (among the polymers employed herein), its cloud point (CP) was studied in detail in presence of varying amounts of IBF containing different fixed concentrations of inorganic salts (NaCl, NaNO3, Na2SO4, KBr and KNO3). Presence of all these salts had CP reducing effect. By means of steady state fluorescence quenching studies, average aggregation number of IBF aggregates (Nagg) in the presence of varying amounts of the mentioned polymers were evaluated and discussed. 1H NMR studies show that the magnitude of chemical shifts (δ) varies with the nature of the polymer.

  15. Structural analysis of complex saponins of Balanites aegyptiaca by 800 MHz 1H NMR spectroscopy.

    PubMed

    Staerk, Dan; Chapagain, Bishnu P; Lindin, Therese; Wiesman, Zeev; Jaroszewski, Jerzy W

    2006-10-01

    The main saponin (1) present in the mesocarp of Balanites aegyptiaca fruit is a mixture of 22R and 22S epimers of 26-(O-beta-D-glucopyranosyl)-3-beta-[4-O-(beta-D-glucopyranosyl)-2-O-(alpha-L-rhamnopyranosyl)-beta-D-glucopyranosyloxy]-22,26-dihydroxyfurost-5-ene. This structure differs from a previously reported saponin isolated from this source by the site of attachment of the rhamnosyl residue, and presumably represents a structural revision of the latter. The main saponin (2) present in the kernel is a xylopyranosyl derivative of 1. The use of high-field NMR enabled the practically complete assignment of 1H and 13C chemical shifts of these complex saponins, existing as a mixture of C-22 epimers. Moreover, the work represents a new approach to structural elucidation of saponins: direct preparative-scale HPLC-RID of crude extracts followed by high-field NMR investigations supported by ESI-MSn.

  16. On the role of experimental imperfections in constructing (1)H spin diffusion NMR plots for domain size measurements.

    PubMed

    Nieuwendaal, Ryan C

    2016-01-01

    We discuss the precision of 1D chemical-shift-based (1)H spin diffusion NMR experiments as well as straightforward experimental protocols for reducing errors. The (1)H spin diffusion NMR experiments described herein are useful for samples that contain components with significant spectral overlap in the (1)H NMR spectrum and also for samples of small mass (<1mg). We show that even in samples that display little spectral contrast, domain sizes can be determined to a relatively high degree of certainty if common experimental variability is accounted for and known. In particular, one should (1) measure flip angles to high precision (≈±1° flip angle), (2) establish a metric for phase transients to ensure their repeatability, (3) establish a reliable spectral deconvolution procedure to ascertain the deconvolved spectra of the neat components in the composite or blend spin diffusion spectrum, and (4) when possible, perform 1D chemical-shift-based (1)H spin diffusion experiments with zero total integral to partially correct for errors and uncertainties if these requirements cannot fully be implemented. We show that minimizing the degree of phase transients is not a requirement for reliable domain size measurement, but their repeatability is essential, as is knowing their contribution to the spectral offset (i.e. the J1 coefficient). When performing experiments with zero total integral in the spin diffusion NMR spectrum with carefully measured flip angles and known phase transient effects, the largest contribution to error arises from an uncertainty in the component lineshapes which can be as high as 7%. This uncertainty can be reduced considerably if the component lineshapes deconvolved from the composite or blend spin diffusion spectra adequately match previously acquired pure component spectra.

  17. Detection of chemical vapor with high sensitivity by using the symmetrical metal-cladding waveguide-enhanced Goos-Hänchen shift.

    PubMed

    Nie, Yiyou; Li, Yuanhua; Wu, Zhijing; Wang, Xianping; Yuan, Wen; Sang, Minghuang

    2014-04-21

    We present a novel and simple optical structure, i.e., the symmetrical metal-cladding waveguide, in which a polymer layer is added into the guiding layer, for sensitive detection of chemical vapor by using the enhanced Goos-Hänchen (GH) shift (nearly a millimeter scale). Owing to the high sensitivity of the excited ultrahigh-order modes, the vapor-induced effect (swelling effect and refractive index change) in the polymer layer will lead to a dramatic variation of the GH shift. The detected GH shift signal is irrelevant to the power fluctuation of the incident light. The detection limit of 9.5 ppm for toluene and 28.5 ppm for benzene has been achieved.

  18. Chemical shifts of K-X-ray absorption edges on copper in different compounds by X-ray absorption spectroscopy (XAS) with Synchrotron radiation

    NASA Astrophysics Data System (ADS)

    Joseph, D.; Basu, S.; Jha, S. N.; Bhattacharyya, D.

    2012-03-01

    Cu K X-ray absorption edges were measured in compounds such as CuO, Cu(CH3CO2)2, Cu(CO3)2, and CuSO4 where Cu is present in oxidation state of 2+, using the energy dispersive EXAFS beamline at INDUS-2 Synchrotron radiation source at RRCAT, Indore. Energy shifts of ˜4-7 eV were observed for Cu K X-ray absorption edge in the above compounds compared to its value in elemental copper. The difference in the Cu K edge energy shifts in the different compounds having same oxidation state of Cu shows the effect of different chemical environments surrounding the cation in the above compounds. The above chemical effect has been quantitatively described by determining the effective charges on Cu cations in the above compounds.

  19. Quantification of the push-pull Effect in disubstituted alkynes - Application of occupation quotients π*/π and 13C chemical shift differences ΔδCtbnd C

    NASA Astrophysics Data System (ADS)

    Kleinpeter, Erich; Klaumünzer, Ute

    2014-09-01

    Structures, 13C chemical shifts, and the occupation quotients of anti-bonding π* and bonding π orbitals of the Ctbnd C triple bond along a series of push-pull alkynes (p)Xsbnd C6H4sbnd C(O)sbnd Ctbnd Csbnd NHsbnd C6H4sbnd Y(p) (X,Y = H, Me, OMe, NMe2, NO2, COMe, COOMe, F, Cl, Br) were computed at the DFT level (B3LYP/6-311G**) of theory. Both the stereochemistry (cis/trans-isomers) by steric twist and the push-pull character by both 13C chemical shift differences (ΔδCtbnd C) and the occupation quotient (π*Ctbnd C/πCtbnd C) were studied; the latter two parameters can be readily employed to precisely quantify the push-pull effect in alkynes.

  20. Use of chemical shift encoded magnetic resonance imaging (CSE-MRI) for high resolution fat-suppressed imaging of the brachial and lumbosacral plexuses

    PubMed Central

    Grayev, Allison; Reeder, Scott; Hanna, Amgad

    2016-01-01

    Purpose In the era of increasingly complex surgical techniques for peripheral nerve repair, there is a need for high spatial resolution imaging of the neural plexuses in the body. We describe our experience with chemical shift encoded MRI and its implications for patient management. Materials and methods IDEAL water-fat separation is a chemical shift based method of homogeneously suppressing signal from fat, while maintaining adequate signal. This technique was used in clinical practice and the patient images reviewed. Results IDEAL water-fat separation was shown to improve visualization of the brachial and lumbosacral plexuses with good fat suppression and high signal to noise ratio. Conclusion IDEAL water − fat separation is an excellent technique to use in the imaging of the brachial and lumbosacral plexuses as it balances the need for homogeneous fat suppression with maintenance of excellent signal to noise ratio. PMID:27161071

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

    PubMed

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

    2010-09-05

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

  2. Free magnesium levels in normal human brain and brain tumors: sup 31 P chemical-shift imaging measurements at 1. 5 T

    SciTech Connect

    Taylor, J.S.; Vigneron, D.B.; Murphy-Boesch, J.; Nelson, S.J.; Kessler, H.B.; Coia, L.; Curran, W.; Brown, T.R. )

    1991-08-01

    The authors have studied a series of normal subjects and patients with brain tumors, by using {sup 31}P three-dimensional chemical shift imaging to obtain localized {sup 31}P spectra of the brain. A significant proportion of brain cytosolic ATP in normal brain is not complexed to Mg{sup 2+}, as indicated by the chemical shift {delta} of the {beta}-P resonance of ATP. The ATP {beta}P resonance position in brain thus is sensitive to changes in intracellular free Mg{sup 2+} concentration and in the proportion of ATP complexed with Mg because this shift lies on the rising portion of the {delta} vs. Mg{sup 2+} titration curve for ATP. They have measured the ATP {beta}-P shift and compared intracellular free Mg{sup 2+} concentration and fractions of free ATP for normal individuals and a limited series of patients with brain tumors. In four of the five spectra obtained from brain tissue containing a substantial proportion of tumor, intracellular free Mg{sup 2+} was increased, and the fraction of free ATP was decreased, compared with normal brain.

  3. The covariance of the differences between experimental and theoretical chemical shifts as an aid for assigning two-dimensional heteronuclear correlation solid-state NMR spectra

    NASA Astrophysics Data System (ADS)

    Czernek, Jiří; Brus, Jiří

    2014-07-01

    A robust method for the assignment of two-dimensional heteronuclear correlations in the solid-state NMR spectra is described. It statistically evaluates the differences between measured and theoretical (obtained from first-principles calculations of the NMR chemical shielding property of periodic materials) chemical shifts. The values of the covariance of these differences, and of the standard deviations of the respective linear correlations, are elucidative for the spectral assignment process. The efficacy of the method is demonstrated for three crystalline systems: L-tyrosine hydrochloride, L-tyrosine ansolvate, and the polymorphic form I of o-acetylsalicylic acid.

  4. Application of cryoprobe 1H nuclear magnetic resonance spectroscopy and multivariate analysis for the verification of corsican honey.

    PubMed

    Donarski, James A; Jones, Stephen A; Charlton, Adrian J

    2008-07-23

    Proton nuclear magnetic resonance spectroscopy ((1)H NMR) and multivariate analysis techniques have been used to classify honey into two groups by geographical origin. Honey from Corsica (Miel de Corse) was used as an example of a protected designation of origin product. Mathematical models were constructed to determine the feasibility of distinguishing between honey from Corsica and that from other geographical locations in Europe, using (1)H NMR spectroscopy. Honey from 10 different regions within five countries was analyzed. (1)H NMR spectra were used as input variables for projection to latent structures (PLS) followed by linear discriminant analysis (LDA) and genetic programming (GP). Models were generated using three methods, PLS-LDA, two-stage GP, and a combination of PLS and GP (PLS-GP). The PLS-GP model used variables selected by PLS for subsequent GP calculations. All models were generated using Venetian blind cross-validation. Overall classification rates for the discrimination of Corsican and non-Corsican honey of 75.8, 94.5, and 96.2% were determined using PLS-LDA, two-stage GP, and PLS-GP, respectively. The variables utilized by PLS-GP were related to their (1)H NMR chemical shifts, and this led to the identification of trigonelline in honey for the first time.

  5. 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.

  6. The RAMANITA method for non-destructive and in situ semi-quantitative chemical analysis of mineral solid-solutions by multidimensional calibration of Raman wavenumber shifts.

    PubMed

    Smith, David C

    2005-08-01

    The "RAMANITA" method, for semi-quantitative chemical analysis of mineral solid-solutions by multidimensional calibration of Raman wavenumber shifts and mathematical calculation by simultaneous equations, is published here in detail in English for the first time. It was conceived by the present writer 20 years ago for binary and ternary pyroxene and garnet systems. The mathematical description was set out in 1989, but in an abstract in an obscure French special publication. Detailed "step-by-step" calibration of two garnet ternaries, followed by their linking, in the early 1990s provided a hexary garnet database. Much later, using this garnet database, which forms part of his personal database called RAMANITA, the present writer began to develop the method by improving the terminology, automating the calculations, discussing problems and experimenting with different real chemical problems in archaeometry. Although this RAMANITA method has been very briefly mentioned in two recent books, the necessary full mathematical explanation is given only here. The method will find application in any study which requires obtaining a non-destructive semi-quantitative chemical analysis from mineral solid solutions that cannot be analysed by any destructive analytical method, in particular for archaeological, geological or extraterrestrial research projects, e.g. Recently some other workers have begun deducing chemical compositions from Raman wavenumber shifts in multivariate chemical space, but the philosophical approach is quite different.

  7. Progress in spin dynamics solid-state nuclear magnetic resonance with the application of Floquet-Magnus expansion to chemical shift anisotropy.

    PubMed

    Mananga, Eugene Stephane

    2013-01-01

    The purpose of this article is to present an historical overview of theoretical approaches used for describing spin dynamics under static or rotating experiments in solid state nuclear magnetic resonance. The article gives a brief historical overview for major theories in nuclear magnetic resonance and the promising theories. We present the first application of Floquet-Magnus expansion to chemical shift anisotropy when irradiated by BABA pulse sequence.

  8. 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.

  9. Progress in Spin Dynamics Solid-State Nuclear Magnetic Resonance with the Application of Floquet-Magnus Expansion to Chemical Shift Anisotropy

    PubMed Central

    Mananga, Eugene Stephane

    2013-01-01

    The purpose of this article is to present an historical overview of theoretical approaches used for describing spin dynamics under static or rotating experiments in solid state nuclear magnetic resonance. The article gives a brief historical overview for major theories in nuclear magnetic resonance and the promising theories. We present the first application of Floquet-Magnus expansion to chemical shift anisotropy when irradiated by BABA pulse sequence. PMID:23711337

  10. Design of a hyperpolarized (15)N NMR probe that induces a large chemical-shift change upon binding of calcium ions.

    PubMed

    Hata, Ryunosuke; Nonaka, Hiroshi; Takakusagi, Yoichi; Ichikawa, Kazuhiro; Sando, Shinsuke

    2015-08-07

    Ca(2+) is a fundamental metal ion for physiological functioning. Therefore, molecular probes for Ca(2+) analysis are required. Recently, a hyperpolarized NMR probe has emerged as a promising tool. Here, we report a new design of a hyperpolarized NMR probe for Ca(2+), which showed a large chemical shift change upon binding to Ca(2+) and was applied for Ca(2+) sensing in a hyperpolarized state.

  11. Chemical shift and diffusion-weighted magnetic resonance imaging of the anterior mediastinum in oncology: Current clinical applications in qualitative and quantitative assessment.

    PubMed

    Priola, Adriano Massimiliano; Gned, Dario; Veltri, Andrea; Priola, Sandro Massimo

    2016-02-01

    Recently, the use of magnetic resonance (MR) in clinical practice for the evaluation of the anterior mediastinum has considerably increased due to technological improvements and standardization of thoracic protocols. Currently, MR imaging is increasingly seen as a useful problem-solving modality, especially in equivocal cases at computed tomography, with the advantage of a higher contrast resolution and no radiation exposure. Chemical shift and diffusion-weighted MR are helpful in tissue characterization and present advantages over conventional MR imaging, first in providing quantitative data, without the need for the administration of contrast medium. By detecting microscopic fat in tissue, chemical shift imaging is useful for differentiating normal thymus and rebound hyperplasia from cancer tissue at diagnosis and after chemotherapy in oncologic patients, and for distinguishing lymphoid hyperplasia from thymoma in autoimmune diseases such as myasthenia gravis. Diffusion-weighted MR reflects diffusivity of water molecules within tissue and is increasingly used as a cancer biomarker, even in the thorax, for the detection and characterization of tumors, for their differentiation from benign conditions, and for monitoring treatment response. In this review, based on the current literature, technical considerations about image acquisition and data analysis of chemical shift and diffusion-weighted MR are discussed along with clinical applications in the field of benign and malignant disease of the anterior mediastinum.

  12. A device for the measurement of residual chemical shift anisotropy and residual dipolar coupling in soluble and membrane-associated proteins

    PubMed Central

    Liu, Yizhou

    2010-01-01

    Residual dipolar coupling (RDC) and residual chemical shift anisotropy (RCSA) report on orientational properties of a dipolar bond vector and a chemical shift anisotropy principal axis system, respectively. They can be highly complementary in the analysis of backbone structure and dynamics in proteins as RCSAs generally include a report on vectors out of a peptide plane while RDCs usually report on in-plane vectors. Both RDC and RCSA average to zero in isotropic solutions and require partial orientation in a magnetic field to become observable. While the alignment and measurement of RDC has become routine, that of RCSA is less common. This is partly due to difficulties in providing a suitable isotopic reference spectrum for the measurement of the small chemical shift offsets coming from RCSA. Here we introduce a device (modified NMR tube) specifically designed for accurate measurement of reference and aligned spectra for RCSA measurements, but with a capacity for RDC measurements as well. Applications to both soluble and membrane anchored proteins are illustrated. PMID:20506033

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  14. Adsorption mechanism at the molecular level between polymers and uremic octapeptide by the 2D 1H NMR Technique.

    PubMed

    Li, Guohua; Li, Jihong; Wang, Wei; Yang, Mei; Zhang, Yuanwei; Sun, Pingchuan; Yuan, Zhi; He, Binglin; Yu, Yaoting

    2006-06-01

    To remove uremic octapeptide from the blood stream of uremic patients, various modified polyacylamide cross-linked absorbents were prepared. Adsorption experiments showed these absorbents have significant differences in adsorption capacity to the target peptide. In this paper, two-dimension proton nuclear magnetic resonance (2D 1H NMR) spectroscopy was used to investigate the interaction mechanism between the peptide and the adsorbents. Because of the insolubility of the absorbent, some soluble linear polymers with the same functional groups as the absorbents were employed as the model adsorbents in 2D 1H NMR. The preferred binding site for the peptide and polymers was identified to be at the C-terminal carboxyl group of the octapeptide via chemical shift perturbation effects. In this study, we found that hydrogen bonding, electrostatic, and hydrophobic interactions all play a role in the interaction force but had different contributions. Especially, the great chemical shift changes of the aromatic amino acid residues (Trp) during the interaction between butyl-modified polyacrylamide and octapeptide suggested the hydrophobic interaction, incorporated with the electrostatic force, played an important role in the binding reaction in aqueous solutions. This information not only rationally explained the results of the adsorption experiments, but also identified the effective binding site and mechanism, and shall provide a structural basis for designing better affinity-type adsorbents for the target peptide.

  15. Elucidating connectivity and metal-binding structures of unlabeled paramagnetic complexes by 13C and 1H solid-state NMR under fast magic angle spinning.

    PubMed

    Wickramasinghe, Nalinda P; Shaibat, Medhat A; Ishii, Yoshitaka

    2007-08-23

    Characterizing paramagnetic complexes in solids is an essential step toward understanding their molecular functions. However, methodologies to characterize chemical and electronic structures of paramagnetic systems at the molecular level have been notably limited, particularly for noncrystalline solids. We present an approach to obtain connectivities of chemical groups and metal-binding structures for unlabeled paramagnetic complexes by 13C and 1H high-resolution solid-state NMR (SSNMR) using very fast magic angle spinning (VFMAS, spinning speed >or=20 kHz). It is experimentally shown for unlabeled Cu(II)(Ala-Thr) that 2D 13C/1H correlation SSNMR under VFMAS provides the connectivity of chemical groups and assignments for the characterization of unlabeled paramagnetic systems in solids. We demonstrate that on the basis of the assignments provided by the VFMAS approach multiple 13C-metal distances can be simultaneously elucidated by a combination of measurements of 13C anisotropic hyperfine shifts and 13C T1 relaxation due to hyperfine interactions for this peptide-Cu(II) complex. It is also shown that an analysis of 1H anisotropic hyperfine shifts allows for the determination of electron-spin states in Fe(III)-chloroprotoporphyin-IX in solid states.

  16. Effects of dose shift on line width, line edge roughness, and stochastic defect generation in chemically amplified extreme ultraviolet resist with photodecomposable quencher

    NASA Astrophysics Data System (ADS)

    Kozawa, Takahiro

    2015-01-01

    In chemically amplified resists used for high-volume production of semiconductor devices, the control of acid catalytic reaction is essential for fine patterning. A basic compound, called a quencher, plays an important role in the control of acid catalytic reaction. In particular, the photodecomposable quencher is effective for the enhancement of the chemical gradient. In this study, the effects of photodecomposable quenchers on the dose shift (the deviation from the sizing dose) dependences of line width, line edge roughness (LER), and stochastic defect generation were investigated, assuming line-and-space patterns with 11 nm half-pitch. The exposure latitude of line width in a chemically amplified resist with photodecomposable quenchers was larger than that in a chemically amplified resist with conventional non-photodecomposable quenchers at sizing doses >20 mJ cm-2. By using photodecomposable quenchers, LER and the probability of stochastic defect generation were decreased, while the dose shift dependences of LER and stochastic defect generation did not significantly differ, compared with those observed using conventional non-photodecomposable quenchers.

  17. Calculation of the {sup 13}C NMR chemical shift of ether linkages in lignin derived geopolymers: Constraints on the preservation of lignin primary structure with diagenesis

    SciTech Connect

    Cody, G.D.; Saghi-Szabo, G.

    1999-01-01

    Methodology for the calculation of {sup 13}C NMR shielding on molecular organic fragments, representative of monomers in a type 3 kerogen, is presented. Geometry optimization of each molecular fragment was carried out using Density Functional Theory employing the generalized gradient approximation. NMR shieldings were calculated using the Individual Gauge for Localized orbital Method. Convincing agreement was obtained between calculated and experimentally derived isotropic chemical shielding values over a broad frequency range. Shielding calculations employing the localized orbitals/local origin method resulted in nearly identical results. NMR chemical shift static powder patterns also exhibit excellent agreement with experimental values. These quantum mechanical calculations were applied to determine the extent of lignin primary structure preservation with diagenesis. Specifically, the calculations were used to assess whether inhomogeneous spectral broadening due to both functional group variation and local configurational variability may inhibit the detection of otherwise significant quantities of alkyl-aryl ethers in lignin derived geopolymers. Determination of the chemical-shielding tensor principle axis values reveals a strong correlation between anisotropy and asymmetry with local configuration effects such as dihedral rotation, phenyl group rotation, and bond angle variation. These results indicate that a range of 9 ppm in the isotropic chemical shift can be ascribed to local configuration. Consequently, an upper limit of 5% alkyl-aryl-linkages may go undetected using NMR spectroscopy on lignin-derived geopolymers at the liginite-sub-bituminous transition. It is concluded that the primary structure of lignin does not persist in kerogens even at relatively low thermal maturities.

  18. Calculation of the 13C NMR chemical shift of ether linkages in lignin derived geopolymers: . Constraints on the preservation of lignin primary structure with diagenesis

    NASA Astrophysics Data System (ADS)

    Cody, G. D.; Sághi-Szabó, G.

    1999-01-01

    Methodology for the calculation of 13C NMR shieldings on molecular organic fragments, representative of monomers in a type III kerogen, is presented. Geometry optimization of each molecular fragment was carried out using Density Functional Theory employing the generalized gradient approximation. NMR shieldings were calculated using the Individual Gauge for Localized Orbital Method. Convincing agreement was obtained between calculated and experimentally derived isotropic chemical shielding values over a broad frequency range. Shielding calculations employing the localized orbitals/local origin method resulted in nearly identical results. NMR chemical shift static powder patterns also exhibit excellent agreement with experimental values. These quantum mechanical calculations were applied to determine the extent of lignin primary structure preservation with diagenesis. Specifically, the calculations were used to assess whether inhomogeneous spectral broadening due to both functional group variation and local configurational variability may inhibit the detection of otherwise significant quantities of alkyl-aryl ethers in lignin derived geopolymers. Determination of the chemical-shielding tensor principle axis values reveals a strong correlation between anisotropy and asymmetry with local configuration effects such as dihedral rotation, phenyl group rotation, and bond angle variation. These results indicate that a range of 9 ppm in the isotropic chemical shift can be ascribed to local configuration. Consequently, an upper limit of 5% alkyl-aryl-linkages may go undetected using NMR spectroscopy on lignin-derived geopolymers at the liginite-sub-bituminous transition. It is concluded that the primary structure of lignin does not persist in kerogens even at relatively low thermal maturities.

  19. 1H-detected 1H- 1H correlation spectroscopy of a stereo-array isotope labeled amino acid under fast magic-angle spinning

    NASA Astrophysics Data System (ADS)

    Takahashi, Hiroki; Kainosho, Masatsune; Akutsu, Hideo; Fujiwara, Toshimichi

    2010-04-01

    The combined use of selective deuteration, stereo-array isotope labeling (SAIL), and fast magic-angle spinning effectively suppresses the 1H-1H dipolar couplings in organic solids. This method provided the high-field 1H NMR linewidths comparable to those achieved by combined rotation and multiple-pulse spectroscopy. This technique was applied to two-dimensional 1H-detected 1H-1H polarization transfer CHH experiments of valine. The signal sensitivity for the 1H-detected CHH experiments was greater than that for the 13C-detected 1H-1H polarization transfer experiments by a factor of 2-4. We obtained the 1H-1H distances in SAIL valine by CHH experiments with an accuracy of about 0.2 Å by using a theory developed for 1H-1H polarization transfer in 13C-labeled organic compounds.

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

    NASA Astrophysics Data System (ADS)

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

    1999-10-01

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

  1. In Situ Solid-State Reactions Monitored by X-ray Absorption Spectroscopy: Temperature-Induced Proton Transfer Leads to Chemical Shifts.

    PubMed

    Stevens, Joanna S; Walczak, Monika; Jaye, Cherno; Fischer, Daniel A

    2016-10-24

    The dramatic colour and phase alteration with the solid-state, temperature-dependent reaction between squaric acid and 4,4'-bipyridine has been probed in situ with X-ray absorption spectroscopy. The electronic and chemical sensitivity to the local atomic environment through chemical shifts in the near-edge X-ray absorption fine structure (NEXAFS) revealed proton transfer from the acid to the bipyridine base through the change in nitrogen protonation state in the high-temperature form. Direct detection of proton transfer coupled with structural analysis elucidates the nature of the solid-state process, with intermolecular proton transfer occurring along an acid-base chain followed by a domino effect to the subsequent acid-base chains, leading to the rapid migration along the length of the crystal. NEXAFS thereby conveys the ability to monitor the nature of solid-state chemical reactions in situ, without the need for a priori information or long-range order.

  2. Characterization of heroin samples by 1H NMR and 2D DOSY 1H NMR.

    PubMed

    Balayssac, Stéphane; Retailleau, Emmanuel; Bertrand, Geneviève; Escot, Marie-Pierre; Martino, Robert; Malet-Martino, Myriam; Gilard, Véronique

    2014-01-01

    Twenty-four samples of heroin from different illicit drug seizures were analyzed using proton Nuclear Magnetic Resonance ((1)H NMR) and two-dimensional diffusion-ordered spectroscopy (2D DOSY) (1)H NMR. A careful assignment and quantification of (1)H signals enabled a comprehensive characterization of the substances present in the samples investigated: heroin, its main related impurities (6-acetylmorphine, acetylcodeine, morphine, noscapine and papaverine) and cutting agents (caffeine and acetaminophen in nearly all samples as well as lactose, lidocaine, mannitol, piracetam in one sample only), and hence to establish their spectral signatures. The good agreement between the amounts of heroin, noscapine, caffeine and acetaminophen determined by (1)H NMR and gas chromatography, the reference method in forensic laboratories, demonstrates the validity of the (1)H NMR technique. In this paper, 2D DOSY (1)H NMR offers a new approach for a whole characterization of the various components of these complex mixtures.

  3. An Alternative Scheme for 13C Chemical-Shift Imaging via Inverse Detection of Protons through an MILS (or Inverse SLIM) Technique

    PubMed

    Lee; Tzou; Chiou; Yeung

    1998-01-01

    An alternative scheme in acquiring 13C spectroscopic images using inverse detection via polarization transfer through protons was proposed and experimentally verified by a phantom using a heteronuclear multiple-quantum coherence technique. This scheme has some features that, in special circumstances, can be exploited to one's advantages. These features are: (1) signal enhancement, a feat realizable under favorable conditions; (2) spectroscopic encoding via constant time; and (3) improvement of the time efficiency of the constant-time method via optimization by singular-value decomposition analysis. Features (1) and (2) can, in some cases, yield better sensitivity than the conventional 3DFT technique without sacrificing the most important attribute of 13C, the enormity of the chemical shifts. Such is the case because spectroscopic images acquired by the technique proposed are based on the chemical shifts of carbon, in contrast to the other more prevalent inverse-detection schemes. Feature (2) can also offer higher spatial resolution by shifting the emphasis of signal encoding from a spectral-resolution-first viewpoint to one that favors spatial resolution. Feature (3) was adopted from a method previously known as MILS (metabolite imaging of lines in a spectrum), or the inverse of SLIM, an economical scheme originally proposed by Hu et al. (1988, Magn. Reson. Med. 8, 314) for obtaining a compartmentalized NMR spectrum. Copyright 1998 Academic Press. Copyright 1998 Academic Press

  4. Enhanced Y1H Assays for Arabidopis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Transcription regulation plays a key role in development and response to environment. To understand this mechanism, we need to know which transcription factor (TFs) would bind to which promoter, thus regulate their target gene expression. Yeast one-hybrid (Y1H) technique can be used to map this kind...

  5. [Study on derivatives of 5-amino-4-acylamino-1H-pyrazole as inhibitors of furin].

    PubMed

    Kibirev, V K; Osadchuk, T V; Vadziuk, O B; Shablykin, O V; Kozachenko, A P; Chumachenko, S A; Popil'nichenko, S V; Brovarets, V S

    2011-01-01

    A series of 5-amino-1H-pyrazoles was synthesized and studied as inhibitors of furin. The most potent compound, 5-amino-4-acetylamino-3-(4-methylphenylamino)1H-pyrazole, was found to retard the activity of furin by mixed-type inhibition with K = 288 microM. These findings permit to plan new ways for chemical modifications of the 5-amino-1H-pyrazole structure and design more potent furin inhibitors of non-peptide nature.

  6. Transport-induced shifts in condensate dew-point and composition in multicomponent systems with chemical reaction

    NASA Technical Reports Server (NTRS)

    Rosner, D. E.; Nagarajan, R.

    1985-01-01

    Partial heterogeneous condensation phenomena in multicomponent reacting systems are analyzed taking into consideration the chemical element transport phenomena. It is demonstrated that the dew-point surface temperature in chemically reactive systems is not a purely thermodynamic quantity, but is influenced by the multicomponent diffusion and Soret-mass diffusion phenomena. Several distinct dew-points are shown to exist in such systems and, as a result of transport constraints, the 'sharp' locus between two chemically distinct condensates is systematically moved to a difference mainstream composition.

  7. Applications of high-resolution 1H solid-state NMR.

    PubMed

    Brown, Steven P

    2012-02-01

    This article reviews the large increase in applications of high-resolution (1)H magic-angle spinning (MAS) solid-state NMR, in particular two-dimensional heteronuclear and homonuclear (double-quantum and spin-diffusion NOESY-like exchange) experiments, in the last five years. These applications benefit from faster MAS frequencies (up to 80 kHz), higher magnetic fields (up to 1 GHz) and pulse sequence developments (e.g., homonuclear decoupling sequences applicable under moderate and fast MAS). (1)H solid-state NMR techniques are shown to provide unique structural insight for a diverse range of systems including pharmaceuticals, self-assembled supramolecular structures and silica-based inorganic-organic materials, such as microporous and mesoporous materials and heterogeneous organometallic catalysts, for which single-crystal diffraction structures cannot be obtained. The power of NMR crystallography approaches that combine experiment with first-principles calculations of NMR parameters (notably using the GIPAW approach) are demonstrated, e.g., to yield quantitative insight into hydrogen-bonding and aromatic CH-π interactions, as well as to generate trial three-dimensional packing arrangements. It is shown how temperature-dependent changes in the (1)H chemical shift, linewidth and DQ-filtered signal intensity can be analysed to determine the thermodynamics and kinetics of molecular level processes, such as the making and breaking of hydrogen bonds, with particular application to proton-conducting materials. Other applications to polymers and biopolymers, inorganic compounds and bioinorganic systems, paramagnetic compounds and proteins are presented. The potential of new technological advances such as DNP methods and new microcoil designs is described.

  8. Synthesis, crystal structure analysis, spectral (NMR, FT-IR, FT-Raman and UV-Vis) investigations, molecular docking studies, antimicrobial studies and quantum chemical calculations of a novel 4-chloro-8-methoxyquinoline-2(1H)-one: An effective antimicrobial agent and an inhibition of DNA gyrase and lanosterol-14α-demethylase enzymes

    NASA Astrophysics Data System (ADS)

    Murugavel, S.; Sundramoorthy, S.; Lakshmanan, D.; Subashini, R.; Pavan Kumar, P.

    2017-03-01

    The novel title compound 4-chloro-8-methoxyquinoline-2(1H)-one (4CMOQ) has been synthesized by slow evaporation solution growth technique at room temperature. The synthesized 4CMOQ molecule was characterized experimentally by FT-IR, FT-Raman, UV-Vis, NMR and single crystal diffraction (XRD) and theoretically by quantum chemical calculations. The molecular geometry was also optimized using density functional theory (DFT/B3LYP) method with the 6-311++G (d,p) basis set in ground state and compared with the experimental data. The entire vibrational assignments of wave numbers were made on the basis of potential energy distribution (PED) by VEDA 4 programme. The nuclear magnetic resonance spectra (1H and 13C NMR) are obtained by using the gauge-invariant atomic orbital (GIAO) method. The change in electron density (ED) in the antibonding orbital's and stabilization energies E(2) of the molecule have been evaluated by natural bond orbital (NBO) analysis to give clear evidence of stabilization. Moreover, electronic characteristics such as HOMO and LUMO energies, Mulliken atomic charges and molecular electrostatic potential surface are investigated. Absorption spectrum analysis, nonlinear optical properties, chemical reactivity descriptors and thermodynamic features are also outlined theoretically. Molecular docking studies were executed to understand the inhibitory activity of 4CMOQ against DNA gyrase and Lanosterol 14 α-demethylase. The antimicrobial activity of 4CMOQ was determined against bacterial strains such as Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa and fungal strains such as Aspergillus niger, Monascus purpureus and Penicillium citrinum. The obtained results show that the compound exhibited good to moderate antimicrobial activity.

  9. Hydrogen Atomic Positions of O-H···O Hydrogen Bonds in Solution and in the Solid State: The Synergy of Quantum Chemical Calculations with ¹H-NMR Chemical Shifts and X-ray Diffraction Methods.

    PubMed

    Siskos, Michael G; Choudhary, M Iqbal; Gerothanassis, Ioannis P

    2017-03-07

    The exact knowledge of hydrogen atomic positions of O-H···O hydrogen bonds in solution and in the solid state has been a major challenge in structural and physical organic chemistry. The objective of this review article is to summarize recent developments in the refinement of labile hydrogen positions with the use of: (i) density functional theory (DFT) calculations after a structure has been determined by X-ray from single crystals or from powders; (ii) ¹H-NMR chemical shifts as constraints in DFT calculations, and (iii) use of root-mean-square deviation between experimentally determined and DFT calculated ¹H-NMR chemical shifts considering the great sensitivity of ¹H-NMR shielding to hydrogen bonding properties.

  10. Shift of optical absorption edge in SnO2 films with high concentrations of nitrogen grown by chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Jiang, Jie; Lu, Yinmei; Meyer, Bruno K.; Hofmann, Detlev M.; Eickhoff, Martin

    2016-06-01

    The optical and electrical properties of n-type SnO2 films with high concentrations of nitrogen (SnO2:N) grown by chemical vapor deposition are studied. The carrier concentration increases from 4.1 × 1018 to 3.9 × 1019 cm-3 and the absorption edge shifts from 4.26 to 4.08 eV with increasing NH3 flow rate. Typical Urbach tails were observed from the absorption spectra and the Urbach energy increases from 0.321 to 0.526 eV with increasing NH3 flow rate. An "effective" absorption edge of about 4.61 eV was obtained for all investigated samples from fitting the extrapolations of the Urbach tails. Burstein-Moss effect, electron-impurity, and electron-electron interactions are shown to play a minor role for the shift of the absorption edges in SnO2:N thin films.

  11. 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

  12. The RAMANITA © method for non-destructive and in situ semi-quantitative chemical analysis of mineral solid-solutions by multidimensional calibration of Raman wavenumber shifts

    NASA Astrophysics Data System (ADS)

    Smith, David C.

    2005-08-01

    The "RAMANITA ©" method, for semi-quantitative chemical analysis of mineral solid-solutions by multidimensional calibration of Raman wavenumber shifts and mathematical calculation by simultaneous equations, is published here in detail in English for the first time. It was conceived by the present writer 20 years ago for binary and ternary pyroxene and garnet systems. The mathematical description was set out in 1989, but in an abstract in an obscure French special publication. Detailed "step-by-step" calibration of two garnet ternaries, followed by their linking, by M. Pinet and D.C. Smith in the early 1990s provided a hexary garnet database. Much later, using this garnet database, which forms part of his personal database called RAMANITA ©, the present writer began to develop the method by improving the terminology, automating the calculations, discussing problems and experimenting with different real chemical problems in archaeometry. Although this RAMANITA © method has been very briefly mentioned in two recent books, the necessary full mathematical explanation is given only here. The method will find application in any study which requires obtaining a non-destructive semi-quantitative chemical analysis from mineral solid solutions that cannot be analysed by any destructive analytical method, in particular for archaeological, geological or extraterrestrial research projects, e.g. from gemstones or other crystalline artworks of the cultural heritage (especially by Mobile Raman Microscopy (MRM)) in situ in museums or at archaeological sites, including under water for subaquatic archaeometry; from scientifically precious mineral microinclusions (such as garnet or pyroxene within diamond); from minerals in rocks analysed in situ on planetary bodies by a rover (especially "at distance" by telescopy). Recently some other workers have begun deducing chemical compositions from Raman wavenumber shifts in multivariate chemical space, but the philosophical approach is

  13. Quantification of ethanol methyl 1H magnetic resonance signal intensity following intravenous ethanol administration in primate brain

    PubMed Central

    Flory, Graham S.; O’Malley, Jean; Grant, Kathleen A.; Park, Byung; Kroenke, Christopher D.

    2009-01-01

    In vivo 1H magnetic resonance spectroscopy (MRS) can be used to directly monitor brain ethanol. Previously, studies of human subjects have lead to the suggestion that the ethanol methyl 1H MRS signal intensity relates to tolerance to ethanol’s intoxicating effects. More recently, the ethanol 1H MRS signal intensity has been recognized to vary between brain gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) due to differences in T2 within these environments. The methods presented here extend ethanol MRS techniques to nonhuman primate subjects. Twelve monkeys were administered ethanol while sedated and positioned within a 3T MRI system. Chemical shift imaging (CSI) measurements were performed following intravenous infusion of 1g/kg ethanol. Magnetic resonance imaging (MRI) data were also recorded for each monkey to provide volume fractions of GM, WM, and CSF for each CSI spectrum. To estimate co-variance of ethanol MRS intensity with GM, WM, and CSF volume fractions, the relative contribution of each tissue subtype was determined following corrections for radiofrequency pulse profile non-uniformity, chemical shift artifacts, and differences between the point spread function in the CSI data and the imaging data. The ethanol MRS intensity per unit blood ethanol concentration was found to differ between GM, WM, and CSF. Individual differences in MRS intensity were larger in GM than WM. This methodology demonstrates the feasibility of ethanol MRS experiments and analysis in nonhuman primate subjects, and suggests GM may be a site of significant variation in ethanol MRS intensity between individuals. PMID:20018244

  14. Effect of 1,10-phenanthroline aromaticity in carboxylic acids:1H NMR spectroscopy, GIAO calculations and thermodynamic properties

    NASA Astrophysics Data System (ADS)

    Machado, Camila M. B.; Santos, Vanessa F. C.; Belarmino, Marcia K. D. L.; França, José A. A.; Moura, Gustavo L. C.; Lima, Nathalia B. D.

    2016-08-01

    Hydrogen bonding represents a class of chemical interactions, which are directly responsible for several physical properties, such as: energetic stabilities, boiling points, vibrational modes, bond lengths, etc. In this article, we examine from the point of view of 1H NMR spectroscopy and GIAO calculations, the effects associated with the process of formation of the hydrogen bonds as they appear in the chemical shifts of the acidic hydrogens in the complexes between nitrogenated compounds, PHEN, BIPY and DIBIPY, and carboxylic acids, HOOCH, HOOCCH3 and HOOCC6H5. All computational simulations were performed using the quantum chemical methods B3LYP/6-31++G(d,p) and ωB97X-D/def2-TZVP. The 1H NMR spectroscopy results showed that, in both cases, the hydrogen nucleus of the OH group is the most affected in the process of hydrogen bond formation. For the complexes involving PHEN we observed that the hydrogen nucleus is more strongly shielded when compared with this signal in the corresponding complexes involving BIPY and DIBIPY.

  15. Quantitative and qualitative shifts in defensive metabolites define chemical defense investment during leaf development in Inga, a genus of tropical trees.

    PubMed

    Wiggins, Natasha L; Forrister, Dale L; Endara, María-José; Coley, Phyllis D; Kursar, Thomas A

    2016-01-01

    Selective pressures imposed by herbivores are often positively correlated with investments that plants make in defense. Research based on the framework of an evolutionary arms race has improved our understanding of why the amount and types of defenses differ between plant species. However, plant species are exposed to different selective pressures during the life of a leaf, such that expanding leaves suffer more damage from herbivores and pathogens than mature leaves. We hypothesize that this differential selective pressure may result in contrasting quantitative and qualitative defense investment in plants exposed to natural selective pressures in the field. To characterize shifts in chemical defenses, we chose six species of Inga, a speciose Neotropical tree genus. Focal species represent diverse chemical, morphological, and developmental defense traits and were collected from a single site in the Amazonian rainforest. Chemical defenses were measured gravimetrically and by characterizing the metabolome of expanding and mature leaves. Quantitative investment in phenolics plus saponins, the major classes of chemical defenses identified in Inga, was greater for expanding than mature leaves (46% and 24% of dry weight, respectively). This supports the theory that, because expanding leaves are under greater selective pressure from herbivores, they rely more upon chemical defense as an antiherbivore strategy than do mature leaves. Qualitatively, mature and expanding leaves were distinct and mature leaves contained more total and unique metabolites. Intraspecific variation was greater for mature leaves than expanding leaves, suggesting that leaf development is canalized. This study provides a snapshot of chemical defense investment in a speciose genus of tropical trees during the short, few-week period of leaf development. Exploring the metabolome through quantitative and qualitative profiling enables a more comprehensive examination of foliar chemical defense investment.

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

    PubMed

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

    2015-05-05

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  18. Synthesis, spectroscopic characterization, X-ray structure and DFT studies on 2,6-bis(1-benzyl-1H-benzo[d]imidazol-2-yl)pyridine

    NASA Astrophysics Data System (ADS)

    İnkaya, Ersin; Günnaz, Salih; Özdemir, Namık; Dayan, Osman; Dinçer, Muharrem; Çetinkaya, Bekir

    2013-02-01

    The title molecule, 2,6-bis(1-benzyl-1H-benzo[d]imidazol-2-yl)pyridine (C33H25N5), was synthesized and characterized by elemental analysis, FT-IR spectroscopy, one- and two-dimensional NMR spectroscopies, and single-crystal X-ray diffraction. In addition, the molecular geometry, vibrational frequencies and gauge-independent atomic orbital (GIAO) 1H and 13C NMR chemical shift values of the title compound in the ground state have been calculated using the density functional theory at the B3LYP/6-311G(d,p) level, and compared with the experimental data. The complete assignments of all vibrational modes were performed by potential energy distributions using VEDA 4 program. The geometrical parameters of the optimized structure are in good agreement with the X-ray crystallographic data, and the theoretical vibrational frequencies and GIAO 1H and 13C NMR chemical shifts show good agreement with experimental values. Besides, molecular electrostatic potential (MEP) distribution, frontier molecular orbitals (FMO) and non-linear optical properties of the title compound were investigated by theoretical calculations at the B3LYP/6-311G(d,p) level. The linear polarizabilities and first hyper polarizabilities of the molecule indicate that the compound is a good candidate of nonlinear optical materials. The thermodynamic properties of the compound at different temperatures were calculated, revealing the correlations between standard heat capacity, standard entropy, standard enthalpy changes and temperatures.

  19. Synthesis, spectroscopic characterization, X-ray structure and DFT studies on 2,6-bis(1-benzyl-1H-benzo[d]imidazol-2-yl)pyridine.

    PubMed

    İnkaya, Ersin; Günnaz, Salih; Özdemir, Namık; Dayan, Osman; Dinçer, Muharrem; Çetinkaya, Bekir

    2013-02-15

    The title molecule, 2,6-bis(1-benzyl-1H-benzo[d]imidazol-2-yl)pyridine (C(33)H(25)N(5)), was synthesized and characterized by elemental analysis, FT-IR spectroscopy, one- and two-dimensional NMR spectroscopies, and single-crystal X-ray diffraction. In addition, the molecular geometry, vibrational frequencies and gauge-independent atomic orbital (GIAO) (1)H and (13)C NMR chemical shift values of the title compound in the ground state have been calculated using the density functional theory at the B3LYP/6-311G(d,p) level, and compared with the experimental data. The complete assignments of all vibrational modes were performed by potential energy distributions using VEDA 4 program. The geometrical parameters of the optimized structure are in good agreement with the X-ray crystallographic data, and the theoretical vibrational frequencies and GIAO (1)H and (13)C NMR chemical shifts show good agreement with experimental values. Besides, molecular electrostatic potential (MEP) distribution, frontier molecular orbitals (FMO) and non-linear optical properties of the title compound were investigated by theoretical calculations at the B3LYP/6-311G(d,p) level. The linear polarizabilities and first hyper polarizabilities of the molecule indicate that the compound is a good candidate of nonlinear optical materials. The thermodynamic properties of the compound at different temperatures were calculated, revealing the correlations between standard heat capacity, standard entropy, standard enthalpy changes and temperatures.

  20. Experimental (XRD, IR and NMR) and theoretical investigations on 1-(2-nitrobenzoyl)3,5-bis(4-methoxyphenyl)-4,5-dihydro-1H-pyrazole

    NASA Astrophysics Data System (ADS)

    Evecen, Meryem; Tanak, Hasan; Tinmaz, Feyza; Dege, Necmi; Özer İlhan, İlhan

    2016-12-01

    The pyrazole compound 1-(2-nitrobenzoyl)3,5-bis(4-methoxyphenyl)-4,5-dihydro-1H-pyrazole (I) has been synthesized and characterized by IR, NMR and X-ray diffraction methods. The compound crystallizes in the monoclinic space group C2/c with a = 36.126(5) Ǻ, b = 8.1963(7) Ǻ, c = 14.3983(18) Ǻ, β = 100.825(10)° and Z = 8. The molecular geometry, vibrational frequencies and Gauge-Independent Atomic Orbital (GIAO) 1H and 13C NMR chemical shift values of 1-(2-nitrobenzoyl)3,5-bis(4-methoxyphenyl)-4,5-dihydro-1H-pyrazole in the ground state have been calculated using the density functional method (B3LYP) with the 6-311++G(d,p) basis set. The optimized parameters are in agreement with X-ray data. The calculated vibrational frequencies and chemical shift values were compared with experimental IR and NMR values. In addition, frontier molecular orbitals, molecular electrostatic potential and NBO analysis of (I) were investigated by DFT calculations.

  1. Solvatochromic shift of donor-acceptor substituted bithiophene in solvents of different polarity: quantum chemical and molecular dynamics simulations.

    PubMed

    Meng, Suci; Ma, Jing

    2008-04-10

    The dependence of excitation energies of the solvatochromic dye, 5-dimethylamino-5'-nitro-2,2'-bithiophene (Me(2)N-2T-NO(2)) on the solvent polarity is demonstrated by time-dependent density functional theory (TD-DFT) calculations in combination with molecular dynamics (MD) simulations. Three kinds of solvation models, namely, the continuum dielectric model, the discrete approach, and the combined discrete/continuum strategy, are employed to calculate the lowest dipole-allowed excitation energies of Me(2)N-2T-NO(2) in seven solvents with the dielectric constant, epsilon, ranging from 2.23 to 111.00. Our calculations demonstrate the limitations of the continuum dielectric model in predicting the solvatochromic shift of Me(2)N-2T-NO(2) in very polar solvents with epsilon > 35. The accuracy of the explicit solvent model is largely limited by the size of supermolecular cluster. The combined discrete/continuum solvent model gives a satisfactory description of the bathochromic shift of Me(2)N-2T-NO(2) with increasing solvent polarity, in agreement with the experimental observations.

  2. Ultrasonic degradation of 1-H-benzotriazole in water.

    PubMed

    Zúñiga-Benítez, Henry; Soltan, Jafar; Peñuela, Gustavo

    2014-01-01

    This paper reports on the effect of different parameters of ultrasonic power, pollutant initial concentration, pH and the presence of co-existing chemical species (oxygen, nitrogen, ozone, and radical scavengers) on the ultrasonic degradation of the endocrine disruptor 1-H-benzotriazole. Increasing the 1-H-benzotriazole initial concentration from 41.97 to 167.88 μM increased the pollutant degradation rate by 40%. Likewise, a high applied ultrasonic power enhanced the extent of 1-H-benzotriazole removal and its initial degradation rate, which was accelerated in the presence of ozone and oxygen, but inhibited by nitrogen. The most favorable pH for the ultrasonic degradation was acidic media, reaching ∼90% pollutant removal in 2 h. The hydroxyl free radical concentration in the reaction medium was proportional to the ultrasound power and the irradiation time. Kinetic models based on a Langmuir-type mechanism were used to predict the pollutant sonochemical degradation. It was concluded that degradation takes place at both the bubble-liquid interfacial region and in the bulk solution, and OH radicals were the main species responsible for the reaction. Hydroxyl free radicals were generated by water pyrolysis and then diffused into the interfacial region and the bulk solution where most of the solute molecules were present.

  3. Evaluation of a rabbit model for osteomyelitis by high field, high resolution imaging using the chemical-shift-specific-slice-selection technique.

    PubMed

    Volk, A; Crémieux, A C; Belmatoug, N; Vallois, J M; Pocidalo, J J; Carbon, C

    1994-01-01

    The rabbit model of osteomyelitis introduced by C.W. Norden, based on injection of an infecting solution (Staphylococcus aureus, sodium morrhuate) into the tibia, was studied at 4.7 Tesla with a time-efficient chemical shift selective imaging technique, Chemical Shift Specific Slice Selection (C4S). The evolution of the disease over several weeks was followed on water-selective, fat-selective, and sum images obtained simultaneously with this imaging sequence. Experiments were performed either on different groups of rabbits at different times after infection with subsequent sacrifice of the animal and microbiological analysis of the infected tibia or on the same group of animals imaged several times after infection. Associated analysis of the water and fat selective images revealed marrow modifications very early (Day 5 after inoculation) demonstrating the high sensitivity of the employed imaging technique. Later on, bone modifications were best identified on the sum images. Additional experiments performed on animals injected with a noninfecting solution containing only sodium morrhuate showed however that the sclerosing agent alone can yield images similar to those produced by infection at early stages after inoculation. Therefore, the Norden model would not be suitable for monitoring quantitatively outcome of therapy by magnetic resonance imaging. It is however well adapted for the evaluation and optimization of MRI techniques or protocols intended to detect early changes of bone marrow produced by septic or aseptic infarct.

  4. Free variable selection QSPR study to predict (19)F chemical shifts of some fluorinated organic compounds using Random Forest and RBF-PLS methods.

    PubMed

    Goudarzi, Nasser

    2016-04-05

    In this work, two new and powerful chemometrics methods are applied for the modeling and prediction of the (19)F chemical shift values of some fluorinated organic compounds. The radial basis function-partial least square (RBF-PLS) and random forest (RF) are employed to construct the models to predict the (19)F chemical shifts. In this study, we didn't used from any variable selection method and RF method can be used as variable selection and modeling technique. Effects of the important parameters affecting the ability of the RF prediction power such as the number of trees (nt) and the number of randomly selected variables to split each node (m) were investigated. The root-mean-square errors of prediction (RMSEP) for the training set and the prediction set for the RBF-PLS and RF models were 44.70, 23.86, 29.77, and 23.69, respectively. Also, the correlation coefficients of the prediction set for the RBF-PLS and RF models were 0.8684 and 0.9313, respectively. The results obtained reveal that the RF model can be used as a powerful chemometrics tool for the quantitative structure-property relationship (QSPR) studies.

  5. Triosephosphate isomerase: 15N and 13C chemical shift assignments and conformational change upon ligand binding by magic-angle spinning solid-state NMR spectroscopy.

    PubMed

    Xu, Yimin; Lorieau, Justin; McDermott, Ann E

    2010-03-19

    Microcrystalline uniformly (13)C,(15)N-enriched yeast triosephosphate isomerase (TIM) is sequentially assigned by high-resolution solid-state NMR (SSNMR). Assignments are based on intraresidue and interresidue correlations, using dipolar polarization transfer methods, and guided by solution NMR assignments of the same protein. We obtained information on most of the active-site residues involved in chemistry, including some that were not reported in a previous solution NMR study, such as the side-chain carbons of His95. Chemical shift differences comparing the microcrystalline environment to the aqueous environment appear to be mainly due to crystal packing interactions. Site-specific perturbations of the enzyme's chemical shifts upon ligand binding are studied by SSNMR for the first time. These changes monitor proteinwide conformational adjustment upon ligand binding, including many of the sites probed by solution NMR and X-ray studies. Changes in Gln119, Ala163, and Gly210 were observed in our SSNMR studies, but were not reported in solution NMR studies (chicken or yeast). These studies identify a number of new sites with particularly clear markers for ligand binding, paving the way for future studies of triosephosphate isomerase dynamics and mechanism.

  6. 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.

  7. Understanding Chemical versus Electrostatic Shifts in X-ray Photoelectron Spectra of Organic Self-Assembled Monolayers

    PubMed Central

    2016-01-01

    The focus of the present article is on understanding the insight that X-ray photoelectron spectroscopy (XPS) measurements can provide when studying self-assembled monolayers. Comparing density functional theory calculations to experimental data on deliberately chosen model systems, we show that both the chemical environment and electrostatic effects arising from a superposition of molecular dipoles influence the measured core-level binding energies to a significant degree. The crucial role of the often overlooked electrostatic effects in polar self-assembled monolayers (SAMs) is unambiguously demonstrated by changing the dipole density through varying the SAM coverage. As a consequence of this effect, care has to be taken when extracting chemical information from the XP spectra of ordered organic adsorbate layers. Our results, furthermore, imply that XPS is a powerful tool for probing local variations in the electrostatic energy in nanoscopic systems, especially in SAMs. PMID:26937264

  8. Final Technical Report: A Paradigm Shift in Chemical Processing: New Sustainable Chemistries for Low-VOC Coatings

    SciTech Connect

    Smith, Kenneth F.

    2006-07-26

    The project employed new processes to make emulsion polymers from reduced levels of petroleum-derived chemical feedstocks. Most waterborne paints contain spherical, emulsion polymer particles that serve as the film-forming binder phase. Our goal was to make emulsion polymer particles containing 30 percent feedstock that would function as effectively as commercial emulsions made from higher level feedstock. The processes developed yielded particles maintained their film formation capability and binding capacity while preserving the structural integrity of the particles after film formation. Rohm and Haas Company (ROH) and Archer Daniels Midland Company (ADM) worked together to employ novel polymer binders (ROH) and new, non-volatile, biomass-derived coalescing agents (ADM). The University of Minnesota Department of Chemical Engineering and Material Science utilized its unique microscopy capabilities to characterize films made from the New Emulsion Polymers (NEP).

  9. Nuclear magnetic resonance, vibrational spectroscopic studies, physico-chemical properties and computational calculations on (nitrophenyl) octahydroquinolindiones by DFT method.

    PubMed

    Pasha, M A; Siddekha, Aisha; Mishra, Soni; Azzam, Sadeq Hamood Saleh; Umapathy, S

    2015-02-05

    In the present study, 2'-nitrophenyloctahydroquinolinedione and its 3'-nitrophenyl isomer were synthesized and characterized by FT-IR, FT-Raman, (1)H NMR and (13)C NMR spectroscopy. The molecular geometry, vibrational frequencies, (1)H and (13)C NMR chemical shift values of the synthesized compounds in the ground state have been calculated by using the density functional theory (DFT) method with the 6-311++G (d,p) basis set and compared with the experimental data. The complete vibrational assignments of wave numbers were made on the basis of potential energy distribution using GAR2PED programme. Isotropic chemical shifts for (1)H and (13)C NMR were calculated using gauge-invariant atomic orbital (GIAO) method. The experimental vibrational frequencies, (1)H and (13)C NMR chemical shift values were found to be in good agreement with the theoretical values. On the basis of vibrational analysis, molecular electrostatic potential and the standard thermodynamic functions have been investigated.

  10. Theoretical investigations of the γ- gauche effect on the 13C chemical shifts produced by oxygen atoms at the γ position by quantum chemistry calculations

    NASA Astrophysics Data System (ADS)

    Suzuki, Shinji; Horii, Fumitaka; Kurosu, Hiromichi

    2009-02-01

    The γ- gauche effect on 13C chemical shifts that is produced by the O atoms located at the γ positions has been evaluated by quantum chemistry calculations based on the GAIO-CHF procedure. The γ- gauche effects produced by the O and Cl atoms in n-propanol and n-propyl chloride are found to be, respectively, +1.4 and -0.7 ppm, whereas that due to the C atom in n-butane is -3.0 ppm in good agreement of the values previously calculated. The apparent cause of such a difference in the γ- gauche effect is mainly relatively higher shielding of the CH 3 carbon in the trans conformation for the n-propanol and n-propyl chloride. Extending the n-propanol chain at both ends causes no significant change in the γ- gauche effect produced by the O atom. In 2-butanol and 2-methyl-2-butanol as examples of secondarily and tertiarily substituted compounds, the γ- gauche effects produced by the γ-OH groups are estimated to be -7 to -9 ppm. In addition, the γ- gauche effect due to the C atom is found to increase in n-butane, secondary, and tertiary butanols in this order. The γ- gauche effect produced by the O atom in hydroxyethylcyclohexane is as negligibly small as -0.7 ppm, whereas that produced by the C atom in ethylcyclohexane is about -5 ppm. These results suggest that the γ- gauche effect, including downfield shift, produced by the O atom in a compound greatly depends on its chemical structure, whereas upfield shifts of -3 to -7 ppm are induced in all examined compounds as the γ- gauche effect due to the C atom.

  11. Synthesis, antimicrobial evaluation and theoretical prediction of NMR chemical shifts of thiazole and selenazole derivatives with high antifungal activity against Candida spp.

    NASA Astrophysics Data System (ADS)

    Łączkowski, Krzysztof Z.; Motylewska, Katarzyna; Baranowska-Łączkowska, Angelika; Biernasiuk, Anna; Misiura, Konrad; Malm, Anna; Fernández, Berta

    2016-03-01

    Synthesis and investigation of antimicrobial activities of novel thiazoles and selenazoles is presented. Their structures were determined using NMR, FAB(+)-MS, HRMS and elemental analyses. To support the experiment, theoretical calculations of the 1H NMR shifts were carried out for representative systems within the DFT B3LYP/6-311++G** approximation which additionally confirmed the structure of investigated compounds. Among the derivatives, compounds 4b, 4h, 4j and 4l had very strong activity against reference strains of Candida albicans ATCC and Candida parapsilosis ATCC 22019 with MIC = 0.49-7.81 μg/ml. In the case of compounds 4b, 4c, 4h - 4j and 4l, the activity was very strong against of Candida spp. isolated from clinical materials, i.e. C. albicans, Candida krusei, Candida inconspicua, Candida famata, Candida lusitaniae, Candida sake, C. parapsilosis and Candida dubliniensis with MIC = 0.24-15.62 μg/ml. The activity of several of these was similar to the activity of commonly used antifungal agent fluconazole. Additionally, compounds 4m - 4s were found to be active against Gram-positive bacteria, both pathogenic staphylococci Staphylococcus aureus ATCC with MIC = 31.25-125 μg/ml and opportunistic bacteria, such as Staphylococcus epidermidis ATCC 12228 and Micrococcus luteus ATCC 10240 with MIC = 7.81-31.25 μg/ml.

  12. Tautomeric ratio and prototropic equilibrium constants of tenoxicam, a 1H and 13C NMR theoretical and experimental study.

    PubMed

    Franco-Pérez, Marco; Moya-Hernández, Rosario; Rojas-Hernández, Alberto; Gutiérrez, Atilano; Gómez-Balderas, Rodolfo

    2011-11-24

    The determination of the micro-equilibrium prototropic constants is often a tough task when the tautomeric ratio favors one of the species or when the chemical exchange is not slow enough to allow the quantitative detection of the tautomeric species. There are just few experimental methods available to reveal the constants of the tautomeric micro-equilibriums; its applicability depends on the nature of the tautomeric system. A combination of experimental and quantum chemistry calculated (1)H and (13)C NMR chemical shifts is presented here to estimate the population of the species participating in the tautomeric equilibriums of the tenoxicam, an important anti-inflammatory drug. A multivariate fitting of a fraction-mol-weighted contribution model, for the NMR chemical shifts of the species in solution, was used to find the populations of the tautomers of tenoxicam. To consider and evaluate the effect of the solvent polarity on the tautomers' populations, experimental determinations were carried out in DMSO-d(6), in an equimolar DMSO-H(2)O mixture of deuterated solvents and in D(2)O. Additionally, by employing HYPNMR, it has been possible to refine the acid-base macroscopic constants of tenoxicam.

  13. Spectroscopic (FT-IR, FT-Raman, UV, 1H and 13C NMR) profiling and computational studies on methyl 5-methoxy-1H-indole-2-carboxylate: A potential precursor to biologically active molecules

    NASA Astrophysics Data System (ADS)

    Almutairi, Maha S.; Xavier, S.; Sathish, M.; Ghabbour, Hazem A.; Sebastian, S.; Periandy, S.; Al-Wabli, Reem I.; Attia, Mohamed I.

    2017-04-01

    Methyl 5-methoxy-1H-indole-2-carboxylate (MMIC) was prepared via esterification of commercially available 5-methoxyindole-2-carboxylic acid. The title molecule MMIC was characterised using FT-IR and FT-Raman in the ranges of 4000-500 and 4000-50 cm-1, respectively. The fundamental modes of the vibrations were assigned and the UV-visible spectrum of the MMIC molecule was recorded in the range of 200-400 nm to explore its electronic nature. The HOMO-LUMO energy distribution was calculated and the bonding and anti-bonding structures of the title molecule were studied and analysed using the natural bond orbital (NBO) approach. The reactivity of the MMIC molecule was also investigated and both the positive and negative centres of the molecule were identified using chemical descriptors and molecular electrostatic potential (MEP) analysis. The chemical shifts of the 1H and 13C NMR spectra were noted and the magnetic field environment of the MMIC molecule are discussed. The non-linear optical (NLO) properties of the title molecule were studied based on its calculated values of polarisability and hyperpolarisability. All computations were obtained by DFT methods using the 6-311++G (d,p) basis set.

  14. Measurement of the individual pKa values of acidic residues of hen and turkey lysozymes by two-dimensional 1H NMR.

    PubMed Central

    Bartik, K; Redfield, C; Dobson, C M

    1994-01-01

    The pH dependence of the two-dimensional 1H nuclear magnetic resonance spectra of hen and turkey egg-white lysozymes has been recorded over the pH range 1-7. By monitoring the chemical shifts of the resonances of the various protons of ionizable residues, individual pKa values for the acidic residues have been determined for both proteins. The pKa values are displaced, with the exception of those of the residues in the active site cleft, by an average of 1 unit to low pH compared to model compounds. PMID:8038389

  15. Synthesis and complete assignment of the 1H and 13C NMR spectra of 6-substituted and 2,6-disubstituted pyridazin-3(2H)-ones.

    PubMed

    Besada, Pedro; Costas, Tamara; Vila, Noemi; Chessa, Carla; Terán, Carmen

    2011-07-01

    Several pyridazin-3(2H)-one derivatives were synthesized starting from alkyl furans using oxidation with singlet oxygen to give 4-methoxy or 4-hydroxybutenolides, key intermediates of the synthetic strategy followed. For all pyridazinones reported, a complete assignment of the (1)H and (13)C NMR spectra using one- and two-dimensional NMR spectroscopic methods, which included NOE, DEPT, COSY, HSQC and HMBC experiments, was accomplished. Correlations between the chemical shifts of the heterocyclic ring atoms and substituents at N-2 and C-6 were analyzed.

  16. A 1H, 13C and 15N NMR study in solution and in the solid state of six N-substituted pyrazoles and indazoles.

    PubMed

    Claramunt, Rosa M; Santa María, M Dolores; Sanz, Dionisia; Alkorta, Ibon; Elguero, José

    2006-05-01

    Three N-substituted pyrazoles and three N-substituted indazoles [1-(4-nitrophenyl)-3,5-dimethylpyrazole (1), 1-(2,4-dinitrophenyl)-3,5-dimethylpyrazole (2), 1-tosyl-pyrazole (3), 1-p-chlorobenzoylindazole (4), 1-tosylinda-zole (5) and 2-(2-hydroxy-2-phenylethyl)-indazole (6)] have been studied by NMR spectroscopy in solution (1H, 13C, 15N) and in the solid state (13C, 15N). The chemical shifts have been compared with GIAO/DFT calculated absolute shieldings. Some discrepancies have been analyzed.

  17. Sequence-specific 1H, 15N and 13C resonance assignments of Art v 1: a proline-rich allergen of Artemisia vulgaris pollen.

    PubMed

    Razzera, Guilherme; Gadermaier, Gabriele; Almeida, Marcius S; Ferreira, Fatima; Almeida, Fabio C L; Valente, Ana Paula

    2009-06-01

    Art v 1 is the major allergen of Artemisia vulgaris. The IgE raised against Art v 1 not only can cross-react with other proteins from the Asteraceae family members but also with components of various forms of food. Art v 1 is an important target for immunotherapy strategies, including vaccination with hypoallergenic derivatives or chimeras. We report the (1)H, (13)C, and (15)N resonance assignments of the recombinant Art v 1 and identification of secondary structures based on (13)C chemical shifts.

  18. Chemical potential shift and gap-state formation in SrTiO{sub 3−δ} revealed by photoemission spectroscopy

    SciTech Connect

    Pal, Prabir Kumar, Pramod; Aswin, V.; Dogra, Anjana; Joshi, Amish G.

    2014-08-07

    In this study, we report on investigations of the electronic structure of SrTiO{sub 3} annealed at temperature ranging between 550 and 840 °C in an ultrahigh vacuum. Annealing induced oxygen vacancies (O{sub vac}) impart considerable changes in the electronic structure of SrTiO{sub 3}. Using core-level photoemission spectroscopy, we have studied the chemical potential shift (Δμ) as a function of annealing temperature. The result shows that the chemical potential monotonously increases with electron doping in SrTiO{sub 3−δ}. The monotonous increase of the chemical potential rules out the existence of electronic phase separation in the sample. Using valence band photoemission, we have demonstrated the formation of a low density of states at the near Fermi level electronic spectrum of SrTiO{sub 3−δ}. The gap-states were observed by spectral weight transfer over a large energy scale of the stoichiometric band gap of SrTiO{sub 3} system leading finally to an insulator-metal transition. We have interpreted our results from the point of structural distortions induced by oxygen vacancies.

  19. Mapping of the C3d ligand binding site on complement receptor 2 (CR2/CD21) using nuclear magnetic resonance and chemical shift analysis.

    PubMed

    Kovacs, James M; Hannan, Jonathan P; Eisenmesser, Elan Z; Holers, V Michael

    2009-04-03

    Complement receptor 2 (CR2, CD21) is a cell membrane protein, with 15 or 16 extracellular short consensus repeats (SCRs), that promotes B lymphocyte responses and bridges innate and acquired immunity. The most distally located SCRs (SCR1-2) mediate the interaction of CR2 with its four known ligands (C3d, Epstein-Barr virus gp350, interferon-alpha, and CD23). Inhibitory monoclonal antibodies against SCR1-2 block binding of all ligands. To develop ligand-specific inhibitors that would also assist in identifying residues unique to each receptor-ligand interaction, phage were selected from randomly generated libraries by panning with recombinant SCR1-2, followed by specific ligand-driven elution. Derived peptides were tested by competition ELISA. One peptide, C3dp1 (APQHLSSQYSRT) exhibited ligand-specific inhibition at midmicromolar IC(50). C3d was titrated into (15)N-labeled SCR1-2, which revealed chemical shift changes indicative of specific intermolecular interactions. With backbone assignments made, the chemical shift changes were mapped onto the crystal structure of SCR1-2. With regard to C3d, the binding surface includes regions of SCR1, SCR2, and the inter-SCR linker, specifically residues Arg(13), Tyr(16), Arg(28), Tyr(29), Ser(32), Thr(34), Lys(48), Asp(56), Lys(57), Tyr(68), Arg(83), Gly(84), Asn(101), Asn(105), and Ser(109). SCR1 and SCR2 demonstrated distinct binding modes. The CR2 binding surface incorporating SCR1 is inconsistent with a previous x-ray CR2-C3d co-crystal analysis but consistent with mutagenesis, x-ray neutron scattering, and inhibitory monoclonal antibody epitope mapping. Titration with C3dp1 yielded chemical shift changes (Arg(13), Tyr(16), Thr(34), Lys(48), Asp(56), Lys(57), Tyr(68), Arg(83), Gly(84), Asn(105), and Ser(109)) overlapping with C3d, indicating that C3dp1 interacts at the same CR2 site as C3d.

  20. Size- and site-dependent reconstruction in CdSe QDs evidenced by 77Se{1H} CP-MAS NMR spectroscopy.

    PubMed

    Lovingood, Derek D; Achey, Randall; Paravastu, Anant K; Strouse, Geoffrey F

    2010-03-17

    Evidence of size-dependent reconstruction in quantum dots leading to changes in bonding is observed through analysis of the (77)Se{(1)H} cross-polarization magic angle spinning and (77)Se spin-echo solid-state NMR for Cd(77)Se quantum dots. The CP-MAS and spin-echo data indicate discrete surface and core (77)Se sites exist with the QD, in which the surface is comprised of numerous reconstructed lattice planes. Due to the nearly 100% enrichment level for (77)Se, efficient spin coupling is observed between the surface (77)Se and sublayer (77)Se sites due to spin diffusion in the Cd(77)Se quantum dots. The observed chemical shift for the discrete (77)Se sites can be correlated to the effective mass approximation via the Ramsey expression, indicating a 1/r(2) size dependence for the change in chemical shift with size, while a plot of chemical shift versus the inverse band gap is linear. The correlation of NMR shift for the discrete sites allows a valence bond theory interpretation of the size-dependent changes in bonding character within the reconstructed QD. The NMR results provide a structural model for the QDs in which global reconstruction occurs below 4 nm in diameter, while an apparent self-limiting reconstruction process occurs above 4 nm.

  1. Relative importance of first and second derivatives of nuclear magnetic resonance chemical shifts and spin-spin coupling constants for vibrational averaging.

    PubMed

    Dracínský, Martin; Kaminský, Jakub; Bour, Petr

    2009-03-07

    Relative importance of anharmonic corrections to molecular vibrational energies, nuclear magnetic resonance (NMR) chemical shifts, and J-coupling constants was assessed for a model set of methane derivatives, differently charged alanine forms, and sugar models. Molecular quartic force fields and NMR parameter derivatives were obtained quantum mechanically by a numerical differentiation. In most cases the harmonic vibrational function combined with the property second derivatives provided the largest correction of the equilibrium values, while anharmonic corrections (third and fourth energy derivatives) were found less important. The most computationally expensive off-diagonal quartic energy derivatives involving four different coordinates provided a negligible contribution. The vibrational corrections of NMR shifts were small and yielded a convincing improvement only for very accurate wave function calculations. For the indirect spin-spin coupling constants the averaging significantly improved already the equilibrium values obtained at the density functional theory level. Both first and complete second shielding derivatives were found important for the shift corrections, while for the J-coupling constants the vibrational parts were dominated by the diagonal second derivatives. The vibrational corrections were also applied to some isotopic effects, where the corrected values reasonably well reproduced the experiment, but only if a full second-order expansion of the NMR parameters was included. Contributions of individual vibrational modes for the averaging are discussed. Similar behavior was found for the methane derivatives, and for the larger and polar molecules. The vibrational averaging thus facilitates interpretation of previous experimental results and suggests that it can make future molecular structural studies more reliable. Because of the lengthy numerical differentiation required to compute the NMR parameter derivatives their analytical implementation in

  2. Structural elucidation of dioxa-cage compounds from tetrahydroisobenzofuran-1(3H)-one: analysis of NMR data and GIAO chemical shifts calculations.

    PubMed

    da Costa Resende, Gabriela; Alvarenga, Elson Santiago

    2016-12-01

    The polycyclic compounds, especially the dioxa-cages, have attracted considerable attention in recent years. In our work, a series of 9β-substituted 3-oxo-4,11-dioxatetracyclo[5.2.1.1(5,8) .0(2,6) ]undecane compounds were unexpectedly isolated during bromination, chlorination and epoxidation reactions of the 3-hydroxy-3a,4,7,7a-tetrahydro-4,7-methanoisobenzofuran-1(3H)-one. After careful analysis of the NMR data, the chemical shifts of the isolated and the expected products were predicted by theoretical calculations using density functional theory and gauge including atomic orbitals. The best correlation between calculated and experimental data was evaluated by comparing mean absolute errors and applying DP4 probability methodology. Results from both approaches indicated a correct structural elucidation. Copyright © 2016 John Wiley & Sons, Ltd.

  3. 1H NMR analysis of complexation of hydrotropic agents nicotinamide and caffeine with aromatic biologically active molecules in aqueous solution

    NASA Astrophysics Data System (ADS)

    Lantushenko, Anastasia O.; Mukhina, Yulia V.; Veselkov, Kyrill A.; Davies, David B.; Veselkov, Alexei N.

    2004-07-01

    NMR spectroscopy has been used to elucidate the molecular mechanism of solubilization action of hydrotropic agents nicotinamide (NA) and caffeine (CAF). Hetero-association of NA with riboflavine-mononucleotide (FMN) and CAF with low soluble in aqueous solution synthetic analogue of antibiotic actinomycin D, actinocyl-bis-(3-dimethylaminopropyl) amine (Actill), has been investigated by 500 MHz 1H NMR spectroscopy. Concentration and temperature dependences of proton chemical shifts have been analysed in terms of a statistical-thermodynamic model of indefinite self- and heteroassociation of aromatic molecules. The obtained results enable to conclude that NA-FMN and CAF-Actill intermolecular complexes are mainly stabilized by the stacking interactions of the aromatic chromophores. Hetero-association of the investigated molecules plays an important role in solubilization of aromatic drugs by hydrotropic agents nicotinamide and caffeine.

  4. [Studies by means of 1H NMR spectroscopy of complex formation of aromatic biologically active compounds with antibiotic topotecan].

    PubMed

    Mosunov, A A; Kostiukov, V V; Evstigneev, M P

    2012-01-01

    The analysis of heteroassociation of antibiotic topotecan (TPT) with aromatic biologically active compounds (BAC): caffeine, mutagens ethidium bromide and proflavine, antibiotic daunomycin, vitamins flavin-mononucleotide and nicotinamide, has been carried out in the work using 1H NMR spectroscopy data. The equilibrium constants of heteroassociation and induced chemical shifts of the protons have been obtained in the complexes with BAC. It is found that the complex formation TPT-BAC has the nature of stacking of the chromophores, additionally stabilized in the case of proflavine by intermolecular hydrogen bond. Calculation of the basic components of the Gibbs free energy of the complexation reactions is carried out, and the factors which stabilize and destabilize the heterocomplexes of molecules are revealed.

  5. A new salen base 5-(phenylazo)-N-(2-amino pyridine) salicyliden Schiff base ligand: synthesis, experimental and density functional studies on its crystal structure, FTIR, 1H NMR and 13C NMR spectra.

    PubMed

    Sheikhshoaie, Iran; Saheb, Vahid

    2010-12-01

    A novel Schiff base ligand 5-(phenylazo)-N-(2-amino pyridine) salicyliden is prepared through the condensation of 5-(phenylazo) salicylaldehyde and 2-amino pyridine in methanol at room temperature. The orange crystalline precipitate is used for X-ray crystallography and measuring Fourier transform (FTIR), 1H NMR and 13C NMR spectra. Density functional theory (DFT) calculations at the B3LYP, MPWB1K and B3PW91 levels of theory is used to optimize the geometry and calculate the FTIR, 1H NMR and 13C NMR spectra of the compound. The vibrational frequencies determined experimentally are compared with those obtained theoretically and a vibrational assignment and analysis of the fundamental modes of the compound is performed. We found that the MPWB1K method predicts low vibrational frequencies better than the commonly used B3LYP method. Although the B3PW91 method overestimates the 1H NMR chemical shifts, the values computed at the B3LYP level of theory are in accordance with experimental 1H NMR spectrum. However, both B3LYP and B3PW91 methods tend to overestimate 13C NMR chemical shifts. In addition, a few quantum descriptors of the molecule are calculated and conformational analysis is performed and the result was compared with crystallographic data.

  6. Increasing 14N NQR signal by 1H-14N level crossing with small magnetic fields.

    PubMed

    Thurber, Kent R; Sauer, Karen L; Buess, Michael L; Klug, Christopher A; Miller, Joel B

    2005-11-01

    NQR detection of materials, such as TNT, is hindered by the low signal-to-noise ratio at low NQR frequencies. Sweeping small (0-26 mT) magnetic fields to shift the (1)H NMR frequency relative to the (14)N NQR frequencies can provide a significant increase of the (14)N NQR signal-to-noise ratio. Three effects of (1)H-(14)N level crossing are demonstrated in diglycine hydrochloride and TNT. These effects are (1) transferring (1)H polarization to one or more of the (14)N transitions, including the use of an adiabatic flip of the (1)H polarization during the field sweep, (2) shortening the effective (14)N T(1) by the interaction of (1)H with the (14)N transitions, (3) "level transfer" effect where the third (14)N (spin 1) energy level or other (14)N sites with different NQR frequency are used as a reservoir of polarization which is transferred to the measured (14)N transition by the (1)H. The (14)N NQR signal-to-noise ratio can be increased by a factor of 2.5 for one (14)N site in diglycine hydrochloride (and 2.2 in TNT), even though the maximum (1)H frequency used in this work, 111 6 kHz, is only 30% larger than the measured (14)N frequencies (834 kHz for diglycine hydrochloride and 843 kHz for TNT).

  7. Intrauterine fetal brain NMR spectroscopy: 1H and 31P studies in rats

    SciTech Connect

    Nakada, T.; Kwee, I.L.; Suzuki, N.; Houkin, K. )

    1989-11-01

    Fetal brain metabolism was investigated in utero noninvasively using multinuclear nuclear magnetic resonance spectroscopy in rats at two representative prenatal stages: early (17-18 days) and late (20-21 days) stages. Phosphorus-31 (31P) spectroscopy revealed that phosphocreatine is significantly lower in the early stage and increases to the level of early neonates by the late prenatal stage. Intracellular pH at the early stage was found to be strikingly high (7.52 +/- 0.21) and decreased to a level similar to that of neonates by the late stage (7.29 +/- 0.07). Phosphomonoester levels at both stages were similar to the values reported for early neonates. Water-suppressed proton (1H) spectroscopy demonstrated a distinctive in vivo fetal brain spectral pattern characterized by low levels of N-acetyl aspartate and high levels of taurine. High-resolution proton spectroscopy and homonuclear chemical-shift correlate spectroscopy of brain perchloric acid extracts confirmed these in vivo findings. In vitro 31P spectroscopy of acidified chloroform methanol extracts showed the characteristic membrane phospholipid profiles of fetal brain. The phosphatidylethanolamine (PE)-to-phosphatidylcholine (PC) ratio (PE/PC) did not show significant changes between the two stages at 0.40 +/- 0.11, a value similar to that of early neonates.

  8. 40 CFR 721.8965 - 1H-Pyrole-2, 5-dione, 1-(2,4,6-tribromophenyl)-.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...) TOXIC SUBSTANCES CONTROL ACT SIGNIFICANT NEW USES OF CHEMICAL SUBSTANCES Significant New Uses for Specific Chemical Substances § 721.8965 1H-Pyrole-2, 5-dione, 1-(2,4,6-tribromophenyl)-. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as...

  9. Design, synthesis and 1H NMR study of C3v-symmetric anion receptors with urethane-NH as recognition group

    NASA Astrophysics Data System (ADS)

    Park, Jin-Oh; Sahoo, Suban K.; Choi, Heung-Jin

    2016-01-01

    C3v-Symmetric anion receptors 3 and 4 with urethane groups were synthesized by using trindane triol as tripodal molecular framework. In 1H NMR titration study, the receptors showed noticeable downfield shift/disappearance of the urethane-NH peak in presence of H2PO4- and F- due to the host-guest complexation occurred through multiple hydrogen bonding and/or the deprotonation of urethane-NH groups. Other tested anions such as Cl-, Br-, HSO4-, and NO3- showed either no or negligible chemical shift of the urethane groups. The deprotonation event in 4 allowed selective detection of F- by perceptible color change from colorless to yellowish-red with the appearance of a new charge transfer absorption band at 450 nm.

  10. A lanthanide complex with dual biosensing properties: CEST (chemical exchange saturation transfer) and BIRDS (biosensor imaging of redundant deviation in shifts) with europium DOTA-tetraglycinate.

    PubMed

    Coman, Daniel; Kiefer, Garry E; Rothman, Douglas L; Sherry, A Dean; Hyder, Fahmeed

    2011-12-01

    Responsive contrast agents (RCAs) composed of lanthanide(III) ion (Ln3R) complexes with a variety of1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetate (DOTA4S) derivatives have shown great potential as molecular imaging agents for MR. A variety of LnDOTA–tetraamide complexes have been demonstrated as RCAs for molecular imaging using chemical exchange saturation transfer (CEST). The CEST method detects proton exchange between bulk water and any exchangeable sites on the ligand itself or an inner sphere of bound water that is shifted by a paramagnetic Ln3R ion bound in the core of the macrocycle. It has also been shown that molecular imaging is possible when the RCA itself is observed (i.e. not its effect on bulk water) using a method called biosensor imaging of redundant deviation in shifts (BIRDS). The BIRDS method utilizes redundant information stored in the nonexchangeable proton resonances emanating from the paramagnetic RCA for ambient factors such as temperature and/or pH.Thus, CEST and BIRDS rely on exchangeable and nonexchangeable protons, respectively, for biosensing. We posited that it would be feasible to combine these two biosensing features into the same RCA (i.e. dual CEST and BIRDS properties). A complex between europium(III) ion (Eu3R) and DOTA–tetraglycinate [DOTA–(gly)S4] was used to demonstrate that its CEST characteristics are preserved, while its BIRDS properties are also detectable. The in vitro temperature sensitivity of EuDOTA–(gly)S4 was used to show that qualitative MR contrast with CEST can be calibrated using quantitative MR mapping with BIRDS, thereby enabling quantitative molecular imaging at high spatial resolution.

  11. Crystalline 1H-1,2,3-triazol-5-ylidenes

    SciTech Connect

    Bertrand, Guy; Gulsado-Barrios, Gregorio; Bouffard, Jean; Donnadieu, Bruno

    2016-08-02

    The present invention provides novel and stable crystalline 1H-1,2,3 triazolium carbenes and metal complexes of 1H-1,2,3 triazolium carbenes. The present invention also provides methods of making 1H-1,2,3 triazolium carbenes and metal complexes of 1H-1,2,3 triazolium carbenes. The present invention also provides methods of using 1H-1,2,3 triazolium carbenes and metal complexes of 1H-1,2,3 triazolium carbenes in catalytic reactions.

  12. Characterization of the structure and redox behaviour of cytochrome c3 from Desulfovibrio baculatus by 1H-nuclear-magnetic-resonance spectroscopy.

    PubMed Central

    Coutinho, I B; Turner, D L; LeGall, J; Xavier, A V

    1993-01-01

    Complete assignment of the aromatic and haem proton resonances in the cytochromes c3 isolated from Desulfovibrio baculatus strains (Norway 4, DSM 1741) and (DSM 1743) was achieved using one- and two-dimensional 1H n.m.r. Nuclear Overhauser enhancements observed between haem and aromatic resonances and between resonances due to different haems, together with the ring-current contributions to the chemical shifts of haem resonances, support the argument that the haem core architecture is conserved in the various cytochromes c3, and that the X-ray structure of the D. baculatus cytochrome c3 is erroneous. The relative orientation of the haems for both cytochromes was determined directly from n.m.r. data. The n.m.r. structures have a resolution of approximately 0.25 nm and are found to be in close agreement with the X-ray structure from D. vulgaris cytochrome c3. The proton assignments were used to relate the highest potential to a specific haem in the three-dimensional structure by monitoring the chemical-shift variation of several haem resonances throughout redox titrations followed by 1H n.m.r. The haem with highest redox potential is not the same as that in other cytochromes c3. PMID:8397513

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

    PubMed

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

    2016-10-01

    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 (1)H, (13)C and (15)N 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 (15)N-{(1)H} hetero NOEs. These secondary structure elements suggest the Pa-IF1 adopts the typical β-barrel structure and is composed of an oligomer-binding motif.

  14. [1H NMR analysis of the complex formation of aromatic molecules of antibiotic and vitamin in aqueous solution: heteroassociation of actinomycin D and flavin mononucleotide].

    PubMed

    Veselkov, A N; Evstigneev, M P; Rozvadovskaia, A O; Mukhina, Iu V; Rybakova, K A

    2005-01-01

    The molecular mechanism of the combined action of antibiotic and vitamin was studied by NMR spectroscopy. The heteroassociation of the antitumor antibiotic actinomycin D and flavin mononucleotide was investigated as a function of concentration and temperature by 500 MHz 1H NMR spectroscopy. The equilibrium association constant, the thermodynamic parameters (deltaH, deltaS) of heteroassociation of actinomycin D with flavin mononucleotide, and the limiting values of proton chemical shifts in the heterocomplex were determined from the concentration and temperature dependences of proton chemical shifts of molecules. The most favorable structure of the 1:1 actinomycin D-flavin mononucleotide heteroassociation complex was determined using both the molecular mechanics methods (X-PLOR software) and the limiting values of proton chemical shifts of the molecules. In the calculated structure, the planes of the chromophores of actinomycin D and flavin mononucleotide molecules in the 1:1 heterocomplex are parallel and separated from each other by a distance of about 0.34 nm. At the same time, there is a probability of formation of intermolecular hydrogen bonds in the calculated structure of 1:1 actinomycin D-flavin mononucleotide complex. The analysis of the results obtained suggests that aromatic molecules of vitamins, e.g., flavin mononucleotide, can form energetically favorable heterocomplexes with aromatic antitumor antibiotics in aqueous solution, modulating thereby the efficacy of their medical and biological action.

  15. Unambiguous Metabolite Identification in High-Throughput Metabolomics by Hybrid 1H-NMR/ESI-MS1 Approach

    SciTech Connect

    2016-10-18

    The invention improves accuracy of metabolite identification by combining direct infusion ESI-MS with one-dimensional 1H-NMR spectroscopy. First, we apply a standard 1H-NMR metabolite identification protocol by matching the chemical shift, J-coupling and intensity information of experimental NMR signals against the NMR signals of standard metabolites in a metabolomics reference libraries. This generates a list of candidate metabolites. The list contains both false positive and ambiguous identifications. The software tool (the invention) takes the list of candidate metabolites, generated from NMRbased metabolite identification, and then calculates, for each of the candidate metabolites, the monoisotopic mass-tocharge (m/z) ratios for each commonly observed ion, fragment and adduct feature. These are then used to assign m/z ratios in experimental ESI-MS spectra of the same sample. Detection of the signals of a given metabolite in both NMR and MS spectra resolves the ambiguities, and therefore, significantly improves the confidence of the identification.

  16. High resolution spectroscopy and chemical shift imaging of hyperpolarized 129Xe dissolved in the human brain in vivo at 1.5 tesla

    PubMed Central

    Rao, Madhwesha; Stewart, Neil J.; Norquay, Graham; Griffiths, Paul D.

    2016-01-01

    Purpose Upon inhalation, xenon diffuses into the bloodstream and is transported to the brain, where it dissolves in various compartments of the brain. Although up to five chemically distinct peaks have been previously observed in 129Xe rat head spectra, to date only three peaks have been reported in the human head. This study demonstrates high resolution spectroscopy and chemical shift imaging (CSI) of 129Xe dissolved in the human head at 1.5 Tesla. Methods A 129Xe radiofrequency coil was built in‐house and 129Xe gas was polarized using spin‐exchange optical pumping. Following the inhalation of 129Xe gas, NMR spectroscopy was performed with spectral resolution of 0.033 ppm. Two‐dimensional CSI in all three anatomical planes was performed with spectral resolution of 2.1 ppm and voxel size 20 mm × 20 mm. Results Spectra of hyperpolarized 129Xe dissolved in the human head showed five distinct peaks at 188 ppm, 192 ppm, 196 ppm, 200 ppm, and 217 ppm. Assignment of these peaks was consistent with earlier studies. Conclusion High resolution spectroscopy and CSI of hyperpolarized 129Xe dissolved in the human head has been demonstrated. For the first time, five distinct NMR peaks have been observed in 129Xe spectra from the human head in vivo. Magn Reson Med 75:2227–2234, 2016. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. PMID:27080441

  17. Correlation between ¹⁹⁵Pt chemical shifts and the electronic transitions among d orbitals in pincer NCN Pt(II) complexes: A theoretical study and application of Ramsey's equation.

    PubMed

    Hashemi, Majid

    2015-12-05

    The chemical potentials for two series of [PtCl(NCN-Z-4)] (NCN=2,6-bis[(dimethylamino)methyl]phenyl, Z=H, CHO, COOH, NH2, OH, NO2, SiMe3, I, t-Bu) and [PtCl(NCN-4-CHN-C6H4-Z'-4')] (Z'=NMe2, Me, H, Cl, CN) were calculated. The energies of platinum d orbitals were calculated by NBO analysis. Good correlations were obtained between (195)Pt chemical shifts and the spectral parameters obtained from the energies of electronic transitions between Pt d orbitals in these complexes. The correlations between (195)Pt chemical shifts and the chemical potentials were also good. The correlations were discussed based on Ramsey's equation.

  18. Self-diffusion and interactions in mixtures of imidazolium bis(mandelato)borate ionic liquids with polyethylene glycol: (1) H NMR study.

    PubMed

    Filippov, Andrei; Azancheev, Nail; Taher, Mamoun; Shah, Faiz Ullah; Rabét, Pauline; Glavatskih, Sergei; Antzutkin, Oleg N

    2015-07-01

    We used (1) H nuclear magnetic resonance pulsed-field gradient to study the self-diffusion of polyethylene glycol (PEG) and ions in a mixture of PEG and imidazolium bis(mandelato)borate ionic liquids (ILs) at IL concentrations from 0 to 10 wt% and temperatures from 295 to 370 K. PEG behaves as a solvent for these ILs, allowing observation of separate lines in (1) H NMR spectra assigned to the cation and anion as well as to PEG. The diffusion coefficients of PEG, as well as the imidazolium cation and bis(mandelato)borate (BMB) anion, differ under all experimental conditions tested. This demonstrates that the IL in the mixture is present in at least a partially dissociated state, while the lifetimes of the associated states of the ions and ions with PEG are less than ~30 ms. Generally, increasing the concentration of the IL leads to a decrease in the diffusion coefficients of PEG and both ions. The diffusion coefficient of the anion is less than that of the cation; the molecular mass dependence of diffusion of ions can be described by the Stokes-Einstein model. NMR chemical shift alteration analysis showed that the presence of PEG changes mainly the chemical shifts of protons belonging to imidazole ring of the cation, while chemical shifts of protons of anions and PEG remain unchanged. This demonstrated that the imidazolium cation interacts mainly with PEG, which most probably occurs through the oxygen of PEG and the imidazole ring. The BMB anion does not strongly interact with PEG, but it may be indirectly affected by PEG through interaction with the cation, which directly interacts with PEG.

  19. Intramyocellular lipid dependence on skeletal muscle fiber type and orientation characterized by diffusion tensor imaging and 1H-MRS

    NASA Astrophysics Data System (ADS)

    Valaparla, Sunil K.; Gao, Feng; Abdul-Ghani, Muhammad; Clarke, Geoffrey D.

    2014-03-01

    When muscle fibers are aligned with the B0 field, intramyocellular lipids (IMCL), important for providing energy during physical activity, can be resolved in proton magnetic resonance spectra (1H-MRS). Various muscles of the leg differ significantly in their proportion of fibers and angular distribution. This study determined the influence of muscle fiber type and orientation on IMCL using 1H-MRS and diffusion tensor imaging (DTI). Muscle fiber orientation relative to B0 was estimated by pennation angle (PA) measurements from DTI, providing orientation-specific extramyocellular lipid (EMCL) chemical shift data that were used for subject-specific IMCL quantification. Vastus lateralis (VL), tibialis anterior (TA) and soleus (SO) muscles of 6 healthy subjects (21-40 yrs) were studied on a Siemens 3T MRI system with a flex 4-channel coil. 1H-MRS were acquired using stimulated echo acquisition mode (STEAM, TR=3s, TE=270ms). DTI was performed using single shot EPI (b=600s/mm2, 30 directions, TR=4.5s, TE=82ms, and ten×5mm slices) with center slice indexed to the MRS voxel. The average PA's measured from ROI analysis of primary eigenvectors were PA=19.46+/-5.43 for unipennate VL, 15.65+/-3.73 for multipennate SO, and 7.04+/-3.34 for bipennate TA. Chemical shift (CS) was calculated using [3cos2θ-1] dependence: 0.17+/-0.02 for VL, 0.18+/-0.01 for SO and 0.19+/-0.004 ppm for TA. IMCL-CH2 concentrations from spectral analysis were 12.77+/-6.3 for VL, 3.07+/-1.63 for SO and 0.27+/-0.08 mmol/kg ww for TA. Small PA's were measured in TA and large CS with clear separation between EMCL and IMCL peaks were observed. Larger variations in PA were measured VL and SO resulting in an increased overlap of the EMCL on IMCL peaks.

  20. 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.

  1. 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.

  2. Linear-scaling method for calculating nuclear magnetic resonance chemical shifts using gauge-including atomic orbitals within Hartree-Fock and density-functional theory.

    PubMed

    Kussmann, Jörg; Ochsenfeld, Christian

    2007-08-07

    Details of a new density matrix-based formulation for calculating nuclear magnetic resonance chemical shifts at both Hartree-Fock and density functional theory levels are presented. For systems with a nonvanishing highest occupied molecular orbital-lowest unoccupied molecular orbital gap, the method allows us to reduce the asymptotic scaling order of the computational effort from cubic to linear, so that molecular systems with 1000 and more atoms can be tackled with today's computers. The key feature is a reformulation of the coupled-perturbed self-consistent field (CPSCF) theory in terms of the one-particle density matrix (D-CPSCF), which avoids entirely the use of canonical MOs. By means of a direct solution for the required perturbed density matrices and the adaptation of linear-scaling integral contraction schemes, the overall scaling of the computational effort is reduced to linear. A particular focus of our formulation is to ensure numerical stability when sparse-algebra routines are used to obtain an overall linear-scaling behavior.

  3. VITAL NMR: Using Chemical Shift Derived Secondary Structure Information for a Limited Set of Amino Acids to Assess Homology Model Accuracy

    SciTech Connect

    Brothers, Michael C; Nesbitt, Anna E; Hallock, Michael J; Rupasinghe, Sanjeewa; Tang, Ming; Harris, Jason B; Baudry, Jerome Y; Schuler, Mary A; Rienstra, Chad M

    2011-01-01

    Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR (SSNMR) data. Such data is obtainable in a rapid manner by simple SSNMR experiments (e.g., (13)C-(13)C 2D correlation spectra). To test our homology model scoring procedure for various amino acid labeling schemes, we generated a library of 7,474 homology models for 22 protein targets culled from the TALOS+/SPARTA+ training set of protein structures. Using subsets of amino acids that are plausibly assigned by SSNMR, we discovered that pairs of the residues Val, Ile, Thr, Ala and Leu (VITAL) emulate an ideal dataset where all residues are site specifically assigned. Scoring the models with a predicted VITAL site-specific dataset and calculating secondary structure with the Chemical Shift Index resulted in a Pearson correlation coefficient (-0.75) commensurate to the control (-0.77), where secondary structure was scored site specifically for all amino acids (ALL 20) using STRIDE. This method promises to accelerate structure procurement by SSNMR for proteins with unknown folds through guiding the selection of remotely homologous protein templates and assessing model quality.

  4. Chemical-shift X-ray standing wavefield determination of the local structure of methanethiolate phases on Ni( 1 1 1 )

    NASA Astrophysics Data System (ADS)

    Fisher, C. J.; Woodruff, D. P.; Jones, R. G.; Cowie, B. C. C.; Formoso, V.

    2002-01-01

    By monitoring the X-ray absorption through the chemically-shifted components of the S 1s photoemission signal, normal-incidence X-ray standing wavefield absorption at the (1 1 1) and ( 1¯ 1 1) scatterer planes has been used to determine the local adsorption geometry of the two distinct methanethiolate (CH 3S-) species which occur on Ni(1 1 1) following exposure to methanethiol. The species which is favoured at low temperatures is found to occupy either mixed hollow or bridge sites on a non-reconstructed Ni(1 1 1) surface, whereas that seen at higher temperatures is shown to involve Ni surface layer reconstruction and the data are consistent with hollow site adsorption on a reduced density outermost Ni layer. The relative merits of alternative reconstruction models based on that which occurs due to methanethiolate adsorption on Cu(1 1 1), or the (5√3×2)rect. phase formed by atomic S on Ni(1 1 1), are discussed. Both of these models are based on local square or `pseudo-(1 0 0)' outermost Ni layers. Co-adsorbed atomic sulphur, to which the methanethiolate species decompose at higher temperatures, appears to occupy mainly fcc hollow sites at low temperatures, but is partially converted to the local geometry of the ordered reconstructed (5√3×2)rect.-S phase after higher temperature annealing.

  5. Measurement of sample temperatures under magic-angle spinning from the chemical shift and spin-lattice relaxation rate of 79Br in KBr powder

    NASA Astrophysics Data System (ADS)

    Thurber, Kent R.; Tycko, Robert

    2009-01-01

    Accurate determination of sample temperatures in solid state nuclear magnetic resonance (NMR) with magic-angle spinning (MAS) can be problematic, particularly because frictional heating and heating by radio-frequency irradiation can make the internal sample temperature significantly different from the temperature outside the MAS rotor. This paper demonstrates the use of 79Br chemical shifts and spin-lattice relaxation rates in KBr powder as temperature-dependent parameters for the determination of internal sample temperatures. Advantages of this method include high signal-to-noise, proximity of the 79Br NMR frequency to that of 13C, applicability from 20 K to 320 K or higher, and simultaneity with adjustment of the MAS axis direction. We show that spin-lattice relaxation in KBr is driven by a quadrupolar mechanism. We demonstrate a simple approach to including KBr powder in hydrated samples, such as biological membrane samples, hydrated amyloid fibrils, and hydrated microcrystalline proteins, that allows direct assessment of the effects of frictional and radio-frequency heating under experimentally relevant conditions.

  6. 1H NMR assignments of apo calcyclin and comparative structural analysis with calbindin D9k and S100 beta.

    PubMed Central

    Potts, B. C.; Carlström, G.; Okazaki, K.; Hidaka, H.; Chazin, W. J.

    1996-01-01

    The homodimeric S100 protein calcyclin has been studied in the apo state by two-dimensional 1H NMR spectroscopy. Using a combination of scalar correlation and NOE experiments, sequence-specific 1H NMR assignments were obtained for all but one backbone and > 90% of the side-chain resonances. To our knowledge, the 2 x 90 residue (20 kDa) calcyclin dimer is the largest protein system for which such complete assignments have been made by purely homonuclear methods. Sequential and medium-range NOEs and slowly exchanging backbone amide protons identified directly the four helices and the short antiparallel beta-type interaction between the two binding loops that comprise each subunit of the dimer. Further analysis of NOEs enabled the unambiguous assignment of 556 intrasubunit distance constraints, 24 intrasubunit hydrogen bonding constraints, and 2 x 26 intersubunit distance constraints. The conformation of the monomer subunit was refined by distance geometry and restrained molecular dynamics calculations using the intrasubunit constraints only. Calculation of the dimer structure starting from this conformational ensemble has been reported elsewhere. The extent of structural homology among the apo calcyclin subunit, the monomer subunit of apo S100 beta, and monomeric apo calbindin D9k has been examined in detail by comparing 1H NMR chemical shifts and secondary structures. This analysis was extended to a comprehensive comparison of the three-dimensional structures of the calcyclin monomer subunit and calbindin D9k, which revealed greater similarity in the packing of their hydrophobic cores than was anticipated previously. Together, these results support the hypothesis that all members of the S100 family have similar core structures and similar modes of dimerization. Analysis of the amphiphilicity of Helix IV is used to explain why calbindin D9k is monomeric, but full-length S100 proteins form homodimers. PMID:8931135

  7. Theoretical and spectroscopic (FT-IR, NMR and UV-Vis.) characterizations of 3-p-chlorobenzyl-4-(4-carboxybenzylidenamino)-4,5-dihydro-1H-1,2,4-triazol-5-one molecule

    NASA Astrophysics Data System (ADS)

    Akyıldırım, Onur; Gökce, Halil; Bahçeli, Semiha; Yüksek, Haydar

    2017-01-01

    Fourier transform infrared (FT-IR) spectroscopy in the region 400-4000 cm-1, proton and carbon-13 NMR chemical shifts and UV-Vis. absorption wavelengths of 3-p-chlorobenzyl-4-(4-carboxybenzylidenamino)-4,5-dihydro-1H-1,2,4-triazol-5-one molecule have been experimentally investigated. For monomeric and dimeric forms of the title molecule, the optimized molecular structure analyses, vibrational wavenumbers, 13C and 1H NMR chemical shifts and electronic absorption wavelengths of the title molecule have been performed at DFT/B3LYP method with 6-311G(d,p) basis set. The HOMO and LUMO analyses have been theoretically done by using the mentioned calculation level. The obtained experimental values have been compared with calculated data. The computed vibrational frequencies, NMR chemical shifts and UV-Vis. wavelengths have been found to be in a good agreement with experimental values and spectral results of similar structures in the literature.

  8. Shifting Attention

    ERIC Educational Resources Information Center

    Ingram, Jenni

    2014-01-01

    This article examines the shifts in attention and focus as one teacher introduces and explains an image that represents the processes involved in a numeric problem that his students have been working on. This paper takes a micro-analytic approach to examine how the focus of attention shifts through what the teacher and students do and say in the…

  9. Structural studies on Desulfovibrio gigas cytochrome c3 by two-dimensional 1H-nuclear-magnetic-resonance spectroscopy.

    PubMed Central

    Piçarra-Pereira, M A; Turner, D L; LeGall, J; Xavier, A V

    1993-01-01

    Several aromatic amino acid residues and haem resonances in the fully reduced form of Desulfovibrio gigas cytochrome c3 are assigned, using two-dimensional 1H n.m.r., on the basis of the interactions between the protons of the aromatic amino acids and the haem protons as well as the intrahaem distances known from the X-ray structure [Kissinger (1989) Ph.D. Thesis, Washington State University]. The interhaem interactions observed in the n.m.r. spectra are in full agreement with the D. gigas X-ray structure and also with the n.m.r. data from Desulfovibrio vulgaris (Hildenborough) [Turner, Salgueiro, LeGall and Xavier (1992) Eur. J. Biochem. 210, 931-936]. The good correlation between the calculated ring-current shifts and the observed chemical shifts strongly supports the present assignments. Observation of the two-dimensional nuclear-Overhauser-enhancement spectra of the protein in the reduced, intermediate and fully oxidized stages led to the ordering of the haems in terms of their midpoint redox potentials and their identification in the X-ray structure. The first haem to oxidize is haem I, followed by haems II, III and IV, numbered according to the Cys ligand positions in the amino acid sequences [Mathews (1985) Prog. Biophys. Mol. Biol. 54, 1-56]. Although the haem core architecture is the same for the different Desulfovibrio cytochromes c3, the order of redox potentials is different. PMID:8397514

  10. Optical, electrochemical, and 1H NMR characteristics of Mono-, Bi-, and tetranuclear cyclopalladated complexes with 4,4'-bipyridyl

    NASA Astrophysics Data System (ADS)

    Panova, A. G.; Puzyk, M. V.; Farus, O. A.; Balashev, K. P.

    2011-03-01

    The [Pd(C∧N)(4,4'-bpy)Cl], [Pd(C∧N)NO3]2(μ-4,4'-bpy) and [Pd(C∧N)(μ-4,4'-bpy)]4(NO3)4 complexes (C∧N- are deprotonated forms of 2-phenylpyridine (ppy), 2-(2''-thienyl)pyridine (tpy), and 2-phenylbenzothiazole (bt); bpy is 4,4' bipyridyl) are synthesized and characterized by 1H NMR spectroscopy, electronic absorption and emission spectroscopy, and cyclic voltammetry. The upfield shifts of the chemical shift of a proton in the ortho-position to the donor carbon atom of the cyclopalladated ligand of complexes (Δδ = -(1.1-1.5) ppm) is assigned to the anisotropic effect of the circular current of the pyridine rings of 4,4'-bipyridyl orthogonal to the coordination plane. The characteristic long-wavelength absorption and phosphorescence bands of the complexes are assigned to the chromophore metal-complex fragment {M(C∧N)}. The quasi-reversible reduction waves of complexes are assigned to the ligand-centered processes of successive electron transfer to the π*-orbitals localized mainly on the coordinated pyridine components of 4,4'-bipyridyl.

  11. Structural studies on Desulfovibrio gigas cytochrome c3 by two-dimensional 1H-nuclear-magnetic-resonance spectroscopy.

    PubMed

    Piçarra-Pereira, M A; Turner, D L; LeGall, J; Xavier, A V

    1993-09-15

    Several aromatic amino acid residues and haem resonances in the fully reduced form of Desulfovibrio gigas cytochrome c3 are assigned, using two-dimensional 1H n.m.r., on the basis of the interactions between the protons of the aromatic amino acids and the haem protons as well as the intrahaem distances known from the X-ray structure [Kissinger (1989) Ph.D. Thesis, Washington State University]. The interhaem interactions observed in the n.m.r. spectra are in full agreement with the D. gigas X-ray structure and also with the n.m.r. data from Desulfovibrio vulgaris (Hildenborough) [Turner, Salgueiro, LeGall and Xavier (1992) Eur. J. Biochem. 210, 931-936]. The good correlation between the calculated ring-current shifts and the observed chemical shifts strongly supports the present assignments. Observation of the two-dimensional nuclear-Overhauser-enhancement spectra of the protein in the reduced, intermediate and fully oxidized stages led to the ordering of the haems in terms of their midpoint redox potentials and their identification in the X-ray structure. The first haem to oxidize is haem I, followed by haems II, III and IV, numbered according to the Cys ligand positions in the amino acid sequences [Mathews (1985) Prog. Biophys. Mol. Biol. 54, 1-56]. Although the haem core architecture is the same for the different Desulfovibrio cytochromes c3, the order of redox potentials is different.

  12. Protonation of carbon single-walled nanotubes studied using 13C and 1H-13C cross polarization nuclear magnetic resonance and Raman spectroscopies.

    PubMed

    Engtrakul, Chaiwat; Davis, Mark F; Gennett, Thomas; Dillon, Anne C; Jones, Kim M; Heben, Michael J

    2005-12-14

    The reversible protonation of carbon single-walled nanotubes (SWNTs) in sulfuric acid and Nafion was investigated using solid-state nuclear magnetic resonance (NMR) and Raman spectroscopies. Magic-angle spinning (MAS) was used to obtain high-resolution 13C and 1H-13C cross polarization (CP) NMR spectra. The 13C NMR chemical shifts are reported for bulk SWNTs, H2SO4-treated SWNTs, SWNT-Nafion polymer composites, SWNT-AQ55 polymer composites, and SWNTs in contact with water. Protonation occurs without irreversible oxidation of the nanotube substrate via a charge-transfer process. This is the first report of a chemically induced change in a SWNT 13C resonance brought about by a reversible interaction with an acidic proton, providing additional evidence that carbon nanotubes behave as weak bases. Cross polarization was found to be a powerful technique for providing an additional contrast mechanism for studying nanotubes in contact with other chemical species. The CP studies confirmed polarization transfer from nearby protons to nanotube carbon atoms. The CP technique was also applied to investigate water adsorbed on carbon nanotube surfaces. Finally, the degree of bundling of the SWNTs in Nafion films was probed with the 1H-13C CP-MAS technique.

  13. Synthesis, crystal structures and theoretical calculations of new 1-[2-(5-chloro-2-benzoxazolinone-3-yl)acetyl]-3,5-diphenyl-4,5-dihydro-(1H)-pyrazoles

    NASA Astrophysics Data System (ADS)

    Gökşen, Umut Salgın; Alpaslan, Yelda Bingöl; Kelekçi, Nesrin Gökhan; Işık, Şamil; Ekizoğlu, Melike

    2013-05-01

    1-[2-(5-Chloro-2-benzoxazolinone-3-yl)acetyl]-3-phenyl-5-(3-methoxyphenyl)-4,5-dihydro-(1H)-pyrazole (5a), 1-[2-(5-chloro-2-benzoxazolinone-3-yl)acetyl]-3-phenyl-5-(3,4-dimethoxyphenyl)-4,5-dihydro-(1H)-pyrazole (5b) and 1-[2-(5-chloro-2-benzoxazolinone-3-yl)acetyl]-3-(4-methylphenyl)-5-(2,3-dimethoxyphenyl)-4,5-dihydro-(1H)-pyrazole (5c) were synthesized. The crystal and molecular structures of the compounds 5a, 5b and 5c were determined by elemental analyses, IR, 1H NMR, ESI-MS and single-crystal X-ray diffraction. DFT method with 6-31G(d,p) basis set was used to calculate the optimized geometrical parameters, vibrational frequencies and chemical shift values. The calculated vibrational frequencies and chemical shift values were compared with experimental IR and 1H NMR values. The results represented that there was a good agreement between experimental and calculated values of the compounds 5a-5c. In addition, DFT calculations of the compounds, molecular electrostatic potentials (MEPs) and frontier molecular orbitals were performed at B3LYP/6-31G(d,p) level of theory. Furthermore, compounds were tested against three Gram-positive bacteria: Staphylococcus aureus ATCC 29213 (American Type Culture Collection), methicillin resistant S. aureus (MRSA) ATCC 43300 and Enterococcus faecalis ATCC 29212; two Gram negative bacteria: Escherichia coli ATCC 25922 and Pseudomonas aeruginosa ATCC 27853; and three fungi: Candida albicans ATCC 90028, Candida krusei ATCC 6258 and Candida parapsilosis ATCC 90018. In general, all of the compounds were found to be slightly active against tested microorganisms.

  14. Muscle metabolism and activation heterogeneity by combined 31P chemical shift and T2 imaging, and pulmonary O2 uptake during incremental knee-extensor exercise.

    PubMed

    Cannon, Daniel T; Howe, Franklyn A; Whipp, Brian J; Ward, Susan A; McIntyre, Dominick J; Ladroue, Christophe; Griffiths, John R; Kemp, Graham J; Rossiter, Harry B

    2013-09-01

    The integration of skeletal muscle substrate depletion, metabolite accumulation, and fatigue during large muscle-mass exercise is not well understood. Measurement of intramuscular energy store degradation and metabolite accumulation is confounded by muscle heterogeneity. Therefore, to characterize regional metabolic distribution in the locomotor muscles, we combined 31P magnetic resonance spectroscopy, chemical shift imaging, and T2-weighted imaging with pulmonary oxygen uptake during bilateral knee-extension exercise to intolerance. Six men completed incremental tests for the following: (1) unlocalized 31P magnetic resonance spectroscopy; and (2) spatial determination of 31P metabolism and activation. The relationship of pulmonary oxygen uptake to whole quadriceps phosphocreatine concentration ([PCr]) was inversely linear, and three of four knee-extensor muscles showed activation as assessed by change in T2. The largest changes in [PCr], [inorganic phosphate] ([Pi]) and pH occurred in rectus femoris, but no voxel (72 cm3) showed complete PCr depletion at exercise cessation. The most metabolically active voxel reached 11 ± 9 mM [PCr] (resting, 29 ± 1 mM), 23 ± 11 mM [Pi] (resting, 7 ± 1 mM), and a pH of 6.64 ± 0.29 (resting, 7.08 ± 0.03). However, the distribution of 31P metabolites and pH varied widely between voxels, and the intervoxel coefficient of variation increased between rest (∼10%) and exercise intolerance (∼30-60%). Therefore, the limit of tolerance was attained with wide heterogeneity in substrate depletion and fatigue-related metabolite accumulation, with extreme metabolic perturbation isolated to only a small volume of active muscle (<5%). Regional intramuscular disturbances are thus likely an important requisite for exercise intolerance. How these signals integrate to limit muscle power production, while regional "recruitable muscle" energy stores are presumably still available, remains uncertain.

  15. An optimized method for NMR-based plant seed metabolomic analysis with maximized polar metabolite extraction efficiency, signal-to-noise ratio, and chemical shift consistency.

    PubMed

    Wu, Xiangyu; Li, Ning; Li, Hongde; Tang, Huiru

    2014-04-07

    Plant metabolomic analysis has become an essential part of functional genomics and systems biology and requires effective extraction of both primary and secondary metabolites from plant cells. To establish an optimized extraction method for the NMR-based analysis, we used the seeds of mungbean (Vigna radiata cv. Elü no. 1) as a model and systematically investigated the dependence of the metabolite composition in plant extracts on various extraction parameters including cell-breaking methods, extraction solvents, number of extraction repeats, tissue-to-solvent ratio, and extract-to-buffer ratio (for final NMR analysis). We also compared two NMR approaches for quantitative metabolomic analysis from completely relaxed spectra directly and from partially relaxed spectra calculated with T1. By maximizing the extraction efficiency and signal-to-noise ratio but minimizing inter-sample chemical-shift variations and metabolite degradations, we established a parameter-optimized protocol for NMR-based plant seed metabolomic analysis. We concluded that aqueous methanol was the best extraction solvent with an optimal tissue-to-solvent ratio of about 1 : 10-1 : 15 (mg per μL). The combination of tissuelyser homogenization with ultrasonication was the choice of cell-breaking method with three repeated extractions being necessary. For NMR analysis, the optimal extract-to-solvent was around 5-8 mg mL(-1) and completely relaxed spectra were ideal for intrinsically quantitative metabolomic analysis although partially relaxed spectra were employable for comparative metabolomics. This optimized method will offer ensured data quality for high-throughput and reliable plant metabolomics studies.

  16. Comparison of accelerated 3-D spiral chemical shift imaging and single-voxel spectroscopy at 3T in the pediatric age group.

    PubMed

    Yazbek, Sandrine; Prabhu, Sanjay P; Connaughton, Pauline; Grant, Patricia E; Gagoski, Borjan

    2015-08-01

    Single-voxel spectroscopy (SVS) is usually used in the pediatric population when a short acquisition time is crucial. To overcome the long acquisition time of 3-D phase-encoded chemical shift imaging (CSI) and lack of spatial coverage of single-voxel spectroscopy, efficient encoding schemes using spiral k-space trajectories have been successfully deployed, enabling acquisition of volumetric CSI in <5 min. We assessed feasibility of using 3-D spiral CSI sequence routinely in pediatric clinical settings by comparing its reconstructed spectra against SVS spectra. Volumetric spiral CSI obtained spectra from 2-cc isotropic voxels over a 16×16×10-cm region. SVS acquisition encoded a 3.4-cc (1.5-mm) isotropic voxel. Acquisition time was 3 min for every technique. Data were gathered prospectively from 11 random pediatric patients. Spectra from left basal ganglia were obtained using both techniques and were processed with post-processing software. The following metabolite ratios were calculated: N-acetylaspartate/creatine (NAA/Cr), choline/creatine (Cho/Cr), lactate/creatine (Lac/Cr) and N-acetylapartate/choline (NAA/Cho). We collected data on 11 children ages 4 days to 10 years. In 10/11 cases, spectral quality of both methods was acceptable. Considering 10/11 cases, we found a statistically significant difference between SVS and 3-D spiral CSI for all three ratios. However, this difference was fixed and was probably caused by a fixed bias. This means that 3-D spiral CSI can be used instead of SVS by removing the mean difference between the methods for each ratio. Accelerated 3-D CSI is feasible in pediatric patients and can potentially substitute for SVS.

  17. 1H and 13C NMR assignments for two new angular furanocoumarin glycosides from Peucedanum praeruptorum.

    PubMed

    Chang, Haitao; Okada, Yoshihito; Okuyama, Toru; Tu, Pengfei

    2007-07-01

    Two novel angular-type furanocoumarin glycosides, peucedanoside A (1) and peucedanoside B (2), along with a known compound apterin (3), were isolated from the roots of Peucedanum praeruptorum Dunn. Their chemical structures were determined by MS, NMR spectroscopy and chemical analysis. Complete assignments of the 1H and 13C NMR spectroscopic data were achieved by 1D and 2D NMR experiments including DEPT, HSQC, HMBC and ROESY.

  18. Molecular structure, spectroscopic characterization and DFT calculations of a novel (Z)-1-[(2-Ethylphenylamino)methylene]naphthalene-2(1H)-one

    NASA Astrophysics Data System (ADS)

    Alpaslan, Yelda Bingöl; Gökce, Halil; Macit, Mustafa; Alpaslan, Gökhan; Özdemir, Namık

    2015-09-01

    A novel Schiff base compound (Z)-1-[(2-Ethylphenylamino)methylene]naphthalene-2(1H)-one was synthesized from the reaction of 2-hydroxy-1-naphthaldehyde with 2-ethylaniline. The structural properties of the compound have been characterized by using FT-IR, 1H and 13C NMR, UV-vis and X-ray single-crystal methods. According to X-ray diffraction result, the title compound exists in the keto-amine tautomeric form. The molecular geometry, vibrational frequencies, electronic absorption spectra and gauge including atomic orbital (GIAO) 1H and 13C NMR chemical shift values of the title compound in the ground state have been calculated by using density functional theory (DFT/B3LYP) method with 6-311G++(d,p) basis set, and compared with the experimental data. The obtained results indicate that optimized geometry can well reflect the crystal structural parameters. The theoretical values are in good agreement with the experimental ones. The energetic behavior of the compound in solvent media has been examined using B3LYP method with the 6-311G++(d,p) basis set by applying the polarizable continuum model (PCM). The total energy of the compound decreases with increasing polarity of the solvent. The molecular electrostatic potential (MEP), HOMO-LUMO energy gap and non-linear optical (NLO) properties of the compound were investigated using theoretical calculations.

  19. Spectroscopic characterization and density functional studies of (Z)-1-[(2-methoxy-5-(trifluoromethyl)phenylamino)methylene]naphthalene-2(1H)-one

    NASA Astrophysics Data System (ADS)

    Alpaslan, Yelda Bingöl; Gökce, Halil; Alpaslan, Gökhan; Macit, Mustafa

    2015-10-01

    In the current work, the Schiff base compound (Z)-1-[(2-Methoxy-5-(trifluoromethyl)phenylamino)methylene]naphthalene-2(1H)-one (I) has been characterized by using 13C NMR, 1H NMR, FT-IR and UV-vis spectroscopic techniques. Molecular geometry of the compound I in the ground state, vibrational frequencies, electronic absorption spectra and gauge including atomic orbital (GIAO) 1H and 13C NMR chemical shift values have been calculated by using the density functional method (DFT) with 6-311++G(d,p) basis set and compared with the experimental data. The optimized geometric parameters obtained by using DFT (B3LYP/6-311++G(d,p)) show good agreement with the experimental data. The vibrational frequencies were determined based on the recorded FT-IR spectra in the range of 4000-400 cm-1 for solid state. Using the TD-DFT method, electronic absorption spectra of the compound I have been predicted and good agreement is determined with the experimental ones. In addition, molecular electrostatic potential (MEP), frontier molecular orbital analysis (HOMO-LUMO), non-linear optical (NLO) properties, NBO analysis and NBO atomic charges of the compound I were investigated using same theoretical calculations.

  20. Theoretical and experimental study of inclusion complexes formed by isoniazid and modified β-cyclodextrins: 1H NMR structural determination and antibacterial activity evaluation.

    PubMed

    Teixeira, Milena G; de Assis, João V; Soares, Cássia G P; Venâncio, Mateus F; Lopes, Juliana F; Nascimento, Clebio S; Anconi, Cleber P A; Carvalho, Guilherme S L; Lourenço, Cristina S; de Almeida, Mauro V; Fernandes, Sergio A; de Almeida, Wagner B

    2014-01-09

    Me-β-cyclodextrin (Me-βCD) and HP-β-cyclodextrin (HP-βCD) inclusion complexes with isoniazid (INH) were prepared with the aim of modulating the physicochemical and biopharmaceutical properties of the guest molecule, a well-known antibuberculosis drug. The architectures of the complexes were initially proposed according to NMR data Job plot and ROESY followed by density functional theory (DFT) calculations of (1)H NMR spectra using the PBE1PBE functional and 6-31G(d,p) basis set, including the water solvent effect with the polarizable continuum model (PCM), for various inclusion modes, providing support for the experimental proposal. An analysis of the (1)H NMR chemical shift values for the isoniazid (H6',8' and H5',9') and cyclodextrins (H3,5) C(1)H hydrogens, which are known to be very adequately described by the DFT methodology, revealed them to be extremely useful, promptly confirming the inclusion complex formation. An included mode which describes Me-βCD partially enclosing the hydrazide group of the INH is predicted as the most favorable supramolecular structure that can be used to explain the physicochemical properties of the encapsulated drug. Antibacterial activity was also evaluated, and the results indicated the inclusion complexes are a potential strategy for tuberculosis treatment.

  1. Preliminary 1H NMR study on archaeological waterlogged wood.

    PubMed

    Maccotta, Antonella; Fantazzini, Paola; Garavaglia, Carla; Donato, Ines D; Perzia, Patrizia; Brai, Maria; Morreale, Filippa

    2005-01-01

    Magnetic Resonance Relaxation (MRR) and Magnetic Resonance Imaging (MRI) are powerful tools to obtain detailed information on the pore space structure that one is unlikely to obtain in other ways. These techniques are particularly suitable for Cultural Heritage materials, because they use water 1H nuclei as a probe. Interaction with water is one of the main causes of deterioration of materials. Porous structure in wood, for example, favours the penetration of water, which can carry polluting substances and promote mould growth. A particular case is waterlogged wood from underwater discoveries and moist sites; in fact, these finds are very fragile because of chemical, physical and biological decay from the long contact with the water. When wood artefacts are brought to the surface and directly dried in air, there is the collapse of the cellular structures, and wood loses its original form and dimensions and cannot be used for study and museum exhibits. In this work we have undertaken the study of some wood finds coming from Ercolano's harbour by MRR and MRI under different conditions, and we have obtained a characterization of pore space in wood and images of the spatial distribution of the confined water in the wood.

  2. Vibrational (FT-IR and FT-Raman), electronic (UV-Vis), NMR (1H and 13C) spectra and reactivity analyses of 4,5-dimethyl-o-phenylenediamine

    NASA Astrophysics Data System (ADS)

    Atac, Ahmet; Karaca, Caglar; Gunnaz, Salih; Karabacak, Mehmet

    2014-09-01

    The structure of 4,5-dimethyl-o-phenylenediamine (C8H12N2, DMPDA) was investigated on the basis of spectroscopic data and theoretical calculations. The sterochemical structure was determined by FT-IR, FT-Raman, UV, 1H and 13C NMR spectra. An experimental study and a theoretical analysis were associated by using the B3LYP method with Gaussian09 package program. FT-IR and FT-Raman spectra were recorded in the region of 4000-400 cm-1 and 4000-10 cm-1, respectively. The vibrational spectra were calculated by DFT method and the fundamental vibrations were assigned on the basis of the total energy distribution (TED), calculated with scaled quantum mechanics (SQM) method with Parallel Quantum Solutions (PQS) program. The UV absorption spectrum of the compound that dissolved in ethanol solution were recorded in the range of 190-400 nm. Total density of state (TDOS) and partial density of state (PDOS) of the DMPDA in terms of HOMOs and LUMOs were calculated and analyzed. Chemical shifts were reported in ppm relative to tetramethylsilane (TMS) for 1H and 13C NMR spectra. The compound was dissolved in dimethyl sulfoxide (DMSO). Also, 1H and 13C chemical shifts calculated using the gauge independent atomic orbital (GIAO) method. Mullikan atomic charges and other thermo-dynamical parameters were investigated with the help of B3LYP (DFT) method using 6-311++G** basis set. On the basis of the thermodynamic properties of the title compound at different temperatures have been carried out, revealing the correlations between heat capacity (C), entropy (S), enthalpy changes (H) and temperatures. The optimized bond lengths, bond angles, chemical shifts and vibrational wavenumbers showed the best agreement with the experimental results.

  3. Vibrational (FT-IR and FT-Raman), electronic (UV-Vis), NMR (1H and 13C) spectra and reactivity analyses of 4,5-dimethyl-o-phenylenediamine.

    PubMed

    Atac, Ahmet; Karaca, Caglar; Gunnaz, Salih; Karabacak, Mehmet

    2014-09-15

    The structure of 4,5-dimethyl-o-phenylenediamine (C8H12N2, DMPDA) was investigated on the basis of spectroscopic data and theoretical calculations. The sterochemical structure was determined by FT-IR, FT-Raman, UV, 1H and 13C NMR spectra. An experimental study and a theoretical analysis were associated by using the B3LYP method with Gaussian09 package program. FT-IR and FT-Raman spectra were recorded in the region of 4000-400 cm(-1) and 4000-10 cm(-1), respectively. The vibrational spectra were calculated by DFT method and the fundamental vibrations were assigned on the basis of the total energy distribution (TED), calculated with scaled quantum mechanics (SQM) method with Parallel Quantum Solutions (PQS) program. The UV absorption spectrum of the compound that dissolved in ethanol solution were recorded in the range of 190-400 nm. Total density of state (TDOS) and partial density of state (PDOS) of the DMPDA in terms of HOMOs and LUMOs were calculated and analyzed. Chemical shifts were reported in ppm relative to tetramethylsilane (TMS) for 1H and 13C NMR spectra. The compound was dissolved in dimethyl sulfoxide (DMSO). Also, 1H and 13C chemical shifts calculated using the gauge independent atomic orbital (GIAO) method. Mullikan atomic charges and other thermo-dynamical parameters were investigated with the help of B3LYP (DFT) method using 6-311++G** basis set. On the basis of the thermodynamic properties of the title compound at different temperatures have been carried out, revealing the correlations between heat capacity (C), entropy (S), enthalpy changes (H) and temperatures. The optimized bond lengths, bond angles, chemical shifts and vibrational wavenumbers showed the best agreement with the experimental results.

  4. Cardiac High-Energy Phosphate Metabolism Alters with Age as Studied in 196 Healthy Males with the Help of 31-Phosphorus 2-Dimensional Chemical Shift Imaging

    PubMed Central

    Esterhammer, Regina; Klug, Gert; Wolf, Christian; Mayr, Agnes; Reinstadler, Sebastian; Feistritzer, Hans-Josef; Metzler, Bernhard; Schocke, Michael F. H.

    2014-01-01

    Recently published studies have elucidated alterations of mitochondrial oxidative metabolism during ageing. The intention of the present study was to evaluate the impact of ageing on cardiac high-energy phosphate metabolism and cardiac function in healthy humans. 31-phosphorus 2-dimensional chemical shift imaging (31P 2D CSI) and echocardiography were performed in 196 healthy male volunteers divided into groups of 20 to 40 years (I, n = 43), 40 to 60 years (II, n = 123) and >60 years (III, n = 27) of age. Left ventricular PCr/β-ATP ratio, myocardial mass (MM), ejection fraction and E/A ratio were assessed. Mean PCr/β-ATP ratios were significantly different among the three groups of volunteers (I, 2.10±0.37; II, 1.77±0.37; III, 1.45±0.28; all p<0.001). PCr/β-ATP ratios were inversely related to age (r2 = −0.25; p<0.001) with a decrease from 2.65 by 0.02 per year of ageing. PCr/β-ATP ratios further correlated with MM (r = −0.371; p<0.001) and E/A ratios (r = 0.213; p<0.02). Moreover, E/A ratios (r = −0.502, p<0.001), MM (r = 0.304, p<0.001), glucose-levels (r = 0.157, p<0.05) and systolic blood pressure (r = 0.224, p<0.005) showed significant correlations with age. The ejection fraction did not significantly differ between the groups. This study shows that cardiac PCr/β-ATP ratios decrease moderately with age indicating an impairment of mitochondrial oxidative metabolism due to age. Furthermore, MM increases, and E/A ratio decreases with age. Both correlate with left-ventricular PCr/β-ATP ratios. The findings of the present study confirm numerous experimental studies showing an impairment of cardiac mitochondrial function with age. PMID:24940736

  5. J-edited pure shift NMR for the facile measurement of (n)J(HH) for specific protons.

    PubMed

    Chaudhari, Sachin Rama; Suryaprakash, N

    2015-04-07

    We report a novel 1D J-edited pure shift NMR experiment (J-PSHIFT) that was constructed from a pseudo 2D experiment for the direct measurement of proton-proton scalar couplings. The experiment gives homonuclear broad-band (1)H-decoupled (1)H NMR spectra, which provide a single peak for chemically distinct protons, and only retain the homonuclear-scalar-coupled doublet pattern at the chemical-shift positions of the protons in the coupled network of a specific proton. This permits the direct and unambiguous measurement of the magnitudes of the couplings. The incorporation of a 1D selective correlation spectroscopy (COSY)/ total correlation spectroscopy (TOCSY) block in lieu of the initial selective pulse, results in the exclusive detection of the correlated spectrum of a specific proton.

  6. Fluid Shifts

    NASA Technical Reports Server (NTRS)

    Stenger, M. B.; Hargens, A.; Dulchavsky, S.; Ebert, D.; Lee, S.; Laurie, S.; Garcia, K.; Sargsyan, A.; Martin, D.; Lui, J.; Macias, B.; Arbeille, P.; Danielson, R.; Chang, D.; Gunga, H.; Johnston, S.; Westby, C.; Ribeiro, L.; Ploutz-Snyder, R.; Smith, S.

    2015-01-01

    INTRODUCTION: Mechanisms responsible for the ocular structural and functional changes that characterize the visual impairment and intracranial pressure (ICP) syndrome (VIIP) are unclear, but hypothesized to be secondary to the cephalad fluid shift experienced in spaceflight. This study will relate the fluid distribution and compartmentalization associated with long-duration spaceflight with VIIP symptoms. We also seek to determine whether the magnitude of fluid shifts during spaceflight, as well as the VIIP-related effects of those shifts, can be predicted preflight with acute hemodynamic manipulations, and also if lower body negative pressure (LBNP) can reverse the VIIP effects. METHODS: Physiologic variables will be examined pre-, in- and post-flight in 10 International Space Station crewmembers including: fluid compartmentalization (D2O and NaBr dilution); interstitial tissue thickness (ultrasound); vascular dimensions and dynamics (ultrasound and MRI (including cerebrospinal fluid pulsatility)); ocular measures (optical coherence tomography, intraocular pressure, ultrasound); and ICP measures (tympanic membrane displacement, otoacoustic emissions). Pre- and post-flight measures will be assessed while upright, supine and during 15 deg head-down tilt (HDT). In-flight measures will occur early and late during 6 or 12 month missions. LBNP will be evaluated as a countermeasure during HDT and during spaceflight. RESULTS: The first two crewmembers are in the preflight testing phase. Preliminary results characterize the acute fluid shifts experienced from upright, to supine and HDT postures (increased stroke volume, jugular dimensions and measures of ICP) which are reversed with 25 millimeters Hg LBNP. DISCUSSION: Initial results indicate that acute cephalad fluid shifts may be related to VIIP symptoms, but also may be reversible by LBNP. The effect of a chronic fluid shift has yet to be evaluated. Learning Objectives: Current spaceflight VIIP research is described

  7. Structural study of (±) ethyl 3-acyloxy-1-azabicyclo[2.2.2]octane-3-carboxylates by 1H, 13C NMR spectroscopy, X-ray crystallography and DFT calculations

    NASA Astrophysics Data System (ADS)

    Arias-Pérez, M. S.; Cosme, A.; Gálvez, E.; Morreale, A.; Sanz-Aparicio, J.; Fonseca, I.

    2006-05-01

    1H, 13C NMR spectroscopy and DFT/B3LYP calculations were applied to investigate the conformational preferences of the ethoxycarbonyl and acyloxy groups of some α-acyloxyesters derived from (±) ethyl 3-hydroxy-1-azabicyclo[2.2.2]octane-3-carboxylate. The crystal structure of (±) ethyl 3-diphenylacetoxy-1-azabicyclo[2.2.2]octane-3-carboxylate was determined by X-ray diffraction. To correlate between calculated conformations and the structure in solution, NMR chemical shifts calculations were also performed using the GIAO approach. It has been found that the lowest energetic conformer computed gives the greatest correspondance with experimental solution and solid state data.

  8. Arginine Interactions with Anatase TiO2 (100) Surface and the Perturbation of 49Ti NMR Chemical Shifts - A DFT Investigation: Relevance to Renu-Seeram Bio Solar Cell

    SciTech Connect

    Koch, Rainer; Lipton, Andrew S.; Filipek, S.; Renugopalakrishnan, Venkatesan M.

    2011-06-01

    Density functional theoretical calculations have been utilized to investigate the interaction of the amino acid arginine with the (100) surface of anatase and the reproduction of experimentally measured 49Ti NMR chemical shifts of anatase. Significant binding of arginine through electrostatic interaction and hydrogen bonds of the arginine guanidinium protons to the TiO2 surface oxygen atoms is observed, allowing attachment of proteins to titania surfaces in the construction of bio-sensitized solar cells. GIAO-B3LYP/6-31G(d) NMR calculation of a three-layer model based on the experimental structure of this TiO2 modification gives an excellent reproduction of the experimental value (-927 ppm) within +/- 7 ppm, however, the change in relative chemical shifts, EFGs and CSA suggest that the effect of the electrostatic arginine binding might be too small for experimental detection.

  9. Theoretical and experimental investigations on molecular structure of 7-Chloro-9-phenyl-2,3-dihydroacridin-4(1H)-one with cytotoxic studies

    NASA Astrophysics Data System (ADS)

    Satheeshkumar, Rajendran; Shankar, Ramasamy; Kaminsky, Werner; Kalaiselvi, Sivalingam; Padma, Viswanadha Vijaya; Rajendra Prasad, Karnam Jayarampillai

    2016-04-01

    7-Chloro-9-phenyl-2,3-dihydroacridin-4(1H)-one (3) is synthesized from 2-amino-5-chlorobenzophenone (1) and 1,2-cyclohexanedione (2) in the presence of catalyst InCl3. FT-IR, FT-Raman and FT-NMR spectra of molecule 3 have been recorded and the structure was confirmed by single crystal X-ray diffraction. CDCl3 and DMSO-d6 FT-NMR spectra and 1H and 13C NMR chemical shifts have been measured in molecule 3 and calculated at the B3LYP/6-311G (d,p) and MO6-2x/6-311G (d,p) levels of theory. Similarly calculated vibrational frequencies were found in good agreement with experimental findings. The optimized geometry of molecule 3 was compared with experimental XRD values. DFT calculations of the molecular electrostatic potential (MEP) and HOMO - LUMO frontier orbitals identified chemically active sites of molecule 3 responsible for its bioactivity. The title compound, 3 exhibits higher cytotoxicity in Human breast cancer cells (MCF-7) compared to human lung adenocarcinoma cells (A549).

  10. Synthesis and spectroscopic characterization on 4-(2,5-di-2-thienyl-1H-pyrrol-1-yl) benzoic acid: A DFT approach.

    PubMed

    Kurt, M; Sas, E Babur; Can, M; Okur, S; Icli, S; Demic, S; Karabacak, M; Jayavarthanan, T; Sundaraganesan, N

    2016-01-05

    A complete structural and vibrational analysis of the 4-(2,5-di-2-thienyl-1H-pyrrol-1-yl) benzoic acid (TPBA), was carried out by ab initio calculations, at the density functional theory (DFT) method. Molecular geometry, vibrational wavenumbers and gauge including atomic orbital (GIAO) (13)C NMR and (1)H NMR chemical shift values of (TPBA), in the ground state have been calculated by using ab initio density functional theory (DFT/B3LYP) method with 6-311G(d,p) as basis set for the first time. Comparison of the observed fundamental vibrational modes of (TPBA) and calculated results by DFT/B3LYP method indicates that B3LYP level of theory giving yield good results for quantum chemical studies. Vibrational wavenumbers obtained by the DFT/B3LYP method are in good agreement with the experimental data. The study was complemented with a natural bond orbital (NBO) analysis, to evaluate the significance of hyperconjugative interactions and electrostatic effects on such molecular structure. By using TD-DFT method, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD-DFT method and the experimental one is determined. In addition, the molecular electrostatic potential (MEP), frontier molecular orbitals analysis and thermodynamic properties of TPBA were investigated using theoretical calculations.

  11. Joint Experimental and Computational 17O and 1H Solid State NMR Study of Ba2In2O4(OH)2 Structure and Dynamics

    PubMed Central

    2015-01-01

    A structural characterization of the hydrated form of the brownmillerite-type phase Ba2In2O5, Ba2In2O4(OH)2, is reported using experimental multinuclear NMR spectroscopy and density functional theory (DFT) energy and GIPAW NMR calculations. When the oxygen ions from H2O fill the inherent O vacancies of the brownmillerite structure, one of the water protons remains in the same layer (O3) while the second proton is located in the neighboring layer (O2) in sites with partial occupancies, as previously demonstrated by Jayaraman et al. (Solid State Ionics2004, 170, 25−32) using X-ray and neutron studies. Calculations of possible proton arrangements within the partially occupied layer of Ba2In2O4(OH)2 yield a set of low energy structures; GIPAW NMR calculations on these configurations yield 1H and 17O chemical shifts and peak intensity ratios, which are then used to help assign the experimental MAS NMR spectra. Three distinct 1H resonances in a 2:1:1 ratio are obtained experimentally, the most intense resonance being assigned to the proton in the O3 layer. The two weaker signals are due to O2 layer protons, one set hydrogen bonding to the O3 layer and the other hydrogen bonding alternately toward the O3 and O1 layers. 1H magnetization exchange experiments reveal that all three resonances originate from protons in the same crystallographic phase, the protons exchanging with each other above approximately 150 °C. Three distinct types of oxygen atoms are evident from the DFT GIPAW calculations bare oxygens (O), oxygens directly bonded to a proton (H-donor O), and oxygen ions that are hydrogen bonded to a proton (H-acceptor O). The 17O calculated shifts and quadrupolar parameters are used to assign the experimental spectra, the assignments being confirmed by 1H–17O double resonance experiments. PMID:26321789

  12. Infrared, Raman and NMR spectra, conformational stability, normal coordinate analysis and B3LYP calculations of 5-Amino-3-methyl-1-phenyl-1H-pyrazole-4-carbaldehyde

    NASA Astrophysics Data System (ADS)

    Bahgat, Khaled; EL-Emary, Talaat

    2013-02-01

    FT Raman and IR spectra of the crystallized biologically active molecule, 5-Amino-3-methyl-1-phenyl-1H-pyrazole-4-carbaldehyde (5-APHC, C11H11N3O) have been recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational frequencies of 5-APHC have been investigated with the help of B3LYP density functional theory (DFT) method with 6-31G(d) and 6-311+G(d,p) as basis set. The calculated molecular geometry has been compared with the experimental data. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis (NCA) following the scaled quantum mechanical force field (SQM) technique. The optimized geometry shows the co-planarity of the aldehyde group with pyrazole ring. Potential energy surface (PES) scan studies has also been carried out by ab initio calculations with B3LYP/6-311+G(d,p) basis set. The red shifting of NH2 stretching wavenumber indicates the formation of N-H⋯O hydrogen bonding. 1H and 13C NMR spectra were recorded and 1H and 13C nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. UV-Vis spectrum of the compound was recorded in the region 200-400 nm and the electronic properties HOMO and LUMO energies were calculated by time-dependent TD-DFT approach. Mulliken charges of the 5-APHC molecule was also calculated and interpreted.

  13. 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].

  14. Proton Resonance Frequency Chemical Shift Thermometry: Experimental Design and Validation Towards High-Resolution Non-Invasive Temperature Monitoring, and in vivo Experience in a Non-human Primate Model of Acute Ischemic Stroke

    PubMed Central

    Dehkharghani, Seena; Mao, Hui; Howell, Leonard; Zhang, Xiaodong; Pate, K S; Magrath, P R; Tong, Frank; Wei, L; Qiu, D; Fleischer, C; Oshinski, J N

    2016-01-01

    BACKGROUND AND PURPOSE Applications for non-invasive biological temperature monitoring are widespread in biomedicine, and of particular interest in the context of brain temperature regulation, where traditionally costly and invasive monitoring schemes limit their applicability in many settings. Brain thermal regulation therefore remains controversial, motivating the development of non-invasive approaches such as temperature-sensitive NMR phenomena. The purpose of this work was to compare the utility of competing approaches to MR thermometry (MRT) employing proton resonance frequency chemical shift. Three methodologies were tested, hypothesizing the feasibility of a fast and accurate approach to chemical shift thermometry, in a phantom study at 3.0 Tesla. MATERIALS AND METHODS A conventional, paired approach (DIFF-1), an accelerated single-scan approach (DIFF-2), and a new, further accelerated strategy (DIFF-3) were tested. Phantom temperatures were modulated during real-time fiber optic temperature monitoring, with MRT derived simultaneously from temperature-sensitive changes in the water proton chemical shift (~0.01 ppm/°C). MRT was subsequently performed in a series of in vivo non-human primate experiments under physiologic and ischemic conditions testing its reproducibility and overall performance. RESULTS Chemical shift thermometry demonstrated excellent agreement with phantom temperatures for all three approaches (DIFF-1 linear regression R2=0.994, p<0.001, acquisition time 4 min 40 s; DIFF-2 R2=0.996, p<0.001, acquisition time 4 min; DIFF-3 R2=0.998, p<0.001, acquisition time 40 s). CONCLUSION These findings confirm the comparability in performance of three competing approaches MRT, and present in vivo applications under physiologic and ischemic conditions in a primate stroke model. PMID:25655874

  15. Lanthanide ion (III) complexes of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate for dual biosensing of pH with chemical exchange saturation transfer (CEST) and biosensor imaging of redundant deviation in shifts (BIRDS).

    PubMed

    Huang, Yuegao; Coman, Daniel; Ali, Meser M; Hyder, Fahmeed

    2015-01-01

    Relaxivity-based magnetic resonance of phosphonated ligands chelated with gadolinium (Gd(3+)) shows promise for pH imaging. However instead of monitoring the paramagnetic effect of lanthanide complexes on the relaxivity of water protons, biosensor (or molecular) imaging with magnetic resonance is also possible by detecting either the nonexchangeable or the exchangeable protons on the lanthanide complexes themselves. The nonexchangeable protons (e.g. -CHx, where 3 ≥ x ≥ 1) are detected using a three-dimensional chemical shift imaging method called biosensor imaging of redundant deviation in shifts (BIRDS), whereas the exchangeable protons (e.g. -OH or -NHy , where 2 ≥ y ≥ 1) are measured with chemical exchange saturation transfer (CEST) contrast. Here we tested the feasibility of BIRDS and CEST for pH imaging of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate (DOTA-4AmP(8-)) chelated with thulium (Tm(3+) ) and ytterbium (Yb(3+)). BIRDS and CEST experiments show that both complexes are responsive to pH and temperature changes. Higher pH and temperature sensitivities are obtained with BIRDS for either complex when using the chemical shift difference between two proton resonances vs using the chemical shift of a single proton resonance, thereby eliminating the need to use water resonance as reference. While CEST contrast for both agents is linearly dependent on pH within a relatively large range (i.e. 6.3-7.9), much stronger CEST contrast is obtained with YbDOTA-4AmP(5-) than with TmDOTA-4AmP(5-). In addition, we demonstrate the prospect of using BIRDS to calibrate CEST as new platform for quantitative pH imaging.

  16. Fluid Shifts

    NASA Technical Reports Server (NTRS)

    Stenger, M.; Hargens, A.; Dulchavsky, S.; Ebert, D.; Lee, S.; Lauriie, S.; Garcia, K.; Sargsyan, A.; Martin, D.; Ribeiro, L.; Lui, J.; Macias, B.; Arbeille, P.; Danielson, R.; Chang, D.; Johnston, S.; Ploutz-Snyder, R.; Smith, S.

    2016-01-01

    NASA is focusing on long-duration missions on the International Space Station (ISS) and future exploration-class missions beyond low-Earth orbit. Visual acuity changes observed after short-duration missions were largely transient, but more than 50% of ISS astronauts experienced more profound, chronic changes with objective structural and functional findings such as papilledema and choroidal folds. Globe flattening, optic nerve sheath dilation, and optic nerve tortuosity also are apparent. This pattern is referred to as the visual impairment and intracranial pressure (VIIP) syndrome. VIIP signs and symptoms, as well as postflight lumbar puncture data, suggest that elevated intracranial pressure (ICP) may be associated with the spaceflight-induced cephalad fluid shifts, but this hypothesis has not been tested. The purpose of this study is to characterize fluid distribution and compartmentalization associated with long-duration spaceflight, and to correlate these findings with vision changes and other elements of the VIIP syndrome. We also seek to determine whether the magnitude of fluid shifts during spaceflight, as well as the VIIP-related effects of those shifts, is predicted by the crewmember's preflight conditions and responses to acute hemodynamic manipulations (such as head-down tilt). Lastly, we will evaluate the patterns of fluid distribution in ISS astronauts during acute reversal of fluid shifts through application of lower body negative pressure (LBNP) interventions to characterize and explain general and individual responses. METHODS: We will examine a variety of physiologic variables in 10 long-duration ISS crewmembers using the test conditions and timeline presented in the Figure below. Measures include: (1) fluid compartmentalization (total body water by D2O, extracellular fluid by NaBr, intracellular fluid by calculation, plasma volume by CO rebreathe, interstitial fluid by calculation); (2) forehead/eyelids, tibia, calcaneus tissue thickness (by

  17. 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.

  18. Discrimination of Enantiomers of Dipeptide Derivatives with Two Chiral Centers by Tetraaza Macrocyclic Chiral Solvating Agents Using (1)H NMR Spectroscopy.

    PubMed

    Fang, Lixia; Lv, Caixia; Wang, Guo; Feng, Lei; Stavropoulos, Pericles; Gao, Guangpeng; Ai, Lin; Zhang, Jiaxin

    2016-12-01

    (1)H NMR spectroscopy is often used to discriminate enantiomers of chiral analytes and determine their enantiomeric excess (ee) by various chiral auxiliaries. In reported research, these studies were mainly focused on chiral discriminantion of chiral analytes with only one chiral center. However, many chiral compounds possessing two or more chiral centers are often found in natural products, chiral drugs, products of asymmetric synthesis and biological systems. Therefore, it is necessary to investigate their chiral discrimination by effective chiral auxiliaries using (1)H NMR spectroscopy. In this paper, a new class of tetraaza macrocyclic chiral solvating agents (TAMCSAs) with two amide (CONH), two amino (NH) and two phenolic hydroxyl (PhOH) groups has been designed and synthsized for chiral discrimination towards dipeptide derivatives with two chiral centers. These dipeptide derivatives are important chiral species because some of them are used as clinical drugs and special dietary supplements for treatment of human diseases, such as L-alanyl-L-glutamine and aspartame. The results show that these TAMCSAs have excellent chiral discriminating properties and offer multiple detection possibilities pertaining to (1)H NMR signals of diagnostic split protons. The nonequivalent chemical shifts (up to 0.486 ppm) of various types of protons of these dipeptide derivatives were evaluated with the assistance of well-resolved (1)H NMR signals in most cases. In addition, enantiomeric excesses (ee) of the dipeptide derivatives with different optical compositions have been calculated based on integration of well-separeted proton signals. At the same time, the possible chiral discriminating behaviors have been discussed by means of Job plots, ESI mass spectra and a proposed theoretical model of (±)-G1 with TAMCSA 1c. Additionally, the association constants of enantiomers of (±)-G5 with TAMCSA 1a were calculated by employing the nonlinear curve-fitting method.

  19. Synthesis, molecular structure and spectroscopic characterization of (E)-1-((2-hydroxynaphthalen-1-yl) methyleneamino)-5-(4-methoxybenzoyl)-4-(4-methoxyphenyl) pyrimidine-2(1H)-one with experimental techniques and theoretical calculations

    NASA Astrophysics Data System (ADS)

    Ceylan, Ümit; Hacıyusufoğlu, Mehmet Emin; Yalçınc, Şerife Pınar; Sönmez, Mehmet; Aygün, Muhittin

    2016-04-01

    A new Schiff base compound, (E)-1-((2-hydroxynaphthalen-1-yl) methyleneamino)-5-(4-methoxybenzoyl)-4-(4-methoxyphenyl) pyrimidine-2(1H)-one, formula sum is given by C30H23N3O5, was synthesized and characterized by experimentally and theoretically. Optimized molecular structure was obtained using X-ray diffraction in the ground state. FT-IR, NMR and UV-Vis frequencies have been measured and compared with theoretically obtained data by using by DFT/B3LYP method with 6-31G(d) and 6-311++G(d,p) basis set. In addition, molecular electrostatic potential (MEP), dipole moments, NBO analysis, atomic charges, HOMO-LUMO and molecular electrostatic potential were computed. The calculated results show that the optimized geometry can well reproduce the crystal structure parameters, and the theoretical vibrational frequencies, 1H and 13C NMR chemical shifts show good agreement with experimental values.

  20. Nuclear magnetic resonance, fluorescence correlation spectroscopy and time-resolved fluorescence anisotropy studies of intermolecular interactions in bis(1-methyl-1H-imidazol-3-ium-3-yl)dihydroborate bis(trifluoromethylsulfonyl)amide and its mixtures with various cosolvents

    NASA Astrophysics Data System (ADS)

    Sahu, Prabhat Kumar; Nanda, Raju; Seth, Sudipta; Ghosh, Arindam; Sarkar, Moloy

    2016-09-01

    Keeping in mind the potential usefulness of mixed ionic liquid (IL)-cosolvents systems in several industrial applications, intermolecular interactions between a borate-based IL, bis(1-methyl-1H-imidazol-3-ium-3-yl)dihydroborate bis(trifluoromethylsulfonyl)amide ([BIMIMDBA][TF2N]), and its binary mixtures with several molecular solvents has been investigated through NMR and fluorescence spectroscopy. Analysis of the 1H chemical shifts (δ/ppm) and translational diffusion coefficients (D) of the IL in different solvent mixtures demonstrate interplay of nonspecific (ion-dipole) and specific (hydrogen bonding) interactions in governing the properties of these mixtures. Fluorescence correlation spectroscopy (FCS) and time-resolved fluorescence anisotropy data provide evidence in favour of different IL-solvent interaction for different IL-cosolvent systems.

  1. Synthesis and 1H and 13C NMR spectral study of some r(2),c(4)-bis(isopropylcarbonyl)-c(5)-hydroxy-t(5)-methyl-t(3)-substituted phenyl, cyclohexanones and their oximes

    NASA Astrophysics Data System (ADS)

    Balachander, R.; Sameera, S. A.; Mohan, R. T. Sabapathy

    2016-07-01

    All the synthesized compounds have been characterized by 1H, 13C, 2D NMR and mass spectral studies. The spectral data suggest that compounds 2, 3, 5 and 6 exist in chair conformation with axial orientation of the hydroxyl group and equatorial orientations of all the other substituent. Long-range coupling is observed between OH proton to H-6a proton should be in a W arrangement. Compounds 1 and 4 diamagnetic anisotropic effect of the furyl group is not pronounced and absence of long-rang coupling between OH proton to H-6a proton. The oximation effects were discussed to all synthesized compounds using 1H and 13C chemical shifts.

  2. A 1H NMR study of a ternary peptide complex that mimics the interaction between troponin C and troponin I.

    PubMed Central

    Slupsky, C. M.; Shaw, G. S.; Campbell, A. P.; Sykes, B. D.

    1992-01-01

    The troponin I peptide N alpha-acetyl TnI (104-115) amide (TnIp) represents the minimum sequence necessary for inhibition of actomyosin ATPase activity of skeletal muscle (Talbot, J.A. & Hodges, R.S. 1981, J. Biol. Chem. 256, 2798-3802; Van Eyk, J.E. & Hodges, R.S., 1988, J. Biol. Chem. 263, 1726-1732; Van Eyk, J.E., Kay, C.M., & Hodges, R.S., 1991, Biochemistry 30, 9974-9981). In this study, we have used 1H NMR spectroscopy to compare the binding of this inhibitory TnI peptide to a synthetic peptide heterodimer representing site III and site IV of the C-terminal domain of troponin C (TnC) and to calcium-saturated skeletal TnC. The residues whose 1H NMR chemical shifts are perturbed upon TnIp binding are the same in both the site III/site IV heterodimer and TnC. These residues include F102, I104, F112, I113, I121, I149, D150, F151, and F154, which are all found in the C-terminal domain hydrophobic pocket and antiparallel beta-sheet region of the synthetic site III/site IV heterodimer and of TnC. Further, the affinity of TnIp binding to the heterodimer (Kd = 192 +/- 37 microM) was found to be similar to TnIp binding to TnC (48 +/- 18 microM [Campbell, A.P., Cachia, P.J., & Sykes, B.D., 1991, Biochem. Cell Biol. 69, 674-681]). The results indicate that binding of the inhibitory region of TnI is primarily to the C-terminal domain of TnC. The results also indicate how well the synthetic peptide heterodimer mimics the C-terminal domain of TnC in structure and functional interactions. PMID:1304891

  3. 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.

  4. Implementation of a modified birdcage resonator for 19F/1H MRI at low fields (0.14 T).

    PubMed

    Samaratunga, R C; Pratt, R G; Zhu, Y; Massoth, R J; Thomas, S R

    1994-05-01

    Fluorine-19 nuclear magnetic resonance of perfluorinated blood substitute materials provides a method for determination of oxygen tension (pO2) in vivo. Use of a double resonant 19F/1H radio frequency coil allows convenient correlation between the high resolution anatomic presentation of proton images and the fluorine distribution. However, quantitative 19F measurements require an RF coil with good H1 field homogeneity over the image volume and a high quality factor (Q) to minimize errors caused by the low signal-to-noise levels available in in vivo imaging and image nonuniformities introduced by the large chemical shift of fluorocarbons. The birdcage coil design provides a high Q structure with optimum H1 field uniformity and fill factor. However, at low resonance frequencies, the inherently low inductance of the birdcage geometry requires the use of a large number of chip capacitors giving rise to unwieldy coil fabrication and increased cost. This communication describes a modification to the birdcage design that reduces the chip capacitor requirement by at least a factor of 4 for a given dimension, yet retains the essential characteristics of the birdcage design. The modified structure was tuned for double resonance at 5.7/6.0 MHz for 19F/1H magnetic resonance imaging at 0.14 T. For a coil with a length to diameter ratio of 1.67, an H1 uniformity of +/- 2% for the 19F resonance was obtained over a cylindrical region with radius approximately 0.6r (r = radius of coil) and length approximately 1.8r within the coil.

  5. An unsymmetrical binuclear ruthenium(II) complex of tris(2-pyridyl)-1,3,5-triazine and its identification by sup 1 H NMR spectroscopy

    SciTech Connect

    Chirayil, S.; Hegde, V.; Jahng, Yurngdong; Thummel, R.P. )

    1991-06-26

    The use of tris(2-pyridyl)-1,3,5-triazine (TPT) for use as a bridging ligand that incorporates two Ru(II) atoms in nonequivalent sites such that one Ru(II) is bound in a bidentate fashion and the other is bound in a tridentate manner is described herein. The use of bpy-d{sub 8} as an auxiliary ligand in the formation and characterization of an unsymmetrical mononuclear ruthenium (I) complex has been extended to the perdeuterio analog of 2,2{prime};6,2{double prime}-terpyridine (Tpy), and its use in the characterization of a binuclear complex of TPT are reported. {sup 1}H NMR chemical shift data for the ligands and the ruthenium complexes are presented. 15 refs., 3 figs., 1 tab.

  6. 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.

  7. 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.

  8. 40 CFR 721.9078 - 6-Methoxy-1H-benz[de]isoquinoline-2 [3H]-dione derivative (generic).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 31 2011-07-01 2011-07-01 false 6-Methoxy-1H-benz isoquinoline-2 -dione derivative (generic). 721.9078 Section 721.9078 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT SIGNIFICANT NEW USES OF CHEMICAL SUBSTANCES Significant New Uses for Specific Chemical Substances...

  9. 40 CFR 721.9078 - 6-Methoxy-1H-benz[de]isoquinoline-2 [3H]-dione derivative (generic).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false 6-Methoxy-1H-benz isoquinoline-2 -dione derivative (generic). 721.9078 Section 721.9078 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT SIGNIFICANT NEW USES OF CHEMICAL SUBSTANCES Significant New Uses for Specific Chemical Substances...

  10. 40 CFR 721.9078 - 6-Methoxy-1H-benz[de]isoquinoline-2 [3H]-dione derivative (generic).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false 6-Methoxy-1H-benz isoquinoline-2 -dione derivative (generic). 721.9078 Section 721.9078 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT SIGNIFICANT NEW USES OF CHEMICAL SUBSTANCES Significant New Uses for Specific Chemical Substances...

  11. 40 CFR 721.9078 - 6-Methoxy-1H-benz[de]isoquinoline-2 [3H]-dione derivative (generic).

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 32 2012-07-01 2012-07-01 false 6-Methoxy-1H-benz isoquinoline-2 -dione derivative (generic). 721.9078 Section 721.9078 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT SIGNIFICANT NEW USES OF CHEMICAL SUBSTANCES Significant New Uses for Specific Chemical Substances...

  12. 40 CFR 721.9078 - 6-Methoxy-1H-benz[de]isoquinoline-2 [3H]-dione derivative (generic).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false 6-Methoxy-1H-benz isoquinoline-2 -dione derivative (generic). 721.9078 Section 721.9078 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT SIGNIFICANT NEW USES OF CHEMICAL SUBSTANCES Significant New Uses for Specific Chemical Substances...

  13. Teaching 1H NMR Spectrometry Using Computer Modeling.

    ERIC Educational Resources Information Center

    Habata, Yoichi; Akabori, Sadatoshi

    2001-01-01

    Molecular modeling by computer is used to display stereochemistry, molecular orbitals, structure of transition states, and progress of reactions. Describes new ideas for teaching 1H NMR spectroscopy using computer modeling. (Contains 12 references.) (ASK)

  14. Prediction of (195) Pt NMR chemical shifts of dissolution products of H2 [Pt(OH)6 ] in nitric acid solutions by DFT methods: how important are the counter-ion effects?

    PubMed

    Tsipis, Athanassios C; Karapetsas, Ioannis N

    2016-08-01

    (195) Pt NMR chemical shifts of octahedral Pt(IV) complexes with general formula [Pt(NO3 )n (OH)6 - n ](2-) , [Pt(NO3 )n (OH2 )6 - n ](4 - n) (n = 1-6), and [Pt(NO3 )6 - n  - m (OH)m (OH2 )n ](-2 + n - m) formed by dissolution of platinic acid, H2 [Pt(OH)6 ], in aqueous nitric acid solutions are calculated employing density functional theory methods. Particularly, the gauge-including atomic orbitals (GIAO)-PBE0/segmented all-electron relativistically contracted-zeroth-order regular approximation (SARC-ZORA)(Pt) ∪ 6-31G(d,p)(E)/Polarizable Continuum Model computational protocol performs the best. Excellent second-order polynomial plots of δcalcd ((195) Pt) versus δexptl ((195) Pt) chemical shifts and δcalcd ((195) Pt) versus the natural atomic charge QPt are obtained. Despite of neglecting relativistic and spin orbit effects the good agreement of the calculated δ (195) Pt chemical shifts with experimental values is probably because of the fact that the contribution of relativistic and spin orbit effects to computed σ(iso) (195) Pt magnetic shielding of Pt(IV) coordination compounds is effectively cancelled in the computed δ (195) Pt chemical shifts, because the relativistic corrections are expected to be similar in the complexes and the proper reference standard used. To probe the counter-ion effects on the (195) Pt NMR chemical shifts of the anionic [Pt(NO3 )n (OH)6 - n ](2-) and cationic [Pt(NO3 )n (OH2 )6 - n ](4 - n) (n = 0-3) complexes we calculated the (195) Pt NMR chemical shifts of the neutral (PyH)2 [Pt(NO3 )n (OH)6 - n ] (n = 1-6; PyH = pyridinium cation, C5 H5 NH(+) ) and [Pt(NO3 )n (H2 O)6 - n ](NO3 )4 - n (n = 0-3) complexes. Counter-anion effects are very important for the accurate prediction of the (195) Pt NMR chemical shifts of the cationic [Pt(NO3 )n (OH2 )6 - n ](4 - n) complexes, while counter-cation effects are less important for the anionic [Pt(NO3 )n (OH)6

  15. 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

  16. Fluid Shifts

    NASA Technical Reports Server (NTRS)

    Stenger, Michael; Hargens, A.; Dulchavsky, S.; Ebert, D.; Lee, S.; Sargsyan, A.; Martin, D.; Lui, J.; Macias, B.; Arbeille, P.; Platts, S.

    2014-01-01

    NASA is focusing on long-duration missions on the International Space Station (ISS) and future exploration-class missions beyond low Earth orbit. Visual acuity changes observed after short-duration missions were largely transient, but more than 30% of ISS astronauts experience more profound, chronic changes with objective structural and functional findings such as papilledema and choroidal folds. Globe flattening, optic nerve sheath dilation, and optic nerve tortuosity also are apparent. This pattern is referred to as the visual impairment and intracranial pressure (VIIP) syndrome. VIIP signs and symptoms, as well as postflight lumbar puncture data, suggest that elevated intracranial pressure (ICP) may be associated with the space flight-induced cephalad fluid shifts, but this hypothesis has not been tested. The purpose of this study is to characterize fluid distribution and compartmentalization associated with long-duration space flight, and to correlate these findings with vision changes and other elements of the VIIP syndrome. We also seek to determine whether the magnitude of fluid shifts during space flight, as well as the VIIP-related effects of those shifts, is predicted by the crewmember's pre-flight condition and responses to acute hemodynamic manipulations (such as head-down tilt). Lastly, we will evaluate the patterns of fluid distribution in ISS astronauts during acute reversal of fluid shifts through application of lower body negative pressure (LBNP) interventions to characterize and explain general and individual responses. We will examine a variety of physiologic variables in 10 long-duration ISS crewmembers using the test conditions and timeline presented in the Figure below. Measures include: (1) fluid compartmentalization (total body water by D2O, extracellular fluid by NaBr, intracellular fluid by calculation, plasma volume by CO rebreathe, interstitial fluid by calculation); (2) forehead/eyelids, tibia, calcaneus tissue thickness (by ultrasound

  17. GFT projection NMR for efficient (1)H/ (13)C sugar spin system identification in nucleic acids.

    PubMed

    Atreya, Hanudatta S; Sathyamoorthy, Bharathwaj; Jaipuria, Garima; Beaumont, Victor; Varani, Gabriele; Szyperski, Thomas

    2012-12-01

    A newly implemented G-matrix Fourier transform (GFT) (4,3)D HC(C)CH experiment is presented in conjunction with (4,3)D HCCH to efficiently identify (1)H/(13)C sugar spin systems in (13)C labeled nucleic acids. This experiment enables rapid collection of highly resolved relay 4D HC(C)CH spectral information, that is, shift correlations of (13)C-(1)H groups separated by two carbon bonds. For RNA, (4,3)D HC(C)CH takes advantage of the comparably favorable 1'- and 3'-CH signal dispersion for complete spin system identification including 5'-CH. The (4,3)D HC(C)CH/HCCH based strategy is exemplified for the 30-nucleotide 3'-untranslated region of the pre-mRNA of human U1A protein.

  18. 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.

  19. Full-Quantum chemical calculation of the absorption maximum of bacteriorhodopsin: a comprehensive analysis of the amino acid residues contributing to the opsin shift

    PubMed Central

    Hayashi, Tomohiko; Matsuura, Azuma; Sato, Hiroyuki; Sakurai, Minoru

    2012-01-01

    Herein, the absorption maximum of bacteriorhodopsin (bR) is calculated using our recently developed method in which the whole protein can be treated quantum mechanically at the level of INDO/S-CIS//ONIOM (B3LYP/6-31G(d,p): AMBER). The full quantum mechanical calculation is shown to reproduce the so-called opsin shift of bR with an error of less than 0.04 eV. We also apply the same calculation for 226 different bR mutants, each of which was constructed by replacing any one of the amino acid residues of the wild-type bR with Gly. This substitution makes it possible to elucidate the extent to which each amino acid contributes to the opsin shift and to estimate the inter-residue synergistic effect. It was found that one of the most important contributions to the opsin shift is the electron transfer from Tyr185 to the chromophore upon excitation. We also indicate that some aromatic (Trp86, Trp182) and polar (Ser141, Thr142) residues, located in the vicinity of the retinal polyene chain and the β-ionone ring, respectively, play an important role in compensating for the large blue-shift induced by both the counterion residues (Asp85, Asp212) and an internal water molecule (W402) located near the Schiff base linkage. In particular, the effect of Trp86 is comparable to that of Tyr185. In addition, Ser141 and Thr142 were found to contribute to an increase in the dipole moment of bR in the excited state. Finally, we provide a complete energy diagram for the opsin shift together with the contribution of the chromophore-protein steric interaction. PMID:27493528

  20. Spatially resolved chemical reaction monitoring using magnetic resonance imaging.

    PubMed

    Feindel, Kirk W

    2016-06-01

    Over the previous three decades, the use of MRI for studying dynamic physical and chemical processes of materials systems has grown significantly. This mini-review provides a brief introduction to relevant principles of MRI, including methods of spatial localization, factors contributing to image contrast, and chemical shift imaging. A few historical examples of (1) H MRI for reaction monitoring will be presented, followed by a review of recent research including (1) H MRI studies of gelation and biofilms, (1) H, (7) Li, and (11) B MRI studies of electrochemical systems, in vivo glucose metabolism monitored with (19) F MRI, and in situ temperature monitoring with (27) Al MRI. Copyright © 2015 John Wiley & Sons, Ltd.

  1. Characterization of various magnesium oxides by XRD and {sup 1}H MAS NMR spectroscopy

    SciTech Connect

    Aramendia, M.A.; Benitez, J.A.; Borau, V.; Jimenez, C.; Marinas, J.M.; Ruiz, J.R.; Urbano, F.

    1999-04-01

    A magnesium oxide obtained by thermal decomposition of commercially available magnesium hydroxide was refluxed in water and acetone in order to improve its chemical and textural properties with the purpose of using it as a support for metals in heterogeneous catalysts. X-ray diffraction, CO{sub 2} chemisorption, and {sup 1}H magic-angle spinning nuclear magnetic resonance were used to identify crystal phases, the number of basic sites, and the nature of OH groups in the oxide, respectively.

  2. Aromatic derivatives of 2,3-dihydro-1H-1,5-benzodiazepine

    SciTech Connect

    Orlov, V.D.; Desenko, S.M.; Kiroga, Kh.

    1987-09-01

    The formation of 2,2,4-trisubstituted 2,3-dihydro-1H-1,5-benzodiazepines in the reactions of acetylarenes with 4-ethoxy- and 3,5-dimethyl-1,2-phenylenediamine was studied. The effect of the substituents on the individual stages of the reactions is discussed. A quantum-chemical calculation of the relative nucleophilicity of 1,2-phenylenediamine, 2,3-diaminopyridine, and 3,4-diaminofurazan was undertaken.

  3. 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...

  4. High-Frequency (13)C and (29)Si NMR Chemical Shifts in Diamagnetic Low-Valence Compounds of Tl(I) and Pb(II): Decisive Role of Relativistic Effects.

    PubMed

    Vícha, Jan; Marek, Radek; Straka, Michal

    2016-02-15

    The (13)C and (29)Si NMR signals of ligand atoms directly bonded to Tl(I) or Pb(II) heavy-element centers are predicted to resonate at very high frequencies, up to 400 ppm for (13)C and over 1000 ppm for (29)Si, outside the typical experimental NMR chemical-shift ranges for a given type of nuclei. The large (13)C and (29)Si NMR chemical shifts are ascribed to sizable relativistic spin-orbit effects, which can amount to more than 200 ppm for (13)C and more than 1000 ppm for (29)Si, values unexpected for diamagnetic compounds of the main group elements. The origin of the vast spin-orbit contributions to the (13)C and (29)Si NMR shifts is traced to the highly efficient 6p → 6p* metal-based orbital magnetic couplings and related to the 6p orbital-based bonding together with the low-energy gaps between the occupied and virtual orbital subspaces in the subvalent Tl(I) and Pb(II) compounds. New NMR spectral regions for these compounds are suggested based on the fully relativistic density functional theory calculations in the Dirac-Coulomb framework carefully calibrated on the experimentally known NMR data for Tl(I) and Pb(II) complexes.

  5. Fluid Shifts

    NASA Technical Reports Server (NTRS)

    Stenger, M. B.; Hargens, A. R.; Dulchavsky, S. A.; Arbeille, P.; Danielson, R. W.; Ebert, D. J.; Garcia, K. M.; Johnston, S. L.; Laurie, S. S.; Lee, S. M. C.; Liu, J.; Macias, B.; Martin, D. S.; Minkoff, L.; Ploutz-Snyder, R.; Ribeiro, L. C.; Sargsyan, A.; Smith, S. M.

    2017-01-01

    Introduction. NASA's Human Research Program is focused on addressing health risks associated with long-duration missions on the International Space Station (ISS) and future exploration-class missions beyond low Earth orbit. Visual acuity changes observed after short-duration missions were largely transient, but now more than 50 percent of ISS astronauts have experienced more profound, chronic changes with objective structural findings such as optic disc edema, globe flattening and choroidal folds. These structural and functional changes are referred to as the visual impairment and intracranial pressure (VIIP) syndrome. Development of VIIP symptoms may be related to elevated intracranial pressure (ICP) secondary to spaceflight-induced cephalad fluid shifts, but this hypothesis has not been tested. The purpose of this study is to characterize fluid distribution and compartmentalization associated with long-duration spaceflight and to determine if a relation exists with vision changes and other elements of the VIIP syndrome. We also seek to determine whether the magnitude of fluid shifts during spaceflight, as well as any VIIP-related effects of those shifts, are predicted by the crewmember's pre-flight status and responses to acute hemodynamic manipulations, specifically posture changes and lower body negative pressure. Methods. We will examine a variety of physiologic variables in 10 long-duration ISS crewmembers using the test conditions and timeline presented in the figure below. Measures include: (1) fluid compartmentalization (total body water by D2O, extracellular fluid by NaBr, intracellular fluid by calculation, plasma volume by CO rebreathe, interstitial fluid by calculation); (2) forehead/eyelids, tibia, and calcaneus tissue thickness (by ultrasound); (3) vascular dimensions by ultrasound (jugular veins, cerebral and carotid arteries, vertebral arteries and veins, portal vein); (4) vascular dynamics by MRI (head/neck blood flow, cerebrospinal fluid

  6. Solubilization of flurbiprofen within non-ionic Tween 20 surfactant micelles: a 19F and 1H NMR study.

    PubMed

    Saveyn, Pieter; Cocquyt, Ellen; Zhu, Wuxin; Sinnaeve, Davy; Haustraete, Katrien; Martins, José C; Van der Meeren, Paul

    2009-07-14

    The solubilization of the poorly water soluble anti-inflammatory drug flurbiprofen in non-ionic Tween 20 surfactant micellar solutions was studied by both (19)F and (1)H NMR spectroscopy in an acidic environment. These non-destructive techniques allowed us to investigate the effect of temperature cycling in situ. Using (19)F NMR, an increased solubilisation capacity was observed as the temperature increased. This effect became more pronounced above the cloud point, which was reduced by more than 30 degrees C in the presence of an excess of flurbiprofen. Upon clouding, peak splitting was observed in the (19)F spectrum, which indicates that two pools of solubilised flurbiprofen exist that are in slow exchange on the NMR frequency timescale. The clouding and solubilization processes were found to be reversible, albeit with slow kinetics. Based on chemical shift differences of both Tween 20 and flurbiprofen, as well as NOESY experiments, the flurbiprofen was found to be accumulated within the palisade layer of the Tween 20 micelles.

  7. 1H NMR study of the hetero-association of flavin-mononucleotide with mutagenic dyes: ethidium bromide and proflavine

    NASA Astrophysics Data System (ADS)

    Evstigneev, M. P.; Mukhina, Yu. V.; Davies, D. B.

    The hetero-association of the vitamin B2 derivative, flavin-mononucleotide (FMN), with a mutagenic dye, ethidium bromide (EB) or proflavine (PF), has been studied by 1D and 2D 500 MHz 1H NMR spectroscopy. The variations of proton chemical shifts of both the vitamin and dye as a function of concentration and temperature were analysed in terms of the structural and thermodynamical properties of the FMN-EB and FMN-PF complexes in solution. The structures of the complexes were also investigated by observed intermolecular ROE contacts and molecular mechanics calculations. The results show that the 1 : 1 hetero-association complexes in solution are more stable than the self-association complexes, which is consistent with formation of an intermolecular hydrogen-bond in the hetero-complexes of FMN-EB and FMN-PF. Hence it is possible that the toxicity of aromatic molecules such as EB and PF may be reduced in vitro by the presence of FMN, partly because of the known antimutagenic action of FMN and partly because it has been shown in this work that there is an effective intermolecular association between the mutagens and the vitamin.

  8. Dual 19F/1H MR gene reporter molecules for in vivo detection of β-galactosidase

    PubMed Central

    Yu, Jian-Xin; Kodibagkar, Vikram D.; Hallac, Rami R.; Liu, Li; Mason, Ralph P.

    2012-01-01

    Increased emphasis on personalized medicine and novel therapies require the development of non-invasive strategies for assessing biochemistry in vivo. The detection of enzyme activity and gene expression in vivo is potentially important for the characterization of diseases and gene therapy. Magnetic resonance imaging (MRI) is a particularly promising tool since it is non-invasive, and has no associated radioactivity, yet penetrates deep tissue. We now demonstrate a novel class of dual 1H/19F nuclear magnetic resonance (NMR) lacZ gene reporter molecule to specifically reveal enzyme activity in human tumor xenografts growing in mice. We report the design, synthesis, and characterization of six novel molecules and evaluation of the most effective reporter in mice in vivo. Substrates show a single 19F NMR signal and exposure to β-galactosidase induces a large 19F NMR chemical shift response. In the presence of ferric ions the liberated aglycone generates intense proton MRI T2 contrast. The dual modality approach allows both the detection of substrate and imaging of product enhancing the confidence in enzyme detection. PMID:22352428

  9. Accurate Measurements of Multiple-Bond 13C- 1H Coupling Constants from Phase-Sensitive 2D INEPT Spectra

    NASA Astrophysics Data System (ADS)

    Ding, Keyang

    1999-10-01

    Measurements of multiple-bond 13C-1H coupling constants are of great interest for the assignment of nonprotonated 13C resonances and the elucidation of molecular conformation in solution. Usually, the heteronuclear multiple-bond coupling constants were measured either by the JCH splittings mostly in selective 2D spectra or in 3D spectra, which are time consuming, or by the cross peak intensity analysis in 2D quantitative heteronuclear J correlation spectra (1994, G. Zhu, A. Renwick, and A. Bax, J. Magn. Reson. A 110, 257; 1994, A. Bax, G. W. Vuister, S. Grzesiek, F. Delaglio, A. C. Wang, R. Tschudin, and G. Zhu, Methods Enzymol. 239, 79.), which suffer from the accuracy problem caused by the signal-to-noise ratio and the nonpure absorptive peak patterns. Concerted incrementation of the duration for developing proton antiphase magnetization with respect to carbon-13 and the evolution time for proton chemical shift in different steps in a modified INEPT pulse sequence provides a new method for accurate measurements of heteronuclear multiple-bond coupling constants in a single 2D experiment.

  10. Synthesis, spectral (FT-IR, UV-visible, NMR) features, biological activity prediction and theoretical studies of 4-Amino-3-(4-hydroxybenzyl)-1H-1,2,4-triazole-5(4H)-thione and its tautomer

    NASA Astrophysics Data System (ADS)