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Sample records for 129xe chemical shift

  1. Chemical shift of hyperpolarized 129Xe dissolved in liquid nitrogen

    NASA Astrophysics Data System (ADS)

    Patton, B.; Kuzma, N. N.; Happer, W.

    2002-01-01

    We report NMR measurements of hyperpolarized xenon dissolved in liquid nitrogen. The dependence of the 129Xe frequency shift on liquid nitrogen temperature was measured along the nitrogen saturated vapor curve from 77 to 93 K. Plotted as a function of the liquid nitrogen density, the chemical shift of xenon is very well described by a simple proportionality relation, with a slope of 0.2135(15) ppm/amagat. The relationship between the chemical shift and the longitudinal spin relaxation is considered in terms of the spin-rotation interaction, and estimates of Xe relaxation time in liquid nitrogen are discussed.

  2. Investigation of DOTA-Metal Chelation Effects on the Chemical Shift of (129) Xe.

    PubMed

    Jeong, Keunhong; Slack, Clancy C; Vassiliou, Christophoros C; Dao, Phuong; Gomes, Muller D; Kennedy, Daniel J; Truxal, Ashley E; Sperling, Lindsay J; Francis, Matthew B; Wemmer, David E; Pines, Alexander

    2015-12-01

    Recent work has shown that xenon chemical shifts in cryptophane-cage sensors are affected when tethered chelators bind to metals. Here, we explore the xenon shifts in response to a wide range of metal ions binding to diastereomeric forms of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) linked to cryptophane-A. The shifts induced by the binding of Ca(2+) , Cu(2+) , Ce(3+) , Zn(2+) , Cd(2+) , Ni(2+) , Co(2+) , Cr(2+) , Fe(3+) , and Hg(2+) are distinct. In addition, the different responses of the diastereomers for the same metal ion indicate that shifts are affected by partial folding with a correlation between the expected coordination number of the metal in the DOTA complex and the chemical shift of (129) Xe. These sensors may be used to detect and quantify many important metal ions, and a better understanding of the basis for the induced shifts could enhance future designs. PMID:26376768

  3. 129Xe NMR chemical shift in Xe@C60 calculated at experimental conditions: essential role of the relativity, dynamics, and explicit solvent.

    PubMed

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

    2013-08-15

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

  4. 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

  5. 129Xe NMR of xenon adsorbed on the molecular sieves AlPO 4-11 and SAPO-11. Chemical shift anisotropy related to the asymmetry of the adsorption zones

    NASA Astrophysics Data System (ADS)

    Springuel-Huet, M. A.; Fraissard, J.

    1989-01-01

    The form of the 129Xe NMR signal of xenon adsorbed at low concentration on the molecular sieves SAPO-11 and AlPO 4-11 corresponds to a highly anisotropic chemical shift which expresses the asymmetry of the channels in which the xenon is located. To the asymmetry of the xenon-wall interaction is added that of the xenon-xenon interaction when the channels are largely filled.

  6. Assessment of Lung Function in Asthma and COPD using Hyperpolarized 129Xe Chemical Shift Saturation Recovery Spectroscopy and Dissolved-Phase MR Imaging

    PubMed Central

    Qing, Kun; Mugler, John P.; Altes, Talissa A.; Jiang, Yun; Mata, Jaime F.; Miller, G. Wilson; Ruset, Iulian C.; Hersman, F. William; Ruppert, Kai

    2014-01-01

    Magnetic-resonance spectroscopy and imaging using hyperpolarized xenon-129 show great potential for evaluation of the most important function of the human lung -- gas exchange. In particular, Chemical Shift Saturation Recovery (CSSR) xenon-129 spectroscopy provides important physiological information for the lung as a whole by characterizing the dynamic process of gas exchange, while dissolved-phase xenon-129 imaging captures the time-averaged regional distribution of gas uptake by lung tissue and blood. Herein, we present recent advances in assessing lung function using CSSR spectroscopy and dissolved-phase imaging in a total of 45 subjects (23 healthy, 13 chronic obstructive pulmonary disease (COPD) and 9 asthma). From CSSR acquisitions, the COPD subjects showed red blood cell to tissue/plasma (RBC-to-TP) ratios below the average for the healthy subjects (p<0.001), but significantly higher septal wall thicknesses, as compared with the healthy subjects (p<0.005); the RBC-to-TP ratios for the asthmatics fell outside 2 standard deviations (either higher or lower) from the mean of the healthy subjects although there was no statistically significant difference for the average ratio of the study group as a whole. Similarly, from the 3D DP imaging acquisitions, we found all the ratios (TP-to-GP, RBC-to-GP, RBC-to-TP) measured in the COPD subjects were lower than those from the healthy subjects (p<0.05 for all ratios), while these ratios in the asthmatics differed considerably between subjects. Despite having been performed at different lung inflation levels, the RBC-to-TP ratios measured by CSSR and 3D DP imaging were fairly consistent with each other, with a mean difference of 0.037 (ratios from 3D DP imaging larger). In ten subjects the RBC-to-GP ratios obtained from the 3D DP imaging acquisitions were also highly correlated with their DLCO/Va ratios measured by pulmonary function testing (R=0.91). PMID:25146558

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

    PubMed Central

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

    2014-01-01

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

  8. 129Xe spin relaxation in frozen xenon

    NASA Astrophysics Data System (ADS)

    Fitzgerald, R. J.; Gatzke, M.; Fox, David C.; Cates, G. D.; Happer, W.

    1999-04-01

    We discuss the longitudinal spin relaxation of 129Xe nuclei in frozen xenon. Over a large range of temperatures and magnetic fields, the dominant spin-lattice relaxation mechanism is shown to be nuclear spin-flip Raman scattering of lattice phonons. Two closely related interactions couple the lattice phonons to the spins of 129Xe nuclei: (1) the nuclear spin-rotation interaction between nearest-neighbor atoms, and (2) the paramagnetic antishielding of the externally applied field at the site of 129Xe nuclei by the electrons of neighboring Xe atoms. We show that relaxation rates can be predicted by using measured chemical shifts of gaseous and condensed xenon. The predicted relaxation rates are in good agreement with measurements. We outline a simple way to estimate the spin-rotation coupling and paramagnetic antishielding in terms of the small perturbations of the outermost electron orbitals of one xenon atom due to a neighboring atom.

  9. Detection and characterization of xenon-binding sites in proteins by 129Xe NMR spectroscopy.

    PubMed

    Rubin, Seth M; Lee, Seok-Yong; Ruiz, E Janette; Pines, Alexander; Wemmer, David E

    2002-09-13

    Xenon-binding sites in proteins have led to a number of applications of xenon in biochemical and structural studies. Here we further develop the utility of 129Xe NMR in characterizing specific xenon-protein interactions. The sensitivity of the 129Xe chemical shift to its local environment and the intense signals attainable by optical pumping make xenon a useful NMR reporter of its own interactions with proteins. A method for detecting specific xenon-binding interactions by analysis of 129Xe chemical shift data is illustrated using the maltose binding protein (MBP) from Escherichia coli as an example. The crystal structure of MBP in the presence of 8atm of xenon confirms the binding site determined from NMR data. Changes in the structure of the xenon-binding cavity upon the binding of maltose by the protein can account for the sensitivity of the 129Xe chemical shift to MBP conformation. 129Xe NMR data for xenon in solution with a number of cavity containing phage T4 lysozyme mutants show that xenon can report on cavity structure. In particular, a correlation exists between cavity size and the binding-induced 129Xe chemical shift. Further applications of 129Xe NMR to biochemical assays, including the screening of proteins for xenon binding for crystallography are considered. PMID:12217701

  10. In Vivo MR Imaging of Pulmonary Perfusion and Gas Exchange in Rats via Continuous Extracorporeal Infusion of Hyperpolarized 129Xe

    PubMed Central

    Cleveland, Zackary I.; Möller, Harald E.; Hedlund, Laurence W.; Nouls, John C.; Freeman, Matthew S.; Qi, Yi; Driehuys, Bastiaan

    2012-01-01

    Background Hyperpolarized (HP) 129Xe magnetic resonance imaging (MRI) permits high resolution, regional visualization of pulmonary ventilation. Additionally, its reasonably high solubility (>10%) and large chemical shift range (>200 ppm) in tissues allow HP 129Xe to serve as a regional probe of pulmonary perfusion and gas transport, when introduced directly into the vasculature. In earlier work, vascular delivery was accomplished in rats by first dissolving HP 129Xe in a biologically compatible carrier solution, injecting the solution into the vasculature, and then detecting HP 129Xe as it emerged into the alveolar airspaces. Although easily implemented, this approach was constrained by the tolerable injection volume and the duration of the HP 129Xe signal. Methods and Principal Findings Here, we overcome the volume and temporal constraints imposed by injection, by using hydrophobic, microporous, gas-exchange membranes to directly and continuously infuse 129Xe into the arterial blood of live rats with an extracorporeal (EC) circuit. The resulting gas-phase 129Xe signal is sufficient to generate diffusive gas exchange- and pulmonary perfusion-dependent, 3D MR images with a nominal resolution of 2×2×2 mm3. We also show that the 129Xe signal dynamics during EC infusion are well described by an analytical model that incorporates both mass transport into the blood and longitudinal relaxation. Conclusions Extracorporeal infusion of HP 129Xe enables rapid, 3D MR imaging of rat lungs and, when combined with ventilation imaging, will permit spatially resolved studies of the ventilation-perfusion ratio in small animals. Moreover, EC infusion should allow 129Xe to be delivered elsewhere in the body and make possible functional and molecular imaging approaches that are currently not feasible using inhaled HP 129Xe. PMID:22363613

  11. Continuously Infusing Hyperpolarized 129Xe into Flowing Aqueous Solutions Using Hydrophobic Gas Exchange Membranes

    PubMed Central

    Cleveland, Zackary I.; Möller, Harald E.; Hedlund, Laurence W.; Driehuys, Bastiaan

    2009-01-01

    Hyperpolarized (HP) 129Xe yields high signal intensities in magnetic resonance (MR) and, through its large chemical shift range of ∼300 ppm, provides detailed information about the local chemical environment. To exploit these properties in aqueous solutions and living tissues requires the development of methods for efficiently dissolving HP 129Xe over an extended time period. To this end, we have used commercially available gas exchange modules to continuously infuse concentrated HP 129Xe into flowing liquids, including rat whole blood, for periods as long as one hour, and have demonstrated the feasibility of dissolved-phase MR imaging with sub-millimeter resolution within minutes. These modules, which exchange gases using hydrophobic microporous polymer membranes, are compatible with a variety of liquids and are suitable for infusing HP 129Xe into the bloodstream in vivo. Additionally, we have developed a detailed mathematical model of the infused HP 129Xe signal dynamics that should be useful in designing improved infusion systems that yield even higher dissolved HP 129Xe signal intensities. PMID:19702286

  12. Polarization of metastable 129Xe

    NASA Astrophysics Data System (ADS)

    Xia, Tian; Morgan, Steven; Jau, Yuan-Yu; Happer, William

    2008-05-01

    We have measured atomic polarization of metastable 129Xe in a pyrex cell by optical pumping, while metastability exchange optical pumping of 3He is routinely done. The atomic polarization of metastable Xe is on the order of 10%. Metastable xenon is created by electrodeless rf discharge. The hyperfine transition of metastable 129Xe is observed by microwave excitation. Atomic polarization can be demonstrated by comparison of the intensities of the transitions between different Zeeman sublevels, while pumping a specific optical transition of metastable Xe with circularly polarized light. This work offers insight into attempts to polarize 129Xe nuclei by metastability exchange optical pumping.

  13. About 129Xe ∗ in meteoritic nanodiamonds

    NASA Astrophysics Data System (ADS)

    Fisenko, A. V.; Semjonova, L. F.

    2008-08-01

    The analysis of excess 129Xe in meteoritic nanodiamonds and the kinetics of its release during stepwise pyrolysis allow to suggest that (1) in the solar nebula 129I atoms were adsorbed onto nanodiamond grains and (or) chemisorbed by forming covalent bonds with carbon atoms. Most 129I atoms existed in a surface connected state, but a minor amount of them was in nanopores of the grains. At radioactive decay of 129I the formed 129Xe ( 129Xe ∗) was trapped by diamond grains due to nuclear recoil. (2) During thermal metamorphism or aqueous alteration, the surface-sited 129I atoms were basically lost. On the basis of these assumptions and calculated concentrations of 129Xe ∗ in meteoritic nanodiamonds it is shown that the minimum closing time of the I-Xe system for meteorites of different chemical classes and low petrologic types may be about one million years relative to the minimally thermally metamorphized CO3 meteorite ALHA 77307. With increasing metamorphic grade the closing time of the I-Xe system increases and can range up to several ten millions years. This tendency is in agreement with an onion-shell model of structure and cooling history of meteorite parent bodies where the temperature increases in the direction from surface to center of the asteroids.

  14. Probing zeolite internal structures using very low temperature {sup 129}Xe NMR

    SciTech Connect

    Labouriau, A.; Crawford, S.N.; Earl, W.L.; Pietrass, T.; Weber, W.A.; Panjabi, G.; Gates, B.C.

    1998-08-01

    In recent years, probing pore structure with {sup 129}Xe NMR has received a bad reputation. This is due to the fact that the method is more complex than was originally suggested so the data is somewhat difficult to interpret. The authors find that the use of a wide temperature range (40--350 K) allows them to interpret {sup 129}Xe chemical shifts in terms of van der Waals attraction between the xenon atom and oxygen in zeolite walls. Using rather simple models from the literature, they can extract useful pore size information as well as the van der Waals potential energy.

  15. Hyperpolarized 129Xe magnetic resonance imaging of a rat model of transient Ischemic Stroke

    NASA Astrophysics Data System (ADS)

    Walvick, Ronn P.; Bastan, Birgul; Reno, Austin; Mansour, Joey; Sun, Yanping; Zhou, Xin; Mazzani, Mary; Fisher, Marc; Sotak, Christopher H.; Albert, Mitchell S.

    2009-02-01

    Ischemic stroke accounts for nearly 80% of all stroke cases. Although proton diffusion and perfusion magnetic resonance imaging (MRI) are the gold standards in ischemic stroke diagnostics, the use of hyperpolarized 129Xe MRI has a potential role to contribute to the diagnostic picture. The highly lipophilic hyperpolarized 129Xe can be non-invasively delivered via inhalation into the lungs where it is dissolved into the blood and delivered to other organs such as the brain. As such, we expect hyperpolarized 129Xe to act as a perfusion tracer which will result in a signal deficit in areas of blood deprived tissue. In this work, we present imaging results from an animal model of transient ischemic stroke characterized through 129Xe MRI. In this model, a suture is used to occlude the middle cerebral artery (MCA) in the rat brain, thus causing an ischemic event. After a period of MCA occlusion, the suture can then be removed to reperfuse the ischemic area. During the ischemic phase of the stroke, a signal void was observed in the MCA territory; which was subsequently restored by normal 129Xe MRI signal once perfusion was reinstated. Further, a higher resolution one-dimensional chemical shift image shows a sharp signal drop in the area of ischemia. Validation of ischemic damage was shown through both proton diffusion-weighted MRI (DWI) and by 2,3,5-triphenyltetrazoliumchloride (TTC) staining. The results show the potential of 129Xe to act as a perfusion tracer; information that may add to the diagnostic and prognostic utility of the clinical picture of stroke.

  16. Nuclear spin relaxation of {sup 129}Xe due to persistent xenon dimers

    SciTech Connect

    Berry-Pusey, B. N.; Anger, B. C.; Laicher, G.; Saam, B.

    2006-12-15

    We have measured longitudinal nuclear relaxation rates of {sup 129}Xe in Xe-N{sub 2} mixtures at densities below 0.5 amagats in a magnetic field of 8.0 T. We find that intrinsic spin relaxation in this regime is principally due to fluctuations in the intramolecular spin-rotation (SR) and chemical-shift-anisotropy (CSA) interactions, mediated by the formation of {sup 129}Xe-Xe persistent dimers. Our results are consistent with previous work done in one case at much lower applied fields where the CSA interaction is negligible and in another case at much higher gas densities where transient xenon dimers mediate the interactions. We have verified that a large applied field suppresses the persistent-dimer mechanism, consistent with standard relaxation theory, allowing us to measure room-temperature gas-phase relaxation times T{sub 1} for {sup 129}Xe greater than 25 h at 8.0 T. These data also yield a maximum possible low-field T{sub 1} for pure xenon gas at room temperature of 5.45{+-}0.2 h. The coupling strengths for the SR and CSA interactions that we extract are in fair agreement with estimates based both on previous experimental work and on ab initio calculations. Our results have potential implications for the production and storage of large quantities of hyperpolarized {sup 129}Xe for use in various applications.

  17. Hyperpolarized (129)Xe T (1) in oxygenated and deoxygenated blood

    NASA Technical Reports Server (NTRS)

    Albert, M. S.; Balamore, D.; Kacher, D. F.; Venkatesh, A. K.; Jolesz, F. A.

    2000-01-01

    The viability of the new technique of hyperpolarized (129)Xe MRI (HypX-MRI) for imaging organs other than the lungs depends on whether the spin-lattice relaxation time, T(1), of (129)Xe is sufficiently long in the blood. In previous experiments by the authors, the T(1) was found to be strongly dependent upon the oxygenation of the blood, with T(1) increasing from about 3 s in deoxygenated samples to about 10 s in oxygenated samples. Contrarily, Tseng et al. (J. Magn. Reson. 1997; 126: 79-86) reported extremely long T(1) values deduced from an indirect experiment in which hyperpolarized (129)Xe was used to create a 'blood-foam'. They found that oxygenation decreased T(1). Pivotal to their experiment is the continual and rapid exchange of hyperpolarized (129)Xe between the gas phase (within blood-foam bubbles) and the dissolved phase (in the skin of the bubbles); this necessitated a complicated analysis to extract the T(1) of (129)Xe in blood. In the present study, the experimental design minimizes gas exchange after the initial bolus of hyperpolarized (129)Xe has been bubbled through the sample. This study confirms that oxygenation increases the T(1) of (129)Xe in blood, from about 4 s in freshly drawn venous blood, to about 13 s in blood oxygenated to arterial levels, and also shifts the red blood cell resonance to higher frequency. Copyright 2000 John Wiley & Sons, Ltd. Abbreviations used BOLD blood oxygen level dependent NOE nuclear overhouses effect PO(2) oxygen partial pressure RBC red blood cells RF radio frequency SNR signal-to-noise ratio.

  18. Free volume of poly(perfluorosulfonic acid)/SiO 2 composite proton exchange membranes by 129Xe NMR

    NASA Astrophysics Data System (ADS)

    Utiu, Lavinia; Filipoi, Carmen; Demco, Dan E.; Zhu, Xiaomin; Vinokur, Rostislav; Conradi, Oliver; Graichen, Andreas; Blümich, Bernhard; Möller, Martin

    2011-04-01

    Poly(perfluorosulfonic acid)/silica (PFSA/SiO2) composites were investigated by 129Xe NMR spectroscopy and relaxometry. 129Xe chemical shift extrapolated to zero pressure was used for calculation of average free volume hole size. This quantity reaches a maximum at 2 wt.% SiO2 that could be correlated to the performance of composites proton exchange membrane. 129Xe longitudinal magnetization relaxation revealed a bimodal distribution of the free volume that was explained by the presence of xenon atoms in the backbone and pendant-chain domains. Thus, the free volume is heterogeneous and depends on the content of SiO2. Implications of the free volume changes for the hydrogen crossover through PFSA/SiO2 membranes are also discussed.

  19. Distinguishing multiple chemotaxis Y protein conformations with laser-polarized 129Xe NMR

    SciTech Connect

    Lowery, Thomas J.; Doucleff, Michealeen; Ruiz, E. Janette; Rubin, Seth M.; Pines, Alexander; Wemmer, David E.

    2005-02-01

    The chemical shift of the {sup 129}Xe NMR signal has been shown to be extremely sensitive to the local environment around the atom and has been used to follow processes such as ligand binding by bacterial periplasmic binding proteins (Rubin et al. 2000; Lowery et al. 2004). Here we show that the {sup 129}Xe shift can sense more subtle changes: magnesium binding, BeF{sub 3}{sup -} activation, and peptide binding by the E. coli chemotaxis Y protein. {sup 1}H-{sup 15}N correlation spectroscopy and x-ray crystallography were used to identify two xenon-binding cavities in CheY that are primarily responsible for the shift changes. One site is near the active site, and the other is near the peptide binding site.

  20. Oxygen-dependent hyperpolarized (129) Xe brain MR.

    PubMed

    Li, Haidong; Zhang, Zhiying; Zhong, Jianping; Ruan, Weiwei; Han, Yeqing; Sun, Xianping; Ye, Chaohui; Zhou, Xin

    2016-03-01

    Hyperpolarized (HP) (129) Xe MR offers unique advantages for brain functional imaging (fMRI) because of its extremely high sensitivity to different chemical environments and the total absence of background noise in biological tissues. However, its advancement and applications are currently plagued by issues of signal strength. Generally, xenon atoms found in the brain after inhalation are transferred from the lung via the bloodstream. The longitudinal relaxation time (T1 ) of HP (129) Xe is inversely proportional to the pulmonary oxygen concentration in the lung because oxygen molecules are paramagnetic. However, the T1 of (129) Xe is proportional to the pulmonary oxygen concentration in the blood, because the higher pulmonary oxygen concentration will result in a higher concentration of diamagnetic oxyhemoglobin. Accordingly, there should be an optimal pulmonary oxygen concentration for a given quantity of HP (129) Xe in the brain. In this study, the relationship between pulmonary oxygen concentration and HP (129) Xe signal in the brain was analyzed using a theoretical model and measured through in vivo experiments. The results from the theoretical model and experiments in rats are found to be in good agreement with each other. The optimal pulmonary oxygen concentration predicted by the theoretical model was 21%, and the in vivo experiments confirmed the presence of such an optimal ratio by reporting measurements between 25% and 35%. These findings are helpful for improving the (129) Xe signal in the brain and make the most of the limited spin polarization available for brain experiments. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26915791

  1. 129Xe EDM Search Experiment Using Active Nuclear Spin Maser

    NASA Astrophysics Data System (ADS)

    Sato, Tomoya; Ichikawa, Yuichi; Ohtomo, Yuichi; Sakamoto, Yu; Kojima, Shuichiro; Suzuki, Takahiro; Shirai, Hazuki; Chikamori, Masatoshi; Hikota, Eri; Miyatake, Hirokazu; Nanao, Tsubasa; Suzuki, Kunifumi; Tsuchiya, Masato; Inoue, Takeshi; Furukawa, Takeshi; Yoshimi, Akihiro; Bidinosti, Christopher P.; Ino, Takashi; Ueno, Hideki; Matsuo, Yukari; Fukuyama, Takeshi; Asahi, Koichiro

    An active nuclear spin maser, which enables a precision measurement of spin precession frequency, is employed in the experimental search for permanent electric dipole moment (EDM) in the diamagnetic atom 129Xe. In order to eliminate systematic errors which limit the sensitivity of the experiment to an EDM, the following tactics are adopted: (i) 3He comagnetometry for the cancellation of long-term drifts in the external magnetic fields and (ii) double-cell geometry for the mitigation of frequency shifts due to interaction of 129Xe spin with polarized Rb atoms. In the present work, the design for the double-cell has been changed and a magnetic shield-coil system to provide a highly homogeneous magnetic field has been newly introduced. Thanks to increased polarization and longer 3He spin relaxation time, the dual-species maser of 129Xe and 3He in a double-cell geometry operated successfully. Our experiment is now at the stage of assembling these separate technical elements in order to start the measurement of 129Xe EDM in the 10-28 ecm region.

  2. Rotaxane-mediated suppression and activation of cucurbit[6]uril for molecular detection by (129)Xe hyperCEST NMR.

    PubMed

    Finbloom, Joel A; Slack, Clancy C; Bruns, Carson J; Jeong, Keunhong; Wemmer, David E; Pines, Alexander; Francis, Matthew B

    2016-02-21

    We report a method for blocking interactions between (129)Xe and cucurbit[6]uril (CB6) until activation by a specific chemical event. We synthesized a CB6-rotaxane that allowed no (129)Xe interaction with the CB6 macrocycle component until a cleavage event released the CB6, which then produced a (129)Xe@CB6 NMR signal. This contrast-upon-activation (129)Xe NMR platform allows for modular synthesis and can be expanded to applications in detection and disease imaging. PMID:26795714

  3. {sup 129}Xe nuclear magnetic resonance studies of xenon in zeolite CaA.

    SciTech Connect

    Jameson, C. J.; Jameson, A. K.; Gerald, R. E., II; de Dios, A. C.; Chemical Engineering; Univ. of Illinois at Chicago; Loyola Univ.

    1992-02-01

    The average {sup 129}Xe nuclear magnetic resonance (NMR) chemical shift for xenon atoms in alpha cages of zeolite CaA is observed in a single peak dependent on xenon loading ({l_angle}n{r_angle} = 0.5-8.9 Xe atoms/alpha cage) and temperature (240-360 K). The general increase of the shift with increasing average number of xenon atoms per alpha cage is shown to be due largely to the changing distribution of occupancies with increasing {l_angle}n{r_angle}, coupled with increasing increments in the chemical shifts of Xe{sub n} with increasing n. Except at the highest loadings, the results obtained for xenon in CaA are predicted nicely on the basis of {delta}{sub av}(T) = (1/{l_angle}n{r_angle}){Sigma}{sub n}n{delta}{sub n}(T)P{sub n}({l_angle}n{r_angle},T), where the fractions P{sub n} of alpha cages containing n Xe atoms are imported from the P{sub n} measured in xenon in zeolite NaA. The high loading data in CaA are interpreted in terms of contributions to the average {sup 129}Xe chemical shifts associated with xenon atoms in the window positions.

  4. Large Production of Hyperpolarized 129-Xe for MRI Applications

    NASA Astrophysics Data System (ADS)

    Ruset, Iulian; Hersman, F. W.; Distelbrink, Jan; Ketel, Stephen; Covrig, Silviu; Muradian, Iga; Sindile, Adrian

    2007-03-01

    Although 129-Xe was the first hyperpolarized gas to be used in MRI studies, the research community has focused on 3-He, mainly because of the larger quantities of hyperpolarized gas available. Xenon has advantages over helium, such as natural abundance, lower diffusion, and high solubility in blood. It presents a large frequency chemical shift when dissolved in blood, tissue, brain, or trapped in molecular cages. A new design of a high-flow low-pressure spin-exchange optical pumping Rb-Xe polarizer was recently demonstrated by our group. The concept of counterflowing the gas mixture against laser light and dividing the polarizing cell in three operational zones has resulted in an increase with over an order of magnitude in the output magnetization compared with previously reported polarizers. We were able to produce hyperpolarized xenon at 64% polarization for 0.3 liters/hour flow rate and 22% polarization at 6 liters/hour. We also demonstrated a new design of freezing and thawing hyperpolarized xenon with minimum losses. We will present the concept of the high-flow low-pressure counterflowing xenon polarizer, its performance, as well as new optical pumping laser technologies. We will discuss optimization plans for xenon polarizing systems based on experimental observed limitations and theoretical modeling.

  5. Magnetic decoupling of 129Xe-Rb and 129Xe-Cs binary spin exchange

    NASA Astrophysics Data System (ADS)

    Jau, Yuan-Yu; Kuzma, Nicholas N.; Happer, William

    2003-02-01

    We report calculations of the magnetic decoupling of the nuclear spin relaxation rate of 129Xe atoms caused by binary collisions with Rb or Cs atoms in a gas. A semiclassical approximation, using a classical path for the collision and treating the spin interactions quantum mechanically, gives results that differ by no more than 2% from calculations with the distorted-wave Born approximation. Both computational methods show that the relaxation rate decreases substantially for magnetic fields of a few tens of teslas. For 129Xe-Rb, where recent experimental measurements are available, the calculated rate coefficients at the experimental field of 9.4 T are about 80% of the calculated values at zero field. At 9.4 T, the calculated rate coefficient for 129Xe-Rb is about one-half of the experimentally observed value. This discrepancy is probably due to inaccuracies in the van der Waals and spin-dependent potentials used in the calculations.

  6. A Molecular Imaging Approach to Mercury Sensing Based on Hyperpolarized (129)Xe Molecular Clamp Probe.

    PubMed

    Guo, Qianni; Zeng, Qingbin; Jiang, Weiping; Zhang, Xiaoxiao; Luo, Qing; Zhang, Xu; Bouchard, Louis-S; Liu, Maili; Zhou, Xin

    2016-03-14

    Mercury pollution, in the form of mercury ions (Hg(2+)), is a major health and environmental hazard. Commonly used sensors are invasive and limited to point measurements. Fluorescence-based sensors do not provide depth resolution needed to image spatial distributions. Herein we report a novel sensor capable of yielding spatial distributions by MRI using hyperpolarized (129)Xe. A molecular clamp probe was developed consisting of dipyrrolylquinoxaline (DPQ) derivatives and twocryptophane-A cages. The DPQ derivatives act as cation receptors whereas cryptophane-A acts as a suitable host molecule for xenon. When the DPQ moiety interacts with mercury ions, the molecular clamp closes on the ion. Due to overlap of the electron clouds of the two cryptophane-A cages, the shielding effect on the encapsulated Xe becomes important. This leads to an upfield change of the chemical shift of the encapsulated Xe. This sensor exhibits good selectivity and sensitivity toward the mercury ion. This mercury-activated hyperpolarized (129)Xe-based chemosensor is a new concept method for monitoring Hg(2+) ion distributions by MRI. PMID:26792102

  7. NMR of laser-polarized 129Xe in blood foam

    NASA Technical Reports Server (NTRS)

    Tseng, C. H.; Peled, S.; Nascimben, L.; Oteiza, E.; Walsworth, R. L.; Jolesz, F. A.

    1997-01-01

    Laser-polarized 129Xe dissolved in a foam preparation of fresh human blood was investigated. The NMR signal of 129Xe dissolved in blood was enhanced by creating a foam in which the dissolved 129Xe exchanged with a large reservoir of gaseous laser-polarized 129Xe. The dissolved 129Xe T1 in this system was found to be significantly shorter in oxygenated blood than in deoxygenated blood. The T1 of 129Xe dissolved in oxygenated blood foam was found to be approximately 21 (+/-5) s, and in deoxygenated blood foam to be greater than 40 s. To understand the oxygenation trend, T1 measurements were also made on plasma and hemoglobin foam preparations. The measurement technique using a foam gas-liquid exchange interface may also be useful for studying foam coarsening and other liquid physical properties.

  8. EDM measurement in 129Xe atom using dual active feedback nuclear spin maser

    NASA Astrophysics Data System (ADS)

    Sato, T.; Ichikawa, Y.; Ohtomo, Y.; Sakamoto, Y.; Kojima, S.; Funayama, C.; Suzuki, T.; Chikamori, M.; Hikota, E.; Tsuchiya, M.; Furukawa, T.; Yoshimi, A.; Bidinosti, C. P.; Ino, T.; Ueno, H.; Matsuo, Y.; Fukuyama, T.; Asahi, K.

    2015-04-01

    The technique of an active nuclear spin maser is adopted in the search for electric dipole moment in a diamagnetic atom 129Xe. In order to reduce systematic uncertainties arising from long-term drifts of the external magnetic field and from the contact interaction between longitudinal polarized Rb atoms and 129Xe spin, a 3He comagnetometer with a double-cell geometry was employed. The remaining shift, which turned out to show some correlation with the cell temperature, was mitigated by stabilizing the cell temperature. As a result, the frequency drift of the 129Xe maser was reduced from 12 mHz to 700 μHz, and the determination precision of frequency of 8.7 nHz was obtained for a 2×104 s measurement time using the double-cell geometry cell.

  9. Search for electric dipole moment in 129Xe atom using active nuclear spin maser

    NASA Astrophysics Data System (ADS)

    Ichikawa, Y.; Chikamori, M.; Ohtomo, Y.; Hikota, E.; Sakamoto, Y.; Suzuki, T.; Bidinosti, C. P.; Inoue, T.; Furukawa, T.; Yoshimi, A.; Suzuki, K.; Nanao, T.; Miyatake, H.; Tsuchiya, M.; Yoshida, N.; Shirai, H.; Ino, T.; Ueno, H.; Matsuo, Y.; Fukuyama, T.; Asahi, K.

    2014-03-01

    An experimental search for an electric dipole moment in the diamagnetic atom 129Xe is in progress through the precision measurement of spin precession frequency using an active nuclear spin maser. A 3He comagnetometer has been incorporated into the active spin maser system in order to cancel out the long-term drifts in the external magnetic field. Also, a double-cell geometry has been adopted in order to suppress the frequency shifts due to interaction with polarized Rb atoms. The first EDM measurement with the 129Xe active spin maser and the 3He comagnetometer has been conducted.

  10. NMR spectroscopy of hyperpolarized ^129Xe at high fields: Maintaining spin polarization after optical pumping.

    NASA Astrophysics Data System (ADS)

    Patton, Brian; Kuzma, Nicholas N.; Lisitza, Natalia V.; Happer, William

    2003-05-01

    Spin-polarized ^129Xe has become an invaluable tool in nuclear magnetic resonance research, with applications ranging from medical imaging to high-resolution spectroscopy. High-field NMR studies using hyperpolarized xenon as a spectroscopic probe benefit from the high signal-to-noise ratios and large chemical shifts typical of optically-pumped noble gases. The experimental sensitivity is ultimately determined by the absolute polarization of the xenon in the sample, which can be substantially decreased during purification and transfer. NMR of xenon at high fields (9.4 Tesla) will be discussed, and potential mechanisms of spin relaxation during the distillation, storage(N. N. Kuzma, B. Patton, K. Raman, and W. Happer, Phys. Rev. Lett. 88), 147602 (2002)., and delivery of hyperpolarized xenon will be analyzed.

  11. Understanding cage effects in imidazolium ionic liquids by 129Xe NMR: MD simulations and relativistic DFT calculations.

    PubMed

    Saielli, Giacomo; Bagno, Alessandro; Castiglione, Franca; Simonutti, Roberto; Mauri, Michele; Mele, Andrea

    2014-12-01

    (129)Xe NMR has been recently employed to probe the local structure of ionic liquids (ILs). However, no theoretical investigation has been yet reported addressing the problem of the dependence of the chemical shift of xenon on the cage structure of the IL. Therefore, we present here a study of the chemical shift of (129)Xe in two ionic liquids, [bmim][Cl] and [bmim][PF6], by a combination of classical MD simulations and relativistic DFT calculations of the xenon shielding constant. The bulk structure of the two ILs is investigated by means of the radial distribution functions, paying special attention to the local structure, volume, and charge distribution of the cage surrounding the xenon atom. Relativistic DFT calculations, based on the ZORA formalism, on clusters extracted from the trajectory files of the two systems, yield an average relative chemical shift in good agreement with the experimental data. Our results demonstrate the importance of the cage volume and the average charge surrounding the xenon nucleus in the IL cage as the factors determining the effective shielding. PMID:25394282

  12. Optically polarized {sup 129}Xe NMR investigation of carbon nanotubes

    SciTech Connect

    Clewett, Catherine F. M.; Morgan, Steven W.; Saam, Brian; Pietrass, Tanja

    2008-12-15

    We demonstrate the utility of optically polarized {sup 129}Xe NMR in a convection cell for measuring the surface properties of materials. In particular, we show adsorption of xenon gas on oxidatively purified single- and multiwalled carbon nanotubes. The interaction between xenon and multiwalled nanotubes produced by chemical vapor deposition was stronger than that of single- or multiwalled nanotubes produced by carbon arc discharge. Xenon was observed in gas, liquid, and adsorbed phases. The large polarization and moderate pressures of xenon ({approx}0.2 MPa) allowed resolution of multiple lines in both the gas and condensed phases of xenon in contact with carbon nanotubes. Xe gas exchanges with physisorbed xenon in two different environments. Xe adsorbs preferentially on defects, but if the number of defects is not sufficient, it will also adsorb on surface and interstitial sites. Penetration of Xe in the tube interior was not observed.

  13. Temperature-Ramped 129Xe Spin-Exchange Optical Pumping

    PubMed Central

    2015-01-01

    We describe temperature-ramped spin-exchange optical pumping (TR-SEOP) in an automated high-throughput batch-mode 129Xe hyperpolarizer utilizing three key temperature regimes: (i) “hot”—where the 129Xe hyperpolarization rate is maximal, (ii) “warm”—where the 129Xe hyperpolarization approaches unity, and (iii) “cool”—where hyperpolarized 129Xe gas is transferred into a Tedlar bag with low Rb content (<5 ng per ∼1 L dose) suitable for human imaging applications. Unlike with the conventional approach of batch-mode SEOP, here all three temperature regimes may be operated under continuous high-power (170 W) laser irradiation, and hyperpolarized 129Xe gas is delivered without the need for a cryocollection step. The variable-temperature approach increased the SEOP rate by more than 2-fold compared to the constant-temperature polarization rate (e.g., giving effective values for the exponential buildup constant γSEOP of 62.5 ± 3.7 × 10–3 min–1 vs 29.9 ± 1.2 × 10–3 min–1) while achieving nearly the same maximum %PXe value (88.0 ± 0.8% vs 90.1% ± 0.8%, for a 500 Torr (67 kPa) Xe cell loading—corresponding to nuclear magnetic resonance/magnetic resonance imaging (NMR/MRI) enhancements of ∼3.1 × 105 and ∼2.32 × 108 at the relevant fields for clinical imaging and HP 129Xe production of 3 T and 4 mT, respectively); moreover, the intercycle “dead” time was also significantly decreased. The higher-throughput TR-SEOP approach can be implemented without sacrificing the level of 129Xe hyperpolarization or the experimental stability for automation—making this approach beneficial for improving the overall 129Xe production rate in clinical settings. PMID:25008290

  14. Temperature-ramped (129)Xe spin-exchange optical pumping.

    PubMed

    Nikolaou, Panayiotis; Coffey, Aaron M; Barlow, Michael J; Rosen, Matthew S; Goodson, Boyd M; Chekmenev, Eduard Y

    2014-08-19

    We describe temperature-ramped spin-exchange optical pumping (TR-SEOP) in an automated high-throughput batch-mode (129)Xe hyperpolarizer utilizing three key temperature regimes: (i) "hot"-where the (129)Xe hyperpolarization rate is maximal, (ii) "warm"-where the (129)Xe hyperpolarization approaches unity, and (iii) "cool"-where hyperpolarized (129)Xe gas is transferred into a Tedlar bag with low Rb content (<5 ng per ∼1 L dose) suitable for human imaging applications. Unlike with the conventional approach of batch-mode SEOP, here all three temperature regimes may be operated under continuous high-power (170 W) laser irradiation, and hyperpolarized (129)Xe gas is delivered without the need for a cryocollection step. The variable-temperature approach increased the SEOP rate by more than 2-fold compared to the constant-temperature polarization rate (e.g., giving effective values for the exponential buildup constant γSEOP of 62.5 ± 3.7 × 10(-3) min(-1) vs 29.9 ± 1.2 × 10(-3) min(-1)) while achieving nearly the same maximum %PXe value (88.0 ± 0.8% vs 90.1% ± 0.8%, for a 500 Torr (67 kPa) Xe cell loading-corresponding to nuclear magnetic resonance/magnetic resonance imaging (NMR/MRI) enhancements of ∼3.1 × 10(5) and ∼2.32 × 10(8) at the relevant fields for clinical imaging and HP (129)Xe production of 3 T and 4 mT, respectively); moreover, the intercycle "dead" time was also significantly decreased. The higher-throughput TR-SEOP approach can be implemented without sacrificing the level of (129)Xe hyperpolarization or the experimental stability for automation-making this approach beneficial for improving the overall (129)Xe production rate in clinical settings. PMID:25008290

  15. Hyperpolarized 129Xe MRI of the Human Lung

    PubMed Central

    Mugler, John P.; Altes, Talissa A.

    2012-01-01

    By permitting direct visualization of the airspaces of the lung, MR imaging using hyperpolarized gases provides unique strategies for evaluating pulmonary structure and function. Although the vast majority of research in humans has been performed using hyperpolarized 3He, recent contraction in the supply of 3He and consequent increases in price have turned attention to the alternative agent, hyperpolarized 129Xe. Compared to 3He, 129Xe yields reduced signal due to its smaller magnetic moment. Nonetheless, taking advantage of advances in gas-polarization technology, recent studies in humans using techniques for measuring ventilation, diffusion, and partial pressure of oxygen have demonstrated results for hyperpolarized 129Xe comparable to those previously demonstrated using hyperpolarized 3He. In addition, xenon has the advantage of readily dissolving in lung tissue and blood following inhalation, which makes hyperpolarized 129Xe particularly attractive for exploring certain characteristics of lung function, such as gas exchange and uptake, which cannot be accessed using 3He. Preliminary results from methods for imaging 129Xe dissolved in the human lung suggest that these approaches will provide new opportunities for quantifying relationships among gas delivery, exchange, and transport, and thus show substantial potential to broaden our understanding of lung disease. Finally, recent changes in the commercial landscape of the hyperpolarized-gas field now make it possible for this innovative technology to move beyond the research lab. PMID:23355432

  16. Double-Cell Geometry for 129Xe/3He Co-Magnetometry

    NASA Astrophysics Data System (ADS)

    Ohtomo, Yuichi; Ichikawa, Yuichi; Sato, Tomoya; Sakamoto, Yu; Kojima, Shuichiro; Suzuki, Takahiro; Shirai, Hazuki; Chikamori, Masatoshi; Hikota, Eri; Miyatake, Hirokazu; Nanao, Tsubasa; Suzuki, Kunifumi; Tsuchiya, Masato; Inoue, Takeshi; Furukawa, Takeshi; Yoshimi, Akihiro; Bidinosti, Christopher P.; Ino, Takashi; Ueno, Hideki; Matsuo, Yukari; Fukuyama, Takeshi; Asahi, Koichiro

    Comagnetometers play a key role in EDM experiments. They allow one to quantify, and subsequently correct for, any long-term drifts of the external magnetic field. In order to improve the performance of the 3He comagnetometer for our 129Xe EDM measurements, we have decided to incorporate a double-cell geometry which enables us to suppress a frequency shift due to contact interaction with polarized Rb atoms. In this study, the production and relaxation of 3He spin polarization in the double cell were studied. As a result, the followings were achieved: a polarization of 1.04(8)%, a longitudinal spin relaxation time of 10.1(5) h, and a transverse relaxation time of 2,340 s. With these improvements, concurrent operation of the 129Xe and 3He masers has been realized, and EDM measurement will be started in near future using a cell designed based on the results of this study.

  17. Hyperpolarized 129Xe MRI: A Viable Functional Lung Imaging Modality?

    PubMed Central

    Patz, Samuel; Hersman, F. William; Muradian, Iga; Hrovat, Mirko I.; Ruset, Iulian C.; Ketel, Stephen; Jacobson, Francine; Topulos, George P.; Hatabu, Hiroto; Butler, James P.

    2008-01-01

    The majority of researchers investigating hyperpolarized gas MRI as a candidate functional lung imaging modality have used 3He as their imaging agent of choice rather than 129Xe. This preference has been predominantly due to, 3He providing stronger signals due to higher levels of polarization and higher gyromagnetic ratio, as well as its being easily available to more researchers due to availability of polarizers (USA) or ease of gas transport (Europe). Most researchers agree, however, that hyperpolarized 129Xe will ultimately emerge as the imaging agent of choice due to its unlimited supply in nature and its falling cost. Our recent polarizer technology delivers vast improvements in hyperpolarized 129Xe output. Using this polarizer, we have demonstrated the unique property of xenon to measure alveolar surface area noninvasively. In this article, we describe our human protocols and their safety, and our results for the measurement of the partial pressure of pulmonary oxygen (pO2) by observation of 129Xe signal decay. We note that the measurement of pO2 by observation of 129Xe signal decay is more complex than that for 3He because of an additional signal loss mechanism due to interphase diffusion of 129Xe from alveolar gas spaces to septal tissue. This results in measurements of an equivalent pO2 that accounts for both traditional T1 decay from pO2 and that from interphase diffusion. We also provide an update on new technological advancements that form the foundation for an improved compact design polarizer as well as improvements that provide another order-of-magnitude scale-up in xenon polarizer output. PMID:17890035

  18. A Genetically Encoded β-Lactamase Reporter for Ultrasensitive (129) Xe NMR in Mammalian Cells.

    PubMed

    Wang, Yanfei; Roose, Benjamin W; Palovcak, Eugene J; Carnevale, Vincenzo; Dmochowski, Ivan J

    2016-07-25

    Molecular imaging holds considerable promise for elucidating biological processes in normal physiology as well as disease states, but requires noninvasive methods for identifying analytes at sub-micromolar concentrations. Particularly useful are genetically encoded, single-protein reporters that harness the power of molecular biology to visualize specific molecular processes, but such reporters have been conspicuously lacking for in vivo magnetic resonance imaging (MRI). Herein, we report TEM-1 β-lactamase (bla) as a single-protein reporter for hyperpolarized (HP) (129) Xe NMR, with significant saturation contrast at 0.1 μm. Xenon chemical exchange saturation transfer (CEST) interactions with the primary allosteric site in bla give rise to a unique saturation peak at 255 ppm, well removed (≈60 ppm downfield) from the (129) Xe-H2 O peak. Useful saturation contrast was also observed for bla expressed in bacterial cells and mammalian cells. PMID:27305488

  19. A 3 He-129 Xe co-magnetometer with 87 Rb magnetometry

    NASA Astrophysics Data System (ADS)

    Limes, Mark; Sheng, Dong; Romalis, Mike

    2016-05-01

    We report progress on a 3 He-129 Xe co-magnetometer detected with a 87 Rb magnetometer. The noble-gas co-magnetometer is insensitive to any long-term bias field drifts, but the presence of hot Rb can cause instability in the ratio of 3 He-129 Xe precession frequencies. We use a sequence of Rb π pulses to suppress the instability due to Rb-noble gas interactions by a factor of 104 along all three spatial axes. For detection, our 87 Rb magnetometer operates using single-axis 87 Rb π pulses with σ+ /σ- pumping-this technique decouples the 87 Rb magnetometer from bias fields, and allows for SERF operation. We are presently investigating systematic effects due to combinations of several imperfections, such as longitudinal noble gas polarization, imperfect 87 Rb π pulses, and 87 Rb pump light shifts. Thus far, our 87 Rb magnetometer has a sensitivity of 40 fT/√{Hz}, and our 3 He-129 Xe co-magnetometer has achieved a single-shot precession frequency ratio error of 20 nHz and a long-term bias drift of 8 nHz at 7 h. We are developing the co-magnetometer for use as an NMR gyro, and to search for possible spin-gravity interactions. Supported by DARPA and NSF.

  20. DFT study of the NMR properties of xenon in covalent compounds and van der waals complexes-implications for the use of 129Xe as a molecular probe.

    PubMed

    Bagno, Alessandro; Saielli, Giacomo

    2003-04-01

    The NMR properties (chemical shift and spin-spin coupling constants) of (129)Xe in covalent compounds and weakly bound complexes have been investigated by DFT methods including relativistic effects. For covalent species, a good agreement between experimental and calculated results is achieved without scalar relativistic effects, but their inclusion (with a triple-zeta, double-polarization basis set) leads to some improvement in the quality of the correlation. The spin-orbit coupling term has a significant effect on the shielding constant, but makes a small contribution to the chemical shift. Coupling constants contain substantial contributions from the Fermi contact and paramagnetic spin-orbit terms; unlike light nuclei the spin-dipole term is also large, whereas the diamagnetic spin-orbit term is negligible. For van der Waals dimers, the dependence of the xenon chemical shift and anisotropy is calculated as a function of the distance. Small (<1 Hz) but non-negligible through-space coupling constants between (129)Xe and (13)C or (1)H are predicted. Much larger couplings, of the order of few Hz, are calculated between xenon and (17)O in a model silicate residue. PMID:12658645

  1. Molecular hydrogen and catalytic combustion in the production of hyperpolarized 83Kr and 129Xe MRI contrast agents

    NASA Astrophysics Data System (ADS)

    Rogers, Nicola J.; Hill-Casey, Fraser; Stupic, Karl F.; Six, Joseph S.; Lesbats, Clémentine; Rigby, Sean P.; Fraissard, Jacques; Pavlovskaya, Galina E.; Meersmann, Thomas

    2016-03-01

    Hyperpolarized (hp) 83Kr is a promising MRI contrast agent for the diagnosis of pulmonary diseases affecting the surface of the respiratory zone. However, the distinct physical properties of 83Kr that enable unique MRI contrast also complicate the production of hp 83Kr. This work presents a previously unexplored approach in the generation of hp 83Kr that can likewise be used for the production of hp 129Xe. Molecular nitrogen, typically used as buffer gas in spin-exchange optical pumping (SEOP), was replaced by molecular hydrogen without penalty for the achievable hyperpolarization. In this particular study, the highest obtained nuclear spin polarizations were P = 29% for 83Kr and P = 63% for 129Xe. The results were reproduced over many SEOP cycles despite the laser-induced on-resonance formation of rubidium hydride (RbH). Following SEOP, the H2 was reactively removed via catalytic combustion without measurable losses in hyperpolarized spin state of either 83Kr or 129Xe. Highly spin-polarized 83Kr can now be purified for the first time, to our knowledge, to provide high signal intensity for the advancement of in vivo hp 83Kr MRI. More generally, a chemical reaction appears as a viable alternative to the cryogenic separation process, the primary purification method of hp 129Xe for the past 2 1/2 decades. The inherent simplicity of the combustion process will facilitate hp 129Xe production and should allow for on-demand continuous flow of purified and highly spin-polarized 129Xe.

  2. Molecular hydrogen and catalytic combustion in the production of hyperpolarized 83Kr and 129Xe MRI contrast agents.

    PubMed

    Rogers, Nicola J; Hill-Casey, Fraser; Stupic, Karl F; Six, Joseph S; Lesbats, Clémentine; Rigby, Sean P; Fraissard, Jacques; Pavlovskaya, Galina E; Meersmann, Thomas

    2016-03-22

    Hyperpolarized (hp) (83)Kr is a promising MRI contrast agent for the diagnosis of pulmonary diseases affecting the surface of the respiratory zone. However, the distinct physical properties of (83)Kr that enable unique MRI contrast also complicate the production of hp (83)Kr. This work presents a previously unexplored approach in the generation of hp (83)Kr that can likewise be used for the production of hp (129)Xe. Molecular nitrogen, typically used as buffer gas in spin-exchange optical pumping (SEOP), was replaced by molecular hydrogen without penalty for the achievable hyperpolarization. In this particular study, the highest obtained nuclear spin polarizations were P =29% for(83)Kr and P= 63% for (129)Xe. The results were reproduced over many SEOP cycles despite the laser-induced on-resonance formation of rubidium hydride (RbH). Following SEOP, the H2 was reactively removed via catalytic combustion without measurable losses in hyperpolarized spin state of either (83)Kr or (129)Xe. Highly spin-polarized (83)Kr can now be purified for the first time, to our knowledge, to provide high signal intensity for the advancement of in vivo hp (83)Kr MRI. More generally, a chemical reaction appears as a viable alternative to the cryogenic separation process, the primary purification method of hp(129)Xe for the past 2 1/2 decades. The inherent simplicity of the combustion process will facilitate hp (129)Xe production and should allow for on-demand continuous flow of purified and highly spin-polarized (129)Xe. PMID:26961001

  3. Targeted Molecular Imaging of Cancer Cells Using MS2-Based (129)Xe NMR.

    PubMed

    Jeong, Keunhong; Netirojjanakul, Chawita; Munch, Henrik K; Sun, Jinny; Finbloom, Joel A; Wemmer, David E; Pines, Alexander; Francis, Matthew B

    2016-08-17

    We have synthesized targeted, selective, and highly sensitive (129)Xe NMR nanoscale biosensors using a spherical MS2 viral capsid, Cryptophane A molecules, and DNA aptamers. The biosensors showed strong binding specificity toward targeted lymphoma cells (Ramos line). Hyperpolarized (129)Xe NMR signal contrast and hyper-CEST (129)Xe MRI image contrast indicated its promise as highly sensitive hyperpolarized (129)Xe NMR nanoscale biosensor for future applications in cancer detection in vivo. PMID:27454679

  4. Cryptophane-Folate Biosensor for 129Xe NMR

    PubMed Central

    2015-01-01

    Folate-conjugated cryptophane was developed for targeting cryptophane to membrane-bound folate receptors that are overexpressed in many human cancers. The cryptophane biosensor was synthesized in 20 nonlinear steps, which included functionalization with folate recognition moiety, solubilizing peptide, and Cy3 fluorophore. Hyperpolarized 129Xe NMR studies confirmed xenon binding to the folate-conjugated cryptophane. Cellular internalization of biosensor was monitored by confocal laser scanning microscopy and quantified by flow cytometry. Competitive blocking studies confirmed cryptophane endocytosis through a folate receptor-mediated pathway. Flow cytometry revealed 10-fold higher cellular internalization in KB cancer cells overexpressing folate receptors compared to HT-1080 cells with normal folate receptor expression. The biosensor was determined to be nontoxic in HT-1080 and KB cells by MTT assay at low micromolar concentrations typically used for hyperpolarized 129Xe NMR experiments. PMID:25438187

  5. Resonance technique to probe 129Xe surface interactions

    NASA Astrophysics Data System (ADS)

    Sauer, K. L.; Fitzgerald, R. J.; Happer, W.

    1999-03-01

    We describe a resonance technique to probe the coupling between two spin systems at low magnetic fields. With the use of a single rotating magnetic field we match the Rabi frequency of one spin to the Larmor frequency of a second, thereby affecting the T1 of the second spin species. We have used this technique to demonstrate the contribution of coupling to surface protons to the relaxation of gaseous and liquid laser-polarized 129Xe.

  6. Combustion resistance of the 129Xe hyperpolarized nuclear spin state.

    PubMed

    Stupic, Karl F; Six, Joseph S; Olsen, Michael D; Pavlovskaya, Galina E; Meersmann, Thomas

    2013-01-01

    Using a methane-xenon mixture for spin exchange optical pumping, MRI of combustion was enabled. The (129)Xe hyperpolarized nuclear spin state was found to sufficiently survive the complete passage through the harsh environment of the reaction zone. A velocity profile (V(z)(z)) of a flame was recorded to demonstrate the feasibility of MRI velocimetry of transport processes in combustors. PMID:23165418

  7. Nuclear spin resonance of (129)Xe doped with O(2).

    PubMed

    McNabb, J W; Balakishiyeva, D N; Honig, A

    2007-10-01

    Spin-lattice relaxation of (129)Xe nuclei in solid natural xenon has been investigated in detail over a large range of paramagnetic O(2) impurity concentrations. Direct measurements of the ground state magnetic properties of the O(2) are difficult because the ESR (electron spin resonance) lines of O(2) are rather unstructured, but NMR measurements in the liquid helium temperature region (1.4-4 K) are very sensitive to the effective magnetic moments associated with the spin 1 Zeeman levels of the O(2) molecules and to the O(2) magnetic relaxation. From these measurements, the value of the D[Sz(2)-(1/3)S(2)] spin-Hamiltonian term of the triplet spin ground state of O(2) can be determined. The temperature and magnetic field dependence of the measured paramagnetic O(2)-induced excess line width of the (129)Xe NMR signal agree well with the theoretical model with the spin-Hamiltonian D=0.19 meV (2.3 K), and with the reasonable assumption that the E[S(x)(2)-S(y)(2)] spin-Hamiltonian term is close to 0 meV. An anomalous temperature dependence between 1.4 K and 4.2K of the (129)Xe spin-lattice relaxation rate, T(1n)(-1)(T), is also accounted for by our model. Using an independent determination of the true O(2) concentration in the Xe-O(2) solid, the effective spin lattice relaxation time (which will be seen to be transition dependent) of the O(2) at 2.3 K and 0.96 T is determined to be approximately 1.4 x 10(-8)s. The experimental results, taken together with the relaxation model, suggest routes for bringing highly spin-polarized (129)Xe from the low temperature condensed phase to higher temperatures without excessive depolarization. PMID:17689279

  8. 1H and 129Xe nuclear magnetic resonance studies of hydrogen chemisorption on supported platinum. Application to the metal dispersion and spillover.

    PubMed

    Rouabah, D; Fraissard, J

    1994-06-01

    Chemisorption of hydrogen, electron microscopy and 1H nuclear magnetic resonance (NMR) have confirmed that the chemical shift of hydrogen chemisorbed on platinum is directly related to the size of the metal particles. The influence of the hydrogen adsorbate concentration and the chemisorption temperature on the chemical shift delta H and the distribution of the hydrogen chemisorbed on these particles have been determined. This study also shows how the dispersion can be deduced from the variation of delta H with the H2 concentration and clarifies the effect of temperature on the concentration of spillover H2. 129Xe NMR of adsorbed xenon used as a probe confirmed most of the previous results. PMID:7827982

  9. Hyperfine resonances in metastable ^129Xe discharge cells

    NASA Astrophysics Data System (ADS)

    Morgan, Steven W.; Xia, Tian; Jau, Yuan-Yu; Happer, William

    2008-05-01

    We have measured the hyperfine resonance linewidths of metastable ^129Xe in electrodeless rf discharge cells. The linewidths on the order of 10 kHz for Xe pressures of a few millitorr are dominated by collisions with other Xe atoms and no buffer gases are present. Additional contributions come from collisions with the walls as well as with impurities which may be drawn off the cell walls due to the harsh plasma environment. If used for small atomic clocks, metastable noble gases could require less power and would be relatively insensitive to temperature variations when compared with alkali metal atoms.

  10. Optical hyperpolarization and NMR detection of 129Xe on a microfluidic chip

    NASA Astrophysics Data System (ADS)

    Jiménez-Martínez, Ricardo; Kennedy, Daniel J.; Rosenbluh, Michael; Donley, Elizabeth A.; Knappe, Svenja; Seltzer, Scott J.; Ring, Hattie L.; Bajaj, Vikram S.; Kitching, John

    2014-05-01

    Optically hyperpolarized 129Xe gas has become a powerful contrast agent in nuclear magnetic resonance (NMR) spectroscopy and imaging, with applications ranging from studies of the human lung to the targeted detection of biomolecules. Equally attractive is its potential use to enhance the sensitivity of microfluidic NMR experiments, in which small sample volumes yield poor sensitivity. Unfortunately, most 129Xe polarization systems are large and non-portable. Here we present a microfabricated chip that optically polarizes 129Xe gas. We have achieved 129Xe polarizations >0.5% at flow rates of several microlitres per second, compatible with typical microfluidic applications. We employ in situ optical magnetometry to sensitively detect and characterize the 129Xe polarization at magnetic fields of 1 μT. We construct the device using standard microfabrication techniques, which will facilitate its integration with existing microfluidic platforms. This device may enable the implementation of highly sensitive 129Xe NMR in compact, low-cost, portable devices.

  11. Reducing Relaxation of Hyperpolarized ^129 Xe during Cryogenic Separation

    NASA Astrophysics Data System (ADS)

    Patton, B.; Kuzma, N. N.; Happer, W.

    2004-05-01

    Recent experimental results^1 indicate that the T1 relaxation time of solid ^129Xe is much shorter than previous models had predicted^2 near the xenon melting point of 161 K and at low magnetic fields. This enhanced relaxation is detrimental to commercial xenon polarizers, which cryogenically distill hyperpolarized ^129Xe from a buffer gas mixture. We have measured the fraction of xenon polarization lost during a typical cryogenic collection, using different permanent magnets to vary the holding field from 700 gauss to over a tesla. The results indicate that using a stronger permanent magnet around the cryo-trap is a simple way to increase the final polarization of the pure xenon gas. An additional experiment was conducted in order to determine whether the majority of the xenon relaxation occurs throughout accumulation (possibly as a result of temperature inhomogeneities within the frozen sample) or during the brief thawing time. In pinpointing the polarization loss, this research may suggest new designs for xenon polarizers. 1. Kuzma et al., Phys. Rev. Lett. 88, 147602 (2002). 2. Fitzgerald et al., Phys. Rev. B 59, 8795 (1999).

  12. {sup 129}Xe magic-angle spinning spectra of xenon in zeolite NaA direct observation of mixed clusters of co-adsorbed species.

    SciTech Connect

    Jameson, A. K.; Jameson, C. J.; de Dios, A. C.; Oldfield, E.; Gerald, R. E., II; Turner, G. L.; Chemical Engineering; Loyola Univ.; Univ. of Illinois at Chicago; Univ. of Illinois; Spectral Data Services, Inc.

    1995-01-01

    We present the first demonstration that the individual {sup 129}Xe resonances corresponding to Xe{sub n} (n = 1-8) clusters inside the {alpha}-cages of zeolite NaA can be narrowed under magic-angle spinning (MAS). Under these high-resolution conditions we also observe upon addition of Kr the individual peaks corresponding to mixed clusters, Xe{sub n}Kr{sub m}, inside the a-cages, which will allow the first direct determination of the distribution of co-adsorbates in a microporous solid. Under MAS the chemical shifts of the Xe{sub n} clusters are shown to be highly sensitive to 'disorder' in the zeolite and provides new, quantitative information about the presence of {alpha}-cages of several types.

  13. Fast Nuclear Spin Relaxation in Hyperpolarized Solid 129Xe

    NASA Astrophysics Data System (ADS)

    Kuzma, N. N.; Patton, B.; Raman, K.; Happer, W.

    2002-04-01

    We report extensive new measurements of the longitudinal relaxation time T1 of 129Xe nuclear spins in solid xenon. For temperatures T<120 K and magnetic fields B>0.05 T, we found T1 on the order of hours, in good agreement with previous measurements and with the predicted phonon-scattering limit for the spin-rotation interaction. For T>120 K, our new data show that T1 can be much shorter than the phonon scattering limit. For B = 0.06 T, a field often used to accumulate hyperpolarized xenon, T1 is ~6 s near the Xe melting point Tm = 161.4 K. From T = 50 K to Tm, the new data are in excellent agreement with the theoretical prediction that the relaxation is due to (i) modulation of the spin-rotation interaction by phonons, and (ii) modulation of the dipole-dipole interaction by vacancy diffusion.

  14. (129)Xe NMR Relaxation-Based Macromolecular Sensing.

    PubMed

    Gomes, Muller D; Dao, Phuong; Jeong, Keunhong; Slack, Clancy C; Vassiliou, Christophoros C; Finbloom, Joel A; Francis, Matthew B; Wemmer, David E; Pines, Alexander

    2016-08-10

    We report a (129)Xe NMR relaxation-based sensing approach that exploits changes in the bulk xenon relaxation rate induced by slowed tumbling of a cryptophane-based sensor upon target binding. The amplification afforded by detection of the bulk dissolved xenon allows sensitive detection of targets. The sensor comprises a xenon-binding cryptophane cage, a target interaction element, and a metal chelating agent. Xenon associated with the target-bound cryptophane cage is rapidly relaxed and then detected after exchange with the bulk. Here we show that large macromolecular targets increase the rotational correlation time of xenon, increasing its relaxation rate. Upon binding of a biotin-containing sensor to avidin at 1.5 μM concentration, the free xenon T2 is reduced by a factor of 4. PMID:27472048

  15. Magnetic Field Stabilization for 129Xe EDM Search Experiment

    NASA Astrophysics Data System (ADS)

    Furukawa, Takeshi; Inoue, Takeshi; Nanao, Tsubasa; Yoshimi, Akihiro; Tsuchiya, Masato; Hayashi, Hironori; Uchida, Makoto; Asahi, Koichiro

    2011-09-01

    Magnetic field stabilization is a crucial condition parameter for many kinds of ultra-high precision measurements such as a search for an electric dipole moment (EDM). The instability of magnetic field strength often arises from the drift of current flow in a solenoid coil to generate the magnetic field. For our EDM search experiment with maser oscillating diamagnetic 129Xe atoms, we have developed a new stabilized current source based on a feedback system which is devised to correct the amount of current flow measured precisely with high-precision digital multimeter and standard resistor. Using this new current source, we have successfully reduced the drifts of coil current by at least a factor of 100 compared to commercially available current sources.

  16. 3D MRI of impaired hyperpolarized 129Xe uptake in a rat model of pulmonary fibrosis.

    PubMed

    Cleveland, Zackary I; Virgincar, Rohan S; Qi, Yi; Robertson, Scott H; Degan, Simone; Driehuys, Bastiaan

    2014-12-01

    A variety of pulmonary pathologies, in particular interstitial lung diseases, are characterized by thickening of the pulmonary blood-gas barrier, and this thickening results in reduced gas exchange. Such diffusive impairment is challenging to quantify spatially, because the distributions of the metabolically relevant gases (CO2 and O2) cannot be detected directly within the lungs. Hyperpolarized (HP) (129)Xe is a promising surrogate for these metabolic gases, because MR spectroscopy and imaging allow gaseous alveolar (129)Xe to be detected separately from (129)Xe dissolved in the red blood cells (RBCs) and the adjacent tissues, which comprise blood plasma and lung interstitium. Because (129)Xe reaches the RBCs by diffusing across the same barrier tissues (blood plasma and interstitium) as O2, barrier thickening will delay (129)Xe transit and, thus, reduce RBC-specific (129)Xe MR signal. Here we have exploited these properties to generate 3D, MR images of (129)Xe uptake by the RBCs in two groups of rats. In the experimental group, unilateral fibrotic injury was generated prior to imaging by instilling bleomycin into one lung. In the control group, a unilateral sham instillation of saline was performed. Uptake of (129)Xe by the RBCs, quantified as the fraction of RBC signal relative to total dissolved (129)Xe signal, was significantly reduced (P = 0.03) in the injured lungs of bleomycin-treated animals. In contrast, no significant difference (P = 0.56) was observed between the saline-treated and untreated lungs of control animals. Together, these results indicate that 3D MRI of HP (129)Xe dissolved in the pulmonary tissues can provide useful biomarkers of impaired diffusive gas exchange resulting from fibrotic thickening. PMID:24816478

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

    PubMed

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

    2004-04-01

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

  18. High-spin structures in the 129Xe nucleus

    NASA Astrophysics Data System (ADS)

    Huang, Y.; Xiao, Z. G.; Zhu, S. J.; Qi, C.; Xu, Q.; Cheng, W. J.; Li, H. J.; Lyu, L. M.; Wang, R. S.; Yan, W. H.; Yi, H.; Zhang, Y.; Chen, Q. M.; He, C. Y.; Hu, S. P.; Li, C. B.; Li, H. W.; Luo, P. W.; Wu, X. G.; Wu, Y. H.; Zheng, Y.; Zhong, J.

    2016-06-01

    High-spin states in the 129Xe nucleus are studied with the reaction 124Sn(9Be,4 n ) at a beam energy of 36 MeV. The level scheme is extended significantly. For the positive-parity band, the α =+1 /2 and the α =-1 /2 signature components are combined to form a complete band structure based on the 3 /2+ state with spin and parity up to 21 /2+ . For the negative-parity band based on the 11 /2- state, the α =+1 /2 signature component is newly established and both the α =+1 /2 and the α =-1 /2 signature components also form a complete band structure up to the 35 /2- state. The positive- and negative-parity bands are proposed to originate from ν d3 /23 /2+[402 ] and ν h11 /211 /2-[505 ] Nilsson configurations, respectively. A backbending is observed in the negative-parity band, which originates from the alignments of two h11 /2 protons according to crank shell model calculations. Based on the total Routhian surface and quasiparticle triaxial rotor model calculations, the negative-parity band is interpreted as a triaxially deformed shape with γ ≈-30∘ , while the positive-parity band is associated with γ softness, in accordance with previous studies. In the high-spin states, three decoupled bands and one oblate band with γ ≈-60∘ are newly identified. The systematics and other characteristics of these bands are discussed.

  19. Diffusion of hyperpolarized 129Xe in the lung: a simplified model of 129Xe septal uptake and experimental results

    NASA Astrophysics Data System (ADS)

    Patz, Samuel; Muradyan, Iga; Hrovat, Mirko I.; Dabaghyan, Mikayel; Washko, George R.; Hatabu, Hiroto; Butler, James P.

    2011-01-01

    We used hyperpolarized 129Xe NMR to measure pulmonary alveolar surface area per unit gas volume SA/Vgas, alveolar septal thickness h and capillary transit time τ, three critical determinants of the lung's primary role as a gas exchange organ. An analytical solution for a simplified diffusion model is described, together with a modification of the xenon transfer contrast imaging technique utilizing 90° radio-frequency pulses applied to the dissolved phase, rather than traditional 180° pulses. With this approach, three-dimensional (3D) maps of SA/Vgas were obtained. We measured global SA/Vgas, h and τ in four normal subjects, two subjects with mild interstitial lung disease (ILD) and two subjects with mild chronic obstructive pulmonary disease (COPD). In normals, SA/Vgas decreased with increasing lung volume from ~320 to 80 cm-1 both h~13 μm and τ~1.5 s were relatively constant. For the two ILD subjects, h was, respectively, 36 and 97% larger than normal, quantifying an increased gas/blood tissue barrier; SA/Vgas and τ were normal. The two COPD subjects had SA/Vgas values ~25% that of normals, quantifying septal surface loss in emphysema; h and τ were normal. These are the first noninvasive, non-radiation-based, quantitative measurements of h and τ in patients with pulmonary disease.

  20. Nuclear spin-spin coupling anisotropy in the van der Waals-bonded 129Xe dimer.

    PubMed

    Jokisaari, Jukka; Vaara, Juha

    2013-07-21

    The spin-spin coupling constant, J, in the van der Waals-bonded (129)Xe-(129)Xe dimer cannot be determined experimentally because of the magnetic equivalence of the two nuclei. In contrast, the anisotropy of the coupling tensor, ΔJ, can be obtained from the so called effective dipole-dipole coupling determined in a solid state inclusion compound whose cages accommodate two xenon atoms. For the determination of the experimental ΔJ((129)Xe, (129)Xe) we exploited the data reported earlier in this journal. [D. H. Brouwer et al., Phys. Chem. Chem. Phys., 2007, 9, 1093.] The experimental value and the value obtained from relativistic first-principles computation are in perfect agreement. To the best of our knowledge this is the first investigation of spin-spin coupling anisotropy in a van der Waals-bonded system. PMID:23743998

  1. Magnetic resonance imaging of dissolved hyperpolarized 129Xe using a membrane-based continuous flow system

    NASA Astrophysics Data System (ADS)

    Amor, N.; Zänker, P. P.; Blümler, P.; Meise, F. M.; Schreiber, L. M.; Scholz, A.; Schmiedeskamp, J.; Spiess, H. W.; Münnemann, K.

    2009-11-01

    A technique for continuous production of solutions containing hyperpolarized 129Xe is explored for MRI applications. The method is based on hollow fiber membranes which inhibit the formation of foams and bubbles. A systematic analysis of various carrier agents for hyperpolarized 129Xe has been carried out, which are applicable as contrast agents for in vivo MRI. The image quality of different hyperpolarized Xe solutions is compared and MRI results obtained in a clinical as well as in a nonclinical MRI setting are provided. Moreover, we demonstrate the application of 129Xe contrast agents produced with our dissolution method for lung MRI by imaging hyperpolarized 129Xe that has been both dissolved in and outgassed from a carrier liquid in a lung phantom, illustrating its potential for the measurement of lung perfusion and ventilation.

  2. Search for Spin-Dependent Short-Range Interaction with an 3He/129Xe Clock Comparison Experiment

    NASA Astrophysics Data System (ADS)

    Tullney, Kathlynne; Heil, Werner; Karpuk, Sergei; Sobolev, Yuri; Allmendinger, Fabian; Schmidt, Ulrich

    2016-02-01

    We performed an experiment to search for a new spin-dependent P- and T-violating nucleon-nucleon interaction σ→ ṡr̂ which is mediated by light pseudoscalar bosons such as axions or axionlike particles. This interaction causes a shift Δν in the precession frequency of nuclear spin polarized gases in the presence of an unpolarized mass. In order to measure this frequency shift a 3He/129Xe comagnetometer was used which is based on the detection of free precession of 3He and 129Xe nuclear spins using SQUIDs as detectors. For the upper limit of Δνsp we obtained 7.1nHz. With this value, an upper limit of the scalar-pseudoscalar coupling of the axion to the spin of a bound neutron could be deduced within the axion mass window. For axion masses between 2 and 500μeV, the laboratory upper bounds were improved by up to 4 orders of magnitude.

  3. High-field measurement of the 129Xe-Cs binary spin-exchange rate coefficient

    NASA Astrophysics Data System (ADS)

    Jau, Yuan-Yu; Kuzma, Nicholas N.; Happer, William

    2004-03-01

    We report the first measurement of the binary spin-exchange rate coefficient κ in the ^129Xe-Cs system. Data were taken using ^129Xe NMR in glass cells containing isotopically enriched xenon gas at pressures on the order of atmospheres and a small amount of liquid Cs metal, in the temperature range from 120 to 140^rcC and at a magnetic field of 9.4 T. The contribution of CsXe van der Waals molecules to spin exchange should have been nearly eliminated by the high magnetic field, as confirmed by our measurements of the ^129Xe longitudinal relaxation time T1 in a series of cells with various densities of xenon. The Cs atomic number density [Cs] was controlled by the cell temperature, and was experimentally determined by analysis of the Faraday rotation of linearly polarized probe laser light. We measured κ = d (T_1-1)/d[Cs]= (2.81± 0.2) × 10-16 cm^3 s-1 . This is about 60% larger than the previously measured rate coefficient for the ^129Xe-Rb system(Y.-Y. Jau, N. N. Kuzma, and W. Happer, Phys. Rev. A 66, 052710 (2002).), κ =d (T_1-1)/d[Rb]= (1.75± 0.12) × 10-16 cm^3 s-1 . A comparison with theory(Y.-Y. Jau, N. N. Kuzma, and W. Happer, Phys. Rev. A 67, 022720 (2003).) will be discussed.

  4. Cryogenics free production of hyperpolarized 129Xe and 83Kr for biomedical MRI applications☆

    PubMed Central

    Hughes-Riley, Theodore; Six, Joseph S.; Lilburn, David M.L.; Stupic, Karl F.; Dorkes, Alan C.; Shaw, Dominick E.; Pavlovskaya, Galina E.; Meersmann, Thomas

    2013-01-01

    As an alternative to cryogenic gas handling, hyperpolarized (hp) gas mixtures were extracted directly from the spin exchange optical pumping (SEOP) process through expansion followed by compression to ambient pressure for biomedical MRI applications. The omission of cryogenic gas separation generally requires the usage of high xenon or krypton concentrations at low SEOP gas pressures to generate hp 129Xe or hp 83Kr with sufficient MR signal intensity for imaging applications. Two different extraction schemes for the hp gasses were explored with focus on the preservation of the nuclear spin polarization. It was found that an extraction scheme based on an inflatable, pressure controlled balloon is sufficient for hp 129Xe handling, while 83Kr can efficiently be extracted through a single cycle piston pump. The extraction methods were tested for ex vivo MRI applications with excised rat lungs. Precise mixing of the hp gases with oxygen, which may be of interest for potential in vivo applications, was accomplished during the extraction process using a piston pump. The 83Kr bulk gas phase T1 relaxation in the mixtures containing more than approximately 1% O2 was found to be slower than that of 129Xe in corresponding mixtures. The experimental setup also facilitated 129Xe T1 relaxation measurements as a function of O2 concentration within excised lungs. PMID:24135800

  5. Cryogenics free production of hyperpolarized 129Xe and 83Kr for biomedical MRI applications.

    PubMed

    Hughes-Riley, Theodore; Six, Joseph S; Lilburn, David M L; Stupic, Karl F; Dorkes, Alan C; Shaw, Dominick E; Pavlovskaya, Galina E; Meersmann, Thomas

    2013-12-01

    As an alternative to cryogenic gas handling, hyperpolarized (hp) gas mixtures were extracted directly from the spin exchange optical pumping (SEOP) process through expansion followed by compression to ambient pressure for biomedical MRI applications. The omission of cryogenic gas separation generally requires the usage of high xenon or krypton concentrations at low SEOP gas pressures to generate hp (129)Xe or hp (83)Kr with sufficient MR signal intensity for imaging applications. Two different extraction schemes for the hp gasses were explored with focus on the preservation of the nuclear spin polarization. It was found that an extraction scheme based on an inflatable, pressure controlled balloon is sufficient for hp (129)Xe handling, while (83)Kr can efficiently be extracted through a single cycle piston pump. The extraction methods were tested for ex vivo MRI applications with excised rat lungs. Precise mixing of the hp gases with oxygen, which may be of interest for potential in vivo applications, was accomplished during the extraction process using a piston pump. The (83)Kr bulk gas phase T1 relaxation in the mixtures containing more than approximately 1% O2 was found to be slower than that of (129)Xe in corresponding mixtures. The experimental setup also facilitated (129)Xe T1 relaxation measurements as a function of O2 concentration within excised lungs. PMID:24135800

  6. 3D MR Imaging of Impaired Hyperpolarized 129Xe Uptake in a Rat Model of Pulmonary Fibrosis

    PubMed Central

    Cleveland, Zackary I.; Virgincar, Rohan, S.; Qi, Yi; Robertson, Scott H.; Degan, Simone; Driehuys, Bastiaan

    2014-01-01

    A variety of pulmonary pathologies, in particular interstitial lung diseases, are characterized by thickening of the pulmonary blood-gas barrier tissues, and this thickening results in reduced gas exchange. Such diffusive impairment is challenging to quantify spatially, because the distributions of the metabolically relevant gases (CO2 and O2) cannot be detected directly within the lungs. Hyperpolarized (HP) 129Xe is a promising surrogate for these metabolic gases, because MR spectroscopy and imaging allow gaseous alveolar 129Xe to be detected separately from 129Xe dissolved in the red blood cells (RBCs) and in the adjacent barrier tissues (blood plasma and lung interstitium). Further, because 129Xe reaches the RBCs by diffusing across the same barrier tissues as O2barrier thickening will delay 129Xe transit and, thus, reduce RBC-specific 129Xe MR signal. Here we exploited these properties to generate 3D, MR images of 129Xe uptake by the RBCs in two groups of rats. In the experimental group, unilateral fibrotic injury was generated prior to imaging by instilling Bleomycin into one lung. In the control group, a unilateral sham instillation of saline was performed. Uptake of 129Xe by the RBCs, quantified as the fraction of RBC signal relative to total dissolved 129Xe signal, was significantly reduced (P = 0.03) in the injured lungs of Bleomycin-treated animals. In contrast, no significant difference (P=0.56) was observed between the saline-treated and untreated lungs of control animals. Together, these results indicate that 3D MRI of HP 129Xe dissolved in the pulmonary tissues can provide useful biomarkers of impaired diffusive gas exchange resulting from fibrotic thickening. PMID:24816478

  7. Characterizing and modeling the efficiency limits in large-scale production of hyperpolarized 129Xe

    PubMed Central

    Freeman, M.S.; Emami, K.; Driehuys, B.

    2014-01-01

    The ability to produce liter volumes of highly spin-polarized 129Xe enables a wide range of investigations, most notably in the fields of materials science and biomedical MRI. However, for nearly all polarizers built to date, both peak 129Xe polarization and the rate at which it is produced fall far below those predicted by the standard model of Rb metal vapor, spin-exchange optical pumping (SEOP). In this work, we comprehensively characterized a high-volume, flow-through 129Xe polarizer using three different SEOP cells with internal volumes of 100, 200 and 300 cc and two types of optical sources: a broad-spectrum 111-W laser (FWHM = 1.92 nm) and a line-narrowed 71-W laser (FWHM = 0.39 nm). By measuring 129Xe polarization as a function of gas flow rate, we extracted peak polarization and polarization production rate across a wide range of laser absorption levels. Peak polarization for all cells consistently remained a factor of 2-3 times lower than predicted at all absorption levels. Moreover, although production rates increased with laser absorption, they did so much more slowly than predicted by the standard theoretical model and basic spin exchange efficiency arguments. Underperformance was most notable in the smallest optical cells. We propose that all these systematic deviations from theory can be explained by invoking the presence of paramagnetic Rb clusters within the vapor. Cluster formation within saturated alkali vapors is well established and their interaction with resonant laser light was recently shown to create plasma-like conditions. Such cluster systems cause both Rb and 129Xe depolarization, as well as excess photon scattering. These effects were incorporated into the SEOP model by assuming that clusters are activated in proportion to excited-state Rb number density and by further estimating physically reasonable values for the nanocluster-induced, velocity-averaged spin-destruction cross-section for Rb (<σcluster-Rbv> ≈4×10-7 cm3s-1), 129Xe

  8. Relaxation rates of low-field gas-phase ^129Xe storage cells

    NASA Astrophysics Data System (ADS)

    Limes, Mark; Saam, Brian

    2010-10-01

    A study of longitudinal nuclear relaxation rates T1 of ^129Xe and Xe-N2 mixtures in a magnetic field of 3.8 mT is presented. In this regime, intrinsic spin relaxation is dominated by the intramolecular spin-rotation interaction due to persistent xenon dimers, a mechanism that can be quelled by introducing large amounts of N2 into the storage cell. Extrinsic spin relaxation is dominated by the wall-relaxation rate, which is the primary quantity of interest for the various low-field storage cells and coatings that we have tested. Previous group work has shown that extremely long gas-phase relaxation times T1 can be obtained, but only at large magnetic fields and low xenon densities. The current work is motivated by the practical benefits of retaining hyperpolarized ^129Xe for extended periods of time in a small magnetic field.

  9. Study of gas-fluidization dynamics with laser-polarized 129Xe.

    PubMed

    Wang, Ruopeng; Rosen, Matthew Scott; Candela, Donald; Mair, Ross William; Walsworth, Ronald Lee

    2005-02-01

    We report initial NMR studies of gas dynamics in a particle bed fluidized by laser-polarized xenon (129Xe) gas. We have made preliminary measurements of two important characteristics: gas exchange between the bubble and emulsion phases and the gas velocity distribution in the bed. We used T2* contrast to differentiate the bubble and emulsion phases by choosing solid particles with large magnetic susceptibility. Experimental tests demonstrated that this method was successful in eliminating 129Xe magnetization in the emulsion phase, which enabled us to observe the time dependence of the bubble magnetization. By employing the pulsed field gradient method, we also measured the gas velocity distribution within the bed. These results clearly show the onset of bubbling and can be used to deduce information about gas and particle motion in the fluidized bed. PMID:15833613

  10. Study of Gas-Fluidization Dynamics with Laser-Polarized 129Xe

    NASA Astrophysics Data System (ADS)

    Wang, R.; Rosen, M. S.; Candela, D.; Mair, R. W.; Walsworth, R. L.

    2004-07-01

    We report initial NMR studies of gas dynamics in a particle bed fluidized by laser-polarized xenon (129Xe) gas. We have made preliminary measurements of two important characteristics: gas exchange between the bubble and emulsion phases; and the gas velocity distribution in the bed. We used T2* contrast to differentiate the bubble and emulsion phases by choosing solid particles with large magnetic susceptibility, in order. Experimental tests demonstrated that this method was successful in eliminating 129Xe magnetization in the emulsion phase, which enabled us to observe the time-dependence of the bubble magnetization. By employing the pulsed field gradient method, we also measured the gas velocity distribution within the bed. These results clearly show the onset of bubbling and can be used to deduce information about gas and particle motion in the fluidized bed.

  11. Measurement of 129Xe -Cs binary spin-exchange rate coefficient

    NASA Astrophysics Data System (ADS)

    Jau, Yuan-Yu; Kuzma, Nicholas N.; Happer, William

    2004-06-01

    We report the first measurement of the spin-exchange rate coefficient for binary collisions between Cs and 129Xe atoms in the temperature range 110129Xe gas. We measured 1/ T1 of a thermally polarized Xe gas using the saturation-recovery of conventional nuclear magnetic resonance. We also directly measured the Cs atomic number density [Cs] by using Faraday rotation of the linear polarization of a probing laser beam passing through the sample. The measured rate coefficient is κ (9.4 T) = d (1/ T1 ) / d [Cs] = (2.81±0.2) × 10-16 cm3 /s , which is about a factor of 1.6 higher than the previously measured spin-exchange rate coefficient of 129Xe -Rb binary collisions. Using a calculated magnetic decoupling factor, we extrapolate our result to zero magnetic field: κ (0 T) = (4.1±0.3) × 10-16 cm3 /s .

  12. Investigation of a 129Xe magnetometer for the Neutron Electric Dipole Moment Experiment at TRIUMF

    NASA Astrophysics Data System (ADS)

    Lang, Michael; Nedm At Triumf Collaboration

    2016-03-01

    A non-zero neutron electric dipole moment (nEDM) would signify a previously unknown source of CP (or T) violation. New sources of CP violation are believed to be required to explain the baryon asymmetry of the universe. Employing a newly developed high-density UCN source, an experiment at TRIUMF aims to measure the nEDM to the level of 10-27 e . cm in its initial phase. Precession frequency differences for UCN stored in a bottle subject to parallel and anti-parallel E and B fields signify a permanent nEDM. Magnetic field instability and inhomogeneity, as well as field changes resulting from leakage currents (correlated with E fields) are the dominant systematic effects in nEDM measurements. To address this, passive and active magnetic shielding are in development along with a dual species (129Xe and 199Hg) atomic comagnetometer. Simultaneously introducing both atomic species into the UCN cell, the comagnetometer can mitigate false EDMs. 199Hg precession will be detected by Faraday rotation spectroscopy, and 129Xe precession will measured via two-photon excitation and emission. The present comagnetometer progress will be discussed, with focus on polarized 129Xe production and delivery. Work supported by the Natural Sciences and Engineering Research Council of Canada.

  13. Frequency characteristics of a nuclear spin maser for the search for the electric dipole moment of 129Xe atom

    NASA Astrophysics Data System (ADS)

    Inoue, T.; Tsuchiya, M.; Furukawa, T.; Hayashi, H.; Nanao, T.; Yoshimi, A.; Uchida, M.; Matsuo, Y.; Asahi, K.

    2011-01-01

    Frequency characteristics of a 129Xe nuclear spin maser was studied, which is under development at Tokyo Institute of Technology for the search for a permanent electric dipole moment in diamagnetic 129Xe atom. Drifts in the solenoid current and cell temperature were found to be the most influential factors on the maser frequency. From correlation coefficient analysis, there seem to exist other origins of frequency fluctuation, such as phase drifts in the maser oscillation. In order to improve the stability of the maser frequency, the intensity of the pumping laser required to fully polarize 129Xe nuclei was evaluated. Construction of a polarization assessment system for 129Xe gas cells and development of a new scheme of current stabilization are also remarked.

  14. XeNA: An automated ‘open-source’ 129Xe hyperpolarizer for clinical use

    PubMed Central

    Nikolaou, Panayiotis; Coffey, Aaron M.; Walkup, Laura L.; Gust, Brogan M.; Whiting, Nicholas; Newton, Hayley; Muradyan, Iga; Dabaghyan, Mikayel; Ranta, Kaili; Moroz, Gregory D.; Rosen, Matthew S.; Patz, Samuel; Barlow, Michael J.; Chekmenev, Eduard Y.; Goodson, Boyd M.

    2014-01-01

    Here we provide a full report on the construction, components, and capabilities of our consortium’s “open-source” large-scale (~1 L/hr) 129Xe hyperpolarizer for clinical, pre-clinical, and materials NMR/MRI (Nikolaou et al., Proc. Natl. Acad. Sci. USA, 110, 14150 (2013)). The ‘hyperpolarizer’ is automated and built mostly of off-the-shelf components; moreover, it is designed to be cost-effective and installed in both research laboratories and clinical settings with materials costing less than $125,000. The device runs in the xenon-rich regime (up to 1800 Torr Xe in 0.5 L) in either stopped-flow or single-batch mode—making cryo-collection of the hyperpolarized gas unnecessary for many applications. In-cell 129Xe nuclear spin polarization values of ~30-90% have been measured for Xe loadings of ~300-1600 Torr. Typical 129Xe polarization build-up and T1 relaxation time constants were ~8.5 min and ~1.9 hr respectively under our SEOP conditions; such ratios, combined with near-unity Rb electron spin polarizations enabled by the high resonant laser power (up to ~200 W), permits such high PXe values to be achieved despite the high in-cell Xe densities. Importantly, most of the polarization is maintained during efficient HP gas transfer to other containers, and ultra-long 129Xe relaxation times (up to nearly 6 hr) were observed in Tedlar bags following transport to a clinical 3 T scanner for MR spectroscopy and imaging as a prelude to in vivo experiments. The device has received FDA IND approval for a clinical study of COPD subjects. The primary focus of this paper is on the technical / engineering development of the polarizer, with the explicit goals of facilitating the adaptation of design features and operative modes into other laboratories, and of spurring the further advancement of HP-gas MR applications in biomedicine. PMID:24631715

  15. XeNA: an automated 'open-source' (129)Xe hyperpolarizer for clinical use.

    PubMed

    Nikolaou, Panayiotis; Coffey, Aaron M; Walkup, Laura L; Gust, Brogan M; Whiting, Nicholas; Newton, Hayley; Muradyan, Iga; Dabaghyan, Mikayel; Ranta, Kaili; Moroz, Gregory D; Rosen, Matthew S; Patz, Samuel; Barlow, Michael J; Chekmenev, Eduard Y; Goodson, Boyd M

    2014-06-01

    Here we provide a full report on the construction, components, and capabilities of our consortium's "open-source" large-scale (~1L/h) (129)Xe hyperpolarizer for clinical, pre-clinical, and materials NMR/MRI (Nikolaou et al., Proc. Natl. Acad. Sci. USA, 110, 14150 (2013)). The 'hyperpolarizer' is automated and built mostly of off-the-shelf components; moreover, it is designed to be cost-effective and installed in both research laboratories and clinical settings with materials costing less than $125,000. The device runs in the xenon-rich regime (up to 1800Torr Xe in 0.5L) in either stopped-flow or single-batch mode-making cryo-collection of the hyperpolarized gas unnecessary for many applications. In-cell (129)Xe nuclear spin polarization values of ~30%-90% have been measured for Xe loadings of ~300-1600Torr. Typical (129)Xe polarization build-up and T1 relaxation time constants were ~8.5min and ~1.9h respectively under our spin-exchange optical pumping conditions; such ratios, combined with near-unity Rb electron spin polarizations enabled by the high resonant laser power (up to ~200W), permit such high PXe values to be achieved despite the high in-cell Xe densities. Importantly, most of the polarization is maintained during efficient HP gas transfer to other containers, and ultra-long (129)Xe relaxation times (up to nearly 6h) were observed in Tedlar bags following transport to a clinical 3T scanner for MR spectroscopy and imaging as a prelude to in vivo experiments. The device has received FDA IND approval for a clinical study of chronic obstructive pulmonary disease subjects. The primary focus of this paper is on the technical/engineering development of the polarizer, with the explicit goals of facilitating the adaptation of design features and operative modes into other laboratories, and of spurring the further advancement of HP-gas MR applications in biomedicine. PMID:24631715

  16. Multidimensional Mapping of Spin-Exchange Optical Pumping in Clinical-Scale Batch-Mode 129Xe Hyperpolarizers

    PubMed Central

    2015-01-01

    We present a systematic, multiparameter study of Rb/129Xe spin-exchange optical pumping (SEOP) in the regimes of high xenon pressure and photon flux using a 3D-printed, clinical-scale stopped-flow hyperpolarizer. In situ NMR detection was used to study the dynamics of 129Xe polarization as a function of SEOP-cell operating temperature, photon flux, and xenon partial pressure to maximize 129Xe polarization (PXe). PXe values of 95 ± 9%, 73 ± 4%, 60 ± 2%, 41 ± 1%, and 31 ± 1% at 275, 515, 1000, 1500, and 2000 Torr Xe partial pressure were achieved. These PXe polarization values were separately validated by ejecting the hyperpolarized 129Xe gas and performing low-field MRI at 47.5 mT. It is shown that PXe in this high-pressure regime can be increased beyond already record levels with higher photon flux and better SEOP thermal management, as well as optimization of the polarization dynamics, pointing the way to further improvements in hyperpolarized 129Xe production efficiency. PMID:24731261

  17. Multidimensional mapping of spin-exchange optical pumping in clinical-scale batch-mode 129Xe hyperpolarizers.

    PubMed

    Nikolaou, Panayiotis; Coffey, Aaron M; Ranta, Kaili; Walkup, Laura L; Gust, Brogan M; Barlow, Michael J; Rosen, Matthew S; Goodson, Boyd M; Chekmenev, Eduard Y

    2014-05-01

    We present a systematic, multiparameter study of Rb/(129)Xe spin-exchange optical pumping (SEOP) in the regimes of high xenon pressure and photon flux using a 3D-printed, clinical-scale stopped-flow hyperpolarizer. In situ NMR detection was used to study the dynamics of (129)Xe polarization as a function of SEOP-cell operating temperature, photon flux, and xenon partial pressure to maximize (129)Xe polarization (PXe). PXe values of 95 ± 9%, 73 ± 4%, 60 ± 2%, 41 ± 1%, and 31 ± 1% at 275, 515, 1000, 1500, and 2000 Torr Xe partial pressure were achieved. These PXe polarization values were separately validated by ejecting the hyperpolarized (129)Xe gas and performing low-field MRI at 47.5 mT. It is shown that PXe in this high-pressure regime can be increased beyond already record levels with higher photon flux and better SEOP thermal management, as well as optimization of the polarization dynamics, pointing the way to further improvements in hyperpolarized (129)Xe production efficiency. PMID:24731261

  18. ^129Xe-Rb spin-exchange cross section measurement at high magnetic field

    NASA Astrophysics Data System (ADS)

    Jau, Yuan-Yu; Kuzma, N. N.; Walter, D. K.; Griffith, W. M.; Happer, W.

    2002-05-01

    We report NMR measurements of the velocity-averaged ^129Xe-Rb spin-exchange cross section <σ_exv> using isotopically enriched xenon gas in a sealed aluminosilicate cell. At 9.4 T, it is possible to detect Boltzmann polarization of xenon gas nuclei without optical pumping. Over the temperature range from 160 to 200^rcC, binary collisions with Rb atoms dominate the ^129Xe spin-relaxation rate (1/T_1) through spin-exchange. Our data show that the spin-exchange contribution of van der Waals RbXe molecules at high magnetic field is very small compared to the contribition of binary collisions. From the observed linear dependence of 1/T1 on Rb density, we extract the value <σ_exv>=1.720.29× 10-16 cm^3/sec at 180^rcC and 9.4 T, where we deduce the Rb number density from our Faraday rotation measurements. In addition, we discuss a theoretical prediction of <σ_exv> based on our numerical computations and compare it to the experimental result.

  19. Nondisruptive Dissolution of Hyperpolarized (129)Xe into Viscous Aqueous and Organic Liquid Crystalline Environments.

    PubMed

    Truxal, Ashley E; Slack, Clancy C; Gomes, Muller D; Vassiliou, Christophoros C; Wemmer, David E; Pines, Alexander

    2016-04-01

    Studies of hyperpolarized xenon-129 (hp-(129)Xe) in media such as liquid crystals and cell suspensions are in demand for applications ranging from biomedical imaging to materials engineering but have been hindered by the inability to bubble Xe through the desired media as a result of viscosity or perturbations caused by bubbles. Herein a device is reported that can be reliably used to dissolve hp-(129)Xe into viscous aqueous and organic samples without bubbling. This method is robust, requires small sample volumes (<60 μL), is compatible with existing NMR hardware, and is made from readily available materials. Experiments show that Xe can be introduced into viscous and aligned media without disrupting molecular order. We detected dissolved xenon in an aqueous liquid crystal that is disrupted by the shear forces of bubbling, and we observed liquid-crystal phase transitions in (MBBA). This tool allows an entirely new class of samples to be investigated by hyperpolarized-gas NMR spectroscopy. PMID:26954536

  20. Progress of the 129Xe EDM search using active feedback nuclear spin maser

    NASA Astrophysics Data System (ADS)

    Sato, Tomoya; Ichikawa, Yuichi; Ohtomo, Yuichi; Sakamoto, Yu; Kojima, Shuichiro; Funayama, Chikako; Suzuki, Takahiro; Chikamori, Masatoshi; Hikota, Eri; Tsuchiya, Masato; Furukawa, Takeshi; Yoshimi, Akihiro; Bidinosti, Christopher; Ino, Takashi; Ueno, Hideki; Matsuo, Yukari; Fukuyama, Takeshi; Asahi, Koichiro

    2014-09-01

    A permanent electric dipole moment (EDM) of a particle is an extremely sensitive probe for physics beyond the Standard Model. The objective of the present study is to search for the 129Xe EDM at a level of 10-28 ecm, beyond the current upper limit. In this experiment, an active-feedback nuclear spin maser is employed to achieve a precision measurement. Systematic instability sets a limit on the precision in our study. Co-magnetometry using 3He spin maser was incorporated into the maser system to eliminate the frequency drift caused by magnetic field fluctuations. Moreover, a double-cell geometry with linearly polarized laser was introduced to reduce frequency drifts arising from contact interactions with polarized Rb atoms. Having integrated these improvements, the 3He/129Xe dual spin maser was successfully operated. In the presentation, recent progress will be reported, including an analysis of spin maser frequencies, a study of electrode designs, and an estimation of possible systematic uncertainties.

  1. Development of an antibody-based, modular biosensor for 129Xe NMR molecular imaging of cells at nanomolar concentrations.

    PubMed

    Rose, Honor M; Witte, Christopher; Rossella, Federica; Klippel, Stefan; Freund, Christian; Schröder, Leif

    2014-08-12

    Magnetic resonance imaging (MRI) is seriously limited when aiming for visualization of targeted contrast agents. Images are reconstructed from the weak diamagnetic properties of the sample and require an abundant molecule like water as the reporter. Micromolar to millimolar concentrations of conventional contrast agents are needed to generate image contrast, thus excluding many molecular markers as potential targets. To address this limitation, we developed and characterized a functional xenon NMR biosensor that can identify a specific cell surface marker by targeted (129)Xe MRI. Cells expressing the cell surface protein CD14 can be spatially distinguished from control cells with incorporation of as little as 20 nM of the xenon MRI readout unit, cryptophane-A. Cryptophane-A serves as a chemical host for hyperpolarized nuclei and facilitates the sensitivity enhancement achieved by xenon MRI. Although this paper describes the application of a CD14-specific biosensor, the construct has been designed in a versatile, modular fashion. This allows for quick and easy adaptation of the biosensor to any cell surface target for which there is a specific antibody. In addition, the modular design facilitates the creation of a multifunctional probe that incorporates readout modules for different detection methods, such as fluorescence, to complement the primary MRI readout. This modular antibody-based approach not only offers a practical technique with which to screen targets, but one which can be readily applied as the xenon MRI field moves closer to molecular imaging applications in vivo. PMID:25071165

  2. Development of an antibody-based, modular biosensor for 129Xe NMR molecular imaging of cells at nanomolar concentrations

    PubMed Central

    Rose, Honor M.; Witte, Christopher; Rossella, Federica; Klippel, Stefan; Freund, Christian; Schröder, Leif

    2014-01-01

    Magnetic resonance imaging (MRI) is seriously limited when aiming for visualization of targeted contrast agents. Images are reconstructed from the weak diamagnetic properties of the sample and require an abundant molecule like water as the reporter. Micromolar to millimolar concentrations of conventional contrast agents are needed to generate image contrast, thus excluding many molecular markers as potential targets. To address this limitation, we developed and characterized a functional xenon NMR biosensor that can identify a specific cell surface marker by targeted 129Xe MRI. Cells expressing the cell surface protein CD14 can be spatially distinguished from control cells with incorporation of as little as 20 nM of the xenon MRI readout unit, cryptophane-A. Cryptophane-A serves as a chemical host for hyperpolarized nuclei and facilitates the sensitivity enhancement achieved by xenon MRI. Although this paper describes the application of a CD14-specific biosensor, the construct has been designed in a versatile, modular fashion. This allows for quick and easy adaptation of the biosensor to any cell surface target for which there is a specific antibody. In addition, the modular design facilitates the creation of a multifunctional probe that incorporates readout modules for different detection methods, such as fluorescence, to complement the primary MRI readout. This modular antibody-based approach not only offers a practical technique with which to screen targets, but one which can be readily applied as the xenon MRI field moves closer to molecular imaging applications in vivo. PMID:25071165

  3. Near-unity nuclear polarization with an open-source 129Xe hyperpolarizer for NMR and MRI

    PubMed Central

    Nikolaou, Panayiotis; Coffey, Aaron M.; Walkup, Laura L.; Gust, Brogan M.; Whiting, Nicholas; Newton, Hayley; Barcus, Scott; Muradyan, Iga; Dabaghyan, Mikayel; Moroz, Gregory D.; Rosen, Matthew S.; Patz, Samuel; Barlow, Michael J.; Chekmenev, Eduard Y.; Goodson, Boyd M.

    2013-01-01

    The exquisite NMR spectral sensitivity and negligible reactivity of hyperpolarized xenon-129 (HP129Xe) make it attractive for a number of magnetic resonance applications; moreover, HP129Xe embodies an alternative to rare and nonrenewable 3He. However, the ability to reliably and inexpensively produce large quantities of HP129Xe with sufficiently high 129Xe nuclear spin polarization (PXe) remains a significant challenge—particularly at high Xe densities. We present results from our “open-source” large-scale (∼1 L/h) 129Xe polarizer for clinical, preclinical, and materials NMR and MRI research. Automated and composed mostly of off-the-shelf components, this “hyperpolarizer” is designed to be readily implementable in other laboratories. The device runs with high resonant photon flux (up to 200 W at the Rb D1 line) in the xenon-rich regime (up to 1,800 torr Xe in 500 cc) in either single-batch or stopped-flow mode, negating in part the usual requirement of Xe cryocollection. Excellent agreement is observed among four independent methods used to measure spin polarization. In-cell PXe values of ∼90%, ∼57%, ∼50%, and ∼30% have been measured for Xe loadings of ∼300, ∼500, ∼760, and ∼1,570 torr, respectively. PXe values of ∼41% and ∼28% (with ∼760 and ∼1,545 torr Xe loadings) have been measured after transfer to Tedlar bags and transport to a clinical 3 T scanner for MR imaging, including demonstration of lung MRI with a healthy human subject. Long “in-bag” 129Xe polarization decay times have been measured (T1 ∼38 min and ∼5.9 h at ∼1.5 mT and 3 T, respectively)—more than sufficient for a variety of applications. PMID:23946420

  4. Magnetic resonance imaging of hyperpolarized 129Xe produced by spin exchange with diode-laser pumped Cs

    NASA Astrophysics Data System (ADS)

    Levron, D.; Walter, D. K.; Appelt, S.; Fitzgerald, R. J.; Kahn, D.; Korbly, S. E.; Sauer, K. L.; Happer, W.; Earles, T. L.; Mawst, L. J.; Botez, D.; Harvey, M.; DiMarco, L.; Connolly, J. C.; Möller, H. E.; Chen, X. J.; Cofer, G. P.; Johnson, G. A.

    1998-11-01

    We report the results of experiments leading to the production of an image of a polarized 129Xe sample prepared by spin exchange with Cs, optically pumped with a spectrally narrowed 894.3 nm diode laser. Representative images of the average electron spin polarization are shown. Appreciable cesium electron polarization values were achieved, and a nuclear polarization of about 2.5% was measured for 129Xe. The absolute nuclear polarization was measured by water-calibrated free induction decay of the nuclear magnetic resonance signal, and the polarized xenon imaged using a 2 T magnetic resonance imaging system.

  5. Theory of spin-exchange optical pumping of 3He and 129Xe

    NASA Astrophysics Data System (ADS)

    Appelt, S.; Baranga, A. Ben-Amar; Erickson, C. J.; Romalis, M. V.; Young, A. R.; Happer, W.

    1998-08-01

    We present a comprehensive theory of nuclear spin polarization of 3He and 129Xe gases by spin-exchange collisions with optically pumped alkali-metal vapors. The most important physical processes considered are (1) spin-conserving spin-exchange collisions between like or unlike alkali-metal atoms; (2) spin-destroying collisions of the alkali-metal atoms with each other and with buffer-gas atoms; (3) electron-nuclear spin-exchange collisions between alkali-metal atoms and 3He or 129Xe atoms; (4) spin interactions in van der Waals molecules consisting of a Xe atom bound to an alkali-metal atom; (5) optical pumping by laser photons; (6) spatial diffusion. The static magnetic field is assumed to be small enough that the nuclear spin of the alkali-metal atom is well coupled to the electron spin and the total spin is very nearly a good quantum number. Conditions appropriate for the production of large quantities of spin-polarized 3He or 129Xe gas are assumed, namely, atmospheres of gas pressure and nearly complete quenching of the optically excited alkali-metal atoms by collisions with N2 or H2 gas. Some of the more important results of this work are as follows: (1) Most of the pumping and relaxation processes are sudden with respect to the nuclear polarization. Consequently, the steady-state population distribution of alkali-metal atoms is well described by a spin temperature, whether the rate of spin-exchange collisions between alkali-metal atoms is large or small compared to the optical pumping rate or the collisional spin-relaxation rates. (2) The population distributions that characterize the response to sudden changes in the intensity of the pumping light are not described by a spin temperature, except in the limit of very rapid spin exchange. (3) Expressions given for the radio-frequency (rf) resonance linewidths and areas can be used to make reliable estimates of the local spin polarization of the alkali-metal atoms. (4) Diffusion effects for these high

  6. Search for a permanent electric dipole moment using liquid 129Xe

    SciTech Connect

    PROFESSOR MICHAEL ROMALIS

    2008-11-24

    Search for an electric dipole moment is one of the best motivated low-energy approaches for investigating physics beyond the Standard Model. Our experimental effort is focused on improving the limit on EDM in liquid 129Xe to put constraints on nuclear CP-violating interactions. High nuclear spin density and high electrical breakdown strength make 129Xe a promising medium for EDM searches. At the time the project started, the transverse nuclear spin relaxation time T2 of 129Xe was unknown. We made measurements of T2 using NMR spin-echo techniques and found that it is exceeds 1300 sec, the longest relaxation time ever measured in a liquid [1]. We also began to investigate non-linear dipolar interaction effects in a high-density spin-polarized liquid Xe. In the second iteration of the experiment we setup a high-Tc SQUID system in magnetic shields and performed detailed studies of Xe spin precession. We developed a model for non-linear dipolar interactions and found that for one set of conditions non-linear interactions can delay spin dephasing due to magnetic field gradients, while for another set of conditions they can lead to exponential amplification of the spin precession signals [2]. Our experimental data were in good quantitative agreement with predictions of the model. We also developed a series of numerical simulations to understand various imperfections in the system and made detailed experimental measurements to confirm these numerical predictions [3]. We demonstrated that non-linear interactions can amplify small precession signals and achieved an amplification factor of 10 [4]. This general phenomenon can be used in other precision measurements with non-linear interactions. We also explored practical applications of the liquid Xe system that we developed. We demonstrated that by mixing Xe with organic liquids, such as cyclopentane, one can enhance the proton spin polarization by a factor of 106 [5]. We have used this technique to perform the first

  7. Polarization and Hyperfine Transitions of Metastable ^129Xe in Discharge Cells

    NASA Astrophysics Data System (ADS)

    Xia, Tian; Morgan, Steven; Jau, Yuan-Yu; Happer, William

    2010-03-01

    The polarization and relaxation rates of metastable ^129Xe atoms are measured with magnetic resonance spectroscopy, at both microwave frequencies, where δF = 1 transitions are induced between the sublevels, and at radiofrequencies, corresponding to δF = 0 transitions. The nuclear spin polarization of the resonant velocity group is measured to be 22±2%. However, the relaxation rate of spin polarization is much larger than the velocity changing rate, the narrow line pumping laser produces spin polarization only for atoms with resonant velocity. The relaxation of metastable xenon atoms is dominated by depolarizing collisions with ground state atoms, with lesser contributions from metastability exchange collisions. We also measure the pressure broadening coefficient of the relaxation rate by varying the temperature of the cryogenic part of the cell.

  8. Temperature response of 129Xe depolarization transfer and its application for ultra-sensitive NMR detection

    SciTech Connect

    Schroeder, Leif; Schroder, Leif; Meldrum, Tyler; Smith, Monica; Lowery, Thomas J.; Wemmer, David E.; Pines, Alexander

    2008-03-20

    Temporary trapping of atomic xenon in functionalized cryptophane cages makes the high sensitivity of hyperpolarized (hp) 129Xe available for highly specific NMR detection of biomolecules like proteins in solution. Here, we study the signal transfer onto a reservoir of unbound hp xenon by gating the residence time of the nuclei in the cage through the temperature-dependent exchange rate. Temperature changes were detectable immediately as an altered reservoir signal and yielded a sensitivity of 0.6 K. The temperature response is adjustable with lower concentrations of caged xenon providing more sensitivity at higher temperatures and allows ultra-sensitive detection of such molecular cages at 310 K. Functionalized cryptophane could be detected at concentrations as low as 10nM which corresponds to a 4000-fold sensitivity enhancement compared to conventional detection. This sensitivity makes hp-NMR capable of detecting such constructs in concentrations far belowthe detection limit by UV-visible light absorbance.

  9. Experimental search for EDM in diamagnetic atom 129Xe using active nuclear spin maser

    NASA Astrophysics Data System (ADS)

    Ichikawa, Yuichi; Sato, Tomoya; Ohtomo, Yuichi; Sakamoto, Yu; Kojima, Shuichiro; Funayama, Chikako; Hirao, Chika; Suzuki, Takahiro; Chikamori, Masatoshi; Hikota, Eri; Miyatake, Hirokazu; Nanao, Tsubasa; Suzuki, Kunifumi; Tsuchiya, Masato; Inoue, Takeshi; Furukawa, Takeshi; Yoshimi, Akihiko; Bidinosti, Christopher; Ino, Takashi; Ueno, Hideki; Matsuo, Yukari; Fukuyama, Takeshi; Asahi, Koichiro

    2014-09-01

    A permanent electric dipole moment (EDM) which directly means T-violation attracts much attention, because an unknown CP-violating phase which is necessary to understand the present matter-dominated Universe is expected to be probed by EDM. The present study aims at measuring the EDM in the diamagnetic atom 129Xe to a size of 10-28 ecm, stepping into a domain below the present upper limit by one order of magnitude. In the present experiment, we employ an active nuclear spin maser which has characteristics of the optical detection of the spin precession and the artificial production of the feedback field to sustain the spin precession over a long measurement duration. For the magnetometry in the measurement, a comagnetometer using 3He is incorporated to the spin maser system. In this presentation, the current status of our experiment will be given.

  10. Multifragmentation in intermediate energy {sup 129}Xe-induced heavy-ion reactions

    SciTech Connect

    Tso, Kin

    1996-05-01

    The {sup 129}Xe-induced reactions on {sup nat}Cu, {sup 89}Y, {sup 165}Ho, and {sup 197}Au at bombarding energies of E/A = 40 & 60 MeV have been studied theoretically and experimentally in order to establish the underlying mechanism of multifragmentation at intermediate energy heavy-Ion collisions. Nuclear disks formed in central heavy-ion collisions, as simulated by means of Boltzmann-like kinetic equations, break up into several fragments due to a new kind of Rayleigh-like surface instability. A sheet of liquid, stable in the limit of non-interacting surfaces, is shown to become unstable due to surface-surface interactions. The onset of this instability is determined analytically. A thin bubble behaves like a sheet and is susceptible to the surface instability through the crispation mode. The Coulomb effects associated with the depletion of charges in the central cavity of nuclear bubbles are investigated. The onset of Coulomb instability is demonstrated for perturbations of the radial mode. Experimental intermediate-mass-fragment multiplicity distributions for the {sup 129}Xe-induced reactions are shown to be binomial at each transverse energy. From these distributions, independent of the specific target, an elementary binary decay probability p can be extracted that has a thermal dependence. Thus it is inferred that multifragmentation is reducible to a combination of nearly independent emission processes. If sequential decay is assumed, the increase of p with transverse energy implies a contraction of the emission time scale. The sensitivity of p to the lower Z threshold in the definition of intermediate-mass-fragments points to a physical Poisson simulations of the particle multiplicities show that the weak auto-correlation between the fragment multiplicity and the transverse energy does not distort a Poisson distribution into a binomial distribution. The effect of device efficiency on the experimental results has also been studied.

  11. INSTRUMENTS AND METHODS OF INVESTIGATION: On experiments in search of the T-odd electric dipole moment of atomic 129Xe

    NASA Astrophysics Data System (ADS)

    Sobel'man, Igor I.; Sorokin, Vadim N.

    2005-09-01

    A new method is proposed for the search of the electric dipole moment of atomic 129Xe arising from time reversal symmetry violation. We consider the basic features of the experiment to measure the electric field of T-odd EDMs of spin-polarized 129Xe atoms with the aid of a Stark electrometer involving Rydberg atoms.

  12. High-field measurement of the 129Xe-Rb spin-exchange rate due to binary collisions

    NASA Astrophysics Data System (ADS)

    Jau, Yuan-Yu; Kuzma, Nicholas N.; Happer, William

    2002-11-01

    We have measured the binary spin-exchange rate coefficient for collisions between Rb and 129Xe atoms at a magnetic field B=9.4 T and in the temperature range 160129Xe is dominated by 129Xe-Rb binary collisions. We measured 1/T1 using the methods of conventional nuclear magnetic resonance, with no spin enhancement by optical pumping. At the high magnetic field and large gas pressures used in this work, the contribution of 129Xe-Rb molecules to the spin-exchange rate was less than 0.1% of the binary-collision rate. The Rb atomic number density [Rb] was measured directly from the large Faraday rotation of the polarization of near-resonant light passing through the sample cells. The rate coefficient is κ=d(1/T1)/d [Rb]=(1.75+/-0.12)×10-16 cm3/s.

  13. Abnormalities in hyperpolarized (129)Xe magnetic resonance imaging and spectroscopy in two patients with pulmonary vascular disease.

    PubMed

    Dahhan, Talal; Kaushik, Shiv S; He, Mu; Mammarappallil, Joseph G; Tapson, Victor F; McAdams, Holman P; Sporn, Thomas A; Driehuys, Bastiaan; Rajagopal, Sudarshan

    2016-03-01

    The diagnosis of pulmonary vascular disease (PVD) is usually based on hemodynamic and/or clinical criteria. Noninvasive imaging of the heart and proximal vasculature can also provide useful information. An alternate approach to such criteria in the diagnosis of PVD is to image the vascular abnormalities in the lungs themselves. Hyperpolarized (HP) (129)Xe magnetic resonance imaging (MRI) is a novel technique for assessing abnormalities in ventilation and gas exchange in the lungs. We applied this technique to two patients for whom there was clinical suspicion of PVD. Two patients who had significant hypoxemia and dyspnea with no significant abnormalities on computed tomography imaging or ventilation-perfusion scan and only mild or borderline pulmonary arterial hypertension at catheterization were evaluated. They underwent HP (129)Xe imaging and subsequently had tissue diagnosis obtained from lung pathology. In both patients, HP (129)Xe imaging demonstrated normal ventilation but markedly decreased gas transfer to red blood cells with focal defects on imaging, a pattern distinct from those previously described for idiopathic pulmonary fibrosis or obstructive lung disease. Pathology on both patients later demonstrated severe PVD. These findings suggest that HP (129)Xe MRI may be useful in the diagnosis of PVD and monitoring response to therapy. Further studies are required to determine its sensitivity and specificity in these settings. PMID:27162620

  14. Development of high-homogeneity magnetic field coil for 129Xe EDM experiment

    NASA Astrophysics Data System (ADS)

    Sakamoto, Y.; Bidinosti, C. P.; Ichikawa, Y.; Sato, T.; Ohtomo, Y.; Kojima, S.; Funayama, C.; Suzuki, T.; Tsuchiya, M.; Furukawa, T.; Yoshimi, A.; Ino, T.; Ueno, H.; Matsuo, Y.; Fukuyama, T.; Asahi, K.

    2015-04-01

    We search for 129Xe EDM by using an active nuclear spin maser. In this experiment, the amplitude of the maser oscillation signal is one of the most important parameters that eventually determine the frequency precision. The amplitude is proportional to the ratio of the transverse spin relaxation time T 2 to the effective longitudinal spin relaxation time . In particular, for a spin maser of 3He (a co-magnetometer) for which typically reaches ˜50 h, a long T 2 is needed. T 2 depends on the homogeneity of the magnetic field which is applied with coils in order to keep the spins under precession. In the present report, we discuss on the design and construction of a new coil which provided a root-mean square (rms) field gradient of less than 5.0 μG/cm. The result of the field measurement has shown that the field gradient in the cell fulfills the target condition , and in fact T 2 of 3He has been measured to be as long as 11,000 s.

  15. Performance check of cell with newly designed electrode for 129Xe EDM measurement

    NASA Astrophysics Data System (ADS)

    Sakamoto, Yu; Bidinosti, Christopher; Ichikawa, Yuichi; Sato, Tomoya; Ohtomo, Yuichi; Kojima, Shuichiro; Funayama, Chikako; Suzuki, Takahiro; Tsuchiya, Masato; Furukawa, Takeshi; Yoshimi, Akihiro; Ino, Takashi; Ueno, Hideki; Matuo, Yukari; Fukuyama, Takeshi; Asahi, Koichiro

    2014-09-01

    A permanent electric dipole moment (EDM) can be detected as a difference between the spin precession frequencies measured with an electric field applied parallel and antiparallel to a magnetic field. We aim to make a measurement of the 129Xe EDM at a level of d ~10-28 e cm by using a nuclear spin maser. The amplitude of the maser signal is proportional to the nuclear spin polarization. The polarization of 3He that acts as a co-magnetometer, is sensitive to the interactions with the electrodes used to generate the electric field. Previously, we used a transparent electrode made of ITO (Indium Tin Oxide) to allow transmission linearly polarized laser light into the cell. However, 3He polarization in a cell with such electrodes was measured to be ~0.1%, which is ten times smaller than no electrodes. In order to solve the problem, we adopted an electrode made from a mesh of Molybdenum. The geometry also reduces the contact area between 3He gas and the electrode. We measured 3He polarization at a cell with the mesh electrode by means of adiabatic fast passage NMR.

  16. Performance assessment of a new laser system for efficient spin exchange optical pumping in a spin maser measurement of 129Xe EDM

    NASA Astrophysics Data System (ADS)

    Funayama, C.; Furukawa, T.; Sato, T.; Ichikawa, Y.; Ohtomo, Y.; Sakamoto, Y.; Kojima, S.; Suzuki, T.; Hirao, C.; Chikamori, M.; Hikota, E.; Tsuchiya, M.; Yoshimi, A.; Bidinosti, C. P.; Ino, T.; Ueno, H.; Matsuo, Y.; Fukuyama, T.; Asahi, K.

    2015-11-01

    We demonstrate spin-exchange optical pumping of 129Xe atoms with our newly made laser system. The new laser system was prepared to provide higher laser power required for the stable operation of spin maser oscillations in the 129Xe EDM experiment. We studied the optimum cell temperature and pumping laser power to improve the degree of 129Xe spin polarization. The best performance was achieved at the cell temperature of 100 ∘C with the presently available laser power of 1 W. The results show that a more intense laser is required for further improvement of the spin polarization at higher cell temperatures in our experiment.

  17. Limit on Lorentz-Invariance- and CPT-Violating Neutron Spin Interactions Using a 3He-129Xe Comagnetometer

    NASA Astrophysics Data System (ADS)

    Allmendinger, F.; Schmidt, U.; Heil, W.; Karpuk, S.; Sobolev, Yu.; Tullney, K.

    2016-02-01

    We performed a search for a Lorentz-invariance- and CPT-violating coupling of the 3He and 129Xe nuclear spins to posited background fields. Our experimental approach is to measure the free precession of nuclear spin polarized 3He and 129Xe atoms using SQUIDs as detectors. As the laboratory reference frame rotates with respect to distant stars, we look for a sidereal modulation of the Larmor frequencies of the co-located spin samples. As a result we obtain an upper limit on the equatorial component of the background field b˜⊥n < 8.4 ṡ 10‑34 GeV (68% C.L.). This experiment is currently the most precise test of spin anisotropy due to the excellent long spin-coherence time.

  18. Transverse spin relaxation and diffusion-constant measurements of spin-polarized 129Xe nuclei in the presence of a magnetic field gradient

    NASA Astrophysics Data System (ADS)

    Liu, Xiaohu; Chen, Chang; Qu, Tianliang; Yang, Kaiyong; Luo, Hui

    2016-04-01

    The presence of a magnetic field gradient in a sample cell containing spin-polarized 129Xe atoms will cause an increased relaxation rate. We measured the transverse spin relaxation time of 129Xe verse the applied magnetic field gradient and the cell temperature. We then compared the different transverse spin relaxation behavior of dual isotopes of xenon (129Xe and 131Xe) due to magnetic field gradient in the same cell. The experiment results show the residual magnetic field gradient can be measured and compensated by applying a negative magnetic gradient in the sample cell. The transverse spin relaxation time of 129Xe could be increased 2–7 times longer when applying an appropriate magnetic field gradient. The experiment results can also be used to determine the diffusion constant of 129Xe in H2 and N2 to be 0.4 ± 0.26 cm2/sec and 0.12 ± 0.02 cm2/sec. The results are close with theoretical calculation.

  19. Transverse spin relaxation and diffusion-constant measurements of spin-polarized 129Xe nuclei in the presence of a magnetic field gradient.

    PubMed

    Liu, Xiaohu; Chen, Chang; Qu, Tianliang; Yang, Kaiyong; Luo, Hui

    2016-01-01

    The presence of a magnetic field gradient in a sample cell containing spin-polarized (129)Xe atoms will cause an increased relaxation rate. We measured the transverse spin relaxation time of (129)Xe verse the applied magnetic field gradient and the cell temperature. We then compared the different transverse spin relaxation behavior of dual isotopes of xenon ((129)Xe and (131)Xe) due to magnetic field gradient in the same cell. The experiment results show the residual magnetic field gradient can be measured and compensated by applying a negative magnetic gradient in the sample cell. The transverse spin relaxation time of (129)Xe could be increased 2-7 times longer when applying an appropriate magnetic field gradient. The experiment results can also be used to determine the diffusion constant of (129)Xe in H2 and N2 to be 0.4 ± 0.26 cm(2)/sec and 0.12 ± 0.02 cm(2)/sec. The results are close with theoretical calculation. PMID:27049237

  20. Transverse spin relaxation and diffusion-constant measurements of spin-polarized 129Xe nuclei in the presence of a magnetic field gradient

    PubMed Central

    Liu, Xiaohu; Chen, Chang; Qu, Tianliang; Yang, Kaiyong; Luo, Hui

    2016-01-01

    The presence of a magnetic field gradient in a sample cell containing spin-polarized 129Xe atoms will cause an increased relaxation rate. We measured the transverse spin relaxation time of 129Xe verse the applied magnetic field gradient and the cell temperature. We then compared the different transverse spin relaxation behavior of dual isotopes of xenon (129Xe and 131Xe) due to magnetic field gradient in the same cell. The experiment results show the residual magnetic field gradient can be measured and compensated by applying a negative magnetic gradient in the sample cell. The transverse spin relaxation time of 129Xe could be increased 2–7 times longer when applying an appropriate magnetic field gradient. The experiment results can also be used to determine the diffusion constant of 129Xe in H2 and N2 to be 0.4 ± 0.26 cm2/sec and 0.12 ± 0.02 cm2/sec. The results are close with theoretical calculation. PMID:27049237

  1. Frequency characteristics of nuclear spin oscillator with an artificial feedback toward search for 129Xe atomic electric dipole moment

    NASA Astrophysics Data System (ADS)

    Inoue, Takeshi; Furukawa, Takeshi; Yoshimi, Akihiro; Nanao, Tsubasa; Chikamori, Masatoshi; Suzuki, Kunifumi; Hayashi, Hironori; Miyatake, Hirokazu; Ichikawa, Yuichi; Tsuchiya, Masato; Hatakeyama, Naoto; Kagami, Sota; Uchida, Makoto; Ueno, Hideki; Matsuo, Yukari; Fukuyama, Takeshi; Asahi, Koichiro

    2016-06-01

    A 129Xe nuclear spin oscillator with an artificial feedback was constructed, and detailed studies were conducted on its performance, focusing on the frequency stability. As a result, the major sources of drift of the precession frequency in the present spin oscillator setup were identified to be drifts of a solenoid current and an environmental magnetic field. By introducing stabilization systems for the current and the environmental field, which yielded improvements by one order of magnitude on the solenoid current and by a factor of three on the environmental field, a frequency precision of 7.9 nHz was obtained for a one-shot measurement of 3 × 104 s duration. We found, however, that the Allan deviation leveled off at around 30 μHz, indicating a strong need for the precision monitor of the experimental conditions represented by magnetometry. The frequency stability of the spin oscillator is discussed in relation to an experimental search for an electric dipole moment of the 129Xe atom.

  2. Observation of hyperfine mixing in measurements of a magnetic octupole decay in isotopically pure nickel-like 129Xe and 132Xe ions

    SciTech Connect

    Trabert, E; Beiersdorfer, P; Brown, G V

    2006-12-21

    We present measurements of high statistical significance of the rate of the magnetic octupole (M3) decay in nickel-like ions of isotopically pure {sup 129}Xe and {sup 132}Xe. On {sup 132}Xe, an isotope with zero nuclear spin and therefore without hyperfine structure, the lifetime of the metastable level was established as (15.06 {+-} 0.24) ms. On {sup 129}Xe, an additional fast (2.7 {+-} 0.1 ms) decay component was established that represents hyperfine mixing with a level that decays by electric quadrupole (E2) radiation.

  3. A New Search for the Atomic EDM of 129Xe at FRM-II (Munich Research Reactor)

    NASA Astrophysics Data System (ADS)

    Singh, Jaideep; Fierlinger, Peter; Kraegeloh, Eva; Kuchler, Florian; Lins, Tobias; Marino, Mike; Meinel, Jonas; Neissen, Benjamin; Stuiber, Stefan; Burghoff, Martin; Fan, Isaac; Kilian, Wolfgang; Knappe-Grueneberg, Silvia; Schnabel, Allard; Seifert, Frank; Trahms, Lutz; Voigt, Jens; Chupp, Tim; Degenkolb, Skyler; Gong, Fei; Sachdeva, Natasha; Babcock, Earl

    2014-09-01

    Electric dipole moments (EDMs) arise due to the breaking of time-reversal or, equivalently, CP -symmetry. Although all searches have so far only set upper limits on EDMs, the motivation for more sensitive searches is stronger than ever. The present limit of 6 ×10-27 e * cm (95% CL) for the 129Xe EDM helps constrain CP -violating parameters within nuclei. A new effort at FRM-II incorporating a 3He comagnetometer can potentially improve this limit by over three orders of magnitude. The noble gas mixture is polarized by spin-exchange optical pumping and then transferred into a high-performance magnetically shielded room. A SQUID magnetometer array measures the precession frequencies in the presence of applied electric- & magnetic-fields. Recent test runs indicate that the experiment is capable of an EDM sensitivity of 10-28 e * cm in one day.

  4. A New Search for the Atomic EDM of 129 Xe at FRM-II (Munich Research Reactor)

    NASA Astrophysics Data System (ADS)

    Kuchler, Florian; Fierlinger, Peter; Kraegeloh, Eva; Lins, Tobias; Marino, Mike; Meinel, Jonas; Niessen, Benjamin; Stuiber, Stefan; Burghoff, Martin; Fan, Isaac; Kilian, Wolfgang; Knappe-Grueneberg, Silvia; Schnabel, Allard; Seifert, Frank; Trahms, Lutz; Voigt, Jens; Chupp, Tim; Degenkolb, Skyler; Gong, Fei; Sachdeva, Natasha; Babcock, Earl; Singh, Jaideep

    2015-04-01

    Electric dipole moments (EDMs) arise due to the breaking of time-reversal or, equivalently, CP-symmetry. Although all searches have so far only set upper limits on EDMs, the motivation for more sensitive searches is stronger than ever. The present limit of 6 × 10-27 e*cm (95 % CL) for the 129 Xe EDM helps constrain CP-violating parameters within nuclei. A new effort at FRM-II incorporating a 3 He comagnetometer can potentially improve this limit by over three orders of magnitude. The noble gas mixture is polarized by spin-exchange optical pumping and then transferred into a high-performance magnetically shielded room. A SQUID magnetometer array measures the precession frequencies in the presence of applied electric- and magnetic-fields. Recent test runs indicate that the experiment is capable of an EDM sensitivity of 10-28 e*cm in one day.

  5. Chemical shift driven geometry optimization.

    PubMed

    Witter, Raiker; Priess, Wolfram; Sternberg, Ulrich

    2002-01-30

    A new method for refinement of 3D molecular structures by geometry optimization is presented. Prerequisites are a force field and a very fast procedure for the calculation of chemical shifts in every step of optimization. To the energy, provided by the force field (COSMOS force field), a pseudoenergy, depending on the difference between experimental and calculated chemical shifts, is added. In addition to the energy gradients, pseudoforces are computed. This requires the derivatives of the chemical shifts with respect to the coordinates. The pseudoforces are analytically derived from the integral expressions of the bond polarization theory. Single chemical shift values attributed to corresponding atoms are considered for structural correction. As a first example, this method is applied for proton position refinement of the D-mannitol X-ray structure. A crystal structure refinement with 13C chemical shift pseudoforces is carried out. PMID:11924742

  6. Detection of radiation induced lung injury in rats using dynamic hyperpolarized {sup 129}Xe magnetic resonance spectroscopy

    SciTech Connect

    Fox, Matthew S.; Ouriadov, Alexei; Hegarty, Elaine; Thind, Kundan; Wong, Eugene; Hope, Andrew; Santyr, Giles E.

    2014-07-15

    Purpose: Radiation induced lung injury (RILI) is a common side effect for patients undergoing thoracic radiation therapy (RT). RILI can lead to temporary or permanent loss of lung function and in extreme cases, death. Combining functional lung imaging information with conventional radiation treatment plans may lead to more desirable treatment plans that reduce lung toxicity and improve the quality of life for lung cancer survivors. Magnetic Resonance Imaging of the lung following inhalation of hyperpolarized{sup 129}Xe may provide a useful nonionizing approach for probing changes in lung function and structure associated with RILI before, during, or after RT (early and late time-points). Methods: In this study, dynamic{sup 129}Xe MR spectroscopy was used to measure whole-lung gas transfer time constants for lung tissue and red blood cells (RBC), respectively (T{sub Tr-tissue} and T{sub Tr-RBC}) in groups of rats at two weeks and six weeks following 14 Gy whole-lung exposure to radiation from a {sup 60}Co source. A separate group of six healthy age-matched rats served as a control group. Results: T{sub Tr-tissue} values at two weeks post-irradiation (51.6 ± 6.8 ms) were found to be significantly elevated (p < 0.05) with respect to the healthy control group (37.2 ± 4.8 ms). T{sub Tr-RBC} did not show any significant changes between groups. T{sub Tr-tissue} was strongly correlated with T{sub Tr-RBC} in the control group (r = 0.9601 p < 0.05) and uncorrelated in the irradiated groups. Measurements of arterial partial pressure of oxygen obtained by arterial blood sampling were found to be significantly decreased (p < 0.05) in the two-week group (54.2 ± 12.3 mm Hg) compared to those from a representative control group (85.0 ± 10.0 mm Hg). Histology of a separate group of similarly irradiated animals confirmed the presence of inflammation due to radiation exposure with alveolar wall thicknesses that were significantly different (p < 0.05). At six weeks post

  7. A new ^3He-^129Xe Co-magnetometer using a Ramsey measurement sequence and Rb-K magnetometer for spin detection

    NASA Astrophysics Data System (ADS)

    Kabcenell, Aaron; Kominis, Iannis; Romalis, Michael

    2012-06-01

    Noble gas co-magnetometers have been used for many precision measurements, but their sensitivity is still very far from fundamental limits. We are exploring a new approach for operation of a ^3He-^129Xe co-magnetometer that uses a sensitive Rb-K magnetometer as a spin detector. By placing the noble gas atoms inside the magnetometer cell we can increase their magnetic signal using the Fermi-contact interaction, representing a gain of nearly 500 for ^129Xe, and achieve nearly quantum-noise limited detection of nuclear spins. In order to take advantage of the long coherence times of ^3He and^129Xe, the precession measurement is based on the Ramsey method of separated oscillatory fields and will be performed in an alkali-metal-free volume. The gas is then transported to the spin detector using techniques developed for remote NMR detection. The sensitivity of this approach is estimated to be on the order of 10-13 Hz/day^1/2, making it several orders of magnitude more sensitive than the best existing co-magnetometers. We are currently performing tests of the Ramsey measurement method and the sensitivity of the spin detector.

  8. Projectile-like fragments from {sup 129}Xe+{sup nat}Cu reactions at E/A = 40 MeV

    SciTech Connect

    Russ, D.E.; Mignerey, A.C.; Garcia-Solis, E.J.

    1996-02-01

    The bombarding of heavy nuclei with energetic heavy projectiles has been one of the most important experimental tools for nuclear science. At low beam energies, (E/A) beam <10 MeV, the reactions appear to be dominated by mean field consideration. At higher beam energies, (E/A) beams > 100 MeV, these mean field effects are less important and nucleon-nucleon interactions dominate. Within the intermediate energy region, the situation is less clear because of both the mean field and nucleon-nucleon effects contribute. There is no consensus on the theoretical treatment of nuclear reaction in the intermediate energy regime and statistical, dynamical, and hybrid models have been used with limited success. Previous studies of {sup 136}Xe + {sup 209}Bi at E/A = 28 MeV carried out at Michigan State University (MSU) have been well described by a damped reaction mechanism. On the other hand, {sup 129}Xe + {sup nat}Cu at E/A = 50 MeV also at MSU has been compared with a hybrid model with reasonable success. In order to see a transition from a damped reaction mechanism to more fragmentation-like processes, an experiment was carried out at MSU using {sup 129}Xe beams at E/A = 30, 40, 50, and 60 MeV. The targets were Cu, Sc, and Au. The current study only looks at the projectile-like fragments (PLF) detected in the Maryland Forward Array (MFA).

  9. 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…

  10. Development of a high intensity laser for efficient spin exchange optical pumping in a spin maser measurement of the 129Xe EDM

    NASA Astrophysics Data System (ADS)

    Funayama, Chikako; Furukawa, Takeshi; Sato, Tomoya; Ichikawa, Yuichi; Ohtomo, Yuichi; Sakamoto, Yu; Kojima, Shuichiro; Suzuki, Takahiro; Chikamori, Masatoshi; Hikota, Eri; Tsuchiya, Masato; Yoshimi, Akihiro; Bidinosti, Christopher; Ino, Takashi; Ueno, Hideki; Matsuo, Yukari; Fukuyama, Takeshi; Asahi, Koichiro

    2014-09-01

    We aim to search for an atomic electric dipole moment (EDM) in 129Xe beyond the present upper limit at the level of 10-28 e cm. The enhancement of the spin polarization through the efficient spin-exchange optical pumping process is important for stable maser operation. Previously, a distributed feedback (DFB) laser and a spatially separated tapered amplifier (TA) were used for the optical pumping. The characteristics of the TA-DFB laser, such as its narrow line width and high frequency stability, enable us to produce a large spin polarization. However, the power of the TA-DFB laser was not sufficient for stable operation of the 3He spin-maser comagnetometer. Recently, we have been preparing a new laser system containing an external cavity laser diode (ECLD) and a more intense TA for more efficient pumping. In the presentation, we discuss the Rb and noble gases polarizations achieved with our new ECLD compared to that with the DFB laser, and evaluate the advantages gained by employing the ECLD.

  11. Millimeter-wave spectroscopy and multichannel quantum-defect-theory analysis of high Rydberg states of xenon: The hyperfine structure of {sup 129}Xe{sup +} and {sup 131}Xe{sup +}

    SciTech Connect

    Schaefer, Martin; Raunhardt, Matthias; Merkt, Frederic

    2010-03-15

    Millimeter-wave transitions between high-n Rydberg states of several isotopes of xenon have been recorded at sub-megahertz resolution. The fine and, for {sup 129}Xe and {sup 131}Xe, hyperfine structures of s, p, d, and f Rydberg states with principal quantum number in the range 52{<=}n{<=}64 have been determined from combination differences and analyzed using multichannel quantum defect theory. Improved eigenquantum defects and channel interaction parameters for the odd- and even-parity Rydberg states of xenon and the hyperfine structure of the {sup 2}P{sub 3/2} ground state of {sup 129}Xe{sup +} and {sup 131}Xe{sup +} have been obtained. Nearly degenerate p and d fine or hyperfine levels are very easily mixed by even weak stray electric fields.

  12. NMR crystallography: the use of chemical shifts

    NASA Astrophysics Data System (ADS)

    Harris, Robin K.

    2004-10-01

    Measurements of chemical shifts obtained from magic-angle spinning NMR spectra (together with quantum mechanical computations of shielding) can provide valuable information on crystallography. Examples are given of the determination of crystallographic asymmetric units, of molecular symmetry in the solid-state environment, and of crystallographic space group assignment. Measurements of full tensor components for 199Hg have given additional coordination information. The nature of intermolecular hydrogen bonding in cortisone acetate polymorphs and solvates is obtained from chemical shift information, also involving measurement of the full tensor parameters. The resulting data have been used as restraints, built into the computation algorithm, in the analysis of powder diffraction patterns to give full crystal structures. A combination of quantum mechanical computation of shielding and measurement of proton chemical shifts (obtained by high-speed MAS) leads to the determination of the position of a proton in an intermolecular hydrogen bond. A recently-developed computer program specifically based on crystallographic repetition has been shown to give acceptable results. Moreover, NMR chemical shifts can distinguish between static and dynamic disorder in crystalline materials and can be used to determine modes and rates of molecular exchange motion.

  13. 129Xe NMR of xenon adsorbed on the molecular sieves AlPO 4-5, SAPO-5, MAPO-5, and SAPO-37

    NASA Astrophysics Data System (ADS)

    Chen, Q. J.; Springuel-Huet, M. A.; Fraissard, J.

    1989-06-01

    The solids NaY, SAPO-37, ALPO 4-5, SAPO-5 and MAPO-5 have been studied at 26°C by 129 NMR with adsorbed xenon used as a probe. The equal values of the chemical shifts of NaY and SAPO-37 show that this technique can be used both on zeolites and AlPO 4 or their derivatives. The chemical shifts of AlPO 4-5, SAPO-5 and MAPO-5 are identical at 26°C. The difference with respect to the value determined from the structure cannot therefore be explained by the difference in chemical composition leading to specific Xe-solid interactions.

  14. Accessible surface area from NMR chemical shifts.

    PubMed

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

    2015-07-01

    Accessible surface area (ASA) is the surface area of an atom, amino acid or biomolecule that is exposed to solvent. The calculation of a molecule's ASA requires three-dimensional coordinate data and the use of a "rolling ball" algorithm to both define and calculate the ASA. For polymers such as proteins, the ASA for individual amino acids is closely related to the hydrophobicity of the amino acid as well as its local secondary and tertiary structure. For proteins, ASA is a structural descriptor that can often be as informative as secondary structure. Consequently there has been considerable effort over the past two decades to try to predict ASA from protein sequence data and to use ASA information (derived from chemical modification studies) as a structure constraint. Recently it has become evident that protein chemical shifts are also sensitive to ASA. Given the potential utility of ASA estimates as structural constraints for NMR we decided to explore this relationship further. Using machine learning techniques (specifically a boosted tree regression model) we developed an algorithm called "ShiftASA" that combines chemical-shift and sequence derived features to accurately estimate per-residue fractional ASA values of water-soluble proteins. This method showed a correlation coefficient between predicted and experimental values of 0.79 when evaluated on a set of 65 independent test proteins, which was an 8.2 % improvement over the next best performing (sequence-only) method. On a separate test set of 92 proteins, ShiftASA reported a mean correlation coefficient of 0.82, which was 12.3 % better than the next best performing method. ShiftASA is available as a web server ( http://shiftasa.wishartlab.com ) for submitting input queries for fractional ASA calculation. PMID:26078090

  15. Calculation of Chemical Shift Anisotropy in Proteins

    PubMed Central

    Tang, Sishi; Case, David A.

    2011-01-01

    Individual peptide groups in proteins must exhibit some variation in the chemical shift anisotropy (CSA) of their constituent atoms, but not much is known about the extent or origins of this dispersion. Direct spectroscopic measurement of CSA remains technically challenging, and theoretical methods can help to overcome these limitations by estimating shielding tensors for arbitrary structures. Here we use an automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach to compute 15N, 13C′ and 1H chemical shift tensors for human ubiquitin and the GB1 and GB3 fragments of staphylococcal protein G. The average and range of variation of the anisotropies is in good agreement with experimental estimates from solid-state NMR, and the variation among residues is somewhat smaller than that estimated from solution-state measurements. Hydrogen-bond effects account for much of the variation, both between helix and sheet regions, and within elements of secondary structure, but other effects (including variations in torsion angles) may play a role as well. PMID:21866436

  16. Protein conformation and proton nuclear-magnetic-resonance chemical shifts.

    PubMed

    Pardi, A; Wagner, G; Wüthrich, K

    1983-12-15

    The nuclear magnetic resonance (NMR) chemical shifts of the polypeptide backbone protons in basic pancreatic trypsin inhibitor from bovine organs and the inhibitors E and K from the venom of Dendroaspis polylepis polylepis have been analyzed. Using the corresponding shifts in model peptides, the chemical shifts observed in the proteins were decomposed into random-coil shifts and conformation-dependent shifts. Correlations between contributions to the latter term and the polypeptide conformation were investigated by using the crystal structure of the bovine inhibitor. In addition to the well-known ring-current effects, a correlation was found between chemical shifts of amide and C alpha protons and the length of the hydrogen bonds formed by these protons with nearby oxygen atoms as acceptor groups. There remain sizeable and as yet unexplained residual conformation shifts. Overall, the present treatment provides a satisfactory qualitative explanation for the outstandingly large shifts of backbone hydrogen atoms in these diamagnetic proteins. PMID:6198174

  17. Comment on the reference compound for chemical shift and Knight shift determination of (209)Bi nuclei.

    PubMed

    Nowak, Bogdan

    2015-01-01

    Several groups exploring the (209)Bi NMR in solids, including usual insulators, metallic and magnetic materials and recently diamagnetic topological materials, use different standards (usually old and invalid) for chemical shift (Knight shift) determination, ignoring IUPAC recommendations. As a consequence the published shift values exhibit considerable differences (up to 17,500 ppm). PMID:25534279

  18. 4D prediction of protein (1)H chemical shifts.

    PubMed

    Lehtivarjo, Juuso; Hassinen, Tommi; Korhonen, Samuli-Petrus; Peräkylä, Mikael; Laatikainen, Reino

    2009-12-01

    A 4D approach for protein (1)H chemical shift prediction was explored. The 4th dimension is the molecular flexibility, mapped using molecular dynamics simulations. The chemical shifts were predicted with a principal component model based on atom coordinates from a database of 40 protein structures. When compared to the corresponding non-dynamic (3D) model, the 4th dimension improved prediction by 6-7%. The prediction method achieved RMS errors of 0.29 and 0.50 ppm for Halpha and HN shifts, respectively. However, for individual proteins the RMS errors were 0.17-0.34 and 0.34-0.65 ppm for the Halpha and HN shifts, respectively. X-ray structures gave better predictions than the corresponding NMR structures, indicating that chemical shifts contain invaluable information about local structures. The (1)H chemical shift prediction tool 4DSPOT is available from http://www.uku.fi/kemia/4dspot . PMID:19876601

  19. 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...

  20. 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. PMID:19246221

  1. Probabilistic validation of protein NMR chemical shift assignments.

    PubMed

    Dashti, Hesam; Tonelli, Marco; Lee, Woonghee; Westler, William M; Cornilescu, Gabriel; Ulrich, Eldon L; Markley, John L

    2016-01-01

    Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data . ARECA has been evaluated through its application to 26 case studies and has been shown to be complementary to, and usually more reliable than, approaches based on chemical shift databases. ARECA is available online at http://areca.nmrfam.wisc.edu/. PMID:26724815

  2. Theoretical and experimental NMR chemical shifts of norsanguinarine and norchelerythrine

    NASA Astrophysics Data System (ADS)

    Toušek, Jaromír.; Dostál, Jiří; Marek, Radek

    2004-02-01

    Norchelerythrine and norsanguinarine, tertiary benzo[ c]phenanthridine alkaloids, were examined by gradient-selected 2D NMR spectroscopy and the later also by extensive theoretical calculations. 1H, 13C and 15N chemical shifts assignments of the title isoquinoline alkaloids based on NOE and multiple-bond chemical-shift correlation experiments (GSQMBC) are reported. Various methods were used for the NMR chemical shifts calculations. Molecular mechanics (MM3 forcefield), AM1 method and Ab initio methods were used for optimizing the geometry. Chemical shielding constants were computed by density functional theory, GIAO and IGLO approaches were used. Chemical shifts calculated by all methods display good qualitative agreement with experimentally determined values. The best overall agreement was achieved when geometry was optimized by RHF/6-31G** method and chemical shielding constants were calculated by B3LYP/6-311G** method, GIAO approach.

  3. Prediction of Bioactive Compounds Using Computed NMR Chemical Shifts.

    PubMed

    Karthikeyan, Muthukumarasamy; Rajamohanan, Pattuparambil Ramanpillai; Vyas, Renu

    2015-01-01

    NMR based chemical shifts are an important diagnostic parameter for structure elucidation as they capture rich information related to conformational, electronic and stereochemical arrangement of functional groups in a molecule which is responsible for its activity towards any biological target. The present work discusses the importance of computing NMR chemical shifts from molecular structures. The NMR chemical shift data (experimental or computed) was used to generate fingerprints in binary formats for mapping molecular fragments (as descriptors) and correlating with the bioactivity classes. For this study, chemical shift data derived binary fingerprints were computed for 149 classes and 4800 bioactive molecules. The sensitivity and selectivity of fingerprints in discriminating molecules belonging to different therapeutic categories was assessed using a LibSVM based classifier. An accuracy of 82% for proton and 94% for carbon NMR fingerprints were obtained for anti-psoriatic and anti-psychotic molecules demonstrating the effectiveness of this approach for virtual screening. PMID:26138568

  4. 93Nb NMR chemical shift scale for niobia systems.

    PubMed

    Lapina, Olga B; Khabibulin, Dzhalil F; Romanenko, Konstantin V; Gan, Zhehong; Zuev, Mikhail G; Krasil'nikov, Vladimir N; Fedorov, Vladimir E

    2005-09-01

    93Nb solid-state NMR spectra of a series of inorganic niobates with Nb in different oxygen coordination environments were measured. For all studied compounds the chemical shielding and quadrupole tensor parameters were determined using conventional and ultrahigh field NMR facilities, ultrahigh speed MAS, DQ STMAS, solid-echo and computer modeling. It has been demonstrated that the 93Nb isotropic chemical shift is sensitive to the coordination number of Nb sites. For the first time the 93Nb NMR chemical shift scale for NbOx polyhedra in solid materials has been proposed: for four-coordinated Nb sites, the isotropic shifts occur from -650 to -950 ppm; five-coordinated Nb sites have the isotropic shifts in the range of -900 to -980 ppm; for six-coordinated Nb sites the isotropic shifts vary from -900 to -1360 ppm; the shifts from -1200 to -1600 ppm are typical for seven-coordinated Nb sites; for eight-coordinated Nb sites the shifts are higher than -1400 ppm. The possible correlation between the value of the isotropic chemical shift and the ionic character of the NbOx-MOy polyhedra association has been suggested. The magnitude of the 93Nb quadrupole coupling constant depends on the local symmetry of Nb sites and may vary from hundreds of kHz to hundreds of MHz. PMID:16216475

  5. Chemical shift guided homology modeling of larger proteins

    PubMed Central

    Shen, Yang; Bax, Ad

    2015-01-01

    We describe an alternate approach to protein structure determination that relies on experimental NMR chemical shifts, plus sparse NOEs if available. The newly introduced alignment method, POMONA, directly exploits the powerful bioinformatics algorithms previously developed for sequence-based homology modeling, but does not require significant sequence similarity. Protein templates, generated by POMONA, are subsequently used as input for chemical shift based Rosetta comparative modeling (CS-RosettaCM) to generate reliable full atom models. PMID:26053889

  6. 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.

  7. Bayesian inference of protein structure from chemical shift data

    PubMed Central

    Bratholm, Lars A.; Christensen, Anders S.; Hamelryck, Thomas

    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. PMID:25825683

  8. Counterion influence on chemical shifts in strychnine salts.

    PubMed

    Metaxas, Athena E; Cort, John R

    2013-05-01

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

  9. Interpretation of chemical shifts and coupling constants in macromolecules.

    PubMed

    Case, D A

    2000-04-01

    Recent developments in NMR spectroscopy, along with advances in computational techniques, have produced new approaches to the interpretation of chemical shifts and spin-spin coupling constants in biomolecules. Quantum chemical studies of useful accuracy are now becoming more routine and are increasingly being used in conjunction with experimental studies to map out expected structural patterns for peptides and oligonucleotides. Topics of recent special interest include spin couplings across hydrogen bonds and patterns of chemical shift anisotropies, in both diamagnetic and paramagnetic proteins. PMID:10753812

  10. 15N chemical shift referencing in solid state NMR.

    PubMed

    Bertani, Philippe; Raya, Jésus; Bechinger, Burkhard

    2014-01-01

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

  11. Determination of Relative Configuration from Residual Chemical Shift Anisotropy.

    PubMed

    Nath, Nilamoni; Schmidt, Manuel; Gil, Roberto R; Williamson, R Thomas; Martin, Gary E; Navarro-Vázquez, Armando; Griesinger, Christian; Liu, Yizhou

    2016-08-01

    Determination of relative configuration is frequently a rate-limiting step in the characterization of small organic molecules. Solution NMR-based nuclear Overhauser effect and scalar J-coupling constants can provide useful spatial information but often fail when stereocenters are separated by more than 4-5 Å. Residual dipolar couplings (RDCs) can provide a means of assigning relative configuration without limits of distance between stereocenters. However, sensitivity limits their application. Chemical shift is the most readily measured NMR parameter, and partial molecular alignment can reveal the anisotropic component of the chemical shift tensor, manifested as residual chemical shift anisotropy (RCSA). Hence, (13)C RCSAs provide information on the relative orientations of specific structural moieties including nonprotonated carbons and can be used for stereochemical assignment. Herein, we present two robust and sensitive methods to accurately measure and apply (13)C RCSAs for stereochemical assignment. The complementary techniques are demonstrated with five molecules representing differing structural classes. PMID:27294984

  12. 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

  13. 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.

  14. NMR chemical shifts in periodic systems from first principles

    NASA Astrophysics Data System (ADS)

    Sebastiani, Daniel; Goward, Gillian; Schnell, Ingo; Parrinello, Michele

    2002-08-01

    A recently developed ab-initio method for the calculation of NMR chemical shifts and magnetic susceptibilities in systems under periodic boundary conditions is presented and applied to a hydrogen-bonded molecular crystal. The calculations can unambiguously assign the chemical shifts to individual atoms in experimental spectra, and can further serve for the validation of simulated atomic trajectories and geometries. Apart from the example presented, the method can be applied to crystalline and amorphous insulators, as well as to isolated molecules using a supercell technique. The results are in good agreement with experiment.

  15. SHIFTX2: significantly improved protein chemical shift prediction.

    PubMed

    Han, Beomsoo; Liu, Yifeng; Ginzinger, Simon W; Wishart, David S

    2011-05-01

    A new computer program, called SHIFTX2, is described which is capable of rapidly and accurately calculating diamagnetic (1)H, (13)C and (15)N chemical shifts from protein coordinate data. Compared to its predecessor (SHIFTX) and to other existing protein chemical shift prediction programs, SHIFTX2 is substantially more accurate (up to 26% better by correlation coefficient with an RMS error that is up to 3.3× smaller) than the next best performing program. It also provides significantly more coverage (up to 10% more), is significantly faster (up to 8.5×) and capable of calculating a wider variety of backbone and side chain chemical shifts (up to 6×) than many other shift predictors. In particular, SHIFTX2 is able to attain correlation coefficients between experimentally observed and predicted backbone chemical shifts of 0.9800 ((15)N), 0.9959 ((13)Cα), 0.9992 ((13)Cβ), 0.9676 ((13)C'), 0.9714 ((1)HN), 0.9744 ((1)Hα) and RMS errors of 1.1169, 0.4412, 0.5163, 0.5330, 0.1711, and 0.1231 ppm, respectively. The correlation between SHIFTX2's predicted and observed side chain chemical shifts is 0.9787 ((13)C) and 0.9482 ((1)H) with RMS errors of 0.9754 and 0.1723 ppm, respectively. SHIFTX2 is able to achieve such a high level of accuracy by using a large, high quality database of training proteins (>190), by utilizing advanced machine learning techniques, by incorporating many more features (χ(2) and χ(3) angles, solvent accessibility, H-bond geometry, pH, temperature), and by combining sequence-based with structure-based chemical shift prediction techniques. With this substantial improvement in accuracy we believe that SHIFTX2 will open the door to many long-anticipated applications of chemical shift prediction to protein structure determination, refinement and validation. SHIFTX2 is available both as a standalone program and as a web server ( http://www.shiftx2.ca ). PMID:21448735

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

    NASA Astrophysics Data System (ADS)

    Laskowski, Robert; Blaha, Peter

    2012-01-01

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

  17. Ab initio theory of NMR chemical shifts in solids

    SciTech Connect

    Louie, S.G. |

    1997-12-31

    A new formalism for ab initio calculation of the orbital magnetic susceptibility and the NMR chemical shifts in solids and liquids is presented. The approach can be applied to periodic systems such as crystals, surfaces or polymers, and with a supercell technique, to nonperiodic systems such as amorphous materials, liquids, or solids with defects. The formalism is based on the density functional theory in the local density approximation and makes use of a generalized f-sum rule to eliminate the divergent terms that plagued previous theories. Calculations have been successfully carried out for the diamagnetic susceptibility of a number of insulators and for the NMR chemical shifts of a variety of systems including free molecules, ionic crystals, hydrogen-bonded materials and amorphous carbon.

  18. Chemical Shift Induced Phase Errors in Phase Contrast MRI

    PubMed Central

    Middione, Matthew J.; Ennis, Daniel B.

    2012-01-01

    Phase contrast magnetic resonance imaging (PC-MRI) is subject to numerous sources of error, which decrease clinical confidence in the reported measures. This work outlines how stationary perivascular fat can impart a significant chemical shift induced PC-MRI measurement error using computational simulations, in vitro, and in vivo experiments. This chemical shift error does not subtract in phase difference processing, but can be minimized with proper parameter selection. The chemical shift induced phase errors largely depend on both the receiver bandwidth (BW) and the TE. Both theory and an in vivo comparison of the maximum difference in net forward flow between vessels with and without perivascular fat indicated that the effects of chemically shifted perivascular fat are minimized by the use of high BW (814 Hz/px) and an in-phase TE (HBW-TEIN). In healthy volunteers (N=10) HBW-TEIN significantly improves intrapatient net forward flow agreement compared to low BW (401 Hz/px) and a mid-phase TE as indicated by significantly decreased measurement biases and limits of agreement for the ascending aorta (1.8±0.5 mL vs. 6.4±2.8 mL, P=0.01), main pulmonary artery (2.0±0.9 mL vs. 11.9±5.8 mL, P=0.04), the left pulmonary artery (1.3±0.9 mL vs. 5.4±2.5 mL, P=0.003), and all vessels (1.7±0.8 mL vs. 7.2±4.4 mL, P=0.001). PMID:22488490

  19. 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.

  20. Chemical shift referencing in MAS solid state NMR

    NASA Astrophysics Data System (ADS)

    Morcombe, Corey R.; Zilm, Kurt W.

    2003-06-01

    Solid state 13C magic angle spinning (MAS) NMR spectra are typically referenced externally using a probe which does not incorporate a field frequency lock. Solution NMR shifts on the other hand are more often determined with respect to an internal reference and using a deuterium based field frequency lock. Further differences arise in solution NMR of proteins and nucleic acids where both 13C and 1H shifts are referenced by recording the frequency of the 1H resonance of DSS (sodium salt of 2,2-dimethyl-2-silapentane-5-sulphonic acid) instead of TMS (tetramethylsilane). In this note we investigate the difficulties in relating shifts measured relative to TMS and DSS by these various approaches in solution and solids NMR, and calibrate adamantane as an external 13C standard for solids NMR. We find that external chemical shift referencing of magic angle spinning spectra is typically quite reproducible and accurate, with better than ±0.03 ppm accuracy being straight forward to achieve. Solid state and liquid phase NMR shifts obtained by magic angle spinning with external referencing agree with those measured using typical solution NMR hardware with the sample tube aligned with the applied field as long as magnetic susceptibility corrections and solvent shifts are taken into account. The DSS and TMS reference scales for 13C and 1H are related accurately using MAS NMR. Large solvent shifts for the 13C resonance in TMS in either deuterochloroform or methanol are observed, being +0.71 ppm and -0.74 ppm from external TMS, respectively. The ratio of the 13C resonance frequencies for the two carbons in solid adamantane to the 1H resonance of TMS is reported.

  1. Chemical shift referencing in MAS solid state NMR.

    PubMed

    Morcombe, Corey R; Zilm, Kurt W

    2003-06-01

    Solid state 13C magic angle spinning (MAS) NMR spectra are typically referenced externally using a probe which does not incorporate a field frequency lock. Solution NMR shifts on the other hand are more often determined with respect to an internal reference and using a deuterium based field frequency lock. Further differences arise in solution NMR of proteins and nucleic acids where both 13C and 1H shifts are referenced by recording the frequency of the 1H resonance of DSS (sodium salt of 2,2-dimethyl-2-silapentane-5-sulphonic acid) instead of TMS (tetramethylsilane). In this note we investigate the difficulties in relating shifts measured relative to TMS and DSS by these various approaches in solution and solids NMR, and calibrate adamantane as an external 13C standard for solids NMR. We find that external chemical shift referencing of magic angle spinning spectra is typically quite reproducible and accurate, with better than +/-0.03 ppm accuracy being straight forward to achieve. Solid state and liquid phase NMR shifts obtained by magic angle spinning with external referencing agree with those measured using typical solution NMR hardware with the sample tube aligned with the applied field as long as magnetic susceptibility corrections and solvent shifts are taken into account. The DSS and TMS reference scales for 13C and 1H are related accurately using MAS NMR. Large solvent shifts for the 13C resonance in TMS in either deuterochloroform or methanol are observed, being +0.71 ppm and -0.74 ppm from external TMS, respectively. The ratio of the 13C resonance frequencies for the two carbons in solid adamantane to the 1H resonance of TMS is reported. PMID:12810033

  2. Laser-polarized xenon-129 magnetic resonance spectroscopy and imaging. The development of a method for in vivo perfusion measurement

    NASA Astrophysics Data System (ADS)

    Rosen, Matthew Scot

    2001-07-01

    This thesis presents in vivo nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) studies with laser-polarized 129Xe delivered to living rats by inhalation and transported to tissue via blood flow. The results presented herein include the observation, assignment, and dynamic measurement of 129Xe resonances in the brain and body, the first one- and two-dimensional chemical-shift-resolved images of 129Xe in blood, tissue, and gas in the thorax, and the first images of 129Xe in brain tissue. These results establish that laser-polarized 129Xe can be used as a magnetic resonance tracer in vivo. NMR resonances at 0, 191, 198, and 209 ppm relative to the 129 Xe gas resonance are observed in the rat thorax and assigned to 129Xe in gas, fat, tissue, and blood respectively. Resonances at 189, 192, 195, 198, and 209 ppm are observed in the brain, and the 195 and 209 ppm resonances are assigned to 129Xe in grey matter, and blood, respectively. The design and construction of a laser-polarized 129Xe production and delivery system is described. This system produces liter-volumes of laser- polarized 129Xe by spin-exchange optical- pumping. It represented an order of magnitude increase over previously reported production volumes of polarized 129Xe. At approximately 3-7% polarization, 157 cc-atm of xenon is produced and stored as ice every 5 minutes. This reliable, effective, and simple production method for large volumes of 129Xe can be applied to other areas of research involving the use of laser-polarized noble gases. A model of the in vivo transport of laser polarized 129Xe to tissue under realistic experimental NMR conditions is described. Appropriate control of the NMR parameters is shown to allow tissue perfasion and 129Xe tissue T1 to be extracted from measurement of the steady-state 129Xe tissue signal. In vivo rodent 129Xe NMR results are used to estimate the signal-to-noise ratio of this technique, and an inhaled 30% xenon/70% O2 mixture polarized to 5

  3. Chemical shifts of small heterogeneous Ar/Xe clusters

    SciTech Connect

    Lindblad, A.; Rander, T.; Bradeanu, I.; Oehrwall, G.; Bjoerneholm, O.; Mucke, M.; Ulrich, V.; Lischke, T.; Hergenhahn, U.

    2011-03-15

    Heterogeneous rare-gas clusters produced by a coexpansion of an argon/xenon mixture have been studied using synchrotron-radiation-based photoelectron spectroscopy. Both valence and Xe 4d{sub 5/2} core-level photoelectron spectra were recorded for three different concentrations of the primary argon/xenon mixture and, for those mixtures, spectra were recorded at several different stagnation conditions. The studied size regime of the mixed clusters ranges from large, similar to those studied in an earlier paper [Phys. Rev. A 69, 031210(R) (2004)], to very small--as reflected in the cluster line shapes and chemical shifts. The chemical shifts obtained from a curve fitting procedure similar to that used in our earlier paper are discussed in terms of the mixed cluster structure which can be expected from equilibrium considerations and the Lennard-Jones parameters of the constituent atoms. Molecular dynamics simulations of the vertical polarization shifts allow more specific assignments of ''on-top'' sites and interfacial sites.

  4. Peridotite xenoliths from the Polynesian Austral and Samoa hotspots: Implications for the destruction of ancient 187Os and 142Nd isotopic domains and the preservation of Hadean 129Xe in the modern convecting mantle

    NASA Astrophysics Data System (ADS)

    Jackson, M. G.; Shirey, S. B.; Hauri, E. H.; Kurz, M. D.; Rizo, H.

    2016-07-01

    The Re-Os systematics in 13 peridotite xenoliths hosted in young (<0.39 myr) rejuvenated lavas from the Samoan island of Savai'i and 8 peridotite xenoliths from 6 to 10 myr old lavas from the Austral island of Tubuai have been examined to evaluate the history of the oceanic mantle in this region. Modal mineralogy, trace element compositions and 187Os/188Os ratios suggest that these peridotites are not cognate or residual to mantle plumes but rather samples of Pacific oceanic lithosphere created at the ridge. Savai'i and Tubuai islands lie along a flow line in the Pacific plate, and provide two snapshots (separated by over 40 Ma in time) of Pacific mantle that originated in the same region of the East Pacific rise. Tubuai xenoliths exhibit 187Os/188Os from 0.1163 to 0.1304, and Savai'i (Samoa) xenoliths span a smaller range from 0.1173 to 0.1284. The 187Os/188Os ratios measured in Tubuai xenoliths are lower than (and show no overlap with) basalts from Tubuai. The 187Os/188Os of the Savai'i xenoliths overlap the isotopic compositions of lavas from the island of Savai'i, but also extend to lower 187Os/188Os than the lavas. 3He/4He measurements of a subset of the xenoliths range from 2.5 to 6.4 Ra for Tubuai and 10.8 to 12.4 Ra for Savai'i. Like abyssal peridotites and xenoliths from oceanic hotspots that sample the convecting mantle, Os isotopes from the Savai'i and Tubuai xenolith suites are relatively unradiogenic, but do not preserve a record of depleted early-formed (Hadean and Archean) mantle domains expected from earlier cycles of ridge-related depletion, continent extraction, or subcontinental lithospheric mantle erosion. The lack of preservation of early-formed, geochemically-depleted Os-isotopic and 142Nd/144Nd domains in the modern convecting mantle contrasts with the preservation of early-formed (early-Hadean) 129Xe/130Xe isotopic heterogeneities in the convecting mantle. This can be explained if the initial isotopic signatures in Re-Os and Sm-Nd systems

  5. Errors of fourier chemical-shift imaging and their corrections

    NASA Astrophysics Data System (ADS)

    Wang, Zhiyue; Bolinger, Lizann; Subramanian, V. Harihara; Leigh, John S.

    From a finite and discrete Fourier transform point of view, we discuss the sources of localization errors in Fourier chemical-shift imaging, and demonstrate them explicitly by computer simulations for simple cases. Errors arise from intravoxel dephasing and the intravoxel asymmetry. The spectral leakage due to intravoxel dephasing is roughly 6-8% from one voxel to one of its nearest neighbors. Neighbors further away are influenced less significantly. The loss of localization due to intravoxel asymmetry effect is also severe. Fortunately, these errors can be corrected under certain conditions. The method for correcting the errors by postprocessing the data is described.

  6. 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.

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

    PubMed

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

    2015-04-14

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

  8. Protein Dielectric Constants Determined from NMR Chemical Shift Perturbations

    PubMed Central

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

    2015-01-01

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

  9. Quantum chemical 13Cα chemical shift calculations for protein NMR structure determination, refinement, and validation

    PubMed Central

    Vila, Jorge A.; Aramini, James M.; Rossi, Paolo; Kuzin, Alexandre; Su, Min; Seetharaman, Jayaraman; Xiao, Rong; Tong, Liang; Montelione, Gaetano T.; Scheraga, Harold A.

    2008-01-01

    A recently determined set of 20 NMR-derived conformations of a 48-residue all-α-helical protein, (PDB ID code 2JVD), is validated here by comparing the observed 13Cα chemical shifts with those computed at the density functional level of theory. In addition, a recently introduced physics-based method, aimed at determining protein structures by using NOE-derived distance constraints together with observed and computed 13Cα chemical shifts, was applied to determine a new set of 10 conformations, (Set-bt), as a blind test for the same protein. A cross-validation of these two sets of conformations in terms of the agreement between computed and observed 13Cα chemical shifts, several stereochemical quality factors, and some NMR quality assessment scores reveals the good quality of both sets of structures. We also carried out an analysis of the agreement between the observed and computed 13Cα chemical shifts for a slightly longer construct of the protein solved by x-ray crystallography at 2.0-Å resolution (PDB ID code 3BHP) with an identical amino acid residue sequence to the 2JVD structure for the first 46 residues. Our results reveal that both of the NMR-derived sets, namely 2JVD and Set-bt, are somewhat better representations of the observed 13Cα chemical shifts in solution than the 3BHP crystal structure. In addition, the 13Cα-based validation analysis appears to be more sensitive to subtle structural differences across the three sets of structures than any other NMR quality-assessment scores used here, and, although it is computationally intensive, this analysis has potential value as a standard procedure to determine, refine, and validate protein structures. PMID:18787110

  10. 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

  11. Automated determination of chemical functionalisation addition routes based on magnetic susceptibility and nucleus independent chemical shifts

    NASA Astrophysics Data System (ADS)

    Van Lier, G.; Ewels, C. P.; Geerlings, P.

    2008-07-01

    We present a modified version of our previously reported meta-code SACHA, for systematic analysis of chemical addition. The code automates the generation of structures, running of quantum chemical codes, and selection of preferential isomers based on chosen selection rules. While the selection rules for the previous version were based on the total system energy, predicting purely thermodynamic addition patterns, we examine here the possibility of using other system parameters, notably magnetic susceptibility as a descriptor of global aromaticity, and nucleus independent chemical shifts (NICS) as local aromaticity descriptor.

  12. Pitfalls of adrenal imaging with chemical shift MRI.

    PubMed

    Schieda, N; Al Dandan, O; Kielar, A Z; Flood, T A; McInnes, M D F; Siegelman, E S

    2014-11-01

    Chemical shift (CS) MRI of the adrenal glands exploits the different precessional frequencies of fat and water protons to differentiate the intracytoplasmic lipid-containing adrenal adenoma from other adrenal lesions. The purpose of this review is to illustrate both technical and interpretive pitfalls of adrenal imaging with CS MRI and emphasize the importance of adherence to strict technical specifications and errors that may occur when other imaging features and clinical factors are not incorporated into the diagnosis. When performed properly, the specificity of CS MRI for the diagnosis of adrenal adenoma is over 90%. Sampling the in-phase and opposed-phase echoes in the correct order and during the same breath-hold are essential requirements, and using the first echo pair is preferred, if possible. CS MRI characterizes more adrenal adenomas then unenhanced CT but may be non-diagnostic in a proportion of lipid-poor adenomas; CT washout studies may be able to diagnose these lipid-poor adenomas. Other primary and secondary adrenal tumours and supra-renal disease entities may contain lipid or gross fat and mimic adenoma or myelolipoma. Heterogeneity within an adrenal lesion that contains intracytoplasmic lipid could be due to myelolipoma, lipomatous metaplasia of adenoma, or collision tumour. Correlation with previous imaging, other imaging features, clinical history, and laboratory investigations can minimize interpretive errors. PMID:25062926

  13. 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

  14. Development of hyperpolarized noble gas MRI

    NASA Astrophysics Data System (ADS)

    Albert, M. S.; Balamore, D.

    1998-02-01

    Magnetic resonance imaging using the MR signal from hyperpolarized noble gases 129Xe and 3He may become an important new diagnostic technique. Alex Pines (adapting the hyperpolarization technique pioneered by William Happer) presented MR spectroscopy studies using hyperpolarized 129Xe. The current authors recognized that the enormous enhancement in the detectability of 129Xe, promised by hyperpolarization, would solve the daunting SNR problems impeding their attempts to use 129Xe as an in vivo MR probe, especially in order to study the action of general anesthetics. It was hoped that hyperpolarized 129Xe MRI would yield resolutions equivalent to that achievable with conventional 1H 2O MRI, and that xenon's solubility in lipids would facilitate investigations of lipid-rich tissues that had as yet been hard to image. The publication of hyperpolarized 129Xe images of excised mouse lungs heralded the emergence of hyperpolarized noble-gas MRI. Using hyperpolarized 3He, researchers have obtained images of the lung gas space of guinea pigs and of humans. Lung gas images from patients with pulmonary disease have recently been reported. 3He is easier to hyperpolarize than 129Xe, and it yields a stronger MR signal, but its extremely low solubility in blood precludes its use for the imaging of tissue. Xenon, however, readily dissolves in blood, and the T1 of dissolved 129Xe is long enough for sufficient polarization to be carried by the circulation to distal tissues. Hyperpolarized 129Xe dissolved-phase tissue spectra from the thorax and head of rodents and humans have been obtained, as have chemical shift 129Xe images from the head of rats. Lung gas 129Xe images of rodents, and more recently of humans, have been reported. Hyperpolarized 129Xe MRI (HypX-MRI) may elucidate the link between the structure of the lung and its function. The technique may also be useful in identifying ventilation-perfusion mismatch in patients with pulmonary embolism, in staging and tracking the

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

    PubMed

    Aeschbacher, Thomas; Schubert, Mario; Allain, Frédéric H-T

    2012-02-01

    Chemical shifts reflect the structural environment of a certain nucleus and can be used to extract structural and dynamic information. Proper calibration is indispensable to extract such information from chemical shifts. Whereas a variety of procedures exist to verify the chemical shift calibration for proteins, no such procedure is available for RNAs to date. We present here a procedure to analyze and correct the calibration of (13)C NMR data of RNAs. Our procedure uses five (13)C chemical shifts as a reference, each of them found in a narrow shift range in most datasets deposited in the Biological Magnetic Resonance Bank. In 49 datasets we could evaluate the (13)C calibration and detect errors or inconsistencies in RNA (13)C chemical shifts based on these chemical shift reference values. More than half of the datasets (27 out of those 49) were found to be improperly referenced or contained inconsistencies. This large inconsistency rate possibly explains that no clear structure-(13)C chemical shift relationship has emerged for RNA so far. We were able to recalibrate or correct 17 datasets resulting in 39 usable (13)C datasets. 6 new datasets from our lab were used to verify our method increasing the database to 45 usable datasets. We can now search for structure-chemical shift relationships with this improved list of (13)C chemical shift data. This is demonstrated by a clear relationship between ribose (13)C shifts and the sugar pucker, which can be used to predict a C2'- or C3'-endo conformation of the ribose with high accuracy. The improved quality of the chemical shift data allows statistical analysis with the potential to facilitate assignment procedures, and the extraction of restraints for structure calculations of RNA. PMID:22252483

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

    PubMed

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

    2016-03-21

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

  17. The nature and origin of chemical shift for intracellular water nuclei in artemia cysts.

    PubMed

    Kasturi, S R; Hazlewood, C F; Yamanashi, W S; Dennis, L W

    1987-08-01

    We investigated the possible existence of chemical shift of water nuclei in Artemia cysts using high resolution nuclear magnetic resonance (NMR) methods. The results conducted at 60, 200, and 500 MHz revealed an unusually large chemical shift for intracellular water protons. After correcting for bulk susceptibility effects, a residual downfield chemical shift of 0.11 ppm was observed in fully hydrated cysts. Similar results have been observed for the deuterium and (17)O nuclei.We have ruled out unusual intracellular pH, diamagnetic susceptibility of intracellular water, or interaction of water molecules with lipids, glycerol, and/or trehalose as possible origins of the residual chemical shift. We conclude that the residual chemical shift observed for water nuclei ((1)H, (2)H, and (17)O) is due to significant water-macromolecular interactions. PMID:19431702

  18. Ab Initio Calculation of Nuclear Magnetic Resonance Chemical Shift Anisotropy Tensors 1. Influence of Basis Set on the Calculation of 31P Chemical Shifts

    SciTech Connect

    Alam, T.M.

    1998-09-01

    The influence of changes in the contracted Gaussian basis set used for ab initio calculations of nuclear magnetic resonance (NMR) phosphorous chemical shift anisotropy (CSA) tensors was investigated. The isotropic chemical shitl and chemical shift anisotropy were found to converge with increasing complexity of the basis set at the Hartree-Fock @IF) level. The addition of d polarization function on the phosphorous nucIei was found to have a major impact of the calculated chemical shi~ but diminished with increasing number of polarization fimctions. At least 2 d polarization fimctions are required for accurate calculations of the isotropic phosphorous chemical shift. The introduction of density fictional theory (DFT) techniques through tie use of hybrid B3LYP methods for the calculation of the phosphorous chemical shift tensor resulted in a poorer estimation of the NMR values, even though DFT techniques result in improved energy and force constant calculations. The convergence of the W parametem with increasing basis set complexity was also observed for the DFT calculations, but produced results with consistent large deviations from experiment. The use of a HF 6-31 l++G(242p) basis set represents a good compromise between accuracy of the simulation and the complexity of the calculation for future ab initio calculations of 31P NMR parameters in larger complexes.

  19. Relativistically corrected nuclear magnetic resonance chemical shifts calculated with the normalized elimination of the small component using an effective potential-NMR chemical shifts of molybdenum and tungsten

    NASA Astrophysics Data System (ADS)

    Filatov, Michael; Cremer, Dieter

    2003-07-01

    A new method for relativistically corrected nuclear magnetic resonance (NMR) chemical shifts is developed by combining the individual gauge for the localized orbital approach for density functional theory with the normalized elimination of a small component using an effective potential. The new method is used for the calculation of the NMR chemical shifts of 95Mo and 183W in various molybdenum and tungsten compounds. It is shown that quasirelativistic corrections lead to an average improvement of calculated NMR chemical shift values by 300 and 120 ppm in the case of 95Mo and 183W, respectively, which is mainly due to improvements in the paramagnetic contributions. The relationship between electronic structure of a molecule and the relativistic paramagnetic corrections is discussed. Relativistic effects for the diamagnetic part of the magnetic shielding caused by a relativistic contraction of the s,p orbitals in the core region concern only the shielding values, however, have little consequence for the shift values because of the large independence from electronic structure and a cancellation of these effects in the shift values. It is shown that the relativistic corrections can be improved by level shift operators and a B3LYP hybrid functional, for which Hartree-Fock exchange is reduced to 15%.

  20. Chemically fractionated fission-xenon in meteorites and on the earth

    NASA Astrophysics Data System (ADS)

    Shukolyukov, Yuri A.; Jessberger, Elmar K.; Meshik, Alexander P.; Vu Minh, Dang; Jordan, Jimmy L.

    1994-07-01

    This is a report on the nature of isotopically anomalous xenon, which has been detected in two Ca-Al-rich inclusions of the Allende carbonaceous chondrite. It is extremely enriched in 132Xe, 129Xe, and to a lesser extent in 131Xe. Similar large excesses of 132Xe as well as of 131Xe, 134Xe, and 129Xe have previously been found in material processed in a natural nuclear reactor (Oklo phenomenon). Excess of these isotopes had also been encountered in MORB-glasses, in an ancient Greenland anorthosite. Thus, this Xe-type, which had previously been termed "alien" ( JORDON et al., 1980a) does not seem to be unique. To determine the origin of "alien" Xe, we analysed Xe (a) in neutron irradiated pitchblende and in the irradiation capsule, (b) in non-irradiated extremely fine-grained pitchblende (so-called Colorado-type deposit), and (c) in sandstone taken from the epicentre of an atomic explosion. In addition, the isotopic composition of xenon released by stepwise degassing and after selective dissolving of rocks from the Oklo natural reactor was determined. The results of these dedicated experiments demonstrate that the formation of alien Xe is due to the migration of the radioactive precursors of the stable isotopes 134Xe, 132Xe, 131Xe, and 129Xe. Due to this reason we now call it CFF-Xe - Chemically Fractionated Fission Xenon. Prerequisites for its formation are the simultaneous prevalence of two conditions: (1) fission (of 238U, 235U, and/ or 244Pu) and (2) a physicochemical environment (temperature, pressure, fluidity) at which the precursors of xenon (mainly Te and I) are mobile. Taking into account the occurrence of xenon in meteorites and terrestrial rocks, not all excesses of 129Xe in mantle rocks and natural gases are necessarily connected with the decay of primordial 129I.

  1. Quantum-chemical analyses of aromaticity, UV spectra, and NMR chemical shifts in plumbacyclopentadienylidenes stabilized by Lewis bases.

    PubMed

    Kawamura, Toshiaki; Abe, Minori; Saito, Masaichi; Hada, Masahiko

    2014-04-30

    We carried out a series of zeroth-order regular approximation (ZORA)-density functional theory (DFT) and ZORA-time-dependent (TD)-DFT calculations for molecular geometries, NMR chemical shifts, nucleus-independent chemical shifts (NICS), and electronic transition energies of plumbacyclopentadienylidenes stabilized by several Lewis bases, (Ph)2 ((t) BuMe2 Si)2 C4 PbL1 L2 (L1, L2 = tetrahydrofuran, Pyridine, N-heterocyclic carbene), and their model molecules. We mainly discussed the Lewis-base effect on the aromaticity of these complexes. The NICS was used to examine the aromaticity. The NICS values showed that the aromaticity of these complexes increases when the donation from the Lewis bases to Pb becomes large. This trend seems to be reasonable when the 4n-Huckel rule is applied to the fractional π-electron number. The calculated (13)C- and (207)Pb-NMR chemical shifts and the calculated UV transition energies reasonably reproduced the experimental trends. We found a specific relationship between the (13)C-NMR chemical shifts and the transition energies. As we expected, the relativistic effect was essential to reproduce a trend not only in the (207)Pb-NMR chemical shifts and J[Pb-C] but also in the (13)C-NMR chemical shifts of carbons adjacent to the lead atom. PMID:24643814

  2. Generation of heteronuclear 13C 1H chemical-shift correlations using soft pulses

    NASA Astrophysics Data System (ADS)

    Doddrell, David M.; Brooks, William; Field, James; Lynden-Bell, R. M.

    Two multipulse sequences are analyzed which can be used to generate heteronuclear 13C, 1H chemical-shift correlations without 2D NMR techniques. Both sequences utilize polarization-transfer techniques and generate the required chemical-shift correlation using a single soft proton pulse. The most useful technique is an extension of the DEPT method of polarization transfer since not only are the chemical-shift correlations generated in an easy to interpret form, but depending on the specific form of the pulse train used, the method can be employed to obtain information on the CH n group multiplicity. The methods are illustrated by applying them to generate 13C, 1H chemical-shift correlation spectra for menthol and cholesterol.

  3. 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)

  4. Chemical shifts and coupling constants of C8H10N4O2

    NASA Astrophysics Data System (ADS)

    Jain, M.

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

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

    PubMed

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

    2015-09-01

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

  6. An efficient amplification pulse sequence for measuring chemical shift anisotropy under fast magic-angle spinning.

    PubMed

    Hung, Ivan; Gan, Zhehong

    2011-12-01

    A two-dimensional experiment for measuring chemical shift anisotropy (CSA) under fast magic-angle spinning (MAS) is presented. The chemical shift anisotropy evolution is amplified by a sequence of π-pulses that repetitively interrupt MAS averaging. The amplification generates spinning sideband manifolds in the indirect dimension separated by the isotropic shift along the direct dimension. The basic unit of the pulse sequence is designed based on the magic-angle turning experiment and can be concatenated for larger amplification factors. PMID:21962909

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

    PubMed

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

    2015-10-13

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

  8. 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

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

    PubMed Central

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

    2011-01-01

    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. PMID:22293396

  10. 1H NMR spectra part 31: 1H chemical shifts of amides in DMSO solvent.

    PubMed

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

    2014-07-01

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

  11. Solvation chemical shifts of perylenic antenna molecules from molecular dynamics simulations.

    PubMed

    Özcan, Nergiz; Mareš, Jiří; Sundholm, Dage; Vaara, Juha

    2014-10-28

    Solvation-induced shifts in molecular properties can be realistically simulated by employing a dynamic model with explicit solvent molecules. In this work, (13)C NMR chemical shifts of various candidate antenna molecules for dye-sensitised solar cells have been studied by using density-functional theory calculations both in vacuo and by employing a dynamic solvation model. The solvent effects were investigated using instantaneous molecular dynamics snapshots containing the antenna molecule and surrounding acetonitrile solvent molecules. Such calculations take into account the main mechanisms of solvation-induced chemical shifts. We have analysed the contributions to the solvent shift due to the solvent susceptibility anisotropy, changes in the density of the virtual orbital space and the accessibility of the excited states to the pronouncedly local magnetic hyperfine operator. We present Lorentzian-broadened chemical shift stick spectra in which a comparison of the in vacuo and dynamic-solvation model results is graphically illustrated. The results show that the solvent-accessible atoms at the perimeter of the solute are influenced by the virtual states of the solvent molecules, which are visible to the hyperfine operators of the perimeter nuclei. This enables efficient coupling of the ground state of the solute to the magnetically allowed excited states, resulting in a positive chemical shift contribution of the perimeter nuclei. As a result of solvation, the chemical shift signals of perimeter nuclei are found to be displaced towards larger chemical shift values, whereas the nuclei of the inner region of the solute molecules show the opposite trend. The solvent susceptibility anisotropy is found to cause a small and practically constant contribution. PMID:25222796

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

    NASA Astrophysics Data System (ADS)

    Lomachuk, Yuriy V.; Titov, Anatoly V.

    2013-12-01

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

  13. Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts.

    PubMed

    Neal, Stephen; Nip, Alex M; Zhang, Haiyan; Wishart, David S

    2003-07-01

    A computer program (SHIFTX) is described which rapidly and accurately calculates the diamagnetic 1H, 13C and 15N chemical shifts of both backbone and sidechain atoms in proteins. The program uses a hybrid predictive approach that employs pre-calculated, empirically derived chemical shift hypersurfaces in combination with classical or semi-classical equations (for ring current, electric field, hydrogen bond and solvent effects) to calculate 1H, 13C and 15N chemical shifts from atomic coordinates. The chemical shift hypersurfaces capture dihedral angle, sidechain orientation, secondary structure and nearest neighbor effects that cannot easily be translated to analytical formulae or predicted via classical means. The chemical shift hypersurfaces were generated using a database of IUPAC-referenced protein chemical shifts--RefDB (Zhang et al., 2003), and a corresponding set of high resolution (<2.1 A) X-ray structures. Data mining techniques were used to extract the largest pairwise contributors (from a list of approximately 20 derived geometric, sequential and structural parameters) to generate the necessary hypersurfaces. SHIFTX is rapid (<1 CPU second for a complete shift calculation of 100 residues) and accurate. Overall, the program was able to attain a correlation coefficient (r) between observed and calculated shifts of 0.911 (1Halpha), 0.980 (13Calpha), 0.996 (13Cbeta), 0.863 (13CO), 0.909 (15N), 0.741 (1HN), and 0.907 (sidechain 1H) with RMS errors of 0.23, 0.98, 1.10, 1.16, 2.43, 0.49, and 0.30 ppm, respectively on test data sets. We further show that the agreement between observed and SHIFTX calculated chemical shifts can be an extremely sensitive measure of the quality of protein structures. Our results suggest that if NMR-derived structures could be refined using heteronuclear chemical shifts calculated by SHIFTX, their precision could approach that of the highest resolution X-ray structures. SHIFTX is freely available as a web server at http

  14. NMRDSP: an accurate prediction of protein shape strings from NMR chemical shifts and sequence data.

    PubMed

    Mao, Wusong; Cong, Peisheng; Wang, Zhiheng; Lu, Longjian; Zhu, Zhongliang; Li, Tonghua

    2013-01-01

    Shape string is structural sequence and is an extremely important structure representation of protein backbone conformations. Nuclear magnetic resonance chemical shifts give a strong correlation with the local protein structure, and are exploited to predict protein structures in conjunction with computational approaches. Here we demonstrate a novel approach, NMRDSP, which can accurately predict the protein shape string based on nuclear magnetic resonance chemical shifts and structural profiles obtained from sequence data. The NMRDSP uses six chemical shifts (HA, H, N, CA, CB and C) and eight elements of structure profiles as features, a non-redundant set (1,003 entries) as the training set, and a conditional random field as a classification algorithm. For an independent testing set (203 entries), we achieved an accuracy of 75.8% for S8 (the eight states accuracy) and 87.8% for S3 (the three states accuracy). This is higher than only using chemical shifts or sequence data, and confirms that the chemical shift and the structure profile are significant features for shape string prediction and their combination prominently improves the accuracy of the predictor. We have constructed the NMRDSP web server and believe it could be employed to provide a solid platform to predict other protein structures and functions. The NMRDSP web server is freely available at http://cal.tongji.edu.cn/NMRDSP/index.jsp. PMID:24376713

  15. MP2 calculation of (77) Se NMR chemical shifts taking into account relativistic corrections.

    PubMed

    Rusakov, Yury Yu; Rusakova, Irina L; Krivdin, Leonid B

    2015-07-01

    The main factors affecting the accuracy and computational cost of the Second-order Möller-Plesset perturbation theory (MP2) calculation of (77) Se NMR chemical shifts (methods and basis sets, relativistic corrections, and solvent effects) are addressed with a special emphasis on relativistic effects. For the latter, paramagnetic contribution (390-466 ppm) dominates over diamagnetic term (192-198 ppm) resulting in a total shielding relativistic correction of about 230-260 ppm (some 15% of the total values of selenium absolute shielding constants). Diamagnetic term is practically constant, while paramagnetic contribution spans over 70-80 ppm. In the (77) Se NMR chemical shifts scale, relativistic corrections are about 20-30 ppm (some 5% of the total values of selenium chemical shifts). Solvent effects evaluated within the polarizable continuum solvation model are of the same order of magnitude as relativistic corrections (about 5%). For the practical calculations of (77) Se NMR chemical shifts of the medium-sized organoselenium compounds, the most efficient computational protocols employing relativistic Dyall's basis sets and taking into account relativistic and solvent corrections are suggested. The best result is characterized by a mean absolute error of 17 ppm for the span of (77) Se NMR chemical shifts reaching 2500 ppm resulting in a mean absolute percentage error of 0.7%. PMID:25998325

  16. NMRDSP: An Accurate Prediction of Protein Shape Strings from NMR Chemical Shifts and Sequence Data

    PubMed Central

    Mao, Wusong; Cong, Peisheng; Wang, Zhiheng; Lu, Longjian; Zhu, Zhongliang; Li, Tonghua

    2013-01-01

    Shape string is structural sequence and is an extremely important structure representation of protein backbone conformations. Nuclear magnetic resonance chemical shifts give a strong correlation with the local protein structure, and are exploited to predict protein structures in conjunction with computational approaches. Here we demonstrate a novel approach, NMRDSP, which can accurately predict the protein shape string based on nuclear magnetic resonance chemical shifts and structural profiles obtained from sequence data. The NMRDSP uses six chemical shifts (HA, H, N, CA, CB and C) and eight elements of structure profiles as features, a non-redundant set (1,003 entries) as the training set, and a conditional random field as a classification algorithm. For an independent testing set (203 entries), we achieved an accuracy of 75.8% for S8 (the eight states accuracy) and 87.8% for S3 (the three states accuracy). This is higher than only using chemical shifts or sequence data, and confirms that the chemical shift and the structure profile are significant features for shape string prediction and their combination prominently improves the accuracy of the predictor. We have constructed the NMRDSP web server and believe it could be employed to provide a solid platform to predict other protein structures and functions. The NMRDSP web server is freely available at http://cal.tongji.edu.cn/NMRDSP/index.jsp. PMID:24376713

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  18. NMR Hyperfine Shifts in Blue Copper Proteins: A Quantum Chemical Investigation

    PubMed Central

    Zhang, Yong; Oldfield, Eric

    2009-01-01

    We present the results of the first quantum chemical investigations of 1H NMR hyperfine shifts in the blue copper proteins (BCPs): amicyanin, azurin, pseudoazurin, plastocyanin, stellacyanin, and rusticyanin. We find that very large structural models that incorporate extensive hydrogen bond networks, as well as geometry optimization, are required to reproduce the experimental NMR hyperfine shift results, the best theory vs experiment predictions having R2 = 0.94, a slope = 1.01, and a SD = 40.5 ppm (or ~4.7% of the overall ~860 ppm shift range). We also find interesting correlations between the hyperfine shifts and the bond and ring critical point properties computed using atoms-in-molecules theory, in addition to finding that hyperfine shifts can be well-predicted by using an empirical model, based on the geometry-optimized structures, which in the future should be of use in structure refinement. PMID:18314973

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

    PubMed

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

    2016-08-28

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

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

    PubMed

    Struppe, Jochem; Zhang, Yong; Rozovsky, Sharon

    2015-03-01

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

  1. 77Se Chemical Shift Tensor of L-selenocystine: Experimental NMR Measurements and Quantum Chemical Investigations of Structural Effects

    PubMed Central

    Struppe, Jochem; Zhang, Yong; Rozovsky, Sharon

    2015-01-01

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

  2. Sequential nearest-neighbor effects on computed 13Cα chemical shifts

    PubMed Central

    Vila, Jorge A.; Serrano, Pedro; Wüthrich, Kurt

    2010-01-01

    To evaluate sequential nearest-neighbor effects on quantum-chemical calculations of 13Cα 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 α/β 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 13Cα 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 13Cα 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 13Cα chemical shifts, Δca,i, for the individual residues along the sequence. This indicates that the Δca,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. PMID:20644980

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

    NASA Astrophysics Data System (ADS)

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

    1996-03-01

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

  4. The Chemical Shift Baseline for High-Pressure NMR Spectra of Proteins.

    PubMed

    Frach, Roland; Kibies, Patrick; Böttcher, Saraphina; Pongratz, Tim; Strohfeldt, Steven; Kurrmann, Simon; Koehler, Joerg; Hofmann, Martin; Kremer, Werner; Kalbitzer, Hans Robert; Reiser, Oliver; Horinek, Dominik; Kast, Stefan M

    2016-07-18

    High-pressure (HP) NMR spectroscopy is an important method for detecting rare functional states of proteins by analyzing the pressure response of chemical shifts. However, for the analysis of the shifts it is mandatory to understand the origin of the observed pressure dependence. Here we present experimental HP NMR data on the (15) N-enriched peptide bond model, N-methylacetamide (NMA), in water, combined with quantum-chemical computations of the magnetic parameters using a pressure-sensitive solvation model. Theoretical analysis of NMA and the experimentally used internal reference standard 4,4-dimethyl-4-silapentane-1-sulfonic (DSS) reveal that a substantial part of observed shifts can be attributed to purely solvent-induced electronic polarization of the backbone. DSS is only marginally responsive to pressure changes and is therefore a reliable sensor for variations in the local magnetic field caused by pressure-induced changes of the magnetic susceptibility of the solvent. PMID:27282319

  5. Use of 13Cα Chemical-Shifts in Protein Structure Determination

    PubMed Central

    Vila, Jorge A.; Ripoll, Daniel R.; Scheraga, Harold A.

    2008-01-01

    A physics-based method, aimed at determining protein structures by using NOE-derived distances together with observed and computed 13C chemical shifts, is proposed. The approach makes use of 13Cα chemical shifts, computed at the density functional level of theory, to obtain torsional constraints for all backbone and side-chain torsional angles without making a priori use of the occupancy of any region of the Ramachandran map by the amino acid residues. The torsional constraints are not fixed but are changed dynamically in each step of the procedure, following an iterative self-consistent approach intended to identify a set of conformations for which the computed 13Cα chemical shifts match the experimental ones. A test is carried out on a 76-amino acid all-α-helical protein, namely the B. Subtilis acyl carrier protein. It is shown that, starting from randomly generated conformations, the final protein models are more accurate than an existing NMR-derived structure model of this protein, in terms of both the agreement between predicted and observed 13Cα chemical shifts and some stereochemical quality indicators, and of similar accuracy as one of the protein models solved at a high level of resolution. The results provide evidence that this methodology can be used not only for structure determination but also for additional protein structure refinement of NMR-derived models deposited in the Protein Data Bank. PMID:17516673

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

    NASA Astrophysics Data System (ADS)

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

    1982-11-01

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

  7. 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…

  8. Compressed sensing for chemical shift-based water-fat separation.

    PubMed

    Doneva, Mariya; Börnert, Peter; Eggers, Holger; Mertins, Alfred; Pauly, John; Lustig, Michael

    2010-12-01

    Multi echo chemical shift-based water-fat separation methods allow for uniform fat suppression in the presence of main field inhomogeneities. However, these methods require additional scan time for chemical shift encoding. This work presents a method for water-fat separation from undersampled data (CS-WF), which combines compressed sensing and chemical shift-based water-fat separation. Undersampling was applied in the k-space and in the chemical shift encoding dimension to reduce the total scanning time. The method can reconstruct high quality water and fat images in 2D and 3D applications from undersampled data. As an extension, multipeak fat spectral models were incorporated into the CS-WF reconstruction to improve the water-fat separation quality. In 3D MRI, reduction factors of above three can be achieved, thus fully compensating the additional time needed in three-echo water-fat imaging. The method is demonstrated on knee and abdominal in vivo data. PMID:20859998

  9. Identify Beta-Hairpin Motifs with Quadratic Discriminant Algorithm Based on the Chemical Shifts

    PubMed Central

    YongE, Feng; GaoShan, Kou

    2015-01-01

    Successful prediction of the beta-hairpin motif will be helpful for understanding the of the fold recognition. Some algorithms have been proposed for the prediction of beta-hairpin motifs. However, the parameters used by these methods were primarily based on the amino acid sequences. Here, we proposed a novel model for predicting beta-hairpin structure based on the chemical shift. Firstly, we analyzed the statistical distribution of chemical shifts of six nuclei in not beta-hairpin and beta-hairpin motifs. Secondly, we used these chemical shifts as features combined with three algorithms to predict beta-hairpin structure. Finally, we achieved the best prediction, namely sensitivity of 92%, the specificity of 94% with 0.85 of Mathew’s correlation coefficient using quadratic discriminant analysis algorithm, which is clearly superior to the same method for the prediction of beta-hairpin structure from 20 amino acid compositions in the three-fold cross-validation. Our finding showed that the chemical shift is an effective parameter for beta-hairpin prediction, suggesting the quadratic discriminant analysis is a powerful algorithm for the prediction of beta-hairpin. PMID:26422468

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

    PubMed

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

    2016-08-01

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

  11. A geometrical parametrization of C1'-C5' RNA ribose chemical shifts calculated by density functional theory

    NASA Astrophysics Data System (ADS)

    Suardíaz, Reynier; Sahakyan, Aleksandr B.; Vendruscolo, Michele

    2013-07-01

    It has been recently shown that NMR chemical shifts can be used to determine the structures of proteins. In order to begin to extend this type of approach to nucleic acids, we present an equation that relates the structural parameters and the 13C chemical shifts of the ribose group. The parameters in the equation were determined by maximizing the agreement between the DFT-derived chemical shifts and those predicted through the equation for a database of ribose structures. Our results indicate that this type of approach represents a promising way of establishing quantitative and computationally efficient analytical relationships between chemical shifts and structural parameters in nucleic acids.

  12. Experimental link between the /sup 13/C NMR chemical shift of carbonyl carbons and the energy shifts observed in the n. -->. 3s optical transition of cyclic ketones

    SciTech Connect

    Cornish, T.J.; Baer, T.

    1988-09-14

    The n ..-->.. 3s transition energies of cold methylcyclopentanones and -cyclohexanones, as well as those of some branched-chain and bicyclic ketones, have been measured with 2 + 1 resonance-enhanced multiphoton ionization (REMPI). The energy shifts of the n ..-->.. 3s transition origins are found to correlate in a linear fashion with reported /sup 13/C NMR chemical shifts of the carbonyl carbon atoms. Several possible explanations for the experimental connection to NMR are discussed including consideration of both the paramagnetic and diamagnetic shielding contributions to the total chemical shift. 31 references, 3 figures, 1 table.

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

    SciTech Connect

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

    2012-02-14

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

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

    PubMed

    Shen, Yang; Bax, Ad

    2015-01-01

    Chemical shifts are obtained at the first stage of any protein structural study by NMR spectroscopy. Chemical shifts are known to be impacted by a wide range of structural factors, and the artificial neural network based TALOS-N program has been trained to extract backbone and side-chain torsion angles from (1)H, (15)N, and (13)C shifts. The program is quite robust and typically yields backbone torsion angles for more than 90 % of the residues and side-chain χ 1 rotamer information for about half of these, in addition to reliably predicting secondary structure. The use of TALOS-N is illustrated for the protein DinI, and torsion angles obtained by TALOS-N analysis from the measured chemical shifts of its backbone and (13)C(β) nuclei are compared to those seen in a prior, experimentally determined structure. The program is also particularly useful for generating torsion angle restraints, which then can be used during standard NMR protein structure calculations. PMID:25502373

  15. DFT study of zigzag (n, 0) single-walled carbon nanotubes: (13)C NMR chemical shifts.

    PubMed

    Kupka, Teobald; Stachów, Michal; Stobiński, Leszek; Kaminský, Jakub

    2016-06-01

    (13)C NMR chemical shifts of selected finite-size models of pristine zigzag single walled carbon nanotubes (SWCNTs) with a diameter of ∼0.4-0.8nm and length up to 2.2nm were studied theoretically. Results for finite SWCNTs models containing 1, 4 and 10 adjacent bamboo-type units were compared with data obtained for infinite tubes in order to estimate the reliability of small finite models in predicting magnetic properties of real-size nanotubes and to assess their tube-length dependence. SWCNTs were fully optimized using unrestricted density functional theory (DFT-UB3LYP/6-31G*). Cyclacenes, as the shortest models of open-ended zigzag SWCNTs, with systematically varying diameter were calculated as well. GIAO NMR calculations on the SWCNT and cyclacene models were performed using the BHandH density functional combined with relatively small STO-3Gmag basis set, developed by Leszczyński and coworkers for accurate description of magnetic properties. Regular changes of carbon (13)C chemical shifts along the tube axis of real size (6, 0) and (9, 0) zigzag carbon nanotubes were shown. The (13)C NMR shifts according to increasing diameter calculated for zigzag (n, 0, n=5-10) cyclacenes followed the trends observed for zigzag (n, 0) SWCNTs. The results for 4-units long SWCNTs match reasonably well with the data obtained for infinite zigzag (n, 0) SWCNTs, especially to those with bigger diameter (n=8-15). The presence of rim hydrogens obviously affects theoretical (13)C chemical shieldings and shifts in cyclacenes and thus cyclacenes can provide only approximate estimation of (13)C NMR parameters of real-size SWCNTs. The NMR properties predicted for the longest 10-units long models of SWCNTs reliably correspond to results obtained for infinite nanotubes. They were thus able to accurately predict also recently reported experimental chemical shift of chiral (6, 5) SWCNT. PMID:27155813

  16. 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.

  17. NMR characterization of sodium carboxymethyl cellulose 2: Chemical shift assignment and conformation analysis of substituent groups.

    PubMed

    Kono, Hiroyuki; Oshima, Kazuhiro; Hashimoto, Hisaho; Shimizu, Yuuichi; Tajima, Kenji

    2016-10-01

    The chemical shifts of the substituent groups of sodium carboxymethyl cellulose (CMC) were assigned by examining a series of CMC samples with different degrees of substitution. Comparative analysis of the (1)H-(13)C heteronuclear single quantum coherence (HSQC) and heteronuclear multiple bond correlation (HMBC) spectra allowed the complete assignment of the substituent groups at the 2-, 3-, and 6-positions of the seven substituted monomers comprising the CMC chains, namely, 2-mono-, 3-mono-, 6-mono-, 2,3-di-, 2,6-di-, 3,6-di-, and 2,3,6-tri-substituted anhydroglucose units (AGUs). In addition, the mole fractions of the monomers were determined by lineshape analysis of the carbonyl carbon resonances. The comparison between the chemical shifts of the substituents revealed strong interactions between 2- and 3-substituents in the same AGU, and showed that the steric hindrance by a substituent at the 2- or 3-position suppresses subsequent substitution at the adjacent position. PMID:27312635

  18. Assignment of protein backbone resonances using connectivity, torsion angles and 13Calpha chemical shifts.

    PubMed

    Morris, Laura C; Valafar, Homayoun; Prestegard, James H

    2004-05-01

    A program is presented which will return the most probable sequence location for a short connected set of residues in a protein given just (13)C(alpha) chemical shifts (delta((13)C(alpha))) and data restricting the phi and psi backbone angles. Data taken from both the BioMagResBank and the Protein Data Bank were used to create a probability density function (PDF) using a multivariate normal distribution in delta((13)C(alpha)), phi, and psi space for each amino acid residue. Extracting and combining probabilities for particular amino acid residues in a short proposed sequence yields a score indicative of the correctness of the proposed assignment. The program is illustrated using several proteins for which structure and (13)C(alpha) chemical shift data are available. PMID:15017135

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

    PubMed

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

    2015-12-14

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

  20. Characterization of Tricoordinate Boron Chemical Shift Tensors: Definitive High-Field

    SciTech Connect

    Bryce, David L.; Wasylishen, Roderick E.; Gee, Myrlene

    2001-01-01

    Despite the large known chemical shift (CS) range for boron and the large number of 11B NMR studies of glasses, no boron CS tensors have been characterized to date. We report the application of solid-state NMR techniques at moderate (9.4 T) and high (17.63 T) applied magnetic field strengths to the characterization of the boron CS tensors in trimesitylborane (BMes3) and triphenyl borate (B(OPh)3). The boron CS tensor of the former compound exhibits a remarkably large span,? 121 1 ppm, which encompasses the known range of isotropic chemical shifts for tricoordinate boron compounds. Conversely, the effect of the boron CS tensor on the 11B NMR spectra of B(OPh)3 is difficult to observe and quantify even at field strengths as high

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

    NASA Astrophysics Data System (ADS)

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

    2002-08-01

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

  2. Prediction of 31P nuclear magnetic resonance chemical shifts for phosphines

    NASA Astrophysics Data System (ADS)

    Tong, Jianbo; Liu, Shuling; Zhang, Shengwan; Li, Shengshi Z.

    2007-07-01

    Quantitative relationships of the 31P NMR chemical shifts of the phosphorus atoms in 291 phosphines with the atomic ionicity index (INI) and stereoscopic effect parameters ( ɛα, ɛβ, ɛγ) were primarily investigated in this paper for modeling some fundamental quantitative structure-spectroscopy relationships (QSSR). The results indicated that the 31P NMR chemical shifts of phosphines can be described as the quantitative equation by multiple linear regression (MLR): δp (ppm) = -174.0197 - 2.6724 INI + 40.4755 ɛα + 15.1141 ɛβ - 3.1858 ɛγ, correlation coefficient R = 0.9479, root mean square error (rms) = 13.9, and cross-validated predictive correlation coefficient was found by using the leave-one-out procedure to be Q2 = 0.8919. Furthermore, through way of random sampling, the estimative stability and the predictive power of the proposed MLR model were examined by constructing data set randomly into both the internal training set and external test set of 261 and 30 compounds, respectively, and then the chemical shifts were estimated and predicted with the training correlation coefficient R = 0.9467 and rms = 13.4 and the external predicting correlation coefficient Qext = 0.9598 and rms = 10.8. A partial least square model was developed that produced R = 0.9466, Q = 0.9407 and Qext = 0.9599, respectively. Those good results provided a new, simple, accurate and efficient methodology for calculating 31P NMR chemical shifts of phosphines.

  3. 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. PMID:26556218

  4. Relativistic DFT Calculation of (119)Sn Chemical Shifts and Coupling Constants in Tin Compounds.

    PubMed

    Bagno, Alessandro; Casella, Girolamo; Saielli, Giacomo

    2006-01-01

    The nuclear shielding and spin-spin coupling constants of (119)Sn in stannane, tetramethylstannane, methyltin halides Me4-nSnXn (X = Cl, Br, I; n = 1-3), tin halides, and some stannyl cations have been investigated computationally by DFT methods and Slater all-electron basis sets, including relativistic effects by means of the zeroth order regular approximation (ZORA) method up to spin-orbit coupling. Calculated (119)Sn chemical shifts generally correlate well with experimental values, except when several heavy halogen atoms, especially iodine, are bound to tin. In such cases, calculated chemical shifts are almost constant at the scalar (spin-free) ZORA level; only at the spin-orbit level is a good correlation, which holds for all compounds examined, attained. A remarkable "heavy-atom effect", analogous to that observed for analogous alkyl halides, is evident. The chemical shift of the putative stannyl cation (SnH3(+)) has also been examined, and it is concluded that the spectrum of the species obtained in superacids is inconsistent with a simple SnH3(+) structure; strong coordination to even weak nucleophiles such as FSO3H leads to a very satisfactory agreement. On the contrary, the calculated (119)Sn chemical shift of the trimesitylstannyl cation is in very good agreement with the experimental value. Coupling constants between (119)Sn and halogen nuclei are also well-modeled in general (taking into account the large uncertainties in the experimental values); relativistic spin-orbit effects are again quite evident. Couplings to (13)C and (1)H also fall, on the average, on the same correlation line, but individual values show a significant deviation from the expected unit slope. PMID:26626377

  5. 14N Chemical Shifts and Quadrupole Coupling Constants of Inorganic Nitrates

    NASA Astrophysics Data System (ADS)

    Marburger, Simon P.; Fung, B. M.; Khitrin, A. K.

    2002-02-01

    The isotropic chemical shift and the nuclear quadrupole coupling constant for 14N were obtained for 14 inorganic nitrates by solid-state MAS NMR measurements at two different field strengths, 9.4 and 11.7 T. The compounds studied were polycrystalline powders of AgNO3, Al(NO3)3, Ba(NO3)2, Ca(NO3)2, CsNO3, KNO3, LiNO3, Mg(NO3)2, NaNO3, Pb(NO3)2, RbNO3, Sr(NO3)2, Th(NO3)4·4H2O, and UO2(NO3)2·3H2O. Even though the spectra show broadening due to 14N quadrupole interactions, linewidths of a few hundred hertz and a good signal-to-noise ratio were achieved. From the position of the central peaks at the two fields, the chemical shifts and the nuclear quadrupole coupling constants were calculated. The chemical shifts for all compounds studied range from 282 to 342 ppm with respect to NH4Cl. The nuclear quadrupole coupling constants range from 429 kHz for AgNO3 to 993 kHz for LiNO3. These data are compared with those available in the literature.

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

    PubMed Central

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

    2013-01-01

    Summary A remaining challenge in protein modeling is to predict structures for sequences that do not share recognizable sequence similarity to any experimentally solved structure. This challenge can be addressed by hybrid algorithms that utilize easily obtainable experimental data and carry a limited amount of indirect structural information. Based on earlier observations, the library of protein super-secondary structure motifs (Smotifs) saturated about a decade ago, and new folds discovered since then are novel combinations of existing Smotifs. This observation suggests that it should be possible to build any structure, of either a known or yet to be discovered fold, from a combination of existing Smotifs derived from already known structures. In the absence of any sequence similarity signal, limited experimental data can be used to relate the backbone conformations of Smotifs between target proteins and known experimental structures. Here we present a modeling algorithm that relies on an exhaustive Smotif library and on NMR chemical shift patterns without any input of primary sequence information. In a test of 102 proteins with unique folds, the algorithm delivered 90 homology model quality models, among them 24 high quality ones, and a topologically correct solution for almost all cases. Detailed analysis of the method’s performance suggests that further improvement can be achieved by improving sampling algorithms and developing more precise tools that predict dihedral angle preferences from chemical shift assignments. The current approach opens a venue to address the modeling of larger protein structures for which chemical shifts are available. PMID:23685209

  7. Measurement of proton chemical shifts in invisible states of slowly exchanging protein systems by chemical exchange saturation transfer.

    PubMed

    Bouvignies, Guillaume; Kay, Lewis E

    2012-12-13

    Chemical exchange saturation transfer (CEST) NMR spectroscopy has emerged as a powerful technique for studies of transiently formed, sparsely populated (excited) conformational states of protein molecules in slow exchange with a dominant structure. The most popular form of the experiment, and the version originally developed, uses a weak (1)H radio frequency field to perturb longitudinal magnetization of one state with the effect transferred to magnetization in the second conformation via chemical exchange. A significant limitation of the method for protein applications emerges from (1)H magnetization transfer via dipolar relaxation (NOE effect) that can severely complicate analysis of the resulting CEST profile. This is particularly an issue since the (1)H chemical shifts of the excited state, critical for structural studies of these elusive conformers, become difficult to extract. Here we present a method for measurement of these shifts via CEST experiments in which the NOE effect is not an issue. The methodology is illustrated through applications to a pair of exchanging systems where the results are cross-validated. PMID:23194058

  8. 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.

  9. Blue-shifted and picosecond amplified UV emission from aqueous chemical grown ZnO microrods

    NASA Astrophysics Data System (ADS)

    Empizo, Melvin John F.; Yamanoi, Kohei; Santos-Putungan, Alexandra B.; Arita, Ren; Minami, Yuki; Luong, Mui Viet; Shimizu, Toshihiko; Estacio, Elmer S.; Somintac, Armando S.; Salvador, Arnel A.; Sarmago, Roland V.; Sarukura, Nobuhiko

    2015-10-01

    Room-temperature amplified spontaneous emission (ASE) has been observed from aqueous chemical grown zinc oxide (ZnO) microrods. The well-faceted microrods have only a single narrow ultraviolet (UV) emission at 390 nm (3.2 eV) with average lifetimes as fast as 85-100 ps. The characteristic ASE also exhibits blue-shifted peaks and shortened lifetimes. At present, the peak shifting and the lifetime shortening are attributed to the band filling and photo-induced screening effects and to the nonradiative relaxation process, respectively. Results indicate that the ZnO microrods have good structural and optical quality which leads to their suitable use for optoelectronic applications.

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

    NASA Astrophysics Data System (ADS)

    Durbeej, Bo; Eriksson, Leif A.

    2003-06-01

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

  11. Direct detection of spin chemical potential shift through spin filtering effect

    NASA Astrophysics Data System (ADS)

    Miao, Guoxing; Moodera, Jagadeesh

    2010-03-01

    Spin filtering (SF) effect is a unique way to generate highly spin-polarized tunnel currents from nonmagnetic electrodes. Magnetic tunnel junctions based on pure SF effect have been realized recently [1] as a clear demonstration of principle for the spin manipulation through SF effect. The next challenge is the readout of spin information. In this work, we present the direct detection of the spin chemical potential shift in an Al nano cluster sandwiched between two SF EuS tunnel barriers. The spin channels are split by depositing Al directly onto EuS, and the indirect exchange interaction between the Al conduction electrons and the localized Eu 4f electrons gives rise to an effective Zeeman splitting with the strength of a few mV. EuS on the readout side is isolated from the Al clusters with a natural Al2O3 barrier. In a vertical measurement geometry with no transport current, we directly detected the spin dependent voltage levels by aligning the detection SF barrier parallel or antiparallel to the first SF barrier, corresponding to the equilibrium up- and down-spin chemical potentials. A simple analysis treating the barriers as a set of resistors revealed that the observed voltage difference is the actual chemical potential shift modulated by the SF efficiency.[4pt] [1] G.X. Miao, M. Muller, J.S. Moodera,PRL102,076601(2009)

  12. 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

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

    PubMed Central

    Hong, Mei

    2016-01-01

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

  14. Performance of Density Functional Models to Reproduce Observed 13Cα Chemical Shifts of Proteins in Solution

    PubMed Central

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

    2009-01-01

    The purpose of this work is to test several density functional models (namely, OPBE, O3LYP, OPW91, BPW91, OB98, BPBE, B971, OLYP, PBE1PBE, and B3LYP) to determine their accuracy and speed for computing 13Cα chemical shifts in proteins. The test is applied to 10 NMR-derived conformations of the 76-residue α/β protein ubiquitin (protein data bank id 1D3Z). With each functional, the 13Cα shielding was computed for 760 amino acid residues by using a combination of approaches that includes, but is not limited to, treating each amino acid X in the sequence as a terminally blocked tripeptide with the sequence Ac-GXG-NMe in the conformation of the regularized experimental protein structure. As computation of the 13Cα chemical shifts, not their shielding, is the main goal of this work, a computation of the 13Cα shielding of the reference, namely, tetramethylsilane, is investigated here and an effective and a computed tetramethylsilane shielding value for each of the functionals is provided. Despite observed small differences among all functionals tested, the results indicate that four of them, namely, OPBE, OPW91, OB98, and OLYP, provide the most accurate functionals with which to reproduce observed 13Cα chemical shifts of proteins in solution, and are among the faster ones. This study also provides evidence for the applicability of these functionals to proteins of any size or class, and for the validation of our previous results and conclusions, obtained from calculations with the slower B3LYP functional. PMID:18780343

  15. 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

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

    PubMed Central

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

    2009-01-01

    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 (≤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)≥5 for echo train lengths (ETLs)≥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 ≥4 echoes and for T2* (<1.0%) with ≥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 ≤16 echoes for one- and two-peak systems. Preliminary ex vivo and in vivo

  17. Can the current density map topology be extracted from the nucleus independent chemical shifts?

    PubMed

    Van Damme, Sofie; Acke, Guillaume; Havenith, Remco W A; Bultinck, Patrick

    2016-04-28

    Aromatic compounds are characterised by the presence of a ring current when in a magnetic field. As a consequence, current density maps are used to assess (the degree of) aromaticity of a compound. However, often a more discrete set of so-called Nucleus Independent Chemical Shift (NICS) values is used that is derived from the current density. It is shown here that there is no simple one-to-one relationship that allows reconstructing current density maps from only NICS-values. NICS values should therefore not be used as aromaticity indices without analysis of the ab initio computed current density map. PMID:26762574

  18. 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.

  19. 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.

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

    PubMed

    Görling, Benjamin; Bräse, Stefan; Luy, Burkhard

    2016-01-01

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

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

    PubMed

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

    2016-07-01

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

  2. Correlation between 19F environment and isotropic chemical shift in barium and calcium fluoroaluminates.

    PubMed

    Body, M; Silly, G; Legein, C; Buzaré, J-Y

    2004-04-19

    High-speed MAS (19)F NMR spectra are recorded and reconstructed for 10 compounds from BaF(2)-AlF(3) and CaF(2)-AlF(3) binary systems which leads to the determination of 77 isotropic (19)F chemical shifts in various environments. A first attribution of NMR lines is performed for 8 compounds using a superposition model as initially proposed by B. Bureau et al. The phenomenological parameters of this model are then refined to improve the NMR line assignment. A satisfactory reliability is reached with a root-mean-square (RMS) deviation between calculated and measured values equal to 6 ppm. The refined parameters are then successfully tested on alpha-BaCaAlF(7) whose structure was recently determined. Finally, the isotropic chemical shift ranges are defined for shared, unshared, and "free" fluorine atoms encountered in the investigated binary systems. So, the fluorine surroundings can be deduced from the NMR line positions in compounds whose structure is unknown. Such an approach can also be applied to fluoride glasses. PMID:15074964

  3. High spectral specificity of local chemical components characterization with multichannel shift-excitation Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Chen, Kun; Wu, Tao; Wei, Haoyun; Wu, Xuejian; Li, Yan

    2015-09-01

    Raman spectroscopy has emerged as a promising tool for its noninvasive and nondestructive characterization of local chemical structures. However, spectrally overlapping components prevent the specific identification of hyperfine molecular information of different substances, because of limitations in the spectral resolving power. The challenge is to find a way of preserving scattered photons and retrieving hidden/buried Raman signatures to take full advantage of its chemical specificity. Here, we demonstrate a multichannel acquisition framework based on shift-excitation and slit-modulation, followed by mathematical post-processing, which enables a significant improvement in the spectral specificity of Raman characterization. The present technique, termed shift-excitation blind super-resolution Raman spectroscopy (SEBSR), uses multiple degraded spectra to beat the dispersion-loss trade-off and facilitate high-resolution applications. It overcomes a fundamental problem that has previously plagued high-resolution Raman spectroscopy: fine spectral resolution requires large dispersion, which is accompanied by extreme optical loss. Applicability is demonstrated by the perfect recovery of fine structure of the C-Cl bending mode as well as the clear discrimination of different polymorphs of mannitol. Due to its enhanced discrimination capability, this method offers a feasible route at encouraging a broader range of applications in analytical chemistry, materials and biomedicine.

  4. Density-functional computation of ⁹³Nb NMR chemical shifts.

    PubMed

    Bühl, Michael; Wrackmeyer, Bernd

    2010-12-01

    93Nb chemical shifts of [NbX6](-) (X = Cl, F, CO), [NbXCl4](-) (X = O, S), Nb2(OMe)10, Cp*2Nb(κ2-BH4), (Cp*Nb)2(µ-B2H6)2, CpNb(CO)4, and Cp2NbH3 are computed at the GIAO (gauge-including atomic orbitals)-, BPW91- and B3LYP-, and CSGT (continuous set of gauge transformations)-CAM-B3LYP, -ωB97, and -ωB97X levels, using BP86-optimized or experimental (X-ray) geometries. Experimental chemical shifts are best reproduced at the GIAO-BPW91 level when δ(93Nb) values of inorganic complexes are referenced directly relative to [NbCl6](-) and those of organometallic species are first calculated relative to [Nb(CO)6](-). An inadvertent error in the reported δ(93Nb) values of cyclopentadiene borane complexes (H. Brunner et al., J. Organomet. Chem.1992, 436, 313) is corrected. Trends in the observed 93Nb NMR linewidths for anionic niobates [Nb(CO)5](3-), [Nb(CO)5H](2-), and [Nb(CO)5(NH3)](-) are rationalized in terms of computed electric field gradients at the metal. PMID:20552575

  5. High spectral specificity of local chemical components characterization with multichannel shift-excitation Raman spectroscopy

    PubMed Central

    Chen, Kun; Wu, Tao; Wei, Haoyun; Wu, Xuejian; Li, Yan

    2015-01-01

    Raman spectroscopy has emerged as a promising tool for its noninvasive and nondestructive characterization of local chemical structures. However, spectrally overlapping components prevent the specific identification of hyperfine molecular information of different substances, because of limitations in the spectral resolving power. The challenge is to find a way of preserving scattered photons and retrieving hidden/buried Raman signatures to take full advantage of its chemical specificity. Here, we demonstrate a multichannel acquisition framework based on shift-excitation and slit-modulation, followed by mathematical post-processing, which enables a significant improvement in the spectral specificity of Raman characterization. The present technique, termed shift-excitation blind super-resolution Raman spectroscopy (SEBSR), uses multiple degraded spectra to beat the dispersion-loss trade-off and facilitate high-resolution applications. It overcomes a fundamental problem that has previously plagued high-resolution Raman spectroscopy: fine spectral resolution requires large dispersion, which is accompanied by extreme optical loss. Applicability is demonstrated by the perfect recovery of fine structure of the C-Cl bending mode as well as the clear discrimination of different polymorphs of mannitol. Due to its enhanced discrimination capability, this method offers a feasible route at encouraging a broader range of applications in analytical chemistry, materials and biomedicine. PMID:26350355

  6. 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. PMID:25377116

  7. A general chemical shift decomposition method for hyperpolarized (13) C metabolite magnetic resonance imaging.

    PubMed

    Wang, Jian-Xiong; Merritt, Matthew E; Sherry, Dean; Malloy, Craig R

    2016-08-01

    Metabolic imaging with hyperpolarized carbon-13 allows sequential steps of metabolism to be detected in vivo. Potential applications in cancer, brain, muscular, myocardial, and hepatic metabolism suggest that clinical applications could be readily developed. A primary concern in imaging hyperpolarized nuclei is the irreversible decay of the enhanced magnetization back to thermal equilibrium. Multiple methods for rapid imaging of hyperpolarized substrates and their products have been proposed with a multi-point Dixon method distinguishing itself as a robust protocol for imaging [1-(13) C]pyruvate. We describe here a generalized chemical shift decomposition method that incorporates a single-shot spiral imaging sequence plus a spectroscopic sequence to retain as much spin polarization as possible while allowing detection of metabolites that have a wide range of chemical shift values. The new method is demonstrated for hyperpolarized [1-(13) C]pyruvate, [1-(13) C]acetoacetate, and [2-(13) C]dihydroxyacetone. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27060361

  8. Relativistic environmental effects in (29)Si NMR chemical shifts of halosilanes: light nucleus, heavy environment.

    PubMed

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

    2015-06-01

    Relativistic calculations of (29)Si NMR shielding constants (chemical shifts) in the series of halosilanes SiX(n)H(4-n) (X = F, Cl, Br and I) are performed within a full four-component relativistic Dirac's scheme using relativistic Dyall's basis sets. Three different theoretical levels are tested in the computation of (29)Si NMR chemical shifts in comparison with experiment: namely, four-component relativistic GIAO-DFT, four-component relativistic GIAO-RPA, and a hybrid scheme of a nonrelativistic GIAO-MP2 with taking into account relativistic corrections using the four-component relativistic GIAO-RPA. The DFT results give larger relativistic effects as compared to the RPA data which might be rationalized in terms of the manifestation of correlation effects taken into account at the DFT level and not accounted for at the uncorrelated RPA level. Taking into account solvent effects slightly improves agreement with experiment, however, being not a matter of principle. Generally, relativistic pure nonempirical wave function methods perform much better as compared to relativistic DFT methods when benchmarked to experiment. PMID:25946056

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

    PubMed

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

    2016-10-01

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

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

    PubMed

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

    2009-09-10

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-08-01

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

  12. 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

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

    NASA Astrophysics Data System (ADS)

    An, Li

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

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  16. 125Te NMR chemical-shift trends in PbTe–GeTe and PbTe–SnTe alloys

    SciTech Connect

    Njegic, Bosiljka; Levin, Evgenii M.; Schmidt-Rohr, Klaus

    2013-10-08

    Complex tellurides, such as doped PbTe, GeTe, and their alloys, are among the best thermoelectric materials. Knowledge of the change in 125Te 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 125Te 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 125Te 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 125Te 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.

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

    PubMed

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

    2015-08-01

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

  18. 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…

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

    PubMed Central

    Pandey, Manoj Kumar; Ramamoorthy, Ayyalusamy

    2013-01-01

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

  20. XPS Chemical Shifts for CO Adsorbed on Ni(100):. a Theoretical Study

    NASA Astrophysics Data System (ADS)

    Pedocchi, L.; Rovida, G.; Russo, N.

    Starting from the observed chemical shift of C-1s and O-1s ionization potentials (IP), reported in the literature for the adsorption of CO on Ni(100), and correlated to the different CO adsorption sites at different coverages, we have carried out a theoretical investigation, using a first-principle density-functional method, to calculate ionization energies for adsorbed CO in the atop and bridge sites. In our approach, the Ni(100) surface was simulated with clusters of up to nine metal atoms of different geometry, in order to test the two adsorption sites. For each cluster, the CO adsorption geometry was optimized and the O-1s and C-1s ionizations were calculated. The main result was that the (O-1s-C-1s) difference was very well reproduced even with clusters of modest size, thus confirming the possibility to use this value as a structure-sensitive parameter.

  1. 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

  2. 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.

  3. 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.

  4. Subchondral bone and cartilage thickness from MRI: effects of chemical-shift artifact.

    PubMed

    McGibbon, Chris A; Bencardino, Jenny; Palmer, William E

    2003-02-01

    Magnetic resonance imaging (MRI) is the modality of choice for visualizing and quantifying articular cartilage thickness. However, difficulties persist in MRI of subchondral bone using spoiled gradient-echo (SPGR) and other gradient-echo sequences, primarily due to the effects of chemical-shift artifact. Fat suppression techniques are often used to reduce these artifacts, but they prevent measurement of bone thickness. In this report, we assess the magnitude of chemical-shift effects (phase-cancellation and misregistration artifacts) on subchondral bone and cartilage thickness measurements in human femoral heads using a variety of pulse sequence parameters. Phase-cancellation effects were quantified by comparing measurements from in-phase images (TE=13.5 ms) to out-of-phase images (TE=15.8 ms). We also tested the assumption of the optimal in-phase TE by comparing thickness measures at small variations on TE (13.0, 13.5 and 14.0 ms). Misregistration effects were quantified by comparing measurements from water+fat images (water-only+fat-only images) to the measurements from in-phase (TE=13.5) images. A correction algorithm was developed and applied to the in-phase measurements and then compared to measurements from water+fat images. We also compared thickness measurements at different image resolutions. Results showed that both phase-cancellation artifact and misregistration artifact were significant for bone thickness measurement, but not for cartilage thickness measurement. Using an in-phase TE and correction algorithm for misregistration artifact, the errors in bone thickness relative to water+fat images were non-significant. This information may be useful for developing pulse sequences for optimal imaging of both cartilage and subchondral bone. PMID:12695880

  5. Network of long-range concerted chemical shift displacements upon ligand binding to human angiogenin

    PubMed Central

    Gagné, Donald; Narayanan, Chitra; Doucet, Nicolas

    2015-01-01

    Molecular recognition models of both induced fit and conformational selection rely on coupled networks of flexible residues and/or structural rearrangements to promote protein function. While the atomic details of these motional events still remain elusive, members of the pancreatic ribonuclease superfamily were previously shown to depend on subtle conformational heterogeneity for optimal catalytic function. Human angiogenin, a structural homologue of bovine pancreatic RNase A, induces blood vessel formation and relies on a weak yet functionally mandatory ribonucleolytic activity to promote neovascularization. Here, we use the NMR chemical shift projection analysis (CHESPA) to clarify the mechanism of ligand binding in human angiogenin, further providing information on long-range intramolecular residue networks potentially involved in the function of this enzyme. We identify two main clusters of residue networks displaying correlated linear chemical shift trajectories upon binding of substrate fragments to the purine- and pyrimidine-specific subsites of the catalytic cleft. A large correlated residue network clusters in the region corresponding to the V1 domain, a site generally associated with the angiogenic response and structural stability of the enzyme. Another correlated network (residues 40–42) negatively affects the catalytic activity but also increases the angiogenic activity. 15N-CPMG relaxation dispersion experiments could not reveal the existence of millisecond timescale conformational exchange in this enzyme, a lack of flexibility supported by the very low-binding affinities and catalytic activity of angiogenin. Altogether, the current report potentially highlights the existence of long-range dynamic reorganization of the structure upon distinct subsite binding events in human angiogenin. PMID:25450558

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

    PubMed

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

    2016-05-30

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

  7. A strong 13C chemical shift signature provides the coordination mode of histidines in zinc-binding proteins.

    PubMed

    Barraud, Pierre; Schubert, Mario; Allain, Frédéric H-T

    2012-06-01

    Zinc is the second most abundant metal ion incorporated in proteins, and is in many cases a crucial component of protein three-dimensional structures. Zinc ions are frequently coordinated by cysteine and histidine residues. Whereas cysteines bind to zinc via their unique S(γ) atom, histidines can coordinate zinc with two different coordination modes, either N(δ1) or N(ε2) is coordinating the zinc ion. The determination of this coordination mode is crucial for the accurate structure determination of a histidine-containing zinc-binding site by NMR. NMR chemical shifts contain a vast amount of information on local electronic and structural environments and surprisingly their utilization for the determination of the coordination mode of zinc-ligated histidines has been limited so far to (15)N nuclei. In the present report, we observed that the (13)C chemical shifts of aromatic carbons in zinc-ligated histidines represent a reliable signature of their coordination mode. Using a statistical analysis of (13)C chemical shifts, we show that (13)C(δ2) chemical shift is sensitive to the histidine coordination mode and that the chemical shift difference δ{(13)C(ε1)} - δ{(13)C(δ2)} provides a reference-independent marker of this coordination mode. The present approach allows the direct determination of the coordination mode of zinc-ligated histidines even with non-isotopically enriched protein samples and without any prior structural information. PMID:22528293

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

    PubMed

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

    2016-09-01

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

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

    NASA Astrophysics Data System (ADS)

    Leniak, Arkadiusz; Jaźwiński, Jarosław

    2015-03-01

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

  10. 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.

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

    PubMed

    Holmes, Sean T; Dybowski, Cecil

    2015-11-01

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

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

    PubMed Central

    Holmes, Sean T.; Dybowski, Cecil

    2016-01-01

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

  13. [Evaluation of the Effect of Adiabatic Pulse and B1 Shim to the Radio Frequency Homogeneity in Chemical Shift Imaging].

    PubMed

    Kikuchi, Chie; Inoue, Mitsuhiro; Okawa, Kohei; Taguchi, Jyunichi; Hirota, Yoshifumi; Yanagiya, Yohei

    2016-04-01

    It is considered that the enhancement of chemical shift and the elevation of signal-to-noise ratio (SNR) induced by high magnetic fields are useful for the evaluation of metabolism using magnetic resonance spectroscopy (MRS). However, the reduction of the localization in MRS seems to be caused by the decreased homogeneity of radio frequency (RF) pulses, especially in chemical shift imaging (CSI). To search the influence of B1 shim mode and the significance of adiabatic pulses, we have examined the changes of RF homogeneity using 3 T magnetic resonance imaging (MRI) with the water phantom and the metabolites phantom (containing acetate and lactate) in CSI. The RF homogeneity and chemical shift artifact were obviously improved using the adiabatic pulses. Improvement of the homogeneity of RF pulses was observed when B1 shim was used. These results suggest the usefulness of CSI using adiabatic pulses and B1 shim when small amount of metabolites of target is measured in MRS. PMID:27097994

  14. CAESURA: Measurement of slow molecular dynamics by solid-state nuclear magnetic resonance chemical shift anisotropy modulation amplification

    NASA Astrophysics Data System (ADS)

    Shao, Limin; Titman, Jeremy J.

    2006-08-01

    An alternative magic angle spinning (MAS) exchange NMR experiment based on chemical shift anisotropy (CSA) amplification is described. The CSA amplification experiment correlates a standard MAS spectrum in the ω2 dimension with a sideband pattern in ω1 in which the intensities are identical to those expected for a sample spinning at some fraction 1/N of the actual rate ωr. In common with 2D-PASS, the isotropic shift appears only in the ω2 dimension, and long acquisition times can be avoided without loss of resolution of different chemical sites. The new CSA amplification exchange experiment provides information about the time scale and geometry of molecular motions via their effect on the sideband intensities in a one-dimensional pattern. The one-dimensional patterns from different chemical sites are separated across two frequency dimensions according to the isotropic shifts.

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

    PubMed

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

    2008-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-07-01

    We investigate the importance of relativistic effects on NMR shielding constants and chemical shifts of linear HgL2 (L = Cl, Br, I, CH3) compounds using three different relativistic methods: the fully relativistic four-component approach and the two-component approximations, linear response elimination of small component (LR-ESC) and zeroth-order regular approximation (ZORA). LR-ESC reproduces successfully the four-component results for the C shielding constant in Hg(CH3)2 within 6 ppm, but fails to reproduce the Hg shielding constants and chemical shifts. The latter is mainly due to an underestimation of the change in spin-orbit contribution. Even though ZORA underestimates the absolute Hg NMR shielding constants by ˜2100 ppm, the differences between Hg chemical shift values obtained using ZORA and the four-component approach without spin-density contribution to the exchange-correlation (XC) kernel are less than 60 ppm for all compounds using three different functionals, BP86, B3LYP, and PBE0. However, larger deviations (up to 366 ppm) occur for Hg chemical shifts in HgBr2 and HgI2 when ZORA results are compared with four-component calculations with non-collinear spin-density contribution to the XC kernel. For the ZORA calculations it is necessary to use large basis sets (QZ4P) and the TZ2P basis set may give errors of ˜500 ppm for the Hg chemical shifts, despite deceivingly good agreement with experimental data. A Gaussian nucleus model for the Coulomb potential reduces the Hg shielding constants by ˜100-500 ppm and the Hg chemical shifts by 1-143 ppm compared to the point nucleus model depending on the atomic number Z of the coordinating atom and the level of theory. The effect on the shielding constants of the lighter nuclei (C, Cl, Br, I) is, however, negligible.

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

    PubMed

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

    2011-07-28

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

  18. 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

  19. One-dimensional phosphorus-31 chemical shift imaging of human brain tumors

    SciTech Connect

    Rutter, A.; Hugenholtz, H.; Saunders, J.K.

    1995-06-01

    Phosphorus magnetic resonance spectroscopy has been used noninvasively to determine characteristic spectral parameters for untreated human brain tumors as a prelude to its use in clinical diagnosis. The spectra, which reflect the relative amounts of phosphorus-containing compounds, and the pH within and surrounding the tumors, were obtained in vivo using the the localization technique of one-dimensional chemical shift imaging applied with a surface coil. Phosphorus-31 chemical shift imaging was performed successfully in vivo on 9 volunteers and 27 patients with untreated brain tumors, including 7 with astrocytoma, 4 with glioblastoma, 3 with meningioma, and 11 with metastases. This study provides spectra from within and surrounding the brain tumors, and allows accountability for the heterogeneity of brain tumors by the selection of the maximum data point for each parameter. The ratios of resonance areas, phosphodiesters over nucleoside triphosphate (NTP), and phosphomonoesters over NTP, were found to be higher in glioblastomas (2.55 {plus_minus} 0.22, 1.06 {plus_minus} 0.09) and astorcytomas (3.04 {plus_minus} 0.36, 1.28 {plus_minus} 0.36) than in normal brain (2.00 {plus_minus} 0.32, 0.79 {plus_minus}0.22). The ratios of areas due to inorganic phosphate and NTP, and phosphocreatine and NTP, also were higher in astrocytomas (1.16 {plus_minus} 0.40, 1.17 {plus_minus} 0.41) compared with glioblastomas (0.68 {plus_minus} 0.01, 0.88 {plus_minus} 0.19) and normal brain (0.61 {plus_minus}0.03, 0.77 {plus_minus} 0.03). The pH of brain tumors ranged from alkaline to neutral, with meningiomas consistently having alkaline pH. These data show that there are statistically significant differences in the magnetic resonance parameters of the affected brain hemispheres of patients with astrocytomas, glioblastomas, meningiomas, and normal brain tissue, and underline the need for a multisite clinical trial to establish clinical criteria for diagnosis. 28 refs., 3 figs., 2 tabs.

  20. 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

  1. 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

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

    PubMed

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

    2014-12-16

    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 (r(2)) 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

  3. (39)K NMR of solid potassium salts at 21 T: effect of quadrupolar and chemical shift tensors.

    PubMed

    Moudrakovski, Igor L; Ripmeester, John A

    2007-01-25

    39K Solid State NMR spectra (static and magic angle spinning (MAS)) on a set of potassium salts measured at 21.14 T show that the chemical shift range for K(+) ions in diamagnetic salts is well in excess of 100 ppm contrary to previous assumptions that it was quite small. Inequivalent potassium sites in crystals can be resolved through differences in chemical shifts, with chemically similar sites showing differences of over 10 ppm. The quadrupolar coupling constants obtained from MAS and solid echo experiments on powders cover the range from zero for potassium in cubic environments in halides to over 3 MHz for the highly asymmetric sites in K2CO3. Although the quadrupolar effects generally dominate the 39K spectra, in several instances, we have observed subtle but significant contributions of chemical shift anisotropy with values up to 45 ppm, a first such observation. Careful analysis of static and MAS spectra allows the observation of the various chemical shift and quadrupole coupling tensor components as well as their relative orientations, thereby demonstrating that high-field 39K NMR spectroscopy in the solid state has a substantial sensitivity to the local environment with parameters that will be of considerable value in materials characterization and electronic structure studies. PMID:17228903

  4. Parallel-plate RF resonator imaging of chemical shift resolved capillary flow.

    PubMed

    Zhang, Jing; Balcom, Bruce J

    2010-07-01

    Magnetic resonance imaging has been introduced to study flow in microchannels using pure phase spatial encoding with a microfabricated parallel-plate nuclear magnetic resonance (NMR) probe. The NMR probe and pure phase spatial encoding enhance the sensitivity and resolution of the measurement. In this paper, (1)H NMR spectra and images were acquired at 100 MHz. The B(1) magnetic field is homogeneous and the signal-to-noise ratio of 30 microl doped water for a single scan is 8x10(4). The high sensitivity of the probe enables velocity mapping of the fluids in the micro-channel with a spatial resolution of 13x13 microm. The parallel-plate probe with pure phase encoding permits the acquisition of NMR spectra; therefore, chemical shift resolved velocity mapping was also undertaken. Results are presented which show separate velocity maps for water and methanol flowing through a straight circular micro-channel. Finally, future performance of these techniques for the study of microfluidics is extrapolated and discussed. PMID:20444567

  5. Chemical shift changes and line narrowing in 13C NMR spectra of hydrocarbon clathrate hydrates.

    PubMed

    Kida, Masato; Sakagami, Hirotoshi; Takahashi, Nobuo; Nagao, Jiro

    2013-05-23

    The solid-state (13)C NMR spectra of various guest hydrocarbons (methane, ethane, propane, adamantane) in clathrate hydrates were measured to elucidate the local structural environments around hydrocarbon molecules isolated in guest-host frameworks of clathrate hydrates. The results show that, depending on the cage environment, the trends in the (13)C chemical shift and line width change as a function of temperature. Shielding around the carbons of the guest normal alkanes in looser cage environments tends to decrease with increasing temperature, whereas shielding in tighter cage environments tends to increase continuously with increasing temperature. Furthermore, the (13)C NMR line widths suggest, because of the reorientation of the guest alkanes, that the local structures in structure II are more averaged than those in structure I. The differences between structures I and II tend to be very large in the lower temperature range examined in this study. The (13)C NMR spectra of adamantane guest molecules in structure H hydrate show that the local structures around adamantane guests trapped in structure H hydrate cages are averaged at the same level as in the α phase of solid adamantane. PMID:23607335

  6. Heterogeneous living donor hepatic fat distribution on MRI chemical shift imaging

    PubMed Central

    Choi, YoungRok; Lee, Jeong Min; Yi, Nam-Joon; Kim, Hyeyoung; Park, Min-Su; Hong, Geun; Yoo, Tae; Suh, Suk-Won; Lee, Hae Won; Lee, Kwang-Woong

    2015-01-01

    Purpose We evaluated the heterogeneity of steatosis in living donor livers to determine its regional differences. Methods Between June 2011 and February 2012, 81 liver donors were selected. Fat fraction was estimated using magnetic resonance triple-echo chemical shifting gradient imaging in 13 different regions: segment 1 (S1), S2, S3, and each peripheral and deep region of S4, S5, S6, S7, and S8. Results There were differences (range, 3.2%-5.3%) in fat fractions between each peripheral and deep region of S4, S6, S7, and S8 (P < 0.001, P = 0.004, P < 0.001, and P = 0.006). Fat deposit amount in S1, S2, S3 and deep regions of S4-S8 were significantly different from one another (F [4.003, 58.032] = 8.684, P < 0.001), while there were no differences among the peripheral regions of S4-S8 (F [2.9, 5.3] = 1.3, P = 0.272) by repeated measure analysis of variance method. And regional differences of the amount of fat deposit in the whole liver increased as a peripheral fat fraction of S5 increased (R2 = 0.428, P < 0.001). Conclusion Multifocal fat measurements for the whole liver are needed because a small regional evaluation might not represent the remaining liver completely, especially in patients with severe hepatic steatosis. PMID:26131443

  7. 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. PMID:26493308

  8. 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. PMID:23398371

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

    PubMed Central

    Garay, Pablo G.; Martin, Osvaldo A.; Scheraga, Harold 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 13C chemical shifts of different nuclei to detect methylation, acetylation and glycosylation of protein residues by monitoring the deviation of the 13C chemical shifts from the expected (mean) experimental value of the non-modified residue. As a proof-of-concept, we used 13C 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 13Cε 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 13C-nucleus, with which to determine other modifications commonly seen, such as methylation of arginine and glycosylation of serine, asparagine and threonine, shows encouraging results. PMID:27547559

  10. 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. PMID:27547559

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

    PubMed Central

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

    2015-01-01

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

  12. 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.

  13. Benchmark fragment-based (1)H, (13)C, (15)N and (17)O chemical shift predictions in molecular crystals.

    PubMed

    Hartman, Joshua D; Kudla, Ryan A; Day, Graeme M; Mueller, Leonard J; Beran, Gregory J O

    2016-08-21

    The performance of fragment-based ab initio(1)H, (13)C, (15)N and (17)O chemical shift predictions is assessed against experimental NMR chemical shift data in four benchmark sets of molecular crystals. Employing a variety of commonly used density functionals (PBE0, B3LYP, TPSSh, OPBE, PBE, TPSS), we explore the relative performance of cluster, two-body fragment, and combined cluster/fragment models. The hybrid density functionals (PBE0, B3LYP and TPSSh) generally out-perform their generalized gradient approximation (GGA)-based counterparts. (1)H, (13)C, (15)N, and (17)O isotropic chemical shifts can be predicted with root-mean-square errors of 0.3, 1.5, 4.2, and 9.8 ppm, respectively, using a computationally inexpensive electrostatically embedded two-body PBE0 fragment model. Oxygen chemical shieldings prove particularly sensitive to local many-body effects, and using a combined cluster/fragment model instead of the simple two-body fragment model decreases the root-mean-square errors to 7.6 ppm. These fragment-based model errors compare favorably with GIPAW PBE ones of 0.4, 2.2, 5.4, and 7.2 ppm for the same (1)H, (13)C, (15)N, and (17)O test sets. Using these benchmark calculations, a set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided and their robustness assessed using statistical cross-validation. We demonstrate the utility of these approaches and the reported scaling parameters on applications to 9-tert-butyl anthracene, several histidine co-crystals, benzoic acid and the C-nitrosoarene SnCl2(CH3)2(NODMA)2. PMID:27431490

  14. X-Ray Photoelectron and Anger Electron Spectroscopic Studies of Chemical Shifts in Amorphous Ge-Se System

    NASA Astrophysics Data System (ADS)

    Ueno, Tokihiro

    1983-09-01

    The chemical shifts of the Ge 3d, 3p3/2,1/2 and Se 3d, 3p3/2,1/2 photoelectron lines were measured for the amorphous Ge-Se system and those of the Ge photoelectron lines are corrected for Auger parameter shifts. According to the valence shell potential model, the ratio of the chemical shift in the amorphous Ge-Se system to that in stoichiometric GeSe2 can be approximated by the ratio of the Ge-Se bond number in the Ge-Se system to that in GeSe2. The chemical shift ratios evaluated from the experimental results reveal bond structures at non-stoichiometric compositions. In the excess-Ge range, GeSe is composed of atomic clusters of three-fold co-ordinated Ge and Se atoms, and Ge2Se3 contains atomic clusters of Se3Ge-GeSe3 units. In the excess-Se range, GeSe3 includes GeSe4 tetrahedral units, and Se-Se chains and/or Se8 rings.

  15. 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

  16. Are nucleus-independent (NICS) and 1H NMR chemical shifts good indicators of aromaticity in π-stacked polyfluorenes?

    NASA Astrophysics Data System (ADS)

    Osuna, Sílvia; Poater, Jordi; Bofill, Josep M.; Alemany, Pere; Solà, Miquel

    2006-09-01

    We have analyzed the change of local aromaticity in a series of polyfluorene compounds with the increase of the number of π-stacked layers. The local aromaticity of the aromatic and non-aromatic rings of polyfluorenes remains unchanged when going from one to four layers of π-stacked rings according to HOMA, PDI, and FLU aromaticity descriptors. On the contrary, experimental 1H NMR chemical shifts indicate a reduction of the aromaticity of π-stacked rings with the increase of the number of layers. Calculated NICS also show a change of aromaticity, but opposite to the tendency given by the 1H NMR chemical shifts. We show that this increase (decrease) of local aromaticity in superimposed aromatic rings indicated by NICS ( 1H NMR) is not real but the result of the coupling between the magnetic fields generated by the π-stacked rings.

  17. De novo structure generation using chemical shifts for proteins with high-sequence identity but different folds

    PubMed Central

    Shen, Yang; Bryan, Philip N; He, Yanan; Orban, John; Baker, David; Bax, Ad

    2010-01-01

    Proteins with high-sequence identity but very different folds present a special challenge to sequence-based protein structure prediction methods. In particular, a 56-residue three-helical bundle protein (GA95) and an α/β-fold protein (GB95), which share 95% sequence identity, were targets in the CASP-8 structure prediction contest. With only 12 out of 300 submitted server-CASP8 models for GA95 exhibiting the correct fold, this protein proved particularly challenging despite its small size. Here, we demonstrate that the information contained in NMR chemical shifts can readily be exploited by the CS-Rosetta structure prediction program and yields adequate convergence, even when input chemical shifts are limited to just amide 1HN and 15N or 1HN and 1Hα values. PMID:19998407

  18. Deuterium-induced isotope effects on the 13C chemical shifts of α-D-glucose pentaacetate.

    PubMed

    Pérez-Hernández, Nury; Álvarez-Cisneros, Celina; Cerda-García-Rojas, Carlos M; Morales-Ríos, Martha S; Joseph-Nathan, Pedro

    2013-03-01

    1,2,3,4,6-Penta-O-acetyl-α-D-glucopyranose and the corresponding [1-(2)H], [2-(2)H], [3-(2)H], [4-(2)H], [5-(2)H], and [6,6-(2)H(2)]-labeled compounds were prepared for measuring deuterium/hydrogen-induced effects on (13)C chemical shift (n)Δ (DHIECS) values. A conformational analysis of the nondeuterated compound was achieved using density functional theory (DFT) molecular models that allowed calculation of several structural properties as well as Boltzmann-averaged (13)C NMR chemical shifts by using the gauge-including atomic orbital method. It was found that the DFT-calculated C-H bond lengths correlate with (1)Δ DHIECS. PMID:23315885

  19. Determination of nuclear distances and chemical-shift anisotropy from 1H MAS NMR sideband patterns of surface OH groups

    NASA Astrophysics Data System (ADS)

    Fenzke, Dieter; Hunger, Michael; Pfeifer, Harry

    A procedure is described which allows a separate determination of the proton-aluminum distance and of the chemical-shift anisotropy for the bridging OH groups of crystalline molecular sieves from their 'H MAS NMR sideband patterns. For the bridging OH groups which point into the 6-rings of the framework (line "c"), the 1H- 27Al distance could be determined to be 0.237 ± 0.004 and 0.234 ± 0.004 nm for molecular sieves of type H-Y and SAPO-5, respectively. In contrast, for the bridging OH groups of the 12-rings (line "b"), the corresponding distances are equal and distinctly larger, 0.248 ± 0.004 nm. Within the limits of error, the values of the chemical-shift anisotropy are equal (about 19 ± 2 ppm) except for line b of SAPO-5, which exhibits a much smaller value of 14.5 ± 2 ppm.

  20. Computer programming for nucleic acid studies. II. Total chemical shifts calculation of all protons of double-stranded helices.

    PubMed

    Giessner-Prettre, C; Ribas Prado, F; Pullman, B; Kan, L; Kast, J R; Ts'o, P O

    1981-01-01

    A FORTRAN computer program called SHIFTS is described. Through SHIFTS, one can calculate the NMR chemical shifts of the proton resonances of single and double-stranded nucleic acids of known sequences and of predetermined conformations. The program can handle RNA and DNA for an arbitrary sequence of a set of 4 out of the 6 base types A,U,G,C,I and T. Data files for the geometrical parameters are available for A-, A'-, B-, D- and S-conformations. The positions of all the atoms are calculated using a modified version of the SEQ program [1]. Then, based on this defined geometry three chemical shift effects exerted by the atoms of the neighboring nucleotides on the protons of each monomeric unit are calculated separately: the ring current shielding effect: the local atomic magnetic susceptibility effect (including both diamagnetic and paramagnetic terms); and the polarization or electric field effect. Results of the program are compared with experimental results for a gamma (ApApGpCpUpU) 2 helical duplex and with calculated results on this same helix based on model building of A'-form and B-form and on graphical procedure for evaluating the ring current effects. PMID:6274583

  1. On reasons of 29Si NMR chemical shift/structure relations for silicon oxides, nitrides, and carbides: an individual-gauge-for-localized-orbitals study.

    PubMed

    Wolff, R; Jancke, H; Radeglia, R

    1997-12-01

    For alpha-quartz, monoclinic ZSM-5, alpha- and beta-Si3N4 and SiC-6H polytype, the silicon chemical shifts have been calculated using the IGLO (individual gauge for localized orbitals) method and models of different size in real crystal geometry. The result is a theoretical chemical shift scale, which is very similar to the corresponding experimental scale from 29Si MAS NMR experiments. It is shown that the assignment of isotropic silicon chemical shifts of crystallized solids based on theory is a method of practical applicability, also in cases where experimental methods or empirical relations fail. The two NMR spectral lines of alpha-Si3N4 are for the first time assigned to the crystallographic positions. The partition of the silicon chemical shifts into localized contributions from different parts of the model allows insight into the interactions around the resonance nucleus due to substituent and geometry variations leading to silicon chemical shifts. PMID:9477448

  2. Automated evaluation of chemical shift perturbation spectra: New approaches to quantitative analysis of receptor-ligand interaction NMR spectra

    PubMed Central

    Peng, Chen; Unger, Stephen W.; Filipp, Fabian V.; Sattler, Michael; Szalma, Sándor

    2016-01-01

    This paper presents new methods designed for quantitative analysis of chemical shift perturbation NMR spectra. The methods automatically trace the displacements of cross peaks between a perturbed test spectrum and the reference spectrum (or among a series of titration spectra), and measure the changes of chemical shifts, heights, and widths of the altered peaks. The methods are primary aimed at the 1H-15N HSQC spectra of relatively small proteins (<15 kDa) assuming fast exchange between free and ligand-bound states on the chemical shift time scale, or for comparing spectra of free and fully bound states in the slow exchange situation. Using the 1H-15N HSQC spectra from a titration experiment of the 74-residue Pex13p SH3 domain with a Pex14p peptide ligand (14 residues, Kd = ~ 40µM), we demonstrate the scope and limits of our automatic peak tracing (APET) algorithm for efficient scoring of high-throughput SAR by NMR type HSQC spectra, and progressive peak tracing (PROPET) algorithm for detailed analysis of ligand titration spectra. Simulated spectra with low signal-to-noise ratios (S/N ranged from 20 to 1) were used to demonstrate the reliability and reproducibility of the results when dealing with poor quality spectra. These algorithms have been implemented in a new software module, FELIX-Autoscreen, for streamlined processing, analysis and visualization of SAR by NMR and other high-throughput receptor/ligand interaction experiments. PMID:15243180

  3. Cellular thermal shift and clickable chemical probe assays for the determination of drug-target engagement in live cells.

    PubMed

    Xu, Hua; Gopalsamy, Ariamala; Hett, Erik C; Salter, Shores; Aulabaugh, Ann; Kyne, Robert E; Pierce, Betsy; Jones, Lyn H

    2016-07-14

    Proof of drug-target engagement in physiologically-relevant contexts is a key pillar of successful therapeutic target validation. We developed two orthogonal technologies, the cellular thermal shift assay (CETSA) and a covalent chemical probe reporter approach (harnessing sulfonyl fluoride tyrosine labeling and subsequent click chemistry) to measure the occupancy of the mRNA-decapping scavenger enzyme DcpS by a small molecule inhibitor in live cells. Enzyme affinity determined using isothermal dose response fingerprinting (ITDRFCETSA) and the concentration required to occupy 50% of the enzyme (OC50) using the chemical probe reporter assay were very similar. In this case, the chemical probe method worked well due to the long offset kinetics of the reversible inhibitor (determined using a fluorescent dye-tagged probe). This work suggests that CETSA could become the first choice assay to determine in-cell target engagement due to its simplicity. PMID:27216142

  4. Sub-electron-volt chemical shifts and strong interference effects measured in the resonance x-ray scattering spectra of aniline

    SciTech Connect

    Luo, Y.; Agren, H.; Guo, J.; Skytt, P.; Wassdahl, N.; Nordgren, J.

    1995-11-01

    By exploring the monosubstituted benzene compound aniline, we demonstrate that resonance inelastic x-ray spectroscopy of chemically shifted species is {ital site} {ital selective}. Core-excited levels with distinct, super-electron-volt shifts can be resonantly excited and their x-ray emission spectra analyzed separately. Core-excited levels referring to sites with small, sub-electron-volt, chemical shifts give resonant x-ray spectra that interfere strongly. It is demonstrated that this interference, which is manifested in the one-step model, can be used to monitor chemical shifts in the sub-electron-volt energy region. We show that in the limit when these chemical shifts go to zero some salient symmetry-selective features of the benzene resonant x-ray emission spectrum are restored in the aniline spectra.

  5. Thalassiosira spp. community composition shifts in response to chemical and physical forcing in the northeast Pacific Ocean

    PubMed Central

    Chappell, P. Dreux; Whitney, LeAnn P.; Haddock, Traci L.; Menden-Deuer, Susanne; Roy, Eric G.; Wells, Mark L.; Jenkins, Bethany D.

    2013-01-01

    Diatoms are genetically diverse unicellular photosynthetic eukaryotes that are key primary producers in the ocean. Many of the over 100 extant diatom species in the cosmopolitan genus Thalassiosira are difficult to distinguish in mixed populations using light microscopy. Here, we examine shifts in Thalassiosira spp. composition along a coastal to open ocean transect that encountered a 3-month-old Haida eddy in the northeast Pacific Ocean. To quantify shifts in Thalassiosira species composition, we developed a targeted automated ribosomal intergenic spacer analysis (ARISA) method to identify Thalassiosira spp. in environmental samples. As many specific fragment lengths are indicative of individual Thalassiosira spp., the ARISA method is a useful screening tool to identify changes in the relative abundance and distribution of specific species. The method also enabled us to assess changes in Thalassiosira community composition in response to chemical and physical forcing. Thalassiosira spp. community composition in the core of a 3-month-old Haida eddy remained largely (>80%) similar over a 2-week period, despite moving 24 km southwestward. Shifts in Thalassiosira species correlated with changes in dissolved iron (Fe) and temperature throughout the sampling period. Simultaneously tracking community composition and relative abundance of Thalassiosira species within the physical and chemical context they occurred allowed us to identify quantitative linkages between environmental conditions and community response. PMID:24065961

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

    PubMed

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

    2014-06-14

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

  7. 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. PMID:27335085

  8. 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.

  9. 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. PMID:20806873

  10. Chemical shift and zone-folding effects on the energy gaps of GaAs-AlAs (001) superlattices

    SciTech Connect

    Zhang, S.B. Xerox Palo Alto Research Center, 3333 Coyote Hill Road, Palo Alto, California 94304 ); Cohen, M.L.; Louie, S.G. )

    1991-04-15

    The chemical shift and zone-folding effects obtained from quasiparticle calculations for ultrathin GaAs-AlAs superlattices are incorporated within a Kronig-Penny model for superlattices of the arbitrary lattice period. We determine that superlattices with lattice periods in the range of 3{times}3 to 9{times}9 have an {ital X}-derived pseudodirect gap. This result explains both the results from first-principles calculations for ultrathin superlattices and those from experiments for a broader lattice period.

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

    NASA Technical Reports Server (NTRS)

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

    1978-01-01

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

  12. 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. PMID:26963288

  13. Effect of pH, urea, peptide length, and neighboring amino acids on alanine alpha-proton random coil chemical shifts.

    PubMed

    Carlisle, Elizabeth A; Holder, Jessica L; Maranda, Abby M; de Alwis, Adamberage R; Selkie, Ellen L; McKay, Sonya L

    2007-01-01

    Accurate random coil alpha-proton chemical shift values are essential for precise protein structure analysis using chemical shift index (CSI) calculations. The current study determines the chemical shift effects of pH, urea, peptide length and neighboring amino acids on the alpha-proton of Ala using model peptides of the general sequence GnXaaAYaaGn, where Xaa and Yaa are Leu, Val, Phe, Tyr, His, Trp or Pro, and n = 1-3. Changes in pH (2-6), urea (0-1M), and peptide length (n = 1-3) had no effect on Ala alpha-proton chemical shifts. Denaturing concentrations of urea (8M) caused significant downfield shifts (0.10 +/- 0.01 ppm) relative to an external DSS reference. Neighboring aliphatic residues (Leu, Val) had no effect, whereas aromatic amino acids (Phe, Tyr, His and Trp) and Pro caused significant shifts in the alanine alpha-proton, with the extent of the shifts dependent on the nature and position of the amino acid. Smaller aromatic residues (Phe, Tyr, His) caused larger shift effects when present in the C-terminal position (approximately 0.10 vs. 0.05 ppm N-terminal), and the larger aromatic tryptophan caused greater effects in the N-terminal position (0.15 ppm vs. 0.10 C-terminal). Proline affected both significant upfield (0.06 ppm, N-terminal) and downfield (0.25 ppm, C-terminal) chemical shifts. These new Ala correction factors detail the magnitude and range of variation in environmental chemical shift effects, in addition to providing insight into the molecular level interactions that govern protein folding. PMID:17054116

  14. 13C and 199Hg nuclear magnetic resonance spectroscopic study of alkenemercurinium ions: Effect of methyl substituents on 199Hg chemical shifts

    PubMed Central

    Olah, George A.; Garcia-Luna, Armando

    1980-01-01

    The long-lived ethylene, cyclohexene, and norbornenemercurinium ions prepared in superacidic, low-nucleophilic media have been studied by 13C and 199Hg NMR spectroscopy. The norbornenemercurinium ion shows temperature-dependent 13C and 199Hg NMR spectra, consistent with equilibration via rapid hydride and Wagner-Meerwin shifts. The 199Hg NMR shifts of a series of alkylmercury bromides were also obtained in order to elucidate the effect of methyl substituents on 199Hg NMR chemical shifts. PMID:16592870

  15. 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. PMID:27237841

  16. 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.

  17. 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.

  18. Simultaneous phase unwrapping and removal of chemical shift (SPURS) using graph cuts: application in quantitative susceptibility mapping.

    PubMed

    Dong, Jianwu; Liu, Tian; Chen, Feng; Zhou, Dong; Dimov, Alexey; Raj, Ashish; Cheng, Qiang; Spincemaille, Pascal; Wang, Yi

    2015-02-01

    Quantitative susceptibility mapping (QSM) is a magnetic resonance imaging technique that reveals tissue magnetic susceptibility. It relies on having a high quality field map, typically acquired with a relatively long echo spacing and long final TE. Applications of QSM outside the brain require the removal of fat contributions to the total signal phase. However, current water/fat separation methods applied on typical data acquired for QSM suffer from three issues: inadequacy when using large echo spacing, over-smoothing of the field maps and high computational cost. In this paper, the general phase wrap and chemical shift problem is formulated using a single species fitting and is solved using graph cuts with conditional jump moves. This method is referred as simultaneous phase unwrapping and removal of chemical shift (SPURS). The result from SPURS is then used as the initial guess for a voxel-wise iterative decomposition of water and fat with echo asymmetric and least-squares estimation (IDEAL). The estimated 3-D field maps are used to compute QSM in body regions outside of the brain, such as the liver. Experimental results show substantial improvements in field map estimation, water/fat separation and reconstructed QSM compared to two existing water/fat separation methods on 1.5T and 3T magnetic resonance human data with long echo spacing and rapid field map variation. PMID:25312917

  19. Measuring (13)C/(15)N chemical shift anisotropy in [(13)C,(15)N] uniformly enriched proteins using CSA amplification.

    PubMed

    Hung, Ivan; Ge, Yuwei; Liu, Xiaoli; Liu, Mali; Li, Conggang; Gan, Zhehong

    2015-11-01

    Extended chemical shift anisotropy amplification (xCSA) is applied for measuring (13)C/(15)N chemical shift anisotropy (CSA) of uniformly labeled proteins under magic-angle spinning (MAS). The amplification sequence consists of a sequence of π-pulses that repetitively interrupt MAS averaging of the CSA interaction. The timing of the pulses is designed to generate amplified spinning sideband manifolds which can be fitted to extract CSA parameters. The (13)C/(13)C homonuclear dipolar interactions are not affected by the π-pulses due to the bilinear nature of the spin operators and are averaged by MAS in the xCSA experiment. These features make the constant evolution-time experiment suitable for measuring CSA of uniformly labeled samples. The incorporation of xCSA with multi-dimensional (13)C/(15)N correlation is demonstrated with a GB1 protein sample as a model system for measuring (13)C/(15)N CSA of all backbone (15)NH, (13)CA and (13)CO sites. PMID:26404770

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

    PubMed Central

    2015-01-01

    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. PMID:26451676

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

    PubMed

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

    2015-11-11

    Fluorine NMR spectroscopy is a powerful tool for studying biomolecular structure, dynamics, and ligand binding, yet the origins of (19)F chemical shifts are not well understood. Herein, we use electronic structure calculations to describe the changes in (19)F chemical shifts of 2F- and 4F-histidine/(5-methyl)-imidazole upon acid titration. While the protonation of the 2F species results in a deshielded chemical shift, protonation of the 4F isomer results in an opposite, shielded chemical shift. The deshielding of 2F-histidine/(5-methyl)-imidazole upon protonation can be rationalized by concomitant decreases in charge density on fluorine and a reduced dipole moment. These correlations do not hold for 4F-histidine/(5-methyl)-imidazole, however. Molecular orbital calculations reveal that for the 4F species, there are no lone pair electrons on the fluorine until protonation. Analysis of a series of 4F-imidazole analogues, all with delocalized fluorine electron density, indicates that the deshielding of (19)F chemical shifts through substituent effects correlates with increased C-F bond polarity. In summary, the delocalization of fluorine electrons in the neutral 4F species, with gain of a lone pair upon protonation may help explain the difficulty in developing a predictive framework for fluorine chemical shifts. Ideas debated by chemists over 40 years ago, regarding fluorine's complex electronic effects, are shown to have relevance for understanding and predicting fluorine NMR spectra. PMID:26524669

  2. 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

  3. Observation of Optical Chemical Shift by Precision Nuclear Spin Optical Rotation Measurements and Calculations.

    PubMed

    Shi, Junhui; Ikäläinen, Suvi; Vaara, Juha; Romalis, Michael V

    2013-02-01

    Nuclear spin optical rotation (NSOR) is a recently developed technique for detection of nuclear magnetic resonance via rotation of light polarization, instead of the usual long-range magnetic fields. NSOR signals depend on hyperfine interactions with virtual optical excitations, giving new information about the nuclear chemical environment. We use a multipass optical cell to perform the first precision measurements of NSOR signals for a range of organic liquids and find clear distinction between proton signals for different compounds, in agreement with our earlier theoretical predictions. Detailed first-principles quantum mechanical NSOR calculations are found to be in agreement with the measurements. PMID:26281737

  4. Shifting chemical equilibria in flow--efficient decarbonylation driven by annular flow regimes.

    PubMed

    Gutmann, Bernhard; Elsner, Petteri; Glasnov, Toma; Roberge, Dominique M; Kappe, C Oliver

    2014-10-20

    To efficiently drive chemical reactions, it is often necessary to influence an equilibrium by removing one or more components from the reaction space. Such manipulation is straightforward in open systems, for example, by distillation of a volatile product from the reaction mixture. Herein we describe a unique high-temperature/high-pressure gas/liquid continuous-flow process for the rhodium-catalyzed decarbonylation of aldehydes. The carbon monoxide released during the reaction is carried with a stream of an inert gas through the center of the tubing, whereas the liquid feed travels as an annular film along the wall of the channel. As a consequence, carbon monoxide is effectively vaporized from the liquid phase into the gas phase and stripped from the reaction mixture, thus driving the equilibrium to the product and preventing poisoning of the catalyst. This approach enables the catalytic decarbonylation of a variety of aldehydes with unprecedented efficiency with a standard coil-based flow device. PMID:25196172

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

    We report here theoretical and experimental studies on the molecular structure and vibrational and NMR spectra of both natural enmein type diterpenoids molecule (6, 7-seco-ent-kaurenes enmein type), isolated from the leaves of Isodon japonica (Burm.f.) Hara var. galaucocalyx (maxin) Hara. The optimized geometry, total energy, NMR chemical shifts and vibrational wavenumbers of epinodosinol and epinodosin have been determined using B3LYP method with 6-311G (d,p) basis set. A complete vibrational assignment is provided for the observed IR spectra of studied compounds. The calculated wavenumbers and 13C c.s. are in an excellent agreement with the experimental values. Quantum chemical calculations at the B3LYP/6-311G (d,p) level of theory have been carried out on studied compounds to obtain a set of molecular electronic properties (MEP,HOMO, LUMO and gap energies ΔEg). Electrostatic potential surfaces have been mapped over the electron density isosurfaces to obtain information about the size, shape, charge density distribution and chemical reactivity of the molecules. PMID:24013676

  7. Characterization of interface abruptness and material properties in catalytically grown III-V nanowires: exploiting plasmon chemical shift

    NASA Astrophysics Data System (ADS)

    Tizei, L. H. G.; Chiaramonte, T.; Cotta, M. A.; Ugarte, D.

    2010-07-01

    We have studied the assessment of chemical composition changes in III-V heterostructured semiconductor nanowires (NWs) with nanometric spatial resolution using transmission electron microscopy methods. These materials represent a challenge for conventional spectroscopy techniques due to their high sensitivity to electron beam irradiation. Radiation damage strongly limits the exposure time to a few (5-10) s, which reduces the sensitivity of the traditionally used x-ray spectroscopy. The rather low counting statistics results in significant errors bars for EDS chemical quantification (5-10%) and interface width determination (few nanometers). Plasmon chemical shift is ideal in this situation, as its measurement requires very short exposure times (~100 ms) and the plasmon peak energy can be measured with high precision (~20 meV in this work). This high sensitivity allows the detection of subtle changes (1-2%) in composition or even the detection of a small plasmon energy (33 ± 7) meV change along usually assumed pure and homogeneous InAs segments. We have applied this approach to measure interface widths in heterostructure InAs/InP NWs grown using metal catalysts and also to determine the timescale (~10 s) in which beam irradiation induces material damage in these wires. In particular, we have detected small As concentrations (4.4 ± 0.5)% in the final InP segment close to the Au catalyst, which leads to the conclusion that As diffuses through the metal nanoparticle during growth.

  8. Characterization of interface abruptness and material properties in catalytically grown III-V nanowires: exploiting plasmon chemical shift.

    PubMed

    Tizei, L H G; Chiaramonte, T; Cotta, M A; Ugarte, D

    2010-07-23

    We have studied the assessment of chemical composition changes in III-V heterostructured semiconductor nanowires (NWs) with nanometric spatial resolution using transmission electron microscopy methods. These materials represent a challenge for conventional spectroscopy techniques due to their high sensitivity to electron beam irradiation. Radiation damage strongly limits the exposure time to a few (5-10) s, which reduces the sensitivity of the traditionally used x-ray spectroscopy. The rather low counting statistics results in significant errors bars for EDS chemical quantification (5-10%) and interface width determination (few nanometers). Plasmon chemical shift is ideal in this situation, as its measurement requires very short exposure times (approximately 100 ms) and the plasmon peak energy can be measured with high precision (approximately 20 meV in this work). This high sensitivity allows the detection of subtle changes (1-2%) in composition or even the detection of a small plasmon energy (33 +/- 7) meV change along usually assumed pure and homogeneous InAs segments. We have applied this approach to measure interface widths in heterostructure InAs/InP NWs grown using metal catalysts and also to determine the timescale (approximately 10 s) in which beam irradiation induces material damage in these wires. In particular, we have detected small As concentrations (4.4 +/- 0.5)% in the final InP segment close to the Au catalyst, which leads to the conclusion that As diffuses through the metal nanoparticle during growth. PMID:20585172

  9. 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. PMID:24655374

  10. 13C and 1H chemical shift assignments and conformation confirmation of trimedlure-Y via 2-D NMR

    NASA Astrophysics Data System (ADS)

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

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

  11. NMR chemical shift analysis of the conformational transition between the monomer and tetramer of melittin in an aqueous solution.

    PubMed

    Miura, Yoshinori

    2016-05-01

    It is known that melittin in an aqueous solution undergoes a conformational transition between the monomer and tetramer by variation in temperature. The transition correlates closely with isomers of the proline residue; monomeric melittin including a trans proline peptide bond (trans-monomer) is involved directly in the transition, whereas monomeric melittin having a cis proline peptide bond (cis-monomer) is virtually not. The transition has been explored by using nuclear magnetic resonance spectroscopy in order to clarify the stability of the tetrameric conformation and the cooperativity of the transition. In the light of temperature dependence of chemical shifts of resonances from the isomeric monomers, we qualitatively estimate the temperature-, salt-, and concentration-dependence of the relative equilibrium populations of the trans-monomer and tetramer, and show that the tetramer has a maximum conformational stability at 30-45 °C and that the transition cooperativity is very low. PMID:26658745

  12. Non‐invasive Localization of Thymol Accumulation in Carum copticum (Apiaceae) Fruits by Chemical Shift Selective Magnetic Resonance Imaging

    PubMed Central

    GERSBACH, P. V.; REDDY, N.

    2002-01-01

    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. PMID:12197523

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

    PubMed

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

    2015-04-01

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

  14. 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

    2016-08-01

    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. PMID:27273377

  15. Halogen effect on structure and 13C NMR chemical shift of 3,6-disubstituted-N-alkyl carbazoles.

    PubMed

    Radula-Janik, Klaudia; Kupka, Teobald; Ejsmont, Krzysztof; Daszkiewicz, Zdzislaw; Sauer, Stephan P A

    2013-10-01

    Structures of selected 3,6-dihalogeno-N-alkyl carbazole derivatives were calculated at the B3LYP/6-311++G(3df,2pd) level of theory, and their (13) C nuclear magnetic resonance (NMR) isotropic shieldings were predicted using density functional theory (DFT). The model compounds contained 9H, N-methyl and N-ethyl derivatives. The relativistic effect of Br and I atoms on nuclear shieldings was modeled using the spin-orbit zeroth-order regular approximation (ZORA) method. Significant heavy atom shielding effects for the carbon atom directly bonded with Br and I were observed (~-10 and ~-30 ppm while the other carbon shifts were practically unaffected). The decreasing electronegativity of the halogen substituent (F, Cl, Br, and I) was reflected in both nonrelativistic and relativistic NMR results as decreased values of chemical shifts of carbon atoms attached to halogen (C3 and C6) leading to a strong sensitivity to halogen atom type at 3 and 6 positions of the carbazole ring. The predicted NMR data correctly reproduce the available experimental data for unsubstituted N-alkylcarbazoles. PMID:23922027

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  17. 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. PMID:27488185

  18. 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.

  19. Dynamics-based selective 2D (1)H/(1)H chemical shift correlation spectroscopy under ultrafast MAS conditions.

    PubMed

    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 (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 (1)H/(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. PMID:26026440

  20. Correlation between the Temperature Dependence of Intrsinsic Mr Parameters and Thermal Dose Measured by a Rapid Chemical Shift Imaging Technique

    PubMed Central

    Taylor, Brian A.; Elliott, Andrew M.; Hwang, Ken-Pin; Hazle, John D.; Stafford, R. Jason

    2011-01-01

    In order to investigate simultaneous MR temperature imaging and direct validation of tissue damage during thermal therapy, temperature-dependent signal changes in proton resonance frequency (PRF) shifts, R2* values, and T1-weighted amplitudes are measured from one technique in ex vivo tissue heated with a 980-nm laser at 1.5T and 3.0T. Using a multi-gradient echo acquisition and signal modeling with the Stieglitz-McBride algorithm, the temperature sensitivity coefficient (TSC) values of these parameters are measured in each tissue at high spatiotemporal resolutions (1.6×1.6×4mm3,≤5sec) at the range of 25-61 °C. Non-linear changes in MR parameters are examined and correlated with an Arrhenius rate dose model of thermal damage. Using logistic regression, the probability of changes in these parameters is calculated as a function of thermal dose to determine if changes correspond to thermal damage. Temperature calibrations demonstrate TSC values which are consistent with previous studies. Temperature sensitivity of R2* and, in some cases, T1-weighted amplitudes are statistically different before and after thermal damage occurred. Significant changes in the slopes of R2* as a function of temperature are observed. Logistic regression analysis shows that these changes could be accurately predicted using the Arrhenius rate dose model (Ω=1.01±0.03), thereby showing that the changes in R2* could be direct markers of protein denaturation. Overall, by using a chemical shift imaging technique with simultaneous temperature estimation, R2* mapping and T1-W imaging, it is shown that changes in the sensitivity of R2* and, to a lesser degree, T1-W amplitudes are measured in ex vivo tissue when thermal damage is expected to occur according to Arrhenius rate dose models. These changes could possibly be used for direct validation of thermal damage in contrast to model-based predictions. PMID:21721063

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

    PubMed

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

    2016-02-01

    In microemulsions, changes in droplet size and shape and possible transformations occur under various conditions. They are difficult to characterize by most analytical tools because of their nano-sized structure and dynamic nature. Several methods are usually combined to obtain reliable information, guiding the scientist in understanding their physical behavior. We felt that there is a need for a technique that complements those in use today in order to provide more information on the microemulsion behavior, mainly as a function of dilution with water. The improvement of NMR chemical shift measurements independent of bulk magnetization effects makes it possible to study the very weak intermolecular chemical shift effects. In the present study, we used NMR high resolution magic angle spinning to measure the chemical shift very accurately, free of bulk magnetization effects. The chemical shift of microemulsion components is measured as a function of the water content in order to validate the method in an interesting and promising, U-type dilutable microemulsion, which had been previously studied by a variety of techniques. Phase transition points of the microemulsion (O/W, bicontinuous, W/O) and changes in droplet shape were successfully detected using high-accuracy chemical shift measurements. We analyzed the results and found them to be compatible with the previous studies, paving the way for high-accuracy chemical shifts to be used for the study of other microemulsion systems. We detected two transition points along the water dilution line of the concentrate (reverse micelles) corresponding to the transition from swollen W/O nano-droplets to bicontinuous to the O/W droplets along with the changes in the droplets' sizes and shapes. The method seems to be in excellent agreement with other previously studied techniques and shows the advantage of this easy and valid technique. PMID:25113928

  2. Inverted cucurbit[n]urils: density functional investigations on the electronic structure, electrostatic potential, and NMR chemical shifts.

    PubMed

    Pinjari, Rahul V; Gejji, Shridhar P

    2009-02-19

    Inverted cucurbit[n]uril (i(x)CB[n], x = 1, 2; n = 6-8), the enantiomers of cucurbit[n]uril (CB[n]) comprising one or more inverted glycouril units, show distinct selectivity in recognition toward the guest by the virtue of shape and dimensions of its cavity. The iCB[n] (x = 1 and n = 6, 7) are isolated as intermediates during the synthesis of CB[n]. In this work, density functional theory using the hybrid B3LYP functional has been employed to derive the electronic structure and the NMR chemical shifts in the i(x)CB[n] hosts. The present calculations have shown that the inversion of the glycouril unit of CB[6] and CB[7] engenders a destabilization by 4.2 and 5.7 kJ mol(-1), respectively, and, as opposed to this, the iCB[8] is favored by 18.6 kJ mol(-1) over the corresponding CB[8] host. Likewise, i2CB[7] possessing two inverted glycourils are highly destabilized over CB[7]. A large separation of the inverted glycouril units reduces the repulsion between methine protons inside the cavity, rendering the 1,4-i2CB[n] (n = 7 or 8) to be of lowest energy. Stabilization energies from the self-consistent reaction field (SCRF) theory are calculated with water, ethanol, and tetrahydrofuran (THF) as solvents. Unlike in gas phase and other solvents, the stabilization hierarchy iCB[6] < iCB[7] < iCB[8] has been predicted in THF. Molecular electrostatic potential (MESP) was used to gauge the cavity shape of these hosts. Consequently the iCB[6] reveals a half-sprocket-like cavity; an additional tooth for each glycouril in the succeeding iCB[n] homologue was noticed. In the case of the 1,5-i2CB[8] enantiomer, the cavity turns out to be rectangular. The deeper MESP minima near the ureido oxygens suggest strong electrostatic interactions with the guest at the iCB[6] portals. The electron-rich region within the cavity explains the large affinity of CB[n] toward the electron deficient guests. The electronic distribution and shape and size of the cavity thus derived provide insights

  3. Calcium-43 chemical shift and electric field gradient tensor interplay: a sensitive probe of structure, polymorphism, and hydration.

    PubMed

    Widdifield, Cory M; Moudrakovski, Igor; Bryce, David L

    2014-07-14

    Calcium is the 5th most abundant element on earth, and is found in numerous biological tissues, proteins, materials, and increasingly in catalysts. However, due to a number of unfavourable nuclear properties, such as a low magnetogyric ratio, very low natural abundance, and its nuclear electric quadrupole moment, development of solid-state (43)Ca NMR has been constrained relative to similar nuclides. In this study, 12 commonly-available calcium compounds are analyzed via(43)Ca solid-state NMR and the information which may be obtained by the measurement of both the (43)Ca electric field gradient (EFG) and chemical shift tensors (the latter of which are extremely rare with only a handful of literature examples) is discussed. Combined with density functional theory (DFT) computations, this 'tensor interplay' is, for the first time for (43)Ca, illustrated to be diagnostic in distinguishing polymorphs (e.g., calcium formate), and the degree of hydration (e.g., CaCl2·2H2O and calcium tartrate tetrahydrate). For Ca(OH)2, we outline the first example of (1)H to (43)Ca cross-polarization on a sample at natural abundance in (43)Ca. Using prior knowledge of the relationship between the isotropic calcium chemical shift and the calcium quadrupolar coupling constant (CQ) with coordination number, we postulate the coordination number in a sample of calcium levulinate dihydrate, which does not have a known crystal structure. Natural samples of CaCO3 (aragonite polymorph) are used to show that the synthetic structure is present in nature. Gauge-including projector augmented-wave (GIPAW) DFT computations using accepted crystal structures for many of these systems generally result in calculated NMR tensor parameters which are in very good agreement with the experimental observations. This combination of (43)Ca NMR measurements with GIPAW DFT ultimately allows us to establish clear correlations between various solid-state (43)Ca NMR observables and selected structural parameters

  4. The contribution of magnetic susceptibility effects to transmembrane chemical shift differences in the 31P NMR spectra of oxygenated erythrocyte suspensions.

    PubMed

    Kirk, K; Kuchel, P W

    1988-01-01

    Triethyl phosphate, dimethyl methylphosphonate, and the hypophosphite ion all contain the phosphoryl functional group. When added to an oxygenated erythrocyte suspension, the former compound gives rise to a single 31P NMR resonance, whereas the latter compounds give rise to separate intra- and extracellular 31P NMR resonances. On the basis of experiments with intact oxygenated cell suspensions (in which the hematocrit was varied) and with oxygenated cell lysates (in which the lysate concentration was varied), it was concluded that the chemical shifts of the intra- and extracellular populations of triethyl phosphate differ as a consequence of the diamagnetic susceptibility of intracellular oxyhemoglobin but that this difference is averaged by the rapid exchange of the compound across the cell membrane. The difference in the magnetic susceptibility of the intra- and extracellular compartments contributes to the observed separation of the intra- and extracellular resonances of dimethyl methylphosphonate and hypophosphite. The magnitude of this contribution is, however, substantially less than that calculated using a simple two-compartment model and varies with the hematocrit of the suspension. Furthermore, it is insufficient to fully account for the transmembrane chemical shift differences observed for dimethyl methylphosphonate and hypophosphite. An additional effect is operating to move the intracellular resonances of these compounds to a lower chemical shift. The effect is mediated by an intracellular component, and the magnitude of the resultant chemical shift variations depends upon the chemical structure of the phosphoryl compound involved. PMID:3275636

  5. DFT-GIAO 1H and 13C NMR prediction of chemical shifts for the configurational assignment of 6beta-hydroxyhyoscyamine diastereoisomers.

    PubMed

    Muñoz, Marcelo A; Joseph-Nathan, Pedro

    2009-07-01

    (1)H and (13)C NMR chemical shift calculations using the density functional theory-gauge including/invariant atomic orbitals (DFT-GIAO) approximation at the B3LYP/6-311G++(d,p) level of theory have been used to assign both natural diastereoisomers of 6beta-hydroxyhyoscyamine. The theoretical chemical shifts of the (1)H and (13)C atoms in both isomers were calculated using a previously determined conformational distribution, and the theoretical and experimental values were cross-compared. For protons, the obtained average absolute differences and root mean square (rms) errors for each comparison showed that the experimental chemical shifts of dextrorotatory and levorotatory 6beta-hydroxyhyoscyamines correlated well with the theoretical values calculated for the (3R,6R,2'S) and (3S,6S,2'S) configurations, respectively, whereas for (13)C atoms the calculations were unable to differentiate between isomers. The nature of the relatively large chemical shift differences observed in nuclei that share similar chemical environments between isomers was asserted from the same calculations. It is shown that the anisotropic effect of the phenyl group in the tropic ester moiety, positioned under the tropane ring, has a larger shielding effect over one ring side than over the other one. PMID:19373852

  6. Contribution of magnetic susceptibility effects to transmembrane chemical shift differences in the /sup 31/P NMR spectra of oxygenated erythrocyte suspensions

    SciTech Connect

    Kirk, K.; Kuchel, P.W.

    1988-01-05

    Triethyl phosphate, dimethyl methylphosphonate, and the hypophosphite ion all contain the phosphoryl functional group. When added to an oxygenated erythrocyte suspension, the former compound gives rise to a single /sup 31/P NMR resonance, whereas the latter compounds give rise to separate intra- and extracellular /sup 31/P NMR resonances. On the basis of experiments with intact oxygenated cell suspensions (in which the hematocrit was varied) and with oxygenated cell lysates (in which the lysate concentration was varied) it was concluded that the chemical shifts of the intra- and extracellular populations of triethyl phosphate differ as a consequence of the diamagnetic susceptibility of intracellular oxyhemoglobin but that this difference is averaged by the rapid exchange of the compound across the cell membrane. The difference is the magnetic susceptibility of the intra- and extracellular compartments contributes to the observed separation of the intra- and extracellular resonances of dimethyl methylphosphonate and hypophosphite. The magnitude of this contribution is, however, substantially less than that calculated using a simple two-compartment model and varies with the hematocrit of the suspension. Furthermore, it is insufficient to fully account for the transmembrane chemical shift differences observed for dimethyl methylphosphonate and hypophosphite. An additional effect is operating to move the intracellular resonances of these compounds to a lower chemical shift. The effect is mediated by an intracellular component, and the magnitude of the resultant chemical shift variations depends upon the chemical structure of the phosphoryl compound involved.

  7. 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

  8. Neonatal body composition: dual-energy X-ray absorptiometry, magnetic resonance imaging, and three-dimensional chemical shift imaging versus chemical analysis in piglets.

    PubMed

    Fusch, C; Slotboom, J; Fuehrer, U; Schumacher, R; Keisker, A; Zimmermann, W; Moessinger, A; Boesch, C; Blum, J

    1999-10-01

    An animal study to evaluate dual-energy x-ray absorptiometry (DXA) and magnetic resonance (MR) imaging and spectroscopy for measurement of neonatal body composition was performed. Twenty-three piglets with body weights ranging from 848 to 7550 g were used. After measuring total body water, animals were killed and body composition was assessed using DXA and MR (1.5 T; MR imaging, T1-weighted sagittal spin-echo sequence; MR spectroscopy, three-dimensional chemical shift imaging) as well as chemical carcass analysis (standard methods) after homogenization. Body composition by chemical analysis (percent of body weight, mean +/- SD) was as follows: body water, 75.3 +/- 3.9%; total protein, 13.9 +/- 8.8%; and total fat, 6.5 +/- 3.7%. Absolute content of fat and total ash was 7-674 and 35-237 g, respectively. Mean hydration of fat-free mass was 0.804 +/- 0.011 g/kg and decreased with increasing body weight (r2 = 0.419) independent of age. Using DXA, bone mineral content was highly correlated with calcium content (r2 = 0.992), and calcium per bone mineral content was 44.1 +/- 4.2%. DXA fat mass correlated with total fat (r2 = 0.961). Using MR, spectroscopy and chemical analysis were highly correlated with fat-to-water ratio (r2 = 0.984) and absolute fat content (r2 = 0.988). Total fat by MR imaging volumetry showed a lower correlation (r2 = 0.913) and overestimated total fat by a factor of 2.46. Conversion equations for DXA were developed (total fat = 1.31 x fat mass measured by DXA--68.8; calcium = 0.402 x bone mineral content + 1.7), which improved precision and accuracy of DXA measurements. In conclusion, both DXA and MR spectroscopy give accurate and precise estimates of neonatal body composition and may become valuable tools for the noninvasive assessment of neonatal growth and nutritional status. PMID:10509370

  9. Centerband-only analysis of rotor-unsynchronized spin echo for measurement of lipid (31) P chemical shift anisotropy.

    PubMed

    Umegawa, Yuichi; Yamaguchi, Toshiyuki; Murata, Michio; Matsuoka, Shigeru

    2015-07-01

    Structural diversity and molecular flexibility of phospholipids are essential for biological membranes to play key roles in numerous cellular processes. Uncovering the behavior of individual lipids in membrane dynamics is crucial for understanding the molecular mechanisms underlying biological functions of cell membranes. In this paper, we introduce a simple method to investigate dynamics of lipid molecules in multi-component systems by measuring the (31) P chemical shift anisotropy (CSA) under magic angle spinning (MAS) conditions. For achieving both signal separation and CSA determination, we utilized a centerband-only analysis of rotor-unsynchronized spin echo (COARSE). This analysis is based on the curve fitting of periodic modulation of centerband intensity along the interpulse delay time in rotor-unsynchronized spin-echo experiments. The utility of COARSE was examined by using phospholipid vesicles, a three-component lipid raft model system, and archaeal purple membranes. We found that the apparent advantages of this method are high resolution and high sensitivity given by the moderate MAS speed and the one-dimensional acquisition with short spin-echo delays. COARSE provides an alternative method for CSA measurement that is effective in the investigation of lipid polymorphologies. PMID:26017552

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

    PubMed

    Toy, Mehmet; Tanak, Hasan

    2016-01-01

    In the present work, a combined experimental and theoretical study on ground state molecular structure, spectroscopic and nonlinear optical properties of azo compound 3'-chloro-4-dimethlamino azobenzene are reported. The molecular geometry, vibrational wavenumbers and the first order hyperpolarizability of the title compound were calculated with the help of density functional theory computations. The optimized geometric parameters obtained by using DFT (B3LYP/6-311++G(d,p)) show good agreement with the experimental data. The vibrational transitions were identified based on the recorded FT-IR spectra in the range of 4000-400cm(-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. PMID:25468435

  11. 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.

  12. Mapping phosphorylation rate of fluoro-deoxy-glucose in rat brain by 19F chemical shift imaging

    PubMed Central

    Coman, Daniel; Sanganahalli, Basavaraju G.; Cheng, David; McCarthy, Timothy; Rothman, Douglas L.; Hyder, Fahmeed

    2014-01-01

    19F magnetic resonance spectroscopy (MRS) studies of 2-fluoro-2-deoxy-D-glucose (FDG) and 2-fluoro-2-deoxy-D-glucose-6-phosphate (FDG-6P) can be used for directly assessing total glucose metabolism in vivo. To date, 19F MRS measurements of FDG phosphorylation in the brain have either been achieved ex vivo from extracted tissue or in vivo by unusually long acquisition times. Electrophysiological and functional magnetic resonance imaging (fMRI) measurements indicate that FDG doses up to 500mg/kg can be tolerated with minimal side effects on cerebral physiology and evoked fMRI-BOLD responses to forepaw stimulation. In halothane-anesthetized rats, we report localized in vivo detection and separation of FDG and FDG-6P MRS signals with 19F 2D chemical shift imaging (CSI) at 11.7T. A metabolic model based on reversible transport between plasma and brain tissue, which included a non-saturable plasma to tissue component, was used to calculate spatial distribution of FDG and FDG-6P concentrations in rat brain. In addition, spatial distribution of rate constants and metabolic fluxes of FDG to FDG-6P conversion were estimated. Mapping the rate of FDG to FDG-6P conversion by 19F CSI provides an MR methodology that could impact other in vivo applications such as characterization of tumor pathophysiology. PMID:24581725

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

    NASA Astrophysics Data System (ADS)

    Toy, Mehmet; Tanak, Hasan

    2016-01-01

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

  14. Polarization and hyperfine transitions of metastable ^{129}Xe in discharge cells

    NASA Astrophysics Data System (ADS)

    Xia, T.; Morgan, S. W.; Jau, Y.-Y.; Happer, W.

    2010-03-01

    The polarization and relaxation rates of metastable Xe129 atoms are measured with magnetic resonance spectroscopy, at both microwave frequencies, where ΔF=1 transitions are induced between the sublevels, and at radiofrequencies, corresponding to ΔF=0 transitions. The nuclear spin polarization of the resonant velocity group is measured to be 22±2%. The relaxation of metastable xenon atoms is dominated by depolarizing collisions with ground-state atoms, with lesser contributions from metastability exchange collisions.

  15. 129Xe NMR studies of pecan shell-based biochar and structure-process correlations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pecan shell-based biochar is being utilized as filtration medium, sequestrant for metallic ions, soil conditioner, and other applications. One process involves the use of phosphoric acid at high temperature in a partial oxygen atmosphere to produce a highly porous carbonaceous material. In this work...

  16. 13C NMR chemical shift correlations in application of “tool of increasing electron demand” to stable long-lived carbocations: Comprehensive evaluation*

    PubMed Central

    Olah, George A.; Berrier, Arthur L.; Prakash, G. K. Surya

    1981-01-01

    The reliability of 13C NMR chemical shift correlations in the application of the “tool of increasing electron demand” to stable long-lived carbocationic systems is demonstrated by a comprehensive analysis of 22 stable aryl-substituted carbocationic systems. The observation of slopes of less than unity in such chemical shift correlations for several cationic systems has been attributed to additional charge delocalizing mechanisms present in the system (such as homoallylic, cyclopropyl, and π conjugations). The onset of nonclassical σ-delocalization in 2-aryl-2-norbornyl cations with electron withdrawing-substituents previously observed was further verified by using σC+ substituent constants. Difficulties in relating the CαNMR shifts in different carbocationic systems are also discussed. PMID:16593000

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

    PubMed

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

    2016-08-01

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

  18. Nuclear magnetic resonance chemical shifts with the statistical average of orbital-dependent model potentials in Kohn-Sham density functional theory

    NASA Astrophysics Data System (ADS)

    Poater, Jordi; van Lenthe, Erik; Baerends, Evert Jan

    2003-05-01

    In this paper, an orbital-dependent Kohn-Sham exchange-correlation potential, the so-called statistical average of (model) orbital potentials, is applied to the calculation of nuclear magnetic resonance chemical shifts of a series of simple molecules containing H, C, N, O, and F. It is shown that the use of this model potential leads to isotropic chemical shifts which are substantially improved over both local and gradient-corrected functionals, especially for nitrogen and oxygen atoms. This improvement in the chemical shift calculations can be attributed to the increase in the gap between highest occupied and lowest unoccupied orbitals, thus correcting the excessively large paramagnetic contributions, which have been identified to give deficient chemical shifts with both the local-density approximation and with gradient-corrected functionals. This is in keeping with the improvement by the statitical average of orbital model potentials for response properties in general and for excitation energies in particular. The present results are comparable in accuracy to those previously reported with self-interaction corrected functionals by Patchovskii et al., but still inferior to those obtained with accurate Kohn-Sham potentials by Wilson and Tozer. However, the present approach is computationally expedient and routinely applicable to all systems, requiring virtually the same computational effort as local-density and generalized-gradient calculations.

  19. Probing the solvent shell with 195Pt chemical shifts: density functional theory molecular dynamics study of Pt(II) and Pt(IV) anionic complexes in aqueous solution.

    PubMed

    Truflandier, Lionel A; Autschbach, Jochen

    2010-03-17

    Ab initio molecular dynamics (aiMD) simulations based on density functional theory (DFT) were performed on a set of five anionic platinum complexes in aqueous solution. (195)Pt nuclear magnetic shielding constants were computed with DFT as averages over the aiMD trajectories, using the two-component relativistic zeroth-order regular approximation (ZORA) in order to treat relativistic effects on the Pt shielding tensors. The chemical shifts obtained from the aiMD averages are in good agreement with experimental data. For Pt(II) and Pt(IV) halide complexes we found an intermediate solvent shell interacting with the complexes that causes pronounced solvent effects on the Pt chemical shifts. For these complexes, the magnitude of solvent effects on the Pt shielding constant can be correlated with the surface charge density. For square-planar Pt complexes the aiMD simulations also clearly demonstrate the influence of closely coordinated non-equatorial water molecules on the Pt chemical shift, relating the structure of the solution around the complex to the solvent effects on the metal NMR chemical shift. For the complex [Pt(CN)(4)](2-), the solvent effects on the Pt shielding constant are surprisingly small. PMID:20166712

  20. Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction.

    PubMed

    Lehtivarjo, Juuso; Tuppurainen, Kari; Hassinen, Tommi; Laatikainen, Reino; Peräkylä, Mikael

    2012-03-01

    While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein (1)H chemical shifts in which molecular motions, the 4th dimension, were modeled using molecular dynamics (MD) simulations. Although the approach clearly improved the prediction, the X-ray structures and single NMR conformers used in the model cannot be considered fully realistic models of protein in solution. In this work, NMR ensembles (NMRE) were used to expand the conformational space of proteins (e.g. side chains, flexible loops, termini), followed by MD simulations for each conformer to map the local fluctuations. Compared with the non-dynamic model, the NMRE+MD model gave 6-17% lower root-mean-square (RMS) errors for different backbone nuclei. The improved prediction indicates that NMR ensembles with MD simulations can be used to obtain a more realistic picture of protein structures in solutions and moreover underlines the importance of short and long time-scale dynamics for the prediction. The RMS errors of the NMRE+MD model were 0.24, 0.43, 0.98, 1.03, 1.16 and 2.39 ppm for (1)Hα, (1)HN, (13)Cα, (13)Cβ, (13)CO and backbone (15)N chemical shifts, respectively. The model is implemented in the prediction program 4DSPOT, available at http://www.uef.fi/4dspot. PMID:22314705

  1. The recognition of multi-class protein folds by adding average chemical shifts of secondary structure elements

    PubMed Central

    Feng, Zhenxing; Hu, Xiuzhen; Jiang, Zhuo; Song, Hangyu; Ashraf, Muhammad Aqeel

    2015-01-01

    The recognition of protein folds is an important step in the prediction of protein structure and function. Recently, an increasing number of researchers have sought to improve the methods for protein fold recognition. Following the construction of a dataset consisting of 27 protein fold classes by Ding and Dubchak in 2001, prediction algorithms, parameters and the construction of new datasets have improved for the prediction of protein folds. In this study, we reorganized a dataset consisting of 76-fold classes constructed by Liu et al. and used the values of the increment of diversity, average chemical shifts of secondary structure elements and secondary structure motifs as feature parameters in the recognition of multi-class protein folds. With the combined feature vector as the input parameter for the Random Forests algorithm and ensemble classification strategy, we propose a novel method to identify the 76 protein fold classes. The overall accuracy of the test dataset using an independent test was 66.69%; when the training and test sets were combined, with 5-fold cross-validation, the overall accuracy was 73.43%. This method was further used to predict the test dataset and the corresponding structural classification of the first 27-protein fold class dataset, resulting in overall accuracies of 79.66% and 93.40%, respectively. Moreover, when the training set and test sets were combined, the accuracy using 5-fold cross-validation was 81.21%. Additionally, this approach resulted in improved prediction results using the 27-protein fold class dataset constructed by Ding and Dubchak. PMID:26980999

  2. Accuracy of Calculated Chemical Shifts in Carbon 1s Ionization Energies from Single-Reference ab Initio Methods and Density Functional Theory.

    PubMed

    Holme, Alf; Børve, Knut J; Sæthre, Leif J; Thomas, T Darrah

    2011-12-13

    A database of 77 adiabatic carbon 1s ionization energies has been prepared, covering linear and cyclic alkanes and alkenes, linear alkynes, and methyl- or fluoro-substituted benzenes. Individual entries are believed to carry uncertainties of less than 30 meV in ionization energies and less than 20 meV for shifts in ionization energies. The database provides an unprecedented opportunity for assessing the accuracy of theoretical schemes for computing inner-shell ionization energies and their corresponding chemical shifts. Chemical shifts in carbon 1s ionization energies have been computed for all molecules in the database using Hartree-Fock, Møller-Plesset (MP) many-body perturbation theory of order 2 and 3 as well as various approximations to full MP4, and the coupled-cluster approximation with single- and double-excitation operators (CCSD) and also including a perturbational estimate of the energy effect of triple-excitation operators (CCSD(T)). Moreover, a wide range of contemporary density functional theory (DFT) methods are also evaluated with respect to computing experimental shifts in C1s ionization energies. Whereas the top ab initio methods reproduce the observed shifts almost to within the experimental uncertainty, even the best-performing DFT approaches meet with twice the root-mean-squared error and thrice the maximum error compared to CCSD(T). However, a number of different density energy functionals still afford sufficient accuracy to become tools in the analysis of complex C1s photoelectron spectra. PMID:26598356

  3. Multilayer MoS2 prepared by one-time and repeated chemical vapor depositions: anomalous Raman shifts and transistors with high ON/OFF ratio

    NASA Astrophysics Data System (ADS)

    Wu, Chong-Rong; Chang, Xiang-Rui; Chang, Shu-Wei; Chang, Chung-En; Wu, Chao-Hsin; Lin, Shih-Yen

    2015-11-01

    We show that multilayer molybdenum disulfide (MoS2) grown with the chemical vapor deposition (CVD) may exhibit quite distinct behaviors of Raman shifts from those of exfoliated ones. The anomalous Raman shifts depend on CVD growth modes and are attributed to the modified dielectric screening and interlayer coupling of MoS2 in various growth conditions. With repeated CVD growths, we demonstrated the precise control over the layer number of MoS2. A decently large drain current, high ON/OFF ratio of 105, and enhanced field-effect mobility can be achieved in transistors fabricated on the six-layer MoS2.

  4. Cytochrome-P450-Cytochrome-b5 Interaction in a Membrane Environment Changes 15N Chemical Shift Anisotropy Tensors

    PubMed Central

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

    2013-01-01

    It has been well realized that the dependence of chemical shift anisotropy (CSA) tensors on the amino acid sequence, secondary structure, dynamics and electrostatic interactions can be utilized in the structural and dynamic studies of proteins by NMR spectroscopy. In addition, CSA tensors could also be utilized to measure the structural interactions between proteins in a protein-protein complex. To this end, here we report the experimentally measured backbone amide-15N CSA tensors for a membrane-bound 16.7-kDa full-length rabbit cytochrome-b5 (cytb5), in complexation with a 55.8-kDa microsomal rabbit cytochrome P450 2B4 (cytP4502B4). The 15N-CSAs, determined using the 15N CSA/15N-1H dipolar coupling transverse cross-correlated rates, for free cytb5 are compared with that for the cytb5 bound to cytP4502B4. An overall increase in backbone amide-15N transverse cross-correlated rates for the cytb5 residues in the cytb5-cytP450 complex was observed as compared to the free cytb5 residues. Due to fast spin-spin relaxation (T2) and subsequent broadening of the signals in the complex, we were able to measure amide-15N CSAs only for 48 residues of cytb5 as compared to 84 residues of free cytb5. We observed a change in 15N CSA for most residues of cytb5 in the complex, when compared to free cytb5, suggesting a dynamic interaction between the oppositely charged surfaces of anionic cytb5 and cationic cytP450. The mean values of 15N CSA determined for residues in helical, sheet and turn regions of cytb5 in the complex are −184.5, −146.8, and −146.2 ppm, respectively, with an overall average value of −165.5 ppm (excluding the values from residues in more flexible termini). The measured CSA value for residues in helical conformation is slightly larger as compared to previously reported values. This may be attributed to the paramagnetic effect from Fe(III) of the heme in cytb5, which is similar to our previously reported values for the free cytb5. PMID:24107224

  5. A relativistic DFT methodology for calculating the structures and NMR chemical shifts of octahedral platinum and iridium complexes.

    PubMed

    Vícha, Jan; Patzschke, Michael; Marek, Radek

    2013-05-28

    A methodology for optimizing the geometry and calculating the NMR shielding constants is calibrated for octahedral complexes of Pt(IV) and Ir(III) with modified nucleic acid bases. The performance of seven different functionals (BLYP, B3LYP, BHLYP, BP86, TPSS, PBE, and PBE0) in optimizing the geometry of transition-metal complexes is evaluated using supramolecular clusters derived from X-ray data. The effects of the size of the basis set (ranging from SVP to QZVPP) and the dispersion correction (D3) on the interatomic distances are analyzed. When structural deviations and computational demands are employed as criteria for evaluating the optimizations of these clusters, the PBE0/def2-TZVPP/D3 approach provides excellent results. In the next step, the PBE0/def2-TZVPP approach is used with the continuum-like screening model (COSMO) to optimize the geometry of single molecules for the subsequent calculation of the NMR shielding constants in solution. The two-component zeroth-order regular approximation (SO-ZORA) is used to calculate the NMR shielding constants (PBE0/TZP/COSMO). The amount of exact exchange in the PBE0 functional is validated for the nuclear magnetic shieldings of atoms in the vicinity of heavy transition metals. For the PBE0/TZP/COSMO setup, an exact exchange of 40% is found to accurately reproduce the experimental NMR shielding constants for both types of complexes. Finally, the effect of the amount of exact exchange on the NMR shielding calculations (which is capable of compensating for the structural deficiencies) is analyzed for various molecular geometries (SCS-MP2, BHLYP, and PBE0) and the influence of a trans-substituent on the NMR chemical shift of nitrogen is discussed. The observed dependencies for an iridium complex cannot be rationalized by visualizing the Fermi-contact (FC) induced spin density and probably originate from changes in the d-d transitions that modulate the spin-orbit (SO) part of the SO/FC term. PMID:23598437

  6. 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. PMID:25199903

  7. Correlation between 1H NMR chemical shifts of hydroxyl protons in n-hexanol/cyclohexane and molecular association properties investigated using density functional theory

    NASA Astrophysics Data System (ADS)

    Flores, Mario E.; Shibue, Toshimichi; Sugimura, Natsuhiko; Nishide, Hiroyuki; Moreno-Villoslada, Ignacio

    2016-01-01

    Association of n-hexanol molecules in cyclohexane forming clusters is studied by DFT and 1H NMR. Geometry optimization, corrected binding energies, charge distributions, charge transfer energies, and 1H NMR chemical shifts have been obtained. The calculated chemical shifts of hydroxyl protons have been correlated to experimental data obtained in the range of n-hexanol molar fraction between 0.002 and 0.2, showing that n-hexanol molecules at a molar fraction around 0.1, where well-structured hydrogen bond networks are observed, tend to form linear pentamers and hexamers. The experimental data are consistent with the continuous linear association thermodynamic model, showing a dimensionless association constant of 284.

  8. 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

  9. Deciphering Noncovalent Interactions Accompanying 7,7,8,8-Tetracyanoquinodimethane Encapsulation within Biphene[n]arenes: Nucleus-Independent Chemical Shifts Approach.

    PubMed

    Lande, Dipali N; Rao, Soniya S; Gejji, Shridhar P

    2016-07-18

    Binding of novel biphene[n]arene hosts to antiaromatic 7,7,8,8-tetracyanoquinodimethane (TCNQ) are investigated by DFT. Biphene[4]arene favors the inclusion complex through noncovalent interactions, such as hydrogen bonding, π-π stacking, C-H⋅⋅⋅π, and C-H⋅⋅⋅H-C dihydrogen bonding. Donor-acceptor complexation renders aromatic character to the guest through charge transfer. The formation of TCNQ anionic radicals through supramolecular π stacking significantly influences its chemical and photophysical behavior. Electron density reorganization consequent to encapsulation of TCNQ reflects in the shift of characteristic vibrations in the IR spectra. The accompanying aromaticities arising from the induced ring currents are analyzed by employing nucleus-independent chemical shifts based profiles. PMID:27028656

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

    PubMed

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

    2015-10-14

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

  11. 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. PMID:16029851

  12. Spin-orbit ZORA and four-component Dirac-Coulomb estimation of relativistic corrections to isotropic nuclear shieldings and chemical shifts of noble gas dimers.

    PubMed

    Jankowska, Marzena; Kupka, Teobald; Stobiński, Leszek; Faber, Rasmus; Lacerda, Evanildo G; Sauer, Stephan P A

    2016-02-01

    Hartree-Fock and density functional theory with the hybrid B3LYP and general gradient KT2 exchange-correlation functionals were used for nonrelativistic and relativistic nuclear magnetic shielding calculations of helium, neon, argon, krypton, and xenon dimers and free atoms. Relativistic corrections were calculated with the scalar and spin-orbit zeroth-order regular approximation Hamiltonian in combination with the large Slater-type basis set QZ4P as well as with the four-component Dirac-Coulomb Hamiltonian using Dyall's acv4z basis sets. The relativistic corrections to the nuclear magnetic shieldings and chemical shifts are combined with nonrelativistic coupled cluster singles and doubles with noniterative triple excitations [CCSD(T)] calculations using the very large polarization-consistent basis sets aug-pcSseg-4 for He, Ne and Ar, aug-pcSseg-3 for Kr, and the AQZP basis set for Xe. For the dimers also, zero-point vibrational (ZPV) corrections are obtained at the CCSD(T) level with the same basis sets were added. Best estimates of the dimer chemical shifts are generated from these nuclear magnetic shieldings and the relative importance of electron correlation, ZPV, and relativistic corrections for the shieldings and chemical shifts is analyzed. PMID:26503739

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

    PubMed

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

    2015-07-01

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

  14. Stereospecificity of (1) H, (13) C and (15) N shielding constants in the isomers of methylglyoxal bisdimethylhydrazone: problem with configurational assignment based on (1) H chemical shifts.

    PubMed

    Afonin, Andrei V; Pavlov, Dmitry V; Ushakov, Igor A; Keiko, Natalia A

    2012-07-01

    In the (13) C NMR spectra of methylglyoxal bisdimethylhydrazone, the (13) C-5 signal is shifted to higher frequencies, while the (13) C-6 signal is shifted to lower frequencies on going from the EE to ZE isomer following the trend found previously. Surprisingly, the (1) H-6 chemical shift and (1) J(C-6,H-6) coupling constant are noticeably larger in the ZE isomer than in the EE isomer, although the configuration around the -CH═N- bond does not change. This paradox can be rationalized by the C-H⋯N intramolecular hydrogen bond in the ZE isomer, which is found from the quantum-chemical calculations including Bader's quantum theory of atoms in molecules analysis. This hydrogen bond results in the increase of δ((1) H-6) and (1) J(C-6,H-6) parameters. The effect of the C-H⋯N hydrogen bond on the (1) H shielding and one-bond (13) C-(1) H coupling complicates the configurational assignment of the considered compound because of these spectral parameters. The (1) H, (13) C and (15) N chemical shifts of the 2- and 8-(CH(3) )(2) N groups attached to the -C(CH(3) )═N- and -CH═N- moieties, respectively, reveal pronounced difference. The ab initio calculations show that the 8-(CH(3) )(2) N group conjugate effectively with the π-framework, and the 2-(CH(3) )(2) N group twisted out from the plane of the backbone and loses conjugation. As a result, the degree of charge transfer from the N-2- and N-8- nitrogen lone pairs to the π-framework varies, which affects the (1) H, (13) C and (15) N shieldings. PMID:22615146

  15. 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.

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

    PubMed Central

    Manda, Hortance; Arce, Luana M.; Foggie, Tarra; Shah, Pankhil; Grieco, John P.; Achee, Nicole L.

    2011-01-01

    Background Previous studies have identified the behavioral responses of Aedes aegypti to irritant and repellent chemicals that can be exploited to reduce man-vector contact. Maximum efficacy of interventions based on irritant chemical actions will, however, require full knowledge of variables that influence vector resting behavior and how untreated “safe sites” contribute to overall impact. Methods Using a laboratory box assay, resting patterns of two population strains of female Ae. aegypti (THAI and PERU) were evaluated against two material types (cotton and polyester) at various dark:light surface area coverage (SAC) ratio and contrast configuration (horizontal and vertical) under chemical-free and treated conditions. Chemicals evaluated were alphacypermethrin and DDT at varying concentrations. Results Under chemical-free conditions, dark material had significantly higher resting counts compared to light material at all SAC, and significantly increased when material was in horizontal configuration. Cotton elicited stronger response than polyester. Within the treatment assays, significantly higher resting counts were observed on chemical-treated dark material compared to untreated light fabric. However, compared to matched controls, significantly less resting observations were made on chemical-treated dark material overall. Most importantly, resting observations on untreated light material (or “safe sites”) in the treatment assay did not significantly increase for many of the tests, even at 25% SAC. Knockdown rates were ≤5% for all assays. Significantly more observations of flying mosquitoes were made in test assays under chemical-treatment conditions as compared to controls. Conclusions/Significance When preferred Ae. aegypti resting sites are treated with chemicals, even at reduced treatment coverage area, mosquitoes do not simply move to safe sites (untreated areas) following contact with the treated material. Instead, they become agitated, using

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. Association of Quadriceps Muscle Fat With Isometric Strength Measurements in Healthy Males Using Chemical Shift Encoding-Based Water-Fat Magnetic Resonance Imaging

    PubMed Central

    Baum, Thomas; Inhuber, Stephanie; Dieckmeyer, Michael; Cordes, Christian; Ruschke, Stefan; Klupp, Elisabeth; Jungmann, Pia M.; Farlock, Rosanna; Eggers, Holger; Kooijman, Hendrik; Rummeny, Ernst J.; Schwirtz, Ansgar; Kirschke, Jan S.; Karampinos, Dimitrios C.

    2016-01-01

    Abstract Magnetic resonance–based assessment of quadriceps muscle fat has been proposed as surrogate marker in sarcopenia, osteoarthritis, and neuromuscular disorders. We presently investigated the association of quadriceps muscle fat with isometric strength measurements in healthy males using chemical shift encoding-based water-fat magnetic resonance imaging. Intermuscular adipose tissue fraction and intramuscular proton density fat fraction correlated significantly (P < 0.05) with isometric strength (up to r = −0.83 and −0.87, respectively). Reproducibility of intermuscular adipose tissue fraction and intramuscular proton density fat fraction was 1.5% and 5.7%, respectively. PMID:26953765

  2. Backbone chemical shift assignments for the sensor domain of the Burkholderia pseudomallei histidine kinase RisS: "missing" resonances at the dimer interface.

    PubMed

    Buchko, Garry W; Edwards, Thomas E; Hewitt, Stephen N; Phan, Isabelle Q H; Van Voorhis, Wesley C; Miller, Samuel I; Myler, Peter J

    2015-10-01

    Using a deuterated sample, all the observable backbone (1)H(N), (15)N, (13)C(a), and (13)C' chemical shifts for the dimeric, periplasmic sensor domain of the Burkholderia pseudomallei histidine kinase RisS were assigned. Approximately one-fifth of the amide resonances are "missing" in the (1)H-(15)N HSQC spectrum and map primarily onto α-helices at the dimer interface observed in a crystal structure suggesting this region either undergoes intermediate timescale motion (μs-ms) and/or is heterogeneous. PMID:25957069

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

    PubMed

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

    2016-04-01

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

  4. NMR structure note: Structure of the Membrane Protein MerF, a Bacterial Mercury Transporter, Improved by the Inclusion of Chemical Shift Anisotropy Constraints

    PubMed Central

    Tian, Ye; Lu, George J.; Marassi, Francesca M.; Opella, Stanley J.

    2014-01-01

    SUMMARY MerF is a mercury transport membrane protein from the bacterial mercury detoxification system. By performing a solid-state INEPT experiment and measuring chemical shift anisotropy frequencies in aligned samples, we are able to improve on the accuracy and precision of the initial structure that we presented. MerF has four N-terminal and eleven C-terminal residues that are mobile and unstructured in phospholipid bilayers. The structure presented here has average pairwise RMSDs of 1.78 Å for heavy atoms and 0.92 Å for backbone atoms. PMID:25103921

  5. Xe-129 NMR of xenon dissolved in biological media.

    NASA Astrophysics Data System (ADS)

    Mazitov, R. K.; Kuzma, N. N.; Happer, W.; Driehuys, B.; Merrill, G. F.

    2002-03-01

    The high solubility and large chemical shift of ^129Xe in various tissues makes it an ideal, non-invasive probe for pathological conditions such as cancer or atherosclerosis. To this end, we report NMR measurements of lineshapes, chemical shifts, and relaxation times of ^129Xe dissolved in the following biological tissues in vitro: heart, muscle, sinew, stomach(R.K. Mazitov, K. M. Enikeev, et al., Dokl. Akad. Nauk) 365, 396 (1999)., and the white and yolk of egg. NMR measurements of xenon dissolved in olive and sunflower oils are also reported. Tissues weighing 160--250 mg, not exposed to freezing, were studied in a 11.75 T field at the ^129Xe resonance frequency of 138.4 MHz; the pressure of xenon in the sealed-sample ampoules was ~20 bar. The influence of drugs and water content on tissues was studied. No xenon-water clathrates(J.A. Ripmeester and D.W. Davidson, J. Mol. Struct. ) 75, 67 (1981). were observed in the tissues, even at the high pressures used. The aim of this study is to establish possible correlations between the NMR parameters of dissolved xenon and the state of the tissue.

  6. 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

  7. 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).

  8. 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

  9. Comparison of the solution and crystal structures of staphylococcal nuclease with /sup 13/C and /sup 15/N chemical shifts used as structural fingerprints

    SciTech Connect

    Cole, H.B.R.; Sparks, S.W.; Torchia, D.A.

    1988-09-01

    The authors report high-resolution /sup 13/C and /sup 15/N NMR spectra of crystalline staphylococcal nuclease (Nase) complexed to thymidine 3',5'-diphosphate and Ca/sup 2+/. High sensitivity and resolution are obtained by applying solid-state NMR techniques-high power proton decoupling and cross-polarization magic angle sample spinning (CPMASS)-to protein samples that have been efficiently synthesized and labeled by an overproducing strain of Escherichia coli. A comparison of CPMASS and solution spectra of Nase labeled with either (methyl-/sup 13/C)methionine or (/sup 15/)valine shows that the chemical shifts in the crystalline and solution states are virtually identical. This result is strong evidence that the protein conformations in the solution and crystalline states are nearly the same. Because of the close correspondence of the crystal and solution chemical shifts, sequential assignments obtained in solution apply to the crystal spectra. It should therefore be possible to study the molecular structure and dynamics of many sequentially assigned atomic sites in Nase crystals. Similar experiments are applicable to the growing number of proteins that can be obtained from efficient expression systems.

  10. Stored waveform inverse fourier-transform (SWIFT) excitation for water-suppressed whole-body slice-selected proton chemical shift spectra at 1.5 tesla

    NASA Astrophysics Data System (ADS)

    Hsu, Annjia T.; Hunter, William W.; Schmalbrock, Petra; Marshall, Alan G.

    Proton NMR spectroscopy for the in vivo study of metabolites in a spatially resolved region with a clinical NMR imaging device must contend with the 70% hydration of normal man. Theoretical and experimental comparisons of several excitation waveforms designed to suppress the H 2O signal in proton NMR spectroscopy and chemical shift imaging have been conducted. In particular, we have compared the 1 overline33 overline1 and 1 overline1 pulse sequences with those obtained via a stored waveform inverse Fourier-transform (SWIFT) time-domain apodized waveform generated by inverse Fourier transformation of a quadratically phase-encoded excitation magnitude spectrum. Theoretical excitation profiles are compared to those measured in a slice selected with a General Electric Signa 1.5 T whole-body imaging system, and demonstrated for a phantom (toluene, dioxane, and dichloromethane). The SWIFT waveform is theoretically and experimentally superior to 1 overline1 and 1 overline33 overline1 for selective suppression of one spectral segment with simultaneous uniform excitation over the rest of the spectral frequency range. SWIFT-excited water-suppressed depth-resolved chemical shift spectra are demonstrated for human brain and human calf muscle of normal volunteers.

  11. Free variable selection QSPR study to predict 19F chemical shifts of some fluorinated organic compounds using Random Forest and RBF-PLS methods

    NASA Astrophysics Data System (ADS)

    Goudarzi, Nasser

    2016-04-01

    In this work, two new and powerful chemometrics methods are applied for the modeling and prediction of the 19F 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 19F 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.

  12. Solid-state NMR chemical-shift perturbations indicate domain reorientation of the DnaG primase in the primosome of Helicobacter pylori.

    PubMed

    Gardiennet, Carole; Wiegand, Thomas; Bazin, Alexandre; Cadalbert, Riccardo; Kunert, Britta; Lacabanne, Denis; Gutsche, Irina; Terradot, Laurent; Meier, Beat H; Böckmann, Anja

    2016-03-01

    We here investigate the interactions between the DnaB helicase and the C-terminal domain of the corresponding DnaG primase of Helicobacter pylori using solid-state NMR. The difficult crystallization of this 387 kDa complex, where the two proteins interact in a six to three ratio, is circumvented by simple co-sedimentation of the two proteins directly into the MAS-NMR rotor. While the amount of information that can be extracted from such a large protein is still limited, we can assign a number of amino-acid residues experiencing significant chemical-shift perturbations upon helicase-primase complex formation. The location of these residues is used as a guide to model the interaction interface between the two proteins in the complex. Chemical-shift perturbations also reveal changes at the interaction interfaces of the hexameric HpDnaB assembly on HpDnaG binding. A structural model of the complex that explains the experimental findings is obtained. PMID:26961129

  13. Nucleotide-type chemical shift assignment of the encapsulated 40 kbp dsDNA in intact bacteriophage T7 by MAS solid-state NMR.

    PubMed

    Abramov, Gili; Goldbourt, Amir

    2014-08-01

    The icosahedral bacteriophage T7 is a 50 MDa double-stranded DNA (dsDNA) virus that infects Escherichia coli. Although there is substantial information on the physical and morphological properties of T7, structural information, based mostly on Raman spectroscopy and cryo-electron microscopy, is limited. Here, we apply the magic-angle spinning (MAS) solid-state NMR (SSNMR) technique to study a uniformly (13)C and (15)N labeled wild-type T7 phage. We describe the details of the large-scale preparation and purification of an isotopically enriched phage sample under fully hydrated conditions, and show a complete (13)C and a near-complete (15)N nucleotide-type specific assignment of the sugar and base moieties in the 40 kbp dsDNA of T7 using two-dimensional (13)C-(13)C and (15)N-(13)C correlation experiments. The chemical shifts are interpreted as reporters of a B-form conformation of the encapsulated dsDNA. While MAS SSNMR was found to be extremely useful in determining the structures of proteins in native-like environments, its application to nucleic acids has lagged behind, leaving a missing (13)C and (15)N chemical shift database. This work therefore expands the (13)C and (15)N database of real B-form DNA systems, and opens routes to characterize more complex nucleic acid systems by SSNMR. PMID:24875850

  14. 4D non-uniformly sampled HCBCACON and ¹J(NCα)-selective HCBCANCO experiments for the sequential assignment and chemical shift analysis of intrinsically disordered proteins.

    PubMed

    Nováček, Jiří; Haba, Noam Y; Chill, Jordan H; Zídek, Lukáš; Sklenář, Vladimír

    2012-06-01

    A pair of 4D NMR experiments for the backbone assignment of disordered proteins is presented. The experiments exploit (13)C direct detection and non-uniform sampling of the indirectly detected dimensions, and provide correlations of the aliphatic proton (H(α), and H(β)) and carbon (C(α), C(β)) resonance frequencies to the protein backbone. Thus, all the chemical shifts regularly used to map the transient secondary structure motifs in the intrinsically disordered proteins (H(α), C(α), C(β), C', and N) can be extracted from each spectrum. Compared to the commonly used assignment strategy based on matching the C(α) and C(β) chemical shifts, inclusion of the H(α) and H(β) provides up to three extra resonance frequencies that decrease the chance of ambiguous assignment. The experiments were successfully applied to the original assignment of a 12.8 kDa intrinsically disordered protein having a high content of proline residues (26 %) in the sequence. PMID:22580891

  15. Comparative molecular field analysis and comparative molecular similarity index analysis studies on 1H NMR chemical shift of NH group of diaryl triazene derivatives.

    PubMed

    Rofouie, M K; Salahinejad, M; Ghasemi, J B; Aghaei, A

    2013-05-01

    Comparative molecular field analysis (CoMFA), comparative molecular field analysis region focusing (CoMFA-RF) for optimizing the region for the final partial least square analysis, and comparative molecular similarity indices analysis (CoMSIA) methods were employed to develop three-dimensional quantitative structure-activity relationship (3D-QSAR) models of (1)H NMR chemical shift of NH proton of diaryl triazene derivatives. The best orientation was searched by all-orientation search (AOS) strategy to minimize the effect of the initial orientation of the structures. The predictive abilities of CoMFA-RF and CoMSIA models were determined using a test set of ten compounds affording predictive correlation coefficients of 0.721 and 0.754, respectively, indicating good predictive power. For further model validation, cross validation (leave one out), progressive scrambling, and bootstrapping were also applied. The accuracy and speed of obtained 3D-QSAR models for the prediction of (1)H NMR chemical shifts of NH group of diaryl triazene derivatives were greater compared to some computational well-known procedures. PMID:23456682

  16. Validation of Relativistic DFT Approaches to the Calculation of NMR Chemical Shifts in Square-Planar Pt(2+) and Au(3+) Complexes.

    PubMed

    Pawlak, Tomasz; Munzarová, Markéta L; Pazderski, Leszek; Marek, Radek

    2011-12-13

    Recently implemented hybrid density functional methods of calculating nuclear magnetic shielding using the two-component zeroth-order regular approximation approach (J. Phys. Chem. A2009, 113, 11495) have been employed for a series of compounds containing heavy transition-metal atoms. These include Pt(2+), Pd(2+), and Au(3+) organometallics and metal complexes with azines, some of which exhibit interesting biological and catalytic activities. In this study we investigate the effects of geometry, exchange-correlation functional, solvent, and scalar relativistic and spin-orbit corrections on the nuclear magnetic shielding-mainly for (13)C and (15)N atoms connected to a heavy-atom center. Our calculations demonstrate that the B3LYP method using effective core potentials and a cc-pwCVTZ-PP/6-31G** basis set augmented with the polarizable continuum model of the dimethylsulfoxide solvent provides geometries for the complexes in question which are compatible with the experimental NMR results in terms of both the trends and the absolute values of the (13)C shifts. The important role of the exact exchange admixture parameter for hybrid functionals based on B3LYP and PBE0 is investigated systematically for selected Pt(2+) and Au(3+) complexes. The (13)C and (15)N NMR chemical shifts are found to be best reproduced by using a B3LYP or PBE0 approach with 30% and 40-50% exact exchange admixtures for the Pt(2+) and Au(3+) complexes, respectively. The spin-orbit contributions to the (15)N NMR chemical shifts reflect metal-ligand bonding that is much more ionic for the Au(3+) than for the Pt(2+) complex. Finally, an optimized density functional method is applied to a series of transition-metal complexes to estimate the scope and the limitations of the current approach. PMID:26598337

  17. Accurate measurement of methyl 13C chemical shifts by solid-state NMR for the determination of protein side chain conformation: the influenza a M2 transmembrane peptide as an example.

    PubMed

    Hong, Mei; Mishanina, Tatiana V; Cady, Sarah D

    2009-06-10

    The use of side chain methyl (13)C chemical shifts for the determination of the rotameric conformation of Val and Leu residues in proteins by solid-state NMR spectroscopy is described. Examination of the solution NMR stereospecifically assigned methyl groups shows significant correlation between the difference in the two methyl carbons' chemical shifts and the side chain conformation. It is found that alpha-helical and beta-sheet backbones cause different side chain methyl chemical shift trends. In alpha-helical Leu's, a relatively large absolute methyl (13)C shift difference of 2.89 ppm is found for the most populated mt rotamer (chi(1) = -60 degrees, chi(2) = 180 degrees), while a much smaller value of 0.73 ppm is found for the next populated tp rotamer (chi(1) = 180 degrees, chi(2) = 60 degrees). For alpha-helical Val residues, the dominant t rotamer (chi(1) = 180 degrees) has more downfield Cgamma2 chemical shifts than Cgamma1 by 1.71 ppm, while the next populated m rotamer (chi(1) = -60 degrees) shows the opposite trend of more downfield Cgamma1 chemical shift by 1.23 ppm. These significantly different methyl (13)C chemical shifts exist despite the likelihood of partial rotameric averaging at ambient temperature. We show that these conformation-dependent methyl (13)C chemical shifts can be utilized for side chain structure determination once the methyl (13)C resonances are accurately measured by double-quantum (DQ) filtered 2D correlation experiments, most notably the dipolar DQ to single-quantum (SQ) correlation technique. The advantage of the DQ-SQ correlation experiment over simple 2D SQ-SQ correlation experiments is demonstrated on the transmembrane peptide of the influenza A M2 proton channel. The methyl chemical shifts led to predictions of the side chain rotameric states for several Val and Leu residues in this tetrameric helical bundle. The predicted Val rotamers were further verified by dipolar correlation experiments that directly measure the chi(1

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

    PubMed

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

    2015-01-01

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

  19. Analysis of the explosion of gas mixtures with a shift in the chemical equilibrium of the products taken into account

    SciTech Connect

    Zhdan, S.A.

    1983-07-01

    Starting from a representation of the detonation products as a reacting medium with an equilibrium chemical composition at each point, a generalized formulation of the problem on the explosion of a reacting gas mixture in air is given. Methaneoxygen and hydrogen-oxygen systems are considered. It is seen that almost half the energy is in the chemical component of the total internal energy behind the detonation wave front. The results of computations by the mathematical model yield greater values of the excess pressures on the shock front. Experimental data and numerical solutions are compared for the dependence of the excess pressures on the shock front radius, and are found to be in good agreement for the hydrogen-oxygen system. The methane-oxygen system shows a systematic excess in the experimental data which is apparently associated with non-one-dimensional effects in formulation of the experiment. The magnitude of the efficiency of an explosion, defined as the energy transferred to the wave during maximal detonation product expansion and the total energy initially included in the mixture, is of interest. For oxygen mixtures, only a third of the total explosion energy performs work on the surrounding air.

  20. 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.

  1. Stereochemistry of Complex Marine Natural Products by Quantum Mechanical Calculations of NMR Chemical Shifts: Solvent and Conformational Effects on Okadaic Acid

    PubMed Central

    Domínguez, Humberto J.; Crespín, Guillermo D.; Santiago-Benítez, Adrián J.; Gavín, José A.; Norte, Manuel; Fernández, José J.; Hernández Daranas, Antonio

    2014-01-01

    Marine organisms are an increasingly important source of novel metabolites, some of which have already inspired or become new drugs. In addition, many of these molecules show a high degree of novelty from a structural and/or pharmacological point of view. Structure determination is generally achieved by the use of a variety of spectroscopic methods, among which NMR (nuclear magnetic resonance) plays a major role and determination of the stereochemical relationships within every new molecule is generally the most challenging part in structural determination. In this communication, we have chosen okadaic acid as a model compound to perform a computational chemistry study to predict 1H and 13C NMR chemical shifts. The effect of two different solvents and conformation on the ability of DFT (density functional theory) calculations to predict the correct stereoisomer has been studied. PMID:24402177

  2. Examination of anticipated chemical shift and shape distortion effect on materials commonly used in prosthetic socket fabrication when measured using MRI: a validation study.

    PubMed

    Safari, Mohammad Reza; Rowe, Philip; Buis, Arjan

    2013-01-01

    The quality of lower-limb prosthetic socket fit is influenced by shape and volume consistency during the residual limb shape-capturing process (i.e., casting). Casting can be quantified with magnetic resonance imaging (MRI) technology. However, chemical shift artifact and image distortion may influence the accuracy of MRI when common socket/casting materials are used. We used a purpose-designed rig to examine seven different materials commonly used in socket fabrication during exposure to MRI. The rig incorporated glass marker tubes filled with water doped with 1 g/L copper sulfate (CS) and 9 plastic sample vials (film containers) to hold the specific material specimens. The specimens were scanned 9 times in different configurations. The absolute mean difference of the glass marker tube length was 1.39 mm (2.98%) (minimum = 0.13 mm [0.30%], maximum = 5.47 mm [14.03%], standard deviation = 0.89 mm). The absolute shift for all materials was <1.7 mm. This was less than the measurement tolerance of +/-2.18 mm based on voxel (three-dimensional pixel) dimensions. The results show that MRI is an accurate and repeatable method for dimensional measurement when using matter containing water. Additionally, silicone and plaster of paris plus 1 g/L CS do not show a significant shape distortion nor do they interfere with the MRI image of the residual limb. PMID:23516081

  3. Nuclear magnetic resonance studies of guest species in clathrate hydrates: Line-shape anisotropies, chemical shifts, and the determination of cage occupancy ratios and hydration numbers

    SciTech Connect

    Collins, M.J.; Ratcliffe, C.I.; Ripmeester, J.A. )

    1990-01-11

    NMR spectra of the guest molecules PH{sub 3}, H{sub 2}Se, D{sub 2}Se, D{sub 2}S, CD{sub 3}F, CD{sub 3}Cl, CD{sub 3}Br, C{sub 2}D{sub 2}, and C{sub 2}D{sub 4} in their structure I clathrate hydrates have been obtained by use of {sup 2}H, {sup 19}F, {sup 31}P, and {sup 77}Se nuclei. Components due to guests in the small and large cages have been distinguished by using isotropic chemical shift and static line-shape anisotropy differences. Low-temperature magic angle spinning was used in some cases to resolve the two components. Guests in the small cages are invariably found to have a lower field isotropic shift than those in the large cage. The static line shapes are isotropic for guests in the small spherical cages, whereas in the large oblate cages they have a residual anisotropy. Relative cage occupancy ratios {theta}{sub S}/{theta}{sub L} have been obtained from the observed NMR intensities, and together with similar results from previous NMR studies, these have been used to derive hydration numbers. This represents a new and nondestructive method of determining structure I hydrate compositions.

  4. On the utility of spectroscopic imaging as a tool for generating geometrically accurate MR images and parameter maps in the presence of field inhomogeneities and chemical shift effects.

    PubMed

    Bakker, Chris J G; de Leeuw, Hendrik; van de Maat, Gerrit H; van Gorp, Jetse S; Bouwman, Job G; Seevinck, Peter R

    2013-01-01

    Lack of spatial accuracy is a recognized problem in magnetic resonance imaging (MRI) which severely detracts from its value as a stand-alone modality for applications that put high demands on geometric fidelity, such as radiotherapy treatment planning and stereotactic neurosurgery. In this paper, we illustrate the potential and discuss the limitations of spectroscopic imaging as a tool for generating purely phase-encoded MR images and parameter maps that preserve the geometry of an object and allow localization of object features in world coordinates. Experiments were done on a clinical system with standard facilities for imaging and spectroscopy. Images were acquired with a regular spin echo sequence and a corresponding spectroscopic imaging sequence. In the latter, successive samples of the acquired echo were used for the reconstruction of a series of evenly spaced images in the time and frequency domain. Experiments were done with a spatial linearity phantom and a series of test objects representing a wide range of susceptibility- and chemical-shift-induced off-resonance conditions. In contrast to regular spin echo imaging, spectroscopic imaging was shown to be immune to off-resonance effects, such as those caused by field inhomogeneity, susceptibility, chemical shift, f(0) offset and field drift, and to yield geometrically accurate images and parameter maps that allowed object structures to be localized in world coordinates. From these illustrative examples and a discussion of the limitations of purely phase-encoded imaging techniques, it is concluded that spectroscopic imaging offers a fundamental solution to the geometric deficiencies of MRI which may evolve toward a practical solution when full advantage will be taken of current developments with regard to scan time reduction. This perspective is backed up by a demonstration of the significant scan time reduction that may be achieved by the use of compressed sensing for a simple phantom. PMID:22898694

  5. A solid-state (11)b NMR and computational study of boron electric field gradient and chemical shift tensors in boronic acids and boronic esters.

    PubMed

    Weiss, Joseph W E; Bryce, David L

    2010-04-22

    The results of a solid-state (11)B NMR study of a series of 10 boronic acids and boronic esters with aromatic substituents are reported. Boron-11 electric field gradient (EFG) and chemical shift (CS) tensors obtained from analyses of spectra acquired in magnetic fields of 9.4 and 21.1 T are demonstrated to be useful for gaining insight into the molecular and electronic structure about the boron nucleus. Data collected at 21.1 T clearly show the effects of chemical shift anisotropy (CSA), with tensor spans (Omega) on the order of 10-40 ppm. Signal enhancements of up to 2.95 were achieved with a DFS-modified QCPMG pulse sequence. To understand the relationship between the measured tensors and the local structure better, calculations of the (11)B EFG and magnetic shielding tensors for these compounds were conducted. The best agreement was found between experimental results and those obtained from GGA revPBE DFT calculations. A positive correlation was found between Omega and the dihedral angle (phi(CCBO)), which describes the orientation of the boronic acid/ester functional group relative to an aromatic system bound to boron. The small boron CSA is discussed in terms of paramagnetic shielding contributions as well as diamagnetic shielding contributions. Although there is a region of overlap, both Omega and the (11)B quadrupolar coupling constants tend to be larger for boronic acids than for the esters. We conclude that the span is generally the most characteristic boron NMR parameter of the molecular and electronic environment for boronic acids and esters, and show that the values result from a delicate interplay of several competing factors, including hydrogen bonding, the value of phi(CCBO), and the electron-donating or withdrawing substituents bound to the aromatic ring. PMID:20337440

  6. 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. PMID:26278514

  7. Anisotropic nuclear spin relaxation in single-crystal xenon

    NASA Astrophysics Data System (ADS)

    Kuzma, N. N.; Babich, D.; Happer, W.

    2002-04-01

    We extend the theory of longitudinal spin relaxation of 129Xe nuclei in frozen xenon to the case of single-crystal samples, where the relaxation rate depends on the direction of the applied magnetic field with respect to the crystalline axes. For sufficiently large magnetic fields, the relaxation is dominated by spin-flip Raman scattering of lattice phonons. Two closely related interactions couple the lattice phonons to the spins of 129Xe nuclei: the nuclear spin-rotation interaction between nearest-neighbor atoms, which leads to an isotropic, field-independent relaxation rate, and the paramagnetic antishielding of the externally applied field at the site of 129Xe nuclei by the electrons of neighboring Xe atoms. The latter interaction, also known as the chemical shift anisotropy (CSA) interaction, leads to an anisotropic relaxation rate proportional to the square of the applied field. This mechanism dominates spin relaxation at fields of the order of the Debye field BD=kBTD/μB=82 T.

  8. Cluster formation restricts dynamic nuclear polarization of xenon in solid mixtures

    NASA Astrophysics Data System (ADS)

    Kuzma, N. N.; Pourfathi, M.; Kara, H.; Manasseh, P.; Ghosh, R. K.; Ardenkjaer-Larsen, J. H.; Kadlecek, S. J.; Rizi, R. R.

    2012-09-01

    During dynamic nuclear polarization (DNP) at 1.5 K and 5 T, 129Xe nuclear magnetic resonance (NMR) spectra of a homogeneous xenon/1-propanol/trityl-radical solid mixture exhibit a single peak, broadened by 1H neighbors. A second peak appears upon annealing for several hours at 125 K. Its characteristic width and chemical shift indicate the presence of spontaneously formed pure Xe clusters. Microwave irradiation at the appropriate frequencies can bring both peaks to either positive or negative polarization. The peculiar time evolution of 129Xe polarization in pure Xe clusters during DNP can be modelled as an interplay of spin diffusion and T1 relaxation. Our simple spherical-cluster model offers a sensitive tool to evaluate major DNP parameters in situ, revealing a severe spin-diffusion bottleneck at the cluster boundaries and a significant sample overheating due to microwave irradiation. Subsequent DNP system modifications designed to reduce the overheating resulted in four-fold increase of 129Xe polarization, from 5.3% to 21%.

  9. Theoretical 13C chemical shift, 14N, and 2H quadrupole coupling- constant studies of hydrogen bonding in L-alanylglycine dipeptide.

    PubMed

    Tafazzoli, M; Amini, S K

    2008-04-01

    (13)C chemical shieldings and (14)N and (2)H electric field gradient (EFG) tensors of L-alanylglycine (L-alagly) dipeptide were calculated at RHF/6-31 + + G** and B3LYP/6-31 + + G** levels of theory respectively. For these calculations a crystal structure of this dipeptide obtained from X-ray crystallography was used. Atomic coordinates of different clusters containing several L-alagly molecules were used as input files for calculations. These clusters consist of central and surrounding L-alagly molecules, the latter forming short, strong, hydrogen bonds with the central molecule. Since the calculations did not converge for these clusters, the surrounding L-alagly molecules were replaced by glycine molecules. In order to improve the accuracy of calculated chemical shifts and nuclear quadrupole coupling constants (NQCCs), different geometry-optimization strategies were applied for hydrogen nuclei. Agreement between calculated and experimental data confirms that our optimized coordinates for hydrogen nuclei are more accurate than those obtained by X-ray diffraction. PMID:18273875

  10. Mechanism of Spin-Orbit Effects on the Ligand NMR Chemical Shift in Transition-Metal Complexes: Linking NMR to EPR.

    PubMed

    Vícha, Jan; Straka, Michal; Munzarová, Markéta L; Marek, Radek

    2014-04-01

    Relativistic effects play an essential role in understanding the nuclear magnetic resonance (NMR) chemical shifts in heavy-atom compounds. Particularly interesting from the chemical point of view are the relativistic effects due to heavy atom (HA) on the NMR chemical shifts of the nearby light atoms (LA), referred to as the HALA effects. The effect of Spin-Orbit (SO) interaction originating from HA on the nuclear magnetic shielding at a neighboring LA, σ(SO), is explored here in detail for a series of d(6) complexes of iridium. Unlike the previous findings, the trends in σ(SO) observed in this study can be fully explained neither in terms of the s-character of the HA-LA bonding nor by trends in the energy differences between occupied and virtual molecular orbitals (MOs). Rather, the σ(SO) contribution to the total NMR shielding is found to be modulated by the d-orbital participation of the heavy atom (Ir) in the occupied and virtual spin-orbit active MOs, i.e., those which contribute significantly to the σ(SO). The correlation between the d-character of σ(SO)-active MOs and the size of the corresponding SO contribution to the nuclear magnetic shielding constant at LA is so tight that the magnitude of σ(SO) can be predicted in a given class of compounds on the basis of d-orbital character of relevant MO with relative error smaller than 15%. This correspondence is supported by an analogy between the perturbation theory expressions for the spin-orbit induced NMR σ-tensor and those for the EPR g-tensor as well as the A-tensor of the ligand. This correlation is demonstrated on a series of d(5) complexes of iridium. Thus, known qualitative relationships between electronic structure and EPR parameters can be newly applied to reproduce, predict, and understand the SO-induced contributions to NMR shielding constants of light atoms in heavy-atom compounds. PMID:26580365

  11. Shifting tools

    SciTech Connect

    Fisher, E.P.; Welch, W.R.

    1984-03-13

    An improved shifting tool connectable in a well tool string and useful to engage and position a slidable sleeve in a sliding sleeve device in a well flow conductor. The selectively profiled shifting tool keys provide better fit with and more contact area between keys and slidable sleeves. When the engaged slidable sleeve cannot be moved up and the shifting tool is not automatically disengaged, emergency disengagement means may be utilized by applying upward force to the shifting tool sufficient to shear pins and cause all keys to be cammed inwardly at both ends to completely disengage for removal of the shifting tool from the sliding sleeve device.

  12. 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.

  13. Concurrent Increases and Decreases in Local Stability and Conformational Heterogeneity in Cu, Zn Superoxide Dismutase Variants Revealed by Temperature-Dependence of Amide Chemical Shifts.

    PubMed

    Doyle, Colleen M; Rumfeldt, Jessica A; Broom, Helen R; Sekhar, Ashok; Kay, Lewis E; Meiering, Elizabeth M

    2016-03-01

    The chemical shifts of backbone amide protons in proteins are sensitive reporters of local structural stability and conformational heterogeneity, which can be determined from their readily measured linear and nonlinear temperature-dependences, respectively. Here we report analyses of amide proton temperature-dependences for native dimeric Cu, Zn superoxide dismutase (holo pWT SOD1) and structurally diverse mutant SOD1s associated with amyotrophic lateral sclerosis (ALS). Holo pWT SOD1 loses structure with temperature first at its periphery and, while having extremely high global stability, nevertheless exhibits extensive conformational heterogeneity, with ∼1 in 5 residues showing evidence for population of low energy alternative states. The holo G93A and E100G ALS mutants have moderately decreased global stability, whereas V148I is slightly stabilized. Comparison of the holo mutants as well as the marginally stable immature monomeric unmetalated and disulfide-reduced (apo(2SH)) pWT with holo pWT shows that changes in the local structural stability of individual amides vary greatly, with average changes corresponding to differences in global protein stability measured by differential scanning calorimetry. Mutants also exhibit altered conformational heterogeneity compared to pWT. Strikingly, substantial increases as well as decreases in local stability and conformational heterogeneity occur, in particular upon maturation and for G93A. Thus, the temperature-dependence of amide shifts for SOD1 variants is a rich source of information on the location and extent of perturbation of structure upon covalent changes and ligand binding. The implications for potential mechanisms of toxic misfolding of SOD1 in disease and for general aspects of protein energetics, including entropy-enthalpy compensation, are discussed. PMID:26849066

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

    PubMed Central

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

    2014-01-01

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

  15. 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

  16. 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.

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

    PubMed

    Komatsu, Takanori; Kikuchi, Jun

    2013-09-17

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

  18. Recoupling of chemical shift anisotropies in solid-state NMR under high-speed magic-angle spinning and in uniformly 13C-labeled systems

    NASA Astrophysics Data System (ADS)

    Chan, Jerry C. C.; Tycko, Robert

    2003-05-01

    We demonstrate the possibility of recoupling chemical shift anisotropy (CSA) interactions in solid-state nuclear magnetic resonance (NMR) under high-speed magic-angle spinning (MAS) while retaining a static CSA powder pattern line shape and simultaneously attenuating homonuclear dipole-dipole interactions. CSA recoupling is accomplished by a rotation-synchronized radio-frequency pulse sequence with symmetry properties that permit static CSA line shapes to be obtained. We suggest a specific recoupling sequence, which we call ROCSA, for which the scaling factors for CSA and homonuclear dipole-dipole interactions are 0.272 and approximately 0.05, respectively. This sequence is suitable for high-speed 13C MAS NMR experiments on uniformly 13C-labeled organic compounds, including biopolymers. We demonstrate the ROCSA sequence experimentally by measuring the 13C CSA patterns of the uniformly labeled, polycrystalline compounds L-alanine and N-acetyl-D,L-valine at MAS frequencies of 11 and 20 kHz. We also present experimental data for amyloid fibrils formed by a 15-residue fragment of the β-amyloid peptide associated with Alzheimer's disease, in which four amino acid residues are uniformly labeled, demonstrating the applicability to biochemical systems of high molecular weight and significant complexity. Analysis of the CSA patterns in the amyloid fibril sample demonstrates the utility of ROCSA measurements as probes of peptide and protein conformation in noncrystalline solids.

  19. 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.

  20. 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.

  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. PMID:26845204

  2. 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…

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

    PubMed

    Kobayashi, Naohiro; Harano, Yoko; Tochio, Naoya; Nakatani, Eiichi; Kigawa, Takanori; Yokoyama, Shigeyuki; Mading, Steve; Ulrich, Eldon L; Markley, John L; Akutsu, Hideo; Fujiwara, Toshimichi

    2012-08-01

    Biomolecular NMR chemical shift data are key information for the functional analysis of biomolecules and the development of new techniques for NMR studies utilizing chemical shift statistical information. Structural genomics projects are major contributors to the accumulation of protein chemical shift information. The management of the large quantities of NMR data generated by each project in a local database and the transfer of the data to the public databases are still formidable tasks because of the complicated nature of NMR data. Here we report an automated and efficient system developed for the deposition and annotation of a large number of data sets including (1)H, (13)C and (15)N resonance assignments used for the structure determination of proteins. We have demonstrated the feasibility of our system by applying it to over 600 entries from the internal database generated by the RIKEN Structural Genomics/Proteomics Initiative (RSGI) to the public database, BioMagResBank (BMRB). We have assessed the quality of the deposited chemical shifts by comparing them with those predicted from the PDB coordinate entry for the corresponding protein. The same comparison for other matched BMRB/PDB entries deposited from 2001-2011 has been carried out and the results suggest that the RSGI entries greatly improved the quality of the BMRB database. Since the entries include chemical shifts acquired under strikingly similar experimental conditions, these NMR data can be expected to be a promising resource to improve current technologies as well as to develop new NMR methods for protein studies. PMID:22689068

  4. Fluid Shifts

    NASA Technical Reports Server (NTRS)

    Stenger, Michael B.; Hargens, Alan R.; Dulchavsky, Scott A.; Ebert, Douglas J.; Lee, Stuart M. C.; Laurie, Steven S.; Garcia, Kathleen M.; Sargsyan, Ashot E.; Martin, David S.; Liu, John; Macias, Brandon R.; Arbeille, Philippe; Danielson, Richard; Chang, Douglas; Gunga, Hanns-Christian; Johnston, Smith L.; Westby, Christian M.; Ploutz-Snyder, Robert J.; Smith, Scott M.

    2016-01-01

    We hypothesize that microgravity-induced cephalad fluid shifts elevate intracranial pressure (ICP) and contribute to VIIP. We will test this hypothesis and a possible countermeasure in ISS astronauts.

  5. The use of chemical shift temperature gradients to establish the paramagnetic susceptibility tensor orientation: implication for structure determination/refinement in paramagnetic metalloproteins.

    PubMed

    Xia, Z; Nguyen, B D; La Mar, G N

    2000-06-01

    The use of dipolar shifts as important constraints in refining molecular structure of paramagnetic metalloproteins by solution NMR is now well established. A crucial initial step in this procedure is the determination of the orientation. of the anisotropic paramagnetic susceptibility tensor in the molecular frame which is generated interactively with the structure refinement. The use of dipolar shifts as constraints demands knowledge of the diamagnetic shift. which, however, is very often not directly and easily accessible. We demonstrate that temperature gradients of dipolar shifts can serve as alternative constraints for determining the orientation of the magnetic axes, thereby eliminating the need to estimate the diamagnetic shifts. This approach is tested on low-spin, ferric sperm whale cyanometmyoglobin by determining the orientation, anisotropies and anisotropy temperature gradients by the alternate routes of using dipolar shifts and dipolar shift gradients as constraints. The alternate routes ultimately lead to very similar orientation of the magnetic axes, magnetic anisotropies and magnetic anisotropy temperature gradients which, by inference, would lead to an equally valid description of the molecular structure. It is expected that the use of the dipolar shift temperature gradients, rather than the dipolar shifts directly, as constraints will provide an accurate shortcut in a solution structure determination of a paramagnetic metalloprotein. PMID:10921780

  6. Alkaline earth chloride hydrates: chlorine quadrupolar and chemical shift tensors by solid-state NMR spectroscopy and plane wave pseudopotential calculations.

    PubMed

    Bryce, David L; Bultz, Elijah B

    2007-01-01

    A series of alkaline earth chloride hydrates has been studied by solid-state (35/37)Cl NMR spectroscopy in order to characterize the chlorine electric field gradient (EFG) and chemical shift (CS) tensors and to relate these observables to the structure around the chloride ions. Chlorine-35/37 NMR spectra of solid powdered samples of pseudopolymorphs (hydrates) of magnesium chloride (MgCl(2).6H(2)O), calcium chloride (CaCl(2).2H(2)O), strontium chloride (SrCl(2), SrCl(2).2H(2)O, and SrCl(2).6H(2)O), and barium chloride (BaCl(2).2H(2)O) have been acquired under stationary and magic-angle spinning conditions in magnetic fields of 11.75 and 21.1 T. Powder X-ray diffraction was used as an additional tool to confirm the purity and identity of the samples. Chlorine-35 quadrupolar coupling constants (C(Q)) range from essentially zero in cubic anhydrous SrCl(2) to 4.26+/-0.03 MHz in calcium chloride dihydrate. CS tensor spans, Omega, are between 40 and 72 ppm, for example, Omega= 45+/-20 ppm for SrCl(2).6H(2)O. Plane wave-pseudopotential density functional theory, as implemented in the CASTEP program, was employed to model the extended solid lattices of these materials for the calculation of their chlorine EFG and nuclear magnetic shielding tensors, and allowed for the assignment of the two-site chlorine NMR spectra of barium chloride dihydrate. This work builds upon our current understanding of the relationship between chlorine NMR interaction tensors and the local molecular and electronic structure, and highlights the particular sensitivity of quadrupolar nucleus solid-state NMR spectroscopy to the differences between various pseudopolymorphic structures in the case of strontium chloride. PMID:17385204

  7. Muscle metabolism and activation heterogeneity by combined 31P chemical shift and T2 imaging, and pulmonary O2 uptake during incremental knee-extensor exercise

    PubMed Central

    Cannon, Daniel T.; Howe, Franklyn A.; Whipp, Brian J.; Ward, Susan A.; McIntyre, Dominick J.; Ladroue, Christophe; Griffiths, John R.; Kemp, Graham J.

    2013-01-01

    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. PMID:23813534

  8. 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

  9. 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

    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 (r(2)  =  -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

  10. 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

  11. 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.

  12. 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

    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

  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. Determination of the tautomeric equilibria of pyridoyl benzoyl β-diketones in the liquid and solid state through the use of deuterium isotope effects on (1)H and (13)C NMR chemical shifts and spin coupling constants.

    PubMed

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

    2015-02-01

    The tautomeric equilibria for 2-pyridoyl-, 3-pyridoyl-, and 4-pyridoyl-benzoyl methane have been investigated using deuterium isotope effects on (1)H and (13)C chemical shifts both in the liquid and the solid state. Equilibria are established both in the liquid and the solid state. In addition, in the solution state the 2-bond and 3-bond J((1)H-(13)C) coupling constants have been used to confirm the equilibrium positions. The isotope effects due to deuteriation at the OH position are shown to be superior to chemical shift in determination of equilibrium positions of these almost symmetrical -pyridoyl-benzoyl methanes. The assignments of the NMR spectra are supported by calculations of the chemical shifts at the DFT level. The equilibrium positions are shown to be different in the liquid and the solid state. In the liquid state the 4-pyridoyl derivative is at the B-form (C-1 is OH), whereas the 2-and 3-pyridoyl derivatives are in the A-form. In the solid state all three compounds are on the B-form. The 4-pyridoyl derivative shows unusual deuterium isotope effects in the solid, which are ascribed to a change of the crystal structure of the deuteriated compound. PMID:24070650

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

    PubMed

    Sieh, Daniel; Kubiak, Clifford P

    2016-07-18

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

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

    SciTech Connect

    Sevelsted, Tine F.; Herfort, Duncan

    2013-10-15

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

  18. 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

  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. 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. PMID:26820039

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

    PubMed

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

    2006-02-01

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

  2. Theoretical Study of the Electrostatic and Steric Effects on the Spectroscopic Characteristics of the Metal-Ligand Unit of Heme Proteins. 2. C-O Vibrational Frequencies, 17O Isotropic Chemical Shifts, and Nuclear Quadrupole Coupling Constants

    PubMed Central

    Kushkuley, Boris; Stavrov, Solomon S.

    1997-01-01

    The quantum chemical calculations, vibronic theory of activation, and London-Pople approach are used to study the dependence of the C-O vibrational frequency, 17O isotropic chemical shift, and nuclear quadrupole coupling constant on the distortion of the porphyrin ring and geometry of the CO coordination, changes in the iron-carbon and iron-imidazole distances, magnitude of the iron displacement out of the porphyrin plane, and presence of the charged groups in the heme environment. It is shown that only the electrostatic interactions can cause the variation of all these parameters experimentally observed in different heme proteins, and the heme distortions could modulate this variation. The correlations between the theoretically calculated parameters are shown to be close to the experimentally observed ones. The study of the effect of the electric field of the distal histidine shows that the presence of the four C-O vibrational bands in the infrared absorption spectra of the carbon monoxide complexes of different myoglobins and hemoglobins can be caused by the different orientations of the different tautomeric forms of the distal histidine. The dependence of the 17O isotropic chemical shift and nuclear quadrupole coupling constant on pH and the distal histidine substitution can be also explained from the same point of view. PMID:9017215

  3. Nuclear magnetic resonance studies of phosphorus(v) pesticides. Part I. Chemical shifts of protons as a means of identification of pesticides

    USGS Publications Warehouse

    Babad, H.; Herbert, W.; Goldberg, M.C.

    1968-01-01

    Correlations of structural and proton chemical-hift data for 40 commercial phosphorus(V) pesticides are reported. Correlations of structure with the phosphorus coupling constants are discussed, and general trends are noted which aid in the use of NMR as a tool for identification and analysis of phosphorus(V) compounds. ?? 1968.

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

    PubMed

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

    2007-12-01

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

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

    PubMed

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

    2009-03-01

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

  6. Hyperfine-shifted 13C resonance assignments in an iron-sulfur protein with quantum chemical verification: aliphatic C-H···S 3-center-4-electron interactions.

    PubMed

    Westler, William M; Lin, I-Jin; Perczel, András; Weinhold, Frank; Markley, John L

    2011-02-01

    Although the majority of noncovalent interactions associated with hydrogen and heavy atoms in proteins and other biomolecules are classical hydrogen bonds between polar N-H or O-H moieties and O atoms or aromatic π electrons, high-resolution X-ray crystallographic models deposited in the Protein Data Bank show evidence for weaker C-H···O hydrogen bonds, including ones involving sp(3)-hybridized carbon atoms. Little evidence is available in proteins for the (even) weaker C-H···S interactions described in the crystallographic literature on small molecules. Here, we report experimental evidence and theoretical verification for the existence of nine aliphatic (sp(3)-hybridized) C-H···S 3-center-4-electron interactions in the protein Clostridium pasteurianum rubredoxin. Our evidence comes from the analysis of carbon-13 NMR chemical shifts assigned to atoms near the iron at the active site of this protein. We detected anomalous chemical shifts for these carbon-13 nuclei and explained their origin in terms of unpaired spin density from the iron atom being delocalized through interactions of the type: C-H···S-Fe, where S is the sulfur of one of the four cysteine side chains covalently bonded to the iron. These results suggest that polarized sulfur atoms in proteins can engage in multiple weak interactions with surrounding aliphatic groups. We analyze the strength and angular dependence of these interactions and conclude that they may contribute small, but significant, stabilization to the molecule. PMID:21207994

  7. Molecular structure and vibrational and chemical shift assignments of 3-(2-Hydroxyphenyl)-4-phenyl-1 H-1,2,4-triazole-5-(4 H)-thione by DFT and ab initio HF calculations

    NASA Astrophysics Data System (ADS)

    Avcı, Davut; Atalay, Yusuf; Şekerci, Mehmet; Dinçer, Muharrem

    2009-07-01

    The molecular geometry, vibrational frequencies, gauge including atomic orbital (GIAO) 1H and 13C chemical shift values and several thermodynamic parameters of 3-(2-Hydroxyphenyl)-4-phenyl-1 H-1,2,4-triazole-5-(4 H)-thione in the ground state have been calculated by using the Hartree-Fock (HF) and density functional methods (BLYP and B3LYP) with 6-31G(d) basis set. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. The molecule contains one O-H···N and one C-H···π (phenyl) intramolecular interactions. The computed vibrational frequencies are used to determine the types of molecular motions associated with each of the experimental bands observed. Data of the title compound display significant structure-correlation and provide the basis for future design of efficient materials having the derivatives of 1,2,4-triazole. Also, calculated 1H chemical shift values compared with the experimental ones.

  8. The influence of Mg(2+) coordination on (13) C and (15) N chemical shifts in CKI1RD protein domain from experiment and molecular dynamics/density functional theory calculations.

    PubMed

    Vícha, Jan; Babinský, Martin; Demo, Gabriel; Otrusinová, Olga; Jansen, Séverine; Pekárová, Blanka; Žídek, Lukáš; Munzarová, Markéta L

    2016-05-01

    Sequence dependence of (13) C and (15) N chemical shifts in the receiver domain of CKI1 protein from Arabidopsis thaliana, CKI1RD , and its complexed form, CKI1RD •Mg(2+) , was studied by means of MD/DFT calculations. MD simulations of a 20-ns production run length were performed. Nine explicitly hydrated structures of increasing complexity were explored, up to a 40-amino-acid structure. The size of the model necessary depended on the type of nucleus, the type of amino acid and its sequence neighbors, other spatially close amino acids, and the orientation of amino acid NH groups and their surface/interior position. Using models covering a 10 and a 15 Å environment of Mg(2+) , a semi-quantitative agreement has been obtained between experiment and theory for the V67-I73 sequence. The influence of Mg(2+) binding was described better by the 15 Å as compared to the 10 Å model. Thirteen chemical shifts were analyzed in terms of the effect of Mg(2+) insertion and geometry preparation. The effect of geometry was significant and opposite in sign to the effect of Mg(2+) binding. The strongest individual effects were found for (15) N of D70, S74, and V68, where the electrostatics dominated; for (13) Cβ of D69 and (15) N of K76, where the influences were equal, and for (13) Cα of F72 and (13) Cβ of K76, where the geometry adjustment dominated. A partial correlation between dominant geometry influence and torsion angle shifts upon the coordination has been observed. Proteins 2016; 84:686-699. © 2016 Wiley Periodicals, Inc. PMID:26879585

  9. On the choice of optimal methodology for calculation of (13)C and (1)H NMR isotropic chemical shifts in cagelike systems. Case studies of adamantane, 2-adamantanone, and 2,4-methano-2,4-dehydroadamantane.

    PubMed

    Vikić-Topić, D; Pejov, L

    2001-01-01

    The (13)C and (1)H isotropic chemical shift values computed at HF, BLYP, B3LYP, and MPW1PW91/6-311+G(2d,p) levels of theory, for the BLYP and B3LYP/6-31G(d,p) optimized geometries of adamantane, 2-adamantanone, and 2,4-methano-2,4-dehydroadamantane ([3.1.1] propellane) are reported and compared with the experimental data. Except for the "inverted" carbon atoms and some of their nearest neighbors, the HF values are superior over the DFT ones, when the isotropic shifts with respect to TMS are in question. However, in case of the relative shifts computed with respect to the most deshielded center within the molecule, the DFT methods yield significantly better agreement with the experimental data than the HF method, the hybrid DFT methods being superior over "pure" DFT ones. The most probable reason for these findings may be the cancellation of errors arising from the inappropriate description of the paramagnetic contributions to the overall shielding tensor within the Kohn-Sham approach when an internal standard (within a molecule) is chosen, instead of an external one. Almost excellent linear correlation was found between the calculated and experimental relative shift values, which is significantly superior at DFT levels than at HF level, further proving the more systematical nature of errors in predicting the second-order magnetic response properties at DFT levels of theory. Among all DFT methods employed, the MPW1PW91 showed the best performance, in line with the significantly improved long-range behavior of this functional, as compared to the B3LYP one. PMID:11749572

  10. 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.

  11. Unusual Physical and Chemical Properties of Ni in Ce1-xNixO2-y Oxides: Structural Characterization and Catalytic Activity for the Water Gas Shift Reaction

    SciTech Connect

    Rodriguez, J.A.; Barrio, L.; Kubacka, A.; Zhou, G.; Estrella, M.; Martınez-Arias, A.; Hanson, J.C.; Fernandez-Garcıa, M.

    2010-07-29

    The structural and electronic properties of Ce{sub 1-x}Ni{sub x}O{sub 2-y} nanosystems prepared by a reverse microemulsion method were characterized with synchrotron-based X-ray diffraction, X-ray absorption spectroscopy, Raman spectroscopy, and density functional calculations. The Ce{sub 1-x}Ni{sub x}O{sub 2-y} systems adopt a lattice with a fluorite-type structure with an acute local order where Ni displays a strongly distorted (oxygen) nearest-neighbor coordination and the presence of Ni atoms as first cation distances, pointing to the existence of Ni-O-Ni entities embedded into the ceria lattice. A Ni {leftrightarrow} Ce exchange within the CeO{sub 2} leads to a charge redistribution and the appearance of O vacancies. The Ni?O bonds in Ce{sub 1-x}Ni{sub x}O{sub 2-y} are more difficult to reduce than the bonds in pure NiO. The specific structural configuration of Ni inside the mixed-metal oxide leads to a unique catalyst with a high activity for the water gas shift (CO + H{sub 2}O {yields} H{sub 2} + CO{sub 2}) reaction and a simultaneous reduction of the methanation activity of nickel. Characterization results indicate that small particles of metallic Ni at the interface position of a ceria network may be the key for high WGS activity and that the formate?carbonate route is operative for the production of hydrogen.

  12. Unusual Physical and Chemical Properties of Ni in Ce1-xNixO2-y Oxides: Structural Characterization and Catalytic Activity for the Water Gas Shift Reaction

    SciTech Connect

    Barrio, L.; Kubacka, A; Zhou, G; Estrella, M; Martinez-Arias, A; Hanson, J; Fernandez-Garcia, M; Rodriguez, J

    2010-01-01

    The structural and electronic properties of Ce{sub 1-x}Ni{sub x}O{sub 2-y} nanosystems prepared by a reverse microemulsion method were characterized with synchrotron-based X-ray diffraction, X-ray absorption spectroscopy, Raman spectroscopy, and density functional calculations. The Ce{sub 1-x}Ni{sub x}O{sub 2-y} systems adopt a lattice with a fluorite-type structure with an acute local order where Ni displays a strongly distorted (oxygen) nearest-neighbor coordination and the presence of Ni atoms as first cation distances, pointing to the existence of Ni-O-Ni entities embedded into the ceria lattice. A Ni {leftrightarrow} Ce exchange within the CeO{sub 2} leads to a charge redistribution and the appearance of O vacancies. The Ni-O bonds in Ce{sub 1-x}Ni{sub x}O{sub 2-y} are more difficult to reduce than the bonds in pure NiO. The specific structural configuration of Ni inside the mixed-metal oxide leads to a unique catalyst with a high activity for the water gas shift (CO + H{sub 2}O {yields} H{sub 2} + CO{sub 2}) reaction and a simultaneous reduction of the methanation activity of nickel. Characterization results indicate that small particles of metallic Ni at the interface position of a ceria network may be the key for high WGS activity and that the formate-carbonate route is operative for the production of hydrogen.

  13. Synthesis, structural characterization and study of blue shift in optical properties of zinc oxide nano particles prepared by chemical route method

    NASA Astrophysics Data System (ADS)

    Taunk, P. B.; Das, R.; Bisen, D. P.; Tamrakar, Raunak Kumar

    2015-12-01

    We report the synthesis and optical properties of ZnO nano particle using TEA (Tri Ethanol Amine) and without TEA by chemical route method. By decreasing the concentration of TEA, reaction rate is decreases and inter planner spacing d is increases, band gap is increased from 4.1 to 4.8 eV. In case of without TEA band gap is obtained 3.4 eV. Morphology, growth and the nature of crystalline of the powder samples were performed by X- ray Diffraction (XRD); UV spectrophotometer, scanning electron microscope (SEM) and Photoluminescence (PL). Luminescence properties are discussed by probing the photoluminescence properties of ZnO nano particles with TEA at different molar concentrations.

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

    SciTech Connect

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

    1987-08-26

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

  15. Towards the design of cyclooxygenase (COX) inhibitors based on 4',5 di-substituted biphenyl acetic acid molecules: a QSAR study with a new DFT based descriptor - nucleus independent chemical shift.

    PubMed

    Sarkar, Ananda; Mostafa, Golam

    2009-10-01

    Cyclooxygenase (COX) is a well-known enzyme, which converts arachidonic acid to prostaglandins H(2) (PGH(2)), which are the effective mediators of inflammation. 4', 5 di-substituted 3-biphenyl acetic acids (BPA) and several alpha-methyl derivatives (MBPA) of it are widely used as powerful nonsteroidal anti-inflammatory and analgesic agents. We have chosen these activity data because the relation between the substituents and activity is not obvious and is hard to explain and also to show the superiority of DFT method. From the DFT results, various quantum chemical based descriptors were computed but the QSAR results showed that the descriptors based on frontier electron density and a new DFT based quantum chemical descriptor, nucleus independent chemical shift (NICS) are likely to be responsible for the in vitro inhibiting activity of BPA and MPBA. It has been proposed that NICS accounts for pi...pi interaction and indeed leads to a better result. To the best of our knowledge, this is the first use of NICS as a descriptor to get a better relationship to facilitate the design of COX inhibitors with potentially higher biological activity. PMID:19266221

  16. Solid-state (185/187)Re NMR and GIPAW DFT study of perrhenates and Re2(CO)10: chemical shift anisotropy, NMR crystallography, and a metal-metal bond.

    PubMed

    Widdifield, Cory M; Perras, Frédéric A; Bryce, David L

    2015-04-21

    Advances in solid-state nuclear magnetic resonance (SSNMR) methods, such as dynamic nuclear polarization (DNP), intricate pulse sequences, and increased applied magnetic fields, allow for the study of systems which even very recently would be impractical. However, SSNMR methods using certain quadrupolar probe nuclei (i.e., I > 1/2), such as (185/187)Re remain far from fully developed due to the exceedingly strong interaction between the quadrupole moment of these nuclei and local electric field gradients (EFGs). We present a detailed high-field (B0 = 21.1 T) experimental SSNMR study on several perrhenates (KReO4, AgReO4, Ca(ReO4)2·2H2O), as well as ReO3 and Re2(CO)10. We propose solid ReO3 as a new rhenium SSNMR chemical shift standard due to its reproducible and sharp (185/187)Re NMR resonances. We show that for KReO4, previously poorly understood high-order quadrupole-induced effects (HOQIE) on the satellite transitions can be used to measure the EFG tensor asymmetry (i.e., ηQ) to nearly an order-of-magnitude greater precision than competing SSNMR and nuclear quadrupole resonance (NQR) approaches. Samples of AgReO4 and Ca(ReO4)2·2H2O enable us to comment on the effects of counter-ions and hydration upon Re(vii) chemical shifts. Calcium-43 and (185/187)Re NMR tensor parameters allow us to conclude that two proposed crystal structures for Ca(ReO4)2·2H2O, which would be considered as distinct, are in fact the same structure. Study of Re2(CO)10 provides insights into the effects of Re-Re bonding on the rhenium NMR tensor parameters and rhenium oxidation state on the Re chemical shift value. As overtone NQR experiments allowed us to precisely measure the (185/187)Re EFG tensor of Re2(CO)10, we were able to measure rhenium chemical shift anisotropy (CSA) for the first time in a powdered sample. Experimental observations are supported by gauge-including projector augmented-wave (GIPAW) density functional theory (DFT) calculations, with NMR tensor calculations also

  17. 3D ¹⁵N/¹⁵N/¹H chemical shift correlation experiment utilizing an RFDR-based ¹H/¹H mixing period at 100 kHz MAS.

    PubMed

    Nishiyama, Yusuke; Malon, Michal; Ishii, Yuji; Ramamoorthy, Ayyalusamy

    2014-07-01

    Homonuclear correlation NMR experiments are commonly used in the high-resolution structural studies of proteins. While (13)C/(13)C chemical shift correlation experiments utilizing dipolar recoupling techniques are fully utilized under MAS, correlation of the chemical shifts of (15)N nuclei in proteins has been a challenge. Previous studies have shown that the negligible (15)N-(15)N dipolar coupling in peptides or proteins necessitates the use of a very long mixing time (typically several seconds) for effective spin diffusion to occur and considerably slows down a (15)N/(15)N correlation experiment. In this study, we show that the use of mixing proton magnetization, instead of (15)N, via the recoupled (1)H-(1)H dipolar couplings enable faster (15)N/(15)N correlation. In addition, the use of proton-detection under ultrafast MAS overcomes the sensitivity loss due to multiple magnetization transfer (between (1)H and (15)N nuclei) steps. In fact, less than 300 nL (∼1.1 micromole quantity) sample is sufficient to acquire the 3D spectrum within 5 h. Our results also demonstrate that a 3D (15)N/(15)N/(1)H experiment can render higher resolution spectra that will be useful in the structural studies of proteins at ultrafast MAS frequencies. 3D (15)N/(15)N/(1)H and 2D radio frequency-driven dipolar recoupling (RFDR)-based (1)H/(1)H experimental results obtained from a powder sample of N-acetyla-L-(15)N-valyl-L-(15)N-leucine at 70 and 100kHz MAS frequencies are presented. PMID:24801998

  18. Using NMR chemical shift imaging to monitor swelling and molecular transport in drug-loaded tablets of hydrophobically modified poly(acrylic acid): methodology and effects of polymer (in)solubility.

    PubMed

    Knöös, Patrik; Topgaard, Daniel; Wahlgren, Marie; Ulvenlund, Stefan; Piculell, Lennart

    2013-11-12

    A new technique has been developed using NMR chemical shift imaging (CSI) to monitor water penetration and molecular transport in initially dry polymer tablets that also contain small low-molecular weight compounds to be released from the tablets. Concentration profiles of components contained in the swelling tablets could be extracted via the intensities and chemical shift changes of peaks corresponding to protons of the components. The studied tablets contained hydrophobically modified poly(acrylic acid) (HMPAA) as the polymer component and griseofulvin and ethanol as hydrophobic and hydrophilic, respectively, low-molecular weight model compounds. The water solubility of HMPAA could be altered by titration with NaOH. In the pure acid form, HMPAA tablets only underwent a finite swelling until the maximum water content of the polymer-rich phase, as confirmed by independent phase studies, had been reached. By contrast, after partial neutralization with NaOH, the polyacid became fully miscible with water. The solubility of the polymer affected the water penetration, the polymer release, and the releases of both ethanol and griseofulvin. The detailed NMR CSI concentration profiles obtained highlighted the clear differences in the disintegration/dissolution/release behavior for the two types of tablet and provided insights into their molecular origin. The study illustrates the potential of the NMR CSI technique to give information of importance for the development of pharmaceutical tablets and, more broadly, for the general understanding of any operation that involves the immersion and ultimate disintegration of a dry polymer matrix in a solvent. PMID:24106807

  19. Nuclear magnetic resonance studies of xenon clusters in zeolite NaA

    SciTech Connect

    Jameson, C. J.; Jameson, A. K.; Gerald, R. E., II; de Dios, A. C.; Chemical Engineering; Univ. of Illinois at Chicago; Loyola Univ.

    1992-02-01

    We have observed the equilibrium distribution of Xe atoms trapped in the alpha cages of zeolite NaA at 300 and at 360 K for low to high xenon loadings. The experimental distributions obtained by nuclear magnetic resonance (NMR) spectroscopy differ from two previously proposed statistical distributions. The experimental deviations from these statistical models can be explained by the attractive Xe-Xe interactions which favor clustering at low to medium loading, and the higher energies associated with the overcrowded cage disfavoring clusters of eight Xe atoms at high loadings. The temperature dependence of the {sup 129}Xe NMR chemical shift of each cluster has been measured in the range 188-421 K, except that for Xe{sub 8}, which was determined only up to 300 K. The observed shifts and their temperature dependence are interpreted by using the results of ab initio calculations of the intermolecular shielding function in the {sup 39}Ar system as a model for the {sup 129}Xe system.

  20. Psychopathology of Shift Work.

    ERIC Educational Resources Information Center

    Akinnawo, Ebenezer Olutope

    1989-01-01

    Examined incidence and nature of general psychopathology among Nigerian shift workers (N=320). Found shift workers more significantly psychopathological than non-shift workers (p<0.001). Prominent disorders among shift workers were intellectual, sleep, mood, and general somatic disorders. No significant difference could be attributed to gender and…

  1. Synthesis, molecular conformation, vibrational and electronic transition, isometric chemical shift, polarizability and hyperpolarizability analysis of 3-(4-Methoxy-phenyl)-2-(4-nitro-phenyl)-acrylonitrile: A combined experimental and theoretical analysis

    NASA Astrophysics Data System (ADS)

    Asiri, Abdullah Mohamed; Karabacak, Mehmet; Kurt, Mustafa; Alamry, Khalid A.

    2011-11-01

    This work presents the synthesis and characterization of a novel compound, 3-(4-Methoxy-phenyl)-2-(4-nitro-phenyl)-acrylonitrile (abbreviated as 3-(4MP)-2-(4-NP)-AN, C 16H 12N 2O 3). The spectroscopic properties of the compound were examined by FT-IR, UV-vis and NMR ( 1H and 13C) techniques. FT-IR spectrum in solid state was observed in the region 4000-400 cm -1. The UV-vis absorption spectrum of the compound which dissolved in chloroform was recorded in the range of 200-800 nm. The 1H and 13C NMR spectra were recorded in CDCl 3 solution. To determine lowest-energy molecular conformation of the title molecule, the selected torsion angle is varied every 10° and molecular energy profile is calculated from 0° to 360°. The structural and spectroscopic data of the molecule in the ground state were calculated using density functional theory (DFT) employing B3LYP/6-31G(d,p) basis set. The dipole moment, linear polarizability and first hyperpolarizability values were also computed using the same basis set. A study on the electronic properties, such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. The HOMO and LUMO analysis were used to elucidate information regarding charge transfer within the molecule. The vibrational wavenumbers were calculated and scaled values were compared with experimental FT-IR spectrum. The complete assignments were performed on the basis of the experimental results and total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. Isotropic chemical shifts were calculated using the gauge-invariant atomic orbital (GIAO) method. Comparison of the calculated frequencies, NMR chemical shifts, absorption wavelengths with the experimental values revealed that DFT and TD-DFT method produce good results. The linear polarizabilities and first hyperpolarizabilities of the studied molecule indicate that the title compound can be used as a good nonlinear optical material

  2. Synthesis, molecular conformation, vibrational and electronic transition, isometric chemical shift, polarizability and hyperpolarizability analysis of 3-(4-methoxy-phenyl)-2-(4-nitro-phenyl)-acrylonitrile: a combined experimental and theoretical analysis.

    PubMed

    Asiri, Abdullah Mohamed; Karabacak, Mehmet; Kurt, Mustafa; Alamry, Khalid A

    2011-11-01

    This work presents the synthesis and characterization of a novel compound, 3-(4-methoxy-phenyl)-2-(4-nitro-phenyl)-acrylonitrile (abbreviated as 3-(4MP)-2-(4-NP)-AN, C(16)H(12)N(2)O(3)). The spectroscopic properties of the compound were examined by FT-IR, UV-vis and NMR ((1)H and (13)C) techniques. FT-IR spectrum in solid state was observed in the region 4000-400 cm(-1). The UV-vis absorption spectrum of the compound which dissolved in chloroform was recorded in the range of 200-800 nm. The (1)H and (13)C NMR spectra were recorded in CDCl(3) solution. To determine lowest-energy molecular conformation of the title molecule, the selected torsion angle is varied every 10° and molecular energy profile is calculated from 0° to 360°. The structural and spectroscopic data of the molecule in the ground state were calculated using density functional theory (DFT) employing B3LYP/6-31G(d,p) basis set. The dipole moment, linear polarizability and first hyperpolarizability values were also computed using the same basis set. A study on the electronic properties, such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. The HOMO and LUMO analysis were used to elucidate information regarding charge transfer within the molecule. The vibrational wavenumbers were calculated and scaled values were compared with experimental FT-IR spectrum. The complete assignments were performed on the basis of the experimental results and total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. Isotropic chemical shifts were calculated using the gauge-invariant atomic orbital (GIAO) method. Comparison of the calculated frequencies, NMR chemical shifts, absorption wavelengths with the experimental values revealed that DFT and TD-DFT method produce good results. The linear polarizabilities and first hyperpolarizabilities of the studied molecule indicate that the title compound can be used as a good nonlinear

  3. Gear shift control mechanism

    SciTech Connect

    Janson, D.A.

    1987-03-10

    A gear shift control mechanism is described comprising: multiple shift rods directed substantially parallel to one another, each rod carrying a shift fork for axial movement; a shift lever supported for pivotal movement about a first axis directed parallel to the axes of the shift rods and for pivotal movement about a second axis directed substantially perpendicular to the axes of the shift rods. The lever is moveable about the first axis and the second axis into engagement with a selected shift fork; interlock means located on each lateral side of the shift lever and mounted for pivotal movement about the first axis for blocking engagement with the shift forks; detent means for holding the shift lever in multiple predetermined angular positions about the second axis; and spring means located on a lateral side of the shift lever and mounted for pivotal movement about the first axis into interference contact with the shift forks for producing a force tending to resiliently bias the shift lever out of engagement with the selected shift fork.

  4. A comparative quantitative analysis of the IDEAL (iterative decomposition of water and fat with echo asymmetry and least-squares estimation) and the CHESS (chemical shift selection suppression) techniques in 3.0 T L-spine MRI

    NASA Astrophysics Data System (ADS)

    Kim, Eng-Chan; Cho, Jae-Hwan; Kim, Min-Hye; Kim, Ki-Hong; Choi, Cheon-Woong; Seok, Jong-min; Na, Kil-Ju; Han, Man-Seok

    2013-03-01

    This study was conducted on 20 patients who had undergone pedicle screw fixation between March and December 2010 to quantitatively compare a conventional fat suppression technique, CHESS (chemical shift selection suppression), and a new technique, IDEAL (iterative decomposition of water and fat with echo asymmetry and least squares estimation). The general efficacy and usefulness of the IDEAL technique was also evaluated. Fat-suppressed transverse-relaxation-weighed images and longitudinal-relaxation-weighted images were obtained before and after contrast injection by using these two techniques with a 1.5T MR (magnetic resonance) scanner. The obtained images were analyzed for image distortion, susceptibility artifacts and homogenous fat removal in the target region. The results showed that the image distortion due to the susceptibility artifacts caused by implanted metal was lower in the images obtained using the IDEAL technique compared to those obtained using the CHESS technique. The results of a qualitative analysis also showed that compared to the CHESS technique, fewer susceptibility artifacts and more homogenous fat removal were found in the images obtained using the IDEAL technique in a comparative image evaluation of the axial plane images before and after contrast injection. In summary, compared to the CHESS technique, the IDEAL technique showed a lower occurrence of susceptibility artifacts caused by metal and lower image distortion. In addition, more homogenous fat removal was shown in the IDEAL technique.

  5. Molecular structure and vibrational bands and chemical shift assignments of 4-allyl-5-(2-hydroxyphenyl)-2,4-dihydro-3H-1,2,4-triazole-3-thione by DFT and ab initio HF calculations

    NASA Astrophysics Data System (ADS)

    Karakurt, Tuncay; Dinçer, Muharrem; Çetin, Ahmet; Şekerci, Memet

    2010-09-01

    The title molecule, 4-allyl-5-(2-hydroxyphenyl)-2,4-dihydro-3H-1,2,4-triazole-3-thione (C 11H 11N 3OS), was synthesized and characterized by IR-NMR spectroscopy and single-crystal X-ray diffraction. The compound crystallizes in the monoclinic space group is P2 1/ c, a = 9.0907(5) Å, b = 9.1288(7) Å, c = 13.6222(7) Å, α = 90°, β = 98.442 (4), γ = 90° and V = 2683.7(6) Å 3, F(000) = 488, Dx = 1.386 g/cm 3. In addition to the molecular geometry from X-ray experiment, the molecular geometry, vibrational frequencies, gauge including atomic orbital (GIAO) 1H and 13C chemical shift values of the title compound in the ground state have been calculated using the Hartree-Fock (HF) and density functional method (DFT/BLYP and DFT/B3LYP) with 6-31G(d) basis set. To determine conformational flexibility, molecular energy profile of the title compound was obtained by HF/6-31G(d) calculations with respect to selected degree of torsional freedom, which was varied from -180° to +180° in steps of 10°. Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMO), and several thermodynamic properties were performed by the HF and DFT methods.

  6. Relativistic coupled-cluster calculations of {sup 20}Ne, {sup 40}Ar, {sup 84}Kr, and {sup 129}Xe: Correlation energies and dipole polarizabilities

    SciTech Connect

    Mani, B. K.; Angom, D.; Latha, K. V. P.

    2009-12-15

    We have carried out a detailed and systematic study of the correlation energies of inert gas atoms Ne, Ar, Kr, and Xe using relativistic many-body perturbation theory and relativistic coupled-cluster theory. In the relativistic coupled-cluster calculations, we implement perturbative triples and include these in the correlation energy calculations. We then calculate the dipole polarizability of the ground states using perturbed coupled-cluster theory.

  7. Biothiol Xenon MRI Sensor Based on Thiol-Addition Reaction.

    PubMed

    Yang, Shengjun; Jiang, Weiping; Ren, Lili; Yuan, Yaping; Zhang, Bin; Luo, Qing; Guo, Qianni; Bouchard, Louis-S; Liu, Maili; Zhou, Xin

    2016-06-01

    Biothiols such as cysteine (Cys), homocysteine (Hcy), and glutathione (GSH) play an important role in regulating the vital functions of living organisms. Knowledge of their biodistribution in real-time could help diagnose a variety of conditions. However, existing methods of biothiol detection are invasive and require assays. Herein we report a molecular biosensor for biothiol detection using the nuclear spin resonance of (129)Xe. The (129)Xe biosensor consists of a cryptophane cage encapsulating a xenon atom and an acrylate group. The latter serves as a reactive site to covalently bond biothiols through a thiol-addition reaction. The biosensor enables discrimination of Cys from Hcy and GSH through the chemical shift and average reaction rate. This biosensor can be detected at a concentration of 10 μM in a single scan and it has been applied to detect biothiols in bovine serum solution. Our results indicate that this biosensor is a promising tool for the real-time imaging of biothiol distributions. PMID:27128102

  8. Host shifts and evolutionary radiations of butterflies

    PubMed Central

    Fordyce, James A.

    2010-01-01

    Ehrlich and Raven proposed a model of coevolution where major host plant shifts of butterflies facilitate a burst of diversification driven by their arrival to a new adaptive zone. One prediction of this model is that reconstructions of historical diversification of butterflies should indicate an increase in diversification rate following major host shifts. Using reconstructed histories of 15 butterfly groups, I tested this prediction and found general agreement with Ehrlich and Raven's model. Butterfly lineages with an inferred major historical host shift showed evidence of diversification rate variation, with a significant acceleration following the host shift. Lineages without an inferred major host shift generally agreed with a constant-rate model of diversification. These results are consistent with the view that host plant associations have played a profound role in the evolutionary history of butterflies, and show that major shifts to chemically distinct plant groups leave a historical footprint that remains detectable today. PMID:20610430

  9. Optimization of Xenon Biosensors for Detection of ProteinInteractions

    SciTech Connect

    Lowery, Thomas J.; Garcia, Sandra; Chavez, Lana; Ruiz, E.Janette; Wu, Tom; Brotin, Thierry; Dutasta, Jean-Pierre; King, David S.; Schultz, Peter G.; Pines, Alex; Wemmer, David E..

    2005-08-03

    Hyperpolarized 129Xe NMR can detect the presence of specific low-concentration biomolecular analytes by means of the xenon biosensor, which consists of a water-soluble, targeted cryptophane-A cage that encapsulates xenon. In this work we use the prototypical biotinylated xenon biosensor to determine the relationship between the molecular composition of the xenon biosensor and the characteristics of protein-bound resonances. The effects of diastereomer overlap, dipole-dipole coupling, chemical shift anisotropy, xenon exchange, and biosensor conformational exchange on protein-bound biosensor signal were assessed. It was found that optimal protein-bound biosensor signal can be obtained by minimizing the number of biosensor diastereomers and using a flexible linker of appropriate length. Both the linewidth and sensitivity of chemical shift to protein binding of the xenon biosensor were found to be inversely proportional to linker length.

  10. Unusual 1H NMR chemical shifts support (His) C(epsilon) 1...O==C H-bond: proposal for reaction-driven ring flip mechanism in serine protease catalysis.

    PubMed

    Ash, E L; Sudmeier, J L; Day, R M; Vincent, M; Torchilin, E V; Haddad, K C; Bradshaw, E M; Sanford, D G; Bachovchin, W W

    2000-09-12

    13C-selective NMR, combined with inhibitor perturbation experiments, shows that the C(epsilon)(1)H proton of the catalytic histidine in resting alpha-lytic protease and subtilisin BPN' resonates, when protonated, at 9.22 ppm and 9.18 ppm, respectively, which is outside the normal range for such protons and approximately 0.6 to 0.8 ppm further downfield than previously reported. They also show that the previous alpha-lytic protease assignments [Markley, J. L., Neves, D. E., Westler, W. M., Ibanez, I. B., Porubcan, M. A. & Baillargeon, M. W. (1980) Front. Protein Chem. 10, 31-61] were to signals from inactive or denatured protein. Simulations of linewidth vs. pH demonstrate that the true signal is more difficult to detect than corresponding signals from inactive derivatives, owing to higher imidazole pK(a) values and larger chemical shift differences between protonated and neutral forms. A compilation and analysis of available NMR data indicates that the true C(epsilon)(1)H signals from other serine proteases are similarly displaced downfield, with past assignments to more upfield signals probably in error. The downfield displacement of these proton resonances is shown to be consistent with an H-bond involving the histidine C(epsilon)(1)H as donor, confirming the original hypothesis of Derewenda et al. [Derewenda, Z. S., Derewenda, U. & Kobos, P. M. (1994) J. Mol. Biol. 241, 83-93], which was based on an analysis of literature x-ray crystal structures of serine hydrolases. The invariability of this H-bond among enzymes containing Asp-His-Ser triads indicates functional importance. Here, we propose that it enables a reaction-driven imidazole ring flip mechanism, overcoming a major dilemma inherent in all previous mechanisms, namely how these enzymes catalyze both the formation and productive breakdown of tetrahedral intermediates. PMID:10984533

  11. Unusual 1H NMR chemical shifts support (His) Cɛ1—H⋅⋅⋅O⩵C H-bond: Proposal for reaction-driven ring flip mechanism in serine protease catalysis

    PubMed Central

    Ash, Elissa L.; Sudmeier, James L.; Day, Regina M.; Vincent, Matthew; Torchilin, Ekaterina V.; Haddad, Kristin Coffman; Bradshaw, Elizabeth M.; Sanford, David G.; Bachovchin, William W.

    2000-01-01

    13C-selective NMR, combined with inhibitor perturbation experiments, shows that the Cɛ1—H proton of the catalytic histidine in resting α-lytic protease and subtilisin BPN′ resonates, when protonated, at 9.22 ppm and 9.18 ppm, respectively, which is outside the normal range for such protons and ≈0.6 to 0.8 ppm further downfield than previously reported. They also show that the previous α-lytic protease assignments [Markley, J. L., Neves, D. E., Westler, W. M., Ibanez, I. B., Porubcan, M. A. & Baillargeon, M. W. (1980) Front. Protein Chem. 10, 31–61] were to signals from inactive or denatured protein. Simulations of linewidth vs. pH demonstrate that the true signal is more difficult to detect than corresponding signals from inactive derivatives, owing to higher imidazole pKa values and larger chemical shift differences between protonated and neutral forms. A compilation and analysis of available NMR data indicates that the true Cɛ1—H signals from other serine proteases are similarly displaced downfield, with past assignments to more upfield signals probably in error. The downfield displacement of these proton resonances is shown to be consistent with an H-bond involving the histidine Cɛ1—H as donor, confirming the original hypothesis of Derewenda et al. [Derewenda, Z. S., Derewenda, U. & Kobos, P. M. (1994) J. Mol. Biol. 241, 83–93], which was based on an analysis of literature x-ray crystal structures of serine hydrolases. The invariability of this H-bond among enzymes containing Asp-His-Ser triads indicates functional importance. Here, we propose that it enables a reaction-driven imidazole ring flip mechanism, overcoming a major dilemma inherent in all previous mechanisms, namely how these enzymes catalyze both the formation and productive breakdown of tetrahedral intermediates. PMID:10984533

  12. Comparison of clinical semi-quantitative assessment of muscle fat infiltration with quantitative assessment using chemical shift-based water/fat separation in MR studies of the calf of post-menopausal women

    PubMed Central

    Nardo, Lorenzo; Karampinos, Dimitrios C.; Joseph, Gabby B.; Yap, Samuel P.; Baum, Thomas; Krug, Roland; Majumdar, Sharmila; Link, Thomas M.

    2013-01-01

    Objective The goal of this study was to compare the semi-quantitative Goutallier classification for fat infiltration with quantitative fat-fraction derived from a magnetic resonance imaging (MRI) chemical shift-based water/fat separation technique. Methods Sixty-two women (age 61±6 years), 27 of whom had diabetes, underwent MRI of the calf using a T1-weighted fast spin-echo sequence and a six-echo spoiled gradient-echo sequence at 3 T. Water/fat images and fat fraction maps were reconstructed using the IDEAL algorithm with T2* correction and a multi-peak model for the fat spectrum. Two radiologists scored fat infiltration on the T1-weighted images using the Goutallier classification in six muscle compartments. Spearman correlations between the Goutallier grades and the fat fraction were calculated; in addition, intra-observer and inter-observer agreement were calculated. Results A significant correlation between the clinical grading and the fat fraction values was found for all muscle compartments (P<0.0001, R values ranging from 0.79 to 0.88). Goutallier grades 0–4 had a fat fraction ranging from 3.5 to 19%. Intra-observer and inter-observer agreement values of 0.83 and 0.81 were calculated for the semi-quantitative grading. Conclusion Semi-quantitative grading of intramuscular fat and quantitative fat fraction were significantly correlated and both techniques had excellent reproducibility. However, the clinical grading was found to overestimate muscle fat. PMID:22411305

  13. Nuclear spin-spin coupling in a van der Waals-bonded system: xenon dimer.

    PubMed

    Vaara, Juha; Hanni, Matti; Jokisaari, Jukka

    2013-03-14

    Nuclear spin-spin coupling over van der Waals bond has recently been observed via the frequency shift of solute protons in a solution containing optically hyperpolarized (129)Xe nuclei. We carry out a first-principles computational study of the prototypic van der Waals-bonded xenon dimer, where the spin-spin coupling between two magnetically non-equivalent isotopes, J((129)Xe - (131)Xe), is observable. We use relativistic theory at the four-component Dirac-Hartree-Fock and Dirac-density-functional theory levels using novel completeness-optimized Gaussian basis sets and choosing the functional based on a comparison with correlated ab initio methods at the nonrelativistic level. J-coupling curves are provided at different levels of theory as functions of the internuclear distance in the xenon dimer, demonstrating cross-coupling effects between relativity and electron correlation for this property. Calculations on small Xe clusters are used to estimate the importance of many-atom effects on J((129)Xe - (131)Xe). Possibilities of observing J((129)Xe - (131)Xe) in liquid xenon are critically examined, based on molecular dynamics simulation. A simplistic spherical model is set up for the xenon dimer confined in a cavity, such as in microporous materials. It is shown that the on the average shorter internuclear distance enforced by the confinement increases the magnitude of the coupling as compared to the bulk liquid case, rendering J((129)Xe - (131)Xe) in a cavity a feasible target for experimental investigation. PMID:23514495

  14. Hyperpolarized Gas MRI: Technique and Applications

    PubMed Central

    McAdams, Holman P.; Kaushik, S. Sivaram; Driehuys, Bastiaan

    2015-01-01

    Synopsis Functional imaging today offers a rich world of information that is more sensitive to changes in lung structure and function than traditionally obtained pulmonary function tests. Hyperpolarized helium (3He) and xenon (129Xe) MR imaging of the lungs provided new sensitive contrast mechanisms to probe changes in pulmonary ventilation, microstructure and gas exchange. With the recent scarcity in the supply of 3He the field of hyperpolarized gas imaging shifted to the use of cheaper and naturally available 129Xe. Xenon is well tolerated and recent technical advances have ensured that the 129Xe image quality is on par with that of 3He. The added advantage of 129Xe is its solubility in pulmonary tissue, which allows exploring specific lung function characteristics involved in gas exchange and alveolar oxygenation. With a plethora of contrast mechanisms, hyperpolarized gases and 129Xe in particular, stands to be an excellent probe of pulmonary structure and function, and provide sensitive and non-invasive biomarkers for a wide variety of pulmonary diseases. PMID:25952516

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

    SciTech Connect

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

    1993-01-01

    Solid-state NMR spectroscopy is well established as a method for describing molecular structure with resolution on the atomic scale. Many of the NMR observables result from anisotropic interactions between the nuclear spin and its environment. These observables can be described by second-rank tensors. For example, the eigenvalues of the traceless symmetric part of the hydrogen chemical shift (CS) tensor provide information about the strength of inter- or intramolecular hydrogen bonding. On the other hand, the eigenvectors of the deuterium electric field gradient (EFG) tensor give deuteron/proton bond directions with an accuracy rivalled only by neutron diffraction. In this paper the authors report structural information of this type for the amide and carboxyl hydrogen sites in a single crystal of the model peptide N-acetyl-D,L-valine (NAV). They use deuterium NMR to infer both the EFG and CS tensors at the amide and carboxyl hydrogen sites in NAV. Advantages of this technique over multiple-pulse proton NMR are that it works in the presence of {sup 14}N spins which are very hard to decouple from protons and that additional information in form of the EFG tensors can be derived. The change in the CS and EFG tensors upon exchange of a deuteron for a proton (the isotope effect) is anticipated to be very small; the effect on the CS tensors is certainly smaller than the experimental errors. NAV has served as a model peptide before in a variety of NMR studies, including those concerned with developing solid-state NMR spectroscopy as a method for determining the structure of proteins. NMR experiments on peptide or protein samples which are oriented in at least one dimension can provide important information about the three-dimensional structure of the peptide or the protein. In order to interpret the NMR data in terms of the structure of the polypeptide, the relationship of the CS and EFG tensors to the local symmetry elements of an amino acide, e.g., the peptide plane, is

  16. Shifting scintillator neutron detector

    SciTech Connect

    Clonts, Lloyd G; Cooper, Ronald G; Crow, Jr., Morris Lowell; Hannah, Bruce W; Hodges, Jason P; Richards, John D; Riedel, Richard A

    2014-03-04

    Provided are sensors and methods for detecting thermal neutrons. Provided is an apparatus having a scintillator for absorbing a neutron, the scintillator having a back side for discharging a scintillation light of a first wavelength in response to the absorbed neutron, an array of wavelength-shifting fibers proximate to the back side of the scintillator for shifting the scintillation light of the first wavelength to light of a second wavelength, the wavelength-shifting fibers being disposed in a two-dimensional pattern and defining a plurality of scattering plane pixels where the wavelength-shifting fibers overlap, a plurality of photomultiplier tubes, in coded optical communication with the wavelength-shifting fibers, for converting the light of the second wavelength to an electronic signal, and a processor for processing the electronic signal to identify one of the plurality of scattering plane pixels as indicative of a position within the scintillator where the neutron was absorbed.

  17. Advanced NMR-based techniques for pore structure analysis of coal. Quarterly report No. 1, September 1, 1991--November 30, 1991

    SciTech Connect

    Smith, D.M.

    1991-12-31

    One of the main problems in coal utilization is the inability to properly characterize its complex pore structure. We propose to investigate the dependence of the common NMR parameters such as chemical shifts and relaxation times of several different nuclei and compounds on the pore structure of model microporous solids, carbons, and coals. In particular, we will study the interaction between several small molecules ({sup 129}Xe, {sup 3}He, {sup 2}H{sub 2}, {sup 14}N{sub 2}, {sup 14}NH{sub 3}, {sup 15}N{sub 2}, {sup 13}CH{sub 4}, {sup 13}CO{sub 2}) and the pore surfaces in coals. These molecules have been selected for their chemical and physical properties.

  18. Advanced NMR-based techniques for pore structure analysis of coal

    SciTech Connect

    Smith, D.M.

    1991-01-01

    One of the main problems in coal utilization is the inability to properly characterize its complex pore structure. We propose to investigate the dependence of the common NMR parameters such as chemical shifts and relaxation times of several different nuclei and compounds on the pore structure of model microporous solids, carbons, and coals. In particular, we will study the interaction between several small molecules ({sup 129}Xe, {sup 3}He, {sup 2}H{sub 2}, {sup 14}N{sub 2}, {sup 14}NH{sub 3}, {sup 15}N{sub 2}, {sup 13}CH{sub 4}, {sup 13}CO{sub 2}) and the pore surfaces in coals. These molecules have been selected for their chemical and physical properties.

  19. Lanthanide ion (III) complexes of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate (DOTA-4AmP8−) for dual biosensing of pH with CEST (chemical exchange saturation transfer) and BIRDS (biosensor imaging of redundant deviation in shifts)

    PubMed Central

    Huang, Yuegao; Coman, Daniel; Ali, Meser M.; Hyder, Fahmeed

    2014-01-01

    Relaxivity based magnetic resonance of phosphonated ligands chelated with gadolinium (Gd3+) 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 non-exchangeable or the exchangeable protons on the lanthanide complexes themselves. The non-exchangeable 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-4AmP8−) chelated with thulium (Tm3+) and ytterbium (Yb3+). 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-4AmP5− than with TmDOTA-4AmP5−. In addition, we demonstrate the prospect of using BIRDS to calibrate CEST as new platform for quantitative pH imaging. PMID:24801742

  20. Effects of Surface Chemistry on the Porous Structure of Coal

    SciTech Connect

    Radovic, Ljubisa R; Hatcher, Patrick G

    1997-05-01

    In this report, 129 Xe nuclear magnetic resonance spectroscopy of xenon gas adsorbed in coal is used to describe some poorly understood features of coal microporous structure, particularly in establishing that a connected network exists, the type of connectivity, and its changes with the rank of coal. Micropore size scale and distribution are also considered. Two methods are developed which are new and versatile tools for the investigation of porous structure. Both utilize xenon gas that is in motion, while undergoing diffusion or exchange in coal, to describe the connectivity of the micropore structure of coal. Time tracking of the adsorption process by NMR, selective saturation, and saturation transfer techniques were used to obtain new information on the coal rank dependence of porous structure. In addition, an existing 129 Xe chemical shift-pore diameter model was used to calculate micropore diameters for coals, as well as for a microporous carbon, before and after pore-size alteration. In the initial study performed, straightforward 129 Xe NMR spectra at equilibrium xenon adsorption at a series of pressures were acquired for a rank-varied set of six coals. Acquisition of the NMR signal as an echo was tested and found to improve spectral quality. The spectra were used to calculate micropore diameters for the six coals. These range from 5.6 to 7.5 and exhibit a minimum value for the intermediate coal rank. The smallest pores occur in coals of about 82-85% carbon; at both lower and higher coal ranks, the average micropore size tends to be larger. The changes in the spectra with coal rank and surface area were explored. Signal linewidths were found to decrease with increasing coal rank and were interpreted in terms of increasing chemical or physical homogeneity of the coal as rank increases. The packing density of powdered coal was found to alter the spectral appearance in a high volatile bituminous coal, which is preliminary evidence that exchange affects the

  1. Our World: Fluid Shift

    NASA Video Gallery

    Learn about the circulatory system and how gravity aids blood flow in our bodies here on Earth. Find out how NASA flight surgeons help the astronauts deal with the fluid shift that happens during s...

  2. Shape-Shifting Plastic

    SciTech Connect

    2015-05-20

    A new plastic developed by ORNL and Washington State University transforms from its original shape through a series of temporary shapes and returns to its initial form. The shape-shifting process is controlled through changes in temperature

  3. Observing and preventing rubidium runaway in a direct-infusion xenon-spin hyperpolarizer optimized for high-resolution hyper-CEST (chemical exchange saturation transfer using hyperpolarized nuclei) NMR

    NASA Astrophysics Data System (ADS)

    Witte, C.; Kunth, M.; Rossella, F.; Schröder, L.

    2014-02-01

    Xenon is well known to undergo host-guest interactions with proteins and synthetic molecules. As xenon can also be hyperpolarized by spin exchange optical pumping, allowing the investigation of highly dilute systems, it makes an ideal nuclear magnetic resonance probe for such host molecules. The utility of xenon as a probe can be further improved using Chemical Exchange Saturation Transfer using hyperpolarized nuclei (Hyper-CEST), but for highly accurate experiments requires a polarizer and xenon infusion system optimized for such measurements. We present the design of a hyperpolarizer and xenon infusion system specifically designed to meet the requirements of Hyper-CEST measurements. One key element of this design is preventing rubidium runaway, a chain reaction induced by laser heating that prevents efficient utilization of high photon densities. Using thermocouples positioned along the pumping cell we identify the sources of heating and conditions for rubidium runaway to occur. We then demonstrate the effectiveness of actively cooling the optical cell to prevent rubidium runaway in a compact setup. This results in a 2-3-fold higher polarization than without cooling, allowing us to achieve a polarization of 25% at continuous flow rates of 9 ml/min of 129Xe. The simplicity of this design also allows it to be retrofitted to many existing polarizers. Combined with a direction infusion system that reduces shot-to-shot noise down to 0.56% we have captured Hyper-CEST spectra in unprecedented detail, allowing us to completely resolve peaks separated by just 1.62 ppm. Due to its high polarization and excellent stability, our design allows the comparison of underlying theories of host-guest systems with experiment at low concentrations, something extremely difficult with previous polarizers.

  4. Observing and preventing rubidium runaway in a direct-infusion xenon-spin hyperpolarizer optimized for high-resolution hyper-CEST (chemical exchange saturation transfer using hyperpolarized nuclei) NMR

    SciTech Connect

    Witte, C.; Kunth, M.; Rossella, F.; Schröder, L.

    2014-02-28

    Xenon is well known to undergo host-guest interactions with proteins and synthetic molecules. As xenon can also be hyperpolarized by spin exchange optical pumping, allowing the investigation of highly dilute systems, it makes an ideal nuclear magnetic resonance probe for such host molecules. The utility of xenon as a probe can be further improved using Chemical Exchange Saturation Transfer using hyperpolarized nuclei (Hyper-CEST), but for highly accurate experiments requires a polarizer and xenon infusion system optimized for such measurements. We present the design of a hyperpolarizer and xenon infusion system specifically designed to meet the requirements of Hyper-CEST measurements. One key element of this design is preventing rubidium runaway, a chain reaction induced by laser heating that prevents efficient utilization of high photon densities. Using thermocouples positioned along the pumping cell we identify the sources of heating and conditions for rubidium runaway to occur. We then demonstrate the effectiveness of actively cooling the optical cell to prevent rubidium runaway in a compact setup. This results in a 2–3-fold higher polarization than without cooling, allowing us to achieve a polarization of 25% at continuous flow rates of 9 ml/min of {sup 129}Xe. The simplicity of this design also allows it to be retrofitted to many existing polarizers. Combined with a direction infusion system that reduces shot-to-shot noise down to 0.56% we have captured Hyper-CEST spectra in unprecedented detail, allowing us to completely resolve peaks separated by just 1.62 ppm. Due to its high polarization and excellent stability, our design allows the comparison of underlying theories of host-guest systems with experiment at low concentrations, something extremely difficult with previous polarizers.

  5. Molecular Electronic Shift Registers

    NASA Technical Reports Server (NTRS)

    Beratan, David N.; Onuchic, Jose N.

    1990-01-01

    Molecular-scale shift registers eventually constructed as parts of high-density integrated memory circuits. In principle, variety of organic molecules makes possible large number of different configurations and modes of operation for such shift-register devices. Several classes of devices and implementations in some specific types of molecules proposed. All based on transfer of electrons or holes along chains of repeating molecular units.

  6. Protein structure prediction using global optimization by basin-hopping with NMR shift restraints

    NASA Astrophysics Data System (ADS)

    Hoffmann, Falk; Strodel, Birgit

    2013-01-01

    Computational methods that utilize chemical shifts to produce protein structures at atomic resolution have recently been introduced. In the current work, we exploit chemical shifts by combining the basin-hopping approach to global optimization with chemical shift restraints using a penalty function. For three peptides, we demonstrate that this approach allows us to find near-native structures from fully extended structures within 10 000 basin-hopping steps. The effect of adding chemical shift restraints is that the α and β secondary structure elements form within 1000 basin-hopping steps, after which the orientation of the secondary structure elements, which produces the tertiary contacts, is driven by the underlying protein force field. We further show that our chemical shift-restraint BH approach also works for incomplete chemical shift assignments, where the information from only one chemical shift type is considered. For the proper implementation of chemical shift restraints in the basin-hopping approach, we determined the optimal weight of the chemical shift penalty energy with respect to the CHARMM force field in conjunction with the FACTS solvation model employed in this study. In order to speed up the local energy minimization procedure, we developed a function, which continuously decreases the width of the chemical shift penalty function as the minimization progresses. We conclude that the basin-hopping approach with chemical shift restraints is a promising method for protein structure prediction.

  7. Absorption driven focus shift

    NASA Astrophysics Data System (ADS)

    Harrop, N.; Wolf, S.; Maerten, O.; Dudek, K.; Ballach, S.; Kramer, R.

    2016-03-01

    Modern high brilliance near infrared lasers have seen a tremendous growth in applications throughout the world. Increased productivity has been achieved by higher laser power and increased brilliance of lasers. Positive impacts on the performance and costs of parts are opposed to threats on process stability and quality, namely shift of focus position over time. A high initial process quality will be reduced by contamination of optics, eventually leading to a focus shift or even destruction of the optics. Focus analysis at full power of multi-kilowatt high brilliance lasers is a very demanding task because of high power densities in the spot and the high power load on optical elements. With the newly developed high power projection optics, the High-Power Micro-Spot Monitor High Brilliance (HP-MSM-HB) is able to measure focus diameter as low as 20 μm at power levels up to 10 kW at very low internal focus shift. A main driving factor behind thermally induced focus shift is the absorption level of the optical element. A newly developed measuring system is designed to determine the relative absorption level in reference to a gold standard. Test results presented show a direct correlation between absorption levels and focus shift. The ability to determine the absorption level of optical elements as well as their performance at full processing power before they are put to use, enables a high level of quality assurance for optics manufacturers and processing head manufacturers alike.

  8. Predicting catastrophic shifts.

    PubMed

    Weissmann, Haim; Shnerb, Nadav M

    2016-05-21

    Catastrophic shifts are known to pose a serious threat to ecology, and a reliable set of early warning indicators is desperately needed. However, the tools suggested so far have two problems. First, they cannot discriminate between a smooth transition and an imminent irreversible shift. Second, they aimed at predicting the tipping point where a state loses its stability, but in noisy spatial system the actual transition occurs when an alternative state invades. Here we suggest a cluster tracking technique that solves both problems, distinguishing between smooth and catastrophic transitions and to identify an imminent shift in both cases. Our method may allow for the prediction, and thus hopefully the prevention of such transitions, avoiding their destructive outcomes. PMID:26970446

  9. Isotope shift in chromium

    NASA Astrophysics Data System (ADS)

    Furmann, B.; Jarosz, A.; Stefańska, D.; Dembczyński, J.; Stachowska, E.

    2005-01-01

    Thirty-three spectral lines of chromium atom in the blue-violet region (425-465 nm) have been investigated with the method of laser-induced resonance fluorescence on an atomic beam. For all the lines, the isotope shifts for every pair of chromium isotopes have been determined. The lines can be divided into six groups, according to the configuration of the upper and lower levels. Electronic factors of the field shift and the specific mass shift ( Fik and MikSMS, respectively) have been evaluated and the values for each pure configuration involved have been determined. Comparison of the values Fik and MikSMS to the ab initio calculations results has been performed. The presence of crossed second order (CSO) effects has been observed.

  10. Shifting Up a Gear.

    ERIC Educational Resources Information Center

    Palmer, Martin

    1997-01-01

    Shift workers are often excluded from educational opportunities on and off the job. General education and leisure learning needs are addressed less than job-specific training needs. Providers should consider open/distance learning, creative marketing, targeted funding, and consortia of employer-developed programs. (SK)

  11. Eluding catastrophic shifts

    PubMed Central

    Villa Martín, Paula; Bonachela, Juan A.; Levin, Simon A.; Muñoz, Miguel A.

    2015-01-01

    Transitions between regimes with radically different properties are ubiquitous in nature. Such transitions can occur either smoothly or in an abrupt and catastrophic fashion. Important examples of the latter can be found in ecology, climate sciences, and economics, to name a few, where regime shifts have catastrophic consequences that are mostly irreversible (e.g., desertification, coral reef collapses, and market crashes). Predicting and preventing these abrupt transitions remains a challenging and important task. Usually, simple deterministic equations are used to model and rationalize these complex situations. However, stochastic effects might have a profound effect. Here we use 1D and 2D spatially explicit models to show that intrinsic (demographic) stochasticity can alter deterministic predictions dramatically, especially in the presence of other realistic features such as limited mobility or spatial heterogeneity. In particular, these ingredients can alter the possibility of catastrophic shifts by giving rise to much smoother and easily reversible continuous ones. The ideas presented here can help further understand catastrophic shifts and contribute to the discussion about the possibility of preventing such shifts to minimize their disruptive ecological, economic, and societal consequences. PMID:25825772

  12. Eluding catastrophic shifts.

    PubMed

    Villa Martín, Paula; Bonachela, Juan A; Levin, Simon A; Muñoz, Miguel A

    2015-04-14

    Transitions between regimes with radically different properties are ubiquitous in nature. Such transitions can occur either smoothly or in an abrupt and catastrophic fashion. Important examples of the latter can be found in ecology, climate sciences, and economics, to name a few, where regime shifts have catastrophic consequences that are mostly irreversible (e.g., desertification, coral reef collapses, and market crashes). Predicting and preventing these abrupt transitions remains a challenging and important task. Usually, simple deterministic equations are used to model and rationalize these complex situations. However, stochastic effects might have a profound effect. Here we use 1D and 2D spatially explicit models to show that intrinsic (demographic) stochasticity can alter deterministic predictions dramatically, especially in the presence of other realistic features such as limited mobility or spatial heterogeneity. In particular, these ingredients can alter the possibility of catastrophic shifts by giving rise to much smoother and easily reversible continuous ones. The ideas presented here can help further understand catastrophic shifts and contribute to the discussion about the possibility of preventing such shifts to minimize their disruptive ecological, economic, and societal consequences. PMID:25825772

  13. Trophic shift, not collapse

    USGS Publications Warehouse

    Madenjian, Charles P.; Rutherford, Edward S.; Stow, Craig A.; Roseman, Edward F.; He, Ji X.

    2013-01-01

    scientists who are closely monitoring Lake Huron’s food web, we believe that the ongoing changes are more accurately characterized as a trophic shift in which benthic pathways have become more prominent. While decreases in abundance have occurred for some species, others are experiencing improved reproduction resulting in the restoration of several important native species.

  14. E-2-Benzylidenebenzocycloalkanones. IV. Studies on transmission of substituent effects on 13C NMR chemical shifts of E-2-(X-benzylidene)-1-tetralones, and -benzosuberones. Comparison with the 13C NMR data of chalcones and E-2-(X-benzylidene)-1-indanones

    NASA Astrophysics Data System (ADS)

    Perjési, Pál; Linnanto, Juha; Kolehmainen, Erkki; Ősz, Erzsébet; Virtanen, Elina

    2005-04-01

    Single substituent parameter (SSP) and dual substituent parameter (DSP) analyses were applied to study the transmission of substituent effects on selected 13C NMR chemical shifts of the cyclic chalcone analogues, E-2-(4'-X-benzylidene)-1-tetralones ( 2) and E-2-(4'-X-benzylidene)-1-benzosuberones ( 3). In order to study how the geometry of the cyclic chalcone analogues affects the transmission of substituent effects similar investigations with the respective chalcones ( 4) were also performed. The results obtained earlier with the five-membered analogue E-2-(4'-X-benzylidene)-1-indanones ( 1) were also involved in the comparisons. Geometry optimization of the unsubstituted 1a, 2a, 3a and 4a as well as the substituted 2 and 3 was performed by ab initio quantum chemical calculations. Both SSP and DSP analyses reflected that resonance effects contribute more to the chemical shift of C-α (C2), while inductive effects primarily affect that of C-β (C10) of the enone moiety of all the four series. This latter effect, however, is far not as pronounced as that of the former one. It was found that DSP analysis data ( ρF and ρR values) of transmission of substituent effects on the δC2 data can serve as a measure of choice to study the conformation (planarity) of the investigated enones in the four series.

  15. A 3D-printed high power nuclear spin polarizer.

    PubMed

    Nikolaou, Panayiotis; Coffey, Aaron M; Walkup, Laura L; Gust, Brogan M; LaPierre, Cristen D; Koehnemann, Edward; Barlow, Michael J; Rosen, Matthew S; Goodson, Boyd M; Chekmenev, Eduard Y

    2014-01-29

    Three-dimensional printing with high-temperature plastic is used to enable spin exchange optical pumping (SEOP) and hyperpolarization of xenon-129 gas. The use of 3D printed structures increases the simplicity of integration of the following key components with a variable temperature SEOP probe: (i) in situ NMR circuit operating at 84 kHz (Larmor frequencies of (129)Xe and (1)H nuclear spins), (ii) <0.3 nm narrowed 200 W laser source, (iii) in situ high-resolution near-IR spectroscopy, (iv) thermoelectric temperature control, (v) retroreflection optics, and (vi) optomechanical alignment system. The rapid prototyping endowed by 3D printing dramatically reduces production time and expenses while allowing reproducibility and integration of "off-the-shelf" components and enables the concept of printing on demand. The utility of this SEOP setup is demonstrated here to obtain near-unity (129)Xe polarization values in a 0.5 L optical pumping cell, including ∼74 ± 7% at 1000 Torr xenon partial pressure, a record value at such high Xe density. Values for the (129)Xe polarization exponential build-up rate [(3.63 ± 0.15) × 10(-2) min(-1)] and in-cell (129)Xe spin-lattice relaxation time (T1 = 2.19 ± 0.06 h) for 1000 Torr Xe were in excellent agreement with the ratio of the gas-phase polarizations for (129)Xe and Rb (PRb ∼ 96%). Hyperpolarization-enhanced (129)Xe gas imaging was demonstrated with a spherical phantom following automated gas transfer from the polarizer. Taken together, these results support the development of a wide range of chemical, biochemical, material science, and biomedical applications. PMID:24400919

  16. A 3D-Printed High Power Nuclear Spin Polarizer

    PubMed Central

    Nikolaou, Panayiotis; Coffey, Aaron M.; Walkup, Laura L.; Gust, Brogan M.; LaPierre, Cristen D.; Koehnemann, Edward; Barlow, Michael J.; Rosen, Matthew S.; Goodson, Boyd M.; Chekmenev, Eduard Y.

    2015-01-01

    Three-dimensional printing with high-temperature plastic is used to enable spin exchange optical pumping (SEOP) and hyperpolarization of xenon-129 gas. The use of 3D printed structures increases the simplicity of integration of the following key components with a variable temperature SEOP probe: (i) in situ NMR circuit operating at 84 kHz (Larmor frequencies of 129Xe and 1H nuclear spins), (ii) <0.3 nm narrowed 200 W laser source, (iii) in situ high-resolution near-IR spectroscopy, (iv) thermoelectric temperature control, (v) retroreflection optics, and (vi) optomechanical alignment system. The rapid prototyping endowed by 3D printing dramatically reduces production time and expenses while allowing reproducibility and integration of “off-the-shelf” components and enables the concept of printing on demand. The utility of this SEOP setup is demonstrated here to obtain near-unity 129Xe polarization values in a 0.5 L optical pumping cell, including ~74 ± 7% at 1000 Torr xenon partial pressure, a record value at such high Xe density. Values for the 129Xe polarization exponential build-up rate [(3.63 ± 0.15) × 10−2 min−1] and in-cell 129Xe spin−lattice relaxation time (T1 = 2.19 ± 0.06 h) for 1000 Torr Xe were in excellent agreement with the ratio of the gas-phase polarizations for 129Xe and Rb (PRb ~ 96%). Hyperpolarization-enhanced 129Xe gas imaging was demonstrated with a spherical phantom following automated gas transfer from the polarizer. Taken together, these results support the development of a wide range of chemical, biochemical, material science, and biomedical applications. PMID:24400919

  17. Energy phase shift as mechanism for catalysis

    NASA Astrophysics Data System (ADS)

    Beke-Somfai, Tamás; Feng, Bobo; Nordén, Bengt

    2012-05-01

    Catalysts are agents that by binding reactant molecules lower the energy barriers to chemical reaction. After reaction the catalyst is regenerated, its unbinding energy recruited from the environment, which is associated with an inevitable loss of energy. We show that combining several catalytic sites to become energetically and temporally phase-shifted relative to each other provides a possibility to sustain the overall reaction by internal 'energy recycling', bypassing the need for thermal activation, and in principle allowing the system to work adiabatically. Using an analytical model for superimposed, phase-shifted potentials of F1-ATP synthase provides a description integrating main characteristics of this rotary enzyme complex.

  18. Problematic chemical shifts of a fluorine-labeled surfactant and oil in some microemulsion systems. [Soap is potassium 11-(2,2,2-trifluoroethoxy)undecanoate oil is 1-(2,2,2-trifluoroethoxy)hexane or a mixture of this material with heptane

    SciTech Connect

    Muller, N.

    1982-05-27

    Fluorine chemical shifts are reported for water/oil/soap/butanol microemulsions in which the soap is potassium 11-(2,2,2-trifluoroethoxy)undecanoate and the oil is 1-(2,2,2-trifluoroethoxy)hexane or a mixture of this material with heptane. In many of the solutions the two fluorinated compounds appear to have identical microenvironments. This reinforces arguments presented recently by others to the effect that microemulsions do not always contain distinct oil-rich and water-rich domains separated by a well-defined interfacial layer.

  19. Redox-dependent structure change and hyperfine nuclear magnetic resonance shifts in cytochrome c

    SciTech Connect

    Feng, Yiquing; Roder, H.; Englander, S.W. )

    1990-04-10

    Proton nuclear magnetic resonance assignments for reduced and oxidized equine cytochrome c show that many individual protons exhibit different chemical shifts in the two protein forms, reflecting diamagnetic shift effects due to structure change, and in addition contact and pseudocontact shifts that occur only in the paramagnetic oxidized form. To evaluate the chemical shift differences for structure change, the authors removed the pseudocontact shift contribution by a calculation based on knowledge of the electron spin g tensor. The g-tensor calculation, when repeated using only 12 available C{sub {alpha}}H proton resonances for cytochrom c from tuna, proved to be remarkably stable. The derived g tensor was then used together with spatial coordinates for the oxidized form to calculate the pseudocontact shift contribution to proton resonances at 400 identifiable sites throughout the protein, so that the redox-dependent chemical shift discrepancy, could be evaluated. Large residual changes in chemical shift define the Fermi contact shifts, where are found as expected to be limited to the immediate covalent structure of the heme and its ligands and to be asymmetrically distributed over the heme. The chemical shift discrepancies observed appear in the main to reflect structure-dependent diamagnetic shifts rather than hyperfine effects due to displacements in the pseudocontact shift field. Although 51 protons in 29 different residues exhibit significant chemical shift changes, the general impressions one of small structural adjustments to redox-dependent strain rather than sizeable structural displacements or rearrangements.

  20. Ambiguous red shifts

    NASA Astrophysics Data System (ADS)

    Wulfman, Carl E.

    2010-12-01

    A one-parameter conformal invariance of Maxwell's equations allows the wavelengths of electromagnetic waves to change as they propagate, and do so even in otherwise field-free space. This produces an ambiguity in interpretations of stellar red shifts. Experiments that will determine the value of the group parameter, and thereby remove the ambiguity, are proposed. They are based on an analysis of the anomalous frequency shifts uncovered in the Pioneer 10 and 11 spacecraft studies, and physical interpretation of an isomorphism discovered by E.L. Hill. If the group parameter is found to be non-zero, Hubble's relations will have to be reinterpreted and space-time metrics will have to be altered. The cosmological consequences of the transformations are even more extensive because, though they change frequencies they do not alter the energy and momentum conservation laws of classical and quantum-electrodynamical fields established by Cunningham and by Białynicki-Birula.

  1. Shifts that divide population

    NASA Astrophysics Data System (ADS)

    Muneepeerakul, Rachata; Qubbaj, Murad; Aggarwal, Rimjhim; Anderies, John M.; Janssen, Marco

    2014-05-01

    How does a population of organisms in an ecosystem or of people in a society respond to rapid shifts in the environment? Answers to this question are critical to our ability to anticipate and cope with a changing ecohydrological system. We have developed a generic model of adaptation mechanisms, based on replicator dynamics, in which we derive a simple and insightful threshold condition that separates two important types of responses: 'cohesive transition' in which the whole population changes gradually together, and 'population-dividing transition' in which the population splits into two groups with one eventually dominating the other. The threshold depends on the magnitude of the shift and the shape of the fitness landscape. Division in populations can fundamentally alter the functioning of and induce subsequent feedbacks within the system; knowing the condition that gives rise to such division is thus fundamentally important.

  2. The shifted penalty method

    NASA Astrophysics Data System (ADS)

    Zavarise, Giorgio

    2015-07-01

    The method presented here is a variation of the classical penalty one, suited to reduce penetration of the contacting surfaces. The slight but crucial modification concerns the introduction of a shift parameter that moves the minimum point of the constrained potential toward the exact value, without any penalty increase. With respect to the classical augmentation procedures, the solution improvement is embedded within the original penalty contribution. The problem is almost consistently linearized, and the shift is updated before each Newton's iteration. However, adding few iterations, with respect to the original penalty method, a reduction of the penetration of several orders of magnitude can be achieved. The numerical tests have shown very attractive characteristics and very stable solution paths. This permits to foresee a wide area of applications, not only in contact mechanics, but for any problem, like e.g. incompressible materials, where a penalty contribution is required.

  3. Label-free surface-enhanced infrared spectro-electro-chemical analysis of the Redox potential shift of cytochrome c complexed with a cardiolipin-containing lipid membrane of varied composition

    NASA Astrophysics Data System (ADS)

    Liu, Li; Wu, Lie; Zeng, Li; Jiang, Xiu-E.

    2015-12-01

    In this study, a lipid membrane was fabricated by fusing cardiolipin-phosphatidylcholine (CL_PC, 1:4) vesicles onto a hydrophobic surface of 1-dodecanethiol (DT) preadsorbed on a nanostructured gold film. By changing the concentration of the DT adsorption solution, we constructed a series of CL_PC-DT bilayers with different hydrophobicity to study the effects of lipid membrane characteristics on the adsorption conformation of cytochrome c (Cyt c). Electrochemical analysis showed that the formal potential is 0.24 V for Cyt c-CL_PC-DT(10), 0.2 V for Cyt c-CL_PC-DT(20), and 0.16 V for Cyt c-CL_PC-DT(40) — a gradual positive shift with the decreasing DT concentration — relative to the potential of native cyt c (0.02 V). Potential-induced surface-enhanced infrared adsorption difference spectroscopy revealed that the gradual positive shift of the formal potential of CL-bound cyt c is determined by the environment with the gradually lowered dielectric constant for the heme cofactor in CL-bound cyt c (Fe3+). Project supported by the National Natural Science Foundation of China (Grant Nos. 91227114, 21322510, and 21105097), the China Postdoctoral Science Foundation (Grant No. 2013M530998), the Natural Science Foundation of Jilin Province, China (Grant No. 201215092), and the President Funds of the Chinese Academy of Sciences.

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

    PubMed

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

    2007-12-01

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

  5. Shifted genus expanded W ∞ algebra and shifted Hurwitz numbers

    NASA Astrophysics Data System (ADS)

    Zheng, Quan

    2016-05-01

    We construct the shifted genus expanded W ∞ algebra, which is isomorphic to the central subalgebra A ∞ of infinite symmetric group algebra and to the shifted Schur symmetrical function algebra Λ* defined by Okounkov and Olshanskii. As an application, we get some differential equations for the generating functions of the shifted Hurwitz numbers; thus, we can express the generating functions in terms of the shifted genus expanded cut-and-join operators.

  6. Transmission shift control assembly

    SciTech Connect

    Dzioba, D.L.

    1989-04-18

    This patent describes a transmission shift control assembly mounted on a steering column having a longitudinal axis comprising: bracket means secured to the steering column; transmission shift cable means having a portion secured to the bracket means and a portion linearly movable relative to the secured portion; mounting means on the bracket cable drive arm means having an axis and being rotatably mounted on the rotary axis on the mounting means oblique to the longitudinal axis and including a cable connecting portion secured to the movable portion of the cable means and lever mounting means adjacent the mounting means; operator control means including lever means, pin means for pivotally mounting the lever means on the lever mounting means on an axis substantially perpendicular to the rotary axis and positioning arm means formed on the lever means and extending from the pin means; and detent gate means disposed on the bracket means in position to abut the positioning arm means for limiting the extent of pivotal movement of the lever means.

  7. Shifted nondiffractive Bessel beams

    NASA Astrophysics Data System (ADS)

    Kovalev, Alexey A.; Kotlyar, Victor V.; Porfirev, Alexey A.

    2015-05-01

    Nondiffractive Bessel beams are well known to have infinite energy and infinite orbital angular momentum (OAM). However, when normalized to unity of energy, their OAM is finite. In this work, we derive an analytical relationship for calculating the normalized OAM of the superposition of off-axis Bessel beams characterized by the same topological charge. We show that if the constituent beams of the superposition have real-valued weight coefficients, the total OAM of the superposition of the Bessel beams equals that of an individual nonshifted Bessel beam. This property enables generating nondiffractive beams with different intensity distributions but identical OAM. The superposition of a set of identical Bessel beams centered on an arbitrary-radius circle is shown to be equivalent to an individual constituent Bessel beam put in the circle center. As a result of a complex shift of the Bessel beam, the transverse intensity distribution and OAM of the beam are also shown to change. We show that, in the superposition of two or more complex-shifted Bessel beams, the OAM may remain unchanged, while the intensity distribution is changed. Numerical simulation is in good agreement with theory.

  8. NMR shifts for polycyclic aromatic hydrocarbons from first-principles

    SciTech Connect

    Thonhauser, Timo; Ceresoli, Davide; Marzari, Nicola N.

    2009-09-03

    We present first-principles, density-functional theory calculations of the NMR chemical shifts for polycyclic aromatic hydrocarbons, starting with benzene and increasing sizes up to the one- and two-dimensional infinite limits of graphene ribbons and sheets. Our calculations are performed using a combination of the recently developed theory of orbital magnetization in solids, and a novel approach to NMR calculations where chemical shifts are obtained from the derivative of the orbital magnetization with respect to a microscopic, localized magnetic dipole. Using these methods we study on equal footing the 1H and 13C shifts in benzene, pyrene, coronene, in naphthalene, anthracene, naphthacene, and pentacene, and finally in graphene, graphite, and an infinite graphene ribbon. Our results show very good agreement with experiments and allow us to characterize the trends for the chemical shifts as a function of system size.

  9. Shifting epidemiology of Flaviviridae.

    PubMed

    Petersen, Lyle R; Marfin, Anthony A

    2005-04-01

    The dengue, West Nile, Japanese encephalitis and yellow fever viruses are important mosquito-borne viruses whose epidemiology is shifting in response to changing societal factors, such as increasing commerce, urbanization of rural areas, and population growth. All four viruses are expanding geographically, as exemplified by the emergence of West Nile virus in the Americas and Japanese encephalitis virus in Australasia. The large, recent global outbreaks of severe neurological disease caused by West Nile virus, the increasing frequency of dengue hemorrhagic fever outbreaks in the Americas, and the emergence of yellow fever virus vaccination-associated viscerotropic disease, are new clinical epidemiologic trends. These worrisome epidemiologic trends will probably continue in coming decades, as a reversal of their societal and biological drivers is not in sight. Nevertheless, the substantial reductions in Japanese encephalitis virus incidence resulting from vaccination programs and economic development in some Asian countries provide some encouragement within this overall guarded outlook. PMID:16225801

  10. Phase shifting diffraction interferometer

    DOEpatents

    Sommargren, Gary E.

    1996-01-01

    An interferometer which has the capability of measuring optical elements and systems with an accuracy of .lambda./1000 where .lambda. is the wavelength of visible light. Whereas current interferometers employ a reference surface, which inherently limits the accuracy of the measurement to about .lambda./50, this interferometer uses an essentially perfect spherical reference wavefront generated by the fundamental process of diffraction. This interferometer is adjustable to give unity fringe visibility, which maximizes the signal-to-noise, and has the means to introduce a controlled prescribed relative phase shift between the reference wavefront and the wavefront from the optics under test, which permits analysis of the interference fringe pattern using standard phase extraction algorithms.

  11. Phase shifting interferometer

    DOEpatents

    Sommargren, G.E.

    1999-08-03

    An interferometer is disclosed which has the capability of measuring optical elements and systems with an accuracy of {lambda}/1000 where {lambda} is the wavelength of visible light. Whereas current interferometers employ a reference surface, which inherently limits the accuracy of the measurement to about {lambda}/50, this interferometer uses an essentially perfect spherical reference wavefront generated by the fundamental process of diffraction. Whereas current interferometers illuminate the optic to be tested with an aberrated wavefront which also limits the accuracy of the measurement, this interferometer uses an essentially perfect spherical measurement wavefront generated by the fundamental process of diffraction. This interferometer is adjustable to give unity fringe visibility, which maximizes the signal-to-noise, and has the means to introduce a controlled prescribed relative phase shift between the reference wavefront and the wavefront from the optics under test, which permits analysis of the interference fringe pattern using standard phase extraction algorithms. 11 figs.

  12. Phase shifting interferometer

    DOEpatents

    Sommargren, Gary E.

    1999-01-01

    An interferometer which has the capability of measuring optical elements and systems with an accuracy of .lambda./1000 where .lambda. is the wavelength of visible light. Whereas current interferometers employ a reference surface, which inherently limits the accuracy of the measurement to about .lambda./50, this interferometer uses an essentially perfect spherical reference wavefront generated by the fundamental process of diffraction. Whereas current interferometers illuminate the optic to be tested with an aberrated wavefront which also limits the accuracy of the measurement, this interferometer uses an essentially perfect spherical measurement wavefront generated by the fundamental process of diffraction. This interferometer is adjustable to give unity fringe visibility, which maximizes the signal-to-noise, and has the means to introduce a controlled prescribed relative phase shift between the reference wavefront and the wavefront from the optics under test, which permits analysis of the interference fringe pattern using standard phase extraction algorithms.

  13. Phase shifting diffraction interferometer

    DOEpatents

    Sommargren, G.E.

    1996-08-29

    An interferometer which has the capability of measuring optical elements and systems with an accuracy of {lambda}/1000 where {lambda} is the wavelength of visible light. Whereas current interferometers employ a reference surface, which inherently limits the accuracy of the measurement to