Science.gov

Sample records for 129xe chemical shift

  1. 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.

  2. 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

  3. 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

  4. 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

  5. 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.

  6. 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.

  7. The Collectivity in Csr 129Xe+129Xe Collisions

    NASA Astrophysics Data System (ADS)

    Xie, Fei; Wu, Kejun; Liu, Feng

    The Heavy Ion Research Facility in Lanzhou (HIRFL) - Cooler Storage Ring (CSR), which can gather few hundreds MeV/nucleon for heavy ion beam energy in the external-target experiments, could make a significant contribution in studying the property of dense matter. By using a Relativistic Transport Model(ART1.0), we study the collectivity of identified hadrons in 129Xe+129Xe collisions in CSR energy regions. Our investigation indicates that the anisotropic flow reaches its extremum around 500 MeV/nucleon of beam energy. The system size and EOS dependence on anisotropic flow show that directed flow is very sensitive to the equation of state.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Elucidation of meso- and microporosity in soil components with 129-Xe NMR spectroscopy of adsorbed xenon

    NASA Astrophysics Data System (ADS)

    Filimonova, Svetlana; Nossov, Andrey; Knicker, Heike; Kögel-Knabner, Ingrid

    2010-05-01

    Soil meso- and micropores (2-50 nm and <2 nm) are usually studied with the use of common adsorption methods. As a complementary technique, 129-Xe NMR spectroscopy of adsorbed xenon was only recently suggested for the use in soil science. In this present study, we applied both conventional, i.e. thermally polarised (TP), and hyperpolarised (HP) 129-Xe NMR for elucidating pore environments of a series of samples representing porous soil constituents. Aluminium (hydr)oxides, Al2O3 and AlOOH, both pure and subjected to the sorption of dissolved organic matter (DOM) were chosen as model mineral systems. Charcoals were used for understanding adsorption behaviour of xenon within organic polymeric structures formed by thermally altered bio-macromolecules. Natural soil particle size fractions were obtained from a non-allophanic Andosol and from Arenosol, i.e. soils containing charred residues and also characterised by a high content of Al oxides (case of the Andosol). DOM sorption on the studied Al oxides occurred inhomogeneously as it was inferred from the existence of the "empty" pores and the pores coated with OM. The latter were evidenced by the different Xe adsorption enthalpies estimated from the temperature dependences of the chemical shift. The increased sensitivity of the HP 129-Xe NMR allowed us detecting micropores in the charcoals, where the N2 adsorption method underestimated porosity due to the restricted diffusion of N2 at 77 K. The observed differences between the HP and TP 129-Xe patterns were explained by the slow diffusion of xenon within an interconnected but highly constricted pore system of the charcoals. The estimated width of those constricted pore openings was of the order of one or two diameters of the Xe atom. Similar "bottle neck" effects may also exist in the natural soil particle size fractions, as it was inferred from the increased pore access for Xe adsorption performed at elevated pressures (2-4 bar). The unusually large 129-Xe shifts (up to

  13. NOTE: Detection of radiation effects in polymer gel dosimeters using 129Xe NMR

    NASA Astrophysics Data System (ADS)

    Joers, J. M.; Fong, P. M.; Gore, J. C.

    2006-01-01

    Polymer gel dosimeters consist of monomers, with or without cross-linking agents, dispersed in a gel. Upon exposure to ionizing radiation, polymerization proceeds within the gel matrix, thereby changing several measurable physical properties that can then be related quantitatively to absorbed dose. Several previous studies have examined how various nuclear magnetic resonance (NMR) properties, such as the relaxation rates of water protons, change with dose, and magnetic resonance imaging (MRI) has been used successfully to measure three-dimensional dose distributions in irradiated polymer gels. Here we report our first observations of the manner in which the chemical shift of xenon gas (129Xe) dissolved in a gel changes with absorbed dose, and we introduce the potential use of high resolution xenon NMR spectra for understanding better the dose response of gels. 129Xe possesses a large chemical shift range and xenon spectra are sensitive to subtle changes in the physical and chemical environments in which the gas is dissolved. For doses ranging from 0 Gy to 40 Gy we found that the mean chemical shift of 129Xe was linearly related to dose, and that the gel dosimeter could be described in terms of a two-component model undergoing fast exchange. We found no evidence of radiation damage to the gelatin matrix at doses between 0 Gy and 40 Gy. At 40 Gy, the fast-exchange model begins to break down, and distinct gelatin and poly(methacrylate) resonances are observed at higher doses. High resolution NMR measurements of xenon provide a novel method for probing radiation dose effects in irradiated polymer gels.

  14. Relaxation Mechanisms in Hyperpolarized Polycrystalline ^129Xe

    NASA Astrophysics Data System (ADS)

    Samuelson, G.; Su, T.; Saam, B.

    2002-10-01

    Through spin exchange with optically polarized Rb vapor, it is possible to achieve upwards of 30% nuclear spin polarization in ^129Xe and a corresponding NMR signal some 5 orders of magnitude stronger than typical thermally polarized ^129Xe. Due to such a strong signal, hyperpolarized ^129Xe is being used for several leading-edge technologies (eg. biochemical spectroscopy, MRI, and polarization transfer). We have measured the nuclear spin relaxation rate of polycrystalline hyperpolarized ^129Xe at 77K (well below the freezing point of 160K) in a magnetic field of only a few Gauss and have observed that the hyperpolarization completely survives the freezing process. Furthermore, in this regime we have observed non-exponential spin relaxation that depends strongly on magnetic field, isotopic concentration (between ^129Xe and ^131Xe) and differences in crystallite formation. We present a simple spin-diffusion model that fits and explains the features of the data. Our results agree with the hypothesis that at low fields and temperatures the dominant spin relaxation mechanism is cross-relaxation with ^131Xe on the surface of the crystallites (Gatzke, et al., PRL b70, 690 (1993)).

  15. Robust solid 129Xe longitudinal relaxation times

    NASA Astrophysics Data System (ADS)

    Limes, M. E.; Ma, Z. L.; Sorte, E. G.; Saam, B.

    2016-09-01

    We find that if solid xenon is formed from liquid xenon, denoted "ice," there is a 10% increase in 129Xe longitudinal relaxation T1 time (taken at 77 K and 2 T) over a trickle-freeze formation, denoted "snow." Forming xenon ice also gives an unprecedented reproducibility of 129Xe T1 measurements across a range of 77-150 K. This temperature dependence roughly follows the theory of spin rotation mediated by Raman scattering of harmonic phonons, though it results in a smaller-than-predicted spin-rotation coupling strength cK 0/h . Enriched ice 129Xe T1 experiments show no isotopic dependence of bulk relaxation mechanisms at 77 K and at kilogauss fields.

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

    PubMed

    Makulski, Włodzimierz

    2015-04-01

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

  17. T1 of 129Xe in Blood and the Role of Oxygenation

    NASA Astrophysics Data System (ADS)

    Albert, Mitchell S.; Kacher, Daniel F.; Balamore, Dilip; Venkatesh, Arvind K.; Jolesz, Ferenc A.

    1999-09-01

    In previous experiments by the authors, in which hyperpolarized 129Xe was dissolved in fresh blood samples, the T1 was found to be strongly dependent on the oxygenation level, the values increasing with oxygenation: T1 was about 4 s in deoxygenated samples and about 13 s in oxygenated samples. C. H. Tseng et al. (1997, J. Magn. Reson. 126, 79-86), on the other hand, recently reported extremely long T1 values using hyperpolarized 129Xe to create a "blood foam" and found that oxygenation decreased T1. In their experiments, the continual and rapid exchange of hyperpolarized 129Xe between the gas phase (within blood-foam bubbles) and the dissolved phase (in the skin of the bubbles) necessitated a complicated analysis to extract the effective blood T1. In the present study, the complications of hyperpolarized 129Xe exchange dynamics have been avoided by using thermally polarized 129Xe dissolved in whole blood and in suspensions of lysed red blood cells (RBC). During T1 measurements in whole blood, the samples were gently and continuously agitated, for the entire course of the experiment, to avert sedimentation. Oxygenation was found to markedly increase the T1 of 129Xe in blood, as originally measured, and it shifts the RBC resonance to a higher frequency. Carbon monoxide has a similar but somewhat stronger effect.

  18. 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.

  19. Live 129I-129Xe dating

    NASA Technical Reports Server (NTRS)

    Marti, K.

    1986-01-01

    A technique of cosmic ray exposure age dating using cosmic ray produced I-129 and Xe-129 components is discussed. The live I-129 - Xe-129 method provides an ideal monitor for cosmic ray flux variations on the 10(7)y - 10(8)y time-scale. It is based on low-energy neutron reactions on Te, and these data, when coupled to those from other methods, may facilitate the detection of complex exposure histories.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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.

  9. 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.

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

    PubMed Central

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

    2016-01-01

    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. PMID:26961001

  11. 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

  12. 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.

  13. 129Xe NMR studies of biochar made from biobased materials

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biochar is created by pyrolysis of biobased materials under controlled oxidative environments. The product is charcoal-like and can be used as filtration medium, sequestrant for metallic ions, soil conditioner, and other applications. In our work we have found 129Xe NMR to be an excellent technique...

  14. 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

  15. 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

  16. Excess /sup 129/Xe in terrestrial samples: A non-primordial hypothesis

    SciTech Connect

    Caffee, M.W.; Hudson, G.B.

    1987-03-01

    Excesses of /sup 129/Xe relative to the isotopic composition in air are observed in some terrestrial samples. Traditionally these /sup 129/Xe excesses have been thought to be related to /sup 129/I that was present in abundance in the early solar system. We propose an alternative hypothesis to explain terrestrial /sup 129/Xe excesses based on the production of /sup 129/I from the spontaneous fission of /sup 238/U.

  17. (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

  18. Behavior of a thermotropic nematic liquid crystal confined to controlled pore glasses as studied by 129Xe NMR spectroscopy.

    PubMed

    Tallavaara, Pekka; Telkki, Ville-Veikko; Jokisaari, Jukka

    2006-11-01

    The behavior of nematic liquid crystal (LC) Merck Phase 4 confined to controlled pore glass (CPG) materials was investigated using 129Xe nuclear magnetic resonance (NMR) spectroscopy of xenon gas dissolved in the LC. The average pore diameters of the materials varied from 81 to 2917 A, and the measurements were carried out within a wide temperature range (approximately 185-370 K). The spectra contain lots of information about the effect of confinement on the phase of the LC. The theoretical model of shielding of noble gases dissolved in liquid crystals on the basis of pairwise additivity approximation was applied to the analysis of the spectra. When pore diameter is small, smaller than approximately 150 A, xenon experiences on average an isotropic environment inside the pore, and no nematic-isotropic phase transition is observed. When the size is larger than approximately 150 A, nematic phase is observed, and the LC molecules are oriented along pore axis. The orientational order parameter of the LC, S, increases with increasing pore size. In the largest pores, the orientation of the molecules deviates from the pore axis direction to magnetic field direction, which implies that the size of the pores (approximately 3000 A) is close to magnetic coherence length. The decrease of magnetic coherence length with increasing temperature is clearly seen from the spectra. When the sample is cooled rapidly by immersing it in liquid nitrogen, xenon atoms do not squeeze out from the solid, as they do during gradual freezing, but they are occluded inside the solid lattice, and their chemical shift is very sensitive to crystal structure. This makes it possible to study the effect of confinement on the solid phases. According to the measured 129Xe NMR spectra, possibly three different solid phases are observed from bulk liquid crystal in the used temperature region. The same is also seen from the samples containing larger pores (pore size larger than approximately 500 A), and the

  19. 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

  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. 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.

  2. 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.

  3. Finite element modeling of 129Xe diffusive gas exchange NMR in the human alveoli

    NASA Astrophysics Data System (ADS)

    Stewart, Neil J.; Parra-Robles, Juan; Wild, Jim M.

    2016-10-01

    Existing models of 129Xe diffusive exchange for lung microstructural modeling with time-resolved MR spectroscopy data have considered analytical solutions to one-dimensional, homogeneous models of the lungs with specific assumptions about the alveolar geometry. In order to establish a model system for simulating the effects of physiologically-realistic changes in physical and microstructural parameters on 129Xe exchange NMR, we have developed a 3D alveolar capillary model for finite element analysis. To account for the heterogeneity of the alveolar geometry across the lungs, we have derived realistic geometries for finite element analysis based on 2D histological samples and 3D micro-CT image volumes obtained from ex vivo biopsies of lung tissue from normal subjects and patients with interstitial lung disease. The 3D alveolar capillary model permits investigation of the impact of alveolar geometrical parameters and diffusion and perfusion coefficients on the in vivo measured 129Xe CSSR signal response. The heterogeneity of alveolar microstructure that is accounted for in image-based models resulted in considerable alterations to the shape of the 129Xe diffusive uptake curve when compared to 1D models. Our findings have important implications for the future design and optimization of 129Xe MR experiments and in the interpretation of lung microstructural changes from this data.

  4. Finite element modeling of (129)Xe diffusive gas exchange NMR in the human alveoli.

    PubMed

    Stewart, Neil J; Parra-Robles, Juan; Wild, Jim M

    2016-10-01

    Existing models of (129)Xe diffusive exchange for lung microstructural modeling with time-resolved MR spectroscopy data have considered analytical solutions to one-dimensional, homogeneous models of the lungs with specific assumptions about the alveolar geometry. In order to establish a model system for simulating the effects of physiologically-realistic changes in physical and microstructural parameters on (129)Xe exchange NMR, we have developed a 3D alveolar capillary model for finite element analysis. To account for the heterogeneity of the alveolar geometry across the lungs, we have derived realistic geometries for finite element analysis based on 2D histological samples and 3D micro-CT image volumes obtained from ex vivo biopsies of lung tissue from normal subjects and patients with interstitial lung disease. The 3D alveolar capillary model permits investigation of the impact of alveolar geometrical parameters and diffusion and perfusion coefficients on the in vivo measured (129)Xe CSSR signal response. The heterogeneity of alveolar microstructure that is accounted for in image-based models resulted in considerable alterations to the shape of the (129)Xe diffusive uptake curve when compared to 1D models. Our findings have important implications for the future design and optimization of (129)Xe MR experiments and in the interpretation of lung microstructural changes from this data.

  5. Finite element modeling of (129)Xe diffusive gas exchange NMR in the human alveoli.

    PubMed

    Stewart, Neil J; Parra-Robles, Juan; Wild, Jim M

    2016-10-01

    Existing models of (129)Xe diffusive exchange for lung microstructural modeling with time-resolved MR spectroscopy data have considered analytical solutions to one-dimensional, homogeneous models of the lungs with specific assumptions about the alveolar geometry. In order to establish a model system for simulating the effects of physiologically-realistic changes in physical and microstructural parameters on (129)Xe exchange NMR, we have developed a 3D alveolar capillary model for finite element analysis. To account for the heterogeneity of the alveolar geometry across the lungs, we have derived realistic geometries for finite element analysis based on 2D histological samples and 3D micro-CT image volumes obtained from ex vivo biopsies of lung tissue from normal subjects and patients with interstitial lung disease. The 3D alveolar capillary model permits investigation of the impact of alveolar geometrical parameters and diffusion and perfusion coefficients on the in vivo measured (129)Xe CSSR signal response. The heterogeneity of alveolar microstructure that is accounted for in image-based models resulted in considerable alterations to the shape of the (129)Xe diffusive uptake curve when compared to 1D models. Our findings have important implications for the future design and optimization of (129)Xe MR experiments and in the interpretation of lung microstructural changes from this data. PMID:27526397

  6. A novel Cs-(129)Xe atomic spin gyroscope with closed-loop Faraday modulation.

    PubMed

    Fang, Jiancheng; Wan, Shuangai; Qin, Jie; Zhang, Chen; Quan, Wei; Yuan, Heng; Dong, Haifeng

    2013-08-01

    We report a novel Cs-(129)Xe atomic spin gyroscope (ASG) with closed-loop Faraday modulation method. This ASG requires approximately 30 min to start-up and 110 °C to operate. A closed-loop Faraday modulation method for measurement of the optical rotation was used in this ASG. This method uses an additional Faraday modulator to suppress the laser intensity fluctuation and Faraday modulator thermal induced fluctuation. We theoretically and experimentally validate this method in the Cs-(129)Xe ASG and achieved a bias stability of approximately 3.25 °∕h.

  7. 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.

  8. Optimized production of hyperpolarized 129Xe at 2 bars for in vivo lung magnetic resonance imaging

    NASA Astrophysics Data System (ADS)

    Norquay, Graham; Parnell, Steven R.; Xu, Xiaojun; Parra-Robles, Juan; Wild, Jim M.

    2013-01-01

    In this work, the production rate of a spin-exchange optical pumping 129Xe gas polarizer was optimized for routine generation of hyperpolarized 129Xe for in vivo lung MRI. This system uses a narrow (˜ 0.1 nm linewidth), tuneable external cavity laser (operating at ˜25 W) for SEOP of 3% gas mixtures of Xe inside a mid-pressure (2 bars) cell of 491 cm3 volume. Under this regime, theoretical and experimentally measured 129Xe polarizations were calculated to be 24% and 12%, respectively, for a gas flow rate of 300 sccm and a cell temperature of 373 K. The photon efficiency was evaluated, yielding theoretical and experimental values of 0.039 and 0.046, respectively. The theoretical efficiency was calculated from spin-exchange and spin-destruction cross sections and the experimental photon efficiency was measured under flow for a gas-cell residency time equal to an empirically determined spin-exchange time of 45 s. In addition, details of the Xe freeze-out process were analyzed with a model of polarization decay during Xe accumulation in the frozen phase, where a T1 of 87 ± 2 min was observed. To demonstrate the system's application, in vivo lung magnetic resonance images (signal-to-noise ratio ˜ 50 from a voxel of 15 mm× 4 mm× 4 mm) were acquired using modest volumes (<400 ml) of isotopically enriched (86% 129Xe) Xe gas polarized to >10%. Despite the experimental polarization being a factor of 2 lower than the predicted polarization for typical operating parameters, the system is close to the theoretical photon efficiency and the system has so far produced polarized gas for more than 100 in vivo 129Xe lung imaging studies.

  9. 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.

  10. 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

  11. Cell uptake of a biosensor detected by hyperpolarized 129Xe NMR: the transferrin case.

    PubMed

    Boutin, Céline; Stopin, Antoine; Lenda, Fatimazohra; Brotin, Thierry; Dutasta, Jean-Pierre; Jamin, Nadège; Sanson, Alain; Boulard, Yves; Leteurtre, François; Huber, Gaspard; Bogaert-Buchmann, Aurore; Tassali, Nawal; Desvaux, Hervé; Carrière, Marie; Berthault, Patrick

    2011-07-01

    For detection of biological events in vitro, sensors using hyperpolarized (129)Xe NMR can become a powerful tool, provided the approach can bridge the gap in sensitivity. Here we propose constructs based on the non-selective grafting of cryptophane precursors on holo-transferrin. This biological system was chosen because there are many receptors on the cell surface, and endocytosis further increases this density. The study of these biosensors with K562 cell suspensions via fluorescence microscopy and (129)Xe NMR indicates a strong interaction, as well as interesting features such as the capacity of xenon to enter the cryptophane even when the biosensor is endocytosed, while keeping a high level of polarization. Despite a lack of specificity for transferrin receptors, undoubtedly due to the hydrophobic character of the cryptophane moiety that attracts the biosensor into the cell membrane, these biosensors allow the first in-cell probing of biological events using hyperpolarized xenon. PMID:21605977

  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. HyperCEST detection of a 129Xe-based contrast agent composed of cryptophane-A molecular cages on a bacteriophage scaffold.

    PubMed

    Stevens, Todd K; Palaniappan, Krishnan K; Ramirez, R Matthew; Francis, Matthew B; Wemmer, David E; Pines, Alex

    2013-05-01

    A hyperpolarized 129Xe contrast agent composed of many cryptophane-A molecular cages assembled on an M13 bacteriophage has been demonstrated. Saturation of xenon bound in the large number of cryptophane cages is transferred to the pool of aqueous-solvated xenon via chemical exchange, resulting in efficient generation of hyperCEST contrast. No significant loss of contrast per cryptophane cage was observed for the multivalent phage when compared with unscaffolded cryptophane. Detection of this phage-based hyperCEST agent is reported at concentrations as low as 230 fM, representing the current lower limit for NMR/MRI-based contrast agents.

  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. Investigation of the microporous structure of clays and pillared clays by {sup 129}Xe NMR.

    SciTech Connect

    Tsaio, C.-J.; Carrado, K. A.; Botto, R. E.; Chemistry

    1998-04-01

    {sup 129}Xe NMR spectroscopy of xenon gas adsorbed in clays and pillared clays has been used to glean information on the interlayer gallery height of clays before and after pillaring. Two clay minerals were studied, a Ca{sup 2+}-montmorillonite and Bentonite L. The NMR results indicate that the effective interlamellar spacing of the montmorillonite increased from 5.4 to 8.0 Angstroms after pillaring with aluminum polyoxohydroxy Keggin cations. These data are consistent with X-ray powder diffraction results, which show a corresponding increase in gallery height from 5.6 to 8.4 Angstroms.

  16. 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

  17. 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.

  18. 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

  19. 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

  20. Xenon isotopes in size separated nanodiamonds from Efremovka: 129Xe*, Xe-P3, and Xe-P6

    NASA Astrophysics Data System (ADS)

    Gilmour, J. D.; Verchovsky, A. B.; Fisenko, A. V.; Holland, G.; Turner, G.

    2005-08-01

    Xenon isotopic data were acquired by high resolution step pyrolysis and combined step pyrolysis/combustion of aliquots of size separated nanodiamonds. 129Xe excess ( 129Xe*) from in situ decay of 129I is preferentially associated with the larger grain size separates. This observation rules out trapping by recoil from surrounding material. The releases of Xe-P3 and 129Xe occur in the same low temperature pyrolysis steps and exhibit similar distributions among the size separates. These observations imply a common site for the components and, in consequence, suggest a common incorporation event. Whether one component or two, our observations require that 129Xe* and Xe-P3 were incorporated into a subpopulation of nanodiamonds before nanodiamonds were mixed and incorporated into parent bodies. Their susceptibilities to loss during heating in the laboratory are similar, but the ratio of 129Xe* to Xe-P3 varies among nanodiamond separates from different meteorites (literature data). We conclude that the 129Xe* we observe today was present as 129I during parent body processing. Furthermore, the range of 129Xe*/ 132Xe P3 ratios across all the separates requires that even nanodiamonds from CI chondrites were at least 5-10× more rich in Xe-P3 during 129I decay than they are today. We present a simple model involving one degassing event per parent body between incorporation of nanodiamonds and final decay of 129I. The observed variations among parent bodies require degassing events separated by several 129I half lives (˜50Ma), consistent with low-temperature processing on parent bodies but longer than expected for nebular processing. In this model, nanodiamonds from ALHA77307 degassed at an unusually early stage, suggesting they alone may retain the signature of processing in the nebula in their P3 and 129Xe* abundances. The isotopic signature associated with Xe-P6 is also found only in the larger size separates. Concentration of Xe-HL increases with increasing grain size

  1. 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

  2. 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.

  3. 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

  4. Hyperpolarized 3He and 129Xe magnetic resonance imaging apparent diffusion coefficients: physiological relevance in older never‐ and ex‐smokers

    PubMed Central

    Kirby, Miranda; Ouriadov, Alexei; Svenningsen, Sarah; Owrangi, Amir; Wheatley, Andrew; Etemad‐Rezai, Roya; Santyr, Giles E.; McCormack, David G.; Parraga, Grace

    2014-01-01

    Abstract Noble gas pulmonary magnetic resonance imaging (MRI) is transitioning away from 3He to 129Xe gas, but the physiological/clinical relevance of 129Xe apparent diffusion coefficient (ADC) parenchyma measurements is not well understood. Therefore, our objective was to generate 129Xe MRI ADC for comparison with 3He ADC and with well‐established measurements of alveolar structure and function in older never‐smokers and ex‐smokers with chronic obstructive pulmonary disease (COPD). In four never‐smokers and 10 COPD ex‐smokers, 3He (b = 1.6 sec/cm2) and 129Xe (b = 12, 20, and 30 sec/cm2) ADC, computed tomography (CT) density‐threshold measurements, and the diffusing capacity for carbon monoxide (DLCO) were measured. To understand regional differences, the anterior–posterior (APG) and superior–inferior (∆SI) ADC differences were evaluated. Compared to never‐smokers, COPD ex‐smokers showed greater 3He ADC (P = 0.006), 129Xe ADCb12 (P = 0.006), and ADCb20 (P = 0.006), but not for ADCb30 (P > 0.05). Never‐smokers and COPD ex‐smokers had significantly different APG for 3He ADC (P = 0.02), 129Xe ADCb12 (P = 0.006), and ADCb20 (P = 0.01), but not for ADCb30 (P > 0.05). ∆SI for never‐ and ex‐smokers was significantly different for 3He ADC (P = 0.046), but not for 129Xe ADC (P > 0.05). There were strong correlations for DLCO with 3He ADC and 129Xe ADCb12 (both r = −0.95, P < 0.05); in a multivariate model 129Xe ADCb12 was the only significant predictor of DLCO (P = 0.049). For COPD ex‐smokers, CT relative area <−950 HU (RA950) correlated with 3He ADC (r = 0.90, P = 0.008) and 129Xe ADCb12 (r = 0.85, P = 0.03). In conclusion, while 129Xe ADCb30 may be appropriate for evaluating subclinical or mild emphysema, in this small group of never‐smokers and ex‐smokers with moderate‐to‐severe emphysema, 129Xe ADCb12 provided a physiologically appropriate estimate of gas exchange abnormalities and alveolar microstructure. PMID:25347853

  5. Hyperpolarized (129) Xe MRI using isobutene as a new quenching gas.

    PubMed

    Hodono, Shota; Imai, Hirohiko; Yamauchi, Yukiko; Kawamura, Ayano; Matsumoto, Hironobu; Okumura, Shintaro; Fujiwara, Hideaki; Kimura, Atsuomi

    2016-10-01

    The use of a quenching gas, isobutene, with a low vapor pressure was investigated to enhance the utility of hyperpolarized (129) Xe (HP Xe) MRI. Xenon mixed with isobutene was hyperpolarized using a home-built apparatus for continuously producing HP Xe. The isobutene was then readily liquefied and separated almost totally by continuous condensation at about 173 K, because the vapor pressure of isobutene (0.247 kPa) is much lower than that of Xe (157 kPa). Finally, the neat Xe gas was continuously delivered to mice by spontaneous inhalation. The HP Xe MRI was enhanced twofold in polarization level and threefold in signal intensity when isobutene was adopted as the quenching gas instead of N2 . The usefulness of the HP Xe MRI was verified by application to pulmonary functional imaging of spontaneously breathing mice, where the parameters of fractional ventilation (ra ) and gas exchange (fD ) were evaluated, aiming at future extension to preclinical studies. This is the first application of isobutene as a quenching gas for HP Xe MRI.

  6. Hyperpolarized (129) Xe MRI using isobutene as a new quenching gas.

    PubMed

    Hodono, Shota; Imai, Hirohiko; Yamauchi, Yukiko; Kawamura, Ayano; Matsumoto, Hironobu; Okumura, Shintaro; Fujiwara, Hideaki; Kimura, Atsuomi

    2016-10-01

    The use of a quenching gas, isobutene, with a low vapor pressure was investigated to enhance the utility of hyperpolarized (129) Xe (HP Xe) MRI. Xenon mixed with isobutene was hyperpolarized using a home-built apparatus for continuously producing HP Xe. The isobutene was then readily liquefied and separated almost totally by continuous condensation at about 173 K, because the vapor pressure of isobutene (0.247 kPa) is much lower than that of Xe (157 kPa). Finally, the neat Xe gas was continuously delivered to mice by spontaneous inhalation. The HP Xe MRI was enhanced twofold in polarization level and threefold in signal intensity when isobutene was adopted as the quenching gas instead of N2 . The usefulness of the HP Xe MRI was verified by application to pulmonary functional imaging of spontaneously breathing mice, where the parameters of fractional ventilation (ra ) and gas exchange (fD ) were evaluated, aiming at future extension to preclinical studies. This is the first application of isobutene as a quenching gas for HP Xe MRI. PMID:27526627

  7. Chemical shifts in biomolecules

    PubMed Central

    Case, David A.

    2013-01-01

    Summary NMR chemical shifts are sensitive probes of stucture and dynamics in proteins. Empirical models, based on a large database of measured shifts, take an input structure and provide increasingly accurate estimates of the corresponding shifts. Quantum chemical calculations can provide the same information, with greater generality but (currently) with less accuracy. These methods are now providing new ways to approach NMR structure determination, and new insights into the conformational dynamics of proteins. PMID:23422068

  8. Quantitative analysis of hyperpolarized 129Xe ventilation imaging in healthy volunteers and subjects with chronic obstructive pulmonary disease.

    PubMed

    Virgincar, Rohan S; Cleveland, Zackary I; Kaushik, S Sivaram; Freeman, Matthew S; Nouls, John; Cofer, Gary P; Martinez-Jimenez, Santiago; He, Mu; Kraft, Monica; Wolber, Jan; McAdams, H Page; Driehuys, Bastiaan

    2013-04-01

    In this study, hyperpolarized (129) Xe MR ventilation and (1) H anatomical images were obtained from three subject groups: young healthy volunteers (HVs), subjects with chronic obstructive pulmonary disease (COPD) and age-matched controls (AMCs). Ventilation images were quantified by two methods: an expert reader-based ventilation defect score percentage (VDS%) and a semi-automated segmentation-based ventilation defect percentage (VDP). Reader-based values were assigned by two experienced radiologists and resolved by consensus. In the semi-automated analysis, (1) H anatomical images and (129) Xe ventilation images were both segmented following registration to obtain the thoracic cavity volume and ventilated volume, respectively, which were then expressed as a ratio to obtain the VDP. Ventilation images were also characterized by generating signal intensity histograms from voxels within the thoracic cavity volume, and heterogeneity was analyzed using the coefficient of variation (CV). The reader-based VDS% correlated strongly with the semi-automatically generated VDP (r = 0.97, p < 0.0001) and with CV (r = 0.82, p < 0.0001). Both (129) Xe ventilation defect scoring metrics readily separated the three groups from one another and correlated significantly with the forced expiratory volume in 1 s (FEV1 ) (VDS%: r = -0.78, p = 0.0002; VDP: r = -0.79, p = 0.0003; CV: r = -0.66, p = 0.0059) and other pulmonary function tests. In the healthy subject groups (HVs and AMCs), the prevalence of ventilation defects also increased with age (VDS%: r = 0.61, p = 0.0002; VDP: r = 0.63, p = 0.0002). Moreover, ventilation histograms and their associated CVs distinguished between subjects with COPD with similar ventilation defect scores, but visibly different ventilation patterns.

  9. Cation location in microporous zeolite, SSZ-13, probed with xenon adsorption measurement and 129Xe NMR spectrum.

    PubMed

    Shin, Na Ra; Kim, Su Hyun; Shin, Hye Sun; Jang, Ik Jun; Cho, Sung June

    2013-06-01

    The location of metal ion, Ag2+, Ca2+, Cu2+ and Y3+ in the SSZ-13 has been investigated with xenon adsorption measurement and 129Xe NMR spectrum. It was referred that the location of the metal ion varies depending on the corresponding charge. The ion-exchanged Ag ion was located in the alpha-cage to interact directly with xenon. Others multivalent cation contributed little with xenon because these were present near the six membered rings where xenon cannot access. PMID:23862500

  10. 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

  11. 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

  12. 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.

  13. Carrier phases for iodine in the Allende meteorite and their associated sup 129 Xe sub r / sup 127 I ratios: A laser microprobe study

    SciTech Connect

    Kirschbaum, C. )

    1988-03-01

    A new mass spectrometer of high sensitivity coupled to a laser microprobe sample extraction system was used to determine the {sup 129}Xe{sub r}/I ratios of minerals which carry {sup 129}Xe{sub r} in the Allende meteorite. In sodalite-rich fine-grained inclusions Ok correlates with Cl verifying that sodalite carries the majority of I. One sample heated above the decomposition point of sodalite had a small amount of residual I indicating the presence of at least one other carrier. The Cl/I ratio of the matrix was different from that of the fine-grained inclusions and the {sup 129}Xe{sub r} correlates with trapped Xe. This implies either a different Cl/I ratio for sodalite in the matrix or a different carrier for I in matrix. In melilite from one coarse-grained inclusion, I is variable and correlates with both Xe and, surprisingly, {sup 131}Xe produced from Ba during the irradiation. In coarse-grained inclusions with Cl-rich alteration products in cracks, most of the {sup 129}Xe{sub r} is found in those cracks. A residual amount of {sup 129}Xe{sub r} is present in melilite samples which show no Cl-rich alteration products, and is a trace impurity in the melilite. The {sup 129}Xe{sub r}/{sup 127}I ratio of sodalite from the fine-grained inclusions, and matrix is similar--between 1.25 and 1.35 {times} 10{sup {minus}4}. This implies an age for these samples within 2 million years of a Bjurbole chondrule included in the irradiation as a standard. The {sup 129}Xe{sub r}/{sup 127}I ratio of a sample of a fine-grained inclusion heated to 1,100{degree}C is 2.4 {times} 10{sup {minus}4} or 16 million years before the Bjurbole chondrule. A coarse-grained inclusion on the other hand showed a {sup 129}Xe{sub r}/{sup 127}I ratio of 3.15 {times} 10{sup {minus}5} or 35 million years after the Bjurbole chondrule.

  14. 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

  15. Laboratory search for a long-range T-odd, P-odd interaction from axionlike particles using dual-species nuclear magnetic resonance with polarized 129Xe and 131Xe gas.

    PubMed

    Bulatowicz, M; Griffith, R; Larsen, M; Mirijanian, J; Fu, C B; Smith, E; Snow, W M; Yan, H; Walker, T G

    2013-09-01

    Various theories beyond the standard model predict new particles with masses in the sub-eV range with very weak couplings to ordinary matter. A new P-odd and T-odd interaction between polarized and unpolarized nucleons proportional to K·r is one such possibility, where r is the distance between the nucleons and K is the spin of the polarized nucleon. Such an interaction involving a scalar coupling gs at one vertex and a pseudoscalar coupling gp at the polarized nucleon vertex can be induced by the exchange of spin-0 bosons. We used the NMR cell test station at Northrop Grumman Corporation to search for NMR frequency shifts in polarized 129Xe and 131Xe when a nonmagnetic zirconia rod is moved near the NMR cell. Long (T2∼20  s) spin-relaxation times allow precision measurements of the NMR frequency ratios, which are insensitive to magnetic field fluctuations. Combined with existing theoretical calculations of the neutron spin contribution to the nuclear angular momentum in xenon nuclei, the measurements improve the laboratory upper bound on the product gsgp(n) by 2 orders of magnitude for distances near 1 mm. The sensitivity of this technique can be increased by at least two more orders of magnitude.

  16. 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).

  17. 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…

  18. 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.

  19. 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.

  20. Chemical shift prediction for denatured proteins.

    PubMed

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

    2013-02-01

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

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

    PubMed

    Kono, Hiroyuki; Hashimoto, Hisaho; Shimizu, Yuuichi

    2015-03-15

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

  2. 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...

  3. 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

  4. 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

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

    PubMed

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

    2015-01-01

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

  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. 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

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. Ultrahigh resolution protein structures using NMR chemical shift tensors

    PubMed Central

    Wylie, Benjamin J.; Sperling, Lindsay J.; Nieuwkoop, Andrew J.; Franks, W. Trent; Oldfield, Eric; Rienstra, Chad M.

    2011-01-01

    NMR chemical shift tensors (CSTs) in proteins, as well as their orientations, represent an important new restraint class for protein structure refinement and determination. Here, we present the first determination of both CST magnitudes and orientations for 13Cα and 15N (peptide backbone) groups in a protein, the β1 IgG binding domain of protein G from Streptococcus spp., GB1. Site-specific 13Cα and 15N CSTs were measured using synchronously evolved recoupling experiments in which 13C and 15N tensors were projected onto the 1H-13C and 1H-15N vectors, respectively, and onto the 15N-13C vector in the case of 13Cα. The orientations of the 13Cα CSTs to the 1H-13C and 13C-15N vectors agreed well with the results of ab initio calculations, with an rmsd of approximately 8°. In addition, the measured 15N tensors exhibited larger reduced anisotropies in α-helical versus β-sheet regions, with very limited variation (18 ± 4°) in the orientation of the z-axis of the 15N CST with respect to the 1H-15N vector. Incorporation of the 13Cα CST restraints into structure calculations, in combination with isotropic chemical shifts, transferred echo double resonance 13C-15N distances and vector angle restraints, improved the backbone rmsd to 0.16 Å (PDB ID code 2LGI) and is consistent with existing X-ray structures (0.51 Å agreement with PDB ID code 2QMT). These results demonstrate that chemical shift tensors have considerable utility in protein structure refinement, with the best structures comparable to 1.0-Å crystal structures, based upon empirical metrics such as Ramachandran geometries and χ1/χ2 distributions, providing solid-state NMR with a powerful tool for de novo structure determination. PMID:21969532

  16. In vivo 1H chemical shift imaging of silicone implants.

    PubMed

    Pfleiderer, B; Ackerman, J L; Garrido, L

    1993-05-01

    In order to study the aging process (i.e., silicone migration, fat infiltration) of silicone (polydimethylsiloxane, PDMS) based biomaterials in living subjects by NMR imaging, a hybrid 1H selective excitation and saturation chemical shift imaging technique (IR/CHESS-CSSE) has been developed. This sequence allows selective mapping of the distribution of silicone protons in vivo, while suppressing the contributions of fat and water. Our results indicate that a combined inversion recovery and CHESS pulse, followed by a spoiler gradient, must be applied to suppress all contributions of fat protons to the NMR signal. The sensitivity of our experiments allows the detection of a chemically unchanged silicone concentration of 5% in a voxel of 0.9 mm3 at a signal/noise ratio of 2.

  17. 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.

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

    PubMed

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

    2008-10-15

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

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

    PubMed

    Lebedev, A V; Rezvukhin, A I

    1984-07-25

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

  20. 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

  1. 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.

  2. SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database.

    PubMed

    Ginzinger, Simon W; Coles, Murray

    2009-03-01

    We present SimShiftDB, a new program to extract conformational data from protein chemical shifts using structural alignments. The alignments are obtained in searches of a large database containing 13,000 structures and corresponding back-calculated chemical shifts. SimShiftDB makes use of chemical shift data to provide accurate results even in the case of low sequence similarity, and with even coverage of the conformational search space. We compare SimShiftDB to HHSearch, a state-of-the-art sequence-based search tool, and to TALOS, the current standard tool for the task. We show that for a significant fraction of the predicted similarities, SimShiftDB outperforms the other two methods. Particularly, the high coverage afforded by the larger database often allows predictions to be made for residues not involved in canonical secondary structure, where TALOS predictions are both less frequent and more error prone. Thus SimShiftDB can be seen as a complement to currently available methods.

  3. 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.

  4. Chemical shift imaging of atherosclerosis at 7.0 Tesla.

    PubMed

    Maynor, C H; Charles, H C; Herfkens, R J; Suddarth, S A; Johnson, G A

    1989-01-01

    Chemical shift imaging (CSI) was performed on cadaveric atherosclerotic fibrous plaques, periaortic adipose tissue, and cholesterol standards using a 7.0 Tesla horizontal bore prototype imaging spectrometer. Proton spectroscopy of intact tissue and deuterated chloroform extracted samples was done at the equivalent field strength of 7.0 Tesla on a vertical bore spectrometer, including studies of temperature dependence and T2 relaxation measurements. Spectra obtained using CSI on the imaging magnet were comparable with those from the conventional vertical spectrometer. Fibrous plaques and adipose tissue had unique spectral features, differing in the ratios of their water and various fat components. Chloroform extractions revealed a typical cholesteric ester spectrum for the fibrous plaque in contrast to the triglyceride spectrum of the adipose tissue. These two tissues also had different T2 relaxation measurements of their major fat resonances, with fibrous plaques having a short T2 compared to adipose tissue (15.9 milliseconds vs. 46.2 milliseconds). Temperature dependence studies showed that spectral signal intensity of the fat resonance of the fibrous plaque increased while linewidth decreased with increasing temperature from 24 degrees C to 37 degrees C. Atherosclerotic lesions may be studied at 7.0 Tesla, and NMR parameters defined in the present study may be used for further studies at other magnetic field strengths.

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

    PubMed

    Lebedev, A V; Rezvukhin, A I

    1984-07-25

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

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

    PubMed

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

    2013-06-01

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

  7. Light-shift measurement and suppression in atomic spin gyroscope.

    PubMed

    Fang, Jiancheng; Wan, Shuangai; Chen, Yao; Li, Rujie

    2012-11-01

    We present a method to determine and suppress the light shift in an atomic spin gyroscope. This method doesn't require additional drive source or frequency modulation, and it is based on the dynamics of an atomic spin gyroscope to determine a clean curve as a function of the frequency of the pump beam that predicts the zero light shift. We experimentally validate the method in a Cs-(129)Xe atomic spin gyroscope and verify the results through numerical simulations. This method can also be applied to an atomic spin magnetometer based on the spin-exchange relaxation-free exchange that experiences light shift. The method is useful for atomic spin devices because it can improve long-term performance and reduce the influence of the laser.

  8. Fluorine Chemical Shift Imaging by Nuclear Magnetic Resonance

    NASA Astrophysics Data System (ADS)

    Lee, Heung Kyu

    1990-01-01

    One of the difficulties encountered in ^{19}F NMR imaging of fluorinated blood substitutes is that these compounds often exhibit complex multi-peak spectra. These peaks result in chemical shift artifacts along the readout direction (mis-registration). In addition, each peak excites a different slice (mis-selection) when a slice selection gradient is applied. Another difficulty is due to its low concentration in the human body. Even after injecting a fluorinated compound into a living system up to the safest level, the concentration still does not appear to be enough to give a sufficient SNR. To solve the inherent problem of mis-selection, a simultaneous multislice method has been developed. The essence of this method is to use the two strongest peaks of the spectrum to excite different multiple slices simultaneously in a controlled fashion, with or without a slice gap. The images corresponding to the two spectral lines are then separated from in and out of phase images (Dixon method). A signed magnitude method is proposed in conjunction with the simultaneous multislice method. Corrected images are obtained from the magnitude of the measured images using the sign determined from the phase images. The method was tested in the presence of phase error, such as static magnetic field inhomogeneity. As alternatives, two deconvolution methods have been devised to eliminate the mis-registration artifacts and utilize the multiple spectral lines. The reblurring deconvolution method, an iterative deconvolution method, is utilized without serious noise amplifications. A pseudo parametric Wiener filter, a variation of the Wiener filter combined with a constrained least square filter, is also devised. Since the point spread function and 2D or 3D object data are already available in the time domain as the FID data, the computational overhead for either method is negligible. To enhance the signal to noise ratio and solve the problems of mis-registration and mis

  9. Chemical bonding of lead in glasses through isotropic vs anisotropic correlation: PASS shifted echo.

    PubMed

    Fayon, F; Bessada, C; Douy, A; Massiot, D

    1999-03-01

    When observing spin I = (1/2) nuclei with important chemical shift anisotropy in disordered materials, the distribution of isotropic shift can become so large that no accessible spinning rate is able to provide a resolved spectrum. This is the case of 207Pb in glasses where static and high-speed MAS spectra are nearly identical. It is still possible in such a case to rebuild a spinning sideband free spectrum using a shifted echo modified PASS sequence. This makes it possible to discuss isotropic and anisotropic chemical shifts of lead in phosphate glasses, to characterize its structural role and its chemical bonding state.

  10. Phosphorus-31 nuclear magnetic resonance chemical shifts of phosphoric acid derivatives.

    PubMed

    Wittmann, Z; Kovács, Z

    1985-07-01

    (31)P nuclear magnetic resonance chemical shifts of alkyi and alkylaryl phosphates, condensed phosphates, phosphoric arids and their salts, are reported. These are listed by classes of compounds so that relationships between chemical shifts and the substituent groups on phosphorus atoms can be recognized. These relationships are useful for qualitative identification of the specific compounds listed and of related compounds by extrapolation.

  11. 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

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

    NASA Astrophysics Data System (ADS)

    Oldfield, Eric

    2002-10-01

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

  13. 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.

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

    PubMed

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

    2015-01-01

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

  15. Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins

    PubMed Central

    Karp, Jerome M.; Erylimaz, Ertan

    2015-01-01

    There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We find that using MD simulation data as input for chemical shift prediction does not consistently improve prediction accuracy over use of a static X-ray crystal structure. This appears to result from the complex conformational ensemble of the disordered protein segments. We show that using accelerated molecular dynamics (aMD) simulations improves chemical shift prediction, suggesting that methods which better sample the conformational ensemble like aMD are more appropriate tools for use in chemical shift prediction for proteins with disordered regions. Moreover, our study suggests that data accurately reflecting protein dynamics must be used as input for chemical shift prediction in order to correctly predict chemical shifts in systems with disorder. PMID:25416617

  16. Protein backbone angle restraints from searching a database for chemical shift and sequence homology.

    PubMed

    Cornilescu, G; Delaglio, F; Bax, A

    1999-03-01

    Chemical shifts of backbone atoms in proteins are exquisitely sensitive to local conformation, and homologous proteins show quite similar patterns of secondary chemical shifts. The inverse of this relation is used to search a database for triplets of adjacent residues with secondary chemical shifts and sequence similarity which provide the best match to the query triplet of interest. The database contains 13C alpha, 13C beta, 13C', 1H alpha and 15N chemical shifts for 20 proteins for which a high resolution X-ray structure is available. The computer program TALOS was developed to search this database for strings of residues with chemical shift and residue type homology. The relative importance of the weighting factors attached to the secondary chemical shifts of the five types of resonances relative to that of sequence similarity was optimized empirically. TALOS yields the 10 triplets which have the closest similarity in secondary chemical shift and amino acid sequence to those of the query sequence. If the central residues in these 10 triplets exhibit similar phi and psi backbone angles, their averages can reliably be used as angular restraints for the protein whose structure is being studied. Tests carried out for proteins of known structure indicate that the root-mean-square difference (rmsd) between the output of TALOS and the X-ray derived backbone angles is about 15 degrees. Approximately 3% of the predictions made by TALOS are found to be in error.

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

    PubMed

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

    2015-11-01

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

  18. In vivo nuclear magnetic resonance chemical shift imaging by selective irradiation.

    PubMed Central

    Bottomley, P A; Foster, T H; Leue, W M

    1984-01-01

    NMR images of preselected chemically shifted species can be obtained by selective irradiation of the remainder of the NMR chemical shift spectrum prior to application of a conventional NMR imaging sequence. The chemical-selective irradiation consists of narrow-bandwidth pi/2 or saturation radio-frequency pulses applied in the absence of imaging gradients. The technique permits substantial reductions in scan and reconstruction times over standard three- and four-dimensional Fourier transform chemical-shift-imaging methods, when images of few spectral peaks are desired. It is also suitable for the elimination of chemical shift artifacts in conventional high-field NMR imaging. In vivo applications of the technique to the head and limbs in a 1.5-T magnetic field yield 1H H2O and -CH2-images, with little detectable -CH2- in muscle and brain. Images PMID:6593729

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

    PubMed

    Altheimer, Benjamin D; Mehta, Manish A

    2014-04-10

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

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

    PubMed

    Dumez, Jean-Nicolas; Pickard, Chris J

    2009-03-14

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

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

    PubMed

    Shahab, Yosif A; Khalil, Rabah A

    2006-10-01

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

  2. 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)

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

    PubMed

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

    2015-10-01

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

  4. Surface structure and thermodynamics of coals. Quarterly report, October 1, 1989--December 31, 1989

    SciTech Connect

    Wernett, P.C.; Larsen, J.W.

    1989-12-31

    Our work has been the determination of the average micropore diameter of an Argonne Illinois No. 6 coal and a spherocarb sample by {sup 129}Xe NMR. {sup 129}Xe NMR spectroscopy has been used to determine pore sizes and surface characteristics in zeolites. The chemical shift of {sup 129}Xe was measured as a function of pressure and the average micropore diameter was calculated using established techniques. For the spherocarb, the calculated pore diameter of 15.4 CA agrees well with the 0 manufacturer`s reported value of 15{Angstrom}. The Illinois No. 6 coal gave two {sup 129}Xe peaks. Extrapolation of the pressure dependent peak gave a micropore diameter of 5.2{Angstrom}. The other peak was not pressure dependent and is tentatively assigned to Xe dissolved in the coal. The NMR chemical shift of {sup 129}Xe is a useful probe of micropore (<20 {Angstrom} diameter) size and surface characteristics. This application was developed principally by Fraissard and coworkers to determine pore size distributions and the degree of crystallinity in zeolites. The observed {sup 129}Xe NMR chemical shift can be attributed to 4 factors: (1) the number of Xe-Xe collisions; (2) the electric field established by neighboring ions` in the solid sample, found to be negligible for monovalent cations in zeolites; (3) the number of Xe-wall collisions; and (4) the nature of the interaction of Xe with the pore wall. The chemical shift due to Xe-wall collisions can be determined by extrapolation of {sup 129}Xe NMR resonances to 0 Xe pressure.

  5. Surface structure and thermodynamics of coals

    SciTech Connect

    Wernett, P.C.; Larsen, J.W.

    1989-01-01

    Our work has been the determination of the average micropore diameter of an Argonne Illinois No. 6 coal and a spherocarb sample by {sup 129}Xe NMR. {sup 129}Xe NMR spectroscopy has been used to determine pore sizes and surface characteristics in zeolites. The chemical shift of {sup 129}Xe was measured as a function of pressure and the average micropore diameter was calculated using established techniques. For the spherocarb, the calculated pore diameter of 15.4 CA agrees well with the 0 manufacturer's reported value of 15{Angstrom}. The Illinois No. 6 coal gave two {sup 129}Xe peaks. Extrapolation of the pressure dependent peak gave a micropore diameter of 5.2{Angstrom}. The other peak was not pressure dependent and is tentatively assigned to Xe dissolved in the coal. The NMR chemical shift of {sup 129}Xe is a useful probe of micropore (<20 {Angstrom} diameter) size and surface characteristics. This application was developed principally by Fraissard and coworkers to determine pore size distributions and the degree of crystallinity in zeolites. The observed {sup 129}Xe NMR chemical shift can be attributed to 4 factors: (1) the number of Xe-Xe collisions; (2) the electric field established by neighboring ions' in the solid sample, found to be negligible for monovalent cations in zeolites; (3) the number of Xe-wall collisions; and (4) the nature of the interaction of Xe with the pore wall. The chemical shift due to Xe-wall collisions can be determined by extrapolation of {sup 129}Xe NMR resonances to 0 Xe pressure.

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

    PubMed Central

    Wang, Xianlong; Wang, Chengfei; Zhao, Hui

    2012-01-01

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

  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.

    PubMed

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

    2015-10-14

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

  9. 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

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

    PubMed

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

    2016-09-01

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

  12. Minimizing lipid signal bleed in brain 1H chemical shift imaging by post-acquisition grid shifting

    PubMed Central

    Zhang, Yi; Zhou, Jinyuan; Bottomley, Paul A.

    2014-01-01

    Purpose Low spatial resolution in conventional 1H brain chemical shifting imaging (CSI) studies causes partial volume error (PVE) or signal ‘bleed’ that is especially deleterious to voxels near the scalp. The standard spatial apodization approach adversely affects spatial resolution. Here, a novel automated post-processing strategy of partial volume correction employing grid shifting (‘PANGS’) is presented, which minimizes residual PVE without compromising spatial resolution. Methods PANGS shifts the locations of the reconstruction coordinates in a designated region of image space—the scalp, to match the tissue ‘centers-of-mass’ instead of the geometric centers of each voxel, by iteratively minimizing the PVE from the scalp into outside voxels. PANGS’ performance was evaluated by numerical simulation, and in 3T 1H CSI human studies employing outer volume suppression and long echo times. Results PANGS reduced lipid contamination of cortical spectra by up to 86% (54% on average). Metabolite maps exhibited significantly less lipid artifact than conventional and spatially-filtered CSI. All methods generated quantitatively identical spectral peak areas from central brain locations, but spatial filtering increased spectral linewidths and reduced spatial resolution. Conclusion PANGS significantly reduces lipid artifacts in 1H brain CSI spectra and metabolite maps, and improves metabolite detection in cortical regions without compromising resolution. PMID:25168657

  13. Stereoelectronic effects on 1H nuclear magnetic resonance chemical shifts in methoxybenzenes.

    PubMed

    Lambert, Maja; Olsen, Lars; Jaroszewski, Jerzy W

    2006-12-01

    Investigation of all O-methyl ethers of 1,2,3-benzenetriol and 4-methyl-1,2,3-benzenetriol (3-16) by 1H NMR spectroscopy and density-functional calculations disclosed practically useful conformational effects on 1H NMR chemical shifts in the aromatic ring. While the conversion of phenol (2) to anisole (1) causes only small positive changes of 1H NMR chemical shifts (Delta delta < 0.08 ppm) that decrease in the order Hortho > Hmeta > Hpara, the experimental O-methylation induced shifts in ortho-disubstituted phenols are largest for Hpara, Delta delta equals; 0.19 +/- 0.02 ppm (n = 11). The differences are due to different conformational behavior of the OH and OCH3 groups; while the ortho-disubstituted OH group remains planar in polyphenols due to hydrogen bonding and conjugative stabilization, the steric congestion in ortho-disubstituted anisoles outweighs the conjugative effects and forces the Ar-OCH3 torsion out of the ring plane, resulting in large stereoelectronic effects on the chemical shift of Hpara. Conformational searches and geometry optimizations for 3-16 at the B3LYP/6-31G** level, followed by B3LYP/6-311++G(2d,2p) calculations for all low-energy conformers, gave excellent correlation between computed and observed 1H NMR chemical shifts, including agreement between computed and observed chemical shift changes caused by O-methylation. The observed regularities can aid structure elucidation of partly O-methylated polyphenols, including many natural products and drugs, and are useful in connection with chemical shift predictions by desktop computer programs. PMID:17137372

  14. Utilizing the charge field effect on amide (15)N chemical shifts for protein structure validation.

    PubMed

    Bader, Reto

    2009-01-01

    Of all the nuclei in proteins, the nuclear magnetic resonance (NMR) chemical shifts of nitrogen are the theoretically least well understood. In this study, quantum chemical methods are used in combination with polarizable-continuum models in order to show that consideration of the effective electric field, including charge screening due to solvation, improves considerably the consistencies of statistical relationships between experimental and computed amide (15)N shifts between various sets of charged and uncharged oligopeptides and small organic molecules. A single conversion scheme between shielding parameters from first principles using density functional theory (DFT) and experimental shifts is derived that holds for all classes of compounds examined here. This relationship is then used to test the accuracy of such (15)N chemical shift predictions in the cyclic decapeptide antibiotic gramicidin S (GS). GS has previously been studied in great detail, both by NMR and X-ray crystallography. It adopts a well-defined backbone conformation, and hence, only a few discrete side chain conformational states need to be considered. Moreover, a charge-relay effect of the two cationic ornithine side chains to the protein backbone has been described earlier by NMR spectroscopy. Here, DFT-derived backbone amide nitrogen chemical shifts were calculated for multiple conformations of GS. Overall, the structural dynamics of GS is revisited in view of chemical shift behavior along with energetic considerations. Together, the study demonstrates proof of concept that (15)N chemical shift information is particularly useful in the analysis and validation of protein conformational states in a charged environment.

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

    PubMed

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

    2014-09-23

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

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

    PubMed

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

    2003-01-01

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

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

    PubMed

    Hansen, Poul Erik

    2015-01-30

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

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

    PubMed

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

    2012-05-21

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

  2. (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

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

    PubMed

    Grigoleit, Sonja; Bühl, Michael

    2004-10-25

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

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

    PubMed

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

    2013-08-13

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

  6. 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…

  7. 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

  8. 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.

  9. Chemical Shift Assignments of Mouse HOXD13 DNA Binding Domain Bound to Duplex DNA

    PubMed Central

    Turner, Matthew; Zhang, Yonghong; Carlson, Hanqian L.; Stadler, H. Scott; Ames, James B.

    2014-01-01

    The homeobox gene (Hoxd13) codes for a transcription factor protein that binds to AT-rich DNA sequences and controls expression of proteins that control embryonic morphogenesis. We report NMR chemical shift assignments of mouse Hoxd13 DNA binding domain bound to an 11-residue DNA duplex (BMRB no. 25133). PMID:25491407

  10. Quantum vs. classical models of the nitro group for proton chemical shift calculations and conformational analysis.

    PubMed

    Mobli, Mehdi; Abraham, Raymond J

    2005-03-01

    A model based on classical concepts is derived to describe the effect of the nitro group on proton chemical shifts. The calculated chemical shifts are then compared to ab initio (GIAO) calculated chemical shifts. The accuracy of the two models is assessed using proton chemical shifts of a set of rigid organic nitro compounds that are fully assigned in CDCl3 at 700 MHz. The two methods are then used to evaluate the accuracy of different popular post-SCF methods (B3LYP and MP2) and molecular mechanics methods (MMX and MMFF94) in calculating the molecular structure of a set of sterically crowded nitro aromatic compounds. Both models perform well on the rigid molecules used as a test set, although when using the GIAO method a general overestimation of the deshielding of protons near the nitro group is observed. The analysis of the sterically crowded molecules shows that the very popular B3LYP/6-31G(d,p) method produces very poor twist angles for these, and that using a larger basis set [6-311++G(2d,p)] gives much more reasonable results. The MP2 calculations, on the other hand, overestimate the twist angles, which for these compounds compensates for the deshielding effect generally observed for protons near electronegative atoms when using the GIAO method at the B3LYP/6-311++G(2d,p) level. The most accurate results are found when the structures are calculated using B3LYP/6-311++G(2d,p) level of theory, and the chemical shifts are calculated using the CHARGE program based on classical models.

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

    PubMed

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

    2016-02-24

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

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

    PubMed

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

    2016-02-24

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

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

    PubMed

    Fukushima, Kenji; Hidaka, Yoshimasa

    2016-09-01

    We discuss the effect of a strong magnetic field on the chemical freeze-out points in ultrarelativistic heavy-ion collisions. As a result of inverse magnetic catalysis or magnetic inhibition, the crossover onset to hot and dense matter out of quarks and gluons should be shifted to a lower temperature. To quantify this shift we employ the hadron resonance gas model and an empirical condition for the chemical freeze-out. We point out that the charged particle abundances are significantly affected by the magnetic field so that the electric charge fluctuation is largely enhanced, especially at high baryon density. The charge conservation partially cancels the enhancement, but our calculation shows that the electric charge fluctuation could serve as a magnetometer. We find that the fluctuation exhibits a crossover behavior rapidly increased for eB≳(0.4  GeV)^{2}, while the charge chemical potential has smoother behavior with an increasing magnetic field. PMID:27636469

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

    NASA Astrophysics Data System (ADS)

    Fukushima, Kenji; Hidaka, Yoshimasa

    2016-09-01

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

  15. 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.

  16. 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.

  17. 13C solid-state NMR chemical shift anisotropy analysis of the anomeric carbon in carbohydrates.

    PubMed

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

    2005-03-21

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

  18. Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations.

    PubMed

    Markin, Craig J; Spyracopoulos, Leo

    2012-12-01

    NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K ( D )) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K ( D ) value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of (1)H-(15)N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k ( off )). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k ( off ) ~ 3,000 s(-1) in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k ( off ) from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k ( off ) values over a wide range, from 100 to 15,000 s(-1). The validity of line shape analysis for k ( off ) values approaching intermediate exchange (~100 s(-1)), may be facilitated by more accurate K ( D ) measurements

  19. 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.

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

    PubMed

    Shen, Yang; Bax, Ad

    2013-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1997-06-01

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

  2. Measurement of 13C chemical shift tensor principal values with a magic-angle turning experiment.

    PubMed

    Hu, J Z; Orendt, A M; Alderman, D W; Pugmire, R J; Ye, C; Grant, D M

    1994-08-01

    The magic-angle turning (MAT) experiment introduced by Gan is developed into a powerful and routine method for measuring the principal values of 13C chemical shift tensors in powdered solids. A large-volume MAT probe with stable rotation frequencies down to 22 Hz is described. A triple-echo MAT pulse sequence is introduced to improve the quality of the two-dimensional baseplane. It is shown that measurements of the principal values of chemical shift tensors in complex compounds can be enhanced by using either short contact times or dipolar dephasing pulse sequences to isolate the powder patterns from protonated or non-protonated carbons, respectively. A model compound, 1,2,3-trimethoxybenzene, is used to demonstrate these techniques, and the 13C principal values in 2,3-dimethylnaphthalene and Pocahontas coal are reported as typical examples.

  3. 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

  4. 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).

  5. 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.

  6. Fragment-Based Electronic Structure Approach for Computing Nuclear Magnetic Resonance Chemical Shifts in Molecular Crystals.

    PubMed

    Hartman, Joshua D; Beran, Gregory J O

    2014-11-11

    First-principles chemical shielding tensor predictions play a critical role in studying molecular crystal structures using nuclear magnetic resonance. Fragment-based electronic structure methods have dramatically improved the ability to model molecular crystal structures and energetics using high-level electronic structure methods. Here, a many-body expansion fragment approach is applied to the calculation of chemical shielding tensors in molecular crystals. First, the impact of truncating the many-body expansion at different orders and the role of electrostatic embedding are examined on a series of molecular clusters extracted from molecular crystals. Second, the ability of these techniques to assign three polymorphic forms of the drug sulfanilamide to the corresponding experimental (13)C spectra is assessed. This challenging example requires discriminating among spectra whose (13)C chemical shifts differ by only a few parts per million (ppm) across the different polymorphs. Fragment-based PBE0/6-311+G(2d,p) level chemical shielding predictions correctly assign these three polymorphs and reproduce the sulfanilamide experimental (13)C chemical shifts with 1 ppm accuracy. The results demonstrate that fragment approaches are competitive with the widely used gauge-invariant projector augmented wave (GIPAW) periodic density functional theory calculations. PMID:26584373

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

    PubMed

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

    2015-08-21

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

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

    PubMed

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

    2009-08-01

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

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

    PubMed

    Reis, Adriana K C A; Rittner, Roberto

    2007-03-01

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

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

    PubMed

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

    2011-04-01

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

  11. RASP: rapid and robust backbone chemical shift assignments from protein structure.

    PubMed

    MacRaild, Christopher A; Norton, Raymond S

    2014-03-01

    Chemical shift prediction has an unappreciated power to guide backbone resonance assignment in cases where protein structure is known. Here we describe Resonance Assignment by chemical Shift Prediction (RASP), a method that exploits this power to derive protein backbone resonance assignments from chemical shift predictions. Robust assignments can be obtained from a minimal set of only the most sensitive triple-resonance experiments, even for spectroscopically challenging proteins. Over a test set of 154 proteins RASP assigns 88 % of residues with an accuracy of 99.7 %, using only information available from HNCO and HNCA spectra. Applied to experimental data from a challenging 34 kDa protein, RASP assigns 90 % of manually assigned residues using only 40 % of the experimental data required for the manual assignment. RASP has the potential to significantly accelerate the backbone assignment process for a wide range of proteins for which structural information is available, including those for which conventional assignment strategies are not feasible. PMID:24445369

  12. K-39 quadrupolar and chemical shift tensors for organic potassium complexes and diatomic molecules.

    PubMed

    Lee, Philip K; Chapman, Rebecca P; Zhang, Lei; Hu, Jiaxin; Barbour, Leonard J; Elliott, Elizabeth K; Gokel, George W; Bryce, David L

    2007-12-20

    Solid-state potassium-39 NMR spectra of two potassium complexes of crown-ether-based organic ligands (1.KI and 2) have been acquired at 11.75 and 21.1 T and interpreted to provide information on the 39K quadrupolar and chemical shift tensors. The analyses reveal a large potassium chemical shift tensor span of 75+/-20 ppm for 1.KI. This appears to be the first such measurement for potassium in an organic complex, thereby suggesting the utility of potassium chemical shift tensors for characterizing organic and biomolecular K+ binding environments. Compound 2 exhibits a cation-pi interaction between K+ and a phenyl group, and therefore, the 39K NMR tensors obtained for this compound must be partly representative of this interaction. Analyses of potassium-39 spin-rotation data for gaseous 39K19F and 39K35Cl available from molecular beam experiments performed by Cederberg and co-workers reveal the largest potassium CS tensor spans known to date, 84.39 and 141 ppm, respectively. Collectively, the results obtained highlight the potential of ultrahigh-field potassium-39 solid-state NMR spectroscopy and, in particular, the wide range of the anisotropy of the potassium CS tensor when organic and diatomic systems are considered.

  13. Electronic structure and nuclear magnetic resonance chemical shift of solids and surfaces

    NASA Astrophysics Data System (ADS)

    Pfrommer, Bernd Georg

    Several different topics related to the electronic structure of solids and surfaces are discussed in this thesis. With the quasi-Newton algorithm for relaxing crystal structures and a new ab initio method to compute nuclear magnetic resonance (NMR) chemical shifts, numerical methods are developed and implemented to efficiently compute properties related to the electronic structure. These techniques are then applied to a range of different materials. The quasi-Newton method is used to study the recently discovered high-pressure R8 phase of silicon, and the fcc-hcp high-pressure structural phase transition of xenon. Using the pressure-induced magnetic phase transition of a model atomic hydrogen crystal as a test system, the accuracy of density functional theory in both the generalized gradient approximation (GGA) and the local spin density approximation (LSDA) is compared to variational quantum Monte Carlo (VQMC) calculations (1). Finally, for the first time, the NMR chemical shift of extended systems such as amorphous carbon and the hydrogenated diamond (111) surface are calculated from first principles. 1. In the first chapter, a model body-centered cubic (bcc) atomic hydrogen solid is studied using density functional theory in LSDA and GGA. 2. How a quasi-Newton method can be used to simultaneously relax the internal coordinates and lattice parameters of crystals under pressure is the subject of the second chapter. 3. Chapter three presents a detailed ab initio study of the electronic and structural properties of the recently discovered R8 phase of silicon. 4. In chapter four, the fcc-hcp high pressure structural phase transition of xenon is calculated. 5. Chapter five describes a theory for the ab initio computation of the NMR chemical shift in extended systems, using periodic boundary conditions. 6. In chapter six, the NMR chemical shift spectra of diamond, CVD diamond, and diamond-like amorphous carbon are computed from first principles. 7. Unexpected features

  14. 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.

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

    PubMed

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

    2009-07-30

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

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

    PubMed

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

    2008-08-14

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

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

    PubMed

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

    2008-08-14

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

  18. 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

  19. 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

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

    PubMed

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

    2016-02-01

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

  1. 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

  2. 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

  3. 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

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

    PubMed

    Görling, Benjamin; Bräse, Stefan; Luy, Burkhard

    2016-09-02

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

  5. Substituent efects on the carbon-13 chemical shifts in α-phenylpyridylacrylic acids

    NASA Astrophysics Data System (ADS)

    Jovanović, B. Ž.; Mis̆ić-Vukovic, M.; Vajs, V. E.; Čanadi, J. J.

    1992-03-01

    The 13C N.M.R. spectra of some substituted α-phenylpyridylacrylic acids, α-phenyl, α-(3-pyrydyl) and α-(3-pyrydyl-N-oxide) cinnamic acids were determined in deuterated dimethyl sulfoxide (d 6-DMSO). It has been shown that the subsitutent chemical shifts (SCS) for C βatom ethylenic bond of the examined compounds correlated linearely with the summ of the corresponding substituent constants in the both rings (σ x + σ Y). This correlation was interpreted as evidence that the electronic effects of both substituents are involved in conjugated aromatic system.

  6. 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.

  7. 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.

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

    PubMed Central

    Görling, Benjamin; Bräse, Stefan; Luy, Burkhard

    2016-01-01

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

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

    PubMed

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

    2011-08-16

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

  10. 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

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

    PubMed

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

    2012-03-01

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

  12. An analysis of the pH-dependent chemical-shift behavior of phosphorus-containing metabolites

    NASA Astrophysics Data System (ADS)

    Robitaille, Pierre-Marie L.; Robitaille, Patricia A.; Gordon Brown, G.; Brown, George G.

    The pH-dependent chemical-shift behavior of phosphorus-containing metabolites was studied. Metabolites of interest included inorganic phosphate, methyl phosphonate, phosphomonoesters, phosphodiesters, phosphonates, phosphagens, and nucleotide phosphates. The data are documented in tabular form in terms of limiting chemical shifts and appropriate p Ka values. Rearranged Henderson-Hasselbalch equations are presented, for both the one- and the two-p Ka cases.

  13. 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.

  14. 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

  15. 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

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

    PubMed

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

    2016-10-01

    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.

  17. 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

  18. Chemical Shift Separation with Controlled Aliasing for Hyperpolarized 13C Metabolic Imaging

    PubMed Central

    Shin, Peter J.; Larson, Peder E.Z.; Uecker, Martin; Reed, Galen D.; Kerr, Adam B.; Tropp, James; Ohliger, Michael A.; Nelson, Sarah J.; Pauly, John M.; Lustig, Michael; Vigneron, Daniel B.

    2014-01-01

    Purpose A chemical shift separation technique for hyperpolarized 13C metabolic imaging with high spatial and temporal resolution was developed. Specifically, a fast 3D pulse sequence and a reconstruction method were implemented to acquire signals from multiple 13C species simultaneously with subsequent separation into individual images. Methods A stack of flyback-EPI readouts and a set of multiband excitation RF pulses were designed to spatially modulate aliasing patterns of the acquired metabolite images, which translated the chemical shift separation problem into parallel imaging reconstruction problem. An eight-channel coil array was used for data acquisition and a parallel imaging method based on nonlinear inversion was developed to separate the aliased images. Results Simultaneous acquisitions of pyruvate and lactate in a phantom study and in vivo rat experiments were performed. The results demonstrated successful separation of the metabolite distributions into individual images having high spatial resolution. Conclusion This method demonstrated the ability to provide accelerated metabolite imaging in hyperpolarized 13C MR utilizing multi-channel coils, tailored readout, and specialized RF pulses. PMID:25298086

  19. The Contribution of Chemical Exchange to MRI Frequency Shifts in Brain Tissue

    PubMed Central

    Shmueli, Karin; Dodd, Stephen J.; Li, Tie-Qiang; Duyn, Jeff H.

    2010-01-01

    Recent high-field MRI studies based on resonance frequency contrast have revealed brain structure with unprecedented detail. Although subtle magnetic susceptibility variations caused by iron and myelin seem to be important to this contrast, recent research on protein solutions suggests that chemical exchange between water and macromolecular protons may contribute substantially to the observed gray-white matter frequency contrast. To investigate this, we performed spectroscopic MRI experiments at 14 Tesla on samples of fixed human visual cortex and fresh pig brain. To allow direct observation of any exchange-induced frequency shifts, these samples were soaked in reference chemicals (TSP and dioxane) that are assumed not to be involved in exchange. For both fresh and fixed tissues and with both reference chemicals, substantial negative exchange-induced gray-white matter frequency contrast (−6.3 to −13.5 ppb) was found, whereas intra-cortical contrast was negligible. The sign of the gray-white matter exchange-induced frequency difference was opposite to the overall gray-white matter frequency difference observed in vivo. This suggests that exchange contributes to, but is not sufficient to explain, the frequency contrast in vivo, and that tissue susceptibility differences may have a greater contribution than previously thought. The exchange-dependent contribution may report on tissue chemical composition and pH. PMID:20928888

  20. Cuticular hydrocarbon divergence in the jewel wasp Nasonia: evolutionary shifts in chemical communication channels?

    PubMed

    Buellesbach, J; Gadau, J; Beukeboom, L W; Echinger, F; Raychoudhury, R; Werren, J H; Schmitt, T

    2013-11-01

    The evolution and maintenance of intraspecific communication channels constitute a key feature of chemical signalling and sexual communication. However, how divergent chemical communication channels evolve while maintaining their integrity for both sender and receiver is poorly understood. In this study, we compare male and female cuticular hydrocarbon (CHC) profiles in the jewel wasp genus Nasonia, analyse their chemical divergence and investigate their role as species-specific sexual signalling cues. Males and females of all four Nasonia species showed unique, nonoverlapping 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 profiles 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.

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed Central

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

    1983-01-01

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

  3. 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

  4. 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.

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

    PubMed

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

    2005-05-26

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

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

    PubMed

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

    2015-08-01

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

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

    PubMed

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

    2015-08-01

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

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Auer, Alexander A.

    2009-01-01

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

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

    PubMed

    Kou, Gaoshan; Feng, Yonge

    2015-09-01

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

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

    PubMed

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

    2016-09-01

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

  12. Chemical shift mapping of RNA interactions with the polypyrimidine tract binding protein

    PubMed Central

    Yuan, Xuemei; Davydova, Natalia; Conte, Maria R.; Curry, Stephen; Matthews, Stephen

    2002-01-01

    The polypyrimidine tract binding protein (PTB), a homodimer that contains four RRM-type RNA binding domains per monomer, plays important roles in both the regulation of alternative splicing and the stimulation of translation initiation as directed by the internal ribosome entry sites of certain picornaviruses. We have used chemical shift mapping experiments to probe the interactions between PTB-34, a recombinant fragment that contains the third and fourth RRM domains of the protein, and a number of short pyrimidine-rich RNA oligonucleotides. The results confirm that the RNAs interact primarily with the β-sheet surface of PTB-34, but also reveal roles for the two long flexible linkers within the protein fragment, a result that is supported by mutagenesis experiments. The mapping indicates distinct binding preferences for RRM3 and RRM4 with the former making a particularly specific interaction with the sequence UCUUC. PMID:11788707

  13. 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.

  14. 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.

  15. Protein apparent dielectric constant and its temperature dependence from remote chemical shift effects.

    PubMed

    An, Liaoyuan; Wang, Yefei; Zhang, Ning; Yan, Shihai; Bax, Ad; Yao, Lishan

    2014-09-17

    A NMR protocol is introduced that permits accurate measurement of minute, remote chemical shift perturbations (CSPs), caused by a mutation-induced change in the electric field. Using protein GB3 as a model system, (1)H(N) CSPs in K19A and K19E mutants can be fitted to small changes in the electric field at distal sites in the protein using the Buckingham equation, yielding an apparent dielectric constant εa of 8.6 ± 0.8 at 298 K. These CSPs, and their derived εa value, scale strongly with temperature. For example, CSPs at 313 K are about ∼30% smaller than those at 278 K, corresponding to an effective εa value of about 7.3 at 278 K and 10.5 at 313 K. Molecular dynamics simulations in explicit solvent indicate that solvent water makes a significant contribution to εa.

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

    PubMed

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

    2013-03-01

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

  17. 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.

  18. 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.

  19. Analyzing and Assigning Carbon-13 Chemical-Shift Tensors in Fructose, Sorbose, and Xylose Single Crystals

    NASA Astrophysics Data System (ADS)

    Liu, Fang; Phung, Cu G.; Alderman, D. W.; Grant, David M.

    Complete carbon-13 chemical-shift tensors are measured in single crystals of the monosaccharides β- D-fructopyranose [57-48-7], α- L-sorbopyranose [87-79-6], and α- D-xylopyranose [58-86-6] using the two-dimensional chemical-shift correlation technique with a multiple-axis sample-reorientation mechanism. Symmetry-constrained fitting of the experimental data extracts the tensors for the four equivalent molecules in the P2 12 12 1unit cells and the directions of the three twofold axes in the orthorhombic crystals. The standard deviations of the symmetry fits to the data are 0.30, 0.40, and 0.29 ppm for the three monosaccharide molecules, respectively. Gauge-invariant atomic orbital (GIAO) computations using the D-95 double-zeta basis set are then used to assign the experimental tensors to the carbons in the molecules and to the molecules in the unit cell. All assignment permutations and combinations are explored, and that which minimizes the RMS deviation between the experimental and computed tensors is accepted as the best assignment. The GIAO results also identify the experimental twofold axes with the crystallographic axes. Because the hydroxymethyl hydroxyl group in sorbose jumps between two positions, it is necessary to compute the tensors for both molecular configurations and then to take a weighted average of the results for comparison with the experimental data. The D-95 GIAO results have RMS deviations from the experimental tensors of 1.90 ppm for fructose, 2.61 ppm for sorbose, and 2.66 ppm for xylose. Similar computations confirm a previous assignment of the carbon-13 tensors in sucrose and yield a 2.85 ppm RMS deviation.

  20. Increased precision for analysis of protein-ligand dissociation constants determined from chemical shift titrations.

    PubMed

    Markin, Craig J; Spyracopoulos, Leo

    2012-06-01

    NMR is ideally suited for the analysis of protein-protein and protein ligand interactions with dissociation constants ranging from ~2 μM to ~1 mM, and with kinetics in the fast exchange regime on the NMR timescale. For the determination of dissociation constants (K ( D )) of 1:1 protein-protein or protein-ligand interactions using NMR, the protein and ligand concentrations must necessarily be similar in magnitude to the K ( D ), and nonlinear least squares analysis of chemical shift changes as a function of ligand concentration is employed to determine estimates for the parameters K ( D ) and the maximum chemical shift change (Δδ(max)). During a typical NMR titration, the initial protein concentration, [P (0)], is held nearly constant. For this condition, to determine the most accurate parameters for K ( D ) and Δδ(max) from nonlinear least squares analyses requires initial protein concentrations that are ~0.5 × K ( D ), and a maximum concentration for the ligand, or titrant, of ~10 × [P (0)]. From a practical standpoint, these requirements are often difficult to achieve. Using Monte Carlo simulations, we demonstrate that co-variation of the ligand and protein concentrations during a titration leads to an increase in the precision of the fitted K ( D ) and Δδ(max) values when [P (0)] > K ( D ). Importantly, judicious choice of protein and ligand concentrations for a given NMR titration, combined with nonlinear least squares analyses using two independent variables (ligand and protein concentrations) and two parameters (K ( D ) and Δδ(max)) is a straightforward approach to increasing the accuracy of measured dissociation constants for 1:1 protein-ligand interactions.

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

    PubMed

    Michaleas, S; Antoniadou-Vyza, E

    2006-10-11

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

  2. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  4. Predicting protein backbone chemical shifts from Cα coordinates: extracting high resolution experimental observables from low resolution models.

    PubMed

    Frank, Aaron T; Law, Sean M; Ahlstrom, Logan S; Brooks, Charles L

    2015-01-13

    Given the demonstrated utility of coarse-grained modeling and simulations approaches in studying protein structure and dynamics, developing methods that allow experimental observables to be directly recovered from coarse-grained models is of great importance. In this work, we develop one such method that enables protein backbone chemical shifts (1HN, 1Hα, 13Cα, 13C, 13Cβ, and 15N) to be predicted from Cα coordinates. We show that our Cα-based method, LARMORCα, predicts backbone chemical shifts with comparable accuracy to some all-atom approaches. More importantly, we demonstrate that LARMORCα predicted chemical shifts are able to resolve native structure from decoy pools that contain both native and non-native models, and so it is sensitive to protein structure. As an application, we use LARMORCα to characterize the transient state of the fast-folding protein gpW using recently published NMR relaxation dispersion derived backbone chemical shifts. The model we obtain is consistent with the previously proposed model based on independent analysis of the chemical shift dispersion pattern of the transient state. We anticipate that LARMORCα will find utility as a tool that enables important protein conformational substates to be identified by “parsing” trajectories and ensembles generated using coarse-grained modeling and simulations.

  5. Environment effects on the CO vibrational shifts in erbium complexes: a quantum chemical study.

    PubMed

    Ottonelli, Massimo; Musso, Gianfranco; Dellepiane, Giovanna

    2008-11-20

    The stability of lanthanide complexes and the efficiency of the energy transfer process, which makes these molecules interesting materials for technological applications, are correlated to the chemical environment surrounding the metal ion. In particular the efficiency depends on the relative position of the antenna (the ligand moiety that acts as photon absorption center) and the lanthanide ion (the emitting center), while the stability of the complex is correlated to the strength of the coordination between the rare earth and the ligands. For these reasons, knowledge of the structural properties of the complex is an interesting task to achieve. Since a large number of ligand structures hold the carboxylate group (COO(-)), which is used as an anchor for binding the antennae to the lanthanide ion, in this work we will show how the vibrational shifts of this group, induced by the interactions between the carboxylate moiety and the metal center of the lanthanide complex, can be used for obtaining in a simple way information on the structure of the chemical environment surrounding the lanthanide ion.

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

    PubMed

    Wood, Ezra C; Charest, John R

    2014-10-21

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

  7. 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.

  8. Temperature dependence of the 31P chemical shifts of nucleic acids. A prode of phosphate ester torsional conformations.

    PubMed

    Gorenstein, D G; Findlay, J B; Momii, R K; Luxon, B A; Kar, D

    1976-08-24

    The temperature dependence of the 31P chemical shifts of the ribodinucleoside monophosphates, ApA, GpC, CpC, UpU, and ApU, of the deoxyribonucleic acids, d-ApT, TpT, d-ApA, and d-pApT, and of the homopolyribonucleic acids poly(G), poly(U), poly(A) is shown to provide information on the helix-coli transition in nucleic acids. The base stacked, helical structure with a gauche,gauche phosphate ester torsional conformation is 0.2-0.6 ppm upfield from the random coil conformation. In contrast, the 31P chemical shifts of dimethyl and diethyl phosphate do not change significantly with temperature. These results support our earlier hypothesis that 31P shifts are sensitive probes of torsional conformations with phosphate esters in gauche,gauche conformations having 31P shifts upfield from nongauche conformations.

  9. Experimental evidence of an age-specific shift in chemical detection of predators in a lizard.

    PubMed

    Head, Megan L; Keogh, J Scott; Doughty, Paul

    2002-03-01

    The risk posed by predation is one of the most fundamental aspects of an animal's environment. Avoidance of predators implies an ability to obtain reliable information about the risk of predation, and for many species, chemosensory cues are likely to be an important source of such information. Chemosensory cues reliably reveal the presence of predators or their presence in the recent past. We used retreat site selection experiments to test whether the Australian scincid lizard Eulamprus heatwolei uses chemical cues for predator detection and avoidance. Both adult and juvenile lizards were given the choice of retreat sites treated with scents from invertebrate predators, as well as sympatric and allopatric snake predators. Some of the snake predators were known to eat E. heatwolei, while others did not pose a predation threat. All invertebrate predators posed a risk to juveniles, but not adults because of their size. We found that juvenile E. heatwolei avoided predator odors more strongly than adults. Juveniles avoided both invertebrate predators and snakes, and the strongest response was toward the funnel web spider, the only ambush predator used in this experiment. This result may demonstrate the importance of predator ecology in the evolution of predator detection mechanisms, with chemical cues being more useful in detecting sedentary predators than active predators. Adult lizards showed no avoidance behavior toward predator odors. This result suggests an age specific shift in predator avoidance behavior as lizards get older and become too large for many predators. However, adults showed no response to the odor from the red-bellied black snake, a known predator of adult E. heatwolei. This finding further demonstrates the importance of predator ecology when examining communication between predators and prey. Chemical cues, which are persistent long after predators have vacated the area, may not be useful in detecting the red-bellied black snake, a wide

  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.

  12. Chemical shift assignments of zinc finger domain of methionine aminopeptidase 1 (MetAP1) from Homo sapiens.

    PubMed

    Rachineni, Kavitha; Arya, Tarun; Singarapu, Kiran Kumar; Addlagatta, Anthony; Bharatam, Jagadeesh

    2015-10-01

    Methionine aminopeptidase Type I (MetAP1) cleaves the initiator methionine from about 70 % of all newly synthesized proteins in almost every living cell. Human MetAP1 is a two domain protein with a zinc finger on the N-terminus and a catalytic domain on the C-terminus. Here, we report the chemical shift assignments of the amino terminal zinc binding domain (ZBD) (1-83 residues) of the human MetAP1 derived by using advanced NMR spectroscopic methods. We were able to assign the chemical shifts of ZBD of MetAP1 nearly complete, which reveal two helical fragments involving residues P44-L49 (α1) and Q59-K82 (α2). The protein structure unfolds upon complex formation with the addition of 2 M excess EDTA, indicated by the appearance of amide resonances in the random coil chemical shift region of (15)NHSQC spectrum.

  13. 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

  14. [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

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

    PubMed

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

    2013-01-24

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

  16. 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

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

    PubMed Central

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

    2012-01-01

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

  18. 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

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

    PubMed

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

    2016-01-01

    Previous studies have reported significant region-dependent differences in the fiber-type composition of human skeletal muscle. It is therefore hypothesized that there is a difference between the deep and superficial parts of muscle energy metabolism during exercise. We hypothesized that the inorganic phosphate (Pi)/phosphocreatine (PCr) ratio of the superficial parts would be higher, compared with the deep parts, as the work rate increases, because the muscle fiber-type composition of the fast-type may be greater in the superficial parts compared with the deep parts. This study used two-dimensional 31Phosphorus Chemical Shift Imaging (31P-CSI) to detect differences between the deep and superficial parts of the human leg muscles during dynamic knee extension exercise. Six healthy men participated in this study (age 27±1 year, height 169.4±4.1 cm, weight 65.9±8.4 kg). The experiments were carried out with a 1.5-T superconducting magnet with a 5-in. diameter circular surface coil. The subjects performed dynamic one-legged knee extension exercise in the prone position, with the transmit-receive coil placed under the right quadriceps muscles in the magnet. The subjects pulled down an elastic rubber band attached to the ankle at a frequency of 0.25, 0.5 and 1 Hz for 320 s each. The intracellular pH (pHi) was calculated from the median chemical shift of the Pi peak relative to PCr. No significant difference in Pi/PCr was observed between the deep and the superficial parts of the quadriceps muscles at rest. The Pi/PCr of the superficial parts was not significantly increased with increasing work rate. Compared with the superficial areas, the Pi/PCr of the deep parts was significantly higher (p<0.05) at 1 Hz. The pHi showed no significant difference between the two parts. These results suggest that muscle oxidative metabolism is different between deep and superficial parts of quadriceps muscles during dynamic exercise. PMID:26782194

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

    PubMed

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

    2016-01-01

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

  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. Chemical shift assignment of the alternative scaffold protein IscA.

    PubMed

    Popovic, Matija; Pastore, Annalisa

    2016-04-01

    The IscA protein (11.5 kDa) is an essential component of the iron sulphur cluster biogenesis machine. In bacteria, the machine components are clustered in operons, amongst which the most important is the isc operon. Bacterial IscA has direct homologues also in eukaryotes. Like the protein IscU, IscA is thought to assist cluster formation as an alternative scaffold protein which receives the cluster before transferring it further to the final acceptors. Several crystal structures have been published. They all report an IscA dimeric form, although the packing of the protomers in the dimers differs amongst structures. No solution studies have currently been reported. Here we report the (1)H, (13)C and (15)N backbone and side-chain chemical shift assignments of the cluster-free E. coli IscA as a starting point for further studies of the structure and functions of this still poorly characterized protein. We show that IscA exists in solution as an equilibrium between different species. Spectrum assignment was thus challenging given the heterogeneous nature of the sample but doable through judicious choice of selective labelling and concentration dependent studies.

  3. Chemical Shift Encoded Water–Fat Separation Using Parallel Imaging and Compressed Sensing

    PubMed Central

    Sharma, Samir D.; Hu, Houchun H.; Nayak, Krishna S.

    2013-01-01

    Chemical shift encoded techniques have received considerable attention recently because they can reliably separate water and fat in the presence of off-resonance. The insensitivity to off-resonance requires that data be acquired at multiple echo times, which increases the scan time as compared to a single echo acquisition. The increased scan time often requires that a compromise be made between the spatial resolution, the volume coverage, and the tolerance to artifacts from subject motion. This work describes a combined parallel imaging and compressed sensing approach for accelerated water–fat separation. In addition, the use of multiscale cubic B-splines for B0 field map estimation is introduced. The water and fat images and the B0 field map are estimated via an alternating minimization. Coil sensitivity information is derived from a calculated k-space convolution kernel and l1-regularization is imposed on the coil-combined water and fat image estimates. Uniform water–fat separation is demonstrated from retrospectively undersampled data in the liver, brachial plexus, ankle, and knee as well as from a prospectively undersampled acquisition of the knee at 8.6x acceleration. PMID:22505285

  4. Multiband excitation pulses for hyperpolarized 13C dynamic chemical-shift imaging

    NASA Astrophysics Data System (ADS)

    Larson, Peder E. Z.; Kerr, Adam B.; Chen, Albert P.; Lustig, Michael S.; Zierhut, Matthew L.; Hu, Simon; Cunningham, Charles H.; Pauly, John M.; Kurhanewicz, John; Vigneron, Daniel B.

    2008-09-01

    Hyperpolarized 13C offers high signal-to-noise ratios for imaging metabolic activity in vivo, but care must be taken when designing pulse sequences because the magnetization cannot be recovered once it has decayed. It has a short lifetime, on the order of minutes, and gets used up by each RF excitation. In this paper, we present a new dynamic chemical-shift imaging method that uses specialized RF pulses designed to maintain most of the hyperpolarized substrate while providing adequate SNR for the metabolic products. These are multiband, variable flip angle, spectral-spatial RF pulses that use spectral selectivity to minimally excite the injected prepolarized 13C-pyruvate substrate. The metabolic products of lactate and alanine are excited with a larger flip angle to increase SNR. This excitation was followed by an RF amplitude insensitive double spin-echo and an echo-planar flyback spectral-spatial readout gradient. In vivo results in rats and mice are presented showing improvements over constant flip angle RF pulses. The metabolic products are observable for a longer window because the low pyruvate flip angle preserves magnetization, allowing for improved observation of spatially varying metabolic reactions.

  5. Xenon NMR of liquid crystals confined to cylindrical nanocavities: a simulation study.

    PubMed

    Karjalainen, Jouni; Vaara, Juha; Straka, Michal; Lantto, Perttu

    2015-03-21

    Applications of liquid crystals (LCs), such as smart windows and the ubiquitous display devices, are based on controlling the orientational and translational order in a small volume of LC medium. Hence, understanding the effects of confinement to the liquid crystal phase behaviour is essential. The NMR shielding of (129)Xe atoms dissolved in LCs constitutes a very sensitive probe to the details of LC environment. Linking the experimental results to microscopic phenomena calls for molecular simulations. In this work, the NMR shielding of atomic (129)Xe dissolved in a uniaxial thermotropic LC confined to nanosized cylindrical cavities is computed from coarse-grained (CG) isobaric Monte Carlo (MC) simulations with a quantum-chemically (QC) pre-parameterised pairwise-additive model for the Xe nuclear shielding tensor. We report the results for the (129)Xe nuclear shielding and its connection to the structure and order of the LC appropriate to two different cavity sizes, as well as a comparison to the results of bulk (non-confined) simulations. We find that the confinement changes the LC phase structure dramatically and gives rise to the coexistence of varying degrees of LC order, which is reflected in the Xe shielding. Furthermore, we qualitatively reproduce the behaviour of the mean (129)Xe chemical shift with respect to temperature for atomic Xe dissolved in LC confined to controlled-pore glass materials. In the small-radius cavity the nematic - paranematic phase transition is revealed only by the anisotropic component of the (129)Xe nuclear shielding. In the larger cavity, the nematic - paranematic - isotropic transition is clearly seen in the Xe shielding. The simulated (129)Xe NMR shielding is insensitive to the smectic-A - nematic transition, since in the smectic-A phase, the Xe atoms largely occupy the imperfect layer structure near the cavity walls. The direct contribution of the cavity wall to (129)Xe nuclear shielding is dependent on the cavity size but

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

    SciTech Connect

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

    1996-02-01

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

  7. 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.

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

    PubMed

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

    2014-09-14

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

  9. 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

  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.

  11. 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

  12. Limiting Values of the 15N Chemical Shift of the Imidazole Ring of Histidine at High-pH§

    PubMed Central

    Vila, Jorge A.

    2012-01-01

    Tautomeric identification by direct observation of 15N chemical shifts of the imidazole ring of histidine (His) has become a common practice in NMR spectroscopy. However, such applications require knowledge of the “canonical” limiting values of the 15N chemical shift of the imidazole ring of His in which each form of His, namely the protonated (H+) and the tautomeric Nε2-H and Nδ1-H forms, respectively, is present to the extent of 100%. So far, the adopted canonical limiting values of the 15N chemical shift have been those available from model compounds. As to whether these canonical values reflect those of the individual pure forms of His is investigated here by carrying out an analysis of the second-order shielding differences, ΔΔ = |Δε − Δδ, with Δξ(ξ = ε or δ) being the DFT-computed average shielding differences between the two nitrogens of the imidazole ring of His in each pure tautomeric form. In the high-pH limit the results indicate that the (i) ΔΔ values from the DFT-computed shielding, but not from the commonly-used canonical limiting values, are in closer agreement with those obtained with experimental chemical shift data from model compounds in solution and solid-state NMR; and (ii) commonly-used canonical limiting values of the 15N chemical shifts lead to an average tautomeric equilibrium constant that differs by a factor of ~2.6 from the one computed by using DFT-based 15N limiting values, raising concern about the practice of using canonical limiting 15N values; this can be avoided by reporting tautomeric equilibrium constants computed by using only limiting 15N values for the Nε2-H tautomer. PMID:22376024

  13. 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

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

    PubMed

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

    2015-09-01

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

  15. 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.

  16. 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

  17. 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.

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

    PubMed

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

    2015-01-01

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

  19. 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

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

    PubMed

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

    2014-01-01

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

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

    SciTech Connect

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

    2012-03-14

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

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

    PubMed

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

    2008-09-01

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

  3. Identification of zinc-ligated cysteine residues based on 13Calpha and 13Cbeta chemical shift data.

    PubMed

    Kornhaber, Gregory J; Snyder, David; Moseley, Hunter N B; Montelione, Gaetano T

    2006-04-01

    Although a significant number of proteins include bound metals as part of their structure, the identification of amino acid residues coordinated to non-paramagnetic metals by NMR remains a challenge. Metal ligands can stabilize the native structure and/or play critical catalytic roles in the underlying biochemistry. An atom's chemical shift is exquisitely sensitive to its electronic environment. Chemical shift data can provide valuable insights into structural features, including metal ligation. In this study, we demonstrate that overlapped 13Cbeta chemical shift distributions of Zn-ligated and non-metal-ligated cysteine residues are largely resolved by the inclusion of the corresponding 13Calpha chemical shift information, together with secondary structural information. We demonstrate this with a bivariate distribution plot, and statistically with a multivariate analysis of variance (MANOVA) and hierarchical logistic regression analysis. Using 287 13Calpha/13Cbeta shift pairs from 79 proteins with known three-dimensional structures, including 86 13Calpha and 13Cbeta shifts for 43 Zn-ligated cysteine residues, along with corresponding oxidation state and secondary structure information, we have built a logistic regression model that distinguishes between oxidized cystines, reduced (non-metal ligated) cysteines, and Zn-ligated cysteines. Classifying cysteines/cystines with a statistical model incorporating all three phenomena resulted in a predictor of Zn ligation with a recall, precision and F-measure of 83.7%, and an accuracy of 95.1%. This model was applied in the analysis of Bacillus subtilis IscU, a protein involved in iron-sulfur cluster assembly. The model predicts that all three cysteines of IscU are metal ligands. We confirmed these results by (i) examining the effect of metal chelation on the NMR spectrum of IscU, and (ii) inductively coupled plasma mass spectrometry analysis. To gain further insight into the frequency of occurrence of non-cysteine Zn

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

    PubMed

    Liu, Yun; Nekvasil, Hanna; Tossell, John

    2005-04-01

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

  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. Effects of surface chemistry on the porous structure of coal. Quarterly technical progress report, July 1996--September 1996

    SciTech Connect

    Anderson, S.A.; Hatcher, P.G.; Radovic, L.R.

    1996-10-01

    The primary objective of this project is to use {sup 129}Xe NMR to characterize the microporous structure of coals. We will use direct information on pore size, as well as indirect information from adsorption rates and evidence for intra/extraparticle diffusion, to characterize the connectivity of the micropore network. A second objective is to use {sup 129}Xe NMR to describe the effect of controlled opening of the micropores in a microporous carbon by oxygen chemi-sorption/desorption. Our experimental focus in this quarter has been the low power presaturation of the NMR signal of {sup 129}Xe adsorbed in coal. Preliminary work on this experiment was reported in the last quarter. Low power presaturation of {sup 129}Xe adsorbed in two coals produces a hole-burning effect in the adsorbed xenon NMR signals, indicating that these signals are broad due to overlap of a series of chemical shifts. Saturation transfer to the entire adsorbed xenon signal and to the extraparticle gas is observed with increasing presaturation time. Differences in timing of saturation transfer to the external gas have implications for the nature of the connectivity of the pore structures in coal.

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

    PubMed

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

    2008-04-01

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

  8. Observed and calculated 1H and 13C chemical shifts induced by the in situ oxidation of model sulfides to sulfoxides and sulfones.

    PubMed

    Dracínský, Martin; Pohl, Radek; Slavetínská, Lenka; Budesínský, Milos

    2010-09-01

    A series of model sulfides was oxidized in the NMR sample tube to sulfoxides and sulfones by the stepwise addition of meta-chloroperbenzoic acid in deuterochloroform. Various methods of quantum chemical calculations have been tested to reproduce the observed (1)H and (13)C chemical shifts of the starting sulfides and their oxidation products. It has been shown that the determination of the energy-minimized conformation is a very important condition for obtaining realistic data in the subsequent calculation of the NMR chemical shifts. The correlation between calculated and observed chemical shifts is very good for carbon atoms (even for the 'cheap' DFT B3LYP/6-31G* method) and somewhat less satisfactory for hydrogen atoms. The calculated chemical shifts induced by oxidation (the Delta delta values) agree even better with the experimental values and can also be used to determine the oxidation state of the sulfur atom (-S-, -SO-, -SO(2)-).

  9. 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

  10. 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

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

    PubMed

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

    2016-06-01

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

  12. 13C and 15N—Chemical Shift Anisotropy of Ampicillin and Penicillin-V Studied by 2D-PASS and CP/MAS NMR

    NASA Astrophysics Data System (ADS)

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

    1998-11-01

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

  13. Carbon-13 chemical shift tensor correlation via spin diffusion in solid tropolone using switched-angle spinning spectroscopy

    SciTech Connect

    Larsen, R.G.; Lee, Y.K.; He, B.; Yang, J.O.; Luz, Z.; Zimmermann, H.; Pines, A.

    1995-12-08

    In switched-angle spinning spectroscopy (SAS) a sample is spun about different angles, {beta}, relative to the magnetic field, during various periods of the experiment. In the present work, SAS is combined with two-dimensional exchange spectroscopy in order to correlate carbon-13 chemical shift tensors of the carbonyl (1) and hydroxyl (2) carbons of tropolone. Experiments were performed on a sample enriched to 25 at. % in each of these sites (at different molecules). At this level of enrichment the dominant exchange mechanism between the two sites involves spin diffusion. The experiment consists of a preparation period during which the sample spins at the magic angle and the magnetization of one of the sites is quenched by means of a selective pulse sequence. During the rest of the experiment the sample spins with its axis away from the magic angle except for a short period just before the detection where the axis is switched to the magic angle in order to select the magnetization to be detected. Experiments were performed for all four possible combinations of the initial and final magnetizations, thus providing chemical shift correlations between carbons 1,1{prime}, 2, and 2{prime} in the two magnetically inequivalent (but symmetry related) molecules in the unit cell. Combining these results with the known crystal structure of tropolone (neglecting a small tilt between the perpendicular to the molecular plane and the crystallographic {bold c}-axis) provides information on the orientation and magnitude of the chemical shift tensors of the two types of carbons. The principal values (in ppm) are {sigma}{sup 1}{sub {ital xx}}=65, {sigma}{sup 1}{sub {ital yy}}=33, {sigma}{sup 1}{sub {ital zz}}={minus}98, {sigma}{sup 2}{sub {ital xx}}=77, {sigma}{sup 2}{sub {ital yy}}=17, and {sigma}{sup 2}{sub {ital zz}}={minus}94. (Abstract Truncated)

  14. 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.

  15. 13C NMR spectra of 1,3-dipyridyl- and pyridylphenylthioureas. Chemical shift assignments and conformational implications

    NASA Astrophysics Data System (ADS)

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

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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. A Bayesian-probability-based method for assigning protein backbone dihedral angles based on chemical shifts and local sequences.

    PubMed

    Wang, Jun; Liu, Haiyan

    2007-01-01

    Chemical shifts contain substantial information about protein local conformations. We present a method to assign individual protein backbone dihedral angles into specific regions on the Ramachandran map based on the amino acid sequences and the chemical shifts of backbone atoms of tripeptide segments. The method uses a scoring function derived from the Bayesian probability for the central residue of a query tripeptide segment to have a particular conformation. The Ramachandran map is partitioned into representative regions at two levels of resolution. The lower resolution partitioning is equivalent to the conventional definitions of different secondary structure regions on the map. At the higher resolution level, the alpha and beta regions are further divided into subregions. Predictions are attempted at both levels of resolution. We compared our method with TALOS using the original TALOS database, and obtained comparable results. Although TALOS may produce the best results with currently available databases which are much enlarged, the Bayesian-probability-based approach can provide a quantitative measure for the reliability of predictions.

  1. Application of multivariate image analysis in QSPR study of 13C chemical shifts of naphthalene derivatives: a comparative study.

    PubMed

    Garkani-Nejad, Zahra; Poshteh-Shirani, Marziyeh

    2010-11-15

    A new implemented QSPR method, whose descriptors achieved from bidimensional images, was applied for predicting (13)C NMR chemical shifts of 25 mono substituted naphthalenes. The resulted descriptors were subjected to principal component analysis (PCA) and the most significant principal components (PCs) were extracted. MIA-QSPR (multivariate image analysis applied to quantitative structure-property relationship) modeling was done by means of principal component regression (PCR) and principal component-artificial neural network (PC-ANN) methods. Eigen value ranking (EV) and correlation ranking (CR) were used here to select the most relevant set of PCs as inputs for PCR and PC-ANN modeling methods. The results supported that the correlation ranking-principal component-artificial neural network (CR-PC-ANN) model could predict the (13)C NMR chemical shifts of all 10 carbon atoms in mono substituted naphthalenes with R(2) ≥ 0.922 for training set, R(2) ≥ 0.963 for validation set and R(2) ≥ 0.936 for the test set. Comparison of the results with other existing factor selection method revealed that less accurate results were obtained by the eigen value ranking procedure. PMID:21035668

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

    PubMed

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

    2015-11-17

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

  3. 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.

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

    PubMed Central

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

    1997-01-01

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

  5. The chemical bond in external electric fields: energies, geometries, and vibrational Stark shifts of diatomic molecules.

    PubMed

    Sowlati-Hashjin, Shahin; Matta, Chérif F

    2013-10-14

    It is shown that the response of molecular properties of diatomics such as the total energy, the bond length, and the vibrational Stark shift to an external homogenous electric field (EF) can be predicted from field-free observable properties such as the equilibrium bond length, the bond dissociation energy, the polarizability and dipole moment functions, and the vibrational frequency. Delley [J. Mol. Struct.: THEOCHEM 434, 229 (1998)] suggested to approximate the potential energy surface under an EF by a Morse function augmented with a EF term proportional to the internuclear separation. In this work, this term is replaced by the expression of the field-induced energy change which yields a field-perturbed Morse potential that tends to a constant asymptotic limit when the EF term itself become proportional to the sum of the polarizabilities of the separated atoms. The model is validated by comparison with direct calculations on nine diatomics, five homo-nuclear (H2, N2, O2, F2, and Cl2) and four hetero-nuclear (HF, HCl, CO, and NO), covering a range and combinations of dipole moments and polarizabilities. Calculations were conducted at the quadratic configuration interaction with single and double excitations (QCISD) and density functional theory (DFT)-B3LYP levels of theory using the 6-311++G(3df,2pd) basis set. All results agree closely at the two levels of theory except for the Stark effect of NO which is not correctly predicted by QCISD calculations as further calculations, including at the coupled cluster with single and double excitation (CCSD) level of theory, demonstrate.

  6. 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.

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

    SciTech Connect

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

    1996-10-01

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

  8. 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.

  9. 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

  10. 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.

  11. 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.

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

    Gersbach, P V; Reddy, N

    2002-08-01

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

  14. 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.

  15. 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.

  16. 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

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

    PubMed Central

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

    1997-01-01

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

  18. 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.

  19. Zero discharge tanning: a shift from chemical to biocatalytic leather processing.

    PubMed

    Thanikaivelan, Palanisamy; Rao, Jonnalagadda Raghava; Nair, Balachandran Unni; Ramasami, Thirumalachari

    2002-10-01

    Beam house processes (Beam house processes generally mean liming-reliming processes, which employ beam.) contribute more than 60% of the total pollution from leather processing. The use of lime and sodium sulfide is of environmental concern (1, 2). Recently, the authors have developed an enzyme-based dehairing assisted with a very low amount of sodium sulfide, which completely avoids the use of lime. However, the dehaired pelt requires opening up of fiber bundles for further processing, where lime is employed to achieve this through osmotic swelling. Huge amounts of lime sludge and total solids are the main drawbacks of lime. An alternative bioprocess, based on alpha-amylase for fiber opening, has been attempted after enzymatic unhairing. This totally eliminates the use of lime in leather processing. This method enables subsequent processes and operations in leather making feasible without a deliming process. A control experiment was run in parallel using conventional liming-reliming processes. It has been found that the extent of opening up of fiber bundles using alpha-amylase is comparable to that of the control. This has been substantiated through scanning electron microscopic, stratigraphic chrome distribution analysis, and softness measurements. Performance of the leathers is shown to be on a par with leathers produced by the conventional process through physical and hand evaluation. Importantly, softness of the leathers is numerically proven to be comparable with that of control. The process also demonstrates reduction in chemical oxygen demand load by 45% and total solids load by 20% compared to the conventional process. The total dry sludge from the beam house processes is brought down from 152 to 8 kg for processing 1 ton of raw hides.

  20. 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...

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

    PubMed

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

    2016-04-01

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

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

    PubMed

    Liu, Zizhong; Goddard, John D

    2009-12-17

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

  3. 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.

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

    PubMed Central

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy

    2015-01-01

    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 1H 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 1H/1H 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

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

    PubMed

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

    2010-10-14

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

  6. 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

  7. Separation of quadrupolar and chemical/paramagnetic shift interactions in two-dimensional 2H (I=1) nuclear magnetic resonance spectroscopy

    NASA Astrophysics Data System (ADS)

    Antonijevic, Sasa; Wimperis, Stephen

    2005-01-01

    A novel two-dimensional 2H (spin I=1) nuclear magnetic resonance technique is introduced for determination of both quadrupole and chemical/paramagnetic shift tensors and their relative orientation. The new method is based upon the well-known quadrupolar-echo experiment and is designed to refocus the quadrupolar interaction at the end of the t1 evolution period while retaining the modulation introduced by the shift interaction. As a result, a projection of the resulting two-dimensional spectrum onto its F1 dimension yields a shift anisotropy powder lineshape free from any quadrupolar broadening. The chemical/paramagnetic shifts appear in both F1 and F2 dimensions and are thus spread along a +1 frequency gradient; hence, a projection orthogonal to this gradient yields the pure quadrupolar powder lineshape, free from all shift interaction effects. The relative orientation of the quadrupole and shift tensors can be obtained by analysis of the full two-dimensional correlation lineshape. Unlike the well-known double-quantum experiment, the new method is, in principle, equally effective for all values of the quadrupolar splitting, including zero. The properties of the new technique are demonstrated using computer simulation and methods for the extraction of quadrupole and shift tensor parameters are described. The new technique is applied to (diamagnetic) benzoic acid-d1 (C6H5CO2D) and (paramagnetic) copper(II) chloride dihydrate-d4 (CuCl2ṡ2D2O).

  8. Separation of quadrupolar and chemical/paramagnetic shift interactions in two-dimensional 2H (I=1) nuclear magnetic resonance spectroscopy.

    PubMed

    Antonijevic, Sasa; Wimperis, Stephen

    2005-01-22

    A novel two-dimensional (2)H (spin I=1) nuclear magnetic resonance technique is introduced for determination of both quadrupole and chemical/paramagnetic shift tensors and their relative orientation. The new method is based upon the well-known quadrupolar-echo experiment and is designed to refocus the quadrupolar interaction at the end of the t(1) evolution period while retaining the modulation introduced by the shift interaction. As a result, a projection of the resulting two-dimensional spectrum onto its F(1) dimension yields a shift anisotropy powder lineshape free from any quadrupolar broadening. The chemical/paramagnetic shifts appear in both F(1) and F(2) dimensions and are thus spread along a +1 frequency gradient; hence, a projection orthogonal to this gradient yields the pure quadrupolar powder lineshape, free from all shift interaction effects. The relative orientation of the quadrupole and shift tensors can be obtained by analysis of the full two-dimensional correlation lineshape. Unlike the well-known double-quantum experiment, the new method is, in principle, equally effective for all values of the quadrupolar splitting, including zero. The properties of the new technique are demonstrated using computer simulation and methods for the extraction of quadrupole and shift tensor parameters are described. The new technique is applied to (diamagnetic) benzoic acid-d(1) (C(6)H(5)CO(2)D) and (paramagnetic) copper(II) chloride dihydrate-d(4) (CuCl(2).2D(2)O). PMID:15740253

  9. 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.

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

    PubMed Central

    CHAI, JUN; LIU, PENG; JIN, ERHU; SU, TIANHAO; ZHANG, JIE; SHI, KAINING; HONG, XU; YIN, JIE; YU, HENGCHI

    2016-01-01

    The present study aimed to investigate the association between the content and distribution of fat in the pancreas and liver in patients with type 2 diabetes mellitus (T2DM). A total of 70 patients newly diagnosed with T2DM (T2DM group) and 30 healthy volunteers (normal control group) were enrolled in the present study. Dual-echo magnetic resonance (MR) chemical shift imaging was used to measure the fat content of the liver and the head, body and tail regions of the pancreas. In addition, the distribution of fat in the various regions of the pancreas, as well as the average fat content of the pancreas versus the liver, were compared. The fat content of the pancreatic head, body and tail regions of the T2DM group were 5.59±4.70, 4.80±3.75 and 4.89±3.86%, respectively. The fat content of these regions in the normal control group were 3.89±2.47, 3.30±2.11 and 3.23±2.23%, respectively. The average fat content of the pancreas was 5.19±3.75% for the T2DM group and 3.47±2.00% for the normal control group. The average fat content of the liver was 9.87±3.19% for the T2DM group and 7.24±2.38% for the normal control group. Therefore, the results from MR chemical shift imaging suggested that there were no significant differences in the distribution of fat between the pancreas of patients newly diagnosed with T2DM and that from the healthy population; however, the average fat content in the pancreas of the T2DM group was significantly higher (F=3.597; P<0.05), as compared with the normal control group. In addition, there was no correlation between the fat contents in the pancreas and liver in patients newly diagnosed with T2DM and the healthy population. PMID:26893633

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

    PubMed

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

    2013-06-11

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

  12. 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

  13. 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

  14. 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

  15. Chemical shifts assignments of the archaeal MC1 protein and a strongly bent 15 base pairs DNA duplex in complex.

    PubMed

    Loth, Karine; Landon, Céline; Paquet, Françoise

    2015-04-01

    MC1 is the most abundant architectural protein present in Methanosarcina thermophila CHTI55 in laboratory growth conditions and is structurally unrelated to other DNA-binding proteins. MC1 functions are to shape and to protect DNA against thermal denaturation by binding to it. Therefore, MC1 has a strong affinity for any double-stranded DNA. However, it recognizes and preferentially binds to bent DNA, such as four-way junctions and negatively supercoiled DNA minicircles. Combining NMR data, electron microscopy data, biochemistry, molecular modelisation and docking approaches, we proposed recently a new type of DNA/protein complex, in which the monomeric protein MC1 binds on the concave side of a strongly bent 15 base pairs DNA. We present here the NMR chemical shifts assignments of each partner in the complex, (1)H (15)N MC1 protein and (1)H (13)C (15)N bent duplex DNA, as first step towards the first experimental 3D structure of this new type of DNA/protein complex.

  16. 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.

  17. (1)H, (13)C, and (15)N chemical shifts assignments for human endothelial monocyte-activating polypeptide EMAP II.

    PubMed

    Lozhko, Dmytro; Stanek, Jan; Kazimierczuk, Krzysztof; Zawadzka-Kazimierczuk, Anna; Kozminski, Wiktor; Zhukov, Igor; Kornelyuk, Alexander

    2013-04-01

    Endothelial and monocyte-activating polypeptide II (EMAP II) is a cytokine that plays an important role in inflammation, apoptosis and angiogenesis processes in tumour tissues. Structurally, the EMAP II is a 169 amino acid residues long C-terminal domain (residues 147-312) of auxiliary tRNA binding protein p43. In spite of existence in pdb databank of two X-ray structures there are some important aspects of EMAP II cytokine function which are still not fully understood in detail. To obtain information about 3D structure and backbone dynamic processes in solution we perform structure evaluation of human EMAP II cytokine by NMR spectroscopy. The standard approach to sequence-specific backbone assignment using 3D NMR data sets was not successful in our studies and was supplemented by recently developed 4D NMR experiments with random sampling of evolution time space. Here we report the backbone and side chain (1)H, (13)C, and (15)N chemical shifts in solution for recombinant EMAP II cytokine together with secondary structure provided by TALOS + software.

  18. 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.

  19. Ultrafast magnetic-resonance-imaging velocimetry of liquid-liquid systems: overcoming chemical-shift artifacts using compressed sensing.

    PubMed

    Tayler, Alexander B; Benning, Martin; Sederman, Andrew J; Holland, Daniel J; Gladden, Lynn F

    2014-06-01

    We present simultaneous measurement of dispersed and continuous phase flow fields for liquid-liquid systems obtained using ultrafast magnetic resonance imaging. Chemical-shift artifacts, which are otherwise highly problematic for this type of measurement, are overcome using a compressed sensing based image reconstruction algorithm that accounts for off-resonant signal components. This scheme is combined with high-temporal-resolution spiral imaging (188 frames per second), which is noted for its robustness to flow. It is demonstrated that both quantitative signal intensity and phase preconditioning are preserved throughout the image reconstruction algorithm. Measurements are acquired of oil droplets of varying viscosity rising through stagnant water. From these data it is apparent that the internal droplet flow fields are heavily influenced by the droplet shape oscillations, and that the accurate modeling of droplet shape is of critical importance in the modeling of droplet-side hydrodynamics. The application of the technique to three-component systems is also demonstrated, as is the measurement of local concentration maps of a mutually soluble species (acetone in polydimethylsiloxane-water). PMID:25019881

  20. Ultrafast magnetic-resonance-imaging velocimetry of liquid-liquid systems: overcoming chemical-shift artifacts using compressed sensing.

    PubMed

    Tayler, Alexander B; Benning, Martin; Sederman, Andrew J; Holland, Daniel J; Gladden, Lynn F

    2014-06-01

    We present simultaneous measurement of dispersed and continuous phase flow fields for liquid-liquid systems obtained using ultrafast magnetic resonance imaging. Chemical-shift artifacts, which are otherwise highly problematic for this type of measurement, are overcome using a compressed sensing based image reconstruction algorithm that accounts for off-resonant signal components. This scheme is combined with high-temporal-resolution spiral imaging (188 frames per second), which is noted for its robustness to flow. It is demonstrated that both quantitative signal intensity and phase preconditioning are preserved throughout the image reconstruction algorithm. Measurements are acquired of oil droplets of varying viscosity rising through stagnant water. From these data it is apparent that the internal droplet flow fields are heavily influenced by the droplet shape oscillations, and that the accurate modeling of droplet shape is of critical importance in the modeling of droplet-side hydrodynamics. The application of the technique to three-component systems is also demonstrated, as is the measurement of local concentration maps of a mutually soluble species (acetone in polydimethylsiloxane-water).

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

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

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

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

    PubMed

    Muñoz, Marcelo A; Joseph-Nathan, Pedro

    2010-06-01

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

  3. 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

  4. 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.

  5. High-resolution electron spin resonance spectroscopy of XeF* in solid argon. The hyperfine structure constants as a probe of relativistic effects in the chemical bonding properties of a heavy noble gas atom.

    PubMed

    Misochko, Eugenii Ya; Akimov, Alexander V; Goldschleger, Ilya U; Tyurin, Danil A; Laikov, Dimitri N

    2005-01-15

    Xenon fluoride radicals were generated by solid-state chemical reactions of mobile fluorine atoms with xenon atoms trapped in Ar matrix. Highly resolved electron spin resonance spectra of XeF* were obtained in the temperature range of 5-25 K and the anisotropic hyperfine parameters were determined for magnetic nuclei 19F, 129Xe, and 131Xe using naturally occurring and isotopically enriched xenon. Signs of parallel and perpendicular hyperfine components were established from analysis of temperature changes in the spectra and from numerical solutions of the spin Hamiltonian for two nonequivalent magnetic nuclei. Thus, the complete set of components of hyperfine- and g-factor tensors of XeF* were obtained: 19F (Aiso=435, Adip=1249 MHz) and 129Xe (Aiso=-1340, Adip=-485 MHz); g(parallel)=1.9822 and g(perpendicular)=2.0570. Comparison of the measured hyperfine parameters with those predicted by density-functional theory (DFT) calculations indicates, that relativistic DFT gives true electron spin distribution in the 2Sigma+ ground-state, whereas nonrelativistic theory underestimates dramatically the electron-nuclear contact Fermi interaction (Aiso) on the Xe atom. Analysis of the obtained magnetic-dipole interaction constants (Adip) shows that fluorine 2p and xenon 5p atomic orbitals make a major contribution to the spin density distribution in XeF*. Both relativistic and nonrelativistic calculations give close magnetic-dipole interaction constants, which are in agreement with the measured values. The other relativistic feature is considerable anisotropy of g-tensor, which results from spin-orbit interaction. The orbital contribution appears due to mixing of the ionic 2Pi states with the 2Sigma+ ground state, and the spin-orbit interaction plays a significant role in the chemical bonding of XeF*.

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

    PubMed

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

    2013-05-01

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

  7. 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

  8. 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.

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

    PubMed

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

    2016-01-01

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

  10. Evaluation of (95)Mo Nuclear Shielding and Chemical Shift of [Mo6X14](2-) Clusters in the Liquid Phase.

    PubMed

    Nguyen, Thi Thuong; Jung, Julie; Trivelli, Xavier; Trébosc, Julien; Cordier, Stéphane; Molard, Yann; Le Pollès, Laurent; Pickard, Chris J; Cuny, Jérôme; Gautier, Régis

    2015-08-17

    [Mo6X14](2-) octahedral molybdenum clusters are the main building blocks of a large range of materials. Although (95)Mo nuclear magnetic resonance was proposed to be a powerful tool to characterize their structural and dynamical properties in solution, these measurements have never been complemented by theoretical studies which can limit their interpretation for complex systems. In this Article, we use quantum chemical calculations to evaluate the (95)Mo chemical shift of three clusters: [Mo6Cl14](2-), [Mo6Br14](2-), and [Mo6I14](2-). In particular, we test various computational parameters influencing the quality of the results: size of the basis set, treatment of relativistic and solvent effects. Furthermore, to provide quantum chemical calculations that are directly comparable with experimental data, we evaluate for the first time the (95)Mo nuclear magnetic shielding of the experimental reference, namely, MoO4(2-) in aqueous solution. This is achieved by combining ab initio molecular dynamics simulations with a periodic approach to evaluate the (95)Mo nuclear shieldings. The results demonstrate that, despite the difficulty to obtain accurate (95)Mo chemical shifts, relative values for a cluster series can be fairly well-reproduced by DFT calculations. We also show that performing an explicit solvent treatment for the reference compound improves by ∼50 ppm the agreement between theory and experiment. Finally, the standard deviation of ∼70 ppm that we calculate for the (95)Mo nuclear shielding of the reference provides an estimation of the accuracy we can achieve for the calculation of the (95)Mo chemical shifts using a static approach. These results demonstrate the growing ability of quantum chemical calculations to complement and interpret complex experimental measurements.

  11. First-principles calculation of spectral features, chemical shift and absolute threshold of ELNES and XANES using a plane wave pseudopotential method

    NASA Astrophysics Data System (ADS)

    Mizoguchi, Teruyasu; Tanaka, Isao; Gao, Shang-Peng; Pickard, Chris J.

    2009-03-01

    Spectral features, chemical shifts, and absolute thresholds of electron energy loss near-edge structure (ELNES) and x-ray absorption near-edge structure (XANES) for selected compounds, i.e. TiO2 (rutile), TiO2 (anatase), SrTiO3, Ti2O3, Al2O3, AlN and β-Ga2O3, were calculated by a plane wave pseudopotential method. Experimental ELNES/XANES of those compounds were well reproduced when an excited pseudopotential, which includes a core hole, was used. In addition to the spectral features, it was found that chemical shifts among different compounds were also reproduced by correcting the contribution of the excited pseudopotentials to the energy of the core orbital.

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

    SciTech Connect

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

    1991-08-01

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

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

    PubMed

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

    2016-04-01

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

  14. Cross-correlation between a carbonyl C' chemical shift anisotropy and a long-range dipolar C'HA coupling in proteins using symmetrical reconversion.

    PubMed

    Loth, Karine; Pelupessy, Philippe; Bodenhausen, Geoffrey

    2003-10-01

    A new sequence is described to measure the cross-correlation rates between the chemical shift anisotropy of the carbonyl carbon-13 nucleus and the dipole-dipole interaction between this carbonyl and the alpha-proton in proteins. The sequence is based on the symmetrical reconversion principle and is insensitive to experimental errors and to violations of the secular approximation. The cross-correlation rate depends on the backbone angle psi. The advantages and limitations of the sequence are discussed.

  15. 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

  16. 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

  17. 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.

  18. 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

  19. 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

  20. Determination of the Optimal Energy Denominator Shift Parameter of KRb Electronic States in Quantum Chemical Computations Using Perturbation Theory

    NASA Astrophysics Data System (ADS)

    Shundalau, M. B.; Minko, A. A.

    2016-01-01

    The influence of the energy denominator shift (EDS) parameter and the quantitative and qualitative compositions of electronic states included in CASSCF(2,14)/XMCQDPT2 ab initio calculations of the ground state equilibrium internuclear distance and dissociation energy of polar KRb was determined.

  1. 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.

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

    PubMed Central

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

    2009-01-01

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

  3. 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.

  4. Effects of surface chemistry on the porous structure of coal. Quarterly technical progress report, October 1995--December 1995

    SciTech Connect

    Anderson, S.A.; Radovic, L.R.; Hatcher, P.G.

    1995-12-31

    The primary objective of this work is to use {sup 129}Xe NMR to characterize the microporous structure of coals. As an aide in this characterization, which is by no means straightforward, another objective is to combine this technique with volumetric adsorption techniques and track the effect of controlled opening of the micropores in a microporous carbon by oxygen chemisorption/desorption. The primary goal of the NMR work is to measure the micropore sizes in coal; more broadly, it is to better tailor the {sup 129}Xe NMR method for use with coal, and to investigate other ways it may be used to describe pore structure in coal, with emphasis on determining whether micropores in coal are connected or isolated. In terms of the primary objectives of the project, the {sup 129}Xe NMR spectra with pressure variation have been obtained for two more coals, completing this task for the sample set of six coals. In terms of the broad objectives of the project, examination of the influence on the xenon signal of packing the powdered coal has been undertaken. These data are of potential value for the determination of whether the porosity is open or closed. Results of powder density and related experiments will be used in the final interpretation of our current data, including the determination of whether, in the NMR of loose powdered, the chemical shift is indicative of the ``true`` gas-solid interaction.

  5. 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

  6. Chemical shift magnetic resonance imaging in differentiation of benign from malignant vertebral collapse in a rural tertiary care hospital in North India

    PubMed Central

    Mittal, Puneet; Gupta, Ranjana; Mittal, Amit; Joshi, Sandeep

    2016-01-01

    Introduction: Magnetic resonance imaging (MRI) is the modality of the first choice for evaluation of vertebral compression/collapse. Many MRI qualitative features help to differentiate benign from malignant collapse. We conducted this study to look for a quantitative difference in chemical shift values in benign and malignant collapse using dual-echo gradient echo in-phase/out-phase imaging. Materials and Methods: MRI examinations of a total of 38 patients were retrospectively included in the study who had vertebral compression/collapse with marrow edema in which final diagnosis was available at the time of imaging/follow-up. Signal intensity value in the region of abnormal marrow signal and adjacent normal vertebra was measured on in phase/out phase images. Signal intensity ratio (SIR) was measured by dividing signal intensity value on opposite phase images to that on in phase images. SIR was compared in normal vertebrae and benign and malignant vertebral collapse. Results: There were 21 males and 17 females with mean age of 52.4 years (range 28–76 years). Out of total 38 patients, 18 were of benign vertebral collapse and 20 of malignant vertebral collapse. SIR in normal vertebrae was 0.30 ± 0.14, 0.67 ± 0.18 in benign vertebral collapse, and 1.20 ± 0.27 in malignant vertebral collapse with significant difference in SIR of normal vertebrae versus benign collapse (P < 0.01) and in benign collapse versus malignant collapse (P < 0.01). Assuming a cutoff of <0.95 for benign collapse and ≥0.95 for malignant collapse, chemical shift imaging had a sensitivity of 90% and specificity of 94.4%. Conclusion: Chemical shift imaging is a rapid and useful sequence in differentiating benign from malignant vertebral collapse with good specificity and sensitivity. PMID:27695225

  7. Chemical shift magnetic resonance imaging in differentiation of benign from malignant vertebral collapse in a rural tertiary care hospital in North India

    PubMed Central

    Mittal, Puneet; Gupta, Ranjana; Mittal, Amit; Joshi, Sandeep

    2016-01-01

    Introduction: Magnetic resonance imaging (MRI) is the modality of the first choice for evaluation of vertebral compression/collapse. Many MRI qualitative features help to differentiate benign from malignant collapse. We conducted this study to look for a quantitative difference in chemical shift values in benign and malignant collapse using dual-echo gradient echo in-phase/out-phase imaging. Materials and Methods: MRI examinations of a total of 38 patients were retrospectively included in the study who had vertebral compression/collapse with marrow edema in which final diagnosis was available at the time of imaging/follow-up. Signal intensity value in the region of abnormal marrow signal and adjacent normal vertebra was measured on in phase/out phase images. Signal intensity ratio (SIR) was measured by dividing signal intensity value on opposite phase images to that on in phase images. SIR was compared in normal vertebrae and benign and malignant vertebral collapse. Results: There were 21 males and 17 females with mean age of 52.4 years (range 28–76 years). Out of total 38 patients, 18 were of benign vertebral collapse and 20 of malignant vertebral collapse. SIR in normal vertebrae was 0.30 ± 0.14, 0.67 ± 0.18 in benign vertebral collapse, and 1.20 ± 0.27 in malignant vertebral collapse with significant difference in SIR of normal vertebrae versus benign collapse (P < 0.01) and in benign collapse versus malignant collapse (P < 0.01). Assuming a cutoff of <0.95 for benign collapse and ≥0.95 for malignant collapse, chemical shift imaging had a sensitivity of 90% and specificity of 94.4%. Conclusion: Chemical shift imaging is a rapid and useful sequence in differentiating benign from malignant vertebral collapse with good specificity and sensitivity.

  8. 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

  9. Liver steatosis (LS) evaluated through chemical-shift magnetic resonance imaging liver enzymes in morbid obesity; effect of weight loss obtained with intragastric balloon gastric banding.

    PubMed

    Folini, Laura; Veronelli, Annamaria; Benetti, Alberto; Pozzato, Carlo; Cappelletti, Marco; Masci, Enzo; Micheletto, Giancarlo; Pontiroli, Antonio E

    2014-01-01

    The aim of this study was to evaluate in morbid obesity clinical and metabolic effects related to weight loss on liver steatosis (LS), measured through chemical-shift magnetic resonance imaging (MRI) and liver enzymes. Forty obese subjects (8 M/32 W; BMI 42.8 ± 7.12 kg/m(2), mean ± SD) were evaluated for LS through ultrasound (US-LS), chemical-shift MRI (MRI-LS), liver enzymes [aspartate aminotransferase (AST), alanine aminotransferase (ALT), γ-glutamyltransferase (GGT), alkaline phosphatase (ALP)], anthropometric parameters [weight, BMI, waist circumference (WC)], lipids, insulin, insulin resistance (HOMA-IR), glycated hemoglobin (HbA1c), oral glucose tolerance test, and body composition [fat mass (FM) and fat-free mass (FFM) at bio-impedance analysis (BIA)]. Anthropometric measures, MRI-LS, BIA, and biochemical parameters were reevaluated 6 months later in 18 subjects undergoing restrictive bariatric approach, i.e., intragastric balloon (BIB, n = 13) or gastric banding (LAGB, n = 5), and in 13 subjects receiving hypocaloric diet. At baseline, US-LS correlates only with MRI-LS, and the latter correlates with ALT, AST, and GGT. After 6 months, subjects undergoing BIB or LAGB had significant changes of BMI, weight, WC, ALT, AST, GGT, ALP, HbA1c, insulin, HOMA-IR, FM, FFM, and MRI-LS. Diet-treated obese subjects had no significant change of any parameter under study; change of BMI, fat mass, and fat-free mass was significantly greater in LAGB/BIB subjects than in diet-treated subjects. Change of MRI-LS showed a significant correlation with changes in weight, BMI, WC, GGT, ALP, and basal MRI-LS. Significant weight loss after BIB or LAGB is associated with decrease in chemical-shift MRI-LS and with reduction in liver enzymes; chemical-shift MRI and liver enzymes allow monitoring of LS in follow-up studies.

  10. Accurate calculation of chemical shifts in highly dynamic H2@C60 through an integrated quantum mechanics/molecular dynamics scheme.

    PubMed

    Jiménez-Osés, Gonzalo; García, José I; Corzana, Francisco; Elguero, José

    2011-05-20

    A new protocol combining classical MD simulations and DFT calculations is presented to accurately estimate the (1)H NMR chemical shifts of highly mobile guest-host systems and their thermal dependence. This strategy has been successfully applied for the hydrogen molecule trapped into C(60) fullerene, an unresolved and challenging prototypical case for which experimental values have never been reproduced. The dependence of the final values on the theoretical method and their implications to avoid over interpretation of the obtained results are carefully described.

  11. 1H, 13C, and 15N chemical shift assignments of cyanobacteriochrome NpR6012g4 in the green-absorbing photoproduct state.

    PubMed

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

    2016-04-01

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

  12. Backbone chemical shift assignments for the sensor domain of the Burkholderia pseudomallei histidine kinase RisS – “missing” resonances at the dimer interface

    PubMed Central

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

    2015-01-01

    Using a deuterated sample, all the observable backbone 1HN, 15N, 13Cα, and 13C′ 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 1H-15N 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

  13. 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.

  14. 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.

  15. 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

  16. 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).

  17. Predict mycobacterial proteins subcellular locations by incorporating pseudo-average chemical shift into the general form of Chou's pseudo amino acid composition.

    PubMed

    Fan, Guo-Liang; Li, Qian-Zhong

    2012-07-01

    Mycobacterium tuberculosis (MTB) is a pathogenic bacterial species in the genus Mycobacterium and the causative agent of most cases of tuberculosis (Berman et al., 2000). Knowledge of the localization of Mycobacterial protein may help unravel the normal function of this protein. Automated prediction of Mycobacterial protein subcellular localization is an important tool for genome annotation and drug discovery. In this work, a benchmark data set with 638 non-redundant mycobacterial proteins is constructed and an approach for predicting Mycobacterium subcellular localization is proposed by combining amino acid composition, dipeptide composition, reduced physicochemical property, evolutionary information, pseudo-average chemical shift. The overall prediction accuracy is 87.77% for Mycobacterial subcellular localizations and 85.03% for three membrane protein types in Integral membranes using the algorithm of increment of diversity combined with support vector machine. The performance of pseudo-average chemical shift is excellent. In order to check the performance of our method, the data set constructed by Rashid was also predicted and the accuracy of 98.12% was obtained. This indicates that our approach was better than other existing methods in literature.

  18. Toward structural dynamics: protein motions viewed by chemical shift modulations and direct detection of C'N multiple-quantum relaxation.

    PubMed

    Mori, Mirko; Kateb, Fatiha; Bodenhausen, Geoffrey; Piccioli, Mario; Abergel, Daniel

    2010-03-17

    Multiple quantum relaxation in proteins reveals unexpected relationships between correlated or anti-correlated conformational backbone dynamics in alpha-helices or beta-sheets. The contributions of conformational exchange to the relaxation rates of C'N coherences (i.e., double- and zero-quantum coherences involving backbone carbonyl (13)C' and neighboring amide (15)N nuclei) depend on the kinetics of slow exchange processes, as well as on the populations of the conformations and chemical shift differences of (13)C' and (15)N nuclei. The relaxation rates of C'N coherences, which reflect concerted fluctuations due to slow chemical shift modulations (CSMs), were determined by direct (13)C detection in diamagnetic and paramagnetic proteins. In well-folded proteins such as lanthanide-substituted calbindin (CaLnCb), copper,zinc superoxide dismutase (Cu,Zn SOD), and matrix metalloproteinase (MMP12), slow conformational exchange occurs along the entire backbone. Our observations demonstrate that relaxation rates of C'N coherences arising from slow backbone dynamics have positive signs (characteristic of correlated fluctuations) in beta-sheets and negative signs (characteristic of anti-correlated fluctuations) in alpha-helices. This extends the prospects of structure-dynamics relationships to slow time scales that are relevant for protein function and enzymatic activity.

  19. Fractional enrichment of proteins using [2-(13)C]-glycerol as the carbon source facilitates measurement of excited state 13Cα chemical shifts with improved sensitivity.

    PubMed

    Ahlner, Alexandra; Andresen, Cecilia; Khan, Shahid N; Kay, Lewis E; Lundström, Patrik

    2015-07-01

    A selective isotope labeling scheme based on the utilization of [2-(13)C]-glycerol as the carbon source during protein overexpression has been evaluated for the measurement of excited state (13)Cα chemical shifts using Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion (RD) experiments. As expected, the fractional incorporation of label at the Cα positions is increased two-fold relative to labeling schemes based on [2-(13)C]-glucose, effectively doubling the sensitivity of NMR experiments. Applications to a binding reaction involving an SH3 domain from the protein Abp1p and a peptide from the protein Ark1p establish that accurate excited state (13)Cα chemical shifts can be obtained from RD experiments, with errors on the order of 0.06 ppm for exchange rates ranging from 100 to 1000 s(-1), despite the small fraction of (13)Cα-(13)Cβ spin-pairs that are present for many residue types. The labeling approach described here should thus be attractive for studies of exchanging systems using (13)Cα spin probes.

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

    PubMed

    Torii, Hajime

    2016-09-15

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

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

    NASA Astrophysics Data System (ADS)

    Tonan, Kenji; Ikawa, Shun-ichi

    2003-01-01

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

  2. 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.

  3. 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

  4. Nuclear magnetic resonance spectra and (207)Pb chemical-shift tensors of lead carboxylates relevant to soap formation in oil paintings.

    PubMed

    Catalano, Jaclyn; Yao, Yao; Murphy, Anna; Zumbulyadis, Nicholas; Centeno, Silvia A; Dybowski, Cecil

    2014-01-01

    Soap formation in traditional oil paintings occurs when heavy-metal-containing pigments, such as lead white, 2PbCO3·Pb(OH)2, and lead tin yellow type I, Pb2SnO4, react with fatty acids in the binding medium. These soaps may form aggregates that can be 100-200 μm in diameter, which swell and protrude through the paint surface, resulting in the degradation of the paint film and damage to the integrity of the artwork. The factors that trigger soap formation and the mechanism(s) of the process are not yet well understood. To elucidate these issues, chemical and structural information is necessary, which can be obtained using solid-state (207)Pb and (13)C nuclear magnetic resonance (NMR). In this article, we report (207)Pb and (13)C solid-state NMR spectra and (207)Pb chemical-shift tensors of lead carboxylates implicated in soap formation: lead stearate, lead palmitate, and lead azelate, in addition to lead oleate and lead heptanoate for comparison. The (13)C cross polarization with magic-angle spinning (MAS) spectra of these lead carboxylates show resonance doubling for the carbons closest to the lead, indicating two different conformations of the fatty acid chains in the asymmetric unit. The (207)Pb NMR spectra, from which tensors were determined, were obtained with direct excitation and spin-temperature alternation, with and without MAS, and with the wide band uniform rate smooth truncation Carr-Purcell-Meiboom-Gill pulse sequence. The results of these experiments show that the local coordination environment of lead azelate is different from lead palmitate and lead stearate and could thus be distinguished from these in a paint film displaying soap formation. In addition, comparing the (207)Pb NMR chemical-shift tensors of the lead carboxylates studied shows that crystal packing of the acyl chains may be a factor in determining the coordination environment around the lead. PMID:24666944

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

    NASA Astrophysics Data System (ADS)

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

    1998-01-01

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

  6. 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.

  7. Relative importance of first and second derivatives of nuclear magnetic resonance chemical shifts and spin-spin coupling constants for vibrational averaging.

    PubMed

    Dracínský, Martin; Kaminský, Jakub; Bour, Petr

    2009-03-01

    Relative importance of anharmonic corrections to molecular vibrational energies, nuclear magnetic resonance (NMR) chemical shifts, and J-coupling constants was assessed for a model set of methane derivatives, differently charged alanine forms, and sugar models. Molecular quartic force fields and NMR parameter derivatives were obtained quantum mechanically by a numerical differentiation. In most cases the harmonic vibrational function combined with the property second derivatives provided the largest correction of the equilibrium values, while anharmonic corrections (third and fourth energy derivatives) were found less important. The most computationally expensive off-diagonal quartic energy derivatives involving four different coordinates provided a negligible contribution. The vibrational corrections of NMR shifts were small and yielded a convincing improvement only for very accurate wave function calculations. For the indirect spin-spin coupling constants the averaging significantly improved already the equilibrium values obtained at the density functional theory level. Both first and complete second shielding derivatives were found important for the shift corrections, while for the J-coupling constants the vibrational parts were dominated by the diagonal second derivatives. The vibrational corrections were also applied to some isotopic effects, where the corrected values reasonably well reproduced the experiment, but only if a full second-order expansion of the NMR parameters was included. Contributions of individual vibrational modes for the averaging are discussed. Similar behavior was found for the methane derivatives, and for the larger and polar molecules. The vibrational averaging thus facilitates interpretation of previous experimental results and suggests that it can make future molecular structural studies more reliable. Because of the lengthy numerical differentiation required to compute the NMR parameter derivatives their analytical implementation in

  8. Chemical shift assignments and secondary structure prediction for Q4DY78, a conserved kinetoplastid-specific protein from Trypanosoma cruzi.

    PubMed

    D'Andréa, Éverton Dias; Diehl, Anne; Schmieder, Peter; Oschkinat, Hartmut; Pires, José Ricardo

    2016-10-01

    Trypanosoma cruzi, Trypanosma brucei and Leishmania spp. are kinetoplastid protozoa causative agents of Chagas disease, sleeping sickness and leishmaniasis, respectively, neglected tropical diseases estimated to infect millions of people worldwide. Their genome sequencing has revealed approximately 50 % of genes encoding hypothetical proteins of unknown function, opening possibilities for novel target identification and drug discovery. Q4DY78 is a putative essential protein from T. cruzi conserved in the related kinetoplastids and divergent from mammalian host proteins. Here we report the (1)H, (15)N, and (13)C chemical shift assignments and secondary structure analysis of the Q4DY78 protein as basis for NMR structure determination, functional analysis and drug screening.

  9. Doubly Selective Multiple Quantum Chemical Shift Imaging and T1 Relaxation Time Measurement of Glutathione (GSH) in the Human Brain In Vivo

    PubMed Central

    Choi, In-Young; Lee, Phil

    2012-01-01

    Mapping of a major antioxidant, glutathione (GSH), was achieved in the human brain in vivo using a doubly selective multiple quantum filtering based chemical shift imaging (CSI) of GSH at 3 T. Both in vivo and phantom tests in CSI and single voxel measurements were consistent with excellent suppression of overlapping signals from creatine, γ-Amino butyric acid (GABA) and macromolecules. The GSH concentration in the fronto-parietal region was 1.20 ± 0.16 µmol/g (mean ± SD, n = 7). The longitudinal relaxation time (T1) of GSH in the human brain was 397 ± 44 ms (mean ± SD, n = 5), which was substantially shorter than those of other metabolites. This GSH CSI method permits us to address regional differences of GSH in the human brain with conditions where oxidative stress has been implicated, including multiple sclerosis, aging and neurodegenerative diseases. PMID:22730142

  10. 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.

  11. Chemical shift assignment of the intrinsically disordered N-terminus and the rubredoxin domain in the folded metal bound and unfolded oxidized state of mycobacterial protein kinase G.

    PubMed

    Wittwer, Matthias; Dames, Sonja A

    2016-10-01

    Mycobacterium tuberculosis protein kinase G (PknG) is a 82 kDa multidomain eukaryotic-like serine/threonine kinase mediating the survival of pathogenic mycobacteria within host macrophages. The N-terminal sequence preceding the catalytic kinase domain contains an approximately 75 residues long tail, which was predicted to show no regulatory secondary structure (1-75 = NORS) but harbors the major in vivo phosphorylation site (T63), and a rubredoxin-like metal binding motif (74-147 = RD). In the reduced rubredoxin motif, four conserved cysteine residues that are present as two C-X-X-C-G motifs coordinate a metal ion. The cysteines are further involved in sensing the redox environment to regulate PknG catalytic activity. Here, we report the (1)H, (13)C, and (15)N resonance assignments of the highly dynamic unstructured N-terminal region NORS and the RD in the reduced, metal bound, presumably folded and the oxidized, presumably unfolded state. Chemical shifts have been deposited at the BioMagResBank under the BMRB accession numbers 26,028 for the His-PknG1-147 with the RD in reduced, metal bound state, 26,027 for His-PknG1-75, and 26,030 and 26,029 for PknG74-147 either in the reduced, metal bound or oxidized state, respectively. The presented chemical shift assignments pave the route for the structural characterization of the regulation of PknG by redox changes and posttranslational modifications (phosphorylation).

  12. Backbone and side-chain chemical shift assignments for the C-terminal domain of Tcb2, a cytoskeletal calcium-binding protein from Tetrahymena thermophila.

    PubMed

    Kilpatrick, Adina M; Gurrola, Theodore E; Sterner, Robert C; Sleister, Heidi M; Honts, Jerry E; Fowler, C Andrew

    2016-10-01

    Tcb2 is a putative calcium-binding protein from the membrane-associated cytoskeleton of the ciliated protozoan Tetrahymena thermophila. It has been hypothesized to participate in several calcium-mediated processes in Tetrahymena, including ciliary movement, cell cortex signaling, and pronuclear exchange. Sequence analysis suggests that the protein belongs to the calmodulin family, with N- and C-terminal domains connected by a central linker, and two helix-loop-helix motifs in each domain. However, its calcium-binding properties, structure and precise biological function remain unknown. Interestingly, Tcb2 is a major component of unique contractile fibers isolated from the Tetrahymena cytoskeleton; in these fibers, addition of calcium triggers an ATP-independent type of contraction. Here we report the (1)H, (13)C and (15)N backbone and side-chain chemical shift assignments of the C-terminal domain of the protein (Tcb2-C) in the absence and presence of calcium ions. (1)H-(15)N HSQC spectra show that the domain is well folded both in the absence and presence of calcium, and undergoes a dramatic conformational change upon calcium addition. Secondary structure prediction from chemical shifts reveals an architecture encountered in other calcium-binding proteins, with paired EF-hand motifs connected by a flexible linker. These studies represent a starting point for the determination of the high-resolution solution structure of Tcb2-C at both low and high calcium levels, and, together with additional structural studies on the full-length protein, will help establish the molecular basis of Tcb2 function and unique contractile properties.

  13. Complete chemical shift assignment of the ssDNA in the filamentous bacteriophage fd reports on its conformation and on its interface with the capsid shell.

    PubMed

    Morag, Omry; Abramov, Gili; Goldbourt, Amir

    2014-02-12

    The fd bacteriophage is a filamentous virus consisting of a circular single-stranded DNA (ssDNA) wrapped by thousands of copies of a major coat protein subunit (the capsid). The coat protein subunits are mostly α-helical and curved, and are arranged in the capsid in consecutive pentamers related by a translation along the main viral axis and a rotation of ~36° (C5S2 symmetry). The DNA is right-handed and helical, but information on its structure and on its interface with the capsid is incomplete. We present here an approach for assigning the DNA nucleotides and studying its interactions with the capsid by magic-angle spinning solid-state NMR. Capsid contacts with the ssDNA are obtained using a two-dimensional (13)C-(13)C correlation experiment and a proton-mediated (31)P-(13)C polarization transfer experiment, both acquired on an aromatic-unlabeled phage sample. Our results allow us to map the residues that face the interior of the capsid and to show that the ssDNA-capsid interactions are sustained mainly by electrostatic interactions between the positively charged lysine side chains and the phosphate backbone. The use of natural abundance aromatic amino acids in the growth media facilitated the complete assignment of the four nucleotides and the observation of internucleotide contacts. Using chemical shift analysis, our study shows that structural features of the deoxyribose carbons reporting on the sugar pucker are strikingly similar to those observed recently for the Pf1 phage. However, the ssDNA-protein interface is different, and chemical shift markers of base pairing are different. This experimental approach can be utilized in other filamentous and icosahedral bacteriophages, and also in other biomolecular complexes involving structurally and functionally important DNA-protein interactions.

  14. 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.

  15. Modification of apparent fission yields by Chemical Fractionation following Fission (CFF)

    NASA Astrophysics Data System (ADS)

    Hohenberg, Charles; Meshik, Alex

    2008-04-01

    Grain-by-grain studies of the 2 billion year old Oklo natural reactor, using laser micro-extraction^1,2, yield detailed information about Oklo, a water-moderated pulsed reactor, cycle times, total neutron fluence and duration, but it also demonstrates Chemical Fractionation following Fission. In the CFF process, members of an isobaric yield chain with long half-lives are subject to migration before decay can occur. Of particular interest is the 129 isobar where 17 million ^129I can migrate out of the host grain before decay, and iodine compounds are water soluble. This is amply demonstated by the variation of Xe spectra between micron-sized uranium-bearing minerals and adjacent uranium-free minerals. Fission 129 yields for the spontaneous fission of ^238U generally come from measured ^129Xe in pitchblend^2, ores emplaced by aqueous activity, and are incorrect due to the CFF process. ^238U yields for the 131 and 129 chains, reported in Hyde^3, as 0.455 +- .02 and < 0.012, respectively, the latter being anomalously low. ^1A Meshik, C Hohenberg and O Pravdivtesva, PRL 93, 182302 (2004); A Meshik Sci. Am. Nov (2005), 55; ^2E K Hyde, Nucl Prop of Heavy Elements III (1964).

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

    PubMed

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

    2014-05-01

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

  17. 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.

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

    NASA Astrophysics Data System (ADS)

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

    1992-03-01

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

  19. Structure of mutagen nucleic acid complexes in solution. Proton chemical shifts in 9-aminoacridine complexes with dG-dC, dC-dG, and dA-dT-dG-dC-dA-dT.

    PubMed

    Reuben, J; Baker, B M; Kallenbach, N R

    1978-07-11

    The influence of self-complementary oligodeoxynucleotides on the chemical shifts of protons of the mutagenic acridine dye 9-aminoacridine has been measured. Upfield shifts indicative of intercalative binding are found in the cases of dG-dC, dC-dG, and dA-dT-dG-dC-dA-dT but not in dA-dT. Geometries for the complexes that are compatibile with the chemical-shift data and the X-ray structure of the complex between ri5C-rG and 9-aminoacridine determined by Sakore et al. [Sakore, T.D., Jain, S.C., Tsai, C., and Sobell, H.M. (1977), Proc. Natl. Acad. Sci. U.S.A. 74, 188--192] can be identified using recent theoretical estimates of shifts induced by nucleotide bases.

  20. 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.

  1. 19F high magnetic field NMR study of beta-ZrF4 and CeF4: from spectra reconstruction to correlation between fluorine sites and 19F isotropic chemical shifts.

    PubMed

    Legein, C; Fayon, F; Martineau, C; Body, M; Buzaré, J-Y; Massiot, D; Durand, E; Tressaud, A; Demourgues, A; Péron, O; Boulard, B

    2006-12-25

    High magnetic field and high spinning frequency one- and two-dimensional one-pulse MAS 19F NMR spectra of beta-ZrF4 and CeF4 were recorded and reconstructed allowing the accurate determination of the 19F chemical shift tensor parameters for the seven different crystallographic fluorine sites of each compound. The attributions of the NMR resonances are performed using the superposition model for 19F isotropic chemical shift calculation initially proposed by Bureau et al. (Bureau, B.; Silly, G.; Emery, J.; Buzaré, J.-Y. Chem. Phys. 1999, 249, 85-104). A satisfactory reliability is reached with a root-mean-square (rms) deviation between calculated and measured isotropic chemical shift values equal to 1.5 and 3.5 ppm for beta-ZrF4 and CeF4, respectively. PMID:17173418

  2. A lanthanide complex with dual biosensing properties: CEST (chemical exchange saturation transfer) and BIRDS (biosensor imaging of redundant deviation in shifts) with europium DOTA-tetraglycinate.

    PubMed

    Coman, Daniel; Kiefer, Garry E; Rothman, Douglas L; Sherry, A Dean; Hyder, Fahmeed

    2011-12-01

    Responsive contrast agents (RCAs) composed of lanthanide(III) ion (Ln3R) complexes with a variety of1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetate (DOTA4S) derivatives have shown great potential as molecular imaging agents for MR. A variety of LnDOTA–tetraamide complexes have been demonstrated as RCAs for molecular imaging using chemical exchange saturation transfer (CEST). The CEST method detects proton exchange between bulk water and any exchangeable sites on the ligand itself or an inner sphere of bound water that is shifted by a paramagnetic Ln3R ion bound in the core of the macrocycle. It has also been shown that molecular imaging is possible when the RCA itself is observed (i.e. not its effect on bulk water) using a method called biosensor imaging of redundant deviation in shifts (BIRDS). The BIRDS method utilizes redundant information stored in the nonexchangeable proton resonances emanating from the paramagnetic RCA for ambient factors such as temperature and/or pH.Thus, CEST and BIRDS rely on exchangeable and nonexchangeable protons, respectively, for biosensing. We posited that it would be feasible to combine these two biosensing features into the same RCA (i.e. dual CEST and BIRDS properties). A complex between europium(III) ion (Eu3R) and DOTA–tetraglycinate [DOTA–(gly)S4] was used to demonstrate that its CEST characteristics are preserved, while its BIRDS properties are also detectable. The in vitro temperature sensitivity of EuDOTA–(gly)S4 was used to show that qualitative MR contrast with CEST can be calibrated using quantitative MR mapping with BIRDS, thereby enabling quantitative molecular imaging at high spatial resolution.

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

    PubMed

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

    2011-04-30

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

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

    PubMed

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

    1990-10-01

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

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

    PubMed

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

    1990-10-01

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

  6. Correlation between ¹⁹⁵Pt chemical shifts and the electronic transitions among d orbitals in pincer NCN Pt(II) complexes: A theoretical study and application of Ramsey's equation.

    PubMed

    Hashemi, Majid

    2015-12-01

    The chemical potentials for two series of [PtCl(NCN-Z-4)] (NCN=2,6-bis[(dimethylamino)methyl]phenyl, Z=H, CHO, COOH, NH2, OH, NO2, SiMe3, I, t-Bu) and [PtCl(NCN-4-CHN-C6H4-Z'-4')] (Z'=NMe2, Me, H, Cl, CN) were calculated. The energies of platinum d orbitals were calculated by NBO analysis. Good correlations were obtained between (195)Pt chemical shifts and the spectral parameters obtained from the energies of electronic transitions between Pt d orbitals in these complexes. The correlations between (195)Pt chemical shifts and the chemical potentials were also good. The correlations were discussed based on Ramsey's equation.

  7. 13C Magic angle spinning NMR analysis and quantum chemical modeling of the bathochromic shift of astaxanthin in alpha-crustacyanin, the blue carotenoprotein complex in the carapace of the lobster Homarus gammarus.

    PubMed

    Weesie, R J; Jansen, F J; Merlin, J C; Lugtenburg, J; Britton, G; de Groot, H J

    1997-06-17

    Selective isotope enrichment, 13C magic angle spinning (MAS) NMR, and semiempirical quantum chemical modeling, have been used to analyze ligand-protein interactions associated with the bathochromic shift of astaxanthin in alpha-crustacyanin, the blue carotenoprotein complex from the carapace of the lobster Homarus gammarus. Spectra of alpha-crustacyanin were obtained after reconstitution with astaxanthins labeled with 13C at positions 4,4', 12,12', 13,13', or 20,20'. The data reveal substantial downfield shifts of 4.9 and 7.0 ppm at positions 12 and 12' in the complex, respectively. In contrast, at the 13 and 13' positions, small upfield shifts of 1.9 ppm were observed upon binding to the protein. These data are in line with previously obtained results for positions 14,14' (3.9 and 6.8 ppm downfield) and 15,15' (0.6 ppm upfield) and confirm the unequal perturbation of both halves after binding of the chromophore. However, these results also show that the main perturbation is of symmetrical origin, since the chemical shift differences exhibit a similar pattern in both halves of the astaxanthin molecule. A small downfield shift of 2.4 ppm was detected for the 4 and 4' positions. Finally, the 20,20' methyl groups are shifted 0.4 ppm upfield by the protein. The full data set provides convincing evidence that charge polarization is of importance for the bathochromic shift. The NMR shifts are compared with calculated charge densities for astaxanthin subjected to variations in protonation states of the ring-functional groups, as models of ligand-protein interactions. Taking into account the color shift and other available optical data, the current model for the mechanisms of interaction with the protein was refined. The results point toward a mechanism in which the astaxanthin is charged and subject to strong electrostatic polarizations originating from both keto groups, most likely a double protonation. PMID:9200677

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

    PubMed Central

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

    2011-01-01

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

  9. 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

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

    PubMed

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

    2000-04-01

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

  11. Measurement of sample temperatures under magic-angle spinning from the chemical shift and spin-lattice relaxation rate of 79Br in KBr powder

    PubMed Central

    Thurber, Kent R.; Tycko, Robert

    2009-01-01

    Accurate determination of sample temperatures in solid state nuclear magnetic resonance (NMR) with magic-angle spinning (MAS) can be problematic, particularly because frictional heating and heating by radio-frequency irradiation can make the internal sample temperature significantly different from the temperature outside the MAS rotor. This paper demonstrates the use of 79Br chemical shifts and spin-lattice relaxation rates in KBr powder as temperature-dependent parameters for the determination of internal sample temperatures. Advantages of this method include high signal-to-noise, proximity of the 79Br NMR frequency to that of 13C, applicability from 20 K to 320 K or higher, and simultaneity with adjustment of the MAS axis direction. We show that spin-lattice relaxation in KBr is driven by a quadrupolar mechanism. We demonstrate a simple approach to including KBr powder in hydrated samples, such as biological membrane samples, hydrated amyloid fibrils, and hydrated microcrystalline proteins, that allows direct assessment of the effects of frictional and radio-frequency heating under experimentally relevant conditions. PMID:18930418

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

    NASA Astrophysics Data System (ADS)

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

    2010-07-01

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

  13. VITAL NMR: using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy.

    PubMed

    Brothers, Michael C; Nesbitt, Anna E; Hallock, Michael J; Rupasinghe, Sanjeewa G; Tang, Ming; Harris, Jason; Baudry, Jerome; Schuler, Mary A; Rienstra, Chad M

    2012-01-01

    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.

  14. 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.

  15. 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.

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

    PubMed

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

    2016-04-01

    Peroxiredoxins (Prx) are ubiquitous enzymes that reduce peroxides as part of antioxidant defenses and redox signaling. While Prx catalytic activity and sensitivity to hyperoxidative inactivation depend on their dynamic properties, there are few examples where their dynamics has been characterized by NMR spectroscopy. Here, we provide a foundation for studies of the solution properties of peroxiredoxin Q from the plant pathogen Xanthomonas campestris (XcPrxQ) by assigning the observable (1)H(N), (15)N, (13)C(α), (13)C(β), and (13)C' chemical shifts for both the reduced (dithiol) and oxidized (disulfide) states. In the reduced state, most of the backbone amide resonances (149/152, 98 %) can be assigned in the XcPrxQ (1)H-(15)N HSQC spectrum. In contrast, a remarkable 51 % (77) of these amide resonances are not visible in the (1)H-(15)N HSQC spectrum of the disulfide state of the enzyme, indicating a substantial change in backbone dynamics associated with the formation of an intramolecular C48-C84 disulfide bond. PMID:26438558

  17. Heavy Halogen Atom Effect on (13)C NMR Chemical Shifts in Monohalo Derivatives of Cyclohexane and Pyran. Experimental and Theoretical Study.

    PubMed

    Neto, Alvaro Cunha; Ducati, Lucas C; Rittner, Roberto; Tormena, Cláudio F; Contreras, Rubén H; Frenking, Gernot

    2009-09-01

    As a first step, a qualitative analysis of the spin-orbit operator was performed to predict the kind of organic compounds, where it could be expected that the SO/FC (spin-orbit/Fermi contact) and SO/SD (spin-orbit/spin dipolar) yield unusually small contributions to the "heavy atom effect" on (13)C SCSs (substituent chemical shifts). This analysis led to the conclusion that compounds presenting strong hyperconjugative interactions involving the σ*C-X orbital (X = halogen) are good examples where such effects can be expected to take place. On the basis of such results, the following set of model compounds was chosen: 2-eq-halocyclohexane (2-eq), 2-ax-halocyclohexane (2-ax), and 2-ax-halopyran (3), to measure (13)C SCSs. Such experimental values, as well as those of methane and halomethanes taken from the literature, were compared to calculated values at a nonrelativistic approach using B3LYP, and at a relativistic approach with BP86 using scalar ZORA, spin-orbit ZORA, scalar PAULI, and spin-orbit PAULI. Results from relativistic calculations are in agreement with the trends predicted by the qualitative model discussed in this work.

  18. In vivo application of sub-second spiral chemical shift imaging (CSI) to hyperpolarized 13C metabolic imaging: Comparison with phase-encoded CSI

    NASA Astrophysics Data System (ADS)

    Mayer, Dirk; Yen, Yi-Fen; Levin, Yakir S.; Tropp, James; Pfefferbaum, Adolf; Hurd, Ralph E.; Spielman, Daniel M.

    2010-06-01

    A fast spiral chemical shift imaging (CSI) has been developed to address the challenge of the limited acquisition window in hyperpolarized 13C metabolic imaging. The sequence exploits the sparsity of the spectra and prior knowledge of resonance frequencies to reduce the measurement time by undersampling the data in the spectral domain. As a consequence, multiple reconstructions are necessary for any given data set as only frequency components within a selected bandwidth are reconstructed "in-focus" while components outside that band are severely blurred ("spectral tomosynthesis"). A variable-flip-angle scheme was used for optimal use of the longitudinal magnetization. The sequence was applied to sub-second metabolic imaging of the rat in vivo after injection of hyperpolarized [1- 13C]-pyruvate on a clinical 3T MR scanner. The comparison with conventional CSI based on phase encoding showed similar signal-to-noise ratio (SNR) and spatial resolution in metabolic maps for the substrate and its metabolic products lactate, alanine, and bicarbonate, despite a 50-fold reduction in scan time for the spiral CSI acquisition. The presented results demonstrate that dramatic reductions in scan time are feasible in hyperpolarized 13C metabolic imaging without a penalty in SNR or spatial resolution.

  19. 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

  20. 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…

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

    PubMed

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

    2000-11-01

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

  2. 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

  3. Integrating diffusion kurtosis imaging, dynamic susceptibility-weighted contrast-enhanced MRI, and short echo time chemical shift imaging for grading gliomas

    PubMed Central

    Van Cauter, Sofie; De Keyzer, Frederik; Sima, Diana M.; Croitor Sava, Anca; D'Arco, Felice; Veraart, Jelle; Peeters, Ronald R.; Leemans, Alexander; Van Gool, Stefaan; Wilms, Guido; Demaerel, Philippe; Van Huffel, Sabine; Sunaert, Stefan; Himmelreich, Uwe

    2014-01-01

    Background We assessed the diagnostic accuracy of diffusion kurtosis imaging (DKI), dynamic susceptibility-weighted contrast-enhanced (DSC) MRI, and short echo time chemical shift imaging (CSI) for grading gliomas. Methods In this prospective study, 35 patients with cerebral gliomas underwent DKI, DSC, and CSI on a 3 T MR scanner. Diffusion parameters were mean diffusivity (MD), fractional anisotropy, and mean kurtosis (MK). Perfusion parameters were mean relative regional cerebral blood volume (rrCBV), mean relative regional cerebral blood flow (rrCBF), mean transit time, and relative decrease ratio (rDR). The diffusion and perfusion parameters along with 12 CSI metabolite ratios were compared among 22 high-grade gliomas and 14 low-grade gliomas (Mann–Whitney U-test, P < .05). Classification accuracy was determined with a linear discriminant analysis for each MR modality independently. Furthermore, the performance of a multimodal analysis is reported, using a decision-tree rule combining the statistically significant DKI, DSC-MRI, and CSI parameters with the lowest P-value. The proposed classifiers were validated on a set of subsequently acquired data from 19 clinical patients. Results Statistically significant differences among tumor grades were shown for MK, MD, mean rrCBV, mean rrCBF, rDR, lipids over total choline, lipids over creatine, sum of myo-inositol, and sum of creatine. DSC-MRI proved to be the modality with the best performance when comparing modalities individually, while the multimodal decision tree proved to be most accurate in predicting tumor grade, with a performance of 86%. Conclusions Combining information from DKI, DSC-MRI, and CSI increases diagnostic accuracy to differentiate low- from high-grade gliomas, possibly providing diagnosis for the individual patient. PMID:24470551

  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. Pure shift NMR.

    PubMed

    Zangger, Klaus

    2015-04-01

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

  6. Theoretical investigation of conformational stabilities and 13C NMR chemical shifts of a seven-membered ring thiosugar, (3R,4R,5R,7S)-7-(hydroxymethyl)thiepane-3,4,5-triol

    NASA Astrophysics Data System (ADS)

    Tai, Chin-Kuen; Yeh, Pao-Ling; Wu, Yun-Sheng; Shih, Tzenge-Lien; Wang, Bo-Cheng

    2014-06-01

    DFT/B3LYP/6-311++G(d,p) calculations have been performed to obtain optimized structures for fourteen conformers of (3R,4R,5R,7S)-7-(hydroxymethyl)thiepane-3,4,5-triol. These conformers are considered as the twist-chair (TC) and twist-boat (TB) conformations. Among all conformers, the TCS5 and TCS6 conformers appear to be the most energetically stable since they contain an intramolecular hydrogen bond between hydroxyl group at C(8) and S atom. Boltzmann weighting factor analysis provides valuable information on the population of the fourteen conformers, including both the TC and TB conformations. The analysis results demonstrate that the TCS2, TCS5, and TCS6 conformers provide a major population contribution with Boltzamann weighting factors larger than 7% as compared to other conformers. For these conformers of (3R,4R,5R,7S)-7-(hydroxymethyl)thiepane-3,4,5-triol, the GIAO/HF, GIAO/DFT/OPBE, GIAO/DFT/B3LYP and GIAO/DFT/mPW1PW91 calculations with the 6-311++G(d,p), 6-311+G(2d,p), cc-pVDZ and cc-pVTZ basis sets were used to obtain their 13C NMR chemical shifts. The calculated 13C NMR chemical shifts of the TCS2, TCS5, and TCS6 conformers show a close correlation with experimental data, within 2.4-3.0 ppm of MAE values. The experimental 13C NMR chemical shifts represent a combination of contributions from all the conformers. In our investigation, the calculated 13C NMR chemical shifts of the mixture of (3R,4R,5R,7S)-7-(hydroxymethyl)thiepane-3,4,5-triol conformers display a remarkable MAE and RMS improvement comparing to those for each individual conformer. The most appropriate calculation method and basis set to evaluate the theoretical 13C NMR chemical shifts for these conformers are OPBE/6-311+G(2d,p). Calculated results represent that the conformation of (3R,4R,5R,7S)-7-(hydroxymethyl)thiepane-3,4,5-triol can be determined by the intramolecular hydrogen bond which could be simulated by the 13C NMR chemical shift calculation.

  7. 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

  8. Cardiac High-Energy Phosphate Metabolism Alters with Age as Studied in 196 Healthy Males with the Help of 31-Phosphorus 2-Dimensional Chemical Shift Imaging

    PubMed Central

    Esterhammer, Regina; Klug, Gert; Wolf, Christian; Mayr, Agnes; Reinstadler, Sebastian; Feistritzer, Hans-Josef; Metzler, Bernhard; Schocke, Michael F. H.

    2014-01-01

    Recently published studies have elucidated alterations of mitochondrial oxidative metabolism during ageing. The intention of the present study was to evaluate the impact of ageing on cardiac high-energy phosphate metabolism and cardiac function in healthy humans. 31-phosphorus 2-dimensional chemical shift imaging (31P 2D CSI) and echocardiography were performed in 196 healthy male volunteers divided into groups of 20 to 40 years (I, n = 43), 40 to 60 years (II, n = 123) and >60 years (III, n = 27) of age. Left ventricular PCr/β-ATP ratio, myocardial mass (MM), ejection fraction and E/A ratio were assessed. Mean PCr/β-ATP ratios were significantly different among the three groups of volunteers (I, 2.10±0.37; II, 1.77±0.37; III, 1.45±0.28; all p<0.001). PCr/β-ATP ratios were inversely related to age (r2 = −0.25; p<0.001) with a decrease from 2.65 by 0.02 per year of ageing. PCr/β-ATP ratios further correlated with MM (r = −0.371; p<0.001) and E/A ratios (r = 0.213; p<0.02). Moreover, E/A ratios (r = −0.502, p<0.001), MM (r = 0.304, p<0.001), glucose-levels (r = 0.157, p<0.05) and systolic blood pressure (r = 0.224, p<0.005) showed significant correlations with age. The ejection fraction did not significantly differ between the groups. This study shows that cardiac PCr/β-ATP ratios decrease moderately with age indicating an impairment of mitochondrial oxidative metabolism due to age. Furthermore, MM increases, and E/A ratio decreases with age. Both correlate with left-ventricular PCr/β-ATP ratios. The findings of the present study confirm numerous experimental studies showing an impairment of cardiac mitochondrial function with age. PMID:24940736

  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. Lanthanide ion (III) complexes of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate for dual biosensing of pH with chemical exchange saturation transfer (CEST) and biosensor imaging of redundant deviation in shifts (BIRDS).

    PubMed

    Huang, Yuegao; Coman, Daniel; Ali, Meser M; Hyder, Fahmeed

    2015-01-01

    Relaxivity-based magnetic resonance of phosphonated ligands chelated with gadolinium (Gd(3+)) shows promise for pH imaging. However instead of monitoring the paramagnetic effect of lanthanide complexes on the relaxivity of water protons, biosensor (or molecular) imaging with magnetic resonance is also possible by detecting either the nonexchangeable or the exchangeable protons on the lanthanide complexes themselves. The nonexchangeable protons (e.g. -CHx, where 3 ≥ x ≥ 1) are detected using a three-dimensional chemical shift imaging method called biosensor imaging of redundant deviation in shifts (BIRDS), whereas the exchangeable protons (e.g. -OH or -NHy , where 2 ≥ y ≥ 1) are measured with chemical exchange saturation transfer (CEST) contrast. Here we tested the feasibility of BIRDS and CEST for pH imaging of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate (DOTA-4AmP(8-)) chelated with thulium (Tm(3+) ) and ytterbium (Yb(3+)). BIRDS and CEST experiments show that both complexes are responsive to pH and temperature changes. Higher pH and temperature sensitivities are obtained with BIRDS for either complex when using the chemical shift difference between two proton resonances vs using the chemical shift of a single proton resonance, thereby eliminating the need to use water resonance as reference. While CEST contrast for both agents is linearly dependent on pH within a relatively large range (i.e. 6.3-7.9), much stronger CEST contrast is obtained with YbDOTA-4AmP(5-) than with TmDOTA-4AmP(5-). In addition, we demonstrate the prospect of using BIRDS to calibrate CEST as new platform for quantitative pH imaging.

  13. 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

  14. 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].

  15. 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

  16. 1H NMR chemical shift studies of pregn-5-ene-3β,20( R)-diol and pregn-5-ene-3β-ol,20-one D-glucopyranoside derivatives

    NASA Astrophysics Data System (ADS)

    Warthen, J. D.; Waters, R. M.; Oliver, J. E.

    The 1H NMR chemical shift and J value data of a series of pregn-5-ene-3β,20( R)-diol/pregn-5-ene-3β-ol, 20-one D-glucopyranosides and D-glucopyranoside derivatives are reported because of their relevance to the structure determination of pregnenediol tri- and diglucosides on tobacco hornworm eggs. Effects of various substituents at the 3β- and 20( R)-positions of the pregn-5-ene nucleus upon chemical shifts of selected protons on the pregn-5-ene nucleus are discussed. Chemical shifts of selected protons on the D-glucopyranoside nucleus/nuclei are also discussed. Differentiation between the pregn-5-ene substitution points, between anomeric glucose configurations and between anomeric protons on β- D-glucosides at 3β and 20( R) is demonstrated. A COSY NMR analysis of the Manduca peracetylated triglucoside is utilized to show the interaction of the three anomeric β- D-glucoside protons and to distinguish the dissimilar one.

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

    PubMed

    Sieh, Daniel; Kubiak, Clifford P

    2016-07-18

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

  18. 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.

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

    PubMed

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

    2003-06-01

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

  20. 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

  1. {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.

  2. 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

  3. Residual compressive stress induced infrared-absorption frequency shift of hexagonal boron nitride in cubic boron nitride films prepared by plasma-enhanced chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Liu, Yong; Jin, Panpan; Chen, Aili; Yang, Hangsheng; Xu, Yabo

    2012-09-01

    The effects of compressive stress on the TO phonon frequencies of hexagonal boron nitride (hBN) in cubic BN (cBN) films were investigated using infrared absorption spectroscopy, showing that the B-N stretching vibration of hBN at 1380 cm-1 shifted to high wavenumbers under biaxial compressive stress with the rate 2.65 cm-1 per GPa, while the B-N-B bending vibration near 780 cm-1 shifted to low wavenumbers with the rate -3.45 cm-1/GPa. The density functional perturbation theoretical calculation was carried out to check the above phonon frequencies under stress for two typical orientations of hBN crystallite. The results are shown to be in fair agreement with the experimental data. Our results suggest that the residual compressive stress accumulated in cBN films can be evaluated from the IR peak position near 780 cm-1.

  4. 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

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

    SciTech Connect

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

    2010-11-19

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

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

    PubMed

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

    2015-04-01

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

  7. 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.

  8. 1H, 15N, and 13C backbone chemical shift assignments, secondary structure, and magnesium-binding characteristics of the Bacillus subtilis response regulator, Spo0F, determined by heteronuclear high-resolution NMR.

    PubMed Central

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

    1995-01-01

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

  9. 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.

  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. Synthesis, antimicrobial evaluation and theoretical prediction of NMR chemical shifts of thiazole and selenazole derivatives with high antifungal activity against Candida spp.

    NASA Astrophysics Data System (ADS)

    Łączkowski, Krzysztof Z.; Motylewska, Katarzyna; Baranowska-Łączkowska, Angelika; Biernasiuk, Anna; Misiura, Konrad; Malm, Anna; Fernández, Berta

    2016-03-01

    Synthesis and investigation of antimicrobial activities of novel thiazoles and selenazoles is presented. Their structures were determined using NMR, FAB(+)-MS, HRMS and elemental analyses. To support the experiment, theoretical calculations of the 1H NMR shifts were carried out for representative systems within the DFT B3LYP/6-311++G** approximation which additionally confirmed the structure of investigated compounds. Among the derivatives, compounds 4b, 4h, 4j and 4l had very strong activity against reference strains of Candida albicans ATCC and Candida parapsilosis ATCC 22019 with MIC = 0.49-7.81 μg/ml. In the case of compounds 4b, 4c, 4h - 4j and 4l, the activity was very strong against of Candida spp. isolated from clinical materials, i.e. C. albicans, Candida krusei, Candida inconspicua, Candida famata, Candida lusitaniae, Candida sake, C. parapsilosis and Candida dubliniensis with MIC = 0.24-15.62 μg/ml. The activity of several of these was similar to the activity of commonly used antifungal agent fluconazole. Additionally, compounds 4m - 4s were found to be active against Gram-positive bacteria, both pathogenic staphylococci Staphylococcus aureus ATCC with MIC = 31.25-125 μg/ml and opportunistic bacteria, such as Staphylococcus epidermidis ATCC 12228 and Micrococcus luteus ATCC 10240 with MIC = 7.81-31.25 μg/ml.

  12. 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.

  13. 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

  14. 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.

  15. Structure-based predictions of 13C-NMR chemical shifts for a series of 2-functionalized 5-(methylsulfonyl)-1-phenyl-1H-indoles derivatives using GA-based MLR method

    NASA Astrophysics Data System (ADS)

    Ghavami, Raouf; Sadeghi, Faridoon; Rasouli, Zolikha; Djannati, Farhad

    2012-12-01

    Experimental values for the 13C NMR chemical shifts (ppm, TMS = 0) at 300 K ranging from 96.28 ppm (C4' of indole derivative 17) to 159.93 ppm (C4' of indole derivative 23) relative to deuteride chloroform (CDCl3, 77.0 ppm) or dimethylsulfoxide (DMSO, 39.50 ppm) as internal reference in CDCl3 or DMSO-d6 solutions have been collected from literature for thirty 2-functionalized 5-(methylsulfonyl)-1-phenyl-1H-indole derivatives containing different substituted groups. An effective quantitative structure-property relationship (QSPR) models were built using hybrid method combining genetic algorithm (GA) based on stepwise selection multiple linear regression (SWS-MLR) as feature-selection tools and correlation models between each carbon atom of indole derivative and calculated descriptors. Each compound was depicted by molecular structural descriptors that encode constitutional, topological, geometrical, electrostatic, and quantum chemical features. The accuracy of all developed models were confirmed using different types of internal and external procedures and various statistical tests. Furthermore, the domain of applicability for each model which indicates the area of reliable predictions was defined.

  16. 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

  17. 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

  18. 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.

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

    PubMed

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

    2014-01-01

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

  20. 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.

  1. Major Groove Width Variations in RNA Structures Determined by NMR and Impact of 13C residual chemical shift anisotropy and 1H-13C residual dipolar coupling on refinement

    PubMed Central

    Tolbert, Blanton S; Miyazaki, Yasuyuki; Barton, Shawn; Kinde, Benyam; Starck, Patrice; Singh, Rashmi; Bax, Ad

    2010-01-01

    Ribonucleic acid structure determination by NMR spectroscopy relies primarily on local structural restraints provided by 1H-1H NOEs and J-couplings. When employed loosely, these restraints are broadly compatible with A- and B-like helical geometries and give rise to calculated structures that are highly sensitive to the force fields employed during refinement. A survey of recently reported NMR structures reveals significant variations in helical parameters, particularly the major groove width. Although helical parameters observed in high-resolution X-ray crystal structures of isolated A-form RNA helices are sensitive to crystal packing effects, variations among the published X-ray structures are significantly smaller than those observed in NMR structures. Here we show that restraints derived from aromatic 1H-13C residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs) can overcome NMR restraint and force field deficiencies and afford structures with helical properties similar to those observed in high-resolution X-ray structures. PMID:20549304

  2. Compressive Shift Retrieval

    NASA Astrophysics Data System (ADS)

    Ohlsson, Henrik; Eldar, Yonina C.; Yang, Allen Y.; Sastry, S. Shankar

    2014-08-01

    The classical shift retrieval problem considers two signals in vector form that are related by a shift. The problem is of great importance in many applications and is typically solved by maximizing the cross-correlation between the two signals. Inspired by compressive sensing, in this paper, we seek to estimate the shift directly from compressed signals. We show that under certain conditions, the shift can be recovered using fewer samples and less computation compared to the classical setup. Of particular interest is shift estimation from Fourier coefficients. We show that under rather mild conditions only one Fourier coefficient suffices to recover the true shift.

  3. 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.

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2003-12-01

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

  6. Solvent effects on 195Pt and 205Tl NMR chemical shifts of the complexes [(NC)5Pt--Tl(CN)n]n- (n=0-3), and [(NC)5Pt--Tl--Pt(CN)5]3- studied by relativistic density functional theory.

    PubMed

    Autschbach, Jochen; Le Guennic, Boris

    2004-05-17

    The 295Pt and 205Tl NMR chemical shifts of the complexes [(NC)5Pt-Tl(CN)n]n- n=0-3, and of the related system [(NC)5Pt--Tl--Pt(CN)5]3- have been computationally investigated. It is demonstrated that based on relativistically optimized geometries, by applying an explicit first solvation shell, an additional implicit solvation model to represent the bulk solvent effects (COSMO model), and a DFT exchange-correlation potential that was specifically designed for the treatment of response properties, that the experimentally observed metal chemical shifts can be calculated with satisfactory accuracy. The metal chemical shifts have been computed by means of a two-component relativistic density functional approach. The effects of electronic spin-orbit coupling were included in all NMR computations. The impact of the choice of the reference, which ideally should not affect the accuracy of the computed chemical shifts, is also demonstrated. Together with recent calculations by us of the Pt and Tl spin-spin coupling constants, all measured metal NMR parameters of these complexes are now computationally determined with sufficient accuracy in order to allow a detailed analysis of the experimental results. In particular, we show that interaction of the complexes with the solvent (water) must be an integral part of such an analysis.

  7. 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

  8. 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.

  9. Comparison of brown and white adipose tissue fat fractions in ob, seipin, and Fsp27 gene knockout mice by chemical shift-selective imaging and (1)H-MR spectroscopy.

    PubMed

    Peng, Xin-Gui; Ju, Shenghong; Fang, Fang; Wang, Yu; Fang, Ke; Cui, Xin; Liu, George; Li, Peng; Mao, Hui; Teng, Gao-Jun

    2013-01-15

    Brown adipose tissue (BAT) plays a key role in thermogenesis to protect the body from cold and obesity. White adipose tissue (WAT) stores excess energy in the form of triglycerides. To better understand the genetic effect on regulation of WAT and BAT, we investigated the fat fraction (FF) in two types of adipose tissues in ob/ob, human BSCL2/seipin gene knockout (SKO), Fsp27 gene knockout (Fsp27(-/-)), and wild-type (WT) mice in vivo using chemical shift selective imaging and (1)H-MR spectroscopy. We reported that the visceral fat volume in WAT was significantly larger in ob/ob mice, but visceral fat volumes were lower in SKO and Fsp27(-/-) mice compared with WT mice. BAT FF was significantly higher in ob/ob mice than the WT group and similar to that of WAT. In contrast, WAT FFs in SKO and Fsp27(-/-) mice were lower and similar to that of BAT. The adipocyte size of WAT in ob/ob mice and the BAT adipocyte size in ob/ob, SKO, and Fsp27 mice were significantly larger compared with WT mice. However, the WAT adipocyte size was significantly smaller in SKO mice than in WT mice. Positive correlations were observed between the adipocyte size and FFs of WAT and BAT. These results suggested that smaller adipocyte size correlates with lower FFs of WAT and BAT. In addition, the differences in FFs in WAT and BAT measured by MR methods in different mouse models were related to the different regulation effects of ob, seipin, or Fsp27 gene on developing WAT and BAT.

  10. 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.

  11. 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

  12. 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

  13. Spectral shift amplification.

    PubMed

    Han, Pin

    2012-12-01

    The behavior of a limited bandwidth light wave reflected from a material interface is studied theoretically. It is shown that near the anomalous dispersion zone, if the incident center wavelength is shifted by a small amount, this shift can be amplified by about three times in the reflected light. PMID:23202082

  14. Style Shift in Translation

    ERIC Educational Resources Information Center

    Al-Qinai, Jamal

    2009-01-01

    The phenomenon of style shift in translated texts is ascribed mainly to textual incompatibility in terms of rhetorical asymmetry and divergence at the formality level. Mandatory shifts result from a systematic dissimilarity between the source language and the target language in terms of the underlying system of syntax, semantics and rhetorical…

  15. Spectral shift amplification.

    PubMed

    Han, Pin

    2012-12-01

    The behavior of a limited bandwidth light wave reflected from a material interface is studied theoretically. It is shown that near the anomalous dispersion zone, if the incident center wavelength is shifted by a small amount, this shift can be amplified by about three times in the reflected light.

  16. Making Shifts toward Proficiency

    ERIC Educational Resources Information Center

    McGatha, Maggie B.; Bay-Williams, Jennifer M.

    2013-01-01

    The Leading for Mathematical Proficiency (LMP) Framework (Bay-Williams et al.) has three components: (1) The Standards for Mathematical Practice; (2) Shifts in classroom practice; and (3) Teaching skills. This article briefly describes each component of the LMP framework and then focuses more in depth on the second component, the shifts in…

  17. 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.

  18. 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

  19. 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

  20. 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...

  1. 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.

  2. Vehicular transmission shift mechanism

    SciTech Connect

    Okubo, K.

    1988-12-27

    This patent describes a vehicular transmission having a main speed change mechanism and a sub speed change mechanism both housed within a transmission case. The main speed change mechanism has gear trains in plural shifting stages provided between input and output shafts and capable of being established selectively and also has a plurality of synchronizing mechanisms operable by shift forks to establish the gear trains selectively. The sub speed change mechanism has a reduction gear train for obtaining a still lower speed than the lowest shifting stage in the main speed change mechanism and also has a sub speed gear shifting synchronizing mechanism operable by a sub speed gear shift fork to establish the reduction gear train. This sub speed change mechanism is disposed in parallel with the main speed change mechanism, the sub speed gear shift fork having means connected to one end of a lever pivotably supported at an intermediate part thereof by a pivot pin, the pivot pin being mounted on the transmission case from the outside thereof.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Catastrophic shifts in ecosystems

    NASA Astrophysics Data System (ADS)

    Scheffer, Marten; Carpenter, Steve; Foley, Jonathan A.; Folke, Carl; Walker, Brian

    2001-10-01

    All ecosystems are exposed to gradual changes in climate, nutrient loading, habitat fragmentation or biotic exploitation. Nature is usually assumed to respond to gradual change in a smooth way. However, studies on lakes, coral reefs, oceans, forests and arid lands have shown that smooth change can be interrupted by sudden drastic switches to a contrasting state. Although diverse events can trigger such shifts, recent studies show that a loss of resilience usually paves the way for a switch to an alternative state. This suggests that strategies for sustainable management of such ecosystems should focus on maintaining resilience.

  13. Elective automatic shift transmission

    SciTech Connect

    Redzinski, G.E.

    1986-09-02

    For use in vehicle of the type having an engine coupled with traction wheels through a driveline including a change-speed transmission, the transmission includes drive direction reversing means, a drive direction selector for manual control of the reversing means and having a forward and reverse position, the transmission including ratio changing means, a manual gear selector for operation of the ratio changing means for shifting the transmission into a selected gear, and control means responsive to a control signal for upshifting and downshifting between first and second gears.

  14. 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.

  15. 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.

  16. 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.

  17. Spectroscopy and quantum chemical modeling reveal a predominant contribution of excitonic interactions to the bathochromic shift in alpha-crustacyanin, the blue carotenoprotein in the carapace of the lobster Homarus gammarus.

    PubMed

    van Wijk, Arjan A C; Spaans, Arnold; Uzunbajakava, Natallia; Otto, Cees; de Groot, Huub J M; Lugtenburg, Johan; Buda, Francesco

    2005-02-01

    To resolve the molecular basis of the coloration mechanism of alpha-crustacyanin, we used (13)C-labeled astaxanthins as chromophores for solid-state (13)C NMR and resonance Raman spectroscopy of [6,6',7,7']-(13)C(4) alpha-crustacyanin and [8,8',9,9',10,10',11,11',20,20']-(13)C(10) alpha-crustacyanin. We complement the experimental data with time-dependent density functional theory calculations on several models based on the structural information available for beta-crustacyanin. The data rule out major changes and strong polarization effects in the ground-state electron density of astaxanthin upon binding to the protein. Conformational changes in the chromophore and hydrogen-bond interactions between the astaxanthin and the protein can account only for about one-third of the total bathochromic shift in alpha-crustacyanin. The exciton coupling due to the proximity of two astaxanthin chromophores is found to be large, suggesting that aggregation effects in the protein represent the primary source of the color change. PMID:15686376

  18. 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.

  19. 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.

  20. 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 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. 8 figs.

  1. 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.

  2. 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.

  3. Hydraulically actuated well shifting tool

    SciTech Connect

    Roth, B.A.

    1992-10-20

    This patent describes a hydraulically actuated shifting tool for actuating a sliding member in a well tool. It comprises: a housing having a hydraulic fluid bore therein; shifting dog means positioned on the housing for movement away and toward the housing; locking dog means positioned on the housing for movement away and toward the body; shifting dog hydraulic actuating means in fluid communication with the bore for causing engagement of the shifting dogs with the sliding member; locking dog hydraulic actuating means in communication with the bore for causing engagement of the locking dogs with the locking means; and hydraulic shifting means in communication with the bore for causing relative movement between the shifting dog means and the locking dog means for shifting the sliding sleeve.

  4. Pyridazine-based Schiff base ligands with N 4O xS 2 ( x = 2, 4) donor set atoms: Synthesis, characterization, spectral studies and 13C chemical shifts computed by the GIAO-DFT and CSGT-DFT methodologies

    NASA Astrophysics Data System (ADS)

    Khanmohammadi, Hamid; Erfantalab, Malihe

    2010-01-01

    Six pyridazine-based Schiff base ligands, H 2L n ( n = 1-5) and H 4L, with N 4O 2S 2 and N 4O 4S 2 donor set atoms, respectively, were prepared by condensation reaction of 3,6-bis-((2-aminoethyl)thio)pyridazine with various salicyladehyde derivatives in ethanol and under solvent-free polyphosphate ester catalyzed conditions. The acid-base properties of H 2L 2 and H 2L 3 in DMSO/water (1:1) solution have been studied by spectrophotometric method at 25 °C. Optimized geometries of all compounds were also obtained at the B3LYP level of theory. Additionally, the 13C chemical shielding of gas phase H 2L 1 and H 2L 2 were studied by the gauge independent atomic orbital (GIAO) and continuous set of gauge transformations (CSGT) methods at the level of density functional theory (DFT). The 6-311++G* basis set was utilized for all of the atoms.

  5. 1H, 13C, and 15N backbone, side-chain, and heme chemical shift assignments for oxidized and reduced forms of the monoheme c-type cytochrome ApcA isolated from the acidophilic metal-reducing bacterium Acidiphilium cryptum.

    SciTech Connect

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

    2011-03-04

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