Mobility of TOAC spin-labelled peptides binding to the Src SH3 domain studied by paramagnetic NMR

International Nuclear Information System (INIS)

Lindfors, Hanna E.; Koning, Peter E. de; Wouter Drijfhout, Jan; Venezia, Brigida; Ubbink, Marcellus

2008-01-01

Paramagnetic relaxation enhancement provides a tool for studying the dynamics as well as the structure of macromolecular complexes. The application of side-chain coupled spin-labels is limited by the mobility of the free radical. The cyclic, rigid amino acid spin-label TOAC (2,2,6,6-Tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid), which can be incorporated straightforwardly by peptide synthesis, provides an attractive alternative. In this study, TOAC was incorporated into a peptide derived from focal adhesion kinase (FAK), and the interaction of the peptide with the Src homology 3 (SH3) domain of Src kinase was studied, using paramagnetic NMR. Placing TOAC within the binding motif of the peptide has a considerable effect on the peptide-protein binding, lowering the affinity substantially. When the TOAC is positioned just outside the binding motif, the binding constant remains nearly unaffected. Although the SH3 domain binds weakly and transiently to proline-rich peptides from FAK, the interaction is not very dynamic and the relative position of the spin-label to the protein is well-defined. It is concluded that TOAC can be used to generate reliable paramagnetic NMR restraints

Sensitivity and Resolution Enhanced Solid-State NMR for Paramagnetic Systems and Biomolecules under Very Fast Magic Angle Spinning

KAUST Repository

Parthasarathy, Sudhakar

2013-09-17

Recent research in fast magic angle spinning (MAS) methods has drastically improved the resolution and sensitivity of NMR spectroscopy of biomolecules and materials in solids. In this Account, we summarize recent and ongoing developments in this area by presenting (13)C and (1)H solid-state NMR (SSNMR) studies on paramagnetic systems and biomolecules under fast MAS from our laboratories. First, we describe how very fast MAS (VFMAS) at the spinning speed of at least 20 kHz allows us to overcome major difficulties in (1)H and (13)C high-resolution SSNMR of paramagnetic systems. As a result, we can enhance both sensitivity and resolution by up to a few orders of magnitude. Using fast recycling (∼ms/scan) with short (1)H T1 values, we can perform (1)H SSNMR microanalysis of paramagnetic systems on the microgram scale with greatly improved sensitivity over that observed for diamagnetic systems. Second, we discuss how VFMAS at a spinning speed greater than ∼40 kHz can enhance the sensitivity and resolution of (13)C biomolecular SSNMR measurements. Low-power (1)H decoupling schemes under VFMAS offer excellent spectral resolution for (13)C SSNMR by nominal (1)H RF irradiation at ∼10 kHz. By combining the VFMAS approach with enhanced (1)H T1 relaxation by paramagnetic doping, we can achieve extremely fast recycling in modern biomolecular SSNMR experiments. Experiments with (13)C-labeled ubiquitin doped with 10 mM Cu-EDTA demonstrate how effectively this new approach, called paramagnetic assisted condensed data collection (PACC), enhances the sensitivity. Lastly, we examine (13)C SSNMR measurements for biomolecules under faster MAS at a higher field. Our preliminary (13)C SSNMR data of Aβ amyloid fibrils and GB1 microcrystals acquired at (1)H NMR frequencies of 750-800 MHz suggest that the combined use of the PACC approach and ultrahigh fields could allow for routine multidimensional SSNMR analyses of proteins at the 50-200 nmol level. Also, we briefly discuss the

Paramagnetic Nanoparticles Leave Their Mark on Nuclear Spins of Transiently Adsorbed Proteins.

Science.gov (United States)

Zanzoni, Serena; Pedroni, Marco; D'Onofrio, Mariapina; Speghini, Adolfo; Assfalg, Michael

2016-01-13

The successful application of nanomaterials in biosciences necessitates an in-depth understanding of how they interface with biomolecules. Transient associations of proteins with nanoparticles (NPs) are accessible by solution NMR spectroscopy, albeit with some limitations. The incorporation of paramagnetic centers into NPs offers new opportunities to explore bio-nano interfaces. We propose NMR paramagnetic relaxation enhancement as a new tool to detect NP-binding surfaces on proteins with increased sensitivity, also extending the applicability of NMR investigations to heterogeneous biomolecular mixtures. The adsorption of ubiquitin on gadolinium-doped fluoride-based NPs produced residue-specific NMR line-broadening effects mapping to a contiguous area on the surface of the protein. Importantly, an identical paramagnetic fingerprint was observed in the presence of a competing protein-protein association equilibrium, exemplifying possible interactions taking place in crowded biological media. The interaction was further characterized using isothermal titration calorimetry and upconversion emission measurements. The data indicate that the used fluoride-based NPs are not biologically inert but rather are capable of biomolecular recognition.

Subnanodimensional thermometrical NMR-sensors on the basis of lanthanide(III) paramagnetic complexes with EDTA for temperature control in aqueous media and magnetoresonance tomography

International Nuclear Information System (INIS)

Babajlov, S.P.

2008-01-01

It is proposed that temperature dependence of paramagnetic lanthanide-induced shifts (LIS) in NMR spectra on nuclei of EDTA type synthetic organic complexes in kinetically unstable compounds with paramagnetic lanthanide(III) cations is used for ascertaining the temperature of samples placed directly into a NMR spectrometer and formed on the basis of aqueous solutions of diverse chemical substances. It was revealed that complex [Ho III (EDTA)] can be used as an internal or an external thermometric NMR-sensor. For identification and control of temperature in a sample one can make use of LIS for individual signals from CH 2 groups (taken in relation to water or inner DCC standard signals). A higher temperature measurement accuracy (≤0.08 K) is attained by using LIS difference corresponding to the relevant nonequivalent CH 2 groups [ru

Magnetic resonance studies of isotopically labeled paramagnetic proteins: (2FE-2S) ferredoxins

Energy Technology Data Exchange (ETDEWEB)

Cheng, H.; Xia, B.; Chae, Y.K.; Westler, W.M.; Markley, J.L. [Univ. of Wisconsin, Madison, WI (United States)

1994-12-01

Recent developments in NMR spectroscopy, especially multidimensional, multinuclear NMR techniques, have made NMR the most versatile tool available for studying protein structure and function in solution. Unlike diamagnetic proteins, paramagnetic proteins contain centers with unpaired electrons. These unpaired electrons interact with magnetic nuclei either through chemical bonds by a contact mechanism or through space by a pseudocontact mechanism. Such interactions make the acquisition and analysis of NMR spectra of paramagnetic proteins more challenging than those of diamagnetic proteins. Some NMR signals from paramagnetic proteins are shifted outside the chemical shift region characteristic of diamagnetic proteins; these {open_quotes}hyperfine-shifted{close_quotes} resonances originate from nuclei that interact with unpaired electrons from the paramagnetic center. The large chemical shift dispersion in spectra of paramagnetic proteins makes it difficult to excite the entire spectral window and leads to distortions in the baseline. Interactions with paramagnetic centers shorten T{sub 1} and T{sub 2} relaxation times of nuclei; the consequences are line broadening and lower spectral sensitivity. Scalar (through bond) and dipolar (through space) interactions between pairs of nuclei are what give rise to crosspeak signals in multi-dimensional NMR spectra of small diamagnetic proteins. When such interactions involve a nucleus that is strongly relaxed by interaction with a paramagnetic center, specialized methods may be needed for its detection or it may be completely undetectable by present nD NMR methods.

Lanthanide paramagnetic probes for NMR spectroscopic studies of fast molecular conformational dynamics and temperature control. Effective six-site proton exchange in 18-crown-6 by exchange spectroscopy.

Science.gov (United States)

Babailov, Sergey P

2012-02-06

(1)H and (13)C NMR measurements are reported for the CDCl(3) and CD(2)Cl(2) solutions of [La(18-crown-6)(NO(3))(3)] (I), [Pr(18-crown-6) (NO(3))(3)] (II), [Ce(18-crown-6)(NO(3))(3)] (III), and [Nd(18-crown-6)(NO(3))(3)] (IV) complexes. Temperature dependencies of the (1)H NMR spectra of paramagnetic II-IV have been analyzed using the dynamic NMR (DNMR) methods for six-site exchange. Two types of conformational dynamic processes were identified (the first one is conditioned by interconversion of complex enantiomeric forms and pseudorotation of a macrocycle molecule upon the C(2) symmetry axis; the second one is conditioned by macrocycle molecule inversion). Application of exchange spectroscopy (2D-EXSY) of DNMR for investigation of this dynamic system (II-IV) simplifies the assignment of the NMR signals and represents the first experimental study of multisite exchange. In the present work, the methodology of paramagnetic 4f (Ce, Pr, and Nd) probe applications for the study of free-energy, enthalpy, and entropy changes in chemical exchange processes, as well as the advantages of this method in a comparison with DNMR studies of diamagnetic substances, is discussed. In particular, as a result of paramagnetic chemical shifts in 4f complexes, the range of measurable rate constants expands considerably compared to the analogous range in diamagnetic compounds. Coordination compounds investigated in the paper represent new types of thermometric NMR sensors and lanthanide paramagnetic probes for in situ temperature control in solution.

Molecular dynamics simulations on PGLa using NMR orientational constraints

Energy Technology Data Exchange (ETDEWEB)

Sternberg, Ulrich, E-mail: ulrich.sternberg@partner.kit.edu; Witter, Raiker [Tallinn University of Technology, Technomedicum (Estonia)

2015-11-15

NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.

Process of Fragment-Based Lead Discovery—A Perspective from NMR

Directory of Open Access Journals (Sweden)

Rongsheng Ma

2016-07-01

Full Text Available Fragment-based lead discovery (FBLD has proven fruitful during the past two decades for a variety of targets, even challenging protein–protein interaction (PPI systems. Nuclear magnetic resonance (NMR spectroscopy plays a vital role, from initial fragment-based screening to lead generation, because of its power to probe the intrinsically weak interactions between targets and low-molecular-weight fragments. Here, we review the NMR FBLD process from initial library construction to lead generation. We describe technical aspects regarding fragment library design, ligand- and protein-observed screening, and protein–ligand structure model generation. For weak binders, the initial hit-to-lead evolution can be guided by structural information retrieved from NMR spectroscopy, including chemical shift perturbation, transferred pseudocontact shifts, and paramagnetic relaxation enhancement. This perspective examines structure-guided optimization from weak fragment screening hits to potent leads for challenging PPI targets.

Monovacancy paramagnetism in neutron-irradiated graphite probed by 13C NMR.

Science.gov (United States)

Zhang, Z T; Xu, C; Dmytriieva, D; Molatta, S; Wosnitza, J; Wang, Y T; Helm, M; Zhou, Shengqiang; Kühne, H

2017-10-20

We report on the magnetic properties of monovacancy defects in neutron-irradiated graphite, probed by 13 C nuclear magnetic resonance spectroscopy. The bulk paramagnetism of the defect moments is revealed by the temperature dependence of the NMR frequency shift and spectral linewidth, both of which follow a Curie behavior, in agreement with measurements of the macroscopic magnetization. Compared to pristine graphite, the fluctuating hyperfine fields generated by the defect moments lead to an enhancement of the 13 C nuclear spin-lattice relaxation rate [Formula: see text] by about two orders of magnitude. With an applied magnetic field of 7.1 T, the temperature dependence of [Formula: see text] below about 10 K can well be described by a thermally activated form, [Formula: see text], yielding a singular Zeeman energy of ([Formula: see text]) meV, in excellent agreement with the sole presence of polarized, non-interacting defect moments.

Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide

International Nuclear Information System (INIS)

Oktaviani, Nur Alia; Risør, Michael W.; Lee, Young-Ho; Megens, Rik P.; Jong, Djurre H. de; Otten, Renee; Scheek, Ruud M.; Enghild, Jan J.; Nielsen, Niels Chr.; Ikegami, Takahisa; Mulder, Frans A. A.

2015-01-01

Co-solute paramagnetic relaxation enhancement (PRE) is an attractive way to speed up data acquisition in NMR spectroscopy by shortening the T 1 relaxation time of the nucleus of interest and thus the necessary recycle delay. Here, we present the rationale to utilize high-spin iron(III) as the optimal transition metal for this purpose and characterize the properties of its neutral chelate form Fe(DO3A) as a suitable PRE agent. Fe(DO3A) effectively reduces the T 1 values across the entire sequence of the intrinsically disordered protein α-synuclein with negligible impact on line width. The agent is better suited than currently used alternatives, shows no specific interaction with the polypeptide chain and, due to its high relaxivity, is effective at low concentrations and in ‘proton-less’ NMR experiments. By using Fe(DO3A) we were able to complete the backbone resonance assignment of a highly fibrillogenic peptide from α 1 -antitrypsin by acquiring the necessary suite of multidimensional NMR datasets in 3 h

Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide

Energy Technology Data Exchange (ETDEWEB)

Oktaviani, Nur Alia [University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute (Netherlands); Risør, Michael W. [University of Aarhus, Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry (Denmark); Lee, Young-Ho [Osaka University, Institute for Protein Research (Japan); Megens, Rik P. [University of Groningen, Stratingh Institute for Chemistry (Netherlands); Jong, Djurre H. de; Otten, Renee; Scheek, Ruud M. [University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute (Netherlands); Enghild, Jan J. [University of Aarhus, Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics (Denmark); Nielsen, Niels Chr. [University of Aarhus, Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry (Denmark); Ikegami, Takahisa [Yokohama City University, Graduate School of Medical Life Science (Japan); Mulder, Frans A. A., E-mail: fmulder@chem.au.dk [University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute (Netherlands)

2015-06-15

Co-solute paramagnetic relaxation enhancement (PRE) is an attractive way to speed up data acquisition in NMR spectroscopy by shortening the T{sub 1} relaxation time of the nucleus of interest and thus the necessary recycle delay. Here, we present the rationale to utilize high-spin iron(III) as the optimal transition metal for this purpose and characterize the properties of its neutral chelate form Fe(DO3A) as a suitable PRE agent. Fe(DO3A) effectively reduces the T{sub 1} values across the entire sequence of the intrinsically disordered protein α-synuclein with negligible impact on line width. The agent is better suited than currently used alternatives, shows no specific interaction with the polypeptide chain and, due to its high relaxivity, is effective at low concentrations and in ‘proton-less’ NMR experiments. By using Fe(DO3A) we were able to complete the backbone resonance assignment of a highly fibrillogenic peptide from α{sub 1}-antitrypsin by acquiring the necessary suite of multidimensional NMR datasets in 3 h.

Two-dimensional NMR measurement and point dipole model prediction of paramagnetic shift tensors in solids

Energy Technology Data Exchange (ETDEWEB)

Walder, Brennan J.; Davis, Michael C.; Grandinetti, Philip J. [Department of Chemistry, Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210 (United States); Dey, Krishna K. [Department of Physics, Dr. H. S. Gour University, Sagar, Madhya Pradesh 470003 (India); Baltisberger, Jay H. [Division of Natural Science, Mathematics, and Nursing, Berea College, Berea, Kentucky 40403 (United States)

2015-01-07

A new two-dimensional Nuclear Magnetic Resonance (NMR) experiment to separate and correlate the first-order quadrupolar and chemical/paramagnetic shift interactions is described. This experiment, which we call the shifting-d echo experiment, allows a more precise determination of tensor principal components values and their relative orientation. It is designed using the recently introduced symmetry pathway concept. A comparison of the shifting-d experiment with earlier proposed methods is presented and experimentally illustrated in the case of {sup 2}H (I = 1) paramagnetic shift and quadrupolar tensors of CuCl{sub 2}⋅2D{sub 2}O. The benefits of the shifting-d echo experiment over other methods are a factor of two improvement in sensitivity and the suppression of major artifacts. From the 2D lineshape analysis of the shifting-d spectrum, the {sup 2}H quadrupolar coupling parameters are 〈C{sub q}〉 = 118.1 kHz and 〈η{sub q}〉 = 0.88, and the {sup 2}H paramagnetic shift tensor anisotropy parameters are 〈ζ{sub P}〉 = − 152.5 ppm and 〈η{sub P}〉 = 0.91. The orientation of the quadrupolar coupling principal axis system (PAS) relative to the paramagnetic shift anisotropy principal axis system is given by (α,β,γ)=((π)/2 ,(π)/2 ,0). Using a simple ligand hopping model, the tensor parameters in the absence of exchange are estimated. On the basis of this analysis, the instantaneous principal components and orientation of the quadrupolar coupling are found to be in excellent agreement with previous measurements. A new point dipole model for predicting the paramagnetic shift tensor is proposed yielding significantly better agreement than previously used models. In the new model, the dipoles are displaced from nuclei at positions associated with high electron density in the singly occupied molecular orbital predicted from ligand field theory.

Monovacancy paramagnetism in neutron-irradiated graphite probed by 13C NMR.

Science.gov (United States)

Zhang, Zhi Tao; Xu, C; Dmytriieva, Daryna; Molatta, Sebastian; Wosnitza, J; Wang, Y T; Helm, Manfred; Zhou, Shengqiang; Kuehne, Hannes

2017-09-18

We report on the magnetic properties of monovacancy defects in neutron-irradiated graphite, probed by $^{13}$C nuclear magnetic resonance spectroscopy. The bulk paramagnetism of the defect moments is revealed by the temperature dependence of the NMR frequency shift and spectral linewidth, both of which follow a Curie behavior, in agreement with measurements of the macroscopic magnetization. Compared to pristine graphite, the fluctuating hyperfine fields generated by the defect moments lead to an enhancement of the $^{13}$C nuclear spin-lattice relaxation rate $1/T_{1}$ by about two orders of magnitude. With an applied magnetic field of 7.1 T, the temperature dependence of $1/T_{1}$ below about 10 K can well be described by a thermally activated form, $1/T_{1}\\propto\\exp(-\\Delta/k_{B}T)$, yielding a singular Zeeman energy of ($0.41\\pm0.01$) meV, in excellent agreement with the sole presence of polarized, non-interacting defect moments. © 2017 IOP Publishing Ltd.

Symmetric Imidazolium-Based Paramagnetic Ionic Liquids

Science.gov (United States)

2017-11-29

Charts N/A Unclassified Unclassified Unclassified SAR 14 Kamran Ghiassi N/A 1 Symmetric Imidazolium-Based Paramagnetic Ionic Liquids Kevin T. Greeson...NUMBER (Include area code) 29 November 2017 Briefing Charts 01 November 2017 - 30 November 2017 Symmetric Imidazolium-Based Paramagnetic Ionic ... Liquids K. Greeson, K. Ghiassi, J. Alston, N. Redeker, J. Marcischak, L. Gilmore, A. Guenthner Air Force Research Laboratory (AFMC) AFRL/RQRP 9 Antares

Trispyrazolylborate Complexes: An Advanced Synthesis Experiment Using Paramagnetic NMR, Variable-Temperature NMR, and EPR Spectroscopies

Science.gov (United States)

Abell, Timothy N.; McCarrick, Robert M.; Bretz, Stacey Lowery; Tierney, David L.

2017-01-01

A structured inquiry experiment for inorganic synthesis has been developed to introduce undergraduate students to advanced spectroscopic techniques including paramagnetic nuclear magnetic resonance and electron paramagnetic resonance. Students synthesize multiple complexes with unknown first row transition metals and identify the unknown metals by…

Paramagnetic probes to study PrNi5?

International Nuclear Information System (INIS)

Hutchinson, W.D.; Harker, S.J.; Stewart, G.A.; Chaplin, D.H.; Kaplan, N.

1996-01-01

The Van-Vleck paramagnet PrNi 5 has been the focus of many studies in the past as a result of its usefulness as a nuclear cooling agent. Extensive continuous wave praseodymium NMR measurements have been carried out on this compound. However pulsed NMR and therefore precise relaxation measurements particularly at mK temperatures have proved elusive. In this work we have proposed to use radiative gamma-ray detection to indirectly measure Pr NMR in PrNi 5 via cross relaxation to suitable paramagnetic impurity probes placed at Ni lattice sites. 57 Co was chosen as the most compatible nuclear orientation isotope with an appropriate nuclear g-factor. The choice of 57 Co also allows the use of Moessbauer spectroscopy to check the site occupancy. This poster details the production of a 57 Co doped PrNi 5 single crystal specimen including the specimen preparation problems encountered, 57 Fe Moessbauer and preliminary nuclear orientation measurements

Demetalation of Fe, Mn, and Cu chelates and complexes: application to the NMR analysis of micronutrient fertilizers.

Science.gov (United States)

López-Rayo, Sandra; Lucena, Juan J; Laghi, Luca; Cremonini, Mauro A

2011-12-28

The application of nuclear magnetic resonance (NMR) for the quality control of fertilizers based on Fe(3+), Mn(2+), and Cu(2+) chelates and complexes is precluded by the strong paramagnetism of metals. Recently, a method based on the use of ferrocyanide has been described to remove iron from commercial iron chelates based on the o,o-EDDHA [ethylenediamine-N,N'bis(2-hydroxyphenylacetic)acid] chelating agent for their analysis and quantification by NMR. The present work extended that procedure to other paramagnetic ions, manganese and copper, and other chelating, EDTA (ethylenediaminetetraacetic acid), IDHA [N-(1,2-dicarboxyethyl)-d,l-aspartic acid], and complexing agents, gluconate and heptagluconate. Results showed that the removal of the paramagnetic ions was complete, allowing us to obtain (1)H NMR spectra characterized by narrow peaks. The quantification of the ligands by NMR and high-performance liquid chromatography showed that their complete recovery was granted. The NMR analysis enabled detection and quantification of unknown impurities without the need of pure compounds as internal standards.

Magic Angle Spinning NMR Structure Determination of Proteins from Pseudocontact Shifts

KAUST Repository

Li, Jianping

2013-06-05

Magic angle spinning solid-state NMR is a unique technique to study atomic-resolution structure of biomacromolecules which resist crystallization or are too large to study by solution NMR techniques. However, difficulties in obtaining sufficient number of long-range distance restraints using dipolar coupling based spectra hamper the process of structure determination of proteins in solid-state NMR. In this study it is shown that high-resolution structure of proteins in solid phase can be determined without the use of traditional dipolar-dipolar coupling based distance restraints by combining the measurements of pseudocontact shifts (PCSs) with Rosetta calculations. The PCSs were generated by chelating exogenous paramagnetic metal ions to a tag 4-mercaptomethyl-dipicolinic acid, which is covalently attached to different residue sites in a 56-residue immunoglobulin-binding domain of protein G (GB1). The long-range structural restraints with metal-nucleus distance of up to ∼20 Å are quantitatively extracted from experimentally observed PCSs, and these are in good agreement with the distances back-calculated using an X-ray structure model. Moreover, we demonstrate that using several paramagnetic ions with varied paramagnetic susceptibilities as well as the introduction of paramagnetic labels at different sites can dramatically increase the number of long-range restraints and cover different regions of the protein. The structure generated from solid-state NMR PCSs restraints combined with Rosetta calculations has 0.7 Å root-mean-square deviation relative to X-ray structure. © 2013 American Chemical Society.

Magic Angle Spinning NMR Structure Determination of Proteins from Pseudocontact Shifts

KAUST Repository

Li, Jianping; Pilla, Kala Bharath; Li, Qingfeng; Zhang, Zhengfeng; Su, Xuncheng; Huber, Thomas; Yang, Jun

2013-01-01

Magic angle spinning solid-state NMR is a unique technique to study atomic-resolution structure of biomacromolecules which resist crystallization or are too large to study by solution NMR techniques. However, difficulties in obtaining sufficient number of long-range distance restraints using dipolar coupling based spectra hamper the process of structure determination of proteins in solid-state NMR. In this study it is shown that high-resolution structure of proteins in solid phase can be determined without the use of traditional dipolar-dipolar coupling based distance restraints by combining the measurements of pseudocontact shifts (PCSs) with Rosetta calculations. The PCSs were generated by chelating exogenous paramagnetic metal ions to a tag 4-mercaptomethyl-dipicolinic acid, which is covalently attached to different residue sites in a 56-residue immunoglobulin-binding domain of protein G (GB1). The long-range structural restraints with metal-nucleus distance of up to ∼20 Å are quantitatively extracted from experimentally observed PCSs, and these are in good agreement with the distances back-calculated using an X-ray structure model. Moreover, we demonstrate that using several paramagnetic ions with varied paramagnetic susceptibilities as well as the introduction of paramagnetic labels at different sites can dramatically increase the number of long-range restraints and cover different regions of the protein. The structure generated from solid-state NMR PCSs restraints combined with Rosetta calculations has 0.7 Å root-mean-square deviation relative to X-ray structure. © 2013 American Chemical Society.

Thermometric nanosize NMR-sensors for temperature determination in weakly polar non-aqueous media on the base of ion pairs of paramagnetic complexes of lanthanides(III)

International Nuclear Information System (INIS)

Babajlov, S.P.

2008-01-01

For temperature determination in solutions it is suggested that the temperature dependence of the paramagnetic lanthanide-induced shifts (LIS) in the NMR spectra on the ligand nuclei be used for [Ln(PTA) 2 (18-crown-6)] + [Ln(PTA) 4 ] - complex ion pairs formed in CCl 4 , CDCl 3 , CD 2 Cl 2 , CD 3 C 6 D 5 , and C 2 D 3 N type low-polar solvents (Ln = La, Ce, Pr, Nd, Eu; PTA is the pivalyltrifluoroacetonate anion). It was found experimentally that the [Ln(PTA) 2 (18-crown-6)] + complex cation molecules (Ln = Ce and Pr) proved most suitable for use as nanosized (∼1.1 nm) probes for temperature determinations in nonaqueous solutions. A linear dependence of the LIS on the 1 H nuclei of different groups and the difference between the LIS corresponding to the CH 2 groups of the 18-crown-6 molecules and the CH groups of the PTA anions on the reciprocal temperature (1/T) was found. The LIS of the individual signals of different groups in Ln paramagnetic complexes (relative to the signals of the diamagnetic analogs, e.g., La or Lu) may be used for temperature control in the sample, although the temperature measurement error is smaller (≤0.04 K) when the difference between the LIS of the CH 2 and CH groups is used. Due to the high thermodynamic and kinetic stability combined with small sizes of [Ln(PTA) 2 (18-crown-6)] + [Ln(PTA) 4 ] - molecules in nonaqueous solutions, these compounds may be used as thermometric NMR sensors directly in reaction media for in situ control over temperature [ru

Paramagnetic relaxation enhancement of membrane proteins by incorporation of the metal-chelating unnatural amino acid 2-amino-3-(8-hydroxyquinolin-3-yl)propanoic acid (HQA)

Energy Technology Data Exchange (ETDEWEB)

Park, Sang Ho; Wang, Vivian S.; Radoicic, Jasmina; Angelis, Anna A. De; Berkamp, Sabrina; Opella, Stanley J., E-mail: sopella@ucsd.edu [University of California, San Diego, Department of Chemistry and Biochemistry (United States)

2015-04-15

The use of paramagnetic constraints in protein NMR is an active area of research because of the benefits of long-range distance measurements (>10 Å). One of the main issues in successful execution is the incorporation of a paramagnetic metal ion into diamagnetic proteins. The most common metal ion tags are relatively long aliphatic chains attached to the side chain of a selected cysteine residue with a chelating group at the end where it can undergo substantial internal motions, decreasing the accuracy of the method. An attractive alternative approach is to incorporate an unnatural amino acid that binds metal ions at a specific site on the protein using the methods of molecular biology. Here we describe the successful incorporation of the unnatural amino acid 2-amino-3-(8-hydroxyquinolin-3-yl)propanoic acid (HQA) into two different membrane proteins by heterologous expression in E. coli. Fluorescence and NMR experiments demonstrate complete replacement of the natural amino acid with HQA and stable metal chelation by the mutated proteins. Evidence of site-specific intra- and inter-molecular PREs by NMR in micelle solutions sets the stage for the use of HQA incorporation in solid-state NMR structure determinations of membrane proteins in phospholipid bilayers.

Study of actinide paramagnetism in solution

International Nuclear Information System (INIS)

Autillo, Matthieu

2015-01-01

The physiochemical properties of actinide (An) solutions are still difficult to explain, particularly the behavioral differences between An(III) and Ln(III). The study of actinide paramagnetic behavior may be a 'simple' method to analyze the electronic properties of actinide elements and to obtain information on the ligand-actinide interaction. The objective of this PhD thesis is to understand the paramagnetic properties of these elements by magnetic susceptibility measurements and chemical shift studies. Studies on actinide electronic properties at various oxidation states in solution were carried out by magnetic susceptibility measurements in solution according to the Evans method. Unlike Ln(III) elements, there is no specific theory describing the magnetic properties of these ions in solution. To obtain accurate data, the influence of experimental measurement technique and radioactivity of these elements was analyzed. Then, to describe the electronic structure of their low energy states, the experimental results were complemented with quantum chemical calculations from which the influence of the ligand field was studied. Finally, these interpretations were applied to better understand the variations in the magnetic properties of actinide cations in chloride and nitrate media. Information about ligand-actinide interactions may be determined from an NMR chemical shift study of actinide complexes. Indeed, modifications induced by a paramagnetic complex can be separated into two components. The first component, a Fermi contact contribution (δ_c) is related to the degree of covalency in coordination bonds with the actinide ions and the second, a dipolar contribution (δ_p_c) is related to the structure of the complex. The paramagnetic induced shift can be used only if we can isolate these two terms. To achieve this study on actinide elements, we chose to work with the complexes of dipicolinic acid (DPA). Firstly, to characterize the geometrical parameters, a

Increasing the sensitivity of NMR diffusion measurements by paramagnetic longitudinal relaxation enhancement, with application to ribosome–nascent chain complexes

International Nuclear Information System (INIS)

Chan, Sammy H. S.; Waudby, Christopher A.; Cassaignau, Anaïs M. E.; Cabrita, Lisa D.; Christodoulou, John

2015-01-01

The translational diffusion of macromolecules can be examined non-invasively by stimulated echo (STE) NMR experiments to accurately determine their molecular sizes. These measurements can be important probes of intermolecular interactions and protein folding and unfolding, and are crucial in monitoring the integrity of large macromolecular assemblies such as ribosome–nascent chain complexes (RNCs). However, NMR studies of these complexes can be severely constrained by their slow tumbling, low solubility (with maximum concentrations of up to 10 μM), and short lifetimes resulting in weak signal, and therefore continuing improvements in experimental sensitivity are essential. Here we explore the use of the paramagnetic longitudinal relaxation enhancement (PLRE) agent NiDO2A on the sensitivity of 15 N XSTE and SORDID heteronuclear STE experiments, which can be used to monitor the integrity of these unstable complexes. We exploit the dependence of the PLRE effect on the gyromagnetic ratio and electronic relaxation time to accelerate recovery of 1 H magnetization without adversely affecting storage on N z during diffusion delays or introducing significant transverse relaxation line broadening. By applying the longitudinal relaxation-optimized SORDID pulse sequence together with NiDO2A to 70S Escherichia coli ribosomes and RNCs, NMR diffusion sensitivity enhancements of up to 4.5-fold relative to XSTE are achieved, alongside ∼1.9-fold improvements in two-dimensional NMR sensitivity, without compromising the sample integrity. We anticipate these results will significantly advance the use of NMR to probe dynamic regions of ribosomes and other large, unstable macromolecular assemblies.Graphical Abstract

NMR study of the paramagnetic state of low-dimensional magnets LiCu{sub 2}O{sub 2} and NaCu{sub 2}O{sub 2}

Energy Technology Data Exchange (ETDEWEB)

Sadykov, A. F., E-mail: sadykov@imp.uran.ru; Piskunov, Yu. V.; Gerashchenko, A. P.; Ogloblichev, V. V.; Smol’nikov, A. G.; Verkhovskii, S. V.; Arapova, I. Yu.; Volkova, Z. N.; Mikhalev, K. N. [Russian Academy of Sciences, Mikheev Institute of Metal Physics, Ural Branch (Russian Federation); Bush, A. A. [Moscow State Technical University of Radio Engineering, Electronics, and Automation (Russian Federation)

2017-02-15

A comprehensive NMR study of the magnetic properties of single crystal LiCu{sub 2}O{sub 2} (LCO) and NaCu{sub 2}O{sub 2} (NCO) is carried out in the paramagnetic region of the compounds for various orientations of single crystals in an external magnetic field. The values of the electric-field gradient (EFG) tensor, as well as the dipole and transferred hyperfine magnetic fields for {sup 63,65}Cu, {sup 7}Li, and {sup 23}Na nuclei are determined. The results are compared with the data obtained in previous NMR studies of the magnetically ordered state of LCO/NCO cuprates.

Paramagnetic relaxation enhancements in NMR peptide-membrane interaction studies

International Nuclear Information System (INIS)

Kosol, S.

2011-01-01

Small membrane-bound proteins or peptides are involved in numerous essential biological processes, like cellular recognition, signaling, channel formation, and cytolysis. The secondary structure, orientation, mode of interaction and dynamics of these peptides can be as varied as their functions. Their localization in the membrane, the immersion depth, and their binding mode are factors critical to the function of these peptides. The atomic 3D solution structure of peptides bound to micelles can be determined by NMR spectroscopy. However, by employing paramagnetic relaxation enhancements (PREs) information on the complete topology of peptide bound to a micelle can be obtained. The antimicrobial peptide maximin H6, fst, a bacterial toxin, and the human peptide hormone ghrelin served as membrane-bound model peptides of similar sizes but strongly differing amino acid sequences. Their structures and binding behavior were determined and compared.The measured PREs provided suitable data for determining and distinguishing the different topologies of the investigated peptides bound to micelles. Maximin H6 and fst fold into α-helices upon insertion into a membrane, whereas the unstructured ghrelin is freely mobile in solution and interacts only via a covalently bound octanoyl group with the lipids. Maximin H6 is oriented parallel to the membrane surface, enabling the peptide to aggregate at the membrane water interface. Fst binds in transmembrane orientation with a protruding intrinsically disordered region near the C-terminus. Aside from determining the orientation of the bound peptides from the PREs, the moieties critical for membrane binding could be mapped in ghrelin. If suitable relaxation-edited spectra are acquired, the complete orientation and immersion depth of a peptide bound to a micelle can readily be obtained. (author) [de

Protein structural studies by paramagnetic solid-state NMR spectroscopy aided by a compact cyclen-type Cu(II) binding tag

Energy Technology Data Exchange (ETDEWEB)

Sengupta, Ishita; Gao, Min; Arachchige, Rajith J.; Nadaud, Philippe S. [The Ohio State University, Department of Chemistry and Biochemistry (United States); Cunningham, Timothy F.; Saxena, Sunil [University of Pittsburgh, Department of Chemistry (United States); Schwieters, Charles D. [National Institutes of Health, Center for Information Technology (United States); Jaroniec, Christopher P., E-mail: jaroniec@chemistry.ohio-state.edu [The Ohio State University, Department of Chemistry and Biochemistry (United States)

2015-01-15

Paramagnetic relaxation enhancements (PREs) are a rich source of structural information in protein solid-state NMR spectroscopy. Here we demonstrate that PRE measurements in natively diamagnetic proteins are facilitated by a thiol-reactive compact, cyclen-based, high-affinity Cu{sup 2+} binding tag, 1-[2-(pyridin-2-yldisulfanyl)ethyl]-1,4,7,10-tetraazacyclododecane (TETAC), that overcomes the key shortcomings associated with the use of larger, more flexible metal-binding tags. Using the TETAC–Cu{sup 2+} K28C mutant of B1 immunoglobulin-binding domain of protein G as a model, we find that amino acid residues located within ∼10 Å of the Cu{sup 2+} center experience considerable transverse PREs leading to severely attenuated resonances in 2D {sup 15}N–{sup 13}C correlation spectra. For more distant residues, electron–nucleus distances are accessible via quantitative measurements of longitudinal PREs, and we demonstrate such measurements for {sup 15}N–Cu{sup 2+} distances up to ∼20 Å.

Paramagnetic properties of the low- and high-spin states of yeast cytochrome c peroxidase

International Nuclear Information System (INIS)

Vanwetswinkel, Sophie; Nuland, Nico A. J. van; Volkov, Alexander N.

2013-01-01

Here we describe paramagnetic NMR analysis of the low- and high-spin forms of yeast cytochrome c peroxidase (CcP), a 34 kDa heme enzyme involved in hydroperoxide reduction in mitochondria. Starting from the assigned NMR spectra of a low-spin CN-bound CcP and using a strategy based on paramagnetic pseudocontact shifts, we have obtained backbone resonance assignments for the diamagnetic, iron-free protein and the high-spin, resting-state enzyme. The derived chemical shifts were further used to determine low- and high-spin magnetic susceptibility tensors and the zero-field splitting constant (D) for the high-spin CcP. The D value indicates that the latter contains a hexacoordinate heme species with a weak field ligand, such as water, in the axial position. Being one of the very few high-spin heme proteins analyzed in this fashion, the resting state CcP expands our knowledge of the heme coordination chemistry in biological systems

Paramagnetic properties of the low- and high-spin states of yeast cytochrome c peroxidase

Energy Technology Data Exchange (ETDEWEB)

Vanwetswinkel, Sophie; Nuland, Nico A. J. van; Volkov, Alexander N., E-mail: ovolkov@vub.ac.be [Vrije Universiteit Brussel, Jean Jeener NMR Centre, Structural Biology Brussels (Belgium)

2013-09-15

Here we describe paramagnetic NMR analysis of the low- and high-spin forms of yeast cytochrome c peroxidase (CcP), a 34 kDa heme enzyme involved in hydroperoxide reduction in mitochondria. Starting from the assigned NMR spectra of a low-spin CN-bound CcP and using a strategy based on paramagnetic pseudocontact shifts, we have obtained backbone resonance assignments for the diamagnetic, iron-free protein and the high-spin, resting-state enzyme. The derived chemical shifts were further used to determine low- and high-spin magnetic susceptibility tensors and the zero-field splitting constant (D) for the high-spin CcP. The D value indicates that the latter contains a hexacoordinate heme species with a weak field ligand, such as water, in the axial position. Being one of the very few high-spin heme proteins analyzed in this fashion, the resting state CcP expands our knowledge of the heme coordination chemistry in biological systems.

Structure determination of uniformly {sup 13}C, {sup 15}N labeled protein using qualitative distance restraints from MAS solid-state {sup 13}C-NMR observed paramagnetic relaxation enhancement

Energy Technology Data Exchange (ETDEWEB)

Tamaki, Hajime [Hokkaido University, Graduate School of Life Science (Japan); Egawa, Ayako [Osaka University, Institute for Protein Research (Japan); Kido, Kouki [Hokkaido University, Graduate School of Life Science (Japan); Kameda, Tomoshi [National Institute of Advanced Industrial Science and Technology, Biotechnology Research Institute for Drug Discovery (Japan); Kamiya, Masakatsu; Kikukawa, Takashi; Aizawa, Tomoyasu [Hokkaido University, Faculty of Advanced Life Science (Japan); Fujiwara, Toshimichi [Osaka University, Institute for Protein Research (Japan); Demura, Makoto, E-mail: demura@sci.hokudai.ac.jp [Hokkaido University, Faculty of Advanced Life Science (Japan)

2016-01-15

Magic angle spinning (MAS) solid-state nuclear magnetic resonance (NMR) is a powerful method for structure determination of insoluble biomolecules. However, structure determination by MAS solid-state NMR remains challenging because it is difficult to obtain a sufficient amount of distance restraints owing to spectral complexity. Collection of distance restraints from paramagnetic relaxation enhancement (PRE) is a promising approach to alleviate this barrier. However, the precision of distance restraints provided by PRE is limited in solid-state NMR because of incomplete averaged interactions and intermolecular PREs. In this report, the backbone structure of the B1 domain of streptococcal protein G (GB1) has been successfully determined by combining the CS-Rosetta protocol and qualitative PRE restraints. The derived structure has a Cα RMSD of 1.49 Å relative to the X-ray structure. It is noteworthy that our protocol can determine the correct structure from only three cysteine-EDTA-Mn{sup 2+} mutants because this number of PRE sites is insufficient when using a conventional structure calculation method based on restrained molecular dynamics and simulated annealing. This study shows that qualitative PRE restraints can be employed effectively for protein structure determination from a limited conformational sampling space using a protein fragment library.

Functional studies using NMR

International Nuclear Information System (INIS)

McCready, V.R.; Leach, M.O.; Sutton; Ell, P.

1986-01-01

The object of this book is to discuss and evaluate an area of Nuclear Magnetic Resonance which to date has been less emphasized than it might be, namely the use of NMR for functional studies. The book commences with a discussion of the areas in which the NMR techniques might be needed due to deficiencies in other techniques. The physics of NMR especially relating to functional measurement are then explained. Technical factors in producing functional images are discussed and the use of paramagnetic substances for carrying out flow studies are detailed. Particular attention is paid to specific studies in the various organs. The book ends with a survey of imaging in each organ and the relation of NMR images to other techniques such as ultrasound, nuclear medicine and X-rays

BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank

International Nuclear Information System (INIS)

Doreleijers, Jurgen F.; Mading, Steve; Maziuk, Dimitri; Sojourner, Kassandra; Yin Lei; Zhu Jun; Markley, John L.; Ulrich, Eldon L.

2003-01-01

Experimental constraints associated with NMR structures are available from the Protein Data Bank (PDB) in the form of 'Magnetic Resonance' (MR) files. These files contain multiple types of data concatenated without boundary markers and are difficult to use for further research. Reported here are the results of a project initiated to annotate, archive, and disseminate these data to the research community from a searchable resource in a uniform format. The MR files from a set of 1410 NMR structures were analyzed and their original constituent data blocks annotated as to data type using a semi-automated protocol. A new software program called Wattos was then used to parse and archive the data in a relational database. From the total number of MR file blocks annotated as constraints, it proved possible to parse 84% (3337/3975). The constraint lists that were parsed correspond to three data types (2511 distance, 788 dihedral angle, and 38 residual dipolar couplings lists) from the three most popular software packages used in NMR structure determination: XPLOR/CNS (2520 lists), DISCOVER (412 lists), and DYANA/DIANA (405 lists). These constraints were then mapped to a developmental version of the BioMagResBank (BMRB) data model. A total of 31 data types originating from 16 programs have been classified, with the NOE distance constraint being the most commonly observed. The results serve as a model for the development of standards for NMR constraint deposition in computer-readable form. The constraints are updated regularly and are available from the BMRB web site (http://www.bmrb.wisc.edu)

Quantum-Chemical Approach to NMR Chemical Shifts in Paramagnetic Solids Applied to LiFePO4 and LiCoPO4.

Science.gov (United States)

Mondal, Arobendo; Kaupp, Martin

2018-04-05

A novel protocol to compute and analyze NMR chemical shifts for extended paramagnetic solids, accounting comprehensively for Fermi-contact (FC), pseudocontact (PC), and orbital shifts, is reported and applied to the important lithium ion battery cathode materials LiFePO 4 and LiCoPO 4 . Using an EPR-parameter-based ansatz, the approach combines periodic (hybrid) DFT computation of hyperfine and orbital-shielding tensors with an incremental cluster model for g- and zero-field-splitting (ZFS) D-tensors. The cluster model allows the use of advanced multireference wave function methods (such as CASSCF or NEVPT2). Application of this protocol shows that the 7 Li shifts in the high-voltage cathode material LiCoPO 4 are dominated by spin-orbit-induced PC contributions, in contrast with previous assumptions, fundamentally changing interpretations of the shifts in terms of covalency. PC contributions are smaller for the 7 Li shifts of the related LiFePO 4 , where FC and orbital shifts dominate. The 31 P shifts of both materials finally are almost pure FC shifts. Nevertheless, large ZFS contributions can give rise to non-Curie temperature dependences for both 7 Li and 31 P shifts.

Solid state NMR of materials

Energy Technology Data Exchange (ETDEWEB)

Taylor, Sharon A; Ferguson, David B; Haw, James F [Texas A and M Univ., College Station, TX (United States). Dept. of Chemistry

1994-12-31

In situ NMR experiments are studied, including probe of several structures such as the structures of the organic adsorbates, Broensted acid sites, other nuclei associated with active sites, and other framework sites. The authors report that in the absence of high concentrations of paramagnetic sites or metal particles, high resolution MAS spectra are relatively easy to obtain and interpret. It is also concluded that NMR can measure spatial distributions and rates of diffusion; and are able to characterize equilibrium structures and the frequencies and amplitudes of molecular motion

NMR-based milk metabolomics

DEFF Research Database (Denmark)

Sundekilde, Ulrik; Larsen, Lotte Bach; Bertram, Hanne Christine S.

2013-01-01

and processing capabilities of bovine milk is closely associated to milk composition. Metabolomics is ideal in the study of the low-molecular-weight compounds in milk, and this review focuses on the recent nuclear magnetic resonance (NMR)-based metabolomics trends in milk research, including applications linking...... compounds. Furthermore, metabolomics applications elucidating how the differential regulated genes affects milk composition are also reported. This review will highlight the recent advances in NMR-based metabolomics on milk, as well as give a brief summary of when NMR spectroscopy can be useful for gaining...

Dynamics of solutions and fluid mixtures by NMR

International Nuclear Information System (INIS)

Delpuech, J.J.

1994-01-01

After a short introduction to NMR spectroscopy, with a special emphasis on dynamical aspects, an overview on two fundamental aspects of molecular dynamics, NMR relaxation and its relationship with molecular reorientation, and magnetization transfer phenomena induced by molecular rate processes (dynamic NMR) is presented, followed by specific mechanisms of relaxation encountered in paramagnetic systems or with quadrupolar nuclei. Application fields are then reviewed: solvent exchange on metal ions with a variable pressure NMR approach, applications of field gradients in NMR, aggregation phenomena and micro-heterogeneity in surfactant solutions, polymers and biopolymers in the liquid state, liquid-like molecules in rigid matrices and in soft matter (swollen polymers and gels, fluids in and on inorganic materials, food)

De novo protein structure determination using sparse NMR data

International Nuclear Information System (INIS)

Bowers, Peter M.; Strauss, Charlie E.M.; Baker, David

2000-01-01

We describe a method for generating moderate to high-resolution protein structures using limited NMR data combined with the ab initio protein structure prediction method Rosetta. Peptide fragments are selected from proteins of known structure based on sequence similarity and consistency with chemical shift and NOE data. Models are built from these fragments by minimizing an energy function that favors hydrophobic burial, strand pairing, and satisfaction of NOE constraints. Models generated using this procedure with ∼1 NOE constraint per residue are in some cases closer to the corresponding X-ray structures than the published NMR solution structures. The method requires only the sparse constraints available during initial stages of NMR structure determination, and thus holds promise for increasing the speed with which protein solution structures can be determined

Susceptibility cancellation of a microcoil wound with a paramagnetic-liquid-filled copper capillary

Science.gov (United States)

Takeda, Kazuyuki; Takasaki, Tomoya; Takegoshi, K.

2015-09-01

Even though microcoils improve the sensitivity of NMR measurement of tiny samples, magnetic-field inhomogeneity due to the bulk susceptibility effect of the coil material can cause serious resonance-line broadening. Here, we propose to fabricate the microcoil using a thin, hollow copper capillary instead of a wire and fill paramagnetic liquid inside the capillary, so as to cancel the diamagnetic contribution of the copper. Susceptibility cancellation is demonstrated using aqueous solution of NiSO4. In addition, the paramagnetic liquid serves as coolant when it is circulated through the copper capillary, effectively transferring the heat generated by radiofrequency pulses.

Chirp echo Fourier transform EPR-detected NMR.

Science.gov (United States)

Wili, Nino; Jeschke, Gunnar

2018-04-01

A new ultra-wide band (UWB) pulse EPR method is introduced for observing all nuclear frequencies of a paramagnetic center in a single shot. It is based on burning spectral holes with a high turning angle (HTA) pulse that excites forbidden transitions and subsequent detection of the hole pattern by a chirp echo. We term this method Chirp Echo Epr SpectroscopY (CHEESY)-detected NMR. The approach is a revival of FT EPR-detected NMR. It yields similar spectra and the same type of information as electron-electron double resonance (ELDOR)-detected NMR, but with a multiplex advantage. We apply CHEESY-detected NMR in Q band to nitroxides and correlate the hyperfine spectrum to the EPR spectrum by varying the frequency of the HTA pulse. Furthermore, a selective π pulse before the HTA pulse allows for detecting hyperfine sublevel correlations between transitions of one nucleus and for elucidating the coupling regime, the same information as revealed by the HYSCORE experiment. This is demonstrated on hexaaquamanganese(II). We expect that CHEESY-detected NMR is generally applicable to disordered systems and that our results further motivate the development of EPR spectrometers capable of coherent UWB excitation and detection, especially at higher fields and frequencies. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Chirp echo Fourier transform EPR-detected NMR

Science.gov (United States)

Wili, Nino; Jeschke, Gunnar

2018-04-01

A new ultra-wide band (UWB) pulse EPR method is introduced for observing all nuclear frequencies of a paramagnetic center in a single shot. It is based on burning spectral holes with a high turning angle (HTA) pulse that excites forbidden transitions and subsequent detection of the hole pattern by a chirp echo. We term this method Chirp Echo Epr SpectroscopY (CHEESY)-detected NMR. The approach is a revival of FT EPR-detected NMR. It yields similar spectra and the same type of information as electron-electron double resonance (ELDOR)-detected NMR, but with a multiplex advantage. We apply CHEESY-detected NMR in Q band to nitroxides and correlate the hyperfine spectrum to the EPR spectrum by varying the frequency of the HTA pulse. Furthermore, a selective π pulse before the HTA pulse allows for detecting hyperfine sublevel correlations between transitions of one nucleus and for elucidating the coupling regime, the same information as revealed by the HYSCORE experiment. This is demonstrated on hexaaquamanganese(II). We expect that CHEESY-detected NMR is generally applicable to disordered systems and that our results further motivate the development of EPR spectrometers capable of coherent UWB excitation and detection, especially at higher fields and frequencies.

NMR study of structure of lanthanide complexes in solution

International Nuclear Information System (INIS)

Choppin, G.R.

1976-01-01

The diagnostic value PMR studies of diamagnetic lanthanide complexes to define the nature of the species in the lanthanide-pyruvate system is discussed. The use of NMR spectra of both diamagnetic and paramagnetic lanthanide complexes to obtain detailed structural information is reviewed

Proton nuclear magnetic resonance in paramagnetic CoCl2.6H2O

International Nuclear Information System (INIS)

Oravcova, J.; Murin, J.; Rakos, M.; Olcak, D.

1978-01-01

Nuclear magnetic resonance (NMR) is studied of protons of the crystal water of paramagnetic CoCl 2 .6H 2 O. The measurements were carried out on powdered samples at room temperature, for values of the external magnetic field ranging from 0.3 to 1.0 T. The NMR signals of protons of the crystal water exhibit asymmetric shape which changes with the applied external magnetic field. We found that the second moment of the resonance line shows a linear dependence on the square of the induction of the externally applied magnetic field. The cause of the asymmetry of the NMR line of protons of the crystal water and the dependence of the second moment of the resonance line on the induction of external magnetic field are interpreted. (author)

Coal liquefaction process streams characterization and evaluation: Estimation of total phenol concentrations in coal liquefaction resids by {sup 31}P NMR spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Mohan, J.T.; Verkade, J.G. [Ames Lab., IA (United States)

1992-11-01

In this study, Iowa State University researchers used {sub 31}P-tagged reagents to derivatize the labile hydrogen functional groups in the THF-soluble portion of 850{degrees}F{sup +} distillation resid materials and the THF-soluble portion of process oils derived from direct coal liquefaction.{sup 31}P-NMR was used to analyze the derivatized samples. NMR peak assignments can be made by comparison to model compounds similarly derivatized. Species can be quantified by integration of the NMR signals. Different {sup 31}P-NMR tagged reagents can be used to produce different degrees of peak resolution in the NMR spectrum. This, in turn, partially dictates the degree of speciation and/or quantification of species, or classes of compounds, that can be accomplished. Iowa State chose a {sup 31}P-tagged reagent (ClPOCMe{sub 2}CMe{sub 2}O) which was shown previously to be particularly useful in the derivatization of phenols. The derivatized samples all exhibited a small group of peaks attributed to amines and a broad group of peaks in the phenol region. The presence of paramagnetic species in the samples caused the NMR signals to broaden. Electron paramagnetic resonance (EPR) spectra confirmed the presence of paramagnetic organic free radicals in selected samples. Various methods were employed to process the NMR data. The complexity and broadness of the phenol peak, however, made speciation of the phenols impractical.

Coal liquefaction process streams characterization and evaluation: Estimation of total phenol concentrations in coal liquefaction resids by [sup 31]P NMR spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Mohan, J.T.; Verkade, J.G. (Ames Lab., IA (United States))

1992-11-01

In this study, Iowa State University researchers used [sub 31]P-tagged reagents to derivatize the labile hydrogen functional groups in the THF-soluble portion of 850[degrees]F[sup +] distillation resid materials and the THF-soluble portion of process oils derived from direct coal liquefaction.[sup 31]P-NMR was used to analyze the derivatized samples. NMR peak assignments can be made by comparison to model compounds similarly derivatized. Species can be quantified by integration of the NMR signals. Different [sup 31]P-NMR tagged reagents can be used to produce different degrees of peak resolution in the NMR spectrum. This, in turn, partially dictates the degree of speciation and/or quantification of species, or classes of compounds, that can be accomplished. Iowa State chose a [sup 31]P-tagged reagent (ClPOCMe[sub 2]CMe[sub 2]O) which was shown previously to be particularly useful in the derivatization of phenols. The derivatized samples all exhibited a small group of peaks attributed to amines and a broad group of peaks in the phenol region. The presence of paramagnetic species in the samples caused the NMR signals to broaden. Electron paramagnetic resonance (EPR) spectra confirmed the presence of paramagnetic organic free radicals in selected samples. Various methods were employed to process the NMR data. The complexity and broadness of the phenol peak, however, made speciation of the phenols impractical.

Solution NMR Spectroscopy in Target-Based Drug Discovery.

Science.gov (United States)

Li, Yan; Kang, Congbao

2017-08-23

Solution NMR spectroscopy is a powerful tool to study protein structures and dynamics under physiological conditions. This technique is particularly useful in target-based drug discovery projects as it provides protein-ligand binding information in solution. Accumulated studies have shown that NMR will play more and more important roles in multiple steps of the drug discovery process. In a fragment-based drug discovery process, ligand-observed and protein-observed NMR spectroscopy can be applied to screen fragments with low binding affinities. The screened fragments can be further optimized into drug-like molecules. In combination with other biophysical techniques, NMR will guide structure-based drug discovery. In this review, we describe the possible roles of NMR spectroscopy in drug discovery. We also illustrate the challenges encountered in the drug discovery process. We include several examples demonstrating the roles of NMR in target-based drug discoveries such as hit identification, ranking ligand binding affinities, and mapping the ligand binding site. We also speculate the possible roles of NMR in target engagement based on recent processes in in-cell NMR spectroscopy.

Synthesis and evaluation of nitroxide-based oligoradicals for low-temperature dynamic nuclear polarization in solid state NMR

Science.gov (United States)

Yau, Wai-Ming; Thurber, Kent R.; Tycko, Robert

2014-07-01

We describe the synthesis of new nitroxide-based biradical, triradical, and tetraradical compounds and the evaluation of their performance as paramagnetic dopants in dynamic nuclear polarization (DNP) experiments in solid state nuclear magnetic resonance (NMR) spectroscopy with magic-angle spinning (MAS). Under our experimental conditions, which include temperatures in the 25-30 K range, a 9.4 T magnetic field, MAS frequencies of 6.2-6.8 kHz, and microwave irradiation at 264.0 GHz from a 800 mW extended interaction oscillator source, the most effective compounds are triradicals that are related to the previously-described compound DOTOPA-TEMPO (see Thurber et al., 2010), but have improved solubility in glycerol/water solvent near neutral pH. Using these compounds at 30 mM total nitroxide concentration, we observe DNP enhancement factors of 92-128 for cross-polarized 13C NMR signals from 15N,13C-labeled melittin in partially protonated glycerol/water, and build-up times of 2.6-3.8 s for 1H spin polarizations. Net sensitivity enhancements with biradical and tetraradical dopants, taking into account absolute 13C NMR signal amplitudes and build-up times, are approximately 2-4 times lower than with the best triradicals.

Study of Paramagnetic Monohydrates MeSO4.1H2O (Me = Mn2+, Co2+, Fe2+, Ni2+, Cu2+

Directory of Open Access Journals (Sweden)

Jelšovská Kamila

2000-09-01

Full Text Available Nuclear magnetic resonance (NMR of protons of crystrallization water in isomorphous paramagnetic monohydrates MeSO4.1H2O with Me = Mn2+ , Co2+ , Fe2+ , Ni2+ , Cu2+ is studied in the present paper. Several physically important parameters characterizing the studied substances were derived from the NMR spectra. In this paper we analysed the dependences of the NMR second moment M2 on the magnitude of the external magnetic field induction Br and the temperature. The proton NMR spectra in paramagnetic hydrates have an asymmetric form caused by the anisotropy of the local magnetic field acting on resonating nuclei and their second moments, M2, depend linearly on the square of the external magnetic field Br. The parameters M20 (the part of the second moment M2 which corresponds to the nuclear dipole-dipole interactions and á which characterize nuclear dipole-dipole interactions of protons and paramagnetic ions, respectively, are derived from experimentally obtained dependences of M2 vs Br2. The measurements were performed at the room temperature. Calculations were realized using the approximation where two nearest neighbour ions Me2+ to each water molecule are considered. The temperature dependence of the second moment, which was realised in the temperature range 123-313 K, was more informative than the field one. Besides the individual dependences M2(T measured at fr1 and fr2 we analysed the temperature dependence of the difference ∆M2(T. Beside the second moment M20 the Curie-Weiss constant è and the magnetic moment µi of paramagnetic ions were determined from the temperature dependences. The parameters è and M20 were determined directly from the experimental data. Some knowledge on the crystalline structure for the studied substance was required for the calculation of the magnetic moment µi. By means of the classification of substances according to the Curie-Weiss parameter, the negative value of the temperature parameter è for all studied

Electron paramagnetic resonance

CERN Document Server

Al'tshuler, S A

2013-01-01

Electron Paramagnetic Resonance is a comprehensive text on the field of electron paramagnetic resonance, covering both the theoretical background and the results of experiment. This book is composed of eight chapters that cover theoretical materials and experimental data on ionic crystals, since these are the materials that have been most extensively studied by the methods of paramagnetic resonance. The opening chapters provide an introduction to the basic principles of electron paramagnetic resonance and the methods of its measurement. The next chapters are devoted to the theory of spectra an

Temperature-induced transitions in disordered proteins probed by NMR spectroscopy

DEFF Research Database (Denmark)

Kjærgaard, Magnus; Poulsen, Flemming Martin; Kragelund, Birthe Brandt

2012-01-01

Intrinsically disordered proteins are abundant in nature and perform many important physiological functions. Multidimensional NMR spectroscopy has been crucial for the understanding of the conformational properties of disordered proteins and is increasingly used to probe their conformational...... ensembles. Compared to folded proteins, disordered proteins are more malleable and more easily perturbed by environmental factors. Accordingly, the experimental conditions and especially the temperature modify the structural and functional properties of disordered proteins. NMR spectroscopy allows analysis...... of temperature-induced structural changes at residue resolution using secondary chemical shift analysis, paramagnetic relaxation enhancement, and residual dipolar couplings. This chapter discusses practical aspects of NMR studies of temperature-induced structural changes in disordered proteins....

APPLICATION OF A C-13 NMR TOPOLOGICAL MODEL TO THE STRUCTURE ELUCIDATION OF ORGANIC COMPOUNDS

Institute of Scientific and Technical Information of China (English)

袁身刚; 彭琛; 郑崇直

1992-01-01

This paper presents an approach which can elucidate automatically the structures of simple organic compounds from their C-13 NMR spectral data by using a computer. Based on a substructure/C-13 NMR chemical shift topological correlation model, the approach deduces the candidate substructures and the constraints for the substructure assembling from the molecular formula and C-13 NMR spectral data. Then, candidate structures are generated under these constraints by assembling the candidate substructures in a partial superposition manner. Candidate substructures or structures are evaluated once they are generated in order to eliminate those conflicting with the original data as early as possible. The evaluation of a (sub)structure is mainly carried out by simulating its C-13 NMR (sub) spectrum, which is again based on the model, and comparing the simulated spectrum with the original data.

Disk-cylinder method for using NMR to measure magnetic susceptibility

International Nuclear Information System (INIS)

Burnham, A.K.

1978-01-01

The sphere-cylinder method of using nuclear magnetic resonance (NMR) to measure the magnetic susceptibility of diamagnetic and paramagnetic materials has been generalized to the disk-cylinder method. A two-fold increase in sensitivity was obtained. Accuracies of 0.1% of the diamagnetism of water should be readily obtainable

13C NMR and EPR spectroscopic evaluation of oil shale mined soil recuperation

International Nuclear Information System (INIS)

Santos, J.V. dos; Mangrich, A.S.; Pereira, B.F.; Pillon, C.N.; Bonagamba, T.J.

2013-01-01

In this work, native forest soil (NFS) organic matter (SOM) sample and SOM samples from a neighboring forest soil area of an oil shale mine which is being rehabilitated for thirty years (RFS) were analyzed. X-band electron paramagnetic resonance (EPR) and solid-state 13 C nuclear magnetic resonance (NMR) spectroscopies were used to evaluate the soil reclamation of the Brazilian oil shale mining process. Two-dimensional heterospectral correlation studies of the results obtained from EPRand 13 C NMR were used to obtain information about SOM structures and their interactions with residual paramagnetic metal ion. The signal of the residual metallic oxycation, VO 2+ correlated positively with uronic acid-type hydrophilic organic structures, determined from the 13 C NMR spectra, and correlated negatively with the organic free radical (OFR) signal associated with oxygen atoms (g = 2.0042). The hydrophobic aromatic structures correlate positively with the EPR OFR signal associated with carbon atoms (g = 2.0022). The data from the two spectroscopic magnetic techniques show that the used recuperation process is effective. (author)

Constraint-based reachability

Directory of Open Access Journals (Sweden)

Arnaud Gotlieb

2013-02-01

Full Text Available Iterative imperative programs can be considered as infinite-state systems computing over possibly unbounded domains. Studying reachability in these systems is challenging as it requires to deal with an infinite number of states with standard backward or forward exploration strategies. An approach that we call Constraint-based reachability, is proposed to address reachability problems by exploring program states using a constraint model of the whole program. The keypoint of the approach is to interpret imperative constructions such as conditionals, loops, array and memory manipulations with the fundamental notion of constraint over a computational domain. By combining constraint filtering and abstraction techniques, Constraint-based reachability is able to solve reachability problems which are usually outside the scope of backward or forward exploration strategies. This paper proposes an interpretation of classical filtering consistencies used in Constraint Programming as abstract domain computations, and shows how this approach can be used to produce a constraint solver that efficiently generates solutions for reachability problems that are unsolvable by other approaches.

Vivaldi: Visualization and validation of biomacromolecular NMR structures from the PDB

Science.gov (United States)

Hendrickx, Pieter M S; Gutmanas, Aleksandras; Kleywegt, Gerard J

2013-01-01

We describe Vivaldi (VIsualization and VALidation DIsplay; http://pdbe.org/vivaldi), a web-based service for the analysis, visualization, and validation of NMR structures in the Protein Data Bank (PDB). Vivaldi provides access to model coordinates and several types of experimental NMR data using interactive visualization tools, augmented with structural annotations and model-validation information. The service presents information about the modeled NMR ensemble, validation of experimental chemical shifts, residual dipolar couplings, distance and dihedral angle constraints, as well as validation scores based on empirical knowledge and databases. Vivaldi was designed for both expert NMR spectroscopists and casual non-expert users who wish to obtain a better grasp of the information content and quality of NMR structures in the public archive. © Proteins 2013. © 2012 Wiley Periodicals, Inc. PMID:23180575

NMR characterization of weak interactions between RhoGDI2 and fragment screening hits.

Science.gov (United States)

Liu, Jiuyang; Gao, Jia; Li, Fudong; Ma, Rongsheng; Wei, Qingtao; Wang, Aidong; Wu, Jihui; Ruan, Ke

2017-01-01

The delineation of intrinsically weak interactions between novel targets and fragment screening hits has long limited the pace of hit-to-lead evolution. Rho guanine-nucleotide dissociation inhibitor 2 (RhoGDI2) is a novel target that lacks any chemical probes for the treatment of tumor metastasis. Protein-observed and ligand-observed NMR spectroscopy was used to characterize the weak interactions between RhoGDI2 and fragment screening hits. We identified three hits of RhoGDI2 using streamlined NMR fragment-based screening. The binding site residues were assigned using non-uniformly sampled C α - and H α -based three dimensional NMR spectra. The molecular docking to the proposed geranylgeranyl binding pocket of RhoGDI2 was guided by NMR restraints of chemical shift perturbations and ligand-observed transferred paramagnetic relaxation enhancement. We further validated the weak RhoGDI2-hit interactions using mutagenesis and structure-affinity analysis. Weak interactions between RhoGDI2 and fragment screening hits were delineated using an integrated NMR approach. Binders to RhoGDI2 as a potential anti-cancer target have been first reported, and their weak interactions were depicted using NMR spectroscopy. Our work highlights the powerfulness and the versatility of the integrative NMR techniques to provide valuable structural insight into the intrinsically weak interactions between RhoGDI2 and the fragment screening hits, which could hardly be conceived using other biochemical techniques. Copyright © 2016 Elsevier B.V. All rights reserved.

{sup 13}C NMR and EPR spectroscopic evaluation of oil shale mined soil recuperation

Energy Technology Data Exchange (ETDEWEB)

Santos, J.V. dos, E-mail: mangrich@ufpr.br [Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil); Mangrich, A.S. [Instituto Nacional de Ciencia e Tecnologia: Energia e Ambiente, Salvador, BA (Brazil); Pereira, B.F. [EMBRAPA Clima Temperado, Pelotas, RS (Brazil); Pillon, C.N. [EMBRAPA Clima Temperado, Pelotas, RS (Brazil). Estacao Experimental Cascata; Novotny, E.H. [EMBRAPA Solos, Rio de Janeiro, RJ (Brazil); Bonagamba, T.J. [Universidade de Sao Paulo (USP), Sao Carlos, SP (Brazil). Instituto de Fisica; Abbt-Braun, G.; Frimmel, F.H. [Engler-Bunte-Institut, Universitaet Karlsruhe, TH (Germany)

2013-02-15

In this work, native forest soil (NFS) organic matter (SOM) sample and SOM samples from a neighboring forest soil area of an oil shale mine which is being rehabilitated for thirty years (RFS) were analyzed. X-band electron paramagnetic resonance (EPR) and solid-state {sup 13}C nuclear magnetic resonance (NMR) spectroscopies were used to evaluate the soil reclamation of the Brazilian oil shale mining process. Two-dimensional heterospectral correlation studies of the results obtained from EPRand {sup 13}C NMR were used to obtain information about SOM structures and their interactions with residual paramagnetic metal ion. The signal of the residual metallic oxycation, VO{sup 2+} correlated positively with uronic acid-type hydrophilic organic structures, determined from the {sup 13}C NMR spectra, and correlated negatively with the organic free radical (OFR) signal associated with oxygen atoms (g = 2.0042). The hydrophobic aromatic structures correlate positively with the EPR OFR signal associated with carbon atoms (g = 2.0022). The data from the two spectroscopic magnetic techniques show that the used recuperation process is effective. (author)

Combined In Situ Illumination-NMR-UV/Vis Spectroscopy: A New Mechanistic Tool in Photochemistry.

Science.gov (United States)

Seegerer, Andreas; Nitschke, Philipp; Gschwind, Ruth M

2018-06-18

Synthetic applications in photochemistry are booming. Despite great progress in the development of new reactions, mechanistic investigations are still challenging. Therefore, we present a fully automated in situ combination of NMR spectroscopy, UV/Vis spectroscopy, and illumination to allow simultaneous and time-resolved detection of paramagnetic and diamagnetic species. This optical fiber-based setup enables the first acquisition of combined UV/Vis and NMR spectra in photocatalysis, as demonstrated on a conPET process. Furthermore, the broad applicability of combined UVNMR spectroscopy for light-induced processes is demonstrated on a structural and quantitative analysis of a photoswitch, including rate modulation and stabilization of transient species by temperature variation. Owing to the flexibility regarding the NMR hardware, temperature, and light sources, we expect wide-ranging applications of this setup in various research fields. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Constraint-based scheduling applying constraint programming to scheduling problems

CERN Document Server

Baptiste, Philippe; Nuijten, Wim

2001-01-01

Constraint Programming is a problem-solving paradigm that establishes a clear distinction between two pivotal aspects of a problem: (1) a precise definition of the constraints that define the problem to be solved and (2) the algorithms and heuristics enabling the selection of decisions to solve the problem. It is because of these capabilities that Constraint Programming is increasingly being employed as a problem-solving tool to solve scheduling problems. Hence the development of Constraint-Based Scheduling as a field of study. The aim of this book is to provide an overview of the most widely used Constraint-Based Scheduling techniques. Following the principles of Constraint Programming, the book consists of three distinct parts: The first chapter introduces the basic principles of Constraint Programming and provides a model of the constraints that are the most often encountered in scheduling problems. Chapters 2, 3, 4, and 5 are focused on the propagation of resource constraints, which usually are responsibl...

NMR-Fragment Based Virtual Screening: A Brief Overview.

Science.gov (United States)

Singh, Meenakshi; Tam, Benjamin; Akabayov, Barak

2018-01-25

Fragment-based drug discovery (FBDD) using NMR has become a central approach over the last twenty years for development of small molecule inhibitors against biological macromolecules, to control a variety of cellular processes. Yet, several considerations should be taken into account for obtaining a therapeutically relevant agent. In this review, we aim to list the considerations that make NMR fragment screening a successful process for yielding potent inhibitors. Factors that may govern the competence of NMR in fragment based drug discovery are discussed, as well as later steps that involve optimization of hits obtained by NMR-FBDD.

NMR-Fragment Based Virtual Screening: A Brief Overview

Directory of Open Access Journals (Sweden)

Meenakshi Singh

2018-01-01

Full Text Available Fragment-based drug discovery (FBDD using NMR has become a central approach over the last twenty years for development of small molecule inhibitors against biological macromolecules, to control a variety of cellular processes. Yet, several considerations should be taken into account for obtaining a therapeutically relevant agent. In this review, we aim to list the considerations that make NMR fragment screening a successful process for yielding potent inhibitors. Factors that may govern the competence of NMR in fragment based drug discovery are discussed, as well as later steps that involve optimization of hits obtained by NMR-FBDD.

Perturbation of nuclear spin polarizations in solid state NMR of nitroxide-doped samples by magic-angle spinning without microwaves

Energy Technology Data Exchange (ETDEWEB)

Thurber, Kent R., E-mail: thurberk@niddk.nih.gov; Tycko, Robert [Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520 (United States)

2014-05-14

We report solid state {sup 13}C and {sup 1}H nuclear magnetic resonance (NMR) experiments with magic-angle spinning (MAS) on frozen solutions containing nitroxide-based paramagnetic dopants that indicate significant perturbations of nuclear spin polarizations without microwave irradiation. At temperatures near 25 K, {sup 1}H and cross-polarized {sup 13}C NMR signals from {sup 15}N,{sup 13}C-labeled L-alanine in trinitroxide-doped glycerol/water are reduced by factors as large as six compared to signals from samples without nitroxide doping. Without MAS or at temperatures near 100 K, differences between signals with and without nitroxide doping are much smaller. We attribute most of the reduction of NMR signals under MAS near 25 K to nuclear spin depolarization through the cross-effect dynamic nuclear polarization mechanism, in which three-spin flips drive nuclear polarizations toward equilibrium with spin polarization differences between electron pairs. When T{sub 1e} is sufficiently long relative to the MAS rotation period, the distribution of electron spin polarization across the nitroxide electron paramagnetic resonance lineshape can be very different from the corresponding distribution in a static sample at thermal equilibrium, leading to the observed effects. We describe three-spin and 3000-spin calculations that qualitatively reproduce the experimental observations.

Perturbation of nuclear spin polarizations in solid state NMR of nitroxide-doped samples by magic-angle spinning without microwaves

International Nuclear Information System (INIS)

Thurber, Kent R.; Tycko, Robert

2014-01-01

We report solid state 13 C and 1 H nuclear magnetic resonance (NMR) experiments with magic-angle spinning (MAS) on frozen solutions containing nitroxide-based paramagnetic dopants that indicate significant perturbations of nuclear spin polarizations without microwave irradiation. At temperatures near 25 K, 1 H and cross-polarized 13 C NMR signals from 15 N, 13 C-labeled L-alanine in trinitroxide-doped glycerol/water are reduced by factors as large as six compared to signals from samples without nitroxide doping. Without MAS or at temperatures near 100 K, differences between signals with and without nitroxide doping are much smaller. We attribute most of the reduction of NMR signals under MAS near 25 K to nuclear spin depolarization through the cross-effect dynamic nuclear polarization mechanism, in which three-spin flips drive nuclear polarizations toward equilibrium with spin polarization differences between electron pairs. When T 1e is sufficiently long relative to the MAS rotation period, the distribution of electron spin polarization across the nitroxide electron paramagnetic resonance lineshape can be very different from the corresponding distribution in a static sample at thermal equilibrium, leading to the observed effects. We describe three-spin and 3000-spin calculations that qualitatively reproduce the experimental observations

Perturbation of nuclear spin polarizations in solid state NMR of nitroxide-doped samples by magic-angle spinning without microwaves.

Science.gov (United States)

Thurber, Kent R; Tycko, Robert

2014-05-14

We report solid state (13)C and (1)H nuclear magnetic resonance (NMR) experiments with magic-angle spinning (MAS) on frozen solutions containing nitroxide-based paramagnetic dopants that indicate significant perturbations of nuclear spin polarizations without microwave irradiation. At temperatures near 25 K, (1)H and cross-polarized (13)C NMR signals from (15)N,(13)C-labeled L-alanine in trinitroxide-doped glycerol/water are reduced by factors as large as six compared to signals from samples without nitroxide doping. Without MAS or at temperatures near 100 K, differences between signals with and without nitroxide doping are much smaller. We attribute most of the reduction of NMR signals under MAS near 25 K to nuclear spin depolarization through the cross-effect dynamic nuclear polarization mechanism, in which three-spin flips drive nuclear polarizations toward equilibrium with spin polarization differences between electron pairs. When T1e is sufficiently long relative to the MAS rotation period, the distribution of electron spin polarization across the nitroxide electron paramagnetic resonance lineshape can be very different from the corresponding distribution in a static sample at thermal equilibrium, leading to the observed effects. We describe three-spin and 3000-spin calculations that qualitatively reproduce the experimental observations.

Contrast-enhanced NMR imaging: animal studies using gadolinium-DTPA complex

International Nuclear Information System (INIS)

Brasch, R.C.; Weinmann, H.J.; Wesbey, G.E.

1984-01-01

Gadolinium (Gd)-DTPA complex was assessed as a nuclear magnetic resonance (NMR) contrast-enhancing agent by experimentally imaging normal and diseased animals. After intravenous injection, Gd-DTPA, a strongly paramagnetic complex by virtue of unpaired electrons, was rapidly excreted into the urine of rats, producing an easily observable contrast enhancement on NMR images in kidney parenchyma and urine. Sterile soft-tissue abscesses demonstrated an obvious rim pattern of enhancement. A focus of radiation-induced brain damage in a canine model was only faintly detectable on spin-echo NMR images before contrast administration; after 0.5 mmol/kg Gd-DTPA administration, the lesion intensity increased from 3867 to 5590. In comparison, the normal brain with an intact blood-brain barrier remained unchanged in NMR characterization. Gd-DTPA is a promising new NMR contrast enhancer for the clinical assessment of renal function, of inflammatory lesions, and of focal disruption of the blood-brain barrier

Tunable paramagnetic relaxation enhancements by [Gd(DPA)3]3- for protein structure analysis

International Nuclear Information System (INIS)

Yagi, Hiromasa; Loscha, Karin V.; Su, Xun-Cheng; Stanton-Cook, Mitchell; Huber, Thomas; Otting, Gottfried

2010-01-01

Paramagnetic relaxation enhancements (PRE) present a powerful source of structural information in nuclear magnetic resonance (NMR) studies of proteins and protein-ligand complexes. In contrast to conventional PRE reagents that are covalently attached to the protein, the complex between gadolinium and three dipicolinic acid (DPA) molecules, [Gd(DPA) 3 ] 3- , can bind to proteins in a non-covalent yet site-specific manner. This offers straightforward access to PREs that can be scaled by using different ratios of [Gd(DPA) 3 ] 3- to protein, allowing quantitative distance measurements for nuclear spins within about 15 A of the Gd 3+ ion. Such data accurately define the metal position relative to the protein, greatly enhancing the interpretation of pseudocontact shifts induced by [Ln(DPA) 3 ] 3- complexes of paramagnetic lanthanide (Ln 3+ ) ions other than gadolinium. As an example we studied the quaternary structure of the homodimeric GCN4 leucine zipper.

Proton NMR study of α-MnH 0.06

Science.gov (United States)

Soloninin, A. V.; Skripov, A. V.; Buzlukov, A. L.; Antonov, V. E.; Antonova, T. E.

2004-07-01

Proton nuclear magnetic resonance (NMR) spectra and spin-lattice relaxation rates for the solid solution α-MnH 0.06 have been measured over the temperature range 11-297 K and the resonance frequency range 20-90 MHz. A considerable shift and broadening of the proton NMR line and a sharp peak of the spin-lattice relaxation rate are observed near 130 K. These effects are attributed to the onset of antiferromagnetic ordering below the Néel temperature TN≈130 K. The proton NMR line does not disappear in the antiferromagnetic phase; this suggests a small magnitude of the local magnetic fields at H-sites in α-MnH 0.06. The spin-lattice relaxation rate in the paramagnetic phase is dominated by the effects of spin fluctuations.

About kinetics of paramagnetic radiation malformations in beryllium ceramics

International Nuclear Information System (INIS)

Polyakov, A.I.; Ryabinkin, Yu.A.; Zashkvara, O.V.; Bitenbaev, M.I.; Petukhov, Yu.V.

1999-01-01

This paper [1] specifies that γ-radiation of the beryllium-oxide-based ceramics results in development of paramagnetic radiation malformations emerging the ESR spectrum in form of doublet with the splitting rate of oestrasid Δ∼1.6 and g-factor of 2.008. This report presents evaluation outcomes of dependence of paramagnetic radiation malformations concentration in beryllium ceramics on gamma-radiation dose ( 60 Co) within the range of 0-100 Mrad. Total paramagnetic parameters of beryllium ceramics in the range 0-100 Mrad of gamma-radiation dose varied slightly, and were specified by the first type of paramagnetic radiation malformations

FANTEN: a new web-based interface for the analysis of magnetic anisotropy-induced NMR data

Energy Technology Data Exchange (ETDEWEB)

Rinaldelli, Mauro; Carlon, Azzurra; Ravera, Enrico; Parigi, Giacomo, E-mail: parigi@cerm.unifi.it; Luchinat, Claudio, E-mail: luchinat@cerm.unifi.it [University of Florence, CERM and Department of Chemistry “Ugo Schiff” (Italy)

2015-01-15

Pseudocontact shifts (PCSs) and residual dipolar couplings (RDCs) arising from the presence of paramagnetic metal ions in proteins as well as RDCs due to partial orientation induced by external orienting media are nowadays routinely measured as a part of the NMR characterization of biologically relevant systems. PCSs and RDCs are becoming more and more popular as restraints (1) to determine and/or refine protein structures in solution, (2) to monitor the extent of conformational heterogeneity in systems composed of rigid domains which can reorient with respect to one another, and (3) to obtain structural information in protein–protein complexes. The use of both PCSs and RDCs proceeds through the determination of the anisotropy tensors which are at the origin of these NMR observables. A new user-friendly web tool, called FANTEN (Finding ANisotropy TENsors), has been developed for the determination of the anisotropy tensors related to PCSs and RDCs and has been made freely available through the WeNMR ( http://fanten-enmr.cerm.unifi.it:8080 http://fanten-enmr.cerm.unifi.it:8080 ) gateway. The program has many new features not available in other existing programs, among which the possibility of a joint analysis of several sets of PCS and RDC data and the possibility to perform rigid body minimizations.

Spying on Fe ions and their role in modified aluminosilicates during the sorption of anions using solid-state NMR spectroscopy

Czech Academy of Sciences Publication Activity Database

Kobera, Libor; Abbrent, Sabina; Holcova, L.; Urbanová, Martina; Koloušek, D.; Doušová, B.; Brus, Jiří

2017-01-01

Roč. 241, 15 March (2017), s. 115-122 ISSN 1387-1811 R&D Projects: GA ČR(CZ) GA13-24155S; GA ČR(CZ) GA16-13778S Institutional support: RVO:61389013 Keywords : paramagnetic NMR shift * solid-state NMR * aluminosilicate Subject RIV: JN - Civil Engineering OBOR OECD: Civil engineering Impact factor: 3.615, year: 2016

Using the methods of radiospectroscopy (EPR, NMR) to study the nature of the defect structure of solid solutions based on lead zirconate titanate (PZT).

Science.gov (United States)

Bykov, Igor; Zagorodniy, Yuriy; Yurchenko, Lesya; Korduban, Alexander; Nejezchleb, Karel; Trachevsky, Vladimir; Dimza, Vilnis; Jastrabik, Lubomir; Dejneka, Alexander

2014-08-01

The nature of intrinsic and impurity point defects in lead zirconate titanate (PZT) ceramics has been explored. Using electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), and X-ray photoelectron spectroscopy (XPS) methods, several impurity sites have been identified in the materials, including the Fe(3+)-oxygen vacancy (VO) complex and Pb ions. Both of these centers are incorporated into the PZT lattice. The Fe(3+) –VО paramagnetic complex serves as a sensitive probe of the local crystal field in the ceramic; the symmetry of this defect roughly correlates with PZT phase diagram as the composition is varied from PbTiO3 to PbZrO3. NMR spectra (207)Pb in PbTiO3, PbZrO3, and PZT with iron content from 0 to 0.4 wt% showed that increasing the iron concentration leads to a distortion of the crystal structure and to improvement of the electrophysical parameters of the piezoceramics. This is due to the formation of a phase which has a higher symmetry, but at high concentrations of iron (>0.4 wt%), it leads to sharp degradation of electrophysical parameters.

Structure and dynamics of paramagnetic transients by pulsed EPR and NMR detection of nuclear resonance

International Nuclear Information System (INIS)

Trifunac, A.D.

1981-01-01

Structure and dynamics of transient radicals in pulse radiolysis can be studied by time resolved EPR and NMR techniques. EPR study of kinetics and relaxation is illustrated. The NMR detection of nuclear resonance in transient radicals is a new method which allows the study of hyperfine coupling, population dynamics, radical kinetics, and reaction mechanism. 9 figures

Topology and immersion depth of an integral membrane protein by paramagnetic rates from dissolved oxygen.

Science.gov (United States)

Al-Abdul-Wahid, M Sameer; Verardi, Raffaello; Veglia, Gianluigi; Prosser, R Scott

2011-09-01

In studies of membrane proteins, knowledge of protein topology can provide useful insight into both structure and function. In this work, we present a solution NMR method for the measurement the tilt angle and average immersion depth of alpha helices in membrane proteins, from analysis of the paramagnetic relaxation rate enhancements arising from dissolved oxygen. No modification to the micelle or protein is necessary, and the topology of both transmembrane and amphipathic helices are readily determined. We apply this method to the measure the topology of a monomeric mutant of phospholamban (AFA-PLN), a 52-residue membrane protein containing both an amphipathic and a transmembrane alpha helix. In dodecylphosphocholine micelles, the amphipathic helix of AFA-PLN was found to have a tilt angle of 87° ± 1° and an average immersion depth of 13.2 Å. The transmembrane helix was found to have an average immersion depth of 5.4 Å, indicating residues 41 and 42 are closest to the micelle centre. The resolution of paramagnetic relaxation rate enhancements from dissolved oxygen compares favourably to those from Ni (II), a hydrophilic paramagnetic species.

Topology and immersion depth of an integral membrane protein by paramagnetic rates from dissolved oxygen

International Nuclear Information System (INIS)

Al-Abdul-Wahid, M. Sameer; Verardi, Raffaello; Veglia, Gianluigi; Prosser, R. Scott

2011-01-01

In studies of membrane proteins, knowledge of protein topology can provide useful insight into both structure and function. In this work, we present a solution NMR method for the measurement the tilt angle and average immersion depth of alpha helices in membrane proteins, from analysis of the paramagnetic relaxation rate enhancements arising from dissolved oxygen. No modification to the micelle or protein is necessary, and the topology of both transmembrane and amphipathic helices are readily determined. We apply this method to the measure the topology of a monomeric mutant of phospholamban (AFA-PLN), a 52-residue membrane protein containing both an amphipathic and a transmembrane alpha helix. In dodecylphosphocholine micelles, the amphipathic helix of AFA-PLN was found to have a tilt angle of 87° ± 1° and an average immersion depth of 13.2 Å. The transmembrane helix was found to have an average immersion depth of 5.4 Å, indicating residues 41 and 42 are closest to the micelle centre. The resolution of paramagnetic relaxation rate enhancements from dissolved oxygen compares favourably to those from Ni (II), a hydrophilic paramagnetic species.

Crystallographically-based analysis of the NMR spectra of maghemite

International Nuclear Information System (INIS)

Spiers, K.M.; Cashion, J.D.

2012-01-01

All possible iron environments with respect to nearest neighbour vacancies in vacancy-ordered and vacancy-disordered maghemite have been evaluated and used as the foundation for a crystallographically-based analysis of the published NMR spectra of maghemite. The spectral components have been assigned to particular configurations and excellent agreement obtained in comparing predicted spectra with published spectra taken in applied magnetic fields. The broadness of the published NMR lines has been explained by calculations of the magnetic dipole fields at the various iron sites and consideration of the supertransferred hyperfine fields. - Highlights: ► Analysis of 57 Fe NMR of maghemite based on vacancy ordering and nearest neighbour vacancies. ► Assignment of NMR spectral components based on crystallographic analysis of unique iron sites. ► Strong agreement between predicted spectra and published spectra taken in applied magnetic fields. ► Maghemite NMR spectral broadening due to various iron sites and supertransferred hyperfine field.

Additivity, redundancy, and complementarity between structural information from NMR and SAXS data

International Nuclear Information System (INIS)

Kojima, Masaki; Nonaka, Takamasa; Morimoto, Yasumasa; Nakagawa, Takashi; Yanagi, Shigeru; Kihara, Hiroshi

2009-01-01

At present protein structure in solution is determined by restrained molecular dynamics with distance restraints mainly derived from NMR. Although the small-angle X-ray scattering (SAXS) method also confers the structural information, its content is too small to determine the structure by itself. We previously developed a new algorithm that refines the protein structure by restrained molecular dynamics with SAXS constrains. In the present study we performed the protein structure calculation by restrained molecular dynamics with both NMR and SAXS constraints, in order to elucidate the essential structural information that defines the protein architecture. We used RNase T1 as a model protein, which has already been determined by NMR alone. At first we added SAXS constraints (h -1 ) into the original NMR-derived restraints for the calculation. The quality of the structure ensemble was significantly increased. Next we removed the original NMR restraints randomly in order to estimate the redundancy among the NMR-derived information. The essential topology of the resultant structures was hardly changed until the restraints were reduced below the half. Then we added the SAXS constraints into the remaining NMR restraints to expect they could complement the lost structural information. However, the structure was not recovered properly. By removing various types of structural information exclusively from the original NMR data set, we investigated whether the SAXS constraints could complement some kinds of structural information. The results showed that the SAXS could complement the tertiary structure to some extent while it could not secondary structure. (author)

UTOPIA NMR: activating unexploited magnetization using interleaved low-gamma detection

Energy Technology Data Exchange (ETDEWEB)

Viegas, Aldino; Viennet, Thibault [Heinrich-Heine-University, Institute of Physical Biology (Germany); Yu, Tsyr-Yan [Academia Sinica, Institute of Atomic and Molecular Sciences (China); Schumann, Frank [Bruker BioSpin GmbH (Switzerland); Bermel, Wolfgang [Bruker BioSpin GmbH (Germany); Wagner, Gerhard [Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology (United States); Etzkorn, Manuel, E-mail: manuel.etzkorn@hhu.de [Heinrich-Heine-University, Institute of Physical Biology (Germany)

2016-01-15

A growing number of nuclear magnetic resonance (NMR) spectroscopic studies are impaired by the limited information content provided by the standard set of experiments conventionally recorded. This is particularly true for studies of challenging biological systems including large, unstructured, membrane-embedded and/or paramagnetic proteins. Here we introduce the concept of unified time-optimized interleaved acquisition NMR (UTOPIA-NMR) for the unified acquisition of standard high-γ (e.g. {sup 1}H) and low-γ (e.g. {sup 13}C) detected experiments using a single receiver. Our aim is to activate the high level of polarization and information content distributed on low-γ nuclei without disturbing conventional magnetization transfer pathways. We show that using UTOPIA-NMR we are able to recover nearly all of the normally non-used magnetization without disturbing the standard experiments. In other words, additional spectra, that can significantly increase the NMR insights, are obtained for free. While we anticipate a broad range of possible applications we demonstrate for the soluble protein Bcl-x{sub L} (ca. 21 kDa) and for OmpX in nanodiscs (ca. 160 kDa) that UTOPIA-NMR is particularly useful for challenging protein systems including perdeuterated (membrane) proteins.

UTOPIA NMR: activating unexploited magnetization using interleaved low-gamma detection

International Nuclear Information System (INIS)

Viegas, Aldino; Viennet, Thibault; Yu, Tsyr-Yan; Schumann, Frank; Bermel, Wolfgang; Wagner, Gerhard; Etzkorn, Manuel

2016-01-01

A growing number of nuclear magnetic resonance (NMR) spectroscopic studies are impaired by the limited information content provided by the standard set of experiments conventionally recorded. This is particularly true for studies of challenging biological systems including large, unstructured, membrane-embedded and/or paramagnetic proteins. Here we introduce the concept of unified time-optimized interleaved acquisition NMR (UTOPIA-NMR) for the unified acquisition of standard high-γ (e.g. 1 H) and low-γ (e.g. 13 C) detected experiments using a single receiver. Our aim is to activate the high level of polarization and information content distributed on low-γ nuclei without disturbing conventional magnetization transfer pathways. We show that using UTOPIA-NMR we are able to recover nearly all of the normally non-used magnetization without disturbing the standard experiments. In other words, additional spectra, that can significantly increase the NMR insights, are obtained for free. While we anticipate a broad range of possible applications we demonstrate for the soluble protein Bcl-x L (ca. 21 kDa) and for OmpX in nanodiscs (ca. 160 kDa) that UTOPIA-NMR is particularly useful for challenging protein systems including perdeuterated (membrane) proteins

UTOPIA NMR: activating unexploited magnetization using interleaved low-gamma detection.

Science.gov (United States)

Viegas, Aldino; Viennet, Thibault; Yu, Tsyr-Yan; Schumann, Frank; Bermel, Wolfgang; Wagner, Gerhard; Etzkorn, Manuel

2016-01-01

A growing number of nuclear magnetic resonance (NMR) spectroscopic studies are impaired by the limited information content provided by the standard set of experiments conventionally recorded. This is particularly true for studies of challenging biological systems including large, unstructured, membrane-embedded and/or paramagnetic proteins. Here we introduce the concept of unified time-optimized interleaved acquisition NMR (UTOPIA-NMR) for the unified acquisition of standard high-γ (e.g. (1)H) and low-γ (e.g. (13)C) detected experiments using a single receiver. Our aim is to activate the high level of polarization and information content distributed on low-γ nuclei without disturbing conventional magnetization transfer pathways. We show that using UTOPIA-NMR we are able to recover nearly all of the normally non-used magnetization without disturbing the standard experiments. In other words, additional spectra, that can significantly increase the NMR insights, are obtained for free. While we anticipate a broad range of possible applications we demonstrate for the soluble protein Bcl-xL (ca. 21 kDa) and for OmpX in nanodiscs (ca. 160 kDa) that UTOPIA-NMR is particularly useful for challenging protein systems including perdeuterated (membrane) proteins.

Measurement of conformational constraints in an elastin-mimetic protein by residue-pair selected solid-state NMR

International Nuclear Information System (INIS)

Hong, Mei; McMillan, R. Andrew; Conticello, Vincent P.

2002-01-01

We introduce a solid-state NMR technique for selective detection of a residue pair in multiply labeled proteins to obtain site-specific structural constraints. The method exploits the frequency-offset dependence of cross polarization to achieve 13 CO i → 15 N i → 13 Cα i transfer between two residues. A 13 C, 15 N-labeled elastin mimetic protein (VPGVG) n is used to demonstrate the method. The technique selected the Gly3 Cα signal while suppressing the Gly5 Cα signal, and allowed the measurement of the Gly3 Cα chemical shift anisotropy to derive information on the protein conformation. This residue-pair selection technique should simplify the study of protein structure at specific residues

Cys-Ph-TAHA: a lanthanide binding tag for RDC and PCS enhanced protein NMR

NARCIS (Netherlands)

Peters, Fabian; Maestre-Martinez, M.; Leonov, A.; Kovacic, L.; Becker, S.; Boelens, R.; Griesinger, C.

2011-01-01

Here we present Cys-Ph-TAHA, a new nonadentate lanthanide tag for the paramagnetic labelling of proteins. The tag can be easily synthesized and is stereochemically homogenous over a wide range of temperatures, yielding NMR spectra with a single set of peaks. Bound to ubiquitin, it induced large

NMR studies concerning base-base interactions in oligonucleotides

International Nuclear Information System (INIS)

Hoogen, Y.T. van den.

1988-01-01

Two main subjects are treated in the present thesis. The firsst part principally deals with the base-base interactions in single-stranded oligoribonucleotides. The second part presents NMR and model-building studies of DNA and RNA duplexes containing an unpaired base. (author). 242 refs.; 26 figs.; 24 tabs

The structure of poly(carbonsuboxide) on the atomic scale: a solid-state NMR study.

Science.gov (United States)

Schmedt auf der Günne, Jörn; Beck, Johannes; Hoffbauer, Wilfried; Krieger-Beck, Petra

2005-07-18

In this contribution we present a study of the structure of amorphous poly(carbonsuboxide) (C3O2)x by 13C solid-state NMR spectroscopy supported by infrared spectroscopy and chemical analysis. Poly(carbonsuboxide) was obtained by polymerization of carbonsuboxide C3O2, which in turn was synthesized from malonic acid bis(trimethylsilylester). Two different 13C labeling schemes were applied to probe inter- and intramonomeric bonds in the polymer by dipolar solid-state NMR methods and also to allow quantitative 13C MAS NMR spectra. Four types of carbon environments can be distinguished in the NMR spectra. Double-quantum and triple-quantum 2D correlation experiments were used to assign the observed peaks using the through-space and through-bond dipolar coupling. In order to obtain distance constraints for the intermonomeric bonds, double-quantum constant-time experiments were performed. In these experiments an additional filter step was applied to suppress contributions from not directly bonded 13C,13C spin pairs. The 13C NMR intensities, chemical shifts, connectivities and distances gave constraints for both the polymerization mechanism and the short-range order of the polymer. The experimental results were complemented by bond lengths predicted by density functional theory methods for several previously suggested models. Based on the presented evidence we can unambiguously exclude models based on gamma-pyronic units and support models based on alpha-pyronic units. The possibility of planar ladder- and bracelet-like alpha-pyronic structures is discussed.

Paramagnetic decoration of DNA origami nanostructures by Eu³⁺ coordination.

Science.gov (United States)

Opherden, Lars; Oertel, Jana; Barkleit, Astrid; Fahmy, Karim; Keller, Adrian

2014-07-15

The folding of DNA into arbitrary two- and three-dimensional shapes, called DNA origami, represents a powerful tool for the synthesis of functional nanostructures. Here, we present the first approach toward the paramagnetic functionalization of DNA origami nanostructures by utilizing postassembly coordination with Eu(3+) ions. In contrast to the usual formation of toroidal dsDNA condensates in the presence of trivalent cations, planar as well as rod-like DNA origami maintain their shape and monomeric state even under high loading with the trivalent lanthanide. Europium coordination was demonstrated by the change in Eu(3+) luminescence upon binding to the two DNA origami. Their natural circular dichroism in the Mg(2+)- and Eu(3+)-bound state was found to be very similar to that of genomic DNA, evidencing little influence of the DNA origami superstructure on the local chirality of the stacked base pairs. In contrast, the magnetic circular dichroism of the Mg(2+)-bound DNA origami deviates from that of genomic DNA. Furthermore, the lanthanide affects the magnetic properties of DNA in a superstructure-dependent fashion, indicative of the existence of superstructure-specific geometry of Eu(3+) binding sites in the DNA origami that are not formed in genomic DNA. This simple approach lays the foundation for the generation of magneto-responsive DNA origami nanostructures. Such systems do not require covalent modifications and can be used for the magnetic manipulation of DNA nanostructures or for the paramagnetic alignment of molecules in NMR spectroscopy.

Information content of long-range NMR data for the characterization of conformational heterogeneity

Energy Technology Data Exchange (ETDEWEB)

Andrałojć, Witold [University of Florence, Center for Magnetic Resonance (CERM) (Italy); Berlin, Konstantin; Fushman, David, E-mail: fushman@umd.edu [University of Maryland, Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization (United States); Luchinat, Claudio, E-mail: luchinat@cerm.unifi.it; Parigi, Giacomo; Ravera, Enrico [University of Florence, Center for Magnetic Resonance (CERM) (Italy); Sgheri, Luca [CNR, Istituto per le Applicazioni del Calcolo, Sezione di Firenze (Italy)

2015-07-15

Long-range NMR data, namely residual dipolar couplings (RDCs) from external alignment and paramagnetic data, are becoming increasingly popular for the characterization of conformational heterogeneity of multidomain biomacromolecules and protein complexes. The question addressed here is how much information is contained in these averaged data. We have analyzed and compared the information content of conformationally averaged RDCs caused by steric alignment and of both RDCs and pseudocontact shifts caused by paramagnetic alignment, and found that, despite the substantial differences, they contain a similar amount of information. Furthermore, using several synthetic tests we find that both sets of data are equally good towards recovering the major state(s) in conformational distributions.

Ga and Pt NMR study of UPtGa sub 5 and UNiGa sub 5

CERN Document Server

Kato, H; Tokunaga, Y; Tokiwa, Y; Ikeda, S; Onuki, Y; Kambe, S; Walstedt, R E

2003-01-01

Ga and Pt NMR measurements have been carried out for two isomorphs compounds, UPtGa sub 5 and UNiGa sub 5 , which exhibit different magnetic structures below T sub N. Knight shift K measurements in the paramagnetic region are reported here. The transferred hyperfine coupling constants at Ga and Pt sites are determined. The temperature independent part K sub 0 of K, which probes the conduction electron polarization at the ligand site, has been successfully evaluated. A nearly identical conduction electron structure in the paramagnetic region is suggested for these two compounds. The origin of the different magnetic structures is discussed.

1H NMR spectroscopy-based interventional metabolic phenotyping

DEFF Research Database (Denmark)

Lauridsen, Michael B; Bliddal, Henning; Christensen, Robin

2010-01-01

1H NMR spectroscopy-based metabolic phenotyping was used to identify biomarkers in the plasma of patients with rheumatoid arthritis (RA). Forty-seven patients with RA (23 with active disease at baseline and 24 in remission) and 51 healthy subjects were evaluated during a one-year follow-up with a......1H NMR spectroscopy-based metabolic phenotyping was used to identify biomarkers in the plasma of patients with rheumatoid arthritis (RA). Forty-seven patients with RA (23 with active disease at baseline and 24 in remission) and 51 healthy subjects were evaluated during a one-year follow......-up with assessments of disease activity (DAS-28) and 1H NMR spectroscopy of plasma samples. Discriminant analysis provided evidence that the metabolic profiles predicted disease severity. Cholesterol, lactate, acetylated glycoprotein, and lipid signatures were found to be candidate biomarkers for disease severity.......0007). However, after 31 days of optimized therapy, the two patient groups were not significantly different (P=0.91). The metabolic profiles of both groups of RA patients were different from the healthy subjects. 1H NMR-based metabolic phenotyping of plasma samples in patients with RA is well suited...

NMR spectroscopic determination of an equilibrium isotope effect on the hydration of cobalt(II)

International Nuclear Information System (INIS)

Evilia, R.F.; Saunders, M.

1985-01-01

A recently reported NMR method for the measurement of deuterium equilibrium isotope effects is applied to the hydration of the paramagnetic cobalt(II) ion. An isotope effect of about 1.3% is measured. A substantial difference between the intrinsic shift of H 2 O and D 2 O when coordinated to cobalt is also measured

Improved paramagnetic chelate for molecular imaging with MRI

International Nuclear Information System (INIS)

Winter, Patrick; Athey, Phillip; Kiefer, Garry; Gulyas, Gyongyi; Frank, Keith; Fuhrhop, Ralph; Robertson, David; Wickline, Samuel; Lanza, Gregory

2005-01-01

The relaxivity and transmetallation of two lipophilic paramagnetic chelates incorporated onto perfluorocarbon nanoparticles, i.e., gadolinium-methoxy-tetraazacyclododecane-tetraacetic acid phosphatidylethanolamine (Gd-MeO-DOTA-PE) and gadolinium-methoxy-tetraazacyclododecane-tetraacetic acid triglycine phosphatidylethanolamine (Gd-MeO-DOTA-triglycine-PE (Gd-MeO-DOTA-triglycine-PE)), were compared to a prototypic gadolinium-diethylene-triamine-pentaacetic acid bis-oleate (Gd-DTPA-BOA) paramagnetic formulation. Nanoparticles with MeO-DOTA-based chelates demonstrated higher relaxivity (40% higher for Gd-MeO-DOTA-PE and 55% higher for Gd-MeO-DOTA-triglycine-PE) and less transmetallation than the original Gd-DTPA-BOA-based agent

Improved paramagnetic chelate for molecular imaging with MRI

Science.gov (United States)

Winter, Patrick; Athey, Phillip; Kiefer, Garry; Gulyas, Gyongyi; Frank, Keith; Fuhrhop, Ralph; Robertson, David; Wickline, Samuel; Lanza, Gregory

2005-05-01

The relaxivity and transmetallation of two lipophilic paramagnetic chelates incorporated onto perfluorocarbon nanoparticles, i.e., gadolinium-methoxy-tetraazacyclododecane-tetraacetic acid phosphatidylethanolamine (Gd-MeO-DOTA-PE) and gadolinium-methoxy-tetraazacyclododecane-tetraacetic acid triglycine phosphatidylethanolamine (Gd-MeO-DOTA-triglycine-PE (Gd-MeO-DOTA-triglycine-PE)), were compared to a prototypic gadolinium-diethylene-triamine-pentaacetic acid bis-oleate (Gd-DTPA-BOA) paramagnetic formulation. Nanoparticles with MeO-DOTA-based chelates demonstrated higher relaxivity (40% higher for Gd-MeO-DOTA-PE and 55% higher for Gd-MeO-DOTA-triglycine-PE) and less transmetallation than the original Gd-DTPA-BOA-based agent.

Demonstrating Paramagnetism Using Liquid Nitrogen.

Science.gov (United States)

Simmonds, Ray; And Others

1994-01-01

Describes how liquid nitrogen is attracted to the poles of neodymium magnets. Nitrogen is not paramagnetic, so the attraction suggests that the liquid nitrogen contains a small amount of oxygen, which causes the paramagnetism. (MVL)

Buckling of paramagnetic chains in soft gels

Science.gov (United States)

Huang, Shilin; Pessot, Giorgio; Cremer, Peet; Weeber, Rudolf; Holm, Christian; Nowak, Johannes; Odenbach, Stefan; Menzel, Andreas M.; Auernhammer, Günter K.

We study the magneto-elastic coupling behavior of paramagnetic chains in soft polymer gels exposed to external magnetic fields. To this end, a laser scanning confocal microscope is used to observe the morphology of the paramagnetic chains together with the deformation field of the surrounding gel network. The paramagnetic chains in soft polymer gels show rich morphological shape changes under oblique magnetic fields, in particular a pronounced buckling deformation. The details of the resulting morphological shapes depend on the length of the chain, the strength of the external magnetic field, and the modulus of the gel. Based on the observation that the magnetic chains are strongly coupled to the surrounding polymer network, a simplified model is developed to describe their buckling behavior. A coarse-grained molecular dynamics simulation model featuring an increased matrix stiffness on the surfaces of the particles leads to morphologies in agreement with the experimentally observed buckling effects.

Measurement of conformational constraints in an elastin-mimetic protein by residue-pair selected solid-state NMR

Energy Technology Data Exchange (ETDEWEB)

Hong, Mei [Iowa State University, Department of Chemistry (United States)], E-mail: mhong@iastate.edu; McMillan, R. Andrew; Conticello, Vincent P. [Emory University, Department of Chemistry (United States)

2002-02-15

We introduce a solid-state NMR technique for selective detection of a residue pair in multiply labeled proteins to obtain site-specific structural constraints. The method exploits the frequency-offset dependence of cross polarization to achieve {sup 13}CO{sub i} {sup {yields}} {sup 15}N{sub i} {sup {yields}} {sup 13}C{alpha}{sub i} transfer between two residues. A {sup 13}C, {sup 15}N-labeled elastin mimetic protein (VPGVG){sub n} is used to demonstrate the method. The technique selected the Gly3 C{alpha} signal while suppressing the Gly5 C{alpha} signal, and allowed the measurement of the Gly3 C{alpha} chemical shift anisotropy to derive information on the protein conformation. This residue-pair selection technique should simplify the study of protein structure at specific residues.

Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences

Energy Technology Data Exchange (ETDEWEB)

Rinaldelli, Mauro; Ravera, Enrico; Calderone, Vito; Parigi, Giacomo [University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (Finland) (Italy); University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (Finland) (Italy); Murshudov, Garib N., E-mail: garib@mrc-lmb.cam.ac.uk [MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH (United Kingdom); Luchinat, Claudio, E-mail: garib@mrc-lmb.cam.ac.uk [University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (Finland) (Italy); University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (Finland) (Italy)

2014-04-01

Paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and diamagnetic residual dipolar couplings can now be used in the program REFMAC5 from CCP4 as structural restraints together with X-ray crystallographic data. These NMR restraints can reveal differences between solid state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints in REFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably ‘ideal’ geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state.

Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences

International Nuclear Information System (INIS)

Rinaldelli, Mauro; Ravera, Enrico; Calderone, Vito; Parigi, Giacomo; Murshudov, Garib N.; Luchinat, Claudio

2014-01-01

Paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and diamagnetic residual dipolar couplings can now be used in the program REFMAC5 from CCP4 as structural restraints together with X-ray crystallographic data. These NMR restraints can reveal differences between solid state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints in REFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably ‘ideal’ geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state

Investigation of the biochemical state of paramagnetic ions in vivo using the magnetic field dependence of 1/T1 of tissue protons (NMRD profile): applications to contrast agents for magnetic resonance imaging

International Nuclear Information System (INIS)

Koenig, S.H.; Brown, R.D. III; Spiller, M.; Wolf, G.L.

1988-01-01

Nuclear magnetic relaxation dispersion (NMRD) profiles of protons are obtained in homogenous aqueous solutions of the paramagnetic ions, Mn 2+ and Gd 3+ and their chelate and macromolecular complexes in vitro, giving information regarding the biochemical state of these ions. Similarly NMRD profiles of protons of excised rabbit tissues containing Mn 2+ and Gd 3+ complexes are obtained. These NMRD profiles are shown to be very useful for determining the fate of potentially useful paramagnetic NMR imaging contrast agents in vivo. (U.K.)

TD-NMR studies on CuSO{sub 4} salt hydrates

Energy Technology Data Exchange (ETDEWEB)

Nestle, Nikolaus; Magin, Peter; Wengeler, Robert [BASF Aktiengesellschaft, Ludwigshafen (Germany); Kleinschmidt, Sebastian [Universitaet Magdeburg, FB Chemie (Germany)

2008-07-01

Despite the high concentration of paramagnetic copper ions, solid CuSO{sub 4} hydrates exhibit surprizingly narrow NMR signals. This is known since the late 1940s. Using TD-NMR methods established for polymer studies, the relaxation behaviour of CuSO{sub 4} preparations with different water content was studied at room temperature. For the water content of the pentahydrate and below, the NMR signal exhibits a pure solid-state-type magnetization decay behaviour. For slightly overstoichiometric moisture contents, a liquid-like signal is observed in addition to the solid signal. However, the relative amplitudes of the solid and the liquid signal do not mirror the stoichiometric composition of the pentahydrate and the excess water. Instead, the solid signal amplitude only accounts for four hydrate water molecules while the fifth water exhibits rapid exchange with the liquid phase and thus contributes to the liquid-type signal. This finding is in good agreement to results from investigations into the crystal structure of solid CuSO4 pentahydrate.

Constraint-Muse: A Soft-Constraint Based System for Music Therapy

Science.gov (United States)

Hölzl, Matthias; Denker, Grit; Meier, Max; Wirsing, Martin

Monoidal soft constraints are a versatile formalism for specifying and solving multi-criteria optimization problems with dynamically changing user preferences. We have developed a prototype tool for interactive music creation, called Constraint Muse, that uses monoidal soft constraints to ensure that a dynamically generated melody harmonizes with input from other sources. Constraint Muse provides an easy to use interface based on Nintendo Wii controllers and is intended to be used in music therapy for people with Parkinson’s disease and for children with high-functioning autism or Asperger’s syndrome.

Improved quantification of alite and belite in anhydrous Portland cements by 29Si MAS NMR: Effects of paramagnetic ions

DEFF Research Database (Denmark)

Poulsen, Søren Lundsted; Kocaba, Vanessa; Le Saoût, Gwenn

2009-01-01

The applicability, reliability, and repeatability of 29Si MAS NMR for determination of the quantities of alite (Ca3SiO5) and belite (Ca2SiO4) in anhydrous Portland cement was investigated in detail for 11 commercial Portland cements and the results compared with phase quantifications based...

Constraint-based Word Segmentation for Chinese

DEFF Research Database (Denmark)

Christiansen, Henning; Bo, Li

2014-01-01

-hoc and statistically based methods. In this paper, we show experiments of implementing different approaches to CWSP in the framework of CHR Grammars [Christiansen, 2005] that provides a constraint solving approach to language analysis. CHR Grammars are based upon Constraint Handling Rules, CHR [Frühwirth, 1998, 2009......], which is a declarative, high-level programming language for specification and implementation of constraint solvers....

Structure determination of helical filaments by solid-state NMR spectroscopy

Science.gov (United States)

Ahmed, Mumdooh; Spehr, Johannes; König, Renate; Lünsdorf, Heinrich; Rand, Ulfert; Lührs, Thorsten; Ritter, Christiane

2016-01-01

The controlled formation of filamentous protein complexes plays a crucial role in many biological systems and represents an emerging paradigm in signal transduction. The mitochondrial antiviral signaling protein (MAVS) is a central signal transduction hub in innate immunity that is activated by a receptor-induced conversion into helical superstructures (filaments) assembled from its globular caspase activation and recruitment domain. Solid-state NMR (ssNMR) spectroscopy has become one of the most powerful techniques for atomic resolution structures of protein fibrils. However, for helical filaments, the determination of the correct symmetry parameters has remained a significant hurdle for any structural technique and could thus far not be precisely derived from ssNMR data. Here, we solved the atomic resolution structure of helical MAVSCARD filaments exclusively from ssNMR data. We present a generally applicable approach that systematically explores the helical symmetry space by efficient modeling of the helical structure restrained by interprotomer ssNMR distance restraints. Together with classical automated NMR structure calculation, this allowed us to faithfully determine the symmetry that defines the entire assembly. To validate our structure, we probed the protomer arrangement by solvent paramagnetic resonance enhancement, analysis of chemical shift differences relative to the solution NMR structure of the monomer, and mutagenesis. We provide detailed information on the atomic contacts that determine filament stability and describe mechanistic details on the formation of signaling-competent MAVS filaments from inactive monomers. PMID:26733681

Structural Studies of Bcl-xL/ligand Complexes using {sup 19}F NMR

Energy Technology Data Exchange (ETDEWEB)

Yu Liping; Hajduk, Philip J.; Mack, Jamey; Olejniczak, Edward T. [GPRD, Abbott Laboratories, Pharmaceutical Discovery Division (United States)], E-mail: Edward.olejniczak@abbott.com

2006-04-15

Fluorine atoms are often incorporated into drug molecules as part of the lead optimization process in order to improve affinity or modify undesirable metabolic and pharmacokinetic profiles. From an NMR perspective, the abundance of fluorinated drug leads provides an exploitable niche for structural studies using {sup 19}F NMR in the drug discovery process. As {sup 19}F has no interfering background signal from biological sources, {sup 19}F NMR studies of fluorinated drugs bound to their protein receptors can yield easily interpretable and unambiguous structural constraints. {sup 19}F can also be selectively incorporated into proteins to obtain additional constraints for structural studies. Despite these advantages, {sup 19}F NMR has rarely been exploited for structural studies due to its broad lines in macromolecules and their ligand complexes, leading to weak signals in {sup 1}H/{sup 19}F heteronuclear NOE experiments. Here we demonstrate several different experimental strategies that use {sup 19}F NMR to obtain ligand-protein structural constraints for ligands bound to the anti-apoptotic protein Bcl-xL, a drug target for anti-cancer therapy. These examples indicate the applicability of these methods to typical structural problems encountered in the drug development process.

NMR of insensitive nuclei enhanced by dynamic nuclear polarization.

Science.gov (United States)

Miéville, Pascal; Jannin, Sami; Helm, Lothar; Bodenhausen, Geoffrey

2011-01-01

Despite the powerful spectroscopic information it provides, Nuclear Magnetic Resonance (NMR) spectroscopy suffers from a lack of sensitivity, especially when dealing with nuclei other than protons. Even though NMR can be applied in a straightforward manner when dealing with abundant protons of organic molecules, it is very challenging to address biomolecules in low concentration and/or many other nuclei of the periodic table that do not provide as intense signals as protons. Dynamic Nuclear Polarization (DNP) is an important technique that provides a way to dramatically increase signal intensities in NMR. It consists in transferring the very high electron spin polarization of paramagnetic centers (usually at low temperature) to the surrounding nuclear spins with appropriate microwave irradiation. DNP can lead to an enhancement of the nuclear spin polarization by up to four orders of magnitude. We present in this article some basic concepts of DNP, describe the DNP apparatus at EPFL, and illustrate the interest of the technique for chemical applications by reporting recent measurements of the kinetics of complexation of 89Y by the DOTAM ligand.

A new carbamidemethyl-linked lanthanoid chelating tag for PCS NMR spectroscopy of proteins in living HeLa cells

Energy Technology Data Exchange (ETDEWEB)

Hikone, Yuya [Tokyo Metropolitan University, Department of Chemistry, Graduate School of Science and Engineering (Japan); Hirai, Go [RIKEN, Synthetic Organic Chemistry Laboratory (Japan); Mishima, Masaki [Tokyo Metropolitan University, Department of Chemistry, Graduate School of Science and Engineering (Japan); Inomata, Kohsuke [RIKEN, Quantitative Biology Center (Japan); Ikeya, Teppei; Arai, Souichiro [Tokyo Metropolitan University, Department of Chemistry, Graduate School of Science and Engineering (Japan); Shirakawa, Masahiro [Japan Agency for Medical Research and Development, AMED-CREST (Japan); Sodeoka, Mikiko [RIKEN, Synthetic Organic Chemistry Laboratory (Japan); Ito, Yutaka, E-mail: ito-yutaka@tmu.ac.jp [Tokyo Metropolitan University, Department of Chemistry, Graduate School of Science and Engineering (Japan)

2016-10-15

Structural analyses of proteins under macromolecular crowding inside human cultured cells by in-cell NMR spectroscopy are crucial not only for explicit understanding of their cellular functions but also for applications in medical and pharmaceutical sciences. In-cell NMR experiments using human cultured cells however suffer from low sensitivity, thus pseudocontact shifts from protein-tagged paramagnetic lanthanoid ions, analysed using sensitive heteronuclear two-dimensional correlation NMR spectra, offer huge potential advantage in obtaining structural information over conventional NOE-based approaches. We synthesised a new lanthanoid-chelating tag (M8-CAM-I), in which the eight-fold, stereospecifically methylated DOTA (M8) scaffold was retained, while a stable carbamidemethyl (CAM) group was introduced as the functional group connecting to proteins. M8-CAM-I successfully fulfilled the requirements for in-cell NMR: high-affinity to lanthanoid, low cytotoxicity and the stability under reducing condition inside cells. Large PCSs for backbone N–H resonances observed for M8-CAM-tagged human ubiquitin mutant proteins, which were introduced into HeLa cells by electroporation, demonstrated that this approach readily provides the useful information enabling the determination of protein structures, relative orientations of domains and protein complexes within human cultured cells.

A new carbamidemethyl-linked lanthanoid chelating tag for PCS NMR spectroscopy of proteins in living HeLa cells.

Science.gov (United States)

Hikone, Yuya; Hirai, Go; Mishima, Masaki; Inomata, Kohsuke; Ikeya, Teppei; Arai, Souichiro; Shirakawa, Masahiro; Sodeoka, Mikiko; Ito, Yutaka

2016-10-01

Structural analyses of proteins under macromolecular crowding inside human cultured cells by in-cell NMR spectroscopy are crucial not only for explicit understanding of their cellular functions but also for applications in medical and pharmaceutical sciences. In-cell NMR experiments using human cultured cells however suffer from low sensitivity, thus pseudocontact shifts from protein-tagged paramagnetic lanthanoid ions, analysed using sensitive heteronuclear two-dimensional correlation NMR spectra, offer huge potential advantage in obtaining structural information over conventional NOE-based approaches. We synthesised a new lanthanoid-chelating tag (M8-CAM-I), in which the eight-fold, stereospecifically methylated DOTA (M8) scaffold was retained, while a stable carbamidemethyl (CAM) group was introduced as the functional group connecting to proteins. M8-CAM-I successfully fulfilled the requirements for in-cell NMR: high-affinity to lanthanoid, low cytotoxicity and the stability under reducing condition inside cells. Large PCSs for backbone N-H resonances observed for M8-CAM-tagged human ubiquitin mutant proteins, which were introduced into HeLa cells by electroporation, demonstrated that this approach readily provides the useful information enabling the determination of protein structures, relative orientations of domains and protein complexes within human cultured cells.

A new carbamidemethyl-linked lanthanoid chelating tag for PCS NMR spectroscopy of proteins in living HeLa cells

International Nuclear Information System (INIS)

Hikone, Yuya; Hirai, Go; Mishima, Masaki; Inomata, Kohsuke; Ikeya, Teppei; Arai, Souichiro; Shirakawa, Masahiro; Sodeoka, Mikiko; Ito, Yutaka

2016-01-01

Structural analyses of proteins under macromolecular crowding inside human cultured cells by in-cell NMR spectroscopy are crucial not only for explicit understanding of their cellular functions but also for applications in medical and pharmaceutical sciences. In-cell NMR experiments using human cultured cells however suffer from low sensitivity, thus pseudocontact shifts from protein-tagged paramagnetic lanthanoid ions, analysed using sensitive heteronuclear two-dimensional correlation NMR spectra, offer huge potential advantage in obtaining structural information over conventional NOE-based approaches. We synthesised a new lanthanoid-chelating tag (M8-CAM-I), in which the eight-fold, stereospecifically methylated DOTA (M8) scaffold was retained, while a stable carbamidemethyl (CAM) group was introduced as the functional group connecting to proteins. M8-CAM-I successfully fulfilled the requirements for in-cell NMR: high-affinity to lanthanoid, low cytotoxicity and the stability under reducing condition inside cells. Large PCSs for backbone N–H resonances observed for M8-CAM-tagged human ubiquitin mutant proteins, which were introduced into HeLa cells by electroporation, demonstrated that this approach readily provides the useful information enabling the determination of protein structures, relative orientations of domains and protein complexes within human cultured cells.

Fragment based drug discovery: practical implementation based on ¹⁹F NMR spectroscopy.

Science.gov (United States)

Jordan, John B; Poppe, Leszek; Xia, Xiaoyang; Cheng, Alan C; Sun, Yax; Michelsen, Klaus; Eastwood, Heather; Schnier, Paul D; Nixey, Thomas; Zhong, Wenge

2012-01-26

Fragment based drug discovery (FBDD) is a widely used tool for discovering novel therapeutics. NMR is a powerful means for implementing FBDD, and several approaches have been proposed utilizing (1)H-(15)N heteronuclear single quantum coherence (HSQC) as well as one-dimensional (1)H and (19)F NMR to screen compound mixtures against a target of interest. While proton-based NMR methods of fragment screening (FBS) have been well documented and are widely used, the use of (19)F detection in FBS has been only recently introduced (Vulpetti et al. J. Am. Chem. Soc.2009, 131 (36), 12949-12959) with the aim of targeting "fluorophilic" sites in proteins. Here, we demonstrate a more general use of (19)F NMR-based fragment screening in several areas: as a key tool for rapid and sensitive detection of fragment hits, as a method for the rapid development of structure-activity relationship (SAR) on the hit-to-lead path using in-house libraries and/or commercially available compounds, and as a quick and efficient means of assessing target druggability.

Modified Sucksmith balances for ferromagnetic and paramagnetic measurements

Energy Technology Data Exchange (ETDEWEB)

Lundquist, N; Myers, H P

1962-02-15

Two balances, one for measurement of ferromagnetic magnetisation, the other for paramagnetic susceptibility measurements, are described. Designs are based on Sucksmith's ring balance but the ring and optical lever system of the latter has been replaced by a strain gauge bridge, which allows the force on the magnetic specimens to be determined via potentiometer readings. The modified balances are very robust, insensitive to vibration and, if desired, suitable for direct recording. Relative accuracies of 0.3 % and 0.5 % are obtained respectively for the ferromagnetic and paramagnetic systems.

Coverage-based constraints for IMRT optimization

Science.gov (United States)

Mescher, H.; Ulrich, S.; Bangert, M.

2017-09-01

Radiation therapy treatment planning requires an incorporation of uncertainties in order to guarantee an adequate irradiation of the tumor volumes. In current clinical practice, uncertainties are accounted for implicitly with an expansion of the target volume according to generic margin recipes. Alternatively, it is possible to account for uncertainties by explicit minimization of objectives that describe worst-case treatment scenarios, the expectation value of the treatment or the coverage probability of the target volumes during treatment planning. In this note we show that approaches relying on objectives to induce a specific coverage of the clinical target volumes are inevitably sensitive to variation of the relative weighting of the objectives. To address this issue, we introduce coverage-based constraints for intensity-modulated radiation therapy (IMRT) treatment planning. Our implementation follows the concept of coverage-optimized planning that considers explicit error scenarios to calculate and optimize patient-specific probabilities q(\\hat{d}, \\hat{v}) of covering a specific target volume fraction \\hat{v} with a certain dose \\hat{d} . Using a constraint-based reformulation of coverage-based objectives we eliminate the trade-off between coverage and competing objectives during treatment planning. In-depth convergence tests including 324 treatment plan optimizations demonstrate the reliability of coverage-based constraints for varying levels of probability, dose and volume. General clinical applicability of coverage-based constraints is demonstrated for two cases. A sensitivity analysis regarding penalty variations within this planing study based on IMRT treatment planning using (1) coverage-based constraints, (2) coverage-based objectives, (3) probabilistic optimization, (4) robust optimization and (5) conventional margins illustrates the potential benefit of coverage-based constraints that do not require tedious adjustment of target volume objectives.

Fuzzy Constraint-Based Agent Negotiation

Institute of Scientific and Technical Information of China (English)

Menq-Wen Lin; K. Robert Lai; Ting-Jung Yu

2005-01-01

Conflicts between two or more parties arise for various reasons and perspectives. Thus, resolution of conflicts frequently relies on some form of negotiation. This paper presents a general problem-solving framework for modeling multi-issue multilateral negotiation using fuzzy constraints. Agent negotiation is formulated as a distributed fuzzy constraint satisfaction problem (DFCSP). Fuzzy constrains are thus used to naturally represent each agent's desires involving imprecision and human conceptualization, particularly when lexical imprecision and subjective matters are concerned. On the other hand, based on fuzzy constraint-based problem-solving, our approach enables an agent not only to systematically relax fuzzy constraints to generate a proposal, but also to employ fuzzy similarity to select the alternative that is subject to its acceptability by the opponents. This task of problem-solving is to reach an agreement that benefits all agents with a high satisfaction degree of fuzzy constraints, and move towards the deal more quickly since their search focuses only on the feasible solution space. An application to multilateral negotiation of a travel planning is provided to demonstrate the usefulness and effectiveness of our framework.

NMR Evidence for the Topologically Nontrivial Nature in a Family of Half-Heusler Compounds

KAUST Repository

Zhang, Xiaoming

2016-03-16

Spin-orbit coupling (SOC) is expected to partly determine the topologically nontrivial electronic structure of heavy half-Heusler ternary compounds. However, to date, attempts to experimentally observe either the strength of SOC or how it modifies the bulk band structure have been unsuccessful. By using bulk-sensitive nuclear magnetic resonance (NMR) spectroscopy combined with first-principles calculations, we reveal that 209Bi NMR isotropic shifts scale with relativity in terms of the strength of SOC and average atomic numbers, indicating strong relativistic effects on NMR parameters. According to first-principles calculations, we further claim that nuclear magnetic shieldings from relativistic p1/2 states and paramagnetic contributions from low-lying unoccupied p3/2 states are both sensitive to the details of band structures tuned by relativity, which explains why the hidden relativistic effects on band structure can be revealed by 209Bi NMR isotropic shifts in topologically nontrivial half-Heusler compounds. Used in complement to surface-sensitive methods, such as angle resolved photon electron spectroscopy and scanning tunneling spectroscopy, NMR can provide valuable information on bulk electronic states.

NMR Evidence for the Topologically Nontrivial Nature in a Family of Half-Heusler Compounds

KAUST Repository

Zhang, Xiaoming; Hou, Zhipeng; Wang, Yue; Xu, Guizhou; Shi, Chenglong; Liu, EnKe; Xi, Xuekui; Wang, Wenhong; Wu, Guangheng; Zhang, Xixiang

2016-01-01

Spin-orbit coupling (SOC) is expected to partly determine the topologically nontrivial electronic structure of heavy half-Heusler ternary compounds. However, to date, attempts to experimentally observe either the strength of SOC or how it modifies the bulk band structure have been unsuccessful. By using bulk-sensitive nuclear magnetic resonance (NMR) spectroscopy combined with first-principles calculations, we reveal that 209Bi NMR isotropic shifts scale with relativity in terms of the strength of SOC and average atomic numbers, indicating strong relativistic effects on NMR parameters. According to first-principles calculations, we further claim that nuclear magnetic shieldings from relativistic p1/2 states and paramagnetic contributions from low-lying unoccupied p3/2 states are both sensitive to the details of band structures tuned by relativity, which explains why the hidden relativistic effects on band structure can be revealed by 209Bi NMR isotropic shifts in topologically nontrivial half-Heusler compounds. Used in complement to surface-sensitive methods, such as angle resolved photon electron spectroscopy and scanning tunneling spectroscopy, NMR can provide valuable information on bulk electronic states.

Ferromagnetic correlations in Yb based heavy fermions probed by NMR relaxation: YbNi{sub 4}P{sub 2} vs. Yb(Rh,Ir){sub 2}Si{sub 2}

Energy Technology Data Exchange (ETDEWEB)

Baenitz, M.; Sarkar, R.; Khuntia, P.; Krellner, C.; Geibel, C.; Steglich, F. [Max - Planck Institute of Chemical Physics of Solids, 01187 Dresden, Germany (Germany)

2012-07-01

Intersite correlations in Ce-based heavy fermion systems close to the quantum critical point separating the magnetic ordered state from the paramagnetic Kondo lattice are in almost all cases predominantly antiferromagnetic (AFM) in nature. The NMR relaxation of these systems show an evolution from localized fluctuations with 1/T{sub 1} nearly constant above the Kondo temperature T{sub K}, to a linear in T Korringa- like behavior with a constant and enhanced (1/T{sub 1}T)- value below T{sub K}. We report on {sup 31}P-NMR results on the ferromagnetic (FM) quantum critical system YbNi{sub 4}P{sub 2} over a wide range in temperature (2-300 K) and field (0.2 - 9 T). Here, {sup 31}(1/T{sub 1}T)(T) does not show such a signature at T{sub K}, instead a continuous increase of (1/T{sub 1}T) down to lowest T is observed. A similar behavior has been reported for YbRh{sub 2}Si{sub 2}, which also exhibits strong FM correlations evidenced by {sup 29}Si - NMR and an enhanced Wilson ratio. Furthermore, in CeFePO, which is likely unique among Ce-based quantum critical system because of its strong FM correlations, (1/T{sub 1}T) also diverges continuously for T {yields}0. This suggests that the difference in the relaxation between most of the Ce systems and the Yb systems is predominantly related to a change from AFM to FM intersite correlations. NMR-results (shift, line width, T{sub 1}) are analyzed and discussed in different models (Korringa, Moriya).

{sup 1}H and {sup 10}B NMR and MRI investigation of boron- and gadolinium-boron compounds in boron neutron capture therapy

Energy Technology Data Exchange (ETDEWEB)

Bonora, M., E-mail: marco.bonora@unipv.it [Physics Department ' A. Volta' , University of Pavia, Via Bassi 6, 27100 Pavia (Italy)] [CNISM Unit (Italy); Corti, M.; Borsa, F. [Physics Department ' A. Volta' , University of Pavia, Via Bassi 6, 27100 Pavia (Italy)] [CNISM Unit (Italy); Bortolussi, S.; Protti, N.; Santoro, D.; Stella, S.; Altieri, S. [Nuclear and Theoretical Physics Department, University of Pavia, Via Bassi 6, 27100 Pavia (Italy)] [INFN Pavia (Italy); Zonta, C.; Clerici, A.M.; Cansolino, L.; Ferrari, C.; Dionigi, P. [Surgical Sciences Department, Experimental Surgery Laboratory, University of Pavia, Pavia (Italy); Porta, A.; Zanoni, G.; Vidari, G. [Organic Chemistry Department, University of Pavia, Via Taramelli 10, 27100 Pavia (Italy)

2011-12-15

{sup 10}B molecular compounds suitable for Boron Neutron Capture Therapy (BNCT) are tagged with a Gd(III) paramagnetic ion. The newly synthesized molecule, Gd-BPA, is investigated as contrast agent in Magnetic Resonance Imaging (MRI) with the final aim of mapping the boron distribution in tissues. Preliminary Nuclear Magnetic Resonance (NMR) measurements, which include {sup 1}H and {sup 10}B relaxometry in animal tissues, proton relaxivity of the paramagnetic Gd-BPA molecule in water and its absorption in tumoral living cells, are reported.

Levitation in paramagnetic liquids

Energy Technology Data Exchange (ETDEWEB)

Dunne, P.A. [School of Physics and CRANN, Trinity Collge, Dublin 2 (Ireland)]. E-mail: pdunne2@tcd.ie; Hilton, J. [School of Physics and CRANN, Trinity Collge, Dublin 2 (Ireland); Coey, J.M.D. [School of Physics and CRANN, Trinity Collge, Dublin 2 (Ireland)

2007-09-15

Magnetic levitation of diamagnetic and paramagnetic substances in a paramagnetic liquid is explored. Materials ranging from graphite to tin and copper can be made to float at ambient temperature in concentrated solutions of dysprosium nitrate, when an electromagnet or four-block permanent magnet array is used to produce a gradient field. Simulations illustrate the stable regions for levitation above the permanent magnets; and a novel eight-block configuration is proposed, which allows denser materials such as gold or lead to be levitated.

Levitation in paramagnetic liquids

International Nuclear Information System (INIS)

Dunne, P.A.; Hilton, J.; Coey, J.M.D.

2007-01-01

Magnetic levitation of diamagnetic and paramagnetic substances in a paramagnetic liquid is explored. Materials ranging from graphite to tin and copper can be made to float at ambient temperature in concentrated solutions of dysprosium nitrate, when an electromagnet or four-block permanent magnet array is used to produce a gradient field. Simulations illustrate the stable regions for levitation above the permanent magnets; and a novel eight-block configuration is proposed, which allows denser materials such as gold or lead to be levitated

Constraint-based scheduling

Science.gov (United States)

Zweben, Monte

1993-01-01

The GERRY scheduling system developed by NASA Ames with assistance from the Lockheed Space Operations Company, and the Lockheed Artificial Intelligence Center, uses a method called constraint-based iterative repair. Using this technique, one encodes both hard rules and preference criteria into data structures called constraints. GERRY repeatedly attempts to improve schedules by seeking repairs for violated constraints. The system provides a general scheduling framework which is being tested on two NASA applications. The larger of the two is the Space Shuttle Ground Processing problem which entails the scheduling of all the inspection, repair, and maintenance tasks required to prepare the orbiter for flight. The other application involves power allocation for the NASA Ames wind tunnels. Here the system will be used to schedule wind tunnel tests with the goal of minimizing power costs. In this paper, we describe the GERRY system and its application to the Space Shuttle problem. We also speculate as to how the system would be used for manufacturing, transportation, and military problems.

Acceleration of natural-abundance solid-state MAS NMR measurements on bone by paramagnetic relaxation from gadolinium-DTPA

Science.gov (United States)

Mroue, Kamal H.; Zhang, Rongchun; Zhu, Peizhi; McNerny, Erin; Kohn, David H.; Morris, Michael D.; Ramamoorthy, Ayyalusamy

2014-07-01

Reducing the data collection time without affecting the signal intensity and spectral resolution is one of the major challenges for the widespread application of multidimensional nuclear magnetic resonance (NMR) spectroscopy, especially in experiments conducted on complex heterogeneous biological systems such as bone. In most of these experiments, the NMR data collection time is ultimately governed by the proton spin-lattice relaxation times (T1). For over two decades, gadolinium(III)-DTPA (Gd-DTPA, DTPA = Diethylene triamine pentaacetic acid) has been one of the most widely used contrast-enhancement agents in magnetic resonance imaging (MRI). In this study, we demonstrate that Gd-DTPA can also be effectively used to enhance the longitudinal relaxation rates of protons in solid-state NMR experiments conducted on bone without significant line-broadening and chemical-shift-perturbation side effects. Using bovine cortical bone samples incubated in different concentrations of Gd-DTPA complex, the 1H T1 values were calculated from data collected by 1H spin-inversion recovery method detected in natural-abundance 13C cross-polarization magic angle spinning (CPMAS) NMR experiments. Our results reveal that the 1H T1 values can be successfully reduced by a factor of 3.5 using as low as 10 mM Gd-DTPA without reducing the spectral resolution and thus enabling faster data acquisition of the 13C CPMAS spectra. These results obtained from 13C-detected CPMAS experiments were further confirmed using 1H-detected ultrafast MAS experiments on Gd-DTPA doped bone samples. This approach considerably improves the signal-to-noise ratio per unit time of NMR experiments applied to bone samples by reducing the experimental time required to acquire the same number of scans.

Assignment of solid-state 13C and 1H NMR spectra of paramagnetic Ni(II) acetylacetonate complexes aided by first-principles computations

DEFF Research Database (Denmark)

Rouf, Syed Awais; Jakobsen, Vibe Boel; Mareš, Jiří

2017-01-01

Recent advances in computational methodology allowed for first-principles calculations of the nuclear shielding tensor for a series of paramagnetic nickel(II) acetylacetonate complexes, [Ni(acac)2L2] with L = H2O, D2O, NH3, ND3, and PMe2Ph have provided detailed insight into the origin of the par......Recent advances in computational methodology allowed for first-principles calculations of the nuclear shielding tensor for a series of paramagnetic nickel(II) acetylacetonate complexes, [Ni(acac)2L2] with L = H2O, D2O, NH3, ND3, and PMe2Ph have provided detailed insight into the origin...

Constraint-based Attribute and Interval Planning

Science.gov (United States)

Jonsson, Ari; Frank, Jeremy

2013-01-01

In this paper we describe Constraint-based Attribute and Interval Planning (CAIP), a paradigm for representing and reasoning about plans. The paradigm enables the description of planning domains with time, resources, concurrent activities, mutual exclusions among sets of activities, disjunctive preconditions and conditional effects. We provide a theoretical foundation for the paradigm, based on temporal intervals and attributes. We then show how the plans are naturally expressed by networks of constraints, and show that the process of planning maps directly to dynamic constraint reasoning. In addition, we de ne compatibilities, a compact mechanism for describing planning domains. We describe how this framework can incorporate the use of constraint reasoning technology to improve planning. Finally, we describe EUROPA, an implementation of the CAIP framework.

Application progress of solid 29Si, 27Al NMR in the research of cement-based materials

International Nuclear Information System (INIS)

Feng Chunhua; Wang Xijian; Li Dongxu

2014-01-01

Background: The solid-state Nuclear Magnetic Resonance (NMR) is an effective method for the research of cement-based materials. Now it focuses on using solid 29 Si and 27 Al NMR to research the hydration structure of the cement-based materials in cement chemistry. Purpose: A theoretical guidance is proposed for solid 29 Si and 27 Al NMR technology used in cement chemistry research. Methods: We reviewed the application of solid 29 Si and 27 Al NMR in the cement-based materials and analyzed the problem among the researches. Results: This paper introduced an fundamental, relevant-conditions and basic parameters of NMR, and studied the technical parameters of solid 29 Si and 27 Ai NMR together with the relationship among the hydration structure of cement based material. Moreover, this paper reviewed the related domestic and overseas achievements in the research of hydration structure of the cement-based materials using solid 29 Si and 27 Al NMR. Conclusion: There were some problems in the research on cement-based materials by technology of solid 29 Si and 27 Al NMR. NMR will promote the Hydration theory of cement-based material greatly. (authors)

One-dimensional scanning of moisture in heated porous building materials with NMR.

Science.gov (United States)

van der Heijden, G H A; Huinink, H P; Pel, L; Kopinga, K

2011-02-01

In this paper we present a new dedicated NMR setup which is capable of measuring one-dimensional moisture profiles in heated porous materials. The setup, which is placed in the bore of a 1.5 T whole-body scanner, is capable of reaching temperatures up to 500 °C. Moisture and temperature profiles can be measured quasi simultaneously with a typical time resolution of 2-5 min. A methodology is introduced for correcting temperature effects on NMR measurements at these elevated temperatures. The corrections are based on the Curie law for paramagnetism and the observed temperature dependence of the relaxation mechanisms occurring in porous materials. Both these corrections are used to obtain a moisture content profile from the raw NMR signal profile. To illustrate the methodology, a one-sided heating experiment of concrete with a moisture content in equilibrium with 97% RH is presented. This kind of heating experiment is of particular interest in the research on fire spalling of concrete, since it directly reveals the moisture and heat transport occurring inside the concrete. The obtained moisture profiles reveal a moisture peak building up behind the boiling front, resulting in a saturated layer. To our knowledge the direct proof of the formation of a moisture peak and subsequent moisture clogging has not been reported before. Copyright © 2010 Elsevier Inc. All rights reserved.

Solid-State-NMR-Structure-Based Inhibitor Design to Achieve Selective Inhibition of the Parallel-in-Register β-Sheet versus Antiparallel Iowa Mutant β-Amyloid Fibrils.

Science.gov (United States)

Cheng, Qinghui; Qiang, Wei

2017-06-08

Solid-state nuclear magnetic resonance (ssNMR) spectroscopy has been widely applied to characterize the high-resolution structures of β-amyloid (Aβ) fibrils. While these structures provide crucial molecular insights on the deposition of amyloid plaques in Alzheimer's diseases (AD), ssNMR structures have been rarely used so far as the basis for designing inhibitors. It remains a challenge because the ssNMR-based Aβ fibril structures were usually obtained with sparsely isotope-labeled peptides with limited experimental constraints, where the structural models, especially the side-chain coordinates, showed restricted precision. However, these structural models often possess a higher accuracy within the hydrophobic core regions with more well-defined experimental data, which provide potential targets for the molecular design. This work presents an ssNMR-based molecular design to achieve selective inhibition of a particular type of Aβ fibrillar structure, which was formed with the Iowa mutant of Aβ with parallel-in-register β-sheet hydrophobic core. The results show that short peptides that mimic the C-terminal β-strands of the fibril may have a preference in binding to the parallel Aβ fibrils rather than the antiparallel fibrils, mainly due to the differences in the high-resolution structures in the fibril elongation interfaces. The Iowa mutant Aβ fibrils are utilized in this work mainly as a model to demonstrate the feasibility of the strategy because it is relatively straightforward to distinguish the parallel and antiparallel fibril structures using ssNMR. Our results suggest that it is potentially feasible to design structure-selective inhibitors and/or diagnostic agents to Aβ fibrils using ssNMR-based structural models.

International NMR-based Environmental Metabolomics Intercomparison Exercise

Science.gov (United States)

Several fundamental requirements must be met so that NMR-based metabolomics and the related technique of metabonomics can be formally adopted into environmental monitoring and chemical risk assessment. Here we report an intercomparison exercise which has evaluated the effectivene...

Multiplex immunoassay for persistent organic pollutants in tilapia: comparison of imaging- and flow cytometry-based platforms using spectrally encoded paramagnetic microspheres

NARCIS (Netherlands)

Meimaridou, A.; Haasnoot, W.; Shelver, W.L.; Franek, M.; Nielen, M.W.F.

2013-01-01

Recent developments in spectrally encoded microspheres (SEMs)-based technologies provide high multiplexing possibilities. Most SEMs-based assays require a flow cytometer with sophisticated fluidics and optics. A new imaging super-paramagnetic SEMs-based alternative platform transports SEMs with

Carbon-13 NMR characterization of actinyl(VI) carbonate complexes in aqueous solution

International Nuclear Information System (INIS)

Clark, D.L.; Hobart, D.E.; Palmer, P.D.; Sullivan, J.C.; Stout, B.E.

1992-01-01

The uranyl(VI) carbonate system has been re-examined using 13 C NMR of 99.9% 13 C-enriched U VI O 2 ( 13 CO 3 ) 3 4- in millimolar concentrations. By careful control of carbonate ion concentration, we have confirmed the existence of the trimer, and observed dynamic equilibrium between the monomer and the timer. In addition, the ligand exchange reaction between free and coordinated carbonate on Pu VI O 2 ( 13 CO 3 ) 3 4- and Am VI O 2 ( 13 CO 3 ) 3 4- systems has been examined by variable temperature 13 C NMR line-broadening techniques 13 C NMR line-broadening techniques. A modified Carr-Purcell-Meiboom-Gill NMR pulse sequence was written to allow for experimental determination of ligand exchange parameters for paramagnetic actinide complexes. Preliminary Eyring analysis has provided activation parameters of ΔG double-dagger 295 = 56 kJ/M, ΔH double-dagger = 38 kJ/M, and ΔS double-dagger = -60 J/M-K for the plutonyl triscarbonate system, suggesting an associative transition state for the plutonyl (VI) carbonate complex self-exchange reaction. Experiments for determination of the activation parameters for the americium (VI) carbonate system are in progress

Microassembly using a Cluster of Paramagnetic Microparticles

NARCIS (Netherlands)

Khalil, I.S.M.; Brink, F.V; Sardan Sukas, Ö.; Misra, Sarthak

2013-01-01

We use a cluster of paramagnetic microparticles to carry out a wireless two-dimensional microassembly operation. A magnetic-based manipulation system is used to control the motion of the cluster under the influence of the applied magnetic fields. Wireless motion control of the cluster is implemented

Biomolecular solid state NMR with magic-angle spinning at 25K.

Science.gov (United States)

Thurber, Kent R; Tycko, Robert

2008-12-01

A magic-angle spinning (MAS) probe has been constructed which allows the sample to be cooled with helium, while the MAS bearing and drive gases are nitrogen. The sample can be cooled to 25K using roughly 3 L/h of liquid helium, while the 4-mm diameter rotor spins at 6.7 kHz with good stability (+/-5 Hz) for many hours. Proton decoupling fields up to at least 130 kHz can be applied. This helium-cooled MAS probe enables a variety of one-dimensional and two-dimensional NMR experiments on biomolecular solids and other materials at low temperatures, with signal-to-noise proportional to 1/T. We show examples of low-temperature (13)C NMR data for two biomolecular samples, namely the peptide Abeta(14-23) in the form of amyloid fibrils and the protein HP35 in frozen glycerol/water solution. Issues related to temperature calibration, spin-lattice relaxation at low temperatures, paramagnetic doping of frozen solutions, and (13)C MAS NMR linewidths are discussed.

Induced Orbital Paramagnetism and Paratropism in Closed-Shell Molecules

Science.gov (United States)

Pelloni, Stefano; Lazzeretti, Paolo; Zanasi, Riccardo

2009-07-01

Three-dimensional models of the quantum-mechanical current density induced by a uniform magnetic field in the electron cloud have been obtained for closed-shell systems BeH-, BH, and CH+, characterized by induced orbital paramagnetism, and in planar unsaturated hydrocarbons C4H4 and clamped C8H8, exhibiting π paramagnetism. It is shown that, even for these paramagnetic systems, the paramagnetic contributions to magnetic susceptibilities and nuclear magnetic shielding, customarily taken into account in perturbation theory approaches, can formally be eliminated via the procedure of continuous transformation of the origin of the current density-paramagnetic zero. The definition of magnetic response properties can therefore be recast as a sum of two formally "diamagnetic" terms for any molecule, including systems showing strong induced orbital paramagnetism. It is shown that the paramagnetism in the compounds studied arises from the nodal topology of the electronic wave function. In particular, paratropic vortices circulate about stagnation lines at the intersection of nodal surfaces of the highest-occupied zero-order molecular orbital and corresponding first-order orbital.

Two superconducting phases in CePt{sub 3}Si confirmed by NMR

Energy Technology Data Exchange (ETDEWEB)

Ueda, Koh-ichi; Motoyama, Gaku; Kohara, Takao, E-mail: ueda@sci.u-hyogo.ac.j [Graduate School of Material Science, University of Hyogo, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan)

2009-03-01

Recent specific heat experiments in CePt{sub 3}Si of good quality gave an evidence of coexistence of two phases, which have distinct T{sub c} and T{sub n} for each phase. NMR spectrum of {sup 29}Si also showed a complicated line shape due to a co-existence of two phases below T{sub n}. One phase is an ordinary AF state and the other is a paramagnetic like phase, in which the internal field is somewhat small. The AF internal field deduced by NMR is expected to be parallel to the c-axis at Si site. With decreasing temperature below T{sub c}, 1/T{sub 1} measured at the satellite peak decreased rapidly followed by T{sup 3} with no enhancement just below T{sub c}.

On the paramagnetism of spin in the classical limit

International Nuclear Information System (INIS)

Hogreve, H.

1985-12-01

We consider particles with spin 1/2 in external electromagnetic fields. Although in many quantum mechanical situations they show a paramagnetic behaviour, within non-relativistic quantum theory a universal paramagnetic influence of spin fails to be true in general. Here we investigate the paramagnetism of spin in the framework of a classical theory. Applying previous results for the classical limit slash-h→O we obtain a classical expression corresponding to the quantum partition function of Hamiltonians with spin variables. For this classical partition function simple estimates lead to a paramagnetic inequality which demonstrates that indeed in the classical limit the spin shows a general paramagnetic behaviour. (author)

Paramagnetic moments in YBa2Cu3O7−δ nanocomposite films

International Nuclear Information System (INIS)

Dias, F.T.; Vieira, V.N.; Silva, D.L.; Albino Aguiar, J.; Valadão, D.R.B.; Obradors, X.; Puig, T.; Wolff-Fabris, F.; Kampert, E.

2014-01-01

Highlights: • The paramagnetic Meissner effect was observed in a nanocomposite YBaCuO thin film. • The paramagnetic moments in FC experiments were observed up to 10 T. • The paramagnetic Meissner effect increases when the magnetic field is increased. • Results may be explained based on the flux compression scenario and vortex pinning. • An apparent saturation tendency of the paramagnetic moments could be observed. - Abstract: We report on magnetization studies in YBa 2 Cu 3 O 7−δ thin films with dispersed Ba 2 YTaO 6 nanoparticles. The magnetization measurements were made using a superconducting quantum interference device (SQUID) and a vibrating sample magnetometer (VSM). Magnetic moments were measured as functions temperature using zero-field cooling (ZFC) and field-cooled (FC) prescriptions for magnetic fields up to 10 T applied parallel and perpendicular to the ab planes. A paramagnetic response related to the superconducting state was observed during the FC experiments. This effect, known as paramagnetic Meissner effect (PME), apparently increases when the magnetic field is increased. We discuss our PME results in terms of the strong pinning scenario modulated by Ba 2 YTaO 6 nanoparticles dispersed into the superconducting matrix

NMR study of thallium(I) ions in molten binary mixtures of nitrates and chlorides

International Nuclear Information System (INIS)

Nakamura, Yoshio; Kitazawa, Yukiharu; Shimoji, Mitsuo; Shimokawa, Shigezo.

1983-01-01

The chemical shifts of 205 Tl NMR in molten binary mixtures of nitrates and those of chlorides have been measured as a function of composition and temperature. The shifts increase in the diamagnetic direction with decreasing the size of foreign cations and increase in the paramagnetic direction with increasing temperature. These results are interpreted by changes in the overlap of orbitals of the Tl + ion and the anion, which depend upon composition and temperature. (author)

Paramagnetic contrast material

International Nuclear Information System (INIS)

McNamara, M.T.

1987-01-01

Paramagnetic contrast materials have certainly demonstrated clinical utility in a variety of organ systems for improved detection of various neoplastic, inflammatory, infectious, and physiologic abnormalities. Although the more commonly employed extracellular agents, such as Gd-DTPA, have been quite safe and useful, particularly in the CNS, it is almost certain that other substances will achieve more success in various other organs, such as iron oxides in the reticuloendothelial system and persisting extracellular agents in the cardiovascular system. Finally, as MRI technology continues to evolve, producing such exciting new sequences as gradient-echo fast scans, the roles of currently existing and newly discovered paramagnetic pharmaceuticals must be continuously reevaluated both to obtain maximum clinical benefit and to guide the search for newer agents that may further optimize the diagnostic efficacy of MRI

Adsorption and collective paramagnetism

CERN Document Server

Selwood, Pierce W

1962-01-01

Adsorption and Collective Paramagnetism describes a novel method for studying chemisorption. The method is based on the change in the number of unpaired electrons in the adsorbent as chemisorption occurs. The method is applicable to almost all adsorbates, but it is restricted to ferromagnetic adsorbents such as nickel, which may be obtained in the form of very small particles, that is to say, to ferromagnetic adsorbents with a high specific surface. While almost all the data used illustratively have been published elsewhere this is the first complete review of the subject. The book is addresse

WaVPeak: Picking NMR peaks through wavelet-based smoothing and volume-based filtering

KAUST Repository

Liu, Zhi

2012-02-10

Motivation: Nuclear magnetic resonance (NMR) has been widely used as a powerful tool to determine the 3D structures of proteins in vivo. However, the post-spectra processing stage of NMR structure determination usually involves a tremendous amount of time and expert knowledge, which includes peak picking, chemical shift assignment and structure calculation steps. Detecting accurate peaks from the NMR spectra is a prerequisite for all following steps, and thus remains a key problem in automatic NMR structure determination. Results: We introduce WaVPeak, a fully automatic peak detection method. WaVPeak first smoothes the given NMR spectrum by wavelets. The peaks are then identified as the local maxima. The false positive peaks are filtered out efficiently by considering the volume of the peaks. WaVPeak has two major advantages over the state-of-the-art peak-picking methods. First, through wavelet-based smoothing, WaVPeak does not eliminate any data point in the spectra. Therefore, WaVPeak is able to detect weak peaks that are embedded in the noise level. NMR spectroscopists need the most help isolating these weak peaks. Second, WaVPeak estimates the volume of the peaks to filter the false positives. This is more reliable than intensity-based filters that are widely used in existing methods. We evaluate the performance of WaVPeak on the benchmark set proposed by PICKY (Alipanahi et al., 2009), one of the most accurate methods in the literature. The dataset comprises 32 2D and 3D spectra from eight different proteins. Experimental results demonstrate that WaVPeak achieves an average of 96%, 91%, 88%, 76% and 85% recall on 15N-HSQC, HNCO, HNCA, HNCACB and CBCA(CO)NH, respectively. When the same number of peaks are considered, WaVPeak significantly outperforms PICKY. The Author(s) 2012. Published by Oxford University Press.

NMR

International Nuclear Information System (INIS)

Kneeland, J.B.; Lee, B.C.P.; Whalen, J.P.; Knowles, R.J.R.; Cahill, P.T.

1984-01-01

Although still quite new, NMR imaging has already emerged as a safe, noninvasive, painless, and effective diagnostic modality requiring no ionizing radiation. Also, NMR appears already to have established itself as the method of choice for the examination of the brain spinal cord (excluding herniated disks). Another area in which NMR excels is in the examination of the pelvis. The use of surface coils offers the promise of visualizing structures with resolution unobtainable by any other means. In addition, NMR, with its superb visualization of vascular structures and potential ability to measure flow, may soon revolutionize the diagnosis of cardiovascular disease. Finally, NMR, through biochemically and physiologically based T/sub 1/ and T/sub 2/ indices or through spectroscopy, may provide a means of monitoring therapeutic response so as to permit tailoring of treatment to the individual patient. In short, NMR is today probably at the same stage as the x-ray was in Roentgen's day

Characterisation of β-tricalcium phosphate-based bone substitute materials by electron paramagnetic resonance spectroscopy

Science.gov (United States)

Matković, Ivo; Maltar-Strmečki, Nadica; Babić-Ivančić, Vesna; Dutour Sikirić, Maja; Noethig-Laslo, Vesna

2012-10-01

β-TCP based materials are frequently used as dental implants. Due to their resorption in the body and direct contact with tissues, in order to inactivate bacteria, fungal spores and viruses, they are usually sterilized by γ-irradiation. However, the current literature provides little information about effects of the γ-irradiation on the formation and stability of the free radicals in the bone graft materials during and after sterilization procedure. In this work five different bone graft substitution materials, composed of synthetic beta tricalcium phosphate (β-TCP) and hydroxyapatite (HAP) present in the market were characterized by electron paramagnetic resonance (EPR) spectroscopy, X-ray powder diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and thermogravimetric analysis (TGA). Paramagnetic species Mn2+, Fe3+, trapped H-atoms and CO2- radicals were detected in the biphasic material (60% HAP, 40% β-TCP), while in β-TCP materials only Mn2+ andor trapped hydrogen atoms were detected. EPR analysis revealed the details of the structure of these materials at the atomic level. The results have shown that EPR spectroscopy is a method which can be used to improve the quality control of bone graft materials after syntering, processing and sterilization procedure.

NMR of proteins (4Fe-4S): structural properties and intramolecular electron transfer

International Nuclear Information System (INIS)

Huber, J.G.

1996-01-01

NMR started to be applied to Fe-S proteins in the seventies. Its use has recently been enlarged as the problems arising from the paramagnetic polymetallic clusters ware overcome. Applications to [4Fe-4S] are presented herein. The information derived thereof deepens the understanding of the redox properties of these proteins which play a central role in the metabolism of bacterial cells. The secondary structure elements and the overall folding of Chromatium vinosum ferredoxin (Cv Fd) in solution have been established by NMR. The unique features of this sequence have been shown to fold as an α helix at the C-terminus and as a loop between two cysteines ligand of one cluster: these two parts localize in close proximity from one another. The interaction between nuclear and electronic spins is a source of additional structural information for (4Fe-AS] proteins. The conformation of the cysteine-ligands, as revealed by the Fe-(S γ -C β -H β )Cys dihedral angles, is related to the chemical shifts of the signals associated with the protons of these residues. The longitudinal relaxation times of the protons depend on their distance to the cluster. A quantitative relationship has been established and used to show that the solution structure of the high-potential ferredoxin from Cv differs significantly from the crystal structure around Phe-48. Both parameters (chemical shifts and longitudinal relaxation times) give also insight into the electronic and magnetic properties of the [4Fe-4S] clusters. The rate of intramolecular electron transfer between the two [4FE-4S] clusters of ferredoxins has been measured by NMR. It is far slower in the case of Cv Fd than for shorter ferredoxins. The difference may be associated with changes in the magnetic and/or electronic properties of one cluster. The strong paramagnetism of the [4Fe-4S] clusters, which originally limited the applicability of NMR to proteins containing these cofactors, has been proven instrumental in affording new

NMR and molecular modeling evidence for a G·A mismatch base pair in a purine-rich DNA duplex

International Nuclear Information System (INIS)

Li, Ying; Wilson, W.D.; Zon, G.

1991-01-01

1 H NMR experiments indicate that the oligomer 5'-d(ATGAGCGAATA) forms an unusual 10-base-pair duplex with 4 G·A base pairs and a 3' unpaired adenosine. NMR results indicate that guanoxine imino protons of the F·A mismatches are not hydrogen bonded but are stacked in the helix. A G→ I substitution in either G·A base pair causes a dramatic decrtease in duplex stability and indicates that hydrogen bonding of the guanosine amino group is critical. Nuclear Overhauser effect spectroscopy (NOESY) and two-dimensional correlated spectroscopy (COSY) results indicate that the overall duplex conformation is in the B-family. Cross-strand NOEs in two-dimensional NOESY spectra between a mismatched AH2 and an AH1' of the other mismatched base pair and between a mismatched GH8 and GNH1 of the other mismatch establish a purine-purine stacking pattern, adenosine over adenosine and guanosine over guanosine, which strongly stabilizes the duplex. A computer graphics molecular model of the ususual duplex was constructed with G·A base pairs containing A-NH 2 to GN3 and G-NH 2 to AN7 hydrogen bonds and B-form base pairs on both sides of the G·A pairs [5'-d(ATGAGC)]. The energy-minimized duplex satisfies all experimental constraints from NOESY and COSY results. A hydrogen bond from G-NH 2 of the mismatch to a phosphate oxygen is predicted

Characterization of partitioning relevant lanthanide and actinide complexes by NMR spectroscopy; Charakterisierung von partitioningrelevanten Lanthaniden- und Actinidenkomplexen mittels NMR-Spektroskopie

Energy Technology Data Exchange (ETDEWEB)

Adam, Christian

2016-01-15

In the present work the interaction of N-donor ligands, such as 2,6-Bis(5,6-dipropyl-1,2,4-triazin-3-yl)pyridine (nPrBTP) and 2,6-Bis(5-(2,2-dimethylpropyl)1H-pyrazol)-3-yl-pyridine (C5-BPP), with trivalent lanthanide and actinide ions was studied. Ligands of this type show a high selectivity for the separation of trivalent actinide ions over lanthanides from nitric acid solutions. However, the reason for this selectivity, which is crucial for future partitioning and transmutation strategies for radioactive wastes, is still unknown. So far, the selectivity of some N-donor ligands is supposed to be an effect of an increased covalency in the actinide-ligand bond, compared to the lanthanide compounds. NMR spectroscopy on paramagnetic metal complexes is an excellent tool for the elucidation of bonding modes. The overall paramagnetic chemical shift consists of two contributions, the Fermi Contact Shift (FCS), due to electron spin delocalisation through covalent bonds, and the Pseudo Contact Shift (PCS), which describes the dipolar coupling of the electron magnetic moment and the nuclear spin. By assessing the FCS share in the paramagnetic shift, the degree of covalency in the metal-ligand bond can be gauged. Several methods to discriminate FCS and PCS have been used on the data of the nPrBTP- and C5-BPP-complexes and were evaluated regarding their applicability on lanthanide and actinide complexes with N-donor ligands. The study comprised the synthesis of all Ln(III) complexes with the exceptions of Pm(III) and Gd(III) as well as the Am(III) complex as a representative of the actinide series with both ligands. All complexes were fully characterised ({sup 1}H, {sup 13}C and {sup 15}N spectra) using NMR spectroscopy. By isotope enrichment with the NMR-active {sup 15}N in positions 8 and 9 in both ligands, resonance signals of these nitrogen atoms were detected for all complexes. The Bleaneymethod relies on different temperature dependencies for FCS (T{sup -1}) and PCS (T

Hydraulic characterisation of iron-oxide-coated sand and gravel based on nuclear magnetic resonance relaxation mode analyses

Directory of Open Access Journals (Sweden)

S. Costabel

2018-03-01

Full Text Available The capability of nuclear magnetic resonance (NMR relaxometry to characterise hydraulic properties of iron-oxide-coated sand and gravel was evaluated in a laboratory study. Past studies have shown that the presence of paramagnetic iron oxides and large pores in coarse sand and gravel disturbs the otherwise linear relationship between relaxation time and pore size. Consequently, the commonly applied empirical approaches fail when deriving hydraulic quantities from NMR parameters. Recent research demonstrates that higher relaxation modes must be taken into account to relate the size of a large pore to its NMR relaxation behaviour in the presence of significant paramagnetic impurities at its pore wall. We performed NMR relaxation experiments with water-saturated natural and reworked sands and gravels, coated with natural and synthetic ferric oxides (goethite, ferrihydrite, and show that the impact of the higher relaxation modes increases significantly with increasing iron content. Since the investigated materials exhibit narrow pore size distributions, and can thus be described by a virtual bundle of capillaries with identical apparent pore radius, recently presented inversion approaches allow for estimation of a unique solution yielding the apparent capillary radius from the NMR data. We found the NMR-based apparent radii to correspond well to the effective hydraulic radii estimated from the grain size distributions of the samples for the entire range of observed iron contents. Consequently, they can be used to estimate the hydraulic conductivity using the well-known Kozeny–Carman equation without any calibration that is otherwise necessary when predicting hydraulic conductivities from NMR data. Our future research will focus on the development of relaxation time models that consider pore size distributions. Furthermore, we plan to establish a measurement system based on borehole NMR for localising iron clogging and controlling its remediation

Hydraulic characterisation of iron-oxide-coated sand and gravel based on nuclear magnetic resonance relaxation mode analyses

Science.gov (United States)

Costabel, Stephan; Weidner, Christoph; Müller-Petke, Mike; Houben, Georg

2018-03-01

The capability of nuclear magnetic resonance (NMR) relaxometry to characterise hydraulic properties of iron-oxide-coated sand and gravel was evaluated in a laboratory study. Past studies have shown that the presence of paramagnetic iron oxides and large pores in coarse sand and gravel disturbs the otherwise linear relationship between relaxation time and pore size. Consequently, the commonly applied empirical approaches fail when deriving hydraulic quantities from NMR parameters. Recent research demonstrates that higher relaxation modes must be taken into account to relate the size of a large pore to its NMR relaxation behaviour in the presence of significant paramagnetic impurities at its pore wall. We performed NMR relaxation experiments with water-saturated natural and reworked sands and gravels, coated with natural and synthetic ferric oxides (goethite, ferrihydrite), and show that the impact of the higher relaxation modes increases significantly with increasing iron content. Since the investigated materials exhibit narrow pore size distributions, and can thus be described by a virtual bundle of capillaries with identical apparent pore radius, recently presented inversion approaches allow for estimation of a unique solution yielding the apparent capillary radius from the NMR data. We found the NMR-based apparent radii to correspond well to the effective hydraulic radii estimated from the grain size distributions of the samples for the entire range of observed iron contents. Consequently, they can be used to estimate the hydraulic conductivity using the well-known Kozeny-Carman equation without any calibration that is otherwise necessary when predicting hydraulic conductivities from NMR data. Our future research will focus on the development of relaxation time models that consider pore size distributions. Furthermore, we plan to establish a measurement system based on borehole NMR for localising iron clogging and controlling its remediation in the gravel pack of

NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment

Energy Technology Data Exchange (ETDEWEB)

Jang, Richard [Huazhong University of Science and Technology, School of Software Engineering (China); Wang, Yan [Huazhong University of Science and Technology, School of Life Science and Technology (China); Xue, Zhidong, E-mail: zdxue@hust.edu.cn [Huazhong University of Science and Technology, School of Software Engineering (China); Zhang, Yang, E-mail: zhng@umich.edu [University of Michigan, Department of Computational Medicine and Bioinformatics (United States)

2015-08-15

NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second round of the CASD-NMR experiment. Unlike many molecular dynamics-based methods, NMR-I-TASSER takes a molecular replacement-like approach to the problem by first threading the target through the PDB to identify structural templates which are then used for iterative NOE assignments and fragment structure assembly refinements. The employment of multiple templates allows NMR-I-TASSER to sample different topologies while convergence to a single structure is not required. Retroactive and blind tests of the CASD-NMR targets from Rounds 1 and 2 demonstrate that even without using NOE peak lists I-TASSER can generate correct structure topology with 15 of 20 targets having a TM-score above 0.5. With the addition of NOE-based distance restraints, NMR-I-TASSER significantly improved the I-TASSER models with all models having the TM-score above 0.5. The average RMSD was reduced from 5.29 to 2.14 Å in Round 1 and 3.18 to 1.71 Å in Round 2. There is no obvious difference in the modeling results with using raw and refined peak lists, indicating robustness of the pipeline to the NOE assignment errors. Overall, despite the low-resolution modeling the current NMR-I-TASSER pipeline provides a coarse-grained structure folding approach complementary to traditional molecular dynamics simulations, which can produce fast near-native frameworks for atomic-level structural refinement.

Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis

Directory of Open Access Journals (Sweden)

Qu Lijia

2009-03-01

Full Text Available Abstract Background Spectral processing and post-experimental data analysis are the major tasks in NMR-based metabonomics studies. While there are commercial and free licensed software tools available to assist these tasks, researchers usually have to use multiple software packages for their studies because software packages generally focus on specific tasks. It would be beneficial to have a highly integrated platform, in which these tasks can be completed within one package. Moreover, with open source architecture, newly proposed algorithms or methods for spectral processing and data analysis can be implemented much more easily and accessed freely by the public. Results In this paper, we report an open source software tool, Automics, which is specifically designed for NMR-based metabonomics studies. Automics is a highly integrated platform that provides functions covering almost all the stages of NMR-based metabonomics studies. Automics provides high throughput automatic modules with most recently proposed algorithms and powerful manual modules for 1D NMR spectral processing. In addition to spectral processing functions, powerful features for data organization, data pre-processing, and data analysis have been implemented. Nine statistical methods can be applied to analyses including: feature selection (Fisher's criterion, data reduction (PCA, LDA, ULDA, unsupervised clustering (K-Mean and supervised regression and classification (PLS/PLS-DA, KNN, SIMCA, SVM. Moreover, Automics has a user-friendly graphical interface for visualizing NMR spectra and data analysis results. The functional ability of Automics is demonstrated with an analysis of a type 2 diabetes metabolic profile. Conclusion Automics facilitates high throughput 1D NMR spectral processing and high dimensional data analysis for NMR-based metabonomics applications. Using Automics, users can complete spectral processing and data analysis within one software package in most cases

Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis.

Science.gov (United States)

Wang, Tao; Shao, Kang; Chu, Qinying; Ren, Yanfei; Mu, Yiming; Qu, Lijia; He, Jie; Jin, Changwen; Xia, Bin

2009-03-16

Spectral processing and post-experimental data analysis are the major tasks in NMR-based metabonomics studies. While there are commercial and free licensed software tools available to assist these tasks, researchers usually have to use multiple software packages for their studies because software packages generally focus on specific tasks. It would be beneficial to have a highly integrated platform, in which these tasks can be completed within one package. Moreover, with open source architecture, newly proposed algorithms or methods for spectral processing and data analysis can be implemented much more easily and accessed freely by the public. In this paper, we report an open source software tool, Automics, which is specifically designed for NMR-based metabonomics studies. Automics is a highly integrated platform that provides functions covering almost all the stages of NMR-based metabonomics studies. Automics provides high throughput automatic modules with most recently proposed algorithms and powerful manual modules for 1D NMR spectral processing. In addition to spectral processing functions, powerful features for data organization, data pre-processing, and data analysis have been implemented. Nine statistical methods can be applied to analyses including: feature selection (Fisher's criterion), data reduction (PCA, LDA, ULDA), unsupervised clustering (K-Mean) and supervised regression and classification (PLS/PLS-DA, KNN, SIMCA, SVM). Moreover, Automics has a user-friendly graphical interface for visualizing NMR spectra and data analysis results. The functional ability of Automics is demonstrated with an analysis of a type 2 diabetes metabolic profile. Automics facilitates high throughput 1D NMR spectral processing and high dimensional data analysis for NMR-based metabonomics applications. Using Automics, users can complete spectral processing and data analysis within one software package in most cases. Moreover, with its open source architecture, interested

NMR study of rare earth and actinide complexes

International Nuclear Information System (INIS)

Villardi de Montlaur de, G.C.

1978-01-01

Proton magnetic resonance studies of lanthanide shift reagents with olefin-transition metal complexes, monoamines and diamines as substrates are described. Shift reagents for olefins are reported: Lnsup(III)(fod) 3 can induce substantial shifts in the nmr spectra of a variety of olefins when silver 1-heptafluororobutyrate is used to complex the olefin. The preparation, properties and efficiency of such systems are described. Configurational aspects and exchange processes of Lnsup(III)(fod) 3 complexes with secondary and tertiary monoamines are analysed by means of dynamic nmr. Factors influencing the stability and the stoichiometry of these complexes and various processes such as nitrogen inversion and ligand exchange are discussed. At low temperature, ring inversion can be slow on an nmr time-scale for Lnsup(III)(fod) 3 -diamino chelates. Barriers to ring inversion in substituted ethylenediamines and propanediamines are obtained. Steric factors appear to play an important role in the stability and kinetics of these bidentate species. The synthesis of uranium-IV crown-ether and cryptate complexes is described. A conformational study of these compounds show evidence of an insertion of the paramagnetic cation as witnessed by the large induced shifts observed. The insertion of uranium in the macrocyclic ligand of a UCl 4 -dicyclohexyl-18-crown-6 complex is confirmed by an X-ray structural determination [fr

Efficient DNP NMR of Membrane Proteins: Sample Preparation Protocols, Sensitivity, and Radical Location

Science.gov (United States)

Liao, Shu Y.; Lee, Myungwoon; Wang, Tuo; Sergeyev, Ivan V.; Hong, Mei

2016-01-01

Although dynamic nuclear polarization (DNP) has dramatically enhanced solid-state NMR spectral sensitivities of many synthetic materials and some biological macromolecules, recent studies of membrane-protein DNP using exogenously doped paramagnetic radicals as polarizing agents have reported varied and sometimes surprisingly limited enhancement factors. This motivated us to carry out a systematic evaluation of sample preparation protocols for optimizing the sensitivity of DNP NMR spectra of membrane-bound peptides and proteins at cryogenic temperatures of ~110 K. We show that mixing the radical with the membrane by direct titration instead of centrifugation gives a significant boost to DNP enhancement. We quantify the relative sensitivity enhancement between AMUPol and TOTAPOL, two commonly used radicals, and between deuterated and protonated lipid membranes. AMUPol shows ~4 fold higher sensitivity enhancement than TOTAPOL, while deuterated lipid membrane does not give net higher sensitivity for the membrane peptides than protonated membrane. Overall, a ~100 fold enhancement between the microwave-on and microwave-off spectra can be achieved on lipid-rich membranes containing conformationally disordered peptides, and absolute sensitivity gains of 105–160 can be obtained between low-temperature DNP spectra and high-temperature non-DNP spectra. We also measured the paramagnetic relaxation enhancement of lipid signals by TOTAPOL and AMUPol, to determine the depths of these two radicals in the lipid bilayer. Our data indicate a bimodal distribution of both radicals, a surface-bound fraction and a membrane-bound fraction where the nitroxides lie at ~10 Å from the membrane surface. TOTAPOL appears to have a higher membrane-embedded fraction than AMUPol. These results should be useful for membrane-protein solid-state NMR studies under DNP conditions and provide insights into how biradicals interact with phospholipid membranes. PMID:26873390

Efficient DNP NMR of membrane proteins: sample preparation protocols, sensitivity, and radical location

Energy Technology Data Exchange (ETDEWEB)

Liao, Shu Y.; Lee, Myungwoon; Wang, Tuo [Massachusetts Institute of Technology, Department of Chemistry (United States); Sergeyev, Ivan V. [Bruker Biospin (United States); Hong, Mei, E-mail: meihong@mit.edu [Massachusetts Institute of Technology, Department of Chemistry (United States)

2016-03-15

Although dynamic nuclear polarization (DNP) has dramatically enhanced solid-state NMR spectral sensitivities of many synthetic materials and some biological macromolecules, recent studies of membrane-protein DNP using exogenously doped paramagnetic radicals as polarizing agents have reported varied and sometimes surprisingly limited enhancement factors. This motivated us to carry out a systematic evaluation of sample preparation protocols for optimizing the sensitivity of DNP NMR spectra of membrane-bound peptides and proteins at cryogenic temperatures of ~110 K. We show that mixing the radical with the membrane by direct titration instead of centrifugation gives a significant boost to DNP enhancement. We quantify the relative sensitivity enhancement between AMUPol and TOTAPOL, two commonly used radicals, and between deuterated and protonated lipid membranes. AMUPol shows ~fourfold higher sensitivity enhancement than TOTAPOL, while deuterated lipid membrane does not give net higher sensitivity for the membrane peptides than protonated membrane. Overall, a ~100 fold enhancement between the microwave-on and microwave-off spectra can be achieved on lipid-rich membranes containing conformationally disordered peptides, and absolute sensitivity gains of 105–160 can be obtained between low-temperature DNP spectra and high-temperature non-DNP spectra. We also measured the paramagnetic relaxation enhancement of lipid signals by TOTAPOL and AMUPol, to determine the depths of these two radicals in the lipid bilayer. Our data indicate a bimodal distribution of both radicals, a surface-bound fraction and a membrane-bound fraction where the nitroxides lie at ~10 Å from the membrane surface. TOTAPOL appears to have a higher membrane-embedded fraction than AMUPol. These results should be useful for membrane-protein solid-state NMR studies under DNP conditions and provide insights into how biradicals interact with phospholipid membranes.

Guiding automated NMR structure determination using a global optimization metric, the NMR DP score

Energy Technology Data Exchange (ETDEWEB)

Huang, Yuanpeng Janet, E-mail: yphuang@cabm.rutgers.edu; Mao, Binchen; Xu, Fei; Montelione, Gaetano T., E-mail: gtm@rutgers.edu [Rutgers, The State University of New Jersey, Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium (United States)

2015-08-15

ASDP is an automated NMR NOE assignment program. It uses a distinct bottom-up topology-constrained network anchoring approach for NOE interpretation, with 2D, 3D and/or 4D NOESY peak lists and resonance assignments as input, and generates unambiguous NOE constraints for iterative structure calculations. ASDP is designed to function interactively with various structure determination programs that use distance restraints to generate molecular models. In the CASD–NMR project, ASDP was tested and further developed using blinded NMR data, including resonance assignments, either raw or manually-curated (refined) NOESY peak list data, and in some cases {sup 15}N–{sup 1}H residual dipolar coupling data. In these blinded tests, in which the reference structure was not available until after structures were generated, the fully-automated ASDP program performed very well on all targets using both the raw and refined NOESY peak list data. Improvements of ASDP relative to its predecessor program for automated NOESY peak assignments, AutoStructure, were driven by challenges provided by these CASD–NMR data. These algorithmic improvements include (1) using a global metric of structural accuracy, the discriminating power score, for guiding model selection during the iterative NOE interpretation process, and (2) identifying incorrect NOESY cross peak assignments caused by errors in the NMR resonance assignment list. These improvements provide a more robust automated NOESY analysis program, ASDP, with the unique capability of being utilized with alternative structure generation and refinement programs including CYANA, CNS, and/or Rosetta.

Evaluating Direct Manipulation Operations for Constraint-Based Layout

OpenAIRE

Zeidler , Clemens; Lutteroth , Christof; Stuerzlinger , Wolfgang; Weber , Gerald

2013-01-01

Part 11: Interface Layout and Data Entry; International audience; Layout managers are used to control the placement of widgets in graphical user interfaces (GUIs). Constraint-based layout managers are more powerful than other ones. However, they are also more complex and their layouts are prone to problems that usually require direct editing of constraints. Today, designers commonly use GUI builders to specify GUIs. The complexities of traditional approaches to constraint-based layouts pose c...

Judgement of Design Scheme Based on Flexible Constraint in ICAD

Institute of Scientific and Technical Information of China (English)

无

2000-01-01

The conception of flexible constraint is proposed in the paper. The solution of flexible constraint is in special range, and maybe different in different instances of same design scheme. The paper emphasis on how to evaluate and optimize a design scheme with flexible constraints based on the satisfaction degree function defined on flexible constraints. The conception of flexible constraint is used to solve constraint conflict and design optimization in complicated constraint-based assembly design by the PFM parametrization assembly design system. An instance of gear-box design is used for verifying optimization method.

The application of electron paramagnetic resonance in biomedical research

International Nuclear Information System (INIS)

Qu Ximei; Wang Liqin; Zhang Wenyi; Liu Zhongchao; Cui Songye; Feng Xin; Jiaoling

2013-01-01

Electron paramagnetic resonance technique has been found more than half a century, for free radicals detection application, it has been applied to various research studies, and promotes the development of the biomedicine. This article summarized the various free radicals measurement by the electron paramagnetic resonance in biology tissue, and the application of the spin labeling and electron paramagnetic resonance imaging technology in biomedicine. (authors)

Paramagnetic form factors from itinerant electron theory

International Nuclear Information System (INIS)

Cooke, J.F.; Liu, S.H.; Liu, A.J.

1985-01-01

Elastic neutron scattering experiments performed over the past two decades have provided accurate information about the magnetic form factors of paramagnetic transition metals. These measurements have traditionally been analyzed in terms of an atomic-like theory. There are, however, some cases where this procedure does not work, and there remains the overall conceptual problem of using an atomistic theory for systems where the unpaired-spin electrons are itinerant. We have recently developed computer codes for efficiently evaluating the induced magnetic form factors of fcc and bcc itinerant electron paramagnets. Results for the orbital and spin contributions have been obtained for Cr, Nb, V, Mo, Pd, and Rh based on local density bands. By using calculated spin enhancement parameters, we find reasonable agreement between theory and neutron form factor data. In addition, these zero parameter calculations yield predictions for the bulk susceptibility on an absolute scale which are in reasonable agreement with experiment in all treated cases except palladium

On kinetics of paramagnetic radiation defects accumulation in beryllium ceramics

International Nuclear Information System (INIS)

Polyakov, A.I.; Ryabikin, Yu.A.; Zashkvara, O.V.; Bitenbaev, M.I.; Petykhov, Yu.V.

1999-01-01

Results of paramagnetic radiation defects concentration dependence study in beryllium ceramics from gamma-irradiation dose ( 60 Co) within interval 0-100 Mrem are cited. Obtained dose dependence has form of accumulation curve with saturation typical of for majority of solids (crystals, different polymers, organic substances and others) , in which under irradiation occur not only formation of paramagnetic radiation defects, but its destruction due to recombination and interaction with radiation fields. Analysis of accumulation curve by the method of distant asymptotics allows to determine that observed in gamma-irradiated beryllium ceramics double line of electron spin resonance is forming of two types of paramagnetic radiation defects. It was defined, that sum paramagnetic characteristics of beryllium ceramics within 1-100 Mrad gamma- irradiation dose field change insignificantly and define from first type of paramagnetic radiation defects

NMR and TRLFS studies of Ln(iii) and An(iii) C5-BPP complexes.

Science.gov (United States)

Adam, Christian; Beele, Björn B; Geist, Andreas; Müllich, Udo; Kaden, Peter; Panak, Petra J

2015-02-01

C5-BPP is a highly efficient N-donor ligand for the separation of trivalent actinides, An(iii), from trivalent lanthanides, Ln(iii). The molecular origin of the selectivity of C5-BPP and many other N-donor ligands of the BTP-type is still not entirely understood. We present here the first NMR studies on C5-BPP Ln(iii) and An(iii) complexes. C5-BPP is synthesized with 10% 15 N labeling and characterized by NMR and LIFDI-MS methods. 15 N NMR spectroscopy gives a detailed insight into the bonding of C5-BPP with lanthanides and Am(iii) as a representative for trivalent actinide cations, revealing significant differences in 15 N chemical shift for coordinating nitrogen atoms compared to Ln(iii) complexes. The temperature dependence of NMR chemical shifts observed for the Am(iii) complex indicates a weak paramagnetism. This as well as the observed large chemical shift for coordinating nitrogen atoms show that metal-ligand bonding in Am(C5-BPP) 3 has a larger share of covalence than in lanthanide complexes, confirming earlier studies. The Am(C5-BPP) 3 NMR sample is furthermore spiked with Cm(iii) and characterized by time-resolved laser fluorescence spectroscopy (TRLFS), yielding important information on the speciation of trace amounts of minor complex species.

Hearing loss and potential hazards of metallic middle-ear implants in NMR-magnetic fields

International Nuclear Information System (INIS)

Huettenbrink, K.B.

1987-01-01

Concurrent with the expanding clinical applications of nuclear magnetic resonance (NMR) imaging, patients with metallic middle-ear implants will certainly be exposed to this strong magnetic field in the future. To determine potential hazards, associated with movements of steel- or Platinium stapes-prostheses, several tests were performed in a 0.5 tesla NMR unit and the induced forces were calculated. Although the commonly used paramagnetic steel-wire or platinium-alloys will not dislodge in vivo, ferromagnetic prostheses may present a hazardous risk. Prior to exposure to the magnetic field, information about the implanted material should therefore be obtained. A side-effect of the induced current flow is the attenuation of the sound-vibrations of the stapes prosthesis. This, 5-10 dB impairment of transmission develops only at a certain position of the patient's head, when the prosthesis vibrates perpendicularly to the magnetic field's Z-axis. Patients with a metallic prosthesis should be informed about this purely physical, harmless phenomenon prior to entering the NMR-cylinder. (orig.) [de

13C NMR investigation of the structure of cationic carbonyls in transition metal zeolites

International Nuclear Information System (INIS)

Ben Taarit, Y.

1979-01-01

13 C NMR spectroscopy was used to investigate the nature of carbon monoxide adsorbed on transition metal ions hosted in a synthetic faujastite type zeolite. The adsorbed CO species was characterised by a highly shielded carbon nucleus. Using the Pople approximation for the paramagnetic shielding term, the observed chemical shift was rationalised assuming the formation of a cationic carbonyl species with an appreciable electronic transfer from the carbon lone pair to the transition metal ion and negligible π back-bonding if at all. (Auth.)

Citrus Quality Control: An NMR/MRI Problem-Based Experiment

Science.gov (United States)

Erhart, Sarah E.; McCarrick, Robert M.; Lorigan, Gary A.; Yezierski, Ellen J.

2016-01-01

An experiment seated in an industrial context can provide an engaging framework and unique learning opportunity for an upper-division physical chemistry laboratory. An experiment that teaches NMR/MRI through a problem-based quality control of citrus products was developed. In this experiment, using a problem-based learning (PBL) approach, students…

Consistency maintenance for constraint in role-based access control model

Institute of Scientific and Technical Information of China (English)

韩伟力; 陈刚; 尹建伟; 董金祥

2002-01-01

Constraint is an important aspect of role-based access control and is sometimes argued to be the principal motivation for role-based access control (RBAC). But so far few authors have discussed consistency maintenance for constraint in RBAC model. Based on researches of constraints among roles and types of inconsistency among constraints, this paper introduces corresponding formal rules, rule-based reasoning and corresponding methods to detect, avoid and resolve these inconsistencies. Finally, the paper introduces briefly the application of consistency maintenance in ZD-PDM, an enterprise-oriented product data management (PDM) system.

Paramagnetism and magnetic relaxation in melt-textured grown GdBa2Cu3O6+y

International Nuclear Information System (INIS)

Qin, M.J.; Fu, X.K.; Ren, H.T.

1996-01-01

Magnetic measurements have been performed on a melt-textured grown (MTG) GdBa 2 Cu 3 O 6+y sample. Because of the paramagnetism of the Gd 3+ ions, the magnetization relaxation rate is increased by a factor of 4πχ. The effect of paramagnetism on the U(J) relationship of the sample has also been discussed. At the end, we extraxted the U(J) relationship based on the field sweep rate H, which is in agreement with the one after corrections for paramagnetism. (orig.)

Constrained optimization for position calibration of an NMR field camera.

Science.gov (United States)

Chang, Paul; Nassirpour, Sahar; Eschelbach, Martin; Scheffler, Klaus; Henning, Anke

2018-07-01

Knowledge of the positions of field probes in an NMR field camera is necessary for monitoring the B 0 field. The typical method of estimating these positions is by switching the gradients with known strengths and calculating the positions using the phases of the FIDs. We investigated improving the accuracy of estimating the probe positions and analyzed the effect of inaccurate estimations on field monitoring. The field probe positions were estimated by 1) assuming ideal gradient fields, 2) using measured gradient fields (including nonlinearities), and 3) using measured gradient fields with relative position constraints. The fields measured with the NMR field camera were compared to fields acquired using a dual-echo gradient recalled echo B 0 mapping sequence. Comparisons were done for shim fields from second- to fourth-order shim terms. The position estimation was the most accurate when relative position constraints were used in conjunction with measured (nonlinear) gradient fields. The effect of more accurate position estimates was seen when compared to fields measured using a B 0 mapping sequence (up to 10%-15% more accurate for some shim fields). The models acquired from the field camera are sensitive to noise due to the low number of spatial sample points. Position estimation of field probes in an NMR camera can be improved using relative position constraints and nonlinear gradient fields. Magn Reson Med 80:380-390, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Exploring translocation of proteins on DNA by NMR

International Nuclear Information System (INIS)

Marius Clore, G.

2011-01-01

While an extensive body of knowledge has accumulated on the structures of transcription factors, DNA and their complexes from both NMR and crystallography, much less is known at a molecular level regarding the mechanisms whereby transcription factors locate their specific DNA target site within an overwhelming sea of non-specific DNA sites. Indirect kinetic data suggested that three processes are involved in the search procedure: jumping by dissociation of the protein from the DNA followed by re-association at another site, direct transfer from one DNA molecule or segment to another, and one-dimensional sliding. In this brief perspective I summarize recent NMR developments from our laboratory that have permitted direct characterization of the species and molecular mechanisms involved in the target search process, including the detection of highly transient sparsely-populated states. The main tool in these studies involves the application of paramagnetic relaxation enhancement, supplemented by z-exchange spectroscopy, lineshape analysis and residual dipolar couplings. These studies led to the first direct demonstration of rotation-coupled sliding of a protein along the DNA and the direct transfer of a protein from one DNA molecule to another without dissociating into free solution.

Method of T2 spectrum inversion with conjugate gradient algorithm from NMR data

International Nuclear Information System (INIS)

Li Pengju; Shi Shangming; Song Yanjie

2010-01-01

Based on the optimization techniques, the T 2 spectrum inversion method of conjugate gradient that is easy to realize non-negativity constraint of T2 spectrum is proposed. The method transforms the linear mixed-determined problem of T2 spectrum inversion into the typical optimization problem of searching the minimum of objective function by building up the objective function according to the basic idea of geophysics modeling. The optimization problem above is solved with the conjugate gradient algorithm that has quick convergence rate and quadratic termination. The method has been applied to the inversion of noise free echo train generated from artificial spectrum, artificial echo train with signal-to-noise ratio (SNR)=25 and NMR experimental data of drilling core. The comparison between the inversion results of this paper and artificial spectrum or the result of software imported in NMR laboratory shows that the method can correctly invert T 2 spectrum from artificial NMR relaxation data even though SNR=25 and that inversion T 2 spectrum with good continuity and smoothness from core NMR experimental data accords perfectly with that of laboratory software imported, and moreover,the absolute error between the NMR porosity computed from T 2 spectrum and helium (He) porosity in laboratory is 0.65%. (authors)

Petroacoustic Modelling of Heterolithic Sandstone Reservoirs: A Novel Approach to Gassmann Modelling Incorporating Sedimentological Constraints and NMR Porosity data

Science.gov (United States)

Matthews, S.; Lovell, M.; Davies, S. J.; Pritchard, T.; Sirju, C.; Abdelkarim, A.

2012-12-01

Heterolithic or 'shaly' sandstone reservoirs constitute a significant proportion of hydrocarbon resources. Petroacoustic models (a combination of petrophysics and rock physics) enhance the ability to extract reservoir properties from seismic data, providing a connection between seismic and fine-scale rock properties. By incorporating sedimentological observations these models can be better constrained and improved. Petroacoustic modelling is complicated by the unpredictable effects of clay minerals and clay-sized particles on geophysical properties. Such effects are responsible for erroneous results when models developed for "clean" reservoirs - such as Gassmann's equation (Gassmann, 1951) - are applied to heterolithic sandstone reservoirs. Gassmann's equation is arguably the most popular petroacoustic modelling technique in the hydrocarbon industry and is used to model elastic effects of changing reservoir fluid saturations. Successful implementation of Gassmann's equation requires well-constrained drained rock frame properties, which in heterolithic sandstones are heavily influenced by reservoir sedimentology, particularly clay distribution. The prevalent approach to categorising clay distribution is based on the Thomas - Stieber model (Thomas & Stieber, 1975), this approach is inconsistent with current understanding of 'shaly sand' sedimentology and omits properties such as sorting and grain size. The novel approach presented here demonstrates that characterising reservoir sedimentology constitutes an important modelling phase. As well as incorporating sedimentological constraints, this novel approach also aims to improve drained frame moduli estimates through more careful consideration of Gassmann's model assumptions and limitations. A key assumption of Gassmann's equation is a pore space in total communication with movable fluids. This assumption is often violated by conventional applications in heterolithic sandstone reservoirs where effective porosity, which

About kinetics of paramagnetic radiation malformations in beryllium ceramics; O kinetike nakopleniya paramagnitnykh radiatsionnykh defectov v berillievykh keramikakh

Energy Technology Data Exchange (ETDEWEB)

Polyakov, A I; Ryabinkin, Yu A; Zashkvara, O V; Bitenbaev, M I [Fiziko-tekhniucheskij Inst. Ministerstva Nauki i Vysshego Obrazovaniya Respubliki Kazakhstan, Almaty (Kazakhstan); Petukhov, Yu V [Inst. Atomnoj Ehnergii Natsional' nogo Yadernogo Tsentra Respubliki Kazakhstan, Almaty (Kazakhstan)

1999-07-01

This paper [1] specifies that {gamma}-radiation of the beryllium-oxide-based ceramics results in development of paramagnetic radiation malformations emerging the ESR spectrum in form of doublet with the splitting rate of oestrasid {delta}{approx}1.6 and g-factor of 2.008. This report presents evaluation outcomes of dependence of paramagnetic radiation malformations concentration in beryllium ceramics on gamma-radiation dose ({sup 60}Co) within the range of 0-100 Mrad. Total paramagnetic parameters of beryllium ceramics in the range 0-100 Mrad of gamma-radiation dose varied slightly, and were specified by the first type of paramagnetic radiation malformations.

The Src SH2 domain interacts dynamically with the focal adhesion kinase binding site as demonstrated by paramagnetic NMR spectroscopy.

Science.gov (United States)

Lindfors, Hanna E; Drijfhout, Jan Wouter; Ubbink, Marcellus

2012-06-01

The interaction between the tyrosine kinases Src and focal adhesion kinase (FAK) is a key step in signaling processes from focal adhesions. The phosphorylated tyrosine residue 397 in FAK is able to bind the Src SH2 domain. To establish the extent of the FAK binding motif, the binding affinity of the SH2 domain for phosphorylated and unphosphorylated FAK-derived peptides of increasing length was determined and compared with that of the internal Src SH2 binding site. It is shown that the FAK peptides have higher affinity than the internal binding site and that seven negative residues adjacent to the core SH2 binding motif increase the binding constant 30-fold. A rigid spin-label incorporated in the FAK peptides was used to establish on the basis of paramagnetic relaxation enhancement whether the peptide-protein complex is well defined. A large spread of the paramagnetic effects on the surface of the SH2 domain suggests that the peptide-protein complex exhibits dynamics, despite the high affinity of the peptide. The strong electrostatic interaction between the positive side of the SH2 domain and the negative peptide results in a high affinity but may also favor a dynamic interaction. Copyright © 2012 Wiley Periodicals, Inc.

NMR spectroscopy up to 35.2T using a series-connected hybrid magnet.

Science.gov (United States)

Gan, Zhehong; Hung, Ivan; Wang, Xiaoling; Paulino, Joana; Wu, Gang; Litvak, Ilya M; Gor'kov, Peter L; Brey, William W; Lendi, Pietro; Schiano, Jeffrey L; Bird, Mark D; Dixon, Iain R; Toth, Jack; Boebinger, Gregory S; Cross, Timothy A

2017-11-01

The National High Magnetic Field Laboratory has brought to field a Series-Connected Hybrid magnet for NMR spectroscopy. As a DC powered magnet it can be operated at fields up to 36.1T. The series connection between a superconducting outsert and a resistive insert dramatically minimizes the high frequency fluctuations of the magnetic field typically observed in purely resistive magnets. Current-density-grading among various resistive coils was used for improved field homogeneity. The 48mm magnet bore and 42mm outer diameter of the probes leaves limited space for conventional shims and consequently a combination of resistive and ferromagnetic shims are used. Field maps corrected for field instabilities were obtained and shimming achieved better than 1ppm homogeneity over a cylindrical volume of 1cm diameter and height. The magnetic field is regulated within 0.2ppm using an external 7 Li lock sample doped with paramagnetic MnCl 2 . The improved field homogeneity and field regulation using a modified AVANCE NEO console enables NMR spectroscopy at 1 H frequencies of 1.0, 1.2 and 1.5GHz. NMR at 1.5GHz reflects a 50% increase in field strength above the highest superconducting magnets currently available. Three NMR probes have been constructed each equipped with an external lock rf coil for field regulation. Initial NMR results obtained from the SCH magnet using these probes illustrate the very exciting potential of ultra-high magnetic fields. Copyright © 2017 Elsevier Inc. All rights reserved.

Dual excitation acoustic paramagnetic logging tool

Energy Technology Data Exchange (ETDEWEB)

Vail, III, William B. (Bothell, WA)

1989-01-01

New methods and apparatus are disclosed which allow measurement of the presence of oil and water in gelogical formations using a new physical effect called the Acoustic Paramagnetic Logging Effect (APLE). The presence of petroleum in formation causes a slight increase in the earth's magnetic field in the vicinity of the reservoir. This is the phenomena of paramagnetism. Application of an acoustic source to a geological formation at the Larmor frequency of the nucleous present causes the paramagnetism of the formation to disappear. This results in a decrease in the earth's magnetic field in the vicinity of the oil bearing formation. Repetitively frequency sweeping the acoustic source through the Larmor frequency of the nucleons present (approx. 2 kHz) causes an amplitude modulation of the earth's magnetic field which is a consequence of the APLE. The amplitude modulation of the earth's magnetic field is measured with an induction coil gradiometer and provides a direct measure of the amount of oil and water in the excitation zone of the formation. The phase of the signal is used to infer the longitudinal relaxation times of the fluids present, which results in the ability in general to separate oil and water and to measure the viscosity of the oil present. Such measurements may be preformed in open boreholes and in cased well bores. The Dual Excitation Acoustic Paramagnetic Logging Tool employing two acoustic sources is also described.

NMR parallel Q-meter with double-balanced-mixer detection for polarized target experiments

International Nuclear Information System (INIS)

Boissevain, J.; Tippens, W.B.

1983-01-01

A constant-voltage, parallel-tuned nuclear magnetic resonance (NMR) circuit, patterned after a Liverpool design, has been developed for polarized target experiments. Measuring the admittance of the resonance circuit allows advantageous use of double-balanced mixer detection. The resonant circuit is tolerant of stray capacitance between the NMR coil and the target cavity, thus easing target-cell-design constraints. The reference leg of the circuit includes a voltage-controlled attenuator and phase shifter for ease of tuning. The NMR output features a flat background and has good linearity and stability

Electron Paramagnetic Resonance Spectroscopy

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 11. Electron Paramagnetic Resonance Spectroscopy: Biological Applications. B G Hegde. General Article Volume 20 Issue 11 November 2015 pp 1017-1032. Fulltext. Click here to view fulltext PDF. Permanent link:

Consistency maintenance for constraint in role-based access control model

Institute of Scientific and Technical Information of China (English)

韩伟力; 陈刚; 尹建伟; 董金祥

2002-01-01

Constraint is an important aspect of role-based access control and is sometimes argued to be the principal motivation for role-based access control (RBAC). But so far'few authors have discussed consistency maintenance for constraint in RBAC model. Based on researches of constraints among roles and types of inconsistency among constraints, this paper introduces correaponding formal rules, rulebased reasoning and corresponding methods to detect, avoid and resolve these inconsistencies. Finally,the paper introduces briefly the application of consistency maintenance in ZD-PDM, an enterprise-ori-ented product data management (PDM) system.

High field electron paramagnetic resonance spectroscopy under ultrahigh vacuum conditions—A multipurpose machine to study paramagnetic species on well defined single crystal surfaces

Energy Technology Data Exchange (ETDEWEB)

Rocker, J.; Cornu, D.; Kieseritzky, E.; Hänsel-Ziegler, W.; Freund, H.-J. [Fritz-Haber-Institut der MPG, Faradayweg 4-6, 14195 Berlin (Germany); Seiler, A. [Fritz-Haber-Institut der MPG, Faradayweg 4-6, 14195 Berlin (Germany); Laboratorium für Applikationen der Synchrotronstrahlung, KIT Campus Süd, Kaiserstr. 12, 76131 Karlsruhe (Germany); Bondarchuk, O. [Fritz-Haber-Institut der MPG, Faradayweg 4-6, 14195 Berlin (Germany); CIC energiGUNE, Parque Tecnologico, C/Albert Einstein 48, CP 01510 Minano (Alava) (Spain); Risse, T., E-mail: risse@chemie.fu-berlin.de [Fritz-Haber-Institut der MPG, Faradayweg 4-6, 14195 Berlin (Germany); Institut für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin (Germany)

2014-08-01

A new ultrahigh vacuum (UHV) electron paramagnetic resonance (EPR) spectrometer operating at 94 GHz to investigate paramagnetic centers on single crystal surfaces is described. It is particularly designed to study paramagnetic centers on well-defined model catalysts using epitaxial thin oxide films grown on metal single crystals. The EPR setup is based on a commercial Bruker E600 spectrometer, which is adapted to ultrahigh vacuum conditions using a home made Fabry Perot resonator. The key idea of the resonator is to use the planar metal single crystal required to grow the single crystalline oxide films as one of the mirrors of the resonator. EPR spectroscopy is solely sensitive to paramagnetic species, which are typically minority species in such a system. Hence, additional experimental characterization tools are required to allow for a comprehensive investigation of the surface. The apparatus includes a preparation chamber hosting equipment, which is required to prepare supported model catalysts. In addition, surface characterization tools such as low energy electron diffraction (LEED)/Auger spectroscopy, temperature programmed desorption (TPD), and infrared reflection absorption spectroscopy (IRAS) are available to characterize the surfaces. A second chamber used to perform EPR spectroscopy at 94 GHz has a room temperature scanning tunneling microscope attached to it, which allows for real space structural characterization. The heart of the UHV adaptation of the EPR experiment is the sealing of the Fabry-Perot resonator against atmosphere. To this end it is possible to use a thin sapphire window glued to the backside of the coupling orifice of the Fabry Perot resonator. With the help of a variety of stabilization measures reducing vibrations as well as thermal drift it is possible to accumulate data for a time span, which is for low temperature measurements only limited by the amount of liquid helium. Test measurements show that the system can detect paramagnetic

Electron Paramagnetic Resonance Imaging

Indian Academy of Sciences (India)

Twentieth century bore witness to remarkable scientists whohave advanced our understanding of the brain. Among them,EPR (Electron Paramagnetic Resonance) imaging is particularlyuseful in monitoring hypoxic zones in tumors which arehighly resistant to radiation and chemotherapeutic treatment.This first part of the ...

Enhanced 29Si spin-lattice relaxation and observation of three-dimensional lattice connectivity in zeolites by two-dimensional 29Si MASS NMR

International Nuclear Information System (INIS)

Sivadinarayana, C.; Choudhary, V.R.; Ganapathy, S.

1994-01-01

It is shown that considerable sensitivity enhancement is achieved in the 29 Si magic angle sample spinning (MASS) NMR spectra of highly siliceous zeolites by pre treating the material with oxygen. The presence of adsorbed molecular oxygen in zeolite channels promotes an efficient 29 Si spin-lattice relaxation via a paramagnetic interaction between the lattice 29 Si T-site and the adsorbed oxygen on zeolite channels. This affords an efficient 2-D data collection and leads to increased sensitivity. The utility of this method is demonstrated in a two-dimensional COSY-45 NMR experiment of a high silica zeolite ZSM-5. (author). 20 refs., 3 figs., 1 tab

Paramagnetic centers in nanocrystalline TiC/C system

International Nuclear Information System (INIS)

Guskos, N.; Bodziony, T.; Maryniak, M.; Typek, J.; Biedunkiewicz, A.

2008-01-01

Electron paramagnetic resonance is applied to study the defect centers in nanocrystalline titanium carbide dispersed in carbon matrix (TiC x /C) synthesized by the non-hydrolytic sol-gel process. The presence of Ti 3+ paramagnetic centers is identified below 120 K along with a minor contribution from localized defect spins coupled with the conduction electron system in the carbon matrix. The temperature dependence of the resonance intensity of the latter signal indicates weak antiferromagnetic interactions. The presence of paramagnetic centers connected with trivalent titanium is suggested to be the result of chemical disorder, which can be further related to the observed anomalous behavior of conductivity, hardness, and corrosion resistance of nanocrystalline TiC x /C

Paramagnetic resonance and electronic conduction in organic semiconductors

International Nuclear Information System (INIS)

Nechtschein, M.

1963-01-01

As some organic bodies simultaneously display semi-conducting properties and a paramagnetism, this report addresses the study of conduction in organic bodies. The author first briefly recalls how relationships between conductibility and Electron Paramagnetic Resonance (EPR) can be noticed in a specific case (mineral and metallic semiconductors). He discusses published results related to paramagnetism and conductibility in organic bodies. He reviews various categories of organic bodies in which both properties are simultaneously present. He notably addresses radical molecular crystals, non-radical molecular crystals, charge transfer complexes, pyrolyzed coals, and pseudo-ferromagnetic organic structures. He discusses the issue of relationships between conduction (charge transfer by electrons) and ERP (which reveals the existence of non-paired electrons which provide free spins)

Sensitivity and Resolution Enhanced Solid-State NMR for Paramagnetic Systems and Biomolecules under Very Fast Magic Angle Spinning

KAUST Repository

Parthasarathy, Sudhakar; Nishiyama, Yusuke; Ishii, Yoshitaka

2013-01-01

Recent research in fast magic angle spinning (MAS) methods has drastically improved the resolution and sensitivity of NMR spectroscopy of biomolecules and materials in solids. In this Account, we summarize recent and ongoing developments

NMR and TRLFS studies of Ln(iii) and An(iii) C5-BPP complexes† †Electronic supplementary information (ESI) available: LIFDI-MS spectra and additional NMR spectra. See DOI: 10.1039/c4sc03103b

Science.gov (United States)

Beele, Björn B.; Geist, Andreas; Müllich, Udo; Kaden, Peter; Panak, Petra J.

2015-01-01

C5-BPP is a highly efficient N-donor ligand for the separation of trivalent actinides, An(iii), from trivalent lanthanides, Ln(iii). The molecular origin of the selectivity of C5-BPP and many other N-donor ligands of the BTP-type is still not entirely understood. We present here the first NMR studies on C5-BPP Ln(iii) and An(iii) complexes. C5-BPP is synthesized with 10% 15N labeling and characterized by NMR and LIFDI-MS methods. 15N NMR spectroscopy gives a detailed insight into the bonding of C5-BPP with lanthanides and Am(iii) as a representative for trivalent actinide cations, revealing significant differences in 15N chemical shift for coordinating nitrogen atoms compared to Ln(iii) complexes. The temperature dependence of NMR chemical shifts observed for the Am(iii) complex indicates a weak paramagnetism. This as well as the observed large chemical shift for coordinating nitrogen atoms show that metal–ligand bonding in Am(C5-BPP)3 has a larger share of covalence than in lanthanide complexes, confirming earlier studies. The Am(C5-BPP)3 NMR sample is furthermore spiked with Cm(iii) and characterized by time-resolved laser fluorescence spectroscopy (TRLFS), yielding important information on the speciation of trace amounts of minor complex species. PMID:29560242

Paramagnetism: an alternative view. Pt. 1

International Nuclear Information System (INIS)

Oudet, X.

1991-01-01

A new calculation of the paramagnetic susceptibility χ is proposed on the basis of the statistical distribution of the thermal energy using the mean value U of this energy as statistical variable. This allows us to replace the molecular field by an equivalent energy barrier that the paramagnetic moment of an atom has to cross to contribute to χ. The variation of χ with U, or T as well, shows a maximum when there is no magnetic order. The asymptotic character of the Curie-Weiss law appears in close connection with that of the Dulong and Petit law. (orig.)

Export constraints facing Lesotho-based manufacturing enterprises

Directory of Open Access Journals (Sweden)

Motšelisi C. Mokhethi

2015-07-01

Full Text Available Orientation: Exporting is preferred by many enterprises as the mode of foreign entry as it requires less commitment of organisational resources and offers flexibility of managerial actions. However, enterprises face a number of challenges when attempting to initiate exports or expand their export operations. Research purpose: This study was undertaken to determine the characteristics and composition of export barriers constraining exporting by Lesotho-based manufacturing enterprises. Motivation for the study: Lesotho is faced with low destination diversity and low diversity in export products. Research design, approach and method: Data was collected from 162 Lesotho-based manufacturing enterprises through a self-administered questionnaire. Main findings: In its findings, the study firstly identified international constraints, distribution constraints and financial constraints as factors constraining exporting. Secondly, it was determined that three exporting constraints, all internal to the enterprise and all related to one factor (namely financial constraint hampered exporting. Lastly, the ANOVA results revealed that the perceptions of export constraints differed according to the enterprise characteristics, enterprise size, ownership and type of industry. Contribution/value-add: With the majority of enterprises in this study being identified as micro-enterprises, the government of Lesotho needs to pay particular attention to addressing the export needs of these enterprises in order to enable them to participate in exporting activities − especially considering that they can play a pivotal role in the alleviation of poverty, job creation and economic rejuvenation.

A QM/MM refinement of an experimental DNA structure with metal-mediated base pairs.

Science.gov (United States)

Kumbhar, Sadhana; Johannsen, Silke; Sigel, Roland K O; Waller, Mark P; Müller, Jens

2013-10-01

A series of hybrid quantum mechanical/molecular mechanical (QM/MM) calculations was performed on models of a DNA duplex with artificial silver(I)-mediated imidazole base pairs. The optimized structures were compared to the original experimental NMR structure (Nat. Chem. 2 (2010) 229-234). The metal⋯metal distances are significantly shorter (~0.5Å) in the QM/MM model than in the original NMR structure. As a result, argentophilic interactions are feasible between the silver(I) ions of neighboring metal-mediated base pairs. Using the computationally determined metal⋯metal distances, a re-refined NMR solution structure of the DNA duplex was obtained. In this new NMR structure, all experimental constraints remain fulfilled. The new NMR structure shows less deviation from the regular B-type conformation than the original one. This investigation shows that the application of QM/MM models to generate additional constraints to be used during NMR structural refinements represents an elegant approach to obtaining high-resolution NMR structures. Copyright © 2013 Elsevier Inc. All rights reserved.

Broad line and pulsed NMR study of molecular motion in furfuryl alcohol resins

International Nuclear Information System (INIS)

Glowinkowski, S.; Pajak, Z.

1978-01-01

Broad line and pulsed nuclear magnetic resonance studies are carried out on a number of furfuryl alcohol resins differentiated by viscosity. Proton NMR spectra and relaxation times T 1 and Tsub(1rho) are measured over a wide temperature range and the results are interpreted in terms of molecular motion. The marked decrease in second moment and existence of high temperature spin-lattice relaxation times minima are presumed to result from rotational motion of polymer chains. The relaxation processes at low temperature are believed to be due to rotational motion of methyl endgroup and paramagnetic centres. (author)

Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR

NARCIS (Netherlands)

Van Der Schot, Gijs; Bonvin, Alexandre M J J

We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on

A direct simulation method for flows with suspended paramagnetic particles

NARCIS (Netherlands)

Kang, T.G.; Hulsen, M.A.; Toonder, den J.M.J.; Anderson, P.D.; Meijer, H.E.H.

2008-01-01

A direct numerical simulation method based on the Maxwell stress tensor and a fictitious domain method has been developed to solve flows with suspended paramagnetic particles. The numerical scheme enables us to take into account both hydrodynamic and magnetic interactions between particles in a

Paramagnetic moments in YBa{sub 2}Cu{sub 3}O{sub 7−δ} nanocomposite films

Energy Technology Data Exchange (ETDEWEB)

Dias, F.T.; Vieira, V.N.; Silva, D.L. [Instituto de Física e Matemática, Universidade Federal de Pelotas, C.P. 354, 96010-900 Pelotas, RS (Brazil); Albino Aguiar, J. [Departamento de Física, Universidade Federal de Pernambuco, 50670-901 Recife, PE (Brazil); Programa de Pós-Graduação em Ciência de Materiais, Universidade Federal de Pernambuco, 50670-901 Recife, PE (Brazil); Valadão, D.R.B., E-mail: danielavaladao.ufpe@gmail.com [Programa de Pós-Graduação em Ciência de Materiais, Universidade Federal de Pernambuco, 50670-901 Recife, PE (Brazil); Obradors, X.; Puig, T. [Institut de Ciència de Materials de Barcelona, ICMAB-CSIC, Campus U.A. Barcelona, 08193 Bellaterra (Spain); Wolff-Fabris, F.; Kampert, E. [Dresden High Magnetic Field Laboratory, HZ Dresden-Rossendorf , 01314 Dresden (Germany)

2014-08-15

Highlights: • The paramagnetic Meissner effect was observed in a nanocomposite YBaCuO thin film. • The paramagnetic moments in FC experiments were observed up to 10 T. • The paramagnetic Meissner effect increases when the magnetic field is increased. • Results may be explained based on the flux compression scenario and vortex pinning. • An apparent saturation tendency of the paramagnetic moments could be observed. - Abstract: We report on magnetization studies in YBa{sub 2}Cu{sub 3}O{sub 7−δ} thin films with dispersed Ba{sub 2}YTaO{sub 6} nanoparticles. The magnetization measurements were made using a superconducting quantum interference device (SQUID) and a vibrating sample magnetometer (VSM). Magnetic moments were measured as functions temperature using zero-field cooling (ZFC) and field-cooled (FC) prescriptions for magnetic fields up to 10 T applied parallel and perpendicular to the ab planes. A paramagnetic response related to the superconducting state was observed during the FC experiments. This effect, known as paramagnetic Meissner effect (PME), apparently increases when the magnetic field is increased. We discuss our PME results in terms of the strong pinning scenario modulated by Ba{sub 2}YTaO{sub 6} nanoparticles dispersed into the superconducting matrix.

Electromagnetic activity of a pulsating paramagnetic neutron star

International Nuclear Information System (INIS)

Bastrukov, S.I.; Podgainy, D.V.; Yang, J.; Weber, F.

2002-01-01

The fact that neutron star matter possesses the capability of maintaining a highly intense magnetic field has been and still is among the most debatable issues in pulsar astrophysics. Over the years, there were several independent suggestions that the dominant source of pulsar magnetism is either the field-induced or the spontaneous magnetic polarization of the baryon material. The Pauli paramagnetism of degenerate neutron matter is one of the plausible and comprehensive mechanisms of the magnetic ordering of neutron magnetic moments, promoted by a seed magnetic field inherited by the neutron star from a massive progenitor and amplified by its implosive contraction due to the magnetic flux conservation. Adhering to this attitude and based on the equations of magnetoelastic dynamics underlying continuum mechanics of single-axis magnetic insulators, we investigate electrodynamics of a paramagnetic neutron star undergoing nonradial pulsations. We show that the suggested approach regains a recent finding of Akhiezer et al. that the spin-polarized neutron matter can transmit perturbations by low-frequency transverse magnetoelastic waves. We found that nonradial torsional magnetoelastic pulsations of a paramagnetic neutron star can serve as a powerful generator of a highly intense electric field producing the magnetospheric polarization charge whose acceleration along the open magnetic field lines leads to the synchrotron and curvature radiation. Analytic and numerical estimates for periods of nonradial torsional magnetoelastic modes are presented and are followed by a discussion of their possible manifestation in currently monitored activity of pulsars and magnetars

Condensed Matter NMR under Extreme Conditions: Challenges and Opportunities

Science.gov (United States)

Reyes, Arneil

2006-11-01

Advances in resistive magnet and power supply technology have made available extremely high magnetic fields suitable for condensed matter broadline NMR experiments. This capability expands the available phase space for investigating a wide variety of materials using magnetic resonance; utilizing the strength of the field to expose or induce new physical phenomena resulting in better understanding of the physics. Continuous fields up to 45T in NHMFL Hybrid magnet have brought new challenges in designing NMR instrumentation. Field strengths and sample space limitations put constraints on RF pulse power, tuning range, bandwidth, and temperature control. The inclusion of other capabilities, including high pressure, optics, and sample rotation requires intricate probe design and construction, while extremely low milliKelvin temperatures are desired in order to explore energy scales where thermal fluctuations are suppressed. Optimization of these devices has been of paramount consideration in NHMFL Condensed Matter NMR user program. Science achieved at high fields, the new initiatives to develop resistively-detected NMR in 2D electron gas and similar systems, and the current new generation Series-Connected Hybrid magnets for NMR work will be discussed. The NHMFL is supported by the National Science Foundation and the State of Florida.

New possibilities for using laser polarimetry technology to study electron paramagnetic resonance

Energy Technology Data Exchange (ETDEWEB)

Aleksandrov, E V; Zapasskii, V S

1982-01-01

Optical methods of recording electron paramagnetic resonance which arose in the early 50's as applied to the problem of recording the magnetic resonance of excited atoms is at the present time widely used in studying the electron paramagnetic resonance of the ground and excited states of free atoms and paramagnetic centers in condensed media. At the present time attention is devoted to the additional possibilities of optical methods of electron paramagnetic resonance which are realized using laser sources.

Ischemic stroke progress evaluation by 31P NMR-based metabonomic of human serum

International Nuclear Information System (INIS)

Grandizoli, Caroline W.P.S.; Barison, Andersson; Lange, Marcos C.; Novak, Felipe T. M.; Campos, Francinete R.

2014-01-01

In this work, chemometric analyses over 31 P{ 1H } NMR (nuclear magnetic resonance) spectra of human blood serum permitted to discriminated ischemic stroke patients from health individuals due to changes in the chemical composition of phosphorus-containing compounds. These results indicate that 31 P NMR-based metabonomic allowed insights over the mechanism triggered by ischemic stroke. (author)

An adaptive ES with a ranking based constraint handling strategy

Directory of Open Access Journals (Sweden)

Kusakci Ali Osman

2014-01-01

Full Text Available To solve a constrained optimization problem, equality constraints can be used to eliminate a problem variable. If it is not feasible, the relations imposed implicitly by the constraints can still be exploited. Most conventional constraint handling methods in Evolutionary Algorithms (EAs do not consider the correlations between problem variables imposed by the constraints. This paper relies on the idea that a proper search operator, which captures mentioned implicit correlations, can improve performance of evolutionary constrained optimization algorithms. To realize this, an Evolution Strategy (ES along with a simplified Covariance Matrix Adaptation (CMA based mutation operator is used with a ranking based constraint-handling method. The proposed algorithm is tested on 13 benchmark problems as well as on a real life design problem. The outperformance of the algorithm is significant when compared with conventional ES-based methods.

NMR spectroscopy study of agar-based polymers electrolytes

Energy Technology Data Exchange (ETDEWEB)

Mattos, R.I.; Tambelli, C.E. [Universidade de Sao Paulo (USP), Pirassununga, SP (Brazil). Fac. de Zootecnia e Engenharia de Alimentos; Raphael, E. [Universidade Federal de Sao Joao del-Rey (UFSJ), MG (Brazil). Dept. de Ciencias Naturais; Silva, I.D.A.; Magon, C.J.; Donoso, J.P. [Universidade de Sao Paulo (IFSC/USP), Sao Carlos, SP (Brazil). Inst. de Fisica

2012-07-01

Full text: This communication presents the results of preparation and characterization of transparent films obtained from agar and acetic acid. The films were characterized by electrochemical impedance spectroscopy (EIS) and nuclear magnetic resonance (NMR). The film formed by agar (Sigma Aldrich) was dispersed in water and kept under stirring and heating at 100 deg C. Next, glycerol, formaldehyde and different quantities of acetic acid (25 and 50 wt%) were added to this solution. The obtained solution was placed on a glass plate and left to dry for 48 hours in oven at 50 deg C to obtain the films, which were kept under vacuum before characterization. The ionic conductivity of the films display an Arrhenius behavior with activation energy E{sub a} = 78 (25 wt% of acetic acid) and E{sub a} = 87 kJ/mol (50 wt% of acetic acid). The conductivity values were 3:0 X 10{sup -6} and 1:2 X 10{sup -4} S/cm at room temperature and 4:4 X 10{sup -4} and 1:5 X 10{sup -3}S/cm at 70 deg C, for the 25 and 50 wt% of acetic acid respectively. To investigate the mechanism of protonic conduction in the polymer proton conductor proton NMR measurements were performed in the temperature range 200-370 K. The {sup 1}H-NMR results exhibit the qualitative feature associated with the proton mobility, namely the presence of well defined {sup 1}H spin-lattice relaxation maxima at 300 K. Activation energy of the order of 40 kJ/mol was obtained from the {sup 1}H-NMR line narrowing data. The ionic conductivity of the film combined with their transparency, flexibility, homogeneity and good adhesion to the glasses or metals indicate that agar-based SPEs are promising materials for used on optoelectronic applications. (author)

The roles of constraint-based and dedication-based influences on user's continued online shopping behavior.

Science.gov (United States)

Chang, Su-Chao; Chou, Chi-Min

2012-11-01

The objective of this study was to determine empirically the role of constraint-based and dedication-based influences as drivers of the intention to continue using online shopping websites. Constraint-based influences consist of two variables: trust and perceived switching costs. Dedication-based influences consist of three variables: satisfaction, perceived usefulness, and trust. The current results indicate that both constraint-based and dedication-based influences are important drivers of the intention to continue using online shopping websites. The data also shows that trust has the strongest total effect on online shoppers' intention to continue using online shopping websites. In addition, the results indicate that the antecedents of constraint-based influences, technical bonds (e.g., perceived operational competence and perceived website interactivity) and social bonds (e.g., perceived relationship investment, community building, and intimacy) have indirect positive effects on the intention to continue using online shopping websites. Based on these findings, this research suggests that online shopping websites should build constraint-based and dedication-based influences to enhance user's continued online shopping behaviors simultaneously.

Enforcement of entailment constraints in distributed service-based business processes.

Science.gov (United States)

Hummer, Waldemar; Gaubatz, Patrick; Strembeck, Mark; Zdun, Uwe; Dustdar, Schahram

2013-11-01

A distributed business process is executed in a distributed computing environment. The service-oriented architecture (SOA) paradigm is a popular option for the integration of software services and execution of distributed business processes. Entailment constraints, such as mutual exclusion and binding constraints, are important means to control process execution. Mutually exclusive tasks result from the division of powerful rights and responsibilities to prevent fraud and abuse. In contrast, binding constraints define that a subject who performed one task must also perform the corresponding bound task(s). We aim to provide a model-driven approach for the specification and enforcement of task-based entailment constraints in distributed service-based business processes. Based on a generic metamodel, we define a domain-specific language (DSL) that maps the different modeling-level artifacts to the implementation-level. The DSL integrates elements from role-based access control (RBAC) with the tasks that are performed in a business process. Process definitions are annotated using the DSL, and our software platform uses automated model transformations to produce executable WS-BPEL specifications which enforce the entailment constraints. We evaluate the impact of constraint enforcement on runtime performance for five selected service-based processes from existing literature. Our evaluation demonstrates that the approach correctly enforces task-based entailment constraints at runtime. The performance experiments illustrate that the runtime enforcement operates with an overhead that scales well up to the order of several ten thousand logged invocations. Using our DSL annotations, the user-defined process definition remains declarative and clean of security enforcement code. Our approach decouples the concerns of (non-technical) domain experts from technical details of entailment constraint enforcement. The developed framework integrates seamlessly with WS-BPEL and the Web

Dosimetry of ionizing radiations by Electron paramagnetic resonance

International Nuclear Information System (INIS)

Azorin N, J.

2005-01-01

In this work, some historical and theoretical aspects about the Electron Paramagnetic Resonance (EPR), its characteristics, the resonance detection, the paramagnetic species, the radiation effects on inorganic and organic materials, the diagrams of the instrumentation for the EPR detection, the performance of an EPR spectrometer, the coherence among EPR and dosimetry and, practical applications as well as in the food science there are presented. (Author)

Route constraints model based on polychromatic sets

Science.gov (United States)

Yin, Xianjun; Cai, Chao; Wang, Houjun; Li, Dongwu

2018-03-01

With the development of unmanned aerial vehicle (UAV) technology, the fields of its application are constantly expanding. The mission planning of UAV is especially important, and the planning result directly influences whether the UAV can accomplish the task. In order to make the results of mission planning for unmanned aerial vehicle more realistic, it is necessary to consider not only the physical properties of the aircraft, but also the constraints among the various equipment on the UAV. However, constraints among the equipment of UAV are complex, and the equipment has strong diversity and variability, which makes these constraints difficult to be described. In order to solve the above problem, this paper, referring to the polychromatic sets theory used in the advanced manufacturing field to describe complex systems, presents a mission constraint model of UAV based on polychromatic sets.

Probing Interactions of N-Donor Molecules with Open Metal Sites within Paramagnetic Cr-MIL-101: A Solid-State NMR Spectroscopic and Density Functional Theory Study.

Science.gov (United States)

Wittmann, Thomas; Mondal, Arobendo; Tschense, Carsten B L; Wittmann, Johannes J; Klimm, Ottokar; Siegel, Renée; Corzilius, Björn; Weber, Birgit; Kaupp, Martin; Senker, Juergen

2018-02-14

Understanding host-guest interactions is one of the key requirements for adjusting properties in metal-organic frameworks (MOFs). In particular, systems with coordinatively unsaturated Lewis acidic metal sites feature highly selective adsorption processes. This is attributed to strong interactions with Lewis basic guest molecules. Here we show that a combination of 13 C MAS NMR spectroscopy with state-of-the-art density functional theory (DFT) calculations allows one to unravel the interactions of water, 2-aminopyridine, 3-aminopyridine, and diethylamine with the open metal sites in Cr-MIL-101. The 13 C MAS NMR spectra, obtained with ultrafast magic-angle spinning, are well resolved, with resonances distributed over 1000 ppm. They present a clear signature for each guest at the open metal sites. Based on competition experiments this leads to the following binding preference: water open metal sites, the NMR data offer additional information about the guest and framework dynamics. We expect that our strategy has the potential for probing the binding situation of adsorbate mixtures at the open metal sites of MOFs in general and thus accesses the microscopic interaction mechanisms for this important material class, which is essential for deriving structure-property relationships.

Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR.

Science.gov (United States)

van der Schot, Gijs; Bonvin, Alexandre M J J

2015-08-01

We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on unassigned NOE lists (Huang et al. in J Am Chem Soc 127:1665-1674, 2005b, doi: 10.1021/ja047109h). We compare the original submissions using a previous version of the server based on Rosetta version 2.6 with recalculated targets using the new R3FP fragment picker for fragment selection and implementing a new annotation of prediction reliability (van der Schot et al. in J Biomol NMR 57:27-35, 2013, doi: 10.1007/s10858-013-9762-6), both implemented in the CS-Rosetta3 WeNMR server. In this second round of CASD-NMR, the WeNMR CS-Rosetta server has demonstrated a much better performance than in the first round since only converged targets were submitted. Further, recalculation of all CASD-NMR targets using the new version of the server demonstrates that our new annotation of prediction quality is giving reliable results. Predictions annotated as weak are often found to provide useful models, but only for a fraction of the sequence, and should therefore only be used with caution.

The application of NMR-based milk metabolite analysis in milk authenticity identification.

Science.gov (United States)

Li, Qiangqiang; Yu, Zunbo; Zhu, Dan; Meng, Xianghe; Pang, Xiumei; Liu, Yue; Frew, Russell; Chen, He; Chen, Gang

2017-07-01

Milk is an important food component in the human diet and is a target for fraud, including many unsafe practices. For example, the unscrupulous adulteration of soymilk into bovine and goat milk or of bovine milk into goat milk in order to gain profit without declaration is a health risk, as the adulterant source and sanitary history are unknown. A robust and fit-for-purpose technique is required to enforce market surveillance and hence protect consumer health. Nuclear magnetic resonance (NMR) is a powerful technique for characterization of food products based on measuring the profile of metabolites. In this study, 1D NMR in conjunction with multivariate chemometrics as well as 2D NMR was applied to differentiate milk types and to identify milk adulteration. Ten metabolites were found which differed among milk types, hence providing characteristic markers for identifying the milk. These metabolites were used to establish mathematical models for milk type differentiation. The limit of quantification (LOQ) of adulteration was 2% (v/v) for soymilk in bovine milk, 2% (v/v) for soymilk in goat milk and 5% (v/v) for bovine milk in goat milk, with relative standard deviation (RSD) less than 10%, which can meet the needs of daily inspection. The NMR method described here is effective for milk authenticity identification, and the study demonstrates that the NMR-based milk metabolite analysis approach provides a means of detecting adulteration at expected levels and can be used for dairy quality monitoring. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Simulating non-holonomic constraints within the LCP-based simulation framework

DEFF Research Database (Denmark)

Ellekilde, Lars-Peter; Petersen, Henrik Gordon

2006-01-01

be incorporated directly, and derive formalism for how the non-holonomic contact constraints can be modelled as a combination of non-holonomic equality constraints and ordinary contacts constraints. For each of these three we are able to guarantee solvability, when using Lemke's algorithm. A number of examples......In this paper, we will extend the linear complementarity problem-based rigid-body simulation framework with non-holonomic constraints. We consider three different types of such, namely equality, inequality and contact constraints. We show how non-holonomic equality and inequality constraints can...... are included to demonstrate the non-holonomic constraints. Udgivelsesdato: Marts...

HPLC-NMR revisited: Using time-slice HPLC-SPE-NMR with database assisted dereplication

DEFF Research Database (Denmark)

Johansen, Kenneth; Wubshet, Sileshi Gizachew; Nyberg, Nils

2013-01-01

Time based trapping of chromatographically separated compounds on to solid-phase extraction cartridges (SPE) and subsequent elution to NMR-tubes was done to emulate the function of HPLC–NMR for dereplication purposes. Sufficient mass sensitivity was obtained by the use of a state-of-the-art HPLC......–SPE–NMR-system with a cryogenically cooled probe head, designed for 1.7 mm NMR-tubes. The resulting 1H NMR spectra (600 MHz) were evaluated against a database of previously acquired and prepared spectra. The in-house developed matching algorithm, based on partitioning of the spectra and allowing for changes in the chemical shifts......, is described and the code included as Supplementary Information. Two mixtures of natural products was used to test the approach; one extract of Carthamus oxyacantha (wild safflower) containing an array of spiro compounds and one extract of the endophytic fungus Penicillum namyslowski containing griseofulvin...

High-resolution structure of the Shigella type-III secretion needle by solid-state NMR and cryo-electron microscopy

Science.gov (United States)

Demers, Jean-Philippe; Habenstein, Birgit; Loquet, Antoine; Kumar Vasa, Suresh; Giller, Karin; Becker, Stefan; Baker, David; Lange, Adam; Sgourakis, Nikolaos G.

2014-09-01

We introduce a general hybrid approach for determining the structures of supramolecular assemblies. Cryo-electron microscopy (cryo-EM) data define the overall envelope of the assembly and rigid-body orientation of the subunits while solid-state nuclear magnetic resonance (ssNMR) chemical shifts and distance constraints define the local secondary structure, protein fold and inter-subunit interactions. Finally, Rosetta structure calculations provide a general framework to integrate the different sources of structural information. Combining a 7.7-Å cryo-EM density map and 996 ssNMR distance constraints, the structure of the type-III secretion system needle of Shigella flexneri is determined to a precision of 0.4 Å. The calculated structures are cross-validated using an independent data set of 691 ssNMR constraints and scanning transmission electron microscopy measurements. The hybrid model resolves the conformation of the non-conserved N terminus, which occupies a protrusion in the cryo-EM density, and reveals conserved pore residues forming a continuous pattern of electrostatic interactions, thereby suggesting a mechanism for effector protein translocation.

Cys-Ph-TAHA: a lanthanide binding tag for RDC and PCS enhanced protein NMR

International Nuclear Information System (INIS)

Peters, Fabian; Maestre-Martinez, Mitcheell; Leonov, Andrei; Kovačič, Lidija; Becker, Stefan; Boelens, Rolf; Griesinger, Christian

2011-01-01

Here we present Cys-Ph-TAHA, a new nonadentate lanthanide tag for the paramagnetic labelling of proteins. The tag can be easily synthesized and is stereochemically homogenous over a wide range of temperatures, yielding NMR spectra with a single set of peaks. Bound to ubiquitin, it induced large residual dipolar couplings and pseudocontact shifts that could be measured easily and agreed very well with the protein structure. We show that Cys-Ph-TAHA can be used to label large proteins that are biochemically challenging such as the Lac repressor in a 90 kDa ternary complex with DNA and inducer.

Morpholino spin-labeling for base-pair sequencing of a 3'-terminal RNA stem by proton homonuclear Overhauser enhancements: yeast ribosomal 5S RNA

International Nuclear Information System (INIS)

Lee, K.M.; Marshall, A.G.

1987-01-01

Base-pair sequences for 5S and 5.8S RNAs are not readily extracted from proton homonuclear nuclear Overhauser enhancement (NOE) connectivity experiments alone, due to extensive peak overlap in the downfield (11-15 ppm) proton NMR spectrum. In this paper, we introduce a new method for base-pair proton peak assignment for ribosomal RNAs, based upon the distance-dependent broadening of the resonances of base-pair protons spatially proximal to a paramagnetic group. Introduction of a nitroxide spin-label covalently attached to the 3'-terminal ribose provides an unequivocal starting point for base-pair hydrogen-bond proton NMR assignment. Subsequent NOE connectivities then establish the base-pair sequence for the terminal stem of a 5S RNA. Periodate oxidation of yeast 5S RNA, followed by reaction with 4-amino-2,2,6,6-tetramethylpiperidinyl-1-oxy (TEMPO-NH2) and sodium borohydride reduction, produces yeast 5S RNA specifically labeled with a paramagnetic nitroxide group at the 3'-terminal ribose. Comparison of the 500-MHz 1H NMR spectra of native and 3'-terminal spin-labeled yeast 5S RNA serves to identify the terminal base pair (G1 . C120) and its adjacent base pair (G2 . U119) on the basis of their proximity to the 3'-terminal spin-label. From that starting point, we have then identified (G . C, A . U, or G . U) and sequenced eight of the nine base pairs in the terminal helix via primary and secondary NOE's

Investigating energy-based pool structure selection in the structure ensemble modeling with experimental distance constraints: The example from a multidomain protein Pub1.

Science.gov (United States)

Zhu, Guanhua; Liu, Wei; Bao, Chenglong; Tong, Dudu; Ji, Hui; Shen, Zuowei; Yang, Daiwen; Lu, Lanyuan

2018-05-01

The structural variations of multidomain proteins with flexible parts mediate many biological processes, and a structure ensemble can be determined by selecting a weighted combination of representative structures from a simulated structure pool, producing the best fit to experimental constraints such as interatomic distance. In this study, a hybrid structure-based and physics-based atomistic force field with an efficient sampling strategy is adopted to simulate a model di-domain protein against experimental paramagnetic relaxation enhancement (PRE) data that correspond to distance constraints. The molecular dynamics simulations produce a wide range of conformations depicted on a protein energy landscape. Subsequently, a conformational ensemble recovered with low-energy structures and the minimum-size restraint is identified in good agreement with experimental PRE rates, and the result is also supported by chemical shift perturbations and small-angle X-ray scattering data. It is illustrated that the regularizations of energy and ensemble-size prevent an arbitrary interpretation of protein conformations. Moreover, energy is found to serve as a critical control to refine the structure pool and prevent data overfitting, because the absence of energy regularization exposes ensemble construction to the noise from high-energy structures and causes a more ambiguous representation of protein conformations. Finally, we perform structure-ensemble optimizations with a topology-based structure pool, to enhance the understanding on the ensemble results from different sources of pool candidates. © 2018 Wiley Periodicals, Inc.

NMR screening in fragment-based drug design: a practical guide.

Science.gov (United States)

Kim, Hai-Young; Wyss, Daniel F

2015-01-01

Fragment-based drug design (FBDD) comprises both fragment-based screening (FBS) to find hits and elaboration of these hits to lead compounds. Typical fragment hits have lower molecular weight (FBDD since it identifies and localizes the binding site of weakly interacting hits on the target protein. Here we describe ligand-based NMR methods for hit identification from fragment libraries and for functional cross-validation of primary hits.

Tannin fingerprinting in vegetable tanned leather by solid state NMR spectroscopy and comparison with leathers tanned by other processes.

Science.gov (United States)

Romer, Frederik H; Underwood, Andrew P; Senekal, Nadine D; Bonnet, Susan L; Duer, Melinda J; Reid, David G; van der Westhuizen, Jan H

2011-01-28

Solid state ¹³C-NMR spectra of pure tannin powders from four different sources--mimosa, quebracho, chestnut and tara--are readily distinguishable from each other, both in pure commercial powder form, and in leather which they have been used to tan. Groups of signals indicative of the source, and type (condensed vs. hydrolyzable) of tannin used in the manufacture are well resolved in the spectra of the finished leathers. These fingerprints are compared with those arising from leathers tanned with other common tanning agents. Paramagnetic chromium (III) tanning causes widespread but selective disappearance of signals from the spectrum of leather collagen, including resonances from acidic aspartyl and glutamyl residues, likely bound to Cr (III) structures. Aluminium (III) and glutaraldehyde tanning both cause considerable leather collagen signal sharpening suggesting some increase in molecular structural ordering. The ²⁷Al-NMR signal from the former material is consistent with an octahedral coordination by oxygen ligands. Solid state NMR thus provides easily recognisable reagent specific spectral fingerprints of the products of vegetable and some other common tanning processes. Because spectra are related to molecular properties, NMR is potentially a powerful tool in leather process enhancement and quality or provenance assurance.

Size-dependent concentration of N0 paramagnetic centres in HPHT nanodiamonds

OpenAIRE

Yavkin, Boris V; Mamin, Georgy V; Gafurov, Marat R.; Orlinskii, Sergei B.

2015-01-01

Size-calibrated commercial nanodiamonds synthesized by high-pressure high-temperature (HPHT) technique were studied by high-frequency W and conventional X band electron paramagnetic resonance (EPR) spectroscopy. The numbers of spins in the studied samples were estimated. The core-shell model of the HPHT nanodiamonds was proposed to explain the observed dependence of the concentration of the N0 paramagnetic centers. Two other observed paramagnetic centers are attributed to the two types of str...

Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR

Energy Technology Data Exchange (ETDEWEB)

Schot, Gijs van der [Uppsala University, Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology (Sweden); Bonvin, Alexandre M. J. J., E-mail: a.m.j.j.bonvin@uu.nl [Utrecht University, Faculty of Science – Chemistry, Bijvoet Center for Biomolecular Research (Netherlands)

2015-08-15

We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on unassigned NOE lists (Huang et al. in J Am Chem Soc 127:1665–1674, 2005b, doi: 10.1021/ja047109h 10.1021/ja047109h ). We compare the original submissions using a previous version of the server based on Rosetta version 2.6 with recalculated targets using the new R3FP fragment picker for fragment selection and implementing a new annotation of prediction reliability (van der Schot et al. in J Biomol NMR 57:27–35, 2013, doi: 10.1007/s10858-013-9762-6 10.1007/s10858-013-9762-6 ), both implemented in the CS-Rosetta3 WeNMR server. In this second round of CASD-NMR, the WeNMR CS-Rosetta server has demonstrated a much better performance than in the first round since only converged targets were submitted. Further, recalculation of all CASD-NMR targets using the new version of the server demonstrates that our new annotation of prediction quality is giving reliable results. Predictions annotated as weak are often found to provide useful models, but only for a fraction of the sequence, and should therefore only be used with caution.

Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR

International Nuclear Information System (INIS)

Schot, Gijs van der; Bonvin, Alexandre M. J. J.

2015-01-01

We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on unassigned NOE lists (Huang et al. in J Am Chem Soc 127:1665–1674, 2005b, doi: 10.1021/ja047109h 10.1021/ja047109h ). We compare the original submissions using a previous version of the server based on Rosetta version 2.6 with recalculated targets using the new R3FP fragment picker for fragment selection and implementing a new annotation of prediction reliability (van der Schot et al. in J Biomol NMR 57:27–35, 2013, doi: 10.1007/s10858-013-9762-6 10.1007/s10858-013-9762-6 ), both implemented in the CS-Rosetta3 WeNMR server. In this second round of CASD-NMR, the WeNMR CS-Rosetta server has demonstrated a much better performance than in the first round since only converged targets were submitted. Further, recalculation of all CASD-NMR targets using the new version of the server demonstrates that our new annotation of prediction quality is giving reliable results. Predictions annotated as weak are often found to provide useful models, but only for a fraction of the sequence, and should therefore only be used with caution

nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.

Science.gov (United States)

Schober, Daniel; Jacob, Daniel; Wilson, Michael; Cruz, Joseph A; Marcu, Ana; Grant, Jason R; Moing, Annick; Deborde, Catherine; de Figueiredo, Luis F; Haug, Kenneth; Rocca-Serra, Philippe; Easton, John; Ebbels, Timothy M D; Hao, Jie; Ludwig, Christian; Günther, Ulrich L; Rosato, Antonio; Klein, Matthias S; Lewis, Ian A; Luchinat, Claudio; Jones, Andrew R; Grauslys, Arturas; Larralde, Martin; Yokochi, Masashi; Kobayashi, Naohiro; Porzel, Andrea; Griffin, Julian L; Viant, Mark R; Wishart, David S; Steinbeck, Christoph; Salek, Reza M; Neumann, Steffen

2018-01-02

NMR is a widely used analytical technique with a growing number of repositories available. As a result, demands for a vendor-agnostic, open data format for long-term archiving of NMR data have emerged with the aim to ease and encourage sharing, comparison, and reuse of NMR data. Here we present nmrML, an open XML-based exchange and storage format for NMR spectral data. The nmrML format is intended to be fully compatible with existing NMR data for chemical, biochemical, and metabolomics experiments. nmrML can capture raw NMR data, spectral data acquisition parameters, and where available spectral metadata, such as chemical structures associated with spectral assignments. The nmrML format is compatible with pure-compound NMR data for reference spectral libraries as well as NMR data from complex biomixtures, i.e., metabolomics experiments. To facilitate format conversions, we provide nmrML converters for Bruker, JEOL and Agilent/Varian vendor formats. In addition, easy-to-use Web-based spectral viewing, processing, and spectral assignment tools that read and write nmrML have been developed. Software libraries and Web services for data validation are available for tool developers and end-users. The nmrML format has already been adopted for capturing and disseminating NMR data for small molecules by several open source data processing tools and metabolomics reference spectral libraries, e.g., serving as storage format for the MetaboLights data repository. The nmrML open access data standard has been endorsed by the Metabolomics Standards Initiative (MSI), and we here encourage user participation and feedback to increase usability and make it a successful standard.

Constraint-based solver for the Military unit path finding problem

CSIR Research Space (South Africa)

Leenen, L

2010-04-01

Full Text Available -based approach because it requires flexibility in modelling. The authors formulate the MUPFP as a constraint satisfaction problem and a constraint-based extension of the search algorithm. The concept demonstrator uses a provided map, for example taken from Google...

HOROPLAN: computer-assisted nurse scheduling using constraint-based programming.

Science.gov (United States)

Darmoni, S J; Fajner, A; Mahé, N; Leforestier, A; Vondracek, M; Stelian, O; Baldenweck, M

1995-01-01

Nurse scheduling is a difficult and time consuming task. The schedule has to determine the day to day shift assignments of each nurse for a specified period of time in a way that satisfies the given requirements as much as possible, taking into account the wishes of nurses as closely as possible. This paper presents a constraint-based, artificial intelligence approach by describing a prototype implementation developed with the Charme language and the first results of its use in the Rouen University Hospital. Horoplan implements a non-cyclical constraint-based scheduling, using some heuristics. Four levels of constraints were defined to give a maximum of flexibility: French level (e.g. number of worked hours in a year), hospital level (e.g. specific day-off), department level (e.g. specific shift) and care unit level (e.g. specific pattern for week-ends). Some constraints must always be verified and can not be overruled and some constraints can be overruled at a certain cost. Rescheduling is possible at any time specially in case of an unscheduled absence.

Utility decay rates of T1-weighted magnetic resonance imaging contrast based on redox-sensitive paramagnetic nitroxyl contrast agents

International Nuclear Information System (INIS)

Matsumoto, Ken-ichiro

2009-01-01

The availability and applicability of the combination of paramagnetic nitroxyl contrast agent and T 1 -weighted gradient echo (GE)-based dynamic magnetic resonance imaging (MRI) measurement for redox imaging are described. The time courses of T 1 -weighted GE MRI signal intensities according to first-order paramagnetic loss of a nitroxyl contrast agent were simulated for several experimental conditions. The apparent decay rate calculated based on decreasing T 1 -weighted MRI contrast (k MRI ) can show an approximate value of the original decay rate (k true ) discretionarily given for simulation with suitable experimental parameters. The difference between k MRI and k true can be sufficiently small under T 1 -weighted spoiled gradient echo (SPGR) scan conditions (repetition time=75 ms, echo time=3 ms, and flip angle=45deg), with a conventional redox-sensitive nitroxyl contrast agent, such as 4-hydroxy-2,2,6,6,-tetramethylpiperidine-N-oxyl (TEMPOL) and/or 3-carbamoyl-2,2,5,5-tetramethylpyrrolidine-N-oxyl (carbamoyl-PROXYL), and with intravenous (i.v.) doses of below 1.5 γmol/g body weight (b.w.) for mice. The results of this simulation suggest that the k MRI of nitroxyl contrast agents can be the primary index of redox status under biological conditions. (author)

A web-based database for EPR centers in semiconductors

International Nuclear Information System (INIS)

Umeda, T.; Hagiwara, S.; Katagiri, M.; Mizuochi, N.; Isoya, J.

2006-01-01

We develop a web-based database system for electron paramagnetic resonance (EPR) centers in semiconductors. This database is available to anyone at http://www.kc.tsukuba.ac.jp/div-media/epr/. It currently has more than 300 records of the spin-Hamiltonian parameters for major known EPR centers. One can upload own new records to the database or can use simulation tools powered by EPR-NMR(C). Here, we describe the features and objectives of this database, and mention some future plans

Model for paramagnetic Fermi systems

International Nuclear Information System (INIS)

Ainsworth, T.L.; Bedell, K.S.; Brown, G.E.; Quader, K.F.

1983-01-01

We develop a mode for paramagnetic Fermi liquids. This model has both direct and induced interactions, the latter including both density-density and current-current response. The direct interactions are chosen to reproduce the Fermi liquid parameters F/sup s/ 0 , F/sup a/ 0 , F/sup s/ 1 and to satify the forward scattering sum rule. The F/sup a/ 1 and F/sup s/,a/sub l/ for l>1 are determined self-consistently by the induced interactions; they are checked aginst experimental determinations. The model is applied in detail to liquid 3 He, using data from spin-echo experiments, sound attenuation, and the velocities of first and zero sound. Consistency with experiments gives definite preferences for values of m. The model is also applied to paramagnetic metals. Arguments are given that this model should provide a basis for calculating effects of magnetic fields

NMR-based metabolomics for identification of α-amylase inhibitors in rowan berries (Sorbus spp.)

DEFF Research Database (Denmark)

Broholm, Sofie L.; Gramsbergen, Simone; Nyberg, Nils

Type 2 diabetes is a metabolic disorder estimated to affect millions of people all over the world.1 One way of reducing diabetes-related complications is to control postprandial glucose.2 Inhibition of the carbohydrate digestive enzyme α-amylase is a therapeutic target for maintaining low blood g...... a 1H-NMR method suitable for NMR-based metabolomics...

A guide to the identification of metabolites in NMR-based metabonomics/metabolomics experiments.

Science.gov (United States)

Dona, Anthony C; Kyriakides, Michael; Scott, Flora; Shephard, Elizabeth A; Varshavi, Dorsa; Veselkov, Kirill; Everett, Jeremy R

2016-01-01

Metabonomics/metabolomics is an important science for the understanding of biological systems and the prediction of their behaviour, through the profiling of metabolites. Two technologies are routinely used in order to analyse metabolite profiles in biological fluids: nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS), the latter typically with hyphenation to a chromatography system such as liquid chromatography (LC), in a configuration known as LC-MS. With both NMR and MS-based detection technologies, the identification of the metabolites in the biological sample remains a significant obstacle and bottleneck. This article provides guidance on methods for metabolite identification in biological fluids using NMR spectroscopy, and is illustrated with examples from recent studies on mice.

A guide to the identification of metabolites in NMR-based metabonomics/metabolomics experiments

Directory of Open Access Journals (Sweden)

Anthony C. Dona

2016-01-01

Full Text Available Metabonomics/metabolomics is an important science for the understanding of biological systems and the prediction of their behaviour, through the profiling of metabolites. Two technologies are routinely used in order to analyse metabolite profiles in biological fluids: nuclear magnetic resonance (NMR spectroscopy and mass spectrometry (MS, the latter typically with hyphenation to a chromatography system such as liquid chromatography (LC, in a configuration known as LC–MS. With both NMR and MS-based detection technologies, the identification of the metabolites in the biological sample remains a significant obstacle and bottleneck. This article provides guidance on methods for metabolite identification in biological fluids using NMR spectroscopy, and is illustrated with examples from recent studies on mice.

Quantification of organic acids in beer by nuclear magnetic resonance (NMR)-based methods

International Nuclear Information System (INIS)

Rodrigues, J.E.A.; Erny, G.L.; Barros, A.S.; Esteves, V.I.; Brandao, T.; Ferreira, A.A.; Cabrita, E.; Gil, A.M.

2010-01-01

The organic acids present in beer provide important information on the product's quality and history, determining organoleptic properties and being useful indicators of fermentation performance. NMR spectroscopy may be used for rapid quantification of organic acids in beer and different NMR-based methodologies are hereby compared for the six main acids found in beer (acetic, citric, lactic, malic, pyruvic and succinic). The use of partial least squares (PLS) regression enables faster quantification, compared to traditional integration methods, and the performance of PLS models built using different reference methods (capillary electrophoresis (CE), both with direct and indirect UV detection, and enzymatic essays) was investigated. The best multivariate models were obtained using CE/indirect detection and enzymatic essays as reference and their response was compared with NMR integration, either using an internal reference or an electrical reference signal (Electronic REference To access In vivo Concentrations, ERETIC). NMR integration results generally agree with those obtained by PLS, with some overestimation for malic and pyruvic acids, probably due to peak overlap and subsequent integral errors, and an apparent relative underestimation for citric acid. Overall, these results make the PLS-NMR method an interesting choice for organic acid quantification in beer.

Quantification of organic acids in beer by nuclear magnetic resonance (NMR)-based methods

Energy Technology Data Exchange (ETDEWEB)

Rodrigues, J.E.A. [CICECO-Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal); Erny, G.L. [CESAM - Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal); Barros, A.S. [QOPNAA-Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal); Esteves, V.I. [CESAM - Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal); Brandao, T.; Ferreira, A.A. [UNICER, Bebidas de Portugal, Leca do Balio, 4466-955 S. Mamede de Infesta (Portugal); Cabrita, E. [Department of Chemistry, New University of Lisbon, 2825-114 Caparica (Portugal); Gil, A.M., E-mail: agil@ua.pt [CICECO-Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal)

2010-08-03

The organic acids present in beer provide important information on the product's quality and history, determining organoleptic properties and being useful indicators of fermentation performance. NMR spectroscopy may be used for rapid quantification of organic acids in beer and different NMR-based methodologies are hereby compared for the six main acids found in beer (acetic, citric, lactic, malic, pyruvic and succinic). The use of partial least squares (PLS) regression enables faster quantification, compared to traditional integration methods, and the performance of PLS models built using different reference methods (capillary electrophoresis (CE), both with direct and indirect UV detection, and enzymatic essays) was investigated. The best multivariate models were obtained using CE/indirect detection and enzymatic essays as reference and their response was compared with NMR integration, either using an internal reference or an electrical reference signal (Electronic REference To access In vivo Concentrations, ERETIC). NMR integration results generally agree with those obtained by PLS, with some overestimation for malic and pyruvic acids, probably due to peak overlap and subsequent integral errors, and an apparent relative underestimation for citric acid. Overall, these results make the PLS-NMR method an interesting choice for organic acid quantification in beer.

Constraints based analysis of extended cybernetic models.

Science.gov (United States)

Mandli, Aravinda R; Venkatesh, Kareenhalli V; Modak, Jayant M

2015-11-01

The cybernetic modeling framework provides an interesting approach to model the regulatory phenomena occurring in microorganisms. In the present work, we adopt a constraints based approach to analyze the nonlinear behavior of the extended equations of the cybernetic model. We first show that the cybernetic model exhibits linear growth behavior under the constraint of no resource allocation for the induction of the key enzyme. We then quantify the maximum achievable specific growth rate of microorganisms on mixtures of substitutable substrates under various kinds of regulation and show its use in gaining an understanding of the regulatory strategies of microorganisms. Finally, we show that Saccharomyces cerevisiae exhibits suboptimal dynamic growth with a long diauxic lag phase when growing on a mixture of glucose and galactose and discuss on its potential to achieve optimal growth with a significantly reduced diauxic lag period. The analysis carried out in the present study illustrates the utility of adopting a constraints based approach to understand the dynamic growth strategies of microorganisms. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Size-dependent concentration of N0 paramagnetic centres in HPHT nanodiamonds

Directory of Open Access Journals (Sweden)

B.V. Yavkin, G.V. Mamin, M.R. Gafurov, S.B. Orlinskii

2015-12-01

Full Text Available Size-calibrated commercial nanodiamonds synthesized by high-pressure high-temperature (HPHT technique were studied by high-frequency W- and conventional X-band electron paramagnetic resonance (EPR spectroscopy. The numbers of spins in the studied samples were estimated. The core-shell model of the HPHT nanodiamonds was proposed to explain the observed dependence of the concentration of the N0 paramagnetic centers. Two other observed paramagnetic centers are attributed to the two types of structures in the nanodiamond shell.

Molecular dynamics computer simulations based on NMR data

International Nuclear Information System (INIS)

Vlieg, J. de.

1989-01-01

In the work described in this thesis atom-atom distance information obtained from two-dimensional cuclear magnetic resonance is combined with molecular dynamics simulaitons. The simulation is used to improve the accuracy of a structure model constructed on the basis of NMR data. During the MD refinement the crude NMR structure is simultaneously optimized with respect to the atomic interaction function and to the set of atom-atom distances or other NMR information. This means that insufficient experimental data is completed with theoretical knowledge and the combination will lead to more reliable structures than would be obtained from one technique alone. (author). 191 refs.; 17 figs.; 12 schemes; 22 tabs

Discriminating binding and positioning of amphiphiles to lipid bilayers by {sup 1}H NMR

Energy Technology Data Exchange (ETDEWEB)

Evanics, F. [Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Rd. North Mississauga, Ont., L5L 1C6 (Canada); Prosser, R.S. [Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Rd. North Mississauga, Ont., L5L 1C6 (Canada)]. E-mail: sprosser@utm.utoronto.ca

2005-04-04

The binding and positioning in lipid bilayers of three well-known drugs--imipramine, nicotine, and caffeine--have been studied using {sup 1}H NMR. The membrane model system consisted of 'fast-tumbling' lipid bicelles, in which a bilayered lipid domain, composed of the unsaturated lipid, 1,2-dimyristelaidoyl-sn-glycero-3-phosphocholine (DMLPC) was surrounded by a rim of deuterated detergent-like lipids, consisting of 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC-d22). Binding and immersion depth information was obtained by three experiments. (1) {sup 1}H chemical shift perturbations, upon transfer of the amphiphiles from water to a bicelle mixture, were used to estimate regions of the amphiphiles that interact with the membrane. (2) Water contact to resolvable protons was measured through a Nuclear Overhauser Effect (NOE) between water and resolvable drug and lipid resonances. In the case of both lipids and membrane bound drugs, positive NOEs with large cross-relaxation rates were measured for most resonances originating from the membrane hydrophilic region, while negative NOEs were observed predominantly to resonances in the hydrophobic region of the membrane. (3) {sup 1}H NMR measurements of oxygen-induced (paramagnetic) spin-lattice relaxation rates, which are known to increase with membrane immersion depth, were used to corroborate conclusions based on chemical shift perturbations and water-ligand NOEs.

NMR approaches in structure-based lead discovery: recent developments and new frontiers for targeting multi-protein complexes.

Science.gov (United States)

Dias, David M; Ciulli, Alessio

2014-01-01

Nuclear magnetic resonance (NMR) spectroscopy is a pivotal method for structure-based and fragment-based lead discovery because it is one of the most robust techniques to provide information on protein structure, dynamics and interaction at an atomic level in solution. Nowadays, in most ligand screening cascades, NMR-based methods are applied to identify and structurally validate small molecule binding. These can be high-throughput and are often used synergistically with other biophysical assays. Here, we describe current state-of-the-art in the portfolio of available NMR-based experiments that are used to aid early-stage lead discovery. We then focus on multi-protein complexes as targets and how NMR spectroscopy allows studying of interactions within the high molecular weight assemblies that make up a vast fraction of the yet untargeted proteome. Finally, we give our perspective on how currently available methods could build an improved strategy for drug discovery against such challenging targets. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

A constraint-based approach to intelligent support of nuclear reactor design

International Nuclear Information System (INIS)

Furuta, Kazuo

1993-01-01

Constraint is a powerful representation to formulate and solve problems in design; a constraint-based approach to intelligent support of nuclear reactor design is proposed. We first discuss the features of the approach, and then present the architecture of a nuclear reactor design support system under development. In this design support system, the knowledge base contains constraints useful to structure the design space as object class definitions, and several types of constraint resolvers are provided as design support subsystems. The adopted method of constraint resolution are explained in detail. The usefulness of the approach is demonstrated using two design problems: Design window search and multiobjective optimization in nuclear reactor design. (orig./HP)

Uniform and selective deuteration in two-dimensional NMR of proteins

International Nuclear Information System (INIS)

LeMaster, D.M.

1990-01-01

This paper reports on the practicality of isotopic labeling, particularly deuteration, that has received considerable impetus from advances in molecular biology, which have allowed ready production of NMR quantities of labeled proteins. Protein expression in Escherichia coli allows use of the considerable metabolic genetics known for the organism in shaping the biosynthetic process to meet the labeling demands of the NMR experiments. In addition to deuteration's common use in spectral assignment problems, it also offers considerable potential for enhancing the quality of the nuclear Overhauser effect (NOE) distance and dihedral angle constraints used for solution structural analysis of proteins. Recent reviews emphasize the sample preparation and spectral benefits of protein deuteration

Determination of the three-dimensional structure for weakly aligned biomolecules by NMR spectroscopy

International Nuclear Information System (INIS)

Shahkhatuni, Astghik A; Shahkhatuni, Aleksan G

2002-01-01

The key achievements and the potential of NMR spectroscopy for weakly aligned biomolecules are considered. Due to weak alignment, it becomes possible to determine a number of NMR parameters dependent on the orientation of biomolecules, which are averaged to zero in usual isotropic media. The addition of new orientational constraints to standard procedures of 3D structure determination markedly increases the achievable accuracy. The possibility of structure determination for biomolecules using only orientation-dependent parameters without invoking other NMR data is discussed. The methods of orientation, experimental techniques, and calculation methods are systematised. The main results obtained and the prospects of using NMR spectroscopy of weakly aligned systems to study different classes of biomolecules and to solve various problems of molecular biology are analysed. Examples of biomolecules whose structures have been determined using orientation-dependent parameters are given. The bibliography includes 508 references.

Use of a paramagnetic substance, colloidal manganese sulfide, as an NMR contrast material in rats

Energy Technology Data Exchange (ETDEWEB)

Chilton, H.M.; Jackels, S.C.; Hinson, W.H.; Ekstrand, K.E.

1984-05-01

To determine whether an insoluble magnetopharmaceutical might be useful in such service, the authors investigated the effect of a colloidal preparation of manganese sulfide (MnSC) upon liver and lung spin-lattice relaxation time (T/sub 1/) in rats following intravenous administration. NMR tissue sample measurements were made at 24 MHz, and showed that after MnSC treatment, liver T/sub 1/ values - and to a lesser extent lung T/sub 1/ values - were depressed below control values. Liver manganese content (as determined by flame atomic absorption spectrophotometry) increased in proportion to the dose of MnSC, and the reciprocal of the liver T/sub 1/ values also increased in proportion to the dose of MnSC.

1H NMR-based metabolomics of time-dependent responses of Eisenia fetida to sub-lethal phenanthrene exposure

International Nuclear Information System (INIS)

Lankadurai, Brian P.; Wolfe, David M.; Simpson, Andre J.; Simpson, Myrna J.

2011-01-01

1 H NMR-based metabolomics was used to examine the response of the earthworm Eisenia fetida after exposure to sub-lethal concentrations of phenanthrene over time. Earthworms were exposed to 0.025 mg/cm 2 of phenanthrene (1/64th of the LC 50 ) via contact tests over four days. Earthworm tissues were extracted using a mixture of chloroform, methanol and water, resulting in polar and non-polar fractions that were analyzed by 1 H NMR after one, two, three and four days. NMR-based metabolomic analyses revealed heightened E. fetida responses with longer phenanthrene exposure times. Amino acids alanine and glutamate, the sugar maltose, the lipids cholesterol and phosphatidylcholine emerged as potential indicators of phenanthrene exposure. The conversion of succinate to fumarate in the Krebs cycle was also interrupted by phenanthrene. Therefore, this study shows that NMR-based metabolomics is a powerful tool for elucidating time-dependent relationships in addition to the mode of toxicity of phenanthrene in earthworm exposure studies. - Highlights: → NMR-based earthworm metabolomic analysis of the mode of action of phenanthrene is presented. → The earthworm species E. fetida were exposed to sub-lethal phenanthrene concentrations. → Both polar and non-polar metabolites of E. fetida tissue extracts were analyzed by 1 H NMR. → Longer phenanthrene exposure times resulted in heightened earthworm responses. → An interruption of the Krebs cycle was also observed due to phenanthrene exposure. - 1 H NMR metabolomics is used to determine the relationship between phenanthrene exposure and the metabolic response of the earthworm E. fetida over time and also to elucidate the phenanthrene mode of toxicity.

Ferro-paramagnetic coupled resonant modes in GdEuCuO4

International Nuclear Information System (INIS)

Fainstein, A.; Tovar, M.

1990-01-01

Two paramagnetic resonances were observed in compound GdEuCuO 4 : one was originated in trivalent gadolinium paramagnetism, while the other is associated to a weak ferromagnetic mode in Cu-O planes. In this work, experimental results are presented that show an anisotropy and a strongly anomalous temperature dependence of Gd 3+ . A theoretical model was introduced which explains the data in terms of coupled ferro-paramagnetic resonant modes originated in spin exchange coupling of Cu and Gd. (Author). 9 refs., 4 figs

Ischemic stroke progress evaluation by {sup 31}P NMR-based metabonomic of human serum

Energy Technology Data Exchange (ETDEWEB)

Grandizoli, Caroline W.P.S.; Barison, Andersson, E-mail: andernmr@ufpr.br [Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil). Departamento de Quimica. Centro de RMN; Lange, Marcos C.; Novak, Felipe T. M. [Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil). Hospital de Clínicas. Divisao de Neurologia; Campos, Francinete R. [Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil). Departmento de Farmacia

2014-07-01

In this work, chemometric analyses over {sup 31}P{"1"H} NMR (nuclear magnetic resonance) spectra of human blood serum permitted to discriminated ischemic stroke patients from health individuals due to changes in the chemical composition of phosphorus-containing compounds. These results indicate that {sup 31}P NMR-based metabonomic allowed insights over the mechanism triggered by ischemic stroke. (author)

Applications of solid-state Nuclear Magnetic Resonance (NMR) in studies of Portland cements-based materials

DEFF Research Database (Denmark)

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

2007-01-01

Solid-state NMR spectroscopy represents an important research tool in the characterization of a range of structural properties for cement-based materials. Different approaches of the technique can be used to obtain information on hydration kinetics, mobile and bound water, porosity, and local...... atomic structures. After a short introduction to these NMR techniques, it is exemplified how magic-angle spinning (MAS) NMR can provide quantitative and structural information about specific phases in anhydrous and hydrated Portland cements with main emphasis on the incorporation of Al3+ ions...

Magnetization and 13C NMR spin-lattice relaxation of nanodiamond powder

Energy Technology Data Exchange (ETDEWEB)

Levin, E.M.; Fang, X.W.; Bud' ko, S.L.; Straszheim, W.E.; McCallum, R.W.; Schmidt-Rohr, K.

2008-02-15

The bulk magnetization at temperatures of 1.8-400 K and in magnetic fields up to 70 kOe, the ambient temperature {sup 13}C NMR spin-lattice relaxation, T{sub 1,c}, and the elemental composition of three nanodiamond powder samples have been studied. The total magnetization of nanodiamond can be explained in terms of contributions from (1) the diamagnetic effect of carbon, (2) the paramagnetic effect of unpaired electrons present in nanodiamond grains, and (3) ferromagnetic-like and (4) superparamagnetic contributions from Fe-containing particles detected in spatially resolved energy-dispersive spectroscopy. Contributions (1) and (2) are intrinsic to nanodiamond, while contributions (3) and (4) arise from impurities naturally present in detonation nanodiamond samples. {sup 13}C NMR T{sub 1,c} relaxation would be unaffected by the presence of the ferromagnetic particles with the bulk magnetization of {approx} 0.01 emu/g at 300 K. Thus, a reduction of T{sub 1,c} by 3 orders of magnitude compared to natural and synthetic microdiamonds confirms the presence of unpaired electrons in the nanodiamond grains. The spin concentration in nanodiamond powder corresponds to {approx}30 unpaired electrons per {approx}4.6 nm diameter nanodiamond grain.

Optimized slice-selective 1H NMR experiments combined with highly accurate quantitative 13C NMR using an internal reference method

Science.gov (United States)

Jézéquel, Tangi; Silvestre, Virginie; Dinis, Katy; Giraudeau, Patrick; Akoka, Serge

2018-04-01

Isotope ratio monitoring by 13C NMR spectrometry (irm-13C NMR) provides the complete 13C intramolecular position-specific composition at natural abundance. It represents a powerful tool to track the (bio)chemical pathway which has led to the synthesis of targeted molecules, since it allows Position-specific Isotope Analysis (PSIA). Due to the very small composition range (which represents the range of variation of the isotopic composition of a given nuclei) of 13C natural abundance values (50‰), irm-13C NMR requires a 1‰ accuracy and thus highly quantitative analysis by 13C NMR. Until now, the conventional strategy to determine the position-specific abundance xi relies on the combination of irm-MS (isotopic ratio monitoring Mass Spectrometry) and 13C quantitative NMR. However this approach presents a serious drawback since it relies on two different techniques and requires to measure separately the signal of all the carbons of the analyzed compound, which is not always possible. To circumvent this constraint, we recently proposed a new methodology to perform 13C isotopic analysis using an internal reference method and relying on NMR only. The method combines a highly quantitative 1H NMR pulse sequence (named DWET) with a 13C isotopic NMR measurement. However, the recently published DWET sequence is unsuited for samples with short T1, which forms a serious limitation for irm-13C NMR experiments where a relaxing agent is added. In this context, we suggest two variants of the DWET called Multi-WET and Profiled-WET, developed and optimized to reach the same accuracy of 1‰ with a better immunity towards T1 variations. Their performance is evaluated on the determination of the 13C isotopic profile of vanillin. Both pulse sequences show a 1‰ accuracy with an increased robustness to pulse miscalibrations compared to the initial DWET method. This constitutes a major advance in the context of irm-13C NMR since it is now possible to perform isotopic analysis with high

Interactive NMR: A Simulation Based Teaching Tool for Fundamentals to Applications with Tangible Analogies

Science.gov (United States)

Griesse-Nascimento, Sarah; Bridger, Joshua; Brown, Keith; Westervelt, Robert

2011-03-01

Interactive computer simulations increase students' understanding of difficult concepts and their ability to explain complex ideas. We created a module of eight interactive programs and accompanying lesson plans for teaching the fundamental concepts of Nuclear Magnetic Resonance (NMR) and Magnetic Resonance Imaging (MRI) that we call interactive NMR (iNMR). We begin with an analogy between nuclear spins and metronomes to start to build intuition about the dynamics of spins in a magnetic field. We continue to explain T1, T2, and pulse sequences with the metronome analogy. The final three programs are used to introduce and explain the Magnetic Resonance Switch, a recent diagnostic technique based on NMR. A modern relevant application is useful to generate interest in the topic and confidence in the students' ability to apply their knowledge. The iNMR module was incorporated into a high school AP physics class. In a preliminary evaluation of implementation, students expressed enthusiasm and demonstrated enhanced understanding of the material relative to the previous year. Funded by NSF PHY-0646094 grant.

Paramagnetic defects in hydrogenated amorphous carbon powders

International Nuclear Information System (INIS)

Keeble, D J; Robb, K M; Smith, G M; Mkami, H El; Rodil, S E; Robertson, J

2003-01-01

Hydrogenated amorphous carbon materials typically contain high concentrations of paramagnetic defects, the density of which can be quantified by electron paramagnetic resonance (EPR). In this work EPR measurements near 9.5, 94, and 189 GHz have been performed on polymeric and diamond-like hydrogenated amorphous carbon (a-C:H) powder samples. A similar single resonance line was observed at all frequencies for the two forms of a-C:H studied. No contributions to the spectrum from centres with resolved anisotropic g-values as reported earlier were detected. An increase in linewidth with microwave frequency was observed. Possible contributions to this frequency dependence are discussed

Correlation-based decimation in constraint satisfaction problems

International Nuclear Information System (INIS)

Higuchi, Saburo; Mezard, Marc

2010-01-01

We study hard constraint satisfaction problems using some decimation algorithms based on mean-field approximations. The message-passing approach is used to estimate, beside the usual one-variable marginals, the pair correlation functions. The identification of strongly correlated pairs allows to use a new decimation procedure, where the relative orientation of a pair of variables is fixed. We apply this novel decimation to locked occupation problems, a class of hard constraint satisfaction problems where the usual belief-propagation guided decimation performs poorly. The pair-decimation approach provides a significant improvement.

Heteronuclear three-dimensional NMR spectroscopy of the inflammatory protein C5a

International Nuclear Information System (INIS)

Zuiderweg, E.R.P.; Fesik, S.W.

1989-01-01

The utility of three-dimensional heteronuclear NMR spectroscopy for the assignment of 1 H and 15 N resonances of the inflammatory protein C5a (MW 8500), uniformly labeled with 15 N, is demonstrated at a protein concentration of 0.7 mM. It is shown that dramatic simplification of the 2D nuclear Overhauser effect spectrum (NOESY) is obtained by editing with respect to the frequency of the 15 N heteronucleus in a third dimension. The improved resolution in the 3D experiment largely facilitates the assignment of protein NMR spectra and allows for the determination of distance constraints from otherwise overlapping NOE cross peaks for purposes of 3D structure determination. The results show that 15 N heteronuclear 3D NMR can facilitate the structure determination of small proteins and promises to be a useful tool for the study of larger systems that cannot be studied by conventional 2D NMR techniques

Heteronuclear three-dimensional NMR spectroscopy of the inflammatory protein C5a

Energy Technology Data Exchange (ETDEWEB)

Zuiderweg, E.R.P.; Fesik, S.W. (Abbott Laboratories, Abbott Park, IL (USA))

1989-03-21

The utility of three-dimensional heteronuclear NMR spectroscopy for the assignment of {sup 1}H and {sup 15}N resonances of the inflammatory protein C5a (MW 8500), uniformly labeled with {sup 15}N, is demonstrated at a protein concentration of 0.7 mM. It is shown that dramatic simplification of the 2D nuclear Overhauser effect spectrum (NOESY) is obtained by editing with respect to the frequency of the {sup 15}N heteronucleus in a third dimension. The improved resolution in the 3D experiment largely facilitates the assignment of protein NMR spectra and allows for the determination of distance constraints from otherwise overlapping NOE cross peaks for purposes of 3D structure determination. The results show that {sup 15}N heteronuclear 3D NMR can facilitate the structure determination of small proteins and promises to be a useful tool for the study of larger systems that cannot be studied by conventional 2D NMR techniques.

Density-Based Clustering with Geographical Background Constraints Using a Semantic Expression Model

Directory of Open Access Journals (Sweden)

Qingyun Du

2016-05-01

Full Text Available A semantics-based method for density-based clustering with constraints imposed by geographical background knowledge is proposed. In this paper, we apply an ontological approach to the DBSCAN (Density-Based Geospatial Clustering of Applications with Noise algorithm in the form of knowledge representation for constraint clustering. When used in the process of clustering geographic information, semantic reasoning based on a defined ontology and its relationships is primarily intended to overcome the lack of knowledge of the relevant geospatial data. Better constraints on the geographical knowledge yield more reasonable clustering results. This article uses an ontology to describe the four types of semantic constraints for geographical backgrounds: “No Constraints”, “Constraints”, “Cannot-Link Constraints”, and “Must-Link Constraints”. This paper also reports the implementation of a prototype clustering program. Based on the proposed approach, DBSCAN can be applied with both obstacle and non-obstacle constraints as a semi-supervised clustering algorithm and the clustering results are displayed on a digital map.

Direct Comparison of 19F qNMR and 1H qNMR by Characterizing Atorvastatin Calcium Content

Directory of Open Access Journals (Sweden)

Yang Liu

2016-01-01

Full Text Available Quantitative nuclear magnetic resonance (qNMR is a powerful tool in measuring drug content because of its high speed, sensitivity, and precision. Most of the reports were based on proton qNMR (1H qNMR and only a few fluorine qNMR (19F qNMR were reported. No research has been conducted to directly compare the advantage and disadvantage between these two methods. In the present study, both 19F and 1H qNMR were performed to characterize the content of atorvastatin calcium with the same internal standard. Linearity, precision, and results from two methods were compared. Results showed that 19F qNMR has similar precision and sensitivity to 1H qNMR. Both methods generate similar results compared to mass balance method. Major advantage from 19F qNMR is that the analyte signal is with less or no interference from impurities. 19F qNMR is an excellent approach to quantify fluorine-containing analytes.

Tannin Fingerprinting in Vegetable Tanned Leather by Solid State NMR Spectroscopy and Comparison with Leathers Tanned by Other Processes

Directory of Open Access Journals (Sweden)

Jan H. van der Westhuizen

2011-01-01

Full Text Available Solid state 13C-NMR spectra of pure tannin powders from four different sources – mimosa, quebracho, chestnut and tara – are readily distinguishable from each other, both in pure commercial powder form, and in leather which they have been used to tan.  Groups of signals indicative of the source, and type (condensed vs. hydrolyzable of tannin used in the manufacture are well resolved in the spectra of the finished leathers.  These fingerprints are compared with those arising from leathers tanned with other common tanning agents.  Paramagnetic chromium (III tanning causes widespread but selective disappearance of signals from the spectrum of leather collagen, including resonances from acidic aspartyl and glutamyl residues, likely bound to Cr (III structures. Aluminium (III and glutaraldehyde tanning both cause considerable leather collagen signal sharpening suggesting some increase in molecular structural ordering. The 27Al-NMR signal from the former material is consistent with an octahedral coordination by oxygen ligands. Solid state NMR thus provides easily recognisable reagent specific spectral fingerprints of the products of vegetable and some other common tanning processes. Because spectra are related to molecular properties, NMR is potentially a powerful tool in leather process enhancement and quality or provenance assurance.

NMR studies of the solution conformation and dynamics of the tyrocidine peptide antibiotics

International Nuclear Information System (INIS)

Zhou, N.

1985-01-01

The tyrocidine B and tyrocidine C 1 H NMR spectra in DMSO-d 6 were assigned by using 2D 1 H- 1 H correlation spectroscopy and 1D double resonance experiments. Based on the proton chemical shifts, 3 J/sub NH-Nα/ coupling constants, the chemical shift temperature dependence, and 1D and 2D 1 H- 1 H NOE values, a backbone conformation consisting of an anti-parallel β-pleated sheet, a type I β-turn and a type II' β-turn was suggested for both tyrocidines B and C. Seven out of ten side chains were determined to exist predominantly in one classical Chi 1 rotamer; while the residues Val 1 and Leu 3 had two Chi 1 rotamers which were significantly populated. Chi 2 angles were determined for residues Phe 4 , Trp 6 , DPhe 7 (D Trp 7 ) and Asn 8 . The natural abundance 13 C spectra of tyrocidine B and tyrocidine C were assigned by using 1 H- 13 C correlation spectroscopy. A study of the effect of soluble paramagnetic nitroxide compounds on tyrocidine A proton T 1 values were performed which confirmed the proposed tyrocidine A conformation. It also proved that these nitroxide compounds are very useful in studying proton solvent exposure, and therefore in delineating hydrogen bonding. A proton NMR study of the opioid peptide dynorphin-(1-13) in aqueous solution was reported which was consistent with a non-ordered molecule in the solution

NMR-based metabolomics in human disease diagnosis: Applications, limitations, and recommendations

KAUST Repository

Emwas, Abdul-Hamid M.

2013-04-03

Metabolomics is a dynamic and emerging research field, similar to proteomics, transcriptomics and genomics in affording global understanding of biological systems. It is particularly useful in functional genomic studies in which metabolism is thought to be perturbed. Metabolomics provides a snapshot of the metabolic dynamics that reflect the response of living systems to both pathophysiological stimuli and/or genetic modification. Because this approach makes possible the examination of interactions between an organism and its diet or environment, it is particularly useful for identifying biomarkers of disease processes that involve the environment. For example, the interaction of a high fat diet with cardiovascular disease can be studied via such a metabolomics approach by modeling the interaction between genes and diet. The high reproducibility of NMR-based techniques gives this method a number of advantages over other analytical techniques in large-scale and long-term metabolomic studies, such as epidemiological studies. This approach has been used to study a wide range of diseases, through the examination of biofluids, including blood plasma/serum, urine, blister fluid, saliva and semen, as well as tissue extracts and intact tissue biopsies. However, complicating the use of NMR spectroscopy in biomarker discovery is the fact that numerous variables can effect metabolic composition including, fasting, stress, drug administration, diet, gender, age, physical activity, life style and the subject\\'s health condition. To minimize the influence of these variations in the datasets, all experimental conditions including sample collection, storage, preparation as well as NMR spectroscopic parameters and data analysis should be optimized carefully and conducted in an identical manner as described by the local standard operating protocol. This review highlights the potential applications of NMR-based metabolomics studies and gives some recommendations to improve sample

Influence of Freezing and Storage Procedure on Human Urine Samples in NMR-Based Metabolomics

OpenAIRE

Rist, Manuela; Muhle-Goll, Claudia; Görling, Benjamin; Bub, Achim; Heissler, Stefan; Watzl, Bernhard; Luy, Burkhard

2013-01-01

It is consensus in the metabolomics community that standardized protocols should be followed for sample handling, storage and analysis, as it is of utmost importance to maintain constant measurement conditions to identify subtle biological differences. The aim of this work, therefore, was to systematically investigate the influence of freezing procedures and storage temperatures and their effect on NMR spectra as a potentially disturbing aspect for NMR-based metabolomics studies. Urine sample...

Cosmological constraints with clustering-based redshifts

Science.gov (United States)

Kovetz, Ely D.; Raccanelli, Alvise; Rahman, Mubdi

2017-07-01

We demonstrate that observations lacking reliable redshift information, such as photometric and radio continuum surveys, can produce robust measurements of cosmological parameters when empowered by clustering-based redshift estimation. This method infers the redshift distribution based on the spatial clustering of sources, using cross-correlation with a reference data set with known redshifts. Applying this method to the existing Sloan Digital Sky Survey (SDSS) photometric galaxies, and projecting to future radio continuum surveys, we show that sources can be efficiently divided into several redshift bins, increasing their ability to constrain cosmological parameters. We forecast constraints on the dark-energy equation of state and on local non-Gaussianity parameters. We explore several pertinent issues, including the trade-off between including more sources and minimizing the overlap between bins, the shot-noise limitations on binning and the predicted performance of the method at high redshifts, and most importantly pay special attention to possible degeneracies with the galaxy bias. Remarkably, we find that once this technique is implemented, constraints on dynamical dark energy from the SDSS imaging catalogue can be competitive with, or better than, those from the spectroscopic BOSS survey and even future planned experiments. Further, constraints on primordial non-Gaussianity from future large-sky radio-continuum surveys can outperform those from the Planck cosmic microwave background experiment and rival those from future spectroscopic galaxy surveys. The application of this method thus holds tremendous promise for cosmology.

NMR spectroscopic studies of membrane-bound biological systems

International Nuclear Information System (INIS)

Hohlweg, W.

2013-01-01

In the course of this thesis, biological NMR spectroscopy was employed in studying membrane-bound peptides and proteins, for which structural information is still comparatively hard to obtain. Initial work focused on various model peptides bound to membrane-mimicking micelles, studying the protonation state of arginine in a membrane environment. Strong evidence for a cation-π complex was found in TM7, a peptide which forms the seventh transmembrane helix of subunit a of the vacuolar-type H+-ATPase (V-ATPase). V-ATPase is a physiologically highly relevant proton pump, which is present in intracellular membranes of all eukaryotic organisms, as well as the plasma membrane of several specialized cells. Loss of functional V-ATPase is associated with human diseases such as osteopetrosis, distal renal tubular acidosis or the spreading of cancer. V-ATPase is considered a potential drug target in the treatment of osteoporosis and cancer, or in the development of novel contraceptives. Results from NMR solution structure determination, NMR titration experiments, paramagnetic relaxation enhancement experiments and tryptophan fluorescence spectroscopy confirm the existence of a buried cation-? complex formed between arginine residue R735, which is essential for proton transport, and neighbouring tryptophan and tyrosine residues. In vivo experiments in the yeast Saccharomyces cerevisiae using selective growth tests and fluorescence microscopy showed that formation of the cation-π complex is essential for V-ATPase function. Deletion of both aromatic residues, as well as only the one tryptophan residue leads to growth defects and inability to maintain vacuolar pH homeostasis. These findings shine new light on the still elusive mechanism of proton transport in V-ATPase, and show that arginine R735 may be directly involved in proton transfer across the membrane. (author) [de

Structure and dynamics of paramagnetic transients by pulsed EPR and NMR detection of nuclear resonance. [Pulse radiolysis of methanol in D/sub 2/O

Energy Technology Data Exchange (ETDEWEB)

Trifunac, A.D.

1981-01-01

Structure and dynamics of transient radicals in pulse radiolysis can be studied by time resolved EPR and NMR techniques. EPR study of kinetics and relaxation is illustrated. The NMR detection of nuclear resonance in transient radicals is a new method which allows the study of hyperfine coupling, population dynamics, radical kinetics, and reaction mechanism. 9 figures.

Stripline-based microfluidic devices for high-resolution NMR spectroscopy

NARCIS (Netherlands)

Bart, J.

2009-01-01

A novel route towards microchip integrated NMR analysis was studied. For NMR analysis of mass-limited samples, research has focussed for decennia on microsolenoidal or planar helical detection coils on microfluidic substrates. Since these approaches suffer from static field distortion resulting in

Decay of paramagnetic centers in polyacetylene

International Nuclear Information System (INIS)

Hola, O.

1994-01-01

The time dependences of the relative concentration of spins in irradiated and unirradiated samples of polyacetylene have been studied. Similar courses of the decay of paramagnetic centers were observed in both types of samples. (author) 6 refs.; 1 fig

{sup 1}H NMR-based metabolomics of time-dependent responses of Eisenia fetida to sub-lethal phenanthrene exposure

Energy Technology Data Exchange (ETDEWEB)

Lankadurai, Brian P.; Wolfe, David M.; Simpson, Andre J. [Department of Chemistry, University of Toronto, 1265 Military Trail, Toronto, Ontario M1C 1A4 Canada (Canada); Simpson, Myrna J., E-mail: myrna.simpson@utoronto.ca [Department of Chemistry, University of Toronto, 1265 Military Trail, Toronto, Ontario M1C 1A4 Canada (Canada)

2011-10-15

{sup 1}H NMR-based metabolomics was used to examine the response of the earthworm Eisenia fetida after exposure to sub-lethal concentrations of phenanthrene over time. Earthworms were exposed to 0.025 mg/cm{sup 2} of phenanthrene (1/64th of the LC{sub 50}) via contact tests over four days. Earthworm tissues were extracted using a mixture of chloroform, methanol and water, resulting in polar and non-polar fractions that were analyzed by {sup 1}H NMR after one, two, three and four days. NMR-based metabolomic analyses revealed heightened E. fetida responses with longer phenanthrene exposure times. Amino acids alanine and glutamate, the sugar maltose, the lipids cholesterol and phosphatidylcholine emerged as potential indicators of phenanthrene exposure. The conversion of succinate to fumarate in the Krebs cycle was also interrupted by phenanthrene. Therefore, this study shows that NMR-based metabolomics is a powerful tool for elucidating time-dependent relationships in addition to the mode of toxicity of phenanthrene in earthworm exposure studies. - Highlights: > NMR-based earthworm metabolomic analysis of the mode of action of phenanthrene is presented. > The earthworm species E. fetida were exposed to sub-lethal phenanthrene concentrations. > Both polar and non-polar metabolites of E. fetida tissue extracts were analyzed by {sup 1}H NMR. > Longer phenanthrene exposure times resulted in heightened earthworm responses. > An interruption of the Krebs cycle was also observed due to phenanthrene exposure. - {sup 1}H NMR metabolomics is used to determine the relationship between phenanthrene exposure and the metabolic response of the earthworm E. fetida over time and also to elucidate the phenanthrene mode of toxicity.

Actinide(IV) and actinide(VI) carbonate speciation studies by PAS and NMR spectroscopies. Yucca Mountain Project: Milestone report 3031-WBS 1.2.3.4.1.3.1

International Nuclear Information System (INIS)

Clark, D.L.; Ekberg, S.A.; Morris, D.E.; Palmer, P.D.; Tait, C.D.

1994-09-01

Pulsed-laser photoacoustic spectroscopy (PAS) and Fourier-transform nuclear magnetic resonance (NMR) spectroscopy were used to study speciation of actinide(IV) and actinide(VI) ions (Np, Pu, Am) in aqueous carbonate solutions vs of pH, carbonate concentration, actinide content, and temperature. PAS focused on Pu(IV) speciation. Stability fields on a pH (8.4 to 12.0) versus total carbonate content (0.003 to 1.0 M) plot for dilute Pu(IV) carbonate species ([Pu] tot = 1 mM) were mapped. Four plutonium species, with absorption peaks at 486, 492, 500, and 512 nm were found. Loss of a single carbonate ligand does not account for the difference in speciation for the 486 and 492 nm absorption peaks, nor can any of the observed species be identified as colloidal Pu(IV). NMR data have been obtained for UO 2 2+ , PuO 2 2+ and AmO 2 2+ . This report focuses on results for PuO 2 2+ . The ligand exchange reaction between free and coordinated carbonate on the PuO 2 (CO 3 ) 3 4- systems has been examined by variable temperature 13 C NMR spectroscopy. In each of the six different PuO 2 (CO 3 ) 3 4- samples, two NMR signals are present, one for the free carbonate ligand and one for the carbonate ligand coordinated to a paramagnetic plutonium metal center. The single 13 C resonance line for coordinated carbonate is consistent with expectations of a monomeric PuO 2 (CO 3 ) 3 4- species in solution. A modified Carr-Purcell-Meiboom-Gill NMR pulse sequence was used for determining of ligand exchange parameters for paramagnetic actinide complexes. Eyring analysis at standard conditions provided activation parameters of ΔH = 38 KJ/M and ΔS = -60 J/K for the plutonyl triscarbonate system, suggesting an associative transition state for the plutonyl(VI) carbonate complex self-exc

Design principles and theory of paramagnetic fluorine-labelled lanthanide complexes as probes for (19)F magnetic resonance: a proof-of-concept study.

Science.gov (United States)

Chalmers, Kirsten H; De Luca, Elena; Hogg, Naomi H M; Kenwright, Alan M; Kuprov, Ilya; Parker, David; Botta, Mauro; Wilson, J Ian; Blamire, Andrew M

2010-01-04

The synthesis and spectroscopic properties of a series of CF(3)-labelled lanthanide(III) complexes (Ln=Gd, Tb, Dy, Ho, Er, Tm) with amide-substituted ligands based on 1,4,7,10-tetraazacyclododecane are described. The theoretical contributions of the (19)F magnetic relaxation processes in these systems are critically assessed and selected volumetric plots are presented. These plots allow an accurate estimation of the increase in the rates of longitudinal and transverse relaxation as a function of the distance between the Ln(III) ion and the fluorine nucleus, the applied magnetic field, and the re-rotational correlation time of the complex, for a given Ln(III) ion. Selected complexes exhibit pH-dependent chemical shift behaviour, and a pK(a) of 7.0 was determined in one example based on the holmium complex of an ortho-cyano DO3A-monoamide ligand, which allowed the pH to be assessed by measuring the difference in chemical shift (varying by over 14 ppm) between two (19)F resonances. Relaxation analyses of variable-temperature and variable-field (19)F, (17)O and (1)H NMR spectroscopy experiments are reported, aided by identification of salient low-energy conformers by using density functional theory. The study of fluorine relaxation rates, over a field range of 4.7 to 16.5 T allowed precise computation of the distance between the Ln(III) ion and the CF(3) reporter group by using global fitting methods. The sensitivity benefits of using such paramagnetic fluorinated probes in (19)F NMR spectroscopic studies are quantified in preliminary spectroscopic and imaging experiments with respect to a diamagnetic yttrium(III) analogue.

Multinuclear NMR characterization of CTAB-hexanol-water, sodium oleate-butanol-water and triton X-100-decanol-water microemulsions

International Nuclear Information System (INIS)

Nagy, J.B.; Bodart-Ravet, I.; Derouane, E.G.; Gourgue, A.; Verfaillie, J.P.

1989-01-01

Multinuclear NMR is a very valuable tool to characterize micellar systems or microemulsions. It allows one to determine c.m.c. values, to study the dissolution of organic molecules, the solvation of cations and anions, the structural changes occurring in a ternary diagram, the mobility of the molecules, etc. This review paper essentially deals with the characterization of cationic (CTAB-hexanol-water), anionic (sodium oleate-butanol-water) and neutral (Triton X-100-decanol-water) reversed micelles. The use of paramagnetic ions [Ni(II), CO(II), Fe(III), etc.] is particularly emphasized to characterize the site of solubilization and their interaction with surfactant and cosurfactant molecules 13 C-NMR). It is concluded, that the metallic ions are basically solvated in the inner water cores and one or more hexanol molecules are included in their first coordination shells in the CTAB-hexanol-water microemulsions. In the Triton X-100-decanol-water microemulsions, both decanol and Triton X-100 molecules enter the first coordination shell of Co(II) ions which are dissolved in both aqeous water cores and the organic medium. 19 F-NMR of a fluorinated probe molecule is particularly useful to study the size of the inner water cores. The method is based on the partition of the molecules between the interface and the organic medium. However, this method has to be applied with great care, and the computed data have to be compared to other physico-chemical results. Both 19 F- and 23 Na-NMR results show a great variation of the behaviour of the sodium oleate-butanol-water system in the so-called bicontinuous region. The Na + ions are oriented independently on a hypothetical inverse micellar droplet. (author). 43 refs.; 18 figs.; 7 tabs

Synergic Investigation Of The Self-Assembly Structure And Mechanism Of Retroviral Capsid Proteins By Solid State NMR, Transmission Electron Microscopy And Multiscale simulation

Science.gov (United States)

2017-03-29

18], a question naturally arises: if our ssNMR constraints actually impart any meaningful differences to the final model. To answer this question...Mitra at University of Auckland. Xin Qiao, Dr. Chen’s student, presented the ssNMR assignment strategy as a poster presentation titled “Methods

Comparative NMR investigation of the Re-based borides

Science.gov (United States)

Lue, C. S.; Tao, Y. F.; Su, T. H.

2008-07-01

We report a systematic study of the rhenium-based borides, ReB2 , Re7B3 , and Re3B , by means of the B11 nuclear magnetic resonance (NMR) spectroscopy. While Re7B3 and Re3B are superconductors, ReB2 exhibits no superconducting signature but is of current interest due to its superhard mechanical property. Since the major focus of this investigation is their electronic characteristics in the normal states, we performed the measurements at temperatures between 77 and 295 K. For Re7B3 and Re3B , s -character electrons were found to be responsible for the observed B11 NMR Knight shift and spin-lattice relaxation rate (1/T1) . From T1 analysis, we thus deduce the partial Bs Fermi-level density of states (DOS) of both borides. On the other hand, the relaxation rate of ReB2 is mainly associated with p electrons, similar to the cases of OsB2 and RuB2 . In addition, the extracted B2p Fermi-level DOS is in good agreement with the theoretical prediction from band-structure calculations.

NMR strategies to study the local magnetic properties of carbon nanotubes

KAUST Repository

Abou-Hamad, Edy; Kim, Younghyun; Bouhrara, Mohamed; Saih, Youssef; Wå gberg, Thomas; Luzzi, David E.; Goze-Bac, Christophe

2012-01-01

The local magnetic properties of the one dimensional inner space of the nanotubes are investigated using 13C nuclear magnetic resonance spectroscopy of encapsulated fullerene molecules inside single walled carbon nanotubes. Isotope engineering and magnetically purified nanotubes have been advantageously used on our study to discriminate between the different diamagnetic and paramagnetic shifts of the resonances. Ring currents originating from the π electrons circulating on the nanotube, are found to actively screen the applied magnetic field by -36.9 ppm. Defects and holes in the nanotube walls cancel this screening locally. What is interesting, that at high magnetic fields, the modifications of the NMR resonances of the molecules from free to encapsulated can be exploited to determine some structural characteristics of the surrounding nanotubes, never observed experimentally. © 2011 Elsevier B.V. All rights reserved.

NMR strategies to study the local magnetic properties of carbon nanotubes

KAUST Repository

Abou-Hamad, Edy

2012-02-01

The local magnetic properties of the one dimensional inner space of the nanotubes are investigated using 13C nuclear magnetic resonance spectroscopy of encapsulated fullerene molecules inside single walled carbon nanotubes. Isotope engineering and magnetically purified nanotubes have been advantageously used on our study to discriminate between the different diamagnetic and paramagnetic shifts of the resonances. Ring currents originating from the π electrons circulating on the nanotube, are found to actively screen the applied magnetic field by -36.9 ppm. Defects and holes in the nanotube walls cancel this screening locally. What is interesting, that at high magnetic fields, the modifications of the NMR resonances of the molecules from free to encapsulated can be exploited to determine some structural characteristics of the surrounding nanotubes, never observed experimentally. © 2011 Elsevier B.V. All rights reserved.

Final Report: Characterization of Hydrogen Adsorption in Carbon-Based Materials by NMR

International Nuclear Information System (INIS)

Wu, Yue; Kleinhammes, Alfred

2011-01-01

In support of DOE/EERE's Fuel Cell Technologies Program Hydrogen Sorption Center of Excellence (HSCoE), UNC conducted Nuclear Magnetic Resonance (NMR) measurements that contributed spectroscopic information as well as quantitative analysis of adsorption processes. While NMR based Langmuir isotherms produce reliable H2 capacity measurements, the most astute contribution to the center is provided by information on dihydrogen adsorption on the scale of nanometers, including the molecular dynamics of hydrogen in micropores, and the diffusion of dihydrogen between macro and micro pores. A new method to assess the pore width using H2 as probe of the pore geometry was developed and is based on the variation of the observed chemical shift of adsorbed dihydrogen as function of H2 pressure. Adsorbents designed and synthesized by the Center were assessed for their H2 capacity, the binding energy of the adsorption site, their pore structure and their ability to release H2. Feedback to the materials groups was provided to improve the materials properties. To enable in situ NMR measurements as a function of H2 pressure and temperature, a unique, specialized NMR system was designed and built. Pressure can be varied between 10-4 and 107 Pa while the temperature can be controlled between 77K and room temperature. In addition to the 1H investigation of the H2 adsorption process, NMR was implemented to measure the atomic content of substituted elements, e.g. boron in boron substituted graphitic material as well as to determine the local environment and symmetry of these substituted nuclei. The primary findings by UNC are the following: (1) Boron substituted for carbon in graphitic material in the planar BC3 configuration enhances the binding energy for adsorbed hydrogen; (2) Arrested kinetics of H2 was observed below 130K in the same boron substituted carbon samples that combine enhanced binding energy with micropore structure; (3) Hydrogen storage material made from activated PEEK

Final Report: Characterization of Hydrogen Adsorption in Carbon-Based Materials by NMR

Energy Technology Data Exchange (ETDEWEB)

Wu, Yue; Kleinhammes, Alfred

2011-07-11

In support of DOE/EERE's Fuel Cell Technologies Program Hydrogen Sorption Center of Excellence (HSCoE), UNC conducted Nuclear Magnetic Resonance (NMR) measurements that contributed spectroscopic information as well as quantitative analysis of adsorption processes. While NMR based Langmuir isotherms produce reliable H2 capacity measurements, the most astute contribution to the center is provided by information on dihydrogen adsorption on the scale of nanometers, including the molecular dynamics of hydrogen in micropores, and the diffusion of dihydrogen between macro and micro pores. A new method to assess the pore width using H2 as probe of the pore geometry was developed and is based on the variation of the observed chemical shift of adsorbed dihydrogen as function of H2 pressure. Adsorbents designed and synthesized by the Center were assessed for their H2 capacity, the binding energy of the adsorption site, their pore structure and their ability to release H2. Feedback to the materials groups was provided to improve the materials’ properties. To enable in situ NMR measurements as a function of H2 pressure and temperature, a unique, specialized NMR system was designed and built. Pressure can be varied between 10-4 and 107 Pa while the temperature can be controlled between 77K and room temperature. In addition to the 1H investigation of the H2 adsorption process, NMR was implemented to measure the atomic content of substituted elements, e.g. boron in boron substituted graphitic material as well as to determine the local environment and symmetry of these substituted nuclei. The primary findings by UNC are the following: • Boron substituted for carbon in graphitic material in the planar BC3 configuration enhances the binding energy for adsorbed hydrogen. • Arrested kinetics of H2 was observed below 130K in the same boron substituted carbon samples that combine enhanced binding energy with micropore structure. • Hydrogen storage material made from

WaVPeak: Picking NMR peaks through wavelet-based smoothing and volume-based filtering

KAUST Repository

Liu, Zhi; Abbas, Ahmed; Jing, Bing-Yi; Gao, Xin

2012-01-01

Motivation: Nuclear magnetic resonance (NMR) has been widely used as a powerful tool to determine the 3D structures of proteins in vivo. However, the post-spectra processing stage of NMR structure determination usually involves a tremendous amount

PASA - A Program for Automated Protein NMR Backbone Signal Assignment by Pattern-Filtering Approach

International Nuclear Information System (INIS)

Xu Yizhuang; Wang Xiaoxia; Yang Jun; Vaynberg, Julia; Qin Jun

2006-01-01

We present a new program, PASA (Program for Automated Sequential Assignment), for assigning protein backbone resonances based on multidimensional heteronuclear NMR data. Distinct from existing programs, PASA emphasizes a per-residue-based pattern-filtering approach during the initial stage of the automated 13 C α and/or 13 C β chemical shift matching. The pattern filter employs one or multiple constraints such as 13 C α /C β chemical shift ranges for different amino acid types and side-chain spin systems, which helps to rule out, in a stepwise fashion, improbable assignments as resulted from resonance degeneracy or missing signals. Such stepwise filtering approach substantially minimizes early false linkage problems that often propagate, amplify, and ultimately cause complication or combinatorial explosion of the automation process. Our program (http://www.lerner.ccf.org/moleccard/qin/) was tested on four representative small-large sized proteins with various degrees of resonance degeneracy and missing signals, and we show that PASA achieved the assignments efficiently and rapidly that are fully consistent with those obtained by laborious manual protocols. The results demonstrate that PASA may be a valuable tool for NMR-based structural analyses, genomics, and proteomics

New Computational Approaches for NMR-based Drug Design: A Protocol for Ligand Docking to Flexible Target Sites

International Nuclear Information System (INIS)

Gracia, Luis; Speidel, Joshua A.; Weinstein, Harel

2006-01-01

NMR-based drug design has met with some success in the last decade, as illustrated in numerous instances by Fesik's ''ligand screening by NMR'' approach. Ongoing efforts to generalize this success have led us to the development of a new paradigm in which quantitative computational approaches are being integrated with NMR derived data and biological assays. The key component of this work is the inclusion of the intrinsic dynamic quality of NMR structures in theoretical models and its use in docking. A new computational protocol is introduced here, designed to dock small molecule ligands to flexible proteins derived from NMR structures. The algorithm makes use of a combination of simulated annealing monte carlo simulations (SA/MC) and a mean field potential informed by the NMR data. The new protocol is illustrated in the context of an ongoing project aimed at developing new selective inhibitors for the PCAF bromodomains that interact with HIV Tat

Large-Scale Constraint-Based Pattern Mining

Science.gov (United States)

Zhu, Feida

2009-01-01

We studied the problem of constraint-based pattern mining for three different data formats, item-set, sequence and graph, and focused on mining patterns of large sizes. Colossal patterns in each data formats are studied to discover pruning properties that are useful for direct mining of these patterns. For item-set data, we observed robustness of…

Defect assessments of pipelines based on the FAD approach incorporating constraint effects

Energy Technology Data Exchange (ETDEWEB)

Ruggieri, Claudio; Cravero, Sebastian [Sao Paulo Univ., SP (Brazil)

2005-07-01

This work presents a framework for including constraint effects in the failure assessment diagram (FAD) approach. The procedure builds upon the constraint-based Q methodology to correct measured toughness values using low constraint fracture specimens which modifies the shape of the FAD curve. The approach is applied to predict the failure (burst pressure) of high pressure pipelines with planar defects having different geometries (i.e., crack depth and crack length). The FAD curves are corrected for effects of constraint based on the L{sub r}-Q trajectories for pin-loaded SE(T) specimens. The article shows that inclusion of constraint effects in the FAD approach provides better agreement between experimentally measured burst pressure and predicted values for high pressure pipelines with planar defects. (author)

Using an Interactive Web-Based Learning NMR Spectroscopy as a Means to Improve Problem Solving Skills for Undergraduates

International Nuclear Information System (INIS)

Supasorn, Saksri; Vibuljun, Sunantha; Panijpan, Bhinyo; Rajviroongit, Shuleewan

2005-10-01

An Interactive Web-Based Learning NMR Spectroscopy course is developed to improve and facilitate student ' s learning as well as achievement of learning objectives in the concepts of multiplicity, chemical shift, and problem solving. This web-based learning course is emphasized on NMR problem solving, therefore, the concepts of multiplicity and chemical shift, basic concepts for practice problem solving, are also emphasized. Most of animations and pictures in this web-based learning are new created and simplified to explain processes and principles in NMR spectroscopy. With meaningful animations and pictures, simplified English language used, step-by-step problem solving, and interactive test, it can be self-learning web site and best on the student ' s convenience

Paramagnetism and plasma beta in a screw-pinch

International Nuclear Information System (INIS)

Lehnert, B.; Scheffel, J.

1991-02-01

Anisotropic resistivity causes paramagnetic effects (B z ' (r) less then 0) in a screw pinch, being basically different to the self-relaxation described by Taylor. We compute, analytically and numerically, the resulting effect on equilibrium in a 1-D straight cylindrical plasma. In particular we compute paramagnetic effects on the plasma radius and on plasma beta. Ohm's law also contains diamagnetic terms; in this paper we consider radial particle diffusion and the Nernst effect. In a Tokamak or rector plasma these effects are shown to be negligible, whereas they may contribute in present ULQ, Extrap and RFP experiments. A basic result is an expression for the coupling between the poloidal and axial magnetic field components with the above effects included. A result of specific importance to the Extrap programme is that plasma current limitation can arise from lack of equilibrium when the plasma radius tends to exceed its upper limit, being defined by a magnetic or material limiter. The paramagnetic effect described in this work lowers the plasma beta further, making D-D reactor depending on safety factors q(a) bigger than 1 seems less attainable. (au)

Structural studies of SpoIIAA using NMR

International Nuclear Information System (INIS)

Comfort, D.M.

1998-01-01

The protein SpoIIAA participates, via phosphorylation and dephosphorylation, in the four-component system that regulates the sporulation sigma factor e. Differential gene expression depends on specialised transcription factors called sigma factors, which direct the RNA polymerase to transcribe specific genes in one or other of the two chambers at various stages of sporulation. The first sporulation-specific sigma factor to be activated is 4 transcription that depends on σ F is essential for the remaining sigma factors to become active in turn. Early in sporulation SpoIIAA is in the phosphorylated state (SpoIIAA-P), as a result of the activity of the ATP-dependent protein kinase, SpoIIAB. About 80 minutes after the initiation of sporulation a specific phosphatase, SpoIIE, begins to hydrolyse SpoIIAA-P, and the resulting SpoIIAA again becomes a substrate for SpoIIAB. SpoIIAB is also an anti-sigma factor which in its free form inhibits a F by binding to it. Competition by SpoIIAA (the anti-anti-sigma factor) for binding to SpoIIAB releases e activity. The three-dimensional structure of SpoIIAA has been determined using high resolution NMR. SpoIIAA has a novel fold, composed of a-helices and P-strand elements. The structural differences between SpoIIAA and its inactive form, SpoIIAA-P, were also investigated by NMR. Tentative evidence points to the observation that phosphorylation of SpoIIAA results in a minor conformational change near the site of phosphorylation, which interferes with the hydrophobic interaction between SpoIIAA and SpoIIAB. Further NMR studies helped to predict the location of SpoIIAA-, GTP-, and ATP-binding sites on the SpoIIAA structure. In addition, the automated iterative NOE assignment algorithm, ARIA, was used to obtain additional NOE-based distance constraints and to calculate a refined structure. (author)

Structural studies of SpoIIAA using NMR

Energy Technology Data Exchange (ETDEWEB)

Comfort, D.M

1998-07-01

The protein SpoIIAA participates, via phosphorylation and dephosphorylation, in the four-component system that regulates the sporulation sigma factor e. Differential gene expression depends on specialised transcription factors called sigma factors, which direct the RNA polymerase to transcribe specific genes in one or other of the two chambers at various stages of sporulation. The first sporulation-specific sigma factor to be activated is 4 transcription that depends on {sigma}{sup F} is essential for the remaining sigma factors to become active in turn. Early in sporulation SpoIIAA is in the phosphorylated state (SpoIIAA-P), as a result of the activity of the ATP-dependent protein kinase, SpoIIAB. About 80 minutes after the initiation of sporulation a specific phosphatase, SpoIIE, begins to hydrolyse SpoIIAA-P, and the resulting SpoIIAA again becomes a substrate for SpoIIAB. SpoIIAB is also an anti-sigma factor which in its free form inhibits a F by binding to it. Competition by SpoIIAA (the anti-anti-sigma factor) for binding to SpoIIAB releases e activity. The three-dimensional structure of SpoIIAA has been determined using high resolution NMR. SpoIIAA has a novel fold, composed of a-helices and P-strand elements. The structural differences between SpoIIAA and its inactive form, SpoIIAA-P, were also investigated by NMR. Tentative evidence points to the observation that phosphorylation of SpoIIAA results in a minor conformational change near the site of phosphorylation, which interferes with the hydrophobic interaction between SpoIIAA and SpoIIAB. Further NMR studies helped to predict the location of SpoIIAA-, GTP-, and ATP-binding sites on the SpoIIAA structure. In addition, the automated iterative NOE assignment algorithm, ARIA, was used to obtain additional NOE-based distance constraints and to calculate a refined structure. (author)

A paramagnetic nearly isodynamic compact magnetic confinement system

International Nuclear Information System (INIS)

Cooper, W.A.; Antonietti, J.M.; Todd, T.N.

2001-01-01

A coreless compact magnetic confinement system that consists of sets of helical windings and vertical magnetic field coils is investigated. The helical coils produce a small toroidal translation of the magnetic field lines and seed paramagnetism. The force-free component of the toroidal current strongly enhances the paramagnetism such that isodynamic conditions near the plasma centre can be approached. At β 5%, the configuration is stable to local MHD modes. Global MHD modes limit the toroidal current 2πJ to about 60kA for peaked J. Bootstrap-like hollow current profiles generate quasiaxisymmetric systems that require a close fitting conducting shell to satisfy external kink stability. (author)

Constraint-Based Local Search for Constrained Optimum Paths Problems

Science.gov (United States)

Pham, Quang Dung; Deville, Yves; van Hentenryck, Pascal

Constrained Optimum Path (COP) problems arise in many real-life applications and are ubiquitous in communication networks. They have been traditionally approached by dedicated algorithms, which are often hard to extend with side constraints and to apply widely. This paper proposes a constraint-based local search (CBLS) framework for COP applications, bringing the compositionality, reuse, and extensibility at the core of CBLS and CP systems. The modeling contribution is the ability to express compositional models for various COP applications at a high level of abstraction, while cleanly separating the model and the search procedure. The main technical contribution is a connected neighborhood based on rooted spanning trees to find high-quality solutions to COP problems. The framework, implemented in COMET, is applied to Resource Constrained Shortest Path (RCSP) problems (with and without side constraints) and to the edge-disjoint paths problem (EDP). Computational results show the potential significance of the approach.

NMR-based urine analysis in rats: prediction of proximal tubule kidney toxicity and phospholipidosis.

Science.gov (United States)

Lienemann, Kai; Plötz, Thomas; Pestel, Sabine

2008-01-01

The aim of safety pharmacology is early detection of compound-induced side-effects. NMR-based urine analysis followed by multivariate data analysis (metabonomics) identifies efficiently differences between toxic and non-toxic compounds; but in most cases multiple administrations of the test compound are necessary. We tested the feasibility of detecting proximal tubule kidney toxicity and phospholipidosis with metabonomics techniques after single compound administration as an early safety pharmacology approach. Rats were treated orally, intravenously, inhalatively or intraperitoneally with different test compounds. Urine was collected at 0-8 h and 8-24 h after compound administration, and (1)H NMR-patterns were recorded from the samples. Variation of post-processing and feature extraction methods led to different views on the data. Support Vector Machines were trained on these different data sets and then aggregated as experts in an Ensemble. Finally, validity was monitored with a cross-validation study using a training, validation, and test data set. Proximal tubule kidney toxicity could be predicted with reasonable total classification accuracy (85%), specificity (88%) and sensitivity (78%). In comparison to alternative histological studies, results were obtained quicker, compound need was reduced, and very importantly fewer animals were needed. In contrast, the induction of phospholipidosis by the test compounds could not be predicted using NMR-based urine analysis or the previously published biomarker PAG. NMR-based urine analysis was shown to effectively predict proximal tubule kidney toxicity after single compound administration in rats. Thus, this experimental design allows early detection of toxicity risks with relatively low amounts of compound in a reasonably short period of time.

Radiation-induced electron paramagnetic resonance signal and soybean isoflavones content

International Nuclear Information System (INIS)

Oliveira, Marcos R.R. de; Mandarino, José M.G.; Mastro, Nelida L. del

2012-01-01

Electron Paramagnetic Resonance (EPR) is a well-known spectroscopic technique that detects paramagnetic centers and can detect free radicals with high sensitivity. In food, free radicals can be generated by several commonly used industrial processes, such as radiosterilization or heat treatment. EPR spectroscopy is used to detect radioinduced free radicals in food. In this work the relation between EPR signal induced by gamma irradiation treatment and soybean isoflavones content was investigated. Present results did not show correlation between total isoflavones content and the EPR signal. Nevertheless, some isoflavone contents had a negative correlation with the radiation-induced EPR signal. - Highlights: ► Electron Paramagnetic Resonance (EPR) detects free radicals. ► Ionizing radiation as free radicals inducer. ► Total soybean isoflvones do not correlate with radiation-induced EPR intensity but a soybean glucosyl glucoside isoflavone does.

Constraint-aware interior layout exploration for pre-cast concrete-based buildings

KAUST Repository

Liu, Han

2013-05-03

Creating desirable layouts of building interiors is a complex task as designers have to manually adhere to various local and global considerations arising from competing practical and design considerations. In this work, we present an interactive design tool to create desirable floorplans by computationally conforming to such design constraints. Specifically, we support three types of constraints: (i) functional constraints such as number of rooms, connectivity among the rooms, target room areas, etc.; (ii) design considerations such as user modifications and preferences, and (iii) fabrication constraints such as cost and convenience of manufacturing. Based on user specifications, our system automatically generates multiple floor layouts with associated 3D geometry that all satisfy the design specifications and constraints, thus exposing only the desirable family of interior layouts to the user. In this work, we focus on pre-cast concrete-based constructions, which lead to interesting discrete and continuous optimization possibilities. We test our framework on a range of complex real-world specifications and demonstrate the control and expressiveness of the exposed design space relieving the users of the task of manually adhering to non-local functional and fabrication constraints. © 2013 Springer-Verlag Berlin Heidelberg.

EPR in characterization of seeds paramagnetic species

International Nuclear Information System (INIS)

Luiz, A.P.C.; Mauro, M.F.F.L.; Portugal, K.O.; Barbana, V.M.; Guedes, C.L.B.; Mauro, E. di; Carneiro, C.E.A.; Zaia, D.A.M.; Prete, C.E.C.

2011-01-01

Full text. In Brazil, since 1970s, renewable fuel programs has been developed in order to replace petroleum. Today a program that has been discussed is the bio diesel, which intend to replace diesel fuel, fossil oil, to bio diesel, renewal fuel. As seeds are the basis for production of oil and consequently processed into bio diesel, the goal of this work is to characterize and compare paramagnetic species present in the seeds by Electron Paramagnetic Resonance (EPR). Samples used in this study were seeds of sorghum, barley, corn, peanuts, soy beans, cotton, wheat, oats, mustard, rice, sunflower and turnip. Some paramagnetic species present in soil was also investigated as goethite (FeOOH), hematite (Fe 2 O 3 ), magnetite (Fe 3 O 4 ), and ferrihydrite (Fe 5 HO 8 · 4H 2 O), since, these species present in appreciable quantities in the soil can be present in the seeds and analyzed for comparison. The characterization of these species is essential to understand the EPR seeds spectra. Each sample is placed in a thin quartz tube 4 mm in diameter, and it is inserted into the cavity of the spectrometer at room temperature, at low temperature (77 K) and variable temperature using liquid nitrogen flow and hot flow through a compressor air. It was used as standard Mg O:Mn 2+ , which is also inserted into the cavity. Shortly after the potency is regulated, frequency, amplitude and sweep the field. The spectroscopic analysis by EPR X-band (∼ 9:5GHz), were performed at the Fluorescence and Electron Paramagnetic Resonance Laboratory, Exact Sciences Center, State University of Londrina, Parana state, Brazil, through an EPR spectrometer JEOL brand (JES-PE-3X). In the EPR spectra, spectroscopic factor or g factor and line width were determined in paramagnetic species. Studies from several seeds with EPR technique detected in all of them presence of same complex of Fe 3+ present in the goethite at g ∼ 2, and in the seeds exist free radicals at g = 2:004, at room temperature

EPR in characterization of seeds paramagnetic species

Energy Technology Data Exchange (ETDEWEB)

Luiz, A.P.C.; Mauro, M.F.F.L.; Portugal, K.O.; Barbana, V.M.; Guedes, C.L.B.; Mauro, E. di; Carneiro, C.E.A.; Zaia, D.A.M.; Prete, C.E.C. [Universidade Estadual de Londrina (UEL), PR (Brazil)

2011-07-01

Full text. In Brazil, since 1970s, renewable fuel programs has been developed in order to replace petroleum. Today a program that has been discussed is the bio diesel, which intend to replace diesel fuel, fossil oil, to bio diesel, renewal fuel. As seeds are the basis for production of oil and consequently processed into bio diesel, the goal of this work is to characterize and compare paramagnetic species present in the seeds by Electron Paramagnetic Resonance (EPR). Samples used in this study were seeds of sorghum, barley, corn, peanuts, soy beans, cotton, wheat, oats, mustard, rice, sunflower and turnip. Some paramagnetic species present in soil was also investigated as goethite (FeOOH), hematite (Fe{sub 2}O{sub 3}), magnetite (Fe{sub 3}O{sub 4}), and ferrihydrite (Fe{sub 5}HO{sub 8} {center_dot} 4H{sub 2}O), since, these species present in appreciable quantities in the soil can be present in the seeds and analyzed for comparison. The characterization of these species is essential to understand the EPR seeds spectra. Each sample is placed in a thin quartz tube 4 mm in diameter, and it is inserted into the cavity of the spectrometer at room temperature, at low temperature (77 K) and variable temperature using liquid nitrogen flow and hot flow through a compressor air. It was used as standard Mg O:Mn{sup 2+}, which is also inserted into the cavity. Shortly after the potency is regulated, frequency, amplitude and sweep the field. The spectroscopic analysis by EPR X-band ({approx} 9:5GHz), were performed at the Fluorescence and Electron Paramagnetic Resonance Laboratory, Exact Sciences Center, State University of Londrina, Parana state, Brazil, through an EPR spectrometer JEOL brand (JES-PE-3X). In the EPR spectra, spectroscopic factor or g factor and line width were determined in paramagnetic species. Studies from several seeds with EPR technique detected in all of them presence of same complex of Fe{sup 3+} present in the goethite at g {approx} 2, and in the seeds

Constraint-based job shop scheduling with ILOG SCHEDULER

NARCIS (Netherlands)

Nuijten, W.P.M.; Le Pape, C.

1998-01-01

We introduce constraint-based scheduling and discuss its main principles. An approximation algorithm based on tree search is developed for the job shop scheduling problem using ILOG SCHEDULER. A new way of calculating lower bounds on the makespan of the job shop scheduling problem is presented and

Monocular Visual Odometry Based on Trifocal Tensor Constraint

Science.gov (United States)

Chen, Y. J.; Yang, G. L.; Jiang, Y. X.; Liu, X. Y.

2018-02-01

For the problem of real-time precise localization in the urban street, a monocular visual odometry based on Extend Kalman fusion of optical-flow tracking and trifocal tensor constraint is proposed. To diminish the influence of moving object, such as pedestrian, we estimate the motion of the camera by extracting the features on the ground, which improves the robustness of the system. The observation equation based on trifocal tensor constraint is derived, which can form the Kalman filter alone with the state transition equation. An Extend Kalman filter is employed to cope with the nonlinear system. Experimental results demonstrate that, compares with Yu’s 2-step EKF method, the algorithm is more accurate which meets the needs of real-time accurate localization in cities.

An NMR log echo data de-noising method based on the wavelet packet threshold algorithm

International Nuclear Information System (INIS)

Meng, Xiangning; Xie, Ranhong; Li, Changxi; Hu, Falong; Li, Chaoliu; Zhou, Cancan

2015-01-01

To improve the de-noising effects of low signal-to-noise ratio (SNR) nuclear magnetic resonance (NMR) log echo data, this paper applies the wavelet packet threshold algorithm to the data. The principle of the algorithm is elaborated in detail. By comparing the properties of a series of wavelet packet bases and the relevance between them and the NMR log echo train signal, ‘sym7’ is found to be the optimal wavelet packet basis of the wavelet packet threshold algorithm to de-noise the NMR log echo train signal. A new method is presented to determine the optimal wavelet packet decomposition scale; this is within the scope of its maximum, using the modulus maxima and the Shannon entropy minimum standards to determine the global and local optimal wavelet packet decomposition scales, respectively. The results of applying the method to the simulated and actual NMR log echo data indicate that compared with the wavelet threshold algorithm, the wavelet packet threshold algorithm, which shows higher decomposition accuracy and better de-noising effect, is much more suitable for de-noising low SNR–NMR log echo data. (paper)

Logic-based methods for optimization combining optimization and constraint satisfaction

CERN Document Server

Hooker, John

2011-01-01

A pioneering look at the fundamental role of logic in optimization and constraint satisfaction While recent efforts to combine optimization and constraint satisfaction have received considerable attention, little has been said about using logic in optimization as the key to unifying the two fields. Logic-Based Methods for Optimization develops for the first time a comprehensive conceptual framework for integrating optimization and constraint satisfaction, then goes a step further and shows how extending logical inference to optimization allows for more powerful as well as flexible

A protocol for the refinement of NMR structures using simultaneously pseudocontact shift restraints from multiple lanthanide ions

Energy Technology Data Exchange (ETDEWEB)

Sala, Davide; Giachetti, Andrea; Luchinat, Claudio, E-mail: luchinat@cerm.unifi.it; Rosato, Antonio, E-mail: rosato@cerm.unifi.it [University of Florence, Magnetic Resonance Center (CERM) (Italy)

2016-11-15

The binding of paramagnetic metal ions to proteins produces a number of different effects on the NMR spectra of the system. In particular, when the magnetic susceptibility of the metal ion is anisotropic, pseudocontact shifts (PCSs) arise and can be easily measured. They constitute very useful restraints for the solution structure determination of metal-binding proteins. In this context, there has been great interest in the use of lanthanide(III) ions to induce PCSs in diamagnetic proteins, e.g. through the replacement native calcium(II) ions. By preparing multiple samples in each of which a different ion of the lanthanide series is introduced, it is possible to obtain multiple independent PCS datasets that can be used synergistically to generate protein structure ensembles (typically called bundles). For typical NMR-based determination of protein structure, it is necessary to perform an energetic refinement of such initial bundles to obtain final structures whose geometric quality is suitable for deposition in the PDB. This can be conveniently done by using restrained molecular dynamics simulations (rMD) in explicit solvent. However, there are no available protocols for rMD using multiple PCS datasets as part of the restraints. In this work, we extended the PCS module of the AMBER MD package to handle multiple datasets and tuned a previously developed protocol for NMR structure refinement to achieve consistent convergence with PCS restraints. Test calculations with real experimental data show that this new implementation delivers the expected improvement of protein geometry, resulting in final structures that are of suitable quality for deposition. Furthermore, we observe that also initial structures generated only with traditional restraints can be successfully refined using traditional and PCS restraints simultaneously.

Paramagnetic ionic liquids for measurements of density using magnetic levitation.

Science.gov (United States)

Bwambok, David K; Thuo, Martin M; Atkinson, Manza B J; Mirica, Katherine A; Shapiro, Nathan D; Whitesides, George M

2013-09-03

Paramagnetic ionic liquids (PILs) provide new capabilities to measurements of density using magnetic levitation (MagLev). In a typical measurement, a diamagnetic object of unknown density is placed in a container containing a PIL. The container is placed between two magnets (typically NdFeB, oriented with like poles facing). The density of the diamagnetic object can be determined by measuring its position in the magnetic field along the vertical axis (levitation height, h), either as an absolute value or relative to internal standards of known density. For density measurements by MagLev, PILs have three advantages over solutions of paramagnetic salts in aqueous or organic solutions: (i) negligible vapor pressures; (ii) low melting points; (iii) high thermal stabilities. In addition, the densities, magnetic susceptibilities, glass transition temperatures, thermal decomposition temperatures, viscosities, and hydrophobicities of PILs can be tuned over broad ranges by choosing the cation-anion pair. The low melting points and high thermal stabilities of PILs provide large liquidus windows for density measurements. This paper demonstrates applications and advantages of PILs in density-based analyses using MagLev.

Effect of magnetic field strength on NMR-based metabonomic human urine data. Comparative study of 250, 400, 500, and 800 MHz

DEFF Research Database (Denmark)

Bertram, Hanne Christine; Malmendal, Anders; Petersen, Bent O.

2007-01-01

Metabonomic analysis of urine utilizing high-resolution NMR spectroscopy and chemometric techniques has proven valuable in characterizing the biochemical response to an intervention. To assess the effect of magnetic field strength on information contained in NMR-based metabonomic data sets, 1H NMR...

Two-frequency radiospectrometer for studying paramagnetics under a strong magnetic field

International Nuclear Information System (INIS)

Vertii, A.A.; Gudym, I.Y.; Ivanchenko, I.V.

1994-01-01

A two-frequency radiospectrometer for studying electron paramagnetic resonance in the 120-150-GHz band and nuclear magnetic resonance in the 180-200-MHz band is described. The spectrometer is used to measure the properties of paramagnetics by a double-resonance technique in a magnetic field of up to 5 T at a temperature ranging from 1.7 to 20 degrees K

Dating by electron paramagnetic resonance

International Nuclear Information System (INIS)

Poupeau, G.; Rossi, A.M.

1984-01-01

Some natural materials behave like dosimeters in front of the ionizing particle flux coming from environmental radioactivity and the cosmic radiation. This property is used for the dating by Electron Paramagnetic Resonance (EPR). Before presenting the basic principles of the EPR analysis and the dating method which uses such a phenomenous, it is reviewed several types of application currently in course of development. (L.C.) [pt

NMR studies at high magnetic fields of LiVGe_2O_6, a quasi one-dimensional spin S=1 system

Science.gov (United States)

Vonlanthen, P.; Tanaka, K. B.; Clark, W. G.; Gavilano, J. L.; Ott, H. R.; Millet, P.; Mila, F.; Kuhns, P.; Reyes, A. P.; Moulton, W. G.

2001-03-01

We report ^7Li NMR studies of LiVGe_2O_6, a quasi one-dimensional spin S=1 system. Our measurements include NMR spectra, the spin-lattice relaxation rate, T_1-1, and the spin-spin relaxation rate, T_2-1, obtained at magnetic fields (B) of 9 and 23 T and temperatures (T) over the range 1.8 - 300 K. The 9 T NMR spectra show a continuous transfer of spectral weight from a paramagnetic phase to an antiferromagnetic one in a narrow temperature range of about 2 K around the transition temperature TN ≈ 25 K. Both phases coexist in this range. Below 10 K, well into the antiferromagnetic phase, the T_1-1 measurements are consistent with electron spin excitations across an energy gap (Δ) with Δ/k_B≈ 14 K at 9 T and 11 K at about 23 T; i.e., applying a large B slightly reduces Δ. Changing B from 9 to 23 T increases TN by 1 K. Thus, TN is influenced only marginally by B up to 23 Tesla. The UCLA part of the work was supported by NSF Grants DMR-9705369 and DMR-0072524.

Electron paramagnetic resonance study of Ce doped partially stabilized ZrO2 crystals

Directory of Open Access Journals (Sweden)

Mikhail А. Borik

2017-09-01

Full Text Available ZrO2 (PSZ solid solutions crystals stabilized with yttrium and cerium oxides have been studied using electron paramagnetic resonance (EPR in the X and Q ranges. Zr3+ have been observed centers in the as-annealed ZrO2 crystals stabilized only by yttrium oxide (2.8 mol% Y2O3. Another type of paramagnetic-O-centers appear as a result of CeO2 addition to ZrO2 crystals along with yttrium oxide. To estimate the concentration of Ce3+ ions in PZS crystals, we recorded the EPR spectra in the presence of a reference at 7 K. Paramagnetic Ce3+ ions have been identified and their relative amount in the PSZ crystals before and after high-temperature heat treatment has been assessed. Annealing in air leads decreases the concentration of Ce3+ ions for all the test compositions and changes the color of the crystals from red to white. After annealing of the sample 2.0Y0.8Ce3Zr, the amount of paramagnetic Ce3+ ions decreased approximately twofold. Paramagnetic centers from Ce3+ have not been detected in the specimen with a low cerium content of 0.1 mol% after annealing which indicates the complete transition of Ce3+ to the Ce4+ state. We show that the forming cerium paramagnetic centers are bound by strong exchange interactions. No angular dependence of the EPR lines of the paramagnetic Ce3+ cations on the applied external magnetic field has been observed. Probable origin of the absence of angular dependence is that the impurity rare-earth ions are located close to one another, forming impurity clusters with an effective spin of Seff=1/2.

High gradient magnetic separation of upconverting lanthanide nanophosphors based on their intrinsic paramagnetism

Energy Technology Data Exchange (ETDEWEB)

Arppe, Riikka, E-mail: riikka.arppe@utu.fi; Salovaara, Oskari; Mattsson, Leena; Lahtinen, Satu; Valta, Timo; Riuttamaeki, Terhi; Soukka, Tero [University of Turku, Department of Biotechnology (Finland)

2013-09-15

Photon upconverting nanophosphors (UCNPs) have the unique luminescent property of converting low-energy infrared light into visible emission which can be widely utilized in nanoreporter and imaging applications. For the use as reporters in these applications, the UCNPs must undergo a series of surface modification and bioconjugation reactions. Efficient purification methods are required to remove the excess reagents and biomolecules from the nanophosphor solution after each step to yield highly responsive reporters for sensitive bioanalytical assays. However, as the particle size of the UCNPs approaches the size of biomolecules, the handling of these reporters becomes cumbersome with traditional purification methods such as centrifugation. Here we introduce a novel approach for purification of bioconjugated 32-nm NaYF{sub 4}: Yb{sup 3+}, Er{sup 3+}-nanophosphors from excess unbound biomolecules utilizing high gradient magnetic separation (HGMS)-system constructed from permanent super magnets which produce magnetic gradients in a magnetizable steel wool matrix amplifying the magnetic field. The non-magnetic biomolecules flowed straight through the magnetized HGMS-column while the UCNPs were eluted only after the magnetic field was removed. In the UCNPs the luminescent centers, i.e., lanthanide-ion dopants are responsible for the strong upconversion luminescence, but in addition they are also paramagnetic. In this study we have shown that the presence of these weakly paramagnetic luminescent lanthanides actually also enables the use of HGMS to capture the UCNPs without incorporating additional optically inactive magnetic core into them.

High gradient magnetic separation of upconverting lanthanide nanophosphors based on their intrinsic paramagnetism

International Nuclear Information System (INIS)

Arppe, Riikka; Salovaara, Oskari; Mattsson, Leena; Lahtinen, Satu; Valta, Timo; Riuttamäki, Terhi; Soukka, Tero

2013-01-01

Photon upconverting nanophosphors (UCNPs) have the unique luminescent property of converting low-energy infrared light into visible emission which can be widely utilized in nanoreporter and imaging applications. For the use as reporters in these applications, the UCNPs must undergo a series of surface modification and bioconjugation reactions. Efficient purification methods are required to remove the excess reagents and biomolecules from the nanophosphor solution after each step to yield highly responsive reporters for sensitive bioanalytical assays. However, as the particle size of the UCNPs approaches the size of biomolecules, the handling of these reporters becomes cumbersome with traditional purification methods such as centrifugation. Here we introduce a novel approach for purification of bioconjugated 32-nm NaYF 4 : Yb 3+ , Er 3+ -nanophosphors from excess unbound biomolecules utilizing high gradient magnetic separation (HGMS)-system constructed from permanent super magnets which produce magnetic gradients in a magnetizable steel wool matrix amplifying the magnetic field. The non-magnetic biomolecules flowed straight through the magnetized HGMS-column while the UCNPs were eluted only after the magnetic field was removed. In the UCNPs the luminescent centers, i.e., lanthanide-ion dopants are responsible for the strong upconversion luminescence, but in addition they are also paramagnetic. In this study we have shown that the presence of these weakly paramagnetic luminescent lanthanides actually also enables the use of HGMS to capture the UCNPs without incorporating additional optically inactive magnetic core into them

Constraint Differentiation

DEFF Research Database (Denmark)

Mödersheim, Sebastian Alexander; Basin, David; Viganò, Luca

2010-01-01

We introduce constraint differentiation, a powerful technique for reducing search when model-checking security protocols using constraint-based methods. Constraint differentiation works by eliminating certain kinds of redundancies that arise in the search space when using constraints to represent...... results show that constraint differentiation substantially reduces search and considerably improves the performance of OFMC, enabling its application to a wider class of problems....

Solution structures of α-conotoxin G1 determined by two-dimensional NMR spectroscopy

International Nuclear Information System (INIS)

Pardi, A.; Galdes, A.; Florance, J.; Maniconte, D.

1989-01-01

Two-dimensional NMR data have been used to generate solution structures of α-conotoxin G1, a potent peptide antagonist of the acetylcholine receptor. Structural information was obtained in the form of proton-proton internuclear distance constraints, and initial structures were produced with a distance geometry algorithm. Energetically more favorable structures were generated by using the distance geometry structures as input for a constrained energy minimization program. The results of both of these calculations indicate that the overall backbone conformation of the molecule is well-defined by the NMR data whereas the side-chain conformations are generally less well-defined. The main structural features derived from the NMR data were the presence of tight turns centered on residues Pro 5 and Arg 9 . The solution structures are compared with previous proposed models of conotoxin G1, and the NMR data are interpreted in conjunction with chemical modification studies and structural properties of other antagonists of the acetylcholine receptor to gain insight into structure-activity relationships in these peptide toxins

Intrinsic Electric Dipole Moments of Paramagnetic Atoms: Rubidium and Cesium

OpenAIRE

Nataraj, H. S.; Sahoo, B. K.; Das, B. P.; Mukherjee, D.

2008-01-01

The electric dipole moment (EDM) of paramagnetic atoms is sensitive to the intrinsic EDM contribution from that of its constituent electrons and a scalar--pseudo-scalar (S-PS) electron-nucleus interactions. The electron EDM and the S-PS EDM contribution to atomic EDM scales as Z^3. Thus, the heavy paramagnetic atomic systems will exhibit large enhancement factors. However, the nature of the coupling is so small that it becomes an interest of high precision atomic experiments. In this work, we...

Organ specific mapping of in vivo redox state in control and cigarette smoke-exposed mice using EPR/NMR co-imaging

Science.gov (United States)

Caia, George L.; Efimova, Olga V.; Velayutham, Murugesan; El-Mahdy, Mohamed A.; Abdelghany, Tamer M.; Kesselring, Eric; Petryakov, Sergey; Sun, Ziqi; Samouilov, Alexandre; Zweier, Jay L.

2014-01-01

In vivo mapping of alterations in redox status is important for understanding organ specific pathology and disease. While electron paramagnetic resonance imaging (EPRI) enables spatial mapping of free radicals, it does not provide anatomic visualization of the body. Proton MRI is well suited to provide anatomical visualization. We applied EPR/NMR co-imaging instrumentation to map and monitor the redox state of living mice under normal or oxidative stress conditions induced by secondhand cigarette smoke (SHS) exposure. A hybrid co-imaging instrument, EPRI (1.2 GHz) / proton MRI (16.18 MHz), suitable for whole-body co-imaging of mice was utilized with common magnet and gradients along with dual EPR/NMR resonators that enable co-imaging without sample movement. The metabolism of the nitroxide probe, 3–carbamoyl–proxyl (3-CP), was used to map the redox state of control and SHS-exposed mice. Co-imaging allowed precise 3D mapping of radical distribution and reduction in major organs such as the heart, lungs, liver, bladder and kidneys. Reductive metabolism was markedly decreased in SHS-exposed mice and EPR/NMR co-imaging allowed quantitative assessment of this throughout the body. Thus, in vivo EPR/NMR co-imaging enables in vivo organ specific mapping of free radical metabolism and redox stress and the alterations that occur in the pathogenesis of disease. PMID:22296801

NMR and NQR studies of 5f-band metamagnetic UCoAl and UCo{sub 1-x}T{sub x}Al (T=Fe,Ni)

Energy Technology Data Exchange (ETDEWEB)

Kohori, Y. [Graduate School of Science and Technology, Chiba University, Chiba 263-8522 (Japan) and Department of Physics, Faculty of Science, Chiba University, Chiba 263-8522 (Japan)]. E-mail: kohori@faculty.chiba-u.jp; Fukazawa, H. [Graduate School of Science and Technology, Chiba University, Chiba 263-8522 (Japan); Department of Physics, Faculty of Science, Chiba University, Chiba 263-8522 (Japan); Iwamoto, Y. [Division of Cargo and Transportation Science, Kobe University, Kobe 658-0022 (Japan); Kohara, T. [Graduate School of Material Science, University of Hyogo, Hyogo 678-1297 (Japan); Andreev, A.V. [Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, 18040 Prague 8 (Czech Republic); Sechovsky, V. [Department of Electronic Structures, Charles University, Ke Karlovu 5, 121 16 Prague 2 (Czech Republic)

2006-05-01

The 5f-band system UCoAl, which crystallizes in the hexagonal ZrNiAl-type structure, has the paramagnetic ground state. The magnetic fields H as low as 0.6T oriented along the c-axis induce the metamagnetic transition below 17K. In order to study the magnetic property of UCoAl, we performed {sup 27}Al and {sup 59}Co NMR/NQR measurements in UCoAl, UCo{sub 0.98}Fe{sub 0.02}Al and UCo{sub 0.95}Ni{sub 0.05}Al single crystals. The substitution of Fe stabilizes the ferromagnetic state, and that of Ni stabilizes the paramagnetic state. The nuclear spin-lattice relaxation rate 1/T{sub 1} obtained with the crystal c-axis perpendicular to H is nearly six times larger than the 1/T{sub 1} with the c-axis parallel to H, which reflects the anisotropy of the spin fluctuations of the system.

Hysteresis modeling based on saturation operator without constraints

International Nuclear Information System (INIS)

Park, Y.W.; Seok, Y.T.; Park, H.J.; Chung, J.Y.

2007-01-01

This paper proposes a simple way to model complex hysteresis in a magnetostrictive actuator by employing the saturation operators without constraints. Having no constraints causes a singularity problem, i.e. the inverse matrix cannot be obtained during calculating the weights. To overcome it, a pseudoinverse concept is introduced. Simulation results are compared with the experimental data, based on a Terfenol-D actuator. It is clear that the proposed model is much closer to the experimental data than the modified PI model. The relative error is calculated as 12% and less than 1% with the modified PI Model and proposed model, respectively

High-field EPR on membrane proteins - crossing the gap to NMR.

Science.gov (United States)

Möbius, Klaus; Lubitz, Wolfgang; Savitsky, Anton

2013-11-01

In this review on advanced EPR spectroscopy, which addresses both the EPR and NMR communities, considerable emphasis is put on delineating the complementarity of NMR and EPR concerning the measurement of molecular interactions in large biomolecules. From these interactions, detailed information can be revealed on structure and dynamics of macromolecules embedded in solution- or solid-state environments. New developments in pulsed microwave and sweepable cryomagnet technology as well as ultrafast electronics for signal data handling and processing have pushed to new horizons the limits of EPR spectroscopy and its multifrequency extensions concerning the sensitivity of detection, the selectivity with respect to interactions, and the resolution in frequency and time domains. One of the most important advances has been the extension of EPR to high magnetic fields and microwave frequencies, very much in analogy to what happens in NMR. This is exemplified by referring to ongoing efforts for signal enhancement in both NMR and EPR double-resonance techniques by exploiting dynamic nuclear or electron spin polarization via unpaired electron spins and their electron-nuclear or electron-electron interactions. Signal and resolution enhancements are particularly spectacular for double-resonance techniques such as ENDOR and PELDOR at high magnetic fields. They provide greatly improved orientational selection for disordered samples that approaches single-crystal resolution at canonical g-tensor orientations - even for molecules with small g-anisotropies. Exchange of experience between the EPR and NMR communities allows for handling polarization and resolution improvement strategies in an optimal manner. Consequently, a dramatic improvement of EPR detection sensitivity could be achieved, even for short-lived paramagnetic reaction intermediates. Unique structural and dynamic information is thus revealed that can hardly be obtained by any other analytical techniques. Micromolar

Investigation of lanthanide ions and other paramagnetic impurities in natural fluorite by electron paramagnetic resonance: examples of application to mining exploration and geochemistry

International Nuclear Information System (INIS)

Chatagnon, B.

1981-01-01

This research thesis reports the application to geology, and more particularly to geochemistry and mining exploration, of a physical method: the electron paramagnetic resonance (EPR). After a report of a bibliographical investigation on mineralogy and geochemistry of fluorite and lanthanides, as well as on paramagnetic centres observed by physicists in synthetic fluorite, the author reports an experimental work, and describes two examples of application of EPR: firstly, the exploration of radioactive ores, and secondly, with the joint use of neutron activation analysis, the characterization of the redox status of the hydrothermal solution which is at the origin of fluorinated mineralisation

NMR of proteins (4Fe-4S): structural properties and intramolecular electron transfer; RMN de proteines (4Fe-4S): proprietes structurales et transfert electronique intramoleculaire

Energy Technology Data Exchange (ETDEWEB)

Huber, J G

1996-10-17

NMR started to be applied to Fe-S proteins in the seventies. Its use has recently been enlarged as the problems arising from the paramagnetic polymetallic clusters ware overcome. Applications to [4Fe-4S] are presented herein. The information derived thereof deepens the understanding of the redox properties of these proteins which play a central role in the metabolism of bacterial cells. The secondary structure elements and the overall folding of Chromatium vinosum ferredoxin (Cv Fd) in solution have been established by NMR. The unique features of this sequence have been shown to fold as an {alpha} helix at the C-terminus and as a loop between two cysteines ligand of one cluster: these two parts localize in close proximity from one another. The interaction between nuclear and electronic spins is a source of additional structural information for (4Fe-AS] proteins. The conformation of the cysteine-ligands, as revealed by the Fe-(S{sub {gamma}}-C{sub {beta}}-H{sub {beta}})Cys dihedral angles, is related to the chemical shifts of the signals associated with the protons of these residues. The longitudinal relaxation times of the protons depend on their distance to the cluster. A quantitative relationship has been established and used to show that the solution structure of the high-potential ferredoxin from Cv differs significantly from the crystal structure around Phe-48. Both parameters (chemical shifts and longitudinal relaxation times) give also insight into the electronic and magnetic properties of the [4Fe-4S] clusters. The rate of intramolecular electron transfer between the two [4FE-4S] clusters of ferredoxins has been measured by NMR. It is far slower in the case of Cv Fd than for shorter ferredoxins. The difference may be associated with changes in the magnetic and/or electronic properties of one cluster. The strong paramagnetism of the [4Fe-4S] clusters, which originally limited the applicability of NMR to proteins containing these cofactors, has been proven

Study on the unified constraint parameter for characterizing in-plane and out-of-plane constraint based on the equivalent plastic strain

International Nuclear Information System (INIS)

Yang Jie; Wang Guozhen; Xuan Fuzhen; Tu Shandong

2013-01-01

Background: Constraint can significantly alter the material's fracture toughness. Purpose: In order to increase accuracy of the structural integrity assessment. It needs to consider the effect of constraint on the fracture toughness of nuclear power materials and structures. A unified measure which can reflect both in-plane and out-of-plane constraint is needed. Methods: In this paper, the finite element numerical simulation method was used, a unified measure and characterization parameter of in-plane and out-of-plane constraint based on crack-tip equivalent plastic strain have been investigated. Results: The results show that the area surrounded by ε p isoline has a good relevance with the material's fracture toughness on different constraint conditions, so it may be a suitable parameter. Based on the area A PEEQ , a unified constraint characterization parameter √A p is defined. It was found that there exists a sole linear relation between the normalized fracture toughness J IC /J re f and √A p regardless of the in-plane, out-of-plane constraint and the selection of the p isolines. The sole J IC /J re f-√A p line exists for a certain material. For different materials, the slope of J IC /J re f-√A p reference line is different. The material whose slope is larger has a higher J IC /J re f and is more sensitive to constraint at the same magnitude of normalized unified parameter. Conclusions: The unified J IC /J re f -√A p reference line may be used to assess the safety of a cracked component with any constraint levels regardless of in-plane or out-of-plane constraint or both. (authors)

Point defects in crystalline zircon (zirconium silicate), ZrSiO4: electron paramagnetic resonance studies

Science.gov (United States)

Tennant, W. C.; Claridge, R. F. C.; Walsby, C. J.; Lees, N. S.

This article outlines the present state of knowledge of paramagnetic defects in crystalline zircon as obtained mainly, but not exclusively, from electron paramagnetic resonance (EPR) studies in crystalline zircon (zirconium silicate, ZrSiO4). The emphasis is on single-crystal studies where, in principle, unambiguous analysis is possible. Firstly, the crystallography of zircon is presented. Secondly, the relationships between available crystal-site symmetries and the symmetries of observed paramagnetic species in zircon, and how these observations lead to unambiguous assignments of point-group symmetries for particular paramagnetic species are detailed. Next, spin-Hamiltonian (SH) analysis is discussed with emphasis on the symmetry relationships that necessarily exist amongst the Laue classes of the crystal sites in zircon, the paramagnetic species occupying those sites and the SH itself. The final sections of the article then survey the results of EPR studies on zircon over the period 1960-2002.

First-principles calculation of the magnetic properties of paramagnetic fcc iron

International Nuclear Information System (INIS)

Johnson, D.D.; Gyorffy, B.L.; Pinski, F.J.; Staunton, J.; Stocks, G.M.

1985-01-01

Using the disordered local moment picture of itinerant magnetism, we present calculations of the temperature and volume dependence of the magnetic moment and spin-spin correlations for fcc Fe in the paramagnetic state. These calculations are based on the parameter-free, first principles approach of local spin density functional theory and the coherent potential approximation is used to treat the disorder associated with the random orientation of the local moments

Teaching Database Design with Constraint-Based Tutors

Science.gov (United States)

Mitrovic, Antonija; Suraweera, Pramuditha

2016-01-01

Design tasks are difficult to teach, due to large, unstructured solution spaces, underspecified problems, non-existent problem solving algorithms and stopping criteria. In this paper, we comment on our approach to develop KERMIT, a constraint-based tutor that taught database design. In later work, we re-implemented KERMIT as EER-Tutor, and…

Modelling the acid/base 1H NMR chemical shift limits of metabolites in human urine.

Science.gov (United States)

Tredwell, Gregory D; Bundy, Jacob G; De Iorio, Maria; Ebbels, Timothy M D

2016-01-01

Despite the use of buffering agents the 1 H NMR spectra of biofluid samples in metabolic profiling investigations typically suffer from extensive peak frequency shifting between spectra. These chemical shift changes are mainly due to differences in pH and divalent metal ion concentrations between the samples. This frequency shifting results in a correspondence problem: it can be hard to register the same peak as belonging to the same molecule across multiple samples. The problem is especially acute for urine, which can have a wide range of ionic concentrations between different samples. To investigate the acid, base and metal ion dependent 1 H NMR chemical shift variations and limits of the main metabolites in a complex biological mixture. Urine samples from five different individuals were collected and pooled, and pre-treated with Chelex-100 ion exchange resin. Urine samples were either treated with either HCl or NaOH, or were supplemented with various concentrations of CaCl 2 , MgCl 2 , NaCl or KCl, and their 1 H NMR spectra were acquired. Nonlinear fitting was used to derive acid dissociation constants and acid and base chemical shift limits for peaks from 33 identified metabolites. Peak pH titration curves for a further 65 unidentified peaks were also obtained for future reference. Furthermore, the peak variations induced by the main metal ions present in urine, Na + , K + , Ca 2+ and Mg 2+ , were also measured. These data will be a valuable resource for 1 H NMR metabolite profiling experiments and for the development of automated metabolite alignment and identification algorithms for 1 H NMR spectra.

De novo fragment-based design of inhibitors of DXS guided by spin-diffusion-based NMR spectroscopy

NARCIS (Netherlands)

Masini, T.; Pilger, J.; Kroezen, B. S.; Illarionov, B.; Lottmann, P.; Fischer, M.; Griesinger, C.; Hirsch, A. K. H.

We applied for the first time an innovative ligand-based NMR methodology (STI) to a medicinal-chemistry project aimed at the development of inhibitors for the enzyme 1-deoxy-D-xylulose-5-phosphate synthase (DXS). DXS is the first enzyme of the 2C-methyl-D-erythritol-4-phosphate (MEP) pathway,

Compressed sensing and the reconstruction of ultrafast 2D NMR data: Principles and biomolecular applications.

Science.gov (United States)

Shrot, Yoav; Frydman, Lucio

2011-04-01

A topic of active investigation in 2D NMR relates to the minimum number of scans required for acquiring this kind of spectra, particularly when these are dictated by sampling rather than by sensitivity considerations. Reductions in this minimum number of scans have been achieved by departing from the regular sampling used to monitor the indirect domain, and relying instead on non-uniform sampling and iterative reconstruction algorithms. Alternatively, so-called "ultrafast" methods can compress the minimum number of scans involved in 2D NMR all the way to a minimum number of one, by spatially encoding the indirect domain information and subsequently recovering it via oscillating field gradients. Given ultrafast NMR's simultaneous recording of the indirect- and direct-domain data, this experiment couples the spectral constraints of these orthogonal domains - often calling for the use of strong acquisition gradients and large filter widths to fulfill the desired bandwidth and resolution demands along all spectral dimensions. This study discusses a way to alleviate these demands, and thereby enhance the method's performance and applicability, by combining spatial encoding with iterative reconstruction approaches. Examples of these new principles are given based on the compressed-sensed reconstruction of biomolecular 2D HSQC ultrafast NMR data, an approach that we show enables a decrease of the gradient strengths demanded in this type of experiments by up to 80%. Copyright © 2011 Elsevier Inc. All rights reserved.

Functional studies using NMR

International Nuclear Information System (INIS)

McCready, V.R.; Leach, M.; Ell, P.J.

1987-01-01

This volume is based on a series of lectures delivered at a one-day teaching symposium on functional and metabolic aspects of NMR measurements held at the Middlesex Hospital Medical School on 1st September 1985 as a part of the European Nuclear Medicine Society Congress. Currently the major emphasis in medical NMR in vivo is on its potential to image and display abnormalities in conventional radiological images, providing increased contrast between normal and abnormal tissue, improved definition of vasculature, and possibly an increased potential for differential diagnosis. Although these areas are undeniably of major importance, it is probable that NMR will continue to complement conventional measurement methods. The major potential benefits to be derived from in vivo NMR measurements are likely to arise from its use as an instrument for functional and metabolic studies in both clinical research and in the everyday management of patients. It is to this area that this volume is directed

Model-based control strategies for systems with constraints of the program type

Science.gov (United States)

Jarzębowska, Elżbieta

2006-08-01

The paper presents a model-based tracking control strategy for constrained mechanical systems. Constraints we consider can be material and non-material ones referred to as program constraints. The program constraint equations represent tasks put upon system motions and they can be differential equations of orders higher than one or two, and be non-integrable. The tracking control strategy relies upon two dynamic models: a reference model, which is a dynamic model of a system with arbitrary order differential constraints and a dynamic control model. The reference model serves as a motion planner, which generates inputs to the dynamic control model. It is based upon a generalized program motion equations (GPME) method. The method enables to combine material and program constraints and merge them both into the motion equations. Lagrange's equations with multipliers are the peculiar case of the GPME, since they can be applied to systems with constraints of first orders. Our tracking strategy referred to as a model reference program motion tracking control strategy enables tracking of any program motion predefined by the program constraints. It extends the "trajectory tracking" to the "program motion tracking". We also demonstrate that our tracking strategy can be extended to a hybrid program motion/force tracking.

Automated Generation of OCL Constraints: NL based Approach vs Pattern Based Approach

Directory of Open Access Journals (Sweden)

IMRAN SARWAR BAJWA

2017-04-01

Full Text Available This paper presents an approach used for automated generations of software constraints. In this model, the SBVR (Semantics of Business Vocabulary and Rules based semi-formal representation is obtained from the syntactic and semantic analysis of a NL (Natural Language (such as English sentence. A SBVR representation is easy to translate to other formal languages as SBVR is based on higher-order logic like other formal languages such as OCL (Object Constraint Language. The proposed model endows with a systematic and powerful system of incorporating NL knowledge on the formal languages. A prototype is constructed in Java (an Eclipse plug-in as a proof of the concept. The performance was tested for a few sample texts taken from existing research thesis reports and books

1H NMR-based spectroscopy detects metabolic alterations in serum of patients with early-stage ulcerative colitis

International Nuclear Information System (INIS)

Zhang, Ying; Lin, Lianjie; Xu, Yanbin; Lin, Yan; Jin, Yu; Zheng, Changqing

2013-01-01

Highlights: •Twenty ulcerative colitis patients and nineteen healthy controls were enrolled. •Increased 3-hydroxybutyrate, glucose, phenylalanine, and decreased lipid were found. •We report early stage diagnosis of ulcerative colitis using NMR-based metabolomics. -- Abstract: Ulcerative colitis (UC) has seriously impaired the health of citizens. Accurate diagnosis of UC at an early stage is crucial to improve the efficiency of treatment and prognosis. In this study, proton nuclear magnetic resonance ( 1 H NMR)-based metabolomic analysis was performed on serum samples collected from active UC patients (n = 20) and healthy controls (n = 19), respectively. The obtained spectral profiles were subjected to multivariate data analysis. Our results showed that consistent metabolic alterations were present between the two groups. Compared to healthy controls, UC patients displayed increased 3-hydroxybutyrate, β-glucose, α-glucose, and phenylalanine, but decreased lipid in serum. These findings highlight the possibilities of NMR-based metabolomics as a non-invasive diagnostic tool for UC

FoodPro: A Web-Based Tool for Evaluating Covariance and Correlation NMR Spectra Associated with Food Processes

Directory of Open Access Journals (Sweden)

Eisuke Chikayama

2016-10-01

Full Text Available Foods from agriculture and fishery products are processed using various technologies. Molecular mixture analysis during food processing has the potential to help us understand the molecular mechanisms involved, thus enabling better cooking of the analyzed foods. To date, there has been no web-based tool focusing on accumulating Nuclear Magnetic Resonance (NMR spectra from various types of food processing. Therefore, we have developed a novel web-based tool, FoodPro, that includes a food NMR spectrum database and computes covariance and correlation spectra to tasting and hardness. As a result, FoodPro has accumulated 236 aqueous (extracted in D2O and 131 hydrophobic (extracted in CDCl3 experimental bench-top 60-MHz NMR spectra, 1753 tastings scored by volunteers, and 139 hardness measurements recorded by a penetrometer, all placed into a core database. The database content was roughly classified into fish and vegetable groups from the viewpoint of different spectrum patterns. FoodPro can query a user food NMR spectrum, search similar NMR spectra with a specified similarity threshold, and then compute estimated tasting and hardness, covariance, and correlation spectra to tasting and hardness. Querying fish spectra exemplified specific covariance spectra to tasting and hardness, giving positive covariance for tasting at 1.31 ppm for lactate and 3.47 ppm for glucose and a positive covariance for hardness at 3.26 ppm for trimethylamine N-oxide.

FoodPro: A Web-Based Tool for Evaluating Covariance and Correlation NMR Spectra Associated with Food Processes.

Science.gov (United States)

Chikayama, Eisuke; Yamashina, Ryo; Komatsu, Keiko; Tsuboi, Yuuri; Sakata, Kenji; Kikuchi, Jun; Sekiyama, Yasuyo

2016-10-19

Foods from agriculture and fishery products are processed using various technologies. Molecular mixture analysis during food processing has the potential to help us understand the molecular mechanisms involved, thus enabling better cooking of the analyzed foods. To date, there has been no web-based tool focusing on accumulating Nuclear Magnetic Resonance (NMR) spectra from various types of food processing. Therefore, we have developed a novel web-based tool, FoodPro, that includes a food NMR spectrum database and computes covariance and correlation spectra to tasting and hardness. As a result, FoodPro has accumulated 236 aqueous (extracted in D₂O) and 131 hydrophobic (extracted in CDCl₃) experimental bench-top 60-MHz NMR spectra, 1753 tastings scored by volunteers, and 139 hardness measurements recorded by a penetrometer, all placed into a core database. The database content was roughly classified into fish and vegetable groups from the viewpoint of different spectrum patterns. FoodPro can query a user food NMR spectrum, search similar NMR spectra with a specified similarity threshold, and then compute estimated tasting and hardness, covariance, and correlation spectra to tasting and hardness. Querying fish spectra exemplified specific covariance spectra to tasting and hardness, giving positive covariance for tasting at 1.31 ppm for lactate and 3.47 ppm for glucose and a positive covariance for hardness at 3.26 ppm for trimethylamine N -oxide.

A novel tridentate Schiff base dioxo-molybdenum(VI) complex: synthesis, experimental and theoretical studies on its crystal structure, FTIR, UV-visible, ¹H NMR and ¹³C NMR spectra.

Science.gov (United States)

Saheb, Vahid; Sheikhshoaie, Iran; Stoeckli-Evans, Helen

2012-09-01

A new dioxo-molybdenum(VI) complex [MoO(2)(L)(H(2)O)] has been synthesized, using 5-methoxy 2-[(2-hydroxypropylimino)methyl]phenol as tridentate ONO donor Schiff base ligand (H(2)L) and MoO(2)(acac)(2). The yellow crystals of the compound are used for single-crystal X-ray analysis and measuring Fourier Transform Infrared (FTIR), UV-visible, (1)H NMR and (13)C NMR spectra. Electronic structure calculations at the B3LYP and PW91PW91 levels of theory are performed to optimize the molecular geometry and to calculate the UV-visible, FTIR, (1)H NMR and (13)C NMR spectra of the compound. Vibrational assignments and analysis of the fundamental modes of the compound are performed. Time-dependent density functional theory (TDDFT) method is used to calculate the electronic transitions of the complex. All theoretical methods can well reproduce the structure of the compound. The (1)H NMR shielding tensors computed at the B3LYP/DGDZVP level of theory is in agreement with experimental (1)H NMR spectra. However, the (13)C NMR shielding tensors computed at the B3LYP level, employing a combined basis set of DGDZVP for Mo and 6-31+G(2df,p) for other atoms, are in better agreement with experimental (13)C NMR spectra. The electronic transitions calculated at the B3LYP/DGDZVP level by using TD-DFT method is in accordance with the observed UV-visible spectrum of the compound. Copyright © 2012 Elsevier B.V. All rights reserved.

Constraint-plane-based synthesis and topology variation of a class of metamorphic parallel mechanisms

International Nuclear Information System (INIS)

Gan, Dongming; Dias, Jorge; Seneviratne, Lakmal; Dai, Jian S.

2014-01-01

This paper investigates various topologies and mobility of a class of metamorphic parallel mechanisms synthesized with reconfigurable rTPS limbs. Based on the reconfigurable Hooke (rT) joint, the rTPS limb has two phases which result in parallel mechanisms having ability of mobility change. While in one phase the limb has no constraint to the platform, in the other it constrains the spherical joint center to lie on a plane which is used to demonstrate different topologies of the nrTPS metamorphic parallel mechanisms by investigating various relations (parallel or intersecting) among the n constraint planes (n = 2,3,..,6). Geometric constraint equations of the platform rotation matrix and translation vector are set up based on the point-plane constraint, which reveals mobility and redundant geometric conditions of the mechanism topologies. By altering the limbs into the non-constraint phase without constraint plane, new mechanism phases are deduced with mobility change based on each mechanism topology.

Bentonite pore structure based on SAXS, chloride exclusion and NMR studies

International Nuclear Information System (INIS)

Muurinen, A.; Carlsson, T.

2013-11-01

Water-saturated bentonite is planned to be used in many countries as an important barrier component in high-level nuclear waste (HLW) repositories. Knowledge about the microstructure of the bentonite and the distribution of water between interlayer and non-interlayer pores is important for modelling of long-term processes. In this work the microstructure of water-saturated samples prepared from Na montmorillonite, Ca-montmorillonite, sodium bentonite MX-80 and calcium bentonite Deponit CaN were studied with nuclear magnetic resonance (NMR) and small-angle xray scattering spectroscopy (SAXS). The sample dry densities ranged between 0.3 and 1.6 g/cm 3 . The NMR technique was used to get information about the volumes of different water types in the bentonite samples. The results were obtained using 1H NMR spin-lattice T 1ρ relaxation time measurements using the short inter-pulse method. The interpretation of the NMR results was made by fitting distributions of exponentials to observed decay curves. The SAXS measurements were used to get information about the size distribution of the interlayer distance of montmorillonite. The chloride porosity measurements and Donnan exclusion calculations were used together with the SAXS results for evaluation of the bentonite microstructure. The NMR studies and SAXS studies coupled with Cl porosity measurements provided very similar pictures of how the porewater is divided in interlayer and non-interlayer water in MX-80 bentonite. In the case where MX-80 of a dry density 1.6 g/cm 3 was equilibrated with 0.1 M NaCl solution, the results indicated an interlayer porosity of 30 % and non-interlayer porosity of 12 %. The interlayer space mainly contained two water layers but also spaces with more water layers were present. The average size of the non-interlayer pores was evaluated to be 120 - 150 A. From the montmorillonite surface area 98 % was interlayer and 2 % non-interlayer. Evaluation of the interlayer and non

Home-based Constraint Induced Movement Therapy Poststroke

OpenAIRE

Stephen Isbel HScD; Christine Chapparo PhD; David McConnell PhD; Judy Ranka PhD

2014-01-01

Background: This study examined the efficacy of a home-based Constraint Induced Movement Therapy (CI Therapy) protocol with eight poststroke survivors. Method: Eight ABA, single case experiments were conducted in the homes of poststroke survivors. The intervention comprised restraint of the intact upper limb in a mitt for 21 days combined with a home-based and self-directed daily activity regime. Motor changes were measured using The Wolf Motor Function Test (WMFT) and the Motor Activity L...

New methods for the correction of 31P NMR spectra in in vivo NMR spectroscopy

International Nuclear Information System (INIS)

Starcuk, Z.; Bartusek, K.; Starcuk, Z. jr.

1994-01-01

The new methods for the correction of 31 P NMR spectra in vivo NMR spectroscopy have been performed. A method for the baseline correction of the spectra which represents a combination of time-domain and frequency-domain has been discussed.The method is very fast and efficient for minimization of base line artifacts of biological tissues impact

Inverse problem for in vivo NMR spatial localization

International Nuclear Information System (INIS)

Hasenfeld, A.C.

1985-11-01

The basic physical problem of NMR spatial localization is considered. To study diseased sites, one must solve the problem of adequately localizing the NMR signal. We formulate this as an inverse problem. As the NMR Bloch equations determine the motion of nuclear spins in applied magnetic fields, a theoretical study is undertaken to answer the question of how to design magnetic field configurations to achieve these localized excited spin populations. Because of physical constraints in the production of the relevant radiofrequency fields, the problem factors into a temporal one and a spatial one. We formulate the temporal problem as a nonlinear transformation, called the Bloch Transform, from the rf input to the magnetization response. In trying to invert this transformation, both linear (for the Fourier Transform) and nonlinear (for the Bloch Transform) modes of radiofrequency excitation are constructed. The spatial problem is essentially a statics problem for the Maxwell equations of electromagnetism, as the wavelengths of the radiation considered are on the order of ten meters, and so propagation effects are negligible. In the general case, analytic solutions are unavailable, and so the methods of computer simulation are used to map the rf field spatial profiles. Numerical experiments are also performed to verify the theoretical analysis, and experimental confirmation of the theory is carried out on the 0.5 Tesla IBM/Oxford Imaging Spectrometer at the LBL NMR Medical Imaging Facility. While no explicit inverse is constructed to ''solve'' this problem, the combined theoretical/numerical analysis is validated experimentally, justifying the approximations made. 56 refs., 31 figs

Inverse problem for in vivo NMR spatial localization

Energy Technology Data Exchange (ETDEWEB)

Hasenfeld, A.C.

1985-11-01

The basic physical problem of NMR spatial localization is considered. To study diseased sites, one must solve the problem of adequately localizing the NMR signal. We formulate this as an inverse problem. As the NMR Bloch equations determine the motion of nuclear spins in applied magnetic fields, a theoretical study is undertaken to answer the question of how to design magnetic field configurations to achieve these localized excited spin populations. Because of physical constraints in the production of the relevant radiofrequency fields, the problem factors into a temporal one and a spatial one. We formulate the temporal problem as a nonlinear transformation, called the Bloch Transform, from the rf input to the magnetization response. In trying to invert this transformation, both linear (for the Fourier Transform) and nonlinear (for the Bloch Transform) modes of radiofrequency excitation are constructed. The spatial problem is essentially a statics problem for the Maxwell equations of electromagnetism, as the wavelengths of the radiation considered are on the order of ten meters, and so propagation effects are negligible. In the general case, analytic solutions are unavailable, and so the methods of computer simulation are used to map the rf field spatial profiles. Numerical experiments are also performed to verify the theoretical analysis, and experimental confirmation of the theory is carried out on the 0.5 Tesla IBM/Oxford Imaging Spectrometer at the LBL NMR Medical Imaging Facility. While no explicit inverse is constructed to ''solve'' this problem, the combined theoretical/numerical analysis is validated experimentally, justifying the approximations made. 56 refs., 31 figs.

Measurement of electron paramagnetic resonance using terahertz time-domain spectroscopy.

Science.gov (United States)

Kozuki, Kohei; Nagashima, Takeshi; Hangyo, Masanori

2011-12-05

We present a frequency-domain electron spin resonance (ESR) measurement system using terahertz time-domain spectroscopy. A crossed polarizer technique is utilized to increase the sensitivity in detecting weak ESR signals of paramagnets caused by magnetic dipole transitions between magnetic sublevels. We demonstrate the measurements of ESR signal of paramagnetic copper(II) sulfate pentahydrate with uniaxial anisotropy of the g-factor under magnetic fields up to 10 T. The lineshape of the obtained ESR signals agrees well with the theoretical predictions for a powder sample with the uniaxial anisotropy.

Towards interpretation of intermolecular paramagnetic relaxation enhancement outside the fast exchange limit.

Science.gov (United States)

Ceccon, Alberto; Marius Clore, G; Tugarinov, Vitali

2016-09-01

In an exchanging system between major and minor species, the transverse paramagnetic relaxation enhancement rate observed on the resonances of the major species (Γ 2 (app) ) is dependent upon the exchange regime between the species. Quantitative analysis of PRE data in such systems typically assumes that the overall exchange rate k ex between the species is fast on the PRE time scale (k ex ≫ Γ2). Recently, we have characterized the kinetics of binding of the model protein ubiquitin to large (LUV) and small (SUV) unilamellar lipid-based nanoparticles or liposomes (Ceccon A, Tugarinov V, Bax A, Clore GM (2016). J Am Chem Soc 138:5789-5792). Building upon these results and taking advantage of a strong paramagnetic agent with an isotropic g-tensor, Gd(3+), we were able to measure intermolecular methyl carbon and proton PREs between paramagnetically-tagged liposomes and ubiquitin. In the limit of fast exchange (k ex ≫ Γ2) the ratio of the apparent proton to carbon methyl PREs, ((1)Hm-Γ 2 (app) )/((13)Cm-Γ 2 (app) ), is equal to the square of the ratio of the gyromagnetic ratios of the two nuclei, (γΗ/γC)(2). However, outside the fast exchange regime, under intermediate exchange conditions (e.g. when Γ2 is comparable in magnitude to k ex) the ((1)Hm-Γ 2 (app) )/((13)Cm-Γ 2 (app) ) ratio provides a reliable measure of the 'true' methyl PREs.

Proton NMR Studies of a Large Protein. pH, Substrate Titrations, and NOESY Experiments with Perdeuterated Yeast Phosphoglycerate Kinase Containing [ 1H]Histidine Residues

Science.gov (United States)

Pappu, K. M.; Serpersu, E. H.

Fully deuterated yeast phosphoglycerate kinase ([ 2H]PGK) was prepared biosynthetically with only histidine side chains of normal ( 1H) isotopic composition. The 1H NMR spectrum of this enzyme([ 1H]His[ 2H]PGK) showed that the histidine side chains are clearly visible as sharp signals. Thus detailed structural studies by 1H NMR became feasible with isotope-hybrid phosphoglycerate kinase which is otherwise too large ( Mr ˜ 46,000) for conventional 1H NMR studies. Proton signals of bound substrates were visible in the 1H NMR spectrum even with a substrate-to-enzyme ratio of less than 1/2 (mol/mol). The 2D NOESY spectrum of enzyme-MgdATP-glycerol 3-phosphate complex showed that, although protein concentration was very high (1.5 m M), no intraprotein cross peaks were observed other than those of intraresidue histidine NOE cross peaks. In addition, intrasubstrate NOEs and intermolecular NOEs between histidine and substrate protons were visible at a 1.5/1 substrate/enzyme (mol/mol) ratio. Paramagnetic effects of a substrate analog, Cr(III)ATP, on some of the histidine side chains indicated that the formation of the ternary enzyme-substrate complex causes large conformational changes in the enzyme.

Zeeman-Stern Gerlach deceleration of supersonic beams of paramagnetic particles with traveling waves of magnetic field

International Nuclear Information System (INIS)

Trimeche, Azer

2013-01-01

This work focuses on the study and implementation of a new technique of deceleration of a supersonic beam of paramagnetic particles using a co-moving progressive wave of magnetic field. This technique relies on a method of slowing based on Stern-Gerlach forces acting on a paramagnetic system in motion in the presence of a co-propagating magnetic field. This highly innovative approach has the advantage of being applicable to a wide range of species and opens up new opportunities. A suitable theoretical approach is followed, that allows for a direct link between theory, programming of experimental parameters, and experimental results in a systematic, rational and predictive manner. The understanding and control of the dynamics of trapping at a given speed, acceleration and deceleration require decoupling between the transverse and longitudinal effects of the wave. These effects are clearly visible when the added uniform magnetic field limits the transverse effects of the progressive wave of magnetic field. The outlooks for the new Zeeman Stern Gerlach decelerator are numerous. Deceleration paramagnetic molecules, free radicals and neutrons are possible. (author) [fr

Application of High-Resolution Magic-Angle Spinning NMR Spectroscopy to Define the Cell Uptake of MRI Contrast Agents

Science.gov (United States)

Calabi, Luisella; Alfieri, Goffredo; Biondi, Luca; De Miranda, Mario; Paleari, Lino; Ghelli, Stefano

2002-06-01

A new method, based on proton high-resolution magic-angle spinning ( 1H HR-MAS) NMR spectroscopy, has been employed to study the cell uptake of magnetic resonance imaging contrast agents (MRI-CAs). The method was tested on human red blood cells (HRBC) and white blood cells (HWBC) by using three gadolinium complexes, widely used in diagnostics, Gd-BOPTA, Gd-DTPA, and Gd-DOTA, and the analogous complexes obtained by replacing Gd(III) with Dy(III), Nd(III), and Tb(III) (i.e., complexes isostructural to the ones of gadolinium but acting as shift agents). The method is based on the evaluation of the magnetic effects, line broadening, or induced lanthanide shift (LIS) caused by these complexes on NMR signals of intra- and extracellular water. Since magnetic effects are directly linked to permeability, this method is direct. In all the tests, these magnetic effects were detected for the extracellular water signal only, providing a direct proof that these complexes are not able to cross the cell membrane. Line broadening effects (i.e., the use of gadolinium complexes) only allow qualitative evaluations. On the contrary, LIS effects can be measured with high precision and they can be related to the concentration of the paramagnetic species in the cellular compartments. This is possible because the HR-MAS technique provides the complete elimination of bulk magnetic susceptibility (BMS) shift and the differentiation of extra- and intracellular water signals. Thus with this method, the rapid quantification of the MRI-CA amount inside and outside the cells is actually feasible.

Single ferromagnetic fluctuations in UCoGe revealed by 73Ge- and 59Co-NMR studies

Science.gov (United States)

Manago, Masahiro; Ishida, Kenji; Aoki, Dai

2018-02-01

73Ge and 59Co nuclear magnetic resonance (NMR) and nuclear quadrupole resonance (NQR) measurements have been performed on a 73Ge-enriched single-crystalline sample of the ferromagnetic superconductor UCoGe in the paramagnetic state. The 73Ge NQR parameters deduced from NQR and NMR are close to those of another isostructural ferromagnetic superconductor URhGe. The Knight shifts of the Ge and Co sites are well scaled to each other when the magnetic field is parallel to the b or c axis. The hyperfine coupling constants of Ge are estimated to be close to those of Co. The large difference of spin susceptibilities between the a and b axes could lead to the different response of the superconductivity and ferromagnetism with the field parallel to these directions. The temperature dependence of the nuclear spin-lattice relaxation rates 1 /T1 at the two sites is similar to each other above 5 K. These results indicate that the itinerant U-5 f electrons are responsible for the ferromagnetism in this compound, consistent with previous studies. The similarities and differences in the three ferromagnetic superconductors are discussed.

APSY-NMR for protein backbone assignment in high-throughput structural biology

Energy Technology Data Exchange (ETDEWEB)

Dutta, Samit Kumar; Serrano, Pedro; Proudfoot, Andrew; Geralt, Michael [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States); Pedrini, Bill [Paul Scherrer Institute (PSI), SwissFEL Project (Switzerland); Herrmann, Torsten [Université de Lyon, Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1 (France); Wüthrich, Kurt, E-mail: wuthrich@scripps.edu [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States)

2015-01-15

A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90 % of the residues. For most proteins the APSY data acquisition was completed in less than 30 h. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [{sup 1}H,{sup 1}H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination.

High resolution NMR theory and chemical applications

CERN Document Server

Becker, Edwin D

1999-01-01

High Resolution NMR provides a broad treatment of the principles and theory of nuclear magnetic resonance (NMR) as it is used in the chemical sciences. It is written at an "intermediate" level, with mathematics used to augment, rather than replace, clear verbal descriptions of the phenomena. The book is intended to allow a graduate student, advanced undergraduate, or researcher to understand NMR at a fundamental level, and to see illustrations of the applications of NMR to the determination of the structure of small organic molecules and macromolecules, including proteins. Emphasis is on the study of NMR in liquids, but the treatment also includes high resolution NMR in the solid state and the principles of NMR imaging and localized spectroscopy. Careful attention is given to developing and interrelating four approaches - steady state energy levels, the rotating vector picture, the density matrix, and the product operator formalism. The presentation is based on the assumption that the reader has an acquaintan...

Nature of the magnetic susceptibility of dysprosium. Paramagnetic susceptibility of dysprosium - yttrium alloys

International Nuclear Information System (INIS)

Demidov, V.G.; Levitin, R.Z.; Chistyakov, O.D.

1976-01-01

The paramagnetic susceptibility of single crystals of dysprosium-yttirum alloys is measured in the basal plane and along the hexagonal axis. It is shown that the susceptibility of the alloys obeys the Curie-Weiss law, the effective magnetic moments allong the different directions being the same and the paramagnetic Curie temperatures being different. The difference between the paramagnetic Curie temperatures in the basal plane and along the hexagonal axis is independent of the dysprosium concentration in the alloy. As a comparison with the theoretical models of magnetic anisotropy shows, this is an indication that the magnetic anisotropy of dysprosium - yttrium alloys is of a single-ion nature

Flow units from integrated WFT and NMR data

Energy Technology Data Exchange (ETDEWEB)

Kasap, E.; Altunbay, M.; Georgi, D.

1997-08-01

Reliable and continuous permeability profiles are vital as both hard and soft data required for delineating reservoir architecture. They can improve the vertical resolution of seismic data, well-to-well stratigraphic correlations, and kriging between the well locations. In conditional simulations, permeability profiles are imposed as the conditioning data. Variograms, covariance functions and other geostatistical indicators are more reliable when based on good quality permeability data. Nuclear Magnetic Resonance (NMR) logging and Wireline Formation Tests (WFT) separately generate a wealth of information, and their synthesis extends the value of this information further by providing continuous and accurate permeability profiles without increasing the cost. NMR and WFT data present a unique combination because WFTs provide discrete, in situ permeability based on fluid-flow, whilst NMR responds to the fluids in the pore space and yields effective porosity, pore-size distribution, bound and moveable fluid saturations, and permeability. The NMR permeability is derived from the T{sub 2}-distribution data. Several equations have been proposed to transform T{sub 2} data to permeability. Regardless of the transform model used, the NMR-derived permeabilities depend on interpretation parameters that may be rock specific. The objective of this study is to integrate WFT permeabilities with NMR-derived, T{sub 2} distribution-based permeabilities and thereby arrive at core quality, continuously measured permeability profiles. We outlined the procedures to integrate NMR and WFT data and applied the procedure to a field case. Finally, this study advocates the use of hydraulic unit concepts to extend the WFT-NMR derived, core quality permeabilities to uncored intervals or uncored wells.

Fast field cycling NMR relaxometry characterization of biochars obtained from an industrial thermochemical process

Energy Technology Data Exchange (ETDEWEB)

De Pasquale, Claudio; Marsala, Valentina; Alonzo, Giuseppe; Conte, Pellegrino [Universita degli Studi di Palermo (Italy). Dipt. dei Sistemi Agro-Ambientali; Berns, Anne E. [Forschungszentrum Juelich GmbH (Germany). Inst. of Bio- and Geosciences (IBG-3); Valagussa, Massimo [M.A.C. Minoprio Analisi e Certificazioni S.r.l., Vertemate con Minoprio, CO (Italy); Pozzi, Alessandro [A.G.T. Advanced Gasification Technology S.r.l., Arosio, CO (Italy)

2012-09-15

Purpose: Biochar has unique properties which make it a powerful tool to increase soil fertility and to contribute to the decrease of the amount of atmospheric carbon dioxide through the mechanisms of C sequestration in soils. Chemical and physical biochar characteristics depend upon the technique used for its production and the biomass nature. For this reason, biochar characterization is very important in order to address its use either for agricultural or environmental purposes. Materials and methods: Three different biochars obtained from an industrial gasification process were selected in order to establish their chemical and physical peculiarities for a possible use in agronomical practices. They were obtained by charring residues from the wine-making industry (marc) and from poplar and conifer forests. Routine analyses such as pH measurements, elemental composition, and ash and metal contents were performed together with the evaluation of the cross-polarization magic angle spinning (CPMAS) {sup 13}C NMR spectra of all the biochar samples. Finally, relaxometry properties of water-saturated biochars were retrieved in order to obtain information on pore size distribution. Results and discussion: All the biochars revealed basic pH values due to their large content of alkaline metals. The quality of CPMAS {sup 13}C NMR spectra, which showed the typical signal pattern for charred systems, was not affected by the presence of paramagnetic centers. Although paramagnetism was negligible for the acquisition of solid state spectra, it was effective in some of the relaxometry experiments. For this reason, no useful information could be retrieved about water dynamics in marc char. Conversely, both relaxograms and nuclear magnetic resonance dispersion profiles of poplar and conifer chars indicated that poplar char is richer in small-sized pores, while larger pores appear to be characteristic for the conifer char. Conclusions: This study showed the potential of relaxometry in

Multiparameter elastic full waveform inversion with facies-based constraints

Science.gov (United States)

Zhang, Zhen-dong; Alkhalifah, Tariq; Naeini, Ehsan Zabihi; Sun, Bingbing

2018-06-01

Full waveform inversion (FWI) incorporates all the data characteristics to estimate the parameters described by the assumed physics of the subsurface. However, current efforts to utilize FWI beyond improved acoustic imaging, like in reservoir delineation, faces inherent challenges related to the limited resolution and the potential trade-off between the elastic model parameters. Some anisotropic parameters are insufficiently updated because of their minor contributions to the surface collected data. Adding rock physics constraints to the inversion helps mitigate such limited sensitivity, but current approaches to add such constraints are based on including them as a priori knowledge mostly valid around the well or as a global constraint for the whole area. Since similar rock formations inside the Earth admit consistent elastic properties and relative values of elasticity and anisotropy parameters (this enables us to define them as a seismic facies), utilizing such localized facies information in FWI can improve the resolution of inverted parameters. We propose a novel approach to use facies-based constraints in both isotropic and anisotropic elastic FWI. We invert for such facies using Bayesian theory and update them at each iteration of the inversion using both the inverted models and a priori information. We take the uncertainties of the estimated parameters (approximated by radiation patterns) into consideration and improve the quality of estimated facies maps. Four numerical examples corresponding to different acquisition, physical assumptions and model circumstances are used to verify the effectiveness of the proposed method.

Multiparameter Elastic Full Waveform Inversion with Facies-based Constraints

Science.gov (United States)

Zhang, Zhen-dong; Alkhalifah, Tariq; Naeini, Ehsan Zabihi; Sun, Bingbing

2018-03-01

Full waveform inversion (FWI) incorporates all the data characteristics to estimate the parameters described by the assumed physics of the subsurface. However, current efforts to utilize full waveform inversion beyond improved acoustic imaging, like in reservoir delineation, faces inherent challenges related to the limited resolution and the potential trade-off between the elastic model parameters. Some anisotropic parameters are insufficiently updated because of their minor contributions to the surface collected data. Adding rock physics constraints to the inversion helps mitigate such limited sensitivity, but current approaches to add such constraints are based on including them as a priori knowledge mostly valid around the well or as a global constraint for the whole area. Since similar rock formations inside the Earth admit consistent elastic properties and relative values of elasticity and anisotropy parameters (this enables us to define them as a seismic facies), utilizing such localized facies information in FWI can improve the resolution of inverted parameters. We propose a novel approach to use facies-based constraints in both isotropic and anisotropic elastic FWI. We invert for such facies using Bayesian theory and update them at each iteration of the inversion using both the inverted models and a prior information. We take the uncertainties of the estimated parameters (approximated by radiation patterns) into consideration and improve the quality of estimated facies maps. Four numerical examples corresponding to different acquisition, physical assumptions and model circumstances are used to verify the effectiveness of the proposed method.

Multiparameter Elastic Full Waveform Inversion with Facies-based Constraints

KAUST Repository

Zhang, Zhendong

2018-03-20

Full waveform inversion (FWI) incorporates all the data characteristics to estimate the parameters described by the assumed physics of the subsurface. However, current efforts to utilize full waveform inversion beyond improved acoustic imaging, like in reservoir delineation, faces inherent challenges related to the limited resolution and the potential trade-off between the elastic model parameters. Some anisotropic parameters are insufficiently updated because of their minor contributions to the surface collected data. Adding rock physics constraints to the inversion helps mitigate such limited sensitivity, but current approaches to add such constraints are based on including them as a priori knowledge mostly valid around the well or as a global constraint for the whole area. Since similar rock formations inside the Earth admit consistent elastic properties and relative values of elasticity and anisotropy parameters (this enables us to define them as a seismic facies), utilizing such localized facies information in FWI can improve the resolution of inverted parameters. We propose a novel approach to use facies-based constraints in both isotropic and anisotropic elastic FWI. We invert for such facies using Bayesian theory and update them at each iteration of the inversion using both the inverted models and a prior information. We take the uncertainties of the estimated parameters (approximated by radiation patterns) into consideration and improve the quality of estimated facies maps. Four numerical examples corresponding to different acquisition, physical assumptions and model circumstances are used to verify the effectiveness of the proposed method.

Paramagnetic resonance and susceptibility of ilmenite, FeTiO3 crystal

Science.gov (United States)

Mcdonald, P. F.; Parasiris, A.; Pandey, R. K.; Gries, B. L.; Kirk, W. P.

1991-01-01

Large high-purity single crystals of FeTiO3 with ilmenite structure have been grown from a stoichiometric melt of Fe2O3 and TiO2 under an inert atmosphere using the modified Czochralski technique. Susceptibility and X-band paramagnetic resonance studies have been performed. Susceptibility measurements indicate a Neel temperature of about 59 K. The paramagnetic resonance spectrum for magnetic field perpendicular to the crystal c axis consists of a portion of a single, very intense approximately Lorentzian absorption line with its peak at about 600 G and half width at half maximum almost 1200 G. The absorption extends to zero magnetic field. For magnetic field approximately parallel to the c axis, the paramagnetic absorption is much smaller and may be considered a superposition of two approximately Lorentzian line shapes. The magnetic resonance measurements indicate a weak temperature dependence and large angular anisotropy.

Fourier transform NMR

International Nuclear Information System (INIS)

Hallenga, K.

1991-01-01

This paper discusses the concept of Fourier transformation one of the many precious legacies of the French mathematician Jean Baptiste Joseph Fourier, essential for understanding the link between continuous-wave (CW) and Fourier transform (FT) NMR. Although in modern FT NMR the methods used to obtain a frequency spectrum from the time-domain signal may vary greatly, from the efficient Cooley-Tukey algorithm to very elaborate iterative least-square methods based other maximum entropy method or on linear prediction, the principles for Fourier transformation are unchanged and give invaluable insight into the interconnection of many pairs of physical entities called Fourier pairs

A Preliminary Investigation of NSCL/P Plasma and Urine in Guizhou Province in China Using NMR-Based Metabonomics.

Science.gov (United States)

Lei, Huang Guang; Hong, Luo; Kun, Song Ju; Hai, Yin Xin; Dong, Wang Ya; Ke, Zhao; Ping, Xu; Hao, Chen

2013-09-01

Objective : To assess the feasibility of metabonomics in clinical studies. This is a pilot study introducing nuclear magnetic resonance (NMR)-based metabonomics to elucidate and compare the metabolism of patients with nonsyndromic cleft lip and/or palate (NSCL/P) and children without orofacial clefts. Methods : High-resolution (1)H NMR spectroscopy was performed on plasma and urine samples obtained from NSCL/P and healthy children. The (1)H NMR spectra were further analyzed with principal component analysis. Results : Compared to the control group, the level of low-molecular-weight metabolites in plasma such as asparagine was higher in NSCL/P patients, while arginine, lysine, acetate, lactate, proline, glutamine, pyruvate, creatinine, choline, and β-glucose were lower. The carnitine, citrate, and formate excretion in urine appeared to be higher in the healthy children, while the NSCL/P group excreted higher concentrations of aspartic acid and phenylalanine in urine. Conclusion : The present study clearly demonstrated the great potential of NMR-based metabonomics in elucidating NSCL/P plasma metabolism and the possible application of this technology in clinical diagnosis and screening.

A single-board NMR spectrometer based on a software defined radio architecture

International Nuclear Information System (INIS)

Tang, Weinan; Wang, Weimin

2011-01-01

A single-board software defined radio (SDR) spectrometer for nuclear magnetic resonance (NMR) is presented. The SDR-based architecture, realized by combining a single field programmable gate array (FPGA) and a digital signal processor (DSP) with peripheral radio frequency (RF) front-end circuits, makes the spectrometer compact and reconfigurable. The DSP, working as a pulse programmer, communicates with a personal computer via a USB interface and controls the FPGA through a parallel port. The FPGA accomplishes digital processing tasks such as a numerically controlled oscillator (NCO), digital down converter (DDC) and gradient waveform generator. The NCO, with agile control of phase, frequency and amplitude, is part of a direct digital synthesizer that is used to generate an RF pulse. The DDC performs quadrature demodulation, multistage low-pass filtering and gain adjustment to produce a bandpass signal (receiver bandwidth from 3.9 kHz to 10 MHz). The gradient waveform generator is capable of outputting shaped gradient pulse waveforms and supports eddy-current compensation. The spectrometer directly acquires an NMR signal up to 30 MHz in the case of baseband sampling and is suitable for low-field (<0.7 T) application. Due to the featured SDR architecture, this prototype has flexible add-on ability and is expected to be suitable for portable NMR systems

Influence of Freezing and Storage Procedure on Human Urine Samples in NMR-Based Metabolomics

Directory of Open Access Journals (Sweden)

Burkhard Luy

2013-04-01

Full Text Available It is consensus in the metabolomics community that standardized protocols should be followed for sample handling, storage and analysis, as it is of utmost importance to maintain constant measurement conditions to identify subtle biological differences. The aim of this work, therefore, was to systematically investigate the influence of freezing procedures and storage temperatures and their effect on NMR spectra as a potentially disturbing aspect for NMR-based metabolomics studies. Urine samples were collected from two healthy volunteers, centrifuged and divided into aliquots. Urine aliquots were frozen either at −20 °C, on dry ice, at −80 °C or in liquid nitrogen and then stored at −20 °C, −80 °C or in liquid nitrogen vapor phase for 1–5 weeks before NMR analysis. Results show spectral changes depending on the freezing procedure, with samples frozen on dry ice showing the largest deviations. The effect was found to be based on pH differences, which were caused by variations in CO2 concentrations introduced by the freezing procedure. Thus, we recommend that urine samples should be frozen at −20 °C and transferred to lower storage temperatures within one week and that freezing procedures should be part of the publication protocol.

Influence of Freezing and Storage Procedure on Human Urine Samples in NMR-Based Metabolomics.

Science.gov (United States)

Rist, Manuela J; Muhle-Goll, Claudia; Görling, Benjamin; Bub, Achim; Heissler, Stefan; Watzl, Bernhard; Luy, Burkhard

2013-04-09

It is consensus in the metabolomics community that standardized protocols should be followed for sample handling, storage and analysis, as it is of utmost importance to maintain constant measurement conditions to identify subtle biological differences. The aim of this work, therefore, was to systematically investigate the influence of freezing procedures and storage temperatures and their effect on NMR spectra as a potentially disturbing aspect for NMR-based metabolomics studies. Urine samples were collected from two healthy volunteers, centrifuged and divided into aliquots. Urine aliquots were frozen either at -20 °C, on dry ice, at -80 °C or in liquid nitrogen and then stored at -20 °C, -80 °C or in liquid nitrogen vapor phase for 1-5 weeks before NMR analysis. Results show spectral changes depending on the freezing procedure, with samples frozen on dry ice showing the largest deviations. The effect was found to be based on pH differences, which were caused by variations in CO2 concentrations introduced by the freezing procedure. Thus, we recommend that urine samples should be frozen at -20 °C and transferred to lower storage temperatures within one week and that freezing procedures should be part of the publication protocol.

Theoretical study of the electron paramagnetic resonance ...

Indian Academy of Sciences (India)

conveniently investigated by means of electron paramagnetic resonance (EPR). In ... ion Ir2+ can experience the Jahn–Teller effect by means of vibration interaction, ... Similarly, k. (and k ) are the orbital reduction factors arising from the anisotropic interactions of the orbital angular momentum operator. From the cluster ...

Nonequilibrium ensembles. 3. Spin 1/2 paramagnets

International Nuclear Information System (INIS)

Sobouti, Y.; Khajeh-Pour, M.R.H.

1990-07-01

The thermodynamic state of a paramagnetic substance in which the spin vectors precess coherently is investigated. The state is a time dependent one. The corresponding density matrix and the thermodynamics emerging from it is worked out. A laboratory preparation of such a system is discussed. (author). 3 refs

Ehrlich and sarcoma 180 tumour characterisation and early detection by 1H NMR-based metabonomics of mice serum

International Nuclear Information System (INIS)

Grandizoli, Caroline W.P. da S.; Simonelli, Fabio; Nagata, Noemi; Barison, Andersson; Carrenho, Luise Z.B.; Francisco, Thais M.G. de; Campos, Francinete R.; Santana Filho, Arquimedes P. de; Sassaki, Guilherme L.; Kreuger, Maria R.O.

2014-01-01

The success of cancer treatment is directly related to early detection before symptoms emerge, although nowadays few cancers can be detected early. In this sense, 1 H nuclear magnetic resonance ( 1 H NMR)-based metabonomics was used to identify metabolic changes in biofluid as a consequence of tumours growing in mice. Through partial least squares discriminant analysis (PLS-DA) analysis of 1 H NMR spectra from serum samples it was possible to diagnose Ehrlich ascites and Sarcoma 180 tumours five and ten days after cell inoculation, respectively. Lipids, lipoproteins and lactate were the main biomarkers at onset as well as in the progress of carcinogenic process. Thus, NMR-based metabonomics can be a valuable tool to study the effects of tumour establishment on the chemical composition of biofluids. (author)

Characteristic Model-Based Robust Model Predictive Control for Hypersonic Vehicles with Constraints

Directory of Open Access Journals (Sweden)

Jun Zhang

2017-06-01

Full Text Available Designing robust control for hypersonic vehicles in reentry is difficult, due to the features of the vehicles including strong coupling, non-linearity, and multiple constraints. This paper proposed a characteristic model-based robust model predictive control (MPC for hypersonic vehicles with reentry constraints. First, the hypersonic vehicle is modeled by a characteristic model composed of a linear time-varying system and a lumped disturbance. Then, the identification data are regenerated by the accumulative sum idea in the gray theory, which weakens effects of the random noises and strengthens regularity of the identification data. Based on the regenerated data, the time-varying parameters and the disturbance are online estimated according to the gray identification. At last, the mixed H2/H∞ robust predictive control law is proposed based on linear matrix inequalities (LMIs and receding horizon optimization techniques. Using active tackling system constraints of MPC, the input and state constraints are satisfied in the closed-loop control system. The validity of the proposed control is verified theoretically according to Lyapunov theory and illustrated by simulation results.

Faraday effect in γ-Dy2S3 and c-Dy2O3 paramagnetic crystals

International Nuclear Information System (INIS)

Shelykh, A.I.

1987-01-01

Studies of spectral and temperature dependences of Faraday effect in γ-Dy 2 S 3 and C-Dy 2 O 3 paramagnetic crystals are conducted. Paramagnetism of these crystals is brought about by Dy 3+ ions. Estimation of the effect of such factors as the value of paramagnetic ion concentration, width of the forbidden band, crystallochemical composition on magnetooptical effect in the considered compounds of dysprosium is carried out on the basis of the obtained experimental data and theoretical analysis. It is shown, that the Faraday effect in the considered compounds of dysprosium as well as the value of paramagnetic moment may be regarded rather accurately in free ion approximation

Reliability based topology optimization for continuum structures with local failure constraints

DEFF Research Database (Denmark)

Luo, Yangjun; Zhou, Mingdong; Wang, Michael Yu

2014-01-01

This paper presents an effective method for stress constrained topology optimization problems under load and material uncertainties. Based on the Performance Measure Approach (PMA), the optimization problem is formulated as to minimize the objective function under a large number of (stress......-related) target performance constraints. In order to overcome the stress singularity phenomenon caused by the combined stress and reliability constraints, a reduction strategy on target reliability index is proposed and utilized together with the ε-relaxation approach. Meanwhile, an enhanced aggregation method...... is employed to aggregate the selected active constraints using a general K–S function, which avoids expensive computational cost from the large-scale nature of local failure constraints. Several numerical examples are given to demonstrate the validity of the present method....

NMR-based approach to the analysis of radiopharmaceuticals: radiochemical purity, specific activity, and radioactive concentration values by proton and tritium NMR spectroscopy.

Science.gov (United States)

Schenk, David J; Dormer, Peter G; Hesk, David; Pollack, Scott R; Lavey, Carolee Flader

2015-06-15

Compounds containing tritium are widely used across the drug discovery and development landscape. These materials are widely utilized because they can be efficiently synthesized and produced at high specific activity. Results from internally calibrated (3)H and (1)H nuclear magnetic resonance (NMR) spectroscopy suggests that at least in some cases, this calibrated approach could supplement or potentially replace radio-high-performance liquid chromatography for radiochemical purity, dilution and scintillation counting for the measurement of radioactivity per volume, and liquid chromatography/mass spectrometry analysis for the determination of specific activity. In summary, the NMR-derived values agreed with those from the standard approaches to within 1% to 9% for solution count and specific activity. Additionally, the NMR-derived values for radiochemical purity deviated by less than 5%. A benefit of this method is that these values may be calculated at the same time that (3)H NMR analysis provides the location and distribution of tritium atoms within the molecule. Presented and discussed here is the application of this method, advantages and disadvantages of the approach, and a rationale for utilizing internally calibrated (1)H and (3)H NMR spectroscopy for specific activity, radioactive concentration, and radiochemical purity whenever acquiring (3)H NMR for tritium location. Copyright © 2015 John Wiley & Sons, Ltd.

Recommendations and Standardization of Biomarker Quantification Using NMR-based Metabolomics with Particular Focus on Urinary Analysis

KAUST Repository

Emwas, Abdul-Hamid M.

2016-01-08

NMR-based metabolomics has shown considerable promise in disease diagnosis and biomarker discovery because it allows one to non-destructively identify and quantify large numbers of novel metabolite biomarkers in both biofluids and tissues. Indeed, precise metabolite quantification is a necessary prerequisite to move any chemical biomarker or biomarker panel from the lab into the clinic. Among the many biofluids (urine, serum, plasma, cerebrospinal fluid and saliva) commonly used for disease diagnosis and prognosis, urine has several advantages. It is abundant, sterile, easily obtained, needs little sample preparation and does not require any invasive medical procedures for collection. Furthermore, urine captures and concentrates many “unwanted” or “undesirable” compounds throughout the body, thereby providing a rich source of potentially useful disease biomarkers. However, the incredible variation in urine chemical concentrations due to effects such as gender, age, diet, life style, health conditions, and physical activity make the analysis of urine and the identification of useful urinary biomarkers by NMR quite challenging. In this review, we discuss a number of the most significant issues regarding NMR-based urinary metabolomics with a specific emphasis on metabolite quantification for disease biomarker applications. We also propose a number of data collection and instrumental recommendations regarding NMR pulse sequences, acceptable acquisition parameter ranges, relaxation effects on quantitation, proper handling of instrumental differences, as well as recommendations regarding sample preparation and biomarker assessment.

Recommendations and Standardization of Biomarker Quantification Using NMR-based Metabolomics with Particular Focus on Urinary Analysis

KAUST Repository

Emwas, Abdul-Hamid M.; Roy, Raja; McKay, Ryan T.; Ryan, Danielle; Brennan, Lorraine; Tenori, Leonardo; Luchinat, Claudio; Gao, Xin; Zeri, Ana Carolina; Gowda, G. A. Nagana; Raftery, Daniel; Steinbeck, Christoph; Salek, Reza M; Wishart, David S.

2016-01-01

NMR-based metabolomics has shown considerable promise in disease diagnosis and biomarker discovery because it allows one to non-destructively identify and quantify large numbers of novel metabolite biomarkers in both biofluids and tissues. Indeed, precise metabolite quantification is a necessary prerequisite to move any chemical biomarker or biomarker panel from the lab into the clinic. Among the many biofluids (urine, serum, plasma, cerebrospinal fluid and saliva) commonly used for disease diagnosis and prognosis, urine has several advantages. It is abundant, sterile, easily obtained, needs little sample preparation and does not require any invasive medical procedures for collection. Furthermore, urine captures and concentrates many “unwanted” or “undesirable” compounds throughout the body, thereby providing a rich source of potentially useful disease biomarkers. However, the incredible variation in urine chemical concentrations due to effects such as gender, age, diet, life style, health conditions, and physical activity make the analysis of urine and the identification of useful urinary biomarkers by NMR quite challenging. In this review, we discuss a number of the most significant issues regarding NMR-based urinary metabolomics with a specific emphasis on metabolite quantification for disease biomarker applications. We also propose a number of data collection and instrumental recommendations regarding NMR pulse sequences, acceptable acquisition parameter ranges, relaxation effects on quantitation, proper handling of instrumental differences, as well as recommendations regarding sample preparation and biomarker assessment.

Recent results on some columnar paramagnetic metallomesogens

Indian Academy of Sciences (India)

A broader view on some physical properties of columnar paramagnetic ... was evident by X-ray crystal structure determination in the solid state on a homologous ... leading to interfacial polarization as described for other LC materials before [9]. ... dodecyloxy tail on the phenyl rings) was described to exhibit a Colho phase ...

A new Schiff base compound N,N'-(2,2-dimetylpropane)-bis(dihydroxylacetophenone): synthesis, experimental and theoretical studies on its crystal structure, FTIR, UV-visible, 1H NMR and 13C NMR spectra.

Science.gov (United States)

Saheb, Vahid; Sheikhshoaie, Iran

2011-10-15

The Schiff base compound, N,N'-(2,2-dimetylpropane)-bis(dihydroxylacetophenone) (NDHA) is synthesized through the condensation of 2-hydroxylacetophenone and 2,2-dimethyl 1,3-amino propane in methanol at ambient temperature. The yellow crystalline precipitate is used for X-ray single-crystal determination and measuring Fourier transform infrared (FTIR), UV-visible, (1)H NMR and (13)C NMR spectra. Electronic structure calculations at the B3LYP, PBEPBE and PW91PW91 levels of theory are performed to optimize the molecular geometry and to calculate the FTIR, (1)H NMR and (13)C NMR spectra of the compound. Time-dependent density functional theory (TDDFT) method is used to calculate the UV-visible spectrum of NDHA. Vibrational frequencies are determined experimentally and compared with those obtained theoretically. Vibrational assignments and analysis of the fundamental modes of the compound are also performed. All theoretical methods can well reproduce the structure of the compound. The (1)H NMR and (13)C NMR chemical shifts calculated by all DFT methods are consistent with the experimental data. However, the NMR shielding tensors computed at the B3LYP/6-31+G(d,p) level of theory are in better agreement with experimental (1)H NMR and (13)C NMR spectra. The electronic absorption spectrum calculated at the B3LYP/6-31+G(d,p) level by using TD-DFT method is in accordance with the observed UV-visible spectrum of NDHA. In addition, some quantum descriptors of the molecule are calculated and conformational analysis is performed and the results were compared with the crystallographic data. Copyright © 2011 Elsevier B.V. All rights reserved.

Thermal properties of paramagnetic solid helium 3

International Nuclear Information System (INIS)

Goldstein, L.

1983-01-01

It was shown in recent work that over a limited molar volume range and at asymptotically high temperatures the thermal modulations of the pressure along isochores of paramagnetic solid 3 He could be accounted for through the formalism of the Heisenberg model of an antiferromagnetically interacting localized spin- 1/2 system. The internal consistency of this formalism requires the characteristic exchange-interaction parameter of the model derived from pressure modulation data to be identical with that appearing in the other thermal properties of this quantum solid. In a restricted temperature region where the spin excitations are the dominant thermal excitations of the solid, heat capacity data yield exchange-interaction parameters in fair agreement with those derived from pressures along isochores of larger molar volume. At higher temperatures, within well-defined limitations, thermal excitations involve both spin and phononexcitations. Here, because of the opposite temperature variations of the spin and phonon heat capacity components, the ensuing heat capacity minimum determines exactly the exchange-energy parameter and the relevant limiting Debye temperature as a function of the measured temperature location and value of the heat capacity extremum along the experimentally explored isochore. The exchange-energy parameters so derived display larger deviations from their predicted pressure-based values than those resulting from the lower temperature but still asymptotic spin-only heat capacities. At the present time, ambiguities in the experimental determinations of the characteristic Weiss temperatures of the asymptotic paramagnetic susceptibilities prevent one from deriving exchange-energy parameters with them. The present work leads to the prediction, within the limitations of the model formalism, of thermal properties of magnetized solid 3 He

Solid-state (49/47)Ti NMR of titanium-based MCM-41 hybrid materials.

Science.gov (United States)

Ballesteros, Ruth; Fajardo, Mariano; Sierra, Isabel; Force, Carmen; del Hierro, Isabel

2009-11-03

Titanium solid-state NMR spectroscopy data for a series of organic-inorganic titanium MCM-41 based materials have been collected. These materials have been synthesized by first modifying the mesoporous silica MCM-41 in one step with a mixture of silanes: a triazine propyl triethoxysilane acting as functional linker and methyltrimethoxysilane or hexamethyldisilizane as capped agents to mask the remaining silanol groups. Second, the appropiate titanium precursor Ti(OPr(i))(4), [{Ti(OPr(i))(3)(OMent)}(2)] (OMent = 1R,2S,5R-(-)-menthoxo), Ti(OPr(i))(4), or [Ti(eta(5)-C(5)HMe(4))Cl(3)], has been immobilized by reaction with the modified MCM-41. Finally, after Ti(OPr(i))(4) immobilization onto the organomodified support the reaction with the chiral (+)-diethyl-l-tartrate was accomplished. The materials without functional linker have been also prepared by reaction in one step of the capped agent and the titanium precursor with the mesoporous silica. Relevant correlations of titanium NMR resonance chemical shifts and line widths can be inferred depending on different factors. The immobilization procedure used to prepare titanium-based MCM-41 hybrid materials and the choice of the silylating reagents employed to mask the silanol groups present on the silica surfaces produce significant differences in the Ti NMR spectra. Furthermore, depending on the electronic and sterical influence of the substituents directly attached to the titanium center, chemical shifts and line widths are modified providing novel information about titanium structure.

Comparative 1H NMR-based metabonomic analysis of HIV-1 sera

International Nuclear Information System (INIS)

Philippeos, C.; Steffens, F. E.; Meyer, D.

2009-01-01

1 H NMR spectroscopy of sera from HIV-1 infected and uninfected individuals was performed on 300 and 600 MHz instruments. The resultant spectra were automatically data reduced to 90 and 180 integral segments of equal length. Analysis of variance identified significant differences between the sample groups, especially for the samples analyzed on 600 MHz and reduced to fewer segments. Linear discriminant analysis correctly classified 100% of the samples analyzed on the 300 MHz NMR (reduced to 180 segments); an increase in instrument sensitivity resulted in lower percentages of correctly classified samples. Multinomial logistic regression (MLR) resulted in 100% correct classification of all samples from both instruments. Thus 1 H-NMR metabonomics on either instrument distinguishes HIV-positive individuals using or not using anti retroviral therapy, but the sensitivity of the instrument impacts on data reduction. Furthermore, MLR is a novel multivariate statistical technique for improved classification of biological data analyzed in NMR

An Efficient Energy Constraint Based UAV Path Planning for Search and Coverage

Directory of Open Access Journals (Sweden)

German Gramajo

2017-01-01

Full Text Available A path planning strategy for a search and coverage mission for a small UAV that maximizes the area covered based on stored energy and maneuverability constraints is presented. The proposed formulation has a high level of autonomy, without requiring an exact choice of optimization parameters, and is appropriate for real-time implementation. The computed trajectory maximizes spatial coverage while closely satisfying terminal constraints on the position of the vehicle and minimizing the time of flight. Comparisons of this formulation to a path planning algorithm based on those with time constraint show equivalent coverage performance but improvement in prediction of overall mission duration and accuracy of the terminal position of the vehicle.

Correlation induced paramagnetic ground state in FeAl

Czech Academy of Sciences Publication Activity Database

Mohn, P.; Persson, C.; Blaha, P.; Schwarz, K.; Novák, Pavel; Eschrig, H.

2001-01-01

Roč. 87, č. 19 (2001), s. 196401-1-196401-4 ISSN 0031-9007 Institutional research plan: CEZ:AV0Z1010914 Keywords : FeAl * paramagnetic ground state Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 6.668, year: 2001

Model-free nuclear magnetic resonance study of intermolecular free energy landscapes in liquids with paramagnetic Ln3+ spotlights: theory and application to Arg-Gly-Asp.

Science.gov (United States)

Fries, Pascal H

2012-01-28

We propose an easily applicable method for investigating the pair distribution function of a lanthanide Ln(3+) complex LnL (L = ligand) with respect to any solvent or solute molecule A carrying observable nuclear spins. Let r be the distance of Ln(3+) to the observed nuclear spin I. We derive a simple expression of the experimental value of the configurational average of 1/r(6) in terms of longitudinal paramagnetic relaxation (rate) enhancements (PREs) of the spin I measured on a standard high-resolution NMR spectrometer and due to well-chosen concentrations of LnL complexes in which Ln(3+) is a fast-relaxing paramagnetic lanthanide or the slowly-relaxing gadolinium Gd(3+). The derivation is justified in the general case of a molecule A which is by turns in a bound state where it follows the complex and a free state where it moves independently. It rests on the expression of the underlying PRE theory in terms of the angle-dependent pair distribution function of LnL and A. The simplifications of this theory in the high-field regime and under the condition of fast exchange between bound and free states are carefully discussed. We also show that original information on the angle dependence of the molecular pair distribution function can be gained from the measured paramagnetic dipolar shifts induced by complexed fast-relaxing Ln(3+) ions. The method is illustrated by the case study of the anionic Lnttha(3-) = [Ln(3+)(ttha)](3-) (ttha(6-) = triethylene tetraamine hexacetate) complex interacting with the biologically important tripeptide Arg-Gly-Asp (RGD) which carries peripheral ionic groups. The usefulness of an auxiliary reference outer sphere probe solute is emphasized. © 2012 American Institute of Physics

Hysteresis loops of spin-dependent electronic current in a paramagnetic resonant tunnelling diode

International Nuclear Information System (INIS)

Wójcik, P; Spisak, B J; Wołoszyn, M; Adamowski, J

2012-01-01

Nonlinear properties of the spin-dependent electronic transport through a semiconductor resonant tunnelling diode with a paramagnetic quantum well are considered. The spin-dependent Wigner–Poisson model of the electronic transport and the two-current Mott’s formula for the independent spin channels are applied to determine the current–voltage curves of the nanodevice. Two types of the electronic current hysteresis loops are found in the current–voltage characteristics for both the spin components of the electronic current. The physical interpretation of these two types of the electronic current hysteresis loops is given based on the analysis of the spin-dependent electron densities and the potential energy profiles. The differences between the current–voltage characteristics for both the spin components of the electronic current allow us to explore the changes of the spin polarization of the current for different electric fields and determine the influence of the electronic current hysteresis on the spin polarization of the current flowing through the paramagnetic resonant tunnelling diode. (paper)

NMR-based pharmacometabonomics: A new paradigm for personalised or precision medicine

OpenAIRE

Everett, Jeremy R.

2017-01-01

Metabolic profiling by NMR spectroscopy or hyphenated mass spectrometry, known as metabonomics or metabolomics, is an important tool for systems-based approaches in biology and medicine. The experiments are typically done in a diagnostic fashion where changes in metabolite profiles are interpreted as a consequence of an intervention or event; be that a change in diet, the administration of a drug, physical exertion or the onset of a disease. By contrast, pharmacometabonomics takes a prognosti...

SPE-NMR metabolite sub-profiling of urine

NARCIS (Netherlands)

Jacobs, D.M.; Spiesser, L.; Garnier, M.; Roo, de N.; Dorsten, van F.; Hollebrands, B.; Velzen, van E.; Draijer, R.; Duynhoven, van J.P.M.

2012-01-01

NMR-based metabolite profiling of urine is a fast and reproducible method for detection of numerous metabolites with diverse chemical properties. However, signal overlap in the (1)H NMR profiles of human urine may hamper quantification and identification of metabolites. Therefore, a new method has

¹²⁹ Xe NMR Relaxation-Based Macromolecular Sensing

Energy Technology Data Exchange (ETDEWEB)

Gomes, Muller D. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Dao, Phuong [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Jeong, Keunhong [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Slack, Clancy C. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Vassiliou, Christophoros C. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Finbloom, Joel A. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Francis, Matthew B. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Wemmer, David E. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division; Pines, Alexander [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

2016-07-29

A ¹²⁹Xe NMR relaxation-based sensing approach is reported on 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.

Executable specifications for hypothesis-based reasoning with Prolog and Constraint Handling Rules

DEFF Research Database (Denmark)

Christiansen, Henning

2009-01-01

Constraint Handling Rules (CHR) is an extension to Prolog which opens up a  spectrum of hypotheses-based reasoning in logic programs without additional interpretation overhead. Abduction with integrity constraints is one example of hypotheses-based reasoning which can be implemented directly...... in Prolog and CHR with a straightforward use of available and efficiently implemented facilities The present paper clarifies the semantic foundations for this way of doing abduction in CHR and Prolog as well as other examples  of hypotheses-based reasoning that is possible, including assumptive logic...

Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methyl–methyl nuclear overhauser enhancement spectroscopy

International Nuclear Information System (INIS)

Venditti, Vincenzo; Fawzi, Nicolas L.; Clore, G. Marius

2011-01-01

Methyl-transverse relaxation optimized spectroscopy is rapidly becoming the preferred NMR technique for probing structure and dynamics of very large proteins up to ∼1 MDa in molecular size. Data interpretation, however, necessitates assignment of methyl groups which still presents a very challenging and time-consuming process. Here we demonstrate that, in combination with a known 3D structure, paramagnetic relaxation enhancement (PRE), induced by nitroxide spin-labels incorporated at only a few surface-exposed engineered cysteines, provides fast, straightforward and robust access to methyl group resonance assignments, including stereoassignments for the methyl groups of leucine and valine. Neither prior assignments, including backbone assignments, for the protein, nor experiments that transfer magnetization between methyl groups and the protein backbone, are required. PRE-derived assignments are refined by 4D methyl–methyl nuclear Overhauser enhancement data, eliminating ambiguities and errors that may arise due to the high sensitivity of PREs to the potential presence of sparsely-populated transient states.

Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methyl-methyl nuclear overhauser enhancement spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Venditti, Vincenzo; Fawzi, Nicolas L.; Clore, G. Marius, E-mail: mariusc@mail.nih.gov [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Laboratory of Chemical Physics (United States)

2011-11-15

Methyl-transverse relaxation optimized spectroscopy is rapidly becoming the preferred NMR technique for probing structure and dynamics of very large proteins up to {approx}1 MDa in molecular size. Data interpretation, however, necessitates assignment of methyl groups which still presents a very challenging and time-consuming process. Here we demonstrate that, in combination with a known 3D structure, paramagnetic relaxation enhancement (PRE), induced by nitroxide spin-labels incorporated at only a few surface-exposed engineered cysteines, provides fast, straightforward and robust access to methyl group resonance assignments, including stereoassignments for the methyl groups of leucine and valine. Neither prior assignments, including backbone assignments, for the protein, nor experiments that transfer magnetization between methyl groups and the protein backbone, are required. PRE-derived assignments are refined by 4D methyl-methyl nuclear Overhauser enhancement data, eliminating ambiguities and errors that may arise due to the high sensitivity of PREs to the potential presence of sparsely-populated transient states.

A constraints-based approach to the acquisition of expertise in outdoor adventure sports

NARCIS (Netherlands)

Davids, Keith; Brymer, Eric; Seifert, Ludovic; Orth, Dominic

2013-01-01

A constraints-based framework enables a new understanding of expertise in outdoor adventure sports by considering performer-environment couplings through emergent and self-organizing behaviours in relation to interacting constraints. Expert adventure athletes, conceptualized as complex, dynamical

Ehrlich and sarcoma 180 tumour characterisation and early detection by {sup 1}H NMR-based metabonomics of mice serum

Energy Technology Data Exchange (ETDEWEB)

Grandizoli, Caroline W.P. da S.; Simonelli, Fabio; Nagata, Noemi; Barison, Andersson [Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil). Dept. de Quimica; Carrenho, Luise Z.B.; Francisco, Thais M.G. de; Campos, Francinete R. [Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil). Dept. de Farmacia; Santana Filho, Arquimedes P. de; Sassaki, Guilherme L. [Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil). Dept. de Bioquimica; Kreuger, Maria R.O. [Universidade do Vale do Itajai (UNIVALI), (Brazil). Centro de Ciencias da Saude

2014-05-15

The success of cancer treatment is directly related to early detection before symptoms emerge, although nowadays few cancers can be detected early. In this sense, {sup 1}H nuclear magnetic resonance ({sup 1}H NMR)-based metabonomics was used to identify metabolic changes in biofluid as a consequence of tumours growing in mice. Through partial least squares discriminant analysis (PLS-DA) analysis of {sup 1}H NMR spectra from serum samples it was possible to diagnose Ehrlich ascites and Sarcoma 180 tumours five and ten days after cell inoculation, respectively. Lipids, lipoproteins and lactate were the main biomarkers at onset as well as in the progress of carcinogenic process. Thus, NMR-based metabonomics can be a valuable tool to study the effects of tumour establishment on the chemical composition of biofluids. (author)

Depolarization of diffusing spins by paramagnetic impurities

International Nuclear Information System (INIS)

Schillaci, M.E.; Hutson, R.L.; Heffner, R.H.; Leon, M.; Dodds, S.A.; Estle, T.L.

1981-01-01

We study the depolarization of diffusing spins (muons) interacting with dilute paramagnetic impurities in a solid using a simple computational model which properly treats the muon motion and preserves correct muon-impurity distances. Long-range (dipolar) and nearest-neighbor (contact) interactions are treated together. Diffusion parameters are deduced and model comparisons made for AuGd (300 ppm). (orig.)

A superheterodyne spectrometer for electronic paramagnetic. Resonance

International Nuclear Information System (INIS)

Laffon, J.L.

1963-12-01

After a few generalities about electron paramagnetic resonance, a consideration of different experimental techniques authorises the choice of a particular type of apparatus. An EPR superheterodyne spectrometer built in the laboratory and having a novel circuit is described in detail. With this apparatus, many experimental results have been obtained and some of these are described as example. (author) [fr

Constrained Optimization Based on Hybrid Evolutionary Algorithm and Adaptive Constraint-Handling Technique

DEFF Research Database (Denmark)

Wang, Yong; Cai, Zixing; Zhou, Yuren

2009-01-01

A novel approach to deal with numerical and engineering constrained optimization problems, which incorporates a hybrid evolutionary algorithm and an adaptive constraint-handling technique, is presented in this paper. The hybrid evolutionary algorithm simultaneously uses simplex crossover and two...... mutation operators to generate the offspring population. Additionally, the adaptive constraint-handling technique consists of three main situations. In detail, at each situation, one constraint-handling mechanism is designed based on current population state. Experiments on 13 benchmark test functions...... and four well-known constrained design problems verify the effectiveness and efficiency of the proposed method. The experimental results show that integrating the hybrid evolutionary algorithm with the adaptive constraint-handling technique is beneficial, and the proposed method achieves competitive...

Multi-photon Rabi oscillations in high spin paramagnetic impurity

International Nuclear Information System (INIS)

Bertaina, S; Groll, N; Chen, L; Chiorescu, I

2011-01-01

We report on multiple photon monochromatic quantum oscillations (Rabi oscillations) observed by pulsed EPR (Electron Paramagnetic Resonance) of Mn 2+ (S = 5/2) impurities in MgO. We find that when the microwave magnetic field is similar or large than the anisotropy splitting, the Rabi oscillations have a spectrum made of many frequencies not predicted by the S = l/2 Rabi model. We show that these new frequencies come from multiple photon coherent manipulation of the multi-level spin impurity. We develop a model based on the crystal field theory and the rotating frame approximation, describing the observed phenomenon with a very good agreement.

1H NMR-Based Metabolomic Analysis of Sub-Lethal Perfluorooctane Sulfonate Exposure to the Earthworm, Eisenia fetida, in Soil

Directory of Open Access Journals (Sweden)

Myrna J. Simpson

2013-08-01

Full Text Available 1H NMR-based metabolomics was used to measure the response of Eisenia fetida earthworms after exposure to sub-lethal concentrations of perfluorooctane sulfonate (PFOS in soil. Earthworms were exposed to a range of PFOS concentrations (five, 10, 25, 50, 100 or 150 mg/kg for two, seven and fourteen days. Earthworm tissues were extracted and analyzed by 1H NMR. Multivariate statistical analysis of the metabolic response of E. fetida to PFOS exposure identified time-dependent responses that were comprised of two separate modes of action: a non-polar narcosis type mechanism after two days of exposure and increased fatty acid oxidation after seven and fourteen days of exposure. Univariate statistical analysis revealed that 2-hexyl-5-ethyl-3-furansulfonate (HEFS, betaine, leucine, arginine, glutamate, maltose and ATP are potential indicators of PFOS exposure, as the concentrations of these metabolites fluctuated significantly. Overall, NMR-based metabolomic analysis suggests elevated fatty acid oxidation, disruption in energy metabolism and biological membrane structure and a possible interruption of ATP synthesis. These conclusions obtained from analysis of the metabolic profile in response to sub-lethal PFOS exposure indicates that NMR-based metabolomics is an excellent discovery tool when the mode of action (MOA of contaminants is not clearly defined.

First order magnetic transition in single crystal CaFe2As2 detected by 75As NMR

Energy Technology Data Exchange (ETDEWEB)

Baek, Seung Ho [Los Alamos National Laboratory; Curro, Nicholas J [UC - DAVIS

2008-01-01

We report {sup 75}As Nuclear Magnetic Resonance data in a single crystal of CaFe{sub 2}As{sub 2}. The Knight shift, the electric field gradient, and the spin lattice relaxation rate are strongly temperature dependent in the paramagnetic state, and change discontinuously at the structural transition temperature, T{sub S} = T{sub N} = 167 K. Immediately below, the NMR spectra reveal an internal field at the As site associated with the presence of a commensurate magnetic order. These results indicate that the structural and magnetic transitions in CaFe{sub 2}As{sub 2} are first order and strongly coupled, and that the electron density in the FeAs plane is highly sensitive to the out-of-plane structure.

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

Science.gov (United States)

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

2014-01-01

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

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

Directory of Open Access Journals (Sweden)

Diogo A R S Latino

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

Concentration of paramagnetic centres at low-temperature thermal destruction of asphaltenes of heavy petroleum distillates

Directory of Open Access Journals (Sweden)

Dolomatov M.U., Rodionov A.A., Gafurov M.R., Petrov A.V., Biktagirov T.B., Bakhtizin R.Z., Makarchikov S.O., Khairudinov I.Z., Orlinskii S.B.

2016-11-01

Full Text Available Changes of paramagnetic centers (PC concentration in dispersed petroleum systems were studied in the process of low-temperature thermolysis. The kinetic model of PC concentration dynamics based on the processes of unpaired electrons formation during singlet-triplet transitions, weak chemical bonds dissociation and recombination of free radicals is proposed.

In situ NMR observation of the lithium extraction/insertion from LiCoO2 cathode

International Nuclear Information System (INIS)

Shimoda, Keiji; Murakami, Miwa; Takamatsu, Daiko; Arai, Hajime; Uchimoto, Yoshiharu; Ogumi, Zempachi

2013-01-01

Abstract: Rechargeable lithium-ion batteries (LIBs) are currently accepted to be one of the most suitable energy storage resources in portable electronic devices because of their high gravimetric and volumetric energy density. To understand the behavior of Li + ions on electrochemical lithium extraction/insertion process, we performed in situ 7 Li nuclear magnetic resonance (NMR) measurements for LiCoO 2 cathode in a plastic cell battery, and the spectral evolutions of the 7 Li NMR signal of Li x CoO 2 (0 ≤ x ≤ 1) were well investigated. Very narrow solid solution region of Li x CoO 2 (∼0.99 ≤ x 2 signal at ∼0 ppm, which is related to the localized nature of the electronic spin of paramagnetic Co 4+ ion formed at the very early delithiation stage. With further decreasing the signal intensity of LiCoO 2 , a Knight-shifted signal corresponding to an electrically conductive Li x CoO 2 phase emerged at x = 0.97, which then monotonously decreased in intensity for x x CoO 2 . These observations acquired in situ fully confirm the earlier studies obtained in ex situ measurements, although the present study offers more quantitative information. Moreover, it was shown that the peak position of the NMR shift for Li x CoO 2 moved as a function of lithium content, which behavior is analogous to the change in its c lattice parameter. Also, the growth and consumption of dendritic/mossy metallic lithium on the counter electrode was clearly observed during the charge/discharge cycles

Assessment of 1H NMR-based metabolomics analysis for normalization of urinary metals against creatinine.

Science.gov (United States)

Cassiède, Marc; Nair, Sindhu; Dueck, Meghan; Mino, James; McKay, Ryan; Mercier, Pascal; Quémerais, Bernadette; Lacy, Paige

2017-01-01

Proton nuclear magnetic resonance ( 1 H NMR, or NMR) spectroscopy and inductively coupled plasma-mass spectrometry (ICP-MS) are commonly used for metabolomics and metal analysis in urine samples. However, creatinine quantification by NMR for the purpose of normalization of urinary metals has not been validated. We assessed the validity of using NMR analysis for creatinine quantification in human urine samples in order to allow normalization of urinary metal concentrations. NMR and ICP-MS techniques were used to measure metabolite and metal concentrations in urine samples from 10 healthy subjects. For metabolite analysis, two magnetic field strengths (600 and 700MHz) were utilized. In addition, creatinine concentrations were determined by using the Jaffe method. Creatinine levels were strongly correlated (R 2 =0.99) between NMR and Jaffe methods. The NMR spectra were deconvoluted with a target database containing 151 metabolites that are present in urine. A total of 50 metabolites showed good correlation (R 2 =0.7-1.0) at 600 and 700MHz. Metal concentrations determined after NMR-measured creatinine normalization were comparable to previous reports. NMR analysis provided robust urinary creatinine quantification, and was sufficient for normalization of urinary metal concentrations. We found that NMR-measured creatinine-normalized urinary metal concentrations in our control subjects were similar to general population levels in Canada and the United Kingdom. Copyright © 2016 Elsevier B.V. All rights reserved.

Evidence for an anisotropic contact shift. Proton NMR study of line shapes in uranocene and (C5H5)3UCl powders

International Nuclear Information System (INIS)

McGarvey, B.R.; Nagy, S.

1987-01-01

The proton NMR spectra of solid powders of uranocene and (C 5 H 5 ) 3 UCl were measured from 90 to 298 K. The line shapes of both systems became increasingly anisotropic as the temperature was lowered. The cyclooctatetraene rings in uranocene were found to be rotating at a frequency greater than 100 kHz down to 90 K. The (C 5 H 5 ) 3 UCl molecules were found to be reorienting rapidly above 220 K, but below 140 K the NMR spectra were characteristic of a rigid lattice with no rotation of the cyclopentadienyl rings. The spectra of both compounds could be simulated by assuming an axial paramagnetic shift tensor and an orientation-dependent line width. Comparison of the experimental shift tensor with that calculated for a point dipolar interaction revealed a large and very anisotropic paramagnetic shift for uranocene due to unpaired spin transferred into the ligand orbitals. The shift was large when the magnetic field was along the 8-fold symmetry axis of the molecule and nearly zero perpendicular to the axis. It appears conclusive that the contact shift in uranocene is not isotropic at all. A similar anisotropy in the contact shift associated with the cyclopentadienyl rings is evident also in the results for (C 5 H 5 )UCl. The average solid-state shift of uranocene agreed with the solution shift, within experimental error, but the solid state shift of (C 5 H 5 ) 3 UCl was 42 ppm greater than the solution shift at 298 K, indicating a difference in molecular geometry between the crystalline state and solution. 32 references, 8 figures, 3 tables

Towards interpretation of intermolecular paramagnetic relaxation enhancement outside the fast exchange limit

International Nuclear Information System (INIS)

Ceccon, Alberto; Marius Clore, G.; Tugarinov, Vitali

2016-01-01

In an exchanging system between major and minor species, the transverse paramagnetic relaxation enhancement rate observed on the resonances of the major species (Γ_2"a"p"p) is dependent upon the exchange regime between the species. Quantitative analysis of PRE data in such systems typically assumes that the overall exchange rate k_e_x between the species is fast on the PRE time scale (k_e_x ≫ Γ_2). Recently, we have characterized the kinetics of binding of the model protein ubiquitin to large (LUV) and small (SUV) unilamellar lipid-based nanoparticles or liposomes (Ceccon A, Tugarinov V, Bax A, Clore GM (2016). J Am Chem Soc 138:5789–5792). Building upon these results and taking advantage of a strong paramagnetic agent with an isotropic g-tensor, Gd"3"+, we were able to measure intermolecular methyl carbon and proton PREs between paramagnetically-tagged liposomes and ubiquitin. In the limit of fast exchange (k_e_x ≫ Γ_2) the ratio of the apparent proton to carbon methyl PREs, ("1H_m–Γ_2"a"p"p)/("1"3C_m–Γ_2"a"p"p), is equal to the square of the ratio of the gyromagnetic ratios of the two nuclei, (γ_Η/γ_C)"2. However, outside the fast exchange regime, under intermediate exchange conditions (e.g. when Γ_2 is comparable in magnitude to k_e_x) the ("1H_m–Γ_2"a"p"p)/("1"3C_m–Γ_2"a"p"p) ratio provides a reliable measure of the ‘true’ methyl PREs.

On superfluorescent generation of coherent radiation in a paramagnet

International Nuclear Information System (INIS)

Turaev, M.T.; Shumovsky, A.S.

1988-08-01

An exact definition is given of a superradiation intensity for a free system and for a system in cavity. The superradiant generation of the Zeeman transitions in proton paramagnet is described. (author). 7 refs, 2 figs

Deuterium NMR, induced and intrinsic cholesteric lyomesophases

International Nuclear Information System (INIS)

Alcantara, M.R.

1982-01-01

Induced and intrinsic cholesteric lyotropic mesophases were studied. Induced cholesteric lyomesophases based on potassium laurate (KL) system, with small amounts of cholesterol added, were studied by deuterium NMR and by polarizing microscopy. Order profiles obtained from deuterium NMR of KL perdenderated chains in both induced cholesteric and normal mesophases were compared. The intrinsic cholesteric lyotropic mesophases were based on the amphiphile potassium N-lauroyl serinate (KLNS) in the resolved levo form. The study of the type I intrinsic cholesteric mesophase was made by optical microscopy under polarized light and the type II intrinsic cholesteric lyomesophase was characterized by deuterium NMR. The new texture was explained by the use of the theory of disclinations developed for thermotropic liquid crystals, specially for cholesteric type. (M.J.C.) [pt

Extraction of alkaloids for NMR-based profiling

DEFF Research Database (Denmark)

Yilmaz, Ali; Nyberg, Nils; Jaroszewski, Jerzy W.

2012-01-01

A museum collection of Cinchona cortex samples (n = 117), from the period 1850–1950, were extracted with a mixture of chloroform-d1, methanol-d4, water-d2, and perchloric acid in the ratios 5:5:1:1. The extracts were directly analyzed using 1H NMR spectroscopy (600 MHz) and the spectra evaluated...

Clinical Processes - The Killer Application for Constraint-Based Process Interactions

DEFF Research Database (Denmark)

Jiménez-Ramírez, Andrés; Barba, Irene; Reichert, Manfred

2018-01-01

. The scenario is subject to complex temporal constraints and entails the need for coordinating the constraint-based interactions among the processes related to a patient treatment process. As demonstrated in this work, the selected real process scenario can be suitably modeled through a declarative approach....... examples. However, to the best of our knowledge, they have not been used to model complex, real-world scenarios that comprise constraints going beyond control-flow. In this paper, we propose the use of a declarative language for modeling a sophisticated healthcare process scenario from the real world......For more than a decade, the interest in aligning information systems in a process-oriented way has been increasing. To enable operational support for business processes, the latter are usually specified in an imperative way. The resulting process models, however, tend to be too rigid to meet...

Unified integration intervals for the structural characterization of oil, coal or fractions there of by 1h NMR and 13c NMR

International Nuclear Information System (INIS)

Avella, Eliseo; Fierro, Ricardo

2010-01-01

Based on an analysis of publications reported between 1972 and 2006, it became clear that there are inaccuracies in the limits of the ranges of integration that the authors assigned to signals in nuclear magnetic resonance (NMR) to the structural characterization of petroleum, coals and their derived fractions, from their hydrogen (1H NMR) and carbon (13C NMR) spectra. Consequently, consolidated limits were determined for the integration of 1H NMR spectra and 13C NMR of these samples using a statistical treatment applied to the limits of integration intervals already published. With these unified limits, correlation NMR charts were developed that are useful for the allocation of the integral at such intervals, and at smaller intervals defined in terms of the intersection between different assignments. Also raised equations needed to establish the integral attributable to specific fragments in an attempt to make a more accurate structural characterization from NMR spectra of oil, coal or fractions derived.

An unprecedented up-field shift in the 13C NMR spectrum of the carboxyl carbons of the lantern-type dinuclear complex TBA[Ru2(O2CCH3)4Cl2] (TBA+ = tetra(n-butyl)ammonium cation).

Science.gov (United States)

Hiraoka, Yuya; Ikeue, Takahisa; Sakiyama, Hiroshi; Guégan, Frédéric; Luneau, Dominique; Gillon, Béatrice; Hiromitsu, Ichiro; Yoshioka, Daisuke; Mikuriya, Masahiro; Kataoka, Yusuke; Handa, Makoto

2015-08-14

A large up-field shift (-763 ppm) has been observed for the carboxyl carbons of the dichlorido complex TBA[Ru(2)(O(2)CCH(3))(4)Cl(2)] (TBA(+) = tetra(n-butyl)ammonium cation) in the (13)C NMR spectrum (CD(2)Cl(2) at 25 °C). The DFT calculations showed spin delocalization from the paramagnetic Ru(2)(5+) core to the ligands, in agreement with the large up-field shift.

Computational Diffusion Magnetic Resonance Imaging Based on Time-Dependent Bloch NMR Flow Equation and Bessel Functions.

Science.gov (United States)

Awojoyogbe, Bamidele O; Dada, Michael O; Onwu, Samuel O; Ige, Taofeeq A; Akinwande, Ninuola I

2016-04-01

Magnetic resonance imaging (MRI) uses a powerful magnetic field along with radio waves and a computer to produce highly detailed "slice-by-slice" pictures of virtually all internal structures of matter. The results enable physicians to examine parts of the body in minute detail and identify diseases in ways that are not possible with other techniques. For example, MRI is one of the few imaging tools that can see through bones, making it an excellent tool for examining the brain and other soft tissues. Pulsed-field gradient experiments provide a straightforward means of obtaining information on the translational motion of nuclear spins. However, the interpretation of the data is complicated by the effects of restricting geometries as in the case of most cancerous tissues and the mathematical concept required to account for this becomes very difficult. Most diffusion magnetic resonance techniques are based on the Stejskal-Tanner formulation usually derived from the Bloch-Torrey partial differential equation by including additional terms to accommodate the diffusion effect. Despite the early success of this technique, it has been shown that it has important limitations, the most of which occurs when there is orientation heterogeneity of the fibers in the voxel of interest (VOI). Overcoming this difficulty requires the specification of diffusion coefficients as function of spatial coordinate(s) and such a phenomenon is an indication of non-uniform compartmental conditions which can be analyzed accurately by solving the time-dependent Bloch NMR flow equation analytically. In this study, a mathematical formulation of magnetic resonance flow sequence in restricted geometry is developed based on a general second order partial differential equation derived directly from the fundamental Bloch NMR flow equations. The NMR signal is obtained completely in terms of NMR experimental parameters. The process is described based on Bessel functions and properties that can make it

Electron paramagnetic resonance dosimetry using synthetic hydroxyapatite

Energy Technology Data Exchange (ETDEWEB)

Choi, Kwon; Kim, Hwi Young; Ye, Sung Joon [Seoul National University, Seoul (Korea, Republic of); Hirata, Hiroshi [Hokkaido University, Sapporo (Japan); Park, Jong Min [Seoul National University Hospital, Seoul (Korea, Republic of)

2014-11-15

The victims exposed doses under 3.5-4.0 Gy have chance to survive if treated urgently. To determine the priority of treatment among a large number of victims, the triage – distinguishing patients who need an urgent treatment from who may not be urgent – is necessary based on radiation biodosimetry. A current gold standard for radiation biodosimetry is the chromosomal assay using human lymphocytes. But this method requires too much time and skilled labors to cover the mass victims in radiation emergencies. Electron paramagnetic resonance (EPR) has been known for its capability of quantifying radicals in matters. EPR dosimetry is based on the measurement of stable radiation-induced radicals in tooth enamel. Hydroxyapatite (HAP) (Ca10(PO4)6(OH)2) contained in tooth enamel is a major probe for radiation dose reconstruction. This HAP dosimetry study was performed using a novel EPR spectrometer in Hokkaido University, Japan. The EPR dose-response curve was made using HAP samples. The blind test using 250 cGy samples showed the feasibility of EPR dosimetry for the triage purpose.

NMR imaging

International Nuclear Information System (INIS)

Andrew, E.R.

1983-01-01

Since hydrogen is the most abundant element in all living organisms, proton NMR lends itself well as a method of investigation in biology and medicine. NMR imaging has some special advantages as a diagnostic tool: no ionizing radiation is used, it is noninvasive; it provides a safer means of imaging than the use of x-rays, gamma rays, positrons, or heavy ions. In contrast with ultrasound, the radiation penetrates the bony structures without attenuation. In additional to morphological information, NMR imaging provides additional diagnostic insights through relaxation parameters, which are not available from other imaging methods. In the decade since the first primitive NMR images were obtained, the quality of images now obtained approaches those from CT x-ray scanners. Prototype instruments are being constructed for clinical evaluation and the first whole-body scanners are beginning to appear on the market at costs comparable to CT scanners. Primary differences in equipment for conventional NMR and NMR imaging are the much larger aperture magnets that are required for the examination of human subjects and the addition of coils to generate field gradients and facilities for manipulating the gradients. Early results from clinical trials in many parts of the world are encouraging, and in a few years, the usefuleness of this modality of medical imaging to the medical profession in diagnosis and treatment of disease will be defined. 10 figures

Solution NMR characterization of magnetic/electronic properties of azide and cyanide-inhibited substrate complexes of human heme oxygenase: implications for steric ligand tilt.

Science.gov (United States)

Peng, Dungeng; Ogura, Hiroshi; Ma, Li-Hua; Evans, John P; de Montellano, Paul R Ortiz; La Mar, Gerd N

2013-04-01

Solution 2D (1)H NMR was carried out on the azide-ligated substrate complex of human heme oxygenase, hHO, to provide information on the active site molecular structure, chromophore electronic/magnetic properties, and the distal H-bond network linked to the exogenous ligand by catalytically relevant oriented water molecules. While 2D NMR exhibited very similar patterns of two-dimensional nuclear Overhauser spectroscopy cross peaks of residues with substrate and among residues as the previously characterized cyanide complex, significant, broadly distributed chemical shift differences were observed for both labile and non-labile protons. The anisotropy and orientation of the paramagnetic susceptibility tensor, χ, were determined for both the azide and cyanide complexes. The most significant difference observed is the tilt of the major magnetic axes from the heme normal, which is only half as large for the azide than cyanide ligand, with each ligand tilted toward the catalytically cleaved α-meso position. The difference in chemical shifts is quantitatively correlated with differences in dipolar shifts in the respective complexes for all but the distal helix. The necessity of considering dipolar shifts, and hence determination of the orientation/anisotropy of χ, in comparing chemical shifts involving paramagnetic complexes, is emphasized. The analysis shows that the H-bond network cannot detect significant differences in H-bond acceptor properties of cyanide versus azide ligands. Lastly, significant retardation of distal helix labile proton exchange upon replacing cyanide with azide indicates that the dynamic stability of the distal helix is increased upon decreasing the steric interaction of the ligand with the distal helix. Copyright © 2013. Published by Elsevier Inc.

Comparative {sup 1}H NMR-based metabonomic analysis of HIV-1 sera

Energy Technology Data Exchange (ETDEWEB)

Philippeos, C. [University of Johannesburg, Department of Biochemistry (South Africa); Steffens, F. E. [University of Pretoria, Department of Statistics (South Africa); Meyer, D. [University of Pretoria, Department of Biochemistry (South Africa)], E-mail: debra.meyer@up.ac.za

2009-07-15

{sup 1}H NMR spectroscopy of sera from HIV-1 infected and uninfected individuals was performed on 300 and 600 MHz instruments. The resultant spectra were automatically data reduced to 90 and 180 integral segments of equal length. Analysis of variance identified significant differences between the sample groups, especially for the samples analyzed on 600 MHz and reduced to fewer segments. Linear discriminant analysis correctly classified 100% of the samples analyzed on the 300 MHz NMR (reduced to 180 segments); an increase in instrument sensitivity resulted in lower percentages of correctly classified samples. Multinomial logistic regression (MLR) resulted in 100% correct classification of all samples from both instruments. Thus {sup 1}H-NMR metabonomics on either instrument distinguishes HIV-positive individuals using or not using anti retroviral therapy, but the sensitivity of the instrument impacts on data reduction. Furthermore, MLR is a novel multivariate statistical technique for improved classification of biological data analyzed in NMR.

Comparing pharmacophore models derived from crystallography and NMR ensembles

Science.gov (United States)

Ghanakota, Phani; Carlson, Heather A.

2017-11-01

NMR and X-ray crystallography are the two most widely used methods for determining protein structures. Our previous study examining NMR versus X-Ray sources of protein conformations showed improved performance with NMR structures when used in our Multiple Protein Structures (MPS) method for receptor-based pharmacophores (Damm, Carlson, J Am Chem Soc 129:8225-8235, 2007). However, that work was based on a single test case, HIV-1 protease, because of the rich data available for that system. New data for more systems are available now, which calls for further examination of the effect of different sources of protein conformations. The MPS technique was applied to Growth factor receptor bound protein 2 (Grb2), Src SH2 homology domain (Src-SH2), FK506-binding protein 1A (FKBP12), and Peroxisome proliferator-activated receptor-γ (PPAR-γ). Pharmacophore models from both crystal and NMR ensembles were able to discriminate between high-affinity, low-affinity, and decoy molecules. As we found in our original study, NMR models showed optimal performance when all elements were used. The crystal models had more pharmacophore elements compared to their NMR counterparts. The crystal-based models exhibited optimum performance only when pharmacophore elements were dropped. This supports our assertion that the higher flexibility in NMR ensembles helps focus the models on the most essential interactions with the protein. Our studies suggest that the "extra" pharmacophore elements seen at the periphery in X-ray models arise as a result of decreased protein flexibility and make very little contribution to model performance.

NMR-CT scanner

International Nuclear Information System (INIS)

Kose, Katsumi; Sato, Kozo; Sugimoto, Hiroshi; Sato, Masataka.

1983-01-01

A brief explanation is made on the imaging methods for a practical diagnostic NMR-CT scanner : A whole-body NMR-CT scanner utilizing a resistive magnet has been developed by Toshiba in cooperation with the Institute for Solid State Physics, the University of Tokyo. Typical NMR-CT images of volunteers and patients obtained in the clinical experiments using this device are presented. Detailed specifications are also shown about the practical NMR-CTs which are to be put on the market after obtaining the government approval. (author)

Resonance assignment for a particularly challenging protein based on systematic unlabeling of amino acids to complement incomplete NMR data sets

International Nuclear Information System (INIS)

Bellstedt, Peter; Seiboth, Thomas; Häfner, Sabine; Kutscha, Henriette; Ramachandran, Ramadurai; Görlach, Matthias

2013-01-01

NMR-based structure determination of a protein requires the assignment of resonances as indispensable first step. Even though heteronuclear through-bond correlation methods are available for that purpose, challenging situations arise in cases where the protein in question only yields samples of limited concentration and/or stability. Here we present a strategy based upon specific individual unlabeling of all 20 standard amino acids to complement standard NMR experiments and to achieve unambiguous backbone assignments for the fast precipitating 23 kDa catalytic domain of human aprataxin of which only incomplete standard NMR data sets could be obtained. Together with the validation of this approach utilizing the protein GB1 as a model, a comprehensive insight into metabolic interconversion ('scrambling”) of NH and CO groups in a standard Escherichia coli expression host is provided

On kinetics of paramagnetic radiation defects accumulation in beryllium ceramics; O kinetike nakopleniya paramagnitnykh radiatsionnykh defektov v berillievykh keramikakh

Energy Technology Data Exchange (ETDEWEB)

Polyakov, A I; Ryabikin, Yu A; Zashkvara, O V; Bitenbaev, M I; Petykhov, Yu V [Fiziko-Tekhnicheskij Inst., Almaty (Kazakhstan); Inst. Atomnoj Ehnergii, Kurchatov (Kazakhstan)

1999-07-01

Results of paramagnetic radiation defects concentration dependence study in beryllium ceramics from gamma-irradiation dose ({sup 60}Co) within interval 0-100 Mrem are cited. Obtained dose dependence has form of accumulation curve with saturation typical of for majority of solids (crystals, different polymers, organic substances and others) , in which under irradiation occur not only formation of paramagnetic radiation defects, but its destruction due to recombination and interaction with radiation fields. Analysis of accumulation curve by the method of distant asymptotics allows to determine that observed in gamma-irradiated beryllium ceramics double line of electron spin resonance is forming of two types of paramagnetic radiation defects. It was defined, that sum paramagnetic characteristics of beryllium ceramics within 1-100 Mrad gamma- irradiation dose field change insignificantly and define from first type of paramagnetic radiation defects.

An EPR study on tea: Identification of paramagnetic species, effect of heat and sweeteners

Science.gov (United States)

Bıyık, Recep; Tapramaz, Recep

2009-10-01

Tea ( Camellia Sinensis) is the most widely consumed beverage in the world, and is known to be having therapeutic, antioxidant and nutritional effects. Electron paramagnetic resonance (EPR) spectral studies made on the tea cultivated along the shore of Black Sea, Turkey, show Mn 2+ and Fe 3+ centers in green tea leaves and in black tea extract. Dry black tea flakes and dry extract show additional sharp line attributed to semiquinone radical. The origins of the paramagnetic species in black tea are defined and discussed. Effect of humidity and heat are investigated. It is observed that dry extract of black tea melts at 100 °C and the semiquinone radical lives up to 140 °C while Mn 2+ sextet disappears just above 100 °C in tea extract. Natural and synthetics sweeteners have different effects on the paramagnetic centers. White sugar (sucrose) quenches the Mn 2+ and semiquinone lines in black tea EPR spectrum, and glucose, fructose, lactose and maltose quench Fe 3+ line while synthetic sweeteners acesulfam potassium, aspartame and sodium saccharine do not have any effect on paramagnetic species in tea.

Multi-atlas Based Segmentation Editing with Interaction-Guided Constraints

OpenAIRE

Park, Sang Hyun; Gao, Yaozong; Shen, Dinggang

2015-01-01

We propose a novel multi-atlas based segmentation method to address the editing scenario, when given an incomplete segmentation along with a set of training label images. Unlike previous multi-atlas based methods, which depend solely on appearance features, we incorporate interaction-guided constraints to find appropriate training labels and derive their voting weights. Specifically, we divide user interactions, provided on erroneous parts, into multiple local interaction combinations, and th...

Development of 19F-NMR chemical shift detection of DNA B-Z equilibrium using 19F-NMR.

Science.gov (United States)

Nakamura, S; Yang, H; Hirata, C; Kersaudy, F; Fujimoto, K

2017-06-28

Various DNA conformational changes are in correlation with biological events. In particular, DNA B-Z equilibrium showed a high correlation with translation and transcription. In this study, we developed a DNA probe containing 5-trifluoromethylcytidine or 5-trifluoromethylthymidine to detect DNA B-Z equilibrium using 19 F-NMR. Its probe enabled the quantitative detection of B-, Z-, and ss-DNA based on 19 F-NMR chemical shift change.

Invalid-point removal based on epipolar constraint in the structured-light method

Science.gov (United States)

Qi, Zhaoshuai; Wang, Zhao; Huang, Junhui; Xing, Chao; Gao, Jianmin

2018-06-01

In structured-light measurement, there unavoidably exist many invalid points caused by shadows, image noise and ambient light. According to the property of the epipolar constraint, because the retrieved phase of the invalid point is inaccurate, the corresponding projector image coordinate (PIC) will not satisfy the epipolar constraint. Based on this fact, a new invalid-point removal method based on the epipolar constraint is proposed in this paper. First, the fundamental matrix of the measurement system is calculated, which will be used for calculating the epipolar line. Then, according to the retrieved phase map of the captured fringes, the PICs of each pixel are retrieved. Subsequently, the epipolar line in the projector image plane of each pixel is obtained using the fundamental matrix. The distance between the corresponding PIC and the epipolar line of a pixel is defined as the invalidation criterion, which quantifies the satisfaction degree of the epipolar constraint. Finally, all pixels with a distance larger than a certain threshold are removed as invalid points. Experiments verified that the method is easy to implement and demonstrates better performance than state-of-the-art measurement systems.

NMR of lignins

Science.gov (United States)

John Ralph; Larry L. Landucci

2010-01-01

This chapter will consider the basic aspects and findings of several forms of NMR spectroscopy, including separate discussions of proton, carbon, heteronuclear, and multidimensional NMR. Enhanced focus will be on 13C NMR, because of its qualitative and quantitative importance, followed by NMR’s contributions to our understanding of lignin...

Role of paramagnetic chromium in chromium(VI)-induced damage in cultured mammalian cells.

OpenAIRE

Sugiyama, M

1994-01-01

Chromium(VI) compounds are known to be potent toxic and carcinogenic agents. Because chromium(VI) is easily taken up by cells and is subsequently reduced to chromium(III), the formation of paramagnetic chromium such as chromium(V) and chromium(III) is believed to play a role in the adverse biological effects of chromium(VI) compounds. The present report, uses electron spin resonance (ESR) spectroscopy; the importance of the role of paramagnetic chromium in chromium(VI)-induced damage in intac...

Glycerin-Induced Conformational Changes in Bombyx mori Silk Fibroin Film Monitored by (13)C CP/MAS NMR and ¹H DQMAS NMR.

Science.gov (United States)

Asakura, Tetsuo; Endo, Masanori; Hirayama, Misaki; Arai, Hiroki; Aoki, Akihiro; Tasei, Yugo

2016-09-09

In order to improve the stiff and brittle characteristics of pure Bombyx mori (B. mori) silk fibroin (SF) film in the dry state, glycerin (Glyc) has been used as a plasticizer. However, there have been very limited studies on the structural characterization of the Glyc-blended SF film. In this study, (13)C Cross Polarization/Magic Angle Spinning nuclear magnetic resonance (CP/MAS NMR) was used to monitor the conformational changes in the films by changing the Glyc concentration. The presence of only 5 wt % Glyc in the film induced a significant conformational change in SF where Silk I* (repeated type II β-turn and no α-helix) newly appeared. Upon further increase in Glyc concentration, the percentage of Silk I* increased linearly up to 9 wt % Glyc and then tended to be almost constant (30%). This value (30%) was the same as the fraction of Ala residue within the Silk I* form out of all Ala residues of SF present in B. mori mature silkworm. The ¹H DQMAS NMR spectra of Glyc-blended SF films confirmed the appearance of Silk I* in the Glyc-blended SF film. A structural model of Glyc-SF complex including the Silk I* form was proposed with the guidance of the Molecular Dynamics (MD) simulation using ¹H-¹H distance constraints obtained from the ¹H Double-Quantum Magic Angle Spinning (DQMAS) NMR spectra.

Comparison of Fruits of Forsythia suspensa at Two Different Maturation Stages by NMR-Based Metabolomics

Directory of Open Access Journals (Sweden)

Jinping Jia

2015-05-01

Full Text Available Forsythiae Fructus (FF, the dried fruit of Forsythia suspensa, has been widely used as a heat-clearing and detoxifying herbal medicine in China. Green FF (GF and ripe FF (RF are fruits of Forsythia suspensa at different maturity stages collected about a month apart. FF undergoes a complex series of physical and biochemical changes during fruit ripening. However, the clinical uses of GF and RF have not been distinguished to date. In order to comprehensively compare the chemical compositions of GF and RF, NMR-based metabolomics coupled with HPLC and UV spectrophotometry methods were adopted in this study. Furthermore, the in vitro antioxidant and antibacterial activities of 50% methanol extracts of GF and RF were also evaluated. A total of 27 metabolites were identified based on NMR data, and eight of them were found to be different between the GF and RF groups. The GF group contained higher levels of forsythoside A, forsythoside C, cornoside, rutin, phillyrin and gallic acid and lower levels of rengyol and β-glucose compared with the RF group. The antioxidant activity of GF was higher than that of RF, but no significant difference was observed between the antibacterial activities of GF and RF. Given our results showing their distinct chemical compositions, we propose that NMR-based metabolic profiling can be used to discriminate between GF and RF. Differences in the chemical and biological activities of GF and RF, as well as their clinical efficacies in traditional Chinese medicine should be systematically investigated in future studies.

NMR imaging of the cardiovascular system

International Nuclear Information System (INIS)

Canby, R.C.; Evanochko, W.T.; Pohost, G.M.

1986-01-01

Proton nuclear magnetic resonance (NMR) imaging permits high-resolution tomographic and three-dimensional images of the human body to be obtained without exposure to ionizing radiation. Such imaging not only yields anatomic resolution comparable to X-ray examinations but also provides a potential means to discriminate between healthy tissue and diseased tissue. This potential is based on certain NMR properties known as relaxation times, which determine, in part, the signal intensity in an image. These properties are related to such factors as the sizes and concentrations of proteins and mobile lipids and the compartmentalization of the protons of water. Although NMR imaging (also called magnetic resonance imaging, MRI) is becoming widely available for clinical use, application to the cardiovascular system, though promising, remains primarily a research tool. Gated proton NMR imaging can generate cardiac images with excellent morphologic detail and contrast; however, its ultimate importance as a cardiovascular diagnostic modality will depend on the development of several unique applications. These applications are discussed in this paper

Towards interpretation of intermolecular paramagnetic relaxation enhancement outside the fast exchange limit

Energy Technology Data Exchange (ETDEWEB)

Ceccon, Alberto; Marius Clore, G., E-mail: mariusc@mail.nih.gov; Tugarinov, Vitali, E-mail: vitali.tugarinov@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

2016-09-15

In an exchanging system between major and minor species, the transverse paramagnetic relaxation enhancement rate observed on the resonances of the major species (Γ{sub 2}{sup app}) is dependent upon the exchange regime between the species. Quantitative analysis of PRE data in such systems typically assumes that the overall exchange rate k{sub ex} between the species is fast on the PRE time scale (k{sub ex} ≫ Γ{sub 2}). Recently, we have characterized the kinetics of binding of the model protein ubiquitin to large (LUV) and small (SUV) unilamellar lipid-based nanoparticles or liposomes (Ceccon A, Tugarinov V, Bax A, Clore GM (2016). J Am Chem Soc 138:5789–5792). Building upon these results and taking advantage of a strong paramagnetic agent with an isotropic g-tensor, Gd{sup 3+}, we were able to measure intermolecular methyl carbon and proton PREs between paramagnetically-tagged liposomes and ubiquitin. In the limit of fast exchange (k{sub ex} ≫ Γ{sub 2}) the ratio of the apparent proton to carbon methyl PREs, ({sup 1}H{sub m}–Γ{sub 2}{sup app})/({sup 13}C{sub m}–Γ{sub 2}{sup app}), is equal to the square of the ratio of the gyromagnetic ratios of the two nuclei, (γ{sub Η}/γ{sub C}){sup 2}. However, outside the fast exchange regime, under intermediate exchange conditions (e.g. when Γ{sub 2} is comparable in magnitude to k{sub ex}) the ({sup 1}H{sub m}–Γ{sub 2}{sup app})/({sup 13}C{sub m}–Γ{sub 2}{sup app}) ratio provides a reliable measure of the ‘true’ methyl PREs.

Solid-state EPR strategies for the structural characterization of paramagnetic NO adducts of frustrated Lewis pairs (FLPs)

Energy Technology Data Exchange (ETDEWEB)

Oliveira, Marcos de; Magon, Claudio José [Instituto de Física de São Carlos, Universidade de São Paulo, P.O. Box 369, 13560-970 São Carlos, São Paulo (Brazil); Wiegand, Thomas [Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8049 Zürich (Switzerland); Elmer, Lisa-Maria; Sajid, Muhammad; Kehr, Gerald; Erker, Gerhard [Organisch-Chemisches Institut, WWU Münster, Corrensstraße 40, D 48149 Münster (Germany); Eckert, Hellmut, E-mail: eckerth@uni-muenster.de [Instituto de Física de São Carlos, Universidade de São Paulo, P.O. Box 369, 13560-970 São Carlos, São Paulo (Brazil); Institut für Physikalische Chemie, WWU Münster, Corrensstrasse 30, D 48149 Münster (Germany)

2015-03-28

Anisotropic interactions present in three new nitroxide radicals prepared by N,N addition of NO to various borane-phosphane frustrated Lewis pairs (FLPs) have been characterized by continuous-wave (cw) and pulsed X-band EPR spectroscopies in solid FLP-hydroxylamine matrices at 100 K. Anisotropic g-tensor values and {sup 11}B, {sup 14}N, and {sup 31}P hyperfine coupling tensor components have been extracted from continuous-wave lineshape analyses, electron spin echo envelope modulation (ESEEM), and hyperfine sublevel correlation spectroscopy (HYSCORE) experiments with the help of computer simulation techniques. Suitable fitting constraints are developed on the basis of density functional theory (DFT) calculations. These calculations reveal that different from the situation in standard nitroxide radicals (TEMPO), the g-tensors are non-coincident with any of the nuclear hyperfine interaction tensors. The determination of these interaction parameters turns out to be successful, as the cw- and pulse EPR experiments are highly complementary in informational content. While the continuous-wave lineshape is largely influenced by the anisotropic hyperfine coupling to {sup 14}N and {sup 31}P, the ESEEM and HYSCORE spectra contain important information about the {sup 11}B hyperfine coupling and nuclear electric quadrupolar interaction. The set of cw- and pulsed EPR experiments, with fitting constraints developed by DFT calculations, defines an efficient strategy for the structural analysis of paramagnetic FLP adducts.

Medical applications of NMR imaging and NMR spectroscopy with stable isotopes. Summary

International Nuclear Information System (INIS)

Matwiyoff, N.A.

1983-01-01

The current status of NMR imaging and NMR spectroscopy are summarized. For the most part examples from the March 1983 Puerto Rico symposium are used to illustrate the utility of NMR in medicine. 18 refs., 5 figs

Medical applications of NMR imaging and NMR spectroscopy with stable isotopes. Summary

Energy Technology Data Exchange (ETDEWEB)

Matwiyoff, N.A.

1983-01-01

The current status of NMR imaging and NMR spectroscopy are summarized. For the most part examples from the March 1983 Puerto Rico symposium are used to illustrate the utility of NMR in medicine. 18 refs., 5 figs.

Refinement of the ferri and paramagnetic phases of magnetite measured by neutron multiple diffraction

International Nuclear Information System (INIS)

Mazzochi, V.L.; Parente, C.B.R.

1989-10-01

Structural parameters of the ferri and paramagnetic phases of magnetite have been refined from neutron multiple diffraction data. Experimental patterns were obtained by measuring the III primary reflection of a natural single crystal of this compound, at room temperature for the ferrimagnetic phase and 703 0 C for the paramagnetic phase. Theoretical multiple diffraction patterns for both phases have been calculated by the program MULTI which uses the iterative method. In this method intensities are caluclated as Taylor series expansions summed up to a order sufficient for a good approximation. A step by step process has been used in the refinements similarly to the parameter-shift method. Final values for the discrepancy factor found for the ferri and paramagnetic phases were R = 3.96% and R = 3.46%, respectively. (author) [pt

ASIC-based design of NMR system health monitor for mission/safety?critical applications

OpenAIRE

Balasubramanian, P.

2016-01-01

N-modular redundancy (NMR) is a generic fault tolerance scheme that is widely used in safety?critical circuit/system designs to guarantee the correct operation with enhanced reliability. In passive NMR, at least a majority (N?+?1)/2 out of N function modules is expected to operate correctly at any time, where N is odd. Apart from a conventional realization of the NMR system, it would be useful to provide a concurrent indication of the system?s health so that an appropriate remedial action may...

Crystal structure, magnetism, {sup 89}Y solid state NMR, and {sup 121}Sb Moessbauer spectroscopic investigations of YIrSb

Energy Technology Data Exchange (ETDEWEB)

Benndorf, Christopher [Institut fuer Physikalische Chemie, Universitaet Muenster (Germany); Institut fuer Anorganische und Analytische Chemie, Universitaet Muenster (Germany); Heletta, Lukas; Block, Theresa; Poettgen, Rainer [Institut fuer Anorganische und Analytische Chemie, Universitaet Muenster (Germany); Eckert, Hellmut [Institut fuer Physikalische Chemie, Universitaet Muenster (Germany); Institute of Physics in Sao Carlos, University of Sao Paulo, Sao Carlos (Brazil)

2017-02-15

The ternary antimonide YIrSb was synthesized from the binary precursor YIr and elemental antimony by a diffusion controlled solid-state reaction. Single crystals were obtained by a flux technique with elemental bismuth as an inert solvent. The YIrSb structure (TiNiSi type, space group Pnma) was refined from single-crystal X-ray diffractometer data: a = 711.06(9), b = 447.74(5), c = 784.20(8) pm, wR{sub 2} = 0.0455, 535 F{sup 2} values, 20 variables. {sup 89}Y solid state MAS NMR and {sup 121}Sb Moessbauer spectra show single resonance lines in agreement with single-crystal X-ray data. YIrSb is a Pauli paramagnet. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Multifrequency Electron Paramagnetic Resonance Theory and Applications

CERN Document Server

Misra, Sushil K

2011-01-01

Filling the gap for a systematic, authoritative, and up-to-date review of this cutting-edge technique, this book covers both low and high frequency EPR, emphasizing the importance of adopting the multifrequency approach to study paramagnetic systems in full detail by using the EPR method. In so doing, it discusses not only the underlying theory and applications, but also all recent advances -- with a final section devoted to future perspectives.

Synthesis and characterization of thorium(IV) and uranium(IV) complexes with Schiff bases

Energy Technology Data Exchange (ETDEWEB)

Radoske, Thomas; Maerz, Juliane; Kaden, Peter; Patzschke, Michael; Ikeda-Ohno, Atsushi [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Chemistry of the F-Elements

2017-06-01

We report herein the synthesis and characterization of several imine complexes of tetravalent thorium (Th(IV)) and uranium (U(IV)). The ligands investigated in this study are a Schiff base type, including the well-known salen ligand (H{sub 2}Le, Fig. 1). The complexation in solution was investigated by NMR measurements indicating paramagnetic effects of unpaired f-electrons of U(IV) on the ligand molecule. We also determined the solid-state molecular structures of the synthesized complexes by single crystal X-ray diffraction. The synthesized complexes show an eight-fold coordination geometry around the actinide center surrounded by two tetradentate ligands with 2N- and 2O-donor atoms.

Fast and Efficient Fragment-Based Lead Generation by Fully Automated Processing and Analysis of Ligand-Observed NMR Binding Data.

Science.gov (United States)

Peng, Chen; Frommlet, Alexandra; Perez, Manuel; Cobas, Carlos; Blechschmidt, Anke; Dominguez, Santiago; Lingel, Andreas

2016-04-14

NMR binding assays are routinely applied in hit finding and validation during early stages of drug discovery, particularly for fragment-based lead generation. To this end, compound libraries are screened by ligand-observed NMR experiments such as STD, T1ρ, and CPMG to identify molecules interacting with a target. The analysis of a high number of complex spectra is performed largely manually and therefore represents a limiting step in hit generation campaigns. Here we report a novel integrated computational procedure that processes and analyzes ligand-observed proton and fluorine NMR binding data in a fully automated fashion. A performance evaluation comparing automated and manual analysis results on (19)F- and (1)H-detected data sets shows that the program delivers robust, high-confidence hit lists in a fraction of the time needed for manual analysis and greatly facilitates visual inspection of the associated NMR spectra. These features enable considerably higher throughput, the assessment of larger libraries, and shorter turn-around times.

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

Science.gov (United States)

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

2015-01-01

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

Redox-mediated dissolution of paramagnetic nanolids to achieve a smart theranostic system

Science.gov (United States)

Wang, Aifei; Guo, Mingyi; Wang, Nan; Zhao, Jianyun; Qi, Wenxiu; Muhammad, Faheem; Chen, Liang; Guo, Yingjie; Nguyen, Nam-Trung; Zhu, Guangshan

2014-04-01

Manganese oxide (Mn3O4) nanoparticles have recently emerged as a promising T1 contrast agent. In this study, for the first time, we demonstrated an interaction of Mn3O4 with a biological system, and found redox sensitive behavior of these paramagnetic nanoparticles in intracellular reducing environment. Inspired by these findings, we for the first time used this interaction for some therapeutic advantages and designed a versatile mesoporous silica based nanotheranostic system to realize redox-activated enhanced magnetic resonance imaging and responsive anticancer drug delivery. Contrary to previous reports, we firstly prepared high quality amine terminated hydrophilic Mn3O4 nanolids, without using multistep ligand exchange strategies. The resulting water stable and small-sized Mn3O4 nanolids were subsequently used as nanolids to cap drug loaded nanochannels of a porous carrier. Exposure to highly prevalent intracellular reducing environment resulted in the steady-state dissolution of these nanolids and attained an intelligent drug release. Furthermore, the redox receptive dissolution of paramagnetic Mn3O4 nanolids into Mn2+ in turn increases the T1 signal to twofold, providing an added opportunity to even track the feedback of therapy. This study, in addition to simultaneously realizing drug delivery and imaging, also provides a new insight into the fate and interaction of manganese oxide nanoparticles with components of biological systems.Manganese oxide (Mn3O4) nanoparticles have recently emerged as a promising T1 contrast agent. In this study, for the first time, we demonstrated an interaction of Mn3O4 with a biological system, and found redox sensitive behavior of these paramagnetic nanoparticles in intracellular reducing environment. Inspired by these findings, we for the first time used this interaction for some therapeutic advantages and designed a versatile mesoporous silica based nanotheranostic system to realize redox-activated enhanced magnetic resonance

Magnon spin Hall magnetoresistance of a gapped quantum paramagnet

NARCIS (Netherlands)

Ulloa, Camilo; Duine, R.A.

2018-01-01

Motivated by recent experimental work, we consider spin transport between a normal metal and a gapped quantum paramagnet. We model the latter as the magnonic Mott-insulating phase of an easy-plane ferromagnetic insulator. We evaluate the spin current mediated by the interface exchange coupling

Electrically-detected electron paramagnetic resonance of point centers in 6H-SiC nanostructures

Czech Academy of Sciences Publication Activity Database

Bagraev, N.T.; Gets, D.S.; Kalabukhova, E.N.; Klyachkin, L.E.; Malyarenko, A.M.; Mashkov, V.A.; Savchenko, Dariia; Shanina, B.D.

2014-01-01

Roč. 48, č. 11 (2014), s. 1467-1480 ISSN 1063-7826 R&D Projects: GA MŠk(CZ) LM2011029 Grant - others:SAFMAT(XE) CZ.2.16/3.1.00/22132 Institutional support: RVO:68378271 Keywords : electron paramagnetic resonance * electrically- detected electron paramagnetic resonance * 6H -SiC nanostructures * nitrogen-vacancy defect * point defect Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.739, year: 2014

Study of paramagnetic contrast agents for NMR imaging: theoretical and experimental aspects (the case of Mn2+ ion)

International Nuclear Information System (INIS)

Chavoix, M.E.

1984-06-01

The use of contrast enhancing agents and the evaluation of magnetic properties of tissues, extend the diagnostic usefulness of Nuclear Magnetic Resonance (NMR) imaging. From this point of view, proton T 1 (spin-lattice) relaxation times of rat tissue, following parenteral administration of Mn(II) to increase the relaxation rate (R 1 =1/T 1 ), have been studied at 20 MHz. Differenciation of free (MF) and bound (Mb) manganese in these tissues was thus determined by measuring, total exogenous Mn ++ ions by Atomic Absorption spectrometry and free (non protein complexed) ions by Electron Spin Resonance Analysis. From these results, the diffusion of Mn ++ into various organs, was evaluated 15 min. after injection. A significant difference in the fixation of manganese occured between the liver and the pancreas with uptakes of 50% and 1% of the administration dose respectively [fr

A Constraint programming-based genetic algorithm for capacity output optimization

Directory of Open Access Journals (Sweden)

Kate Ean Nee Goh

2014-10-01

Full Text Available Purpose: The manuscript presents an investigation into a constraint programming-based genetic algorithm for capacity output optimization in a back-end semiconductor manufacturing company.Design/methodology/approach: In the first stage, constraint programming defining the relationships between variables was formulated into the objective function. A genetic algorithm model was created in the second stage to optimize capacity output. Three demand scenarios were applied to test the robustness of the proposed algorithm.Findings: CPGA improved both the machine utilization and capacity output once the minimum requirements of a demand scenario were fulfilled. Capacity outputs of the three scenarios were improved by 157%, 7%, and 69%, respectively.Research limitations/implications: The work relates to aggregate planning of machine capacity in a single case study. The constraints and constructed scenarios were therefore industry-specific.Practical implications: Capacity planning in a semiconductor manufacturing facility need to consider multiple mutually influenced constraints in resource availability, process flow and product demand. The findings prove that CPGA is a practical and an efficient alternative to optimize the capacity output and to allow the company to review its capacity with quick feedback.Originality/value: The work integrates two contemporary computational methods for a real industry application conventionally reliant on human judgement.

Investigation of paramagnetic saturation in lanthanum manganese nitrate

NARCIS (Netherlands)

Flokstra, Jakob; Meijer, H.C.; Bots, G.J.C.; Verheij, W.A.; van der Marel, L.C.

1973-01-01

Paramagnetic saturation of lanthanum manganese nitrate, La2Mn3(NO3)12·24H2O, has been investigated at liquid He temperatures in a static as well as a dynamical way. With the aid of the molecular-field theory the Casimir and Du Pré dispersion and absorption curves are adapted explicitly to the

$\\beta$-NMR of copper isotopes in ionic liquids

CERN Multimedia

We propose to test the feasibility of spin-polarization and $\\beta$-NMR studies on several short-lived copper isotopes, $^{58}$ Cu, $^{74}$Cu and $^{75}$Cu in crystals and liquids. The motivation is given by biological studies of Cu with $\\beta$-NMR in liquid samples, since Cu is present in a large number of enzymes involved in electron transfer and activation of oxygen. The technique is based on spin-polarization via optical pumping in the new VITO beamline. We will use the existing lasers, NMR magnet and NMR chambers and we will prepare a new optical pumping system. The studies will be devoted to tests of achieved $\\beta$-asymmetry in solid hosts, the behaviour of asymmetry when increasing vacuum, and finally NMR scans in ionic liquids. The achieved spin polarization will be also relevant for the plans to measure with high precision the magnetic moments of neutron-rich Cu isotopes.

An agent-based analysis of the German electricity market with transmission capacity constraints

International Nuclear Information System (INIS)

Veit, Daniel J.; Weidlich, Anke; Krafft, Jacob A.

2009-01-01

While some agent-based models have been developed for analyzing the German electricity market, there has been little research done on the emerging issue of intra-German congestion and its effects on the bidding behavior of generator agents. Yet, studies of other markets have shown that transmission grid constraints considerably affect strategic behavior in electricity markets. In this paper, the implications of transmission constraints on power markets are analyzed for the case of Germany. Market splitting is applied in the case of congestion in the grid. For this purpose, the agent-based modeling of electricity systems (AMES) market package developed by Sun and Tesfatsion is modified to fit the German context, including a detailed representation of the German high-voltage grid and its interconnections. Implications of transmission constraints on prices and social welfare are analyzed for scenarios that include strategic behavior of market participants and high wind power generation. It can be shown that strategic behavior and transmission constraints are inter-related and may pose severe problems in the future German electricity market.

An agent-based analysis of the German electricity market with transmission capacity constraints

Energy Technology Data Exchange (ETDEWEB)

Veit, Daniel J.; Weidlich, Anke; Krafft, Jacob A. [University of Mannheim, Dieter Schwarz Chair of Business Administration, E-Business and E-Government, 68131 Mannheim (Germany)

2009-10-15

While some agent-based models have been developed for analyzing the German electricity market, there has been little research done on the emerging issue of intra-German congestion and its effects on the bidding behavior of generator agents. Yet, studies of other markets have shown that transmission grid constraints considerably affect strategic behavior in electricity markets. In this paper, the implications of transmission constraints on power markets are analyzed for the case of Germany. Market splitting is applied in the case of congestion in the grid. For this purpose, the agent-based modeling of electricity systems (AMES) market package developed by Sun and Tesfatsion is modified to fit the German context, including a detailed representation of the German high-voltage grid and its interconnections. Implications of transmission constraints on prices and social welfare are analyzed for scenarios that include strategic behavior of market participants and high wind power generation. It can be shown that strategic behavior and transmission constraints are inter-related and may pose severe problems in the future German electricity market. (author)

Theoretical studies of the local structure and electron paramagnetic resonance parameters for tetragonal VO{sup 2+} in C{sub 6}H{sub 7}KO{sub 7}

Energy Technology Data Exchange (ETDEWEB)

Zhou, Ping [Chongqing Jiaotong Univ. (China). School of Science; Li, Ling [Sichuan University of Arts and Science, Dazhou (China). Dept. of Maths and Finance-Economics

2015-07-01

The optical spectra, electron paramagnetic resonance parameters (i.e., the spin Hamiltonian parameters, including paramagnetic g factors and the hyperfine structure constants A{sub i}) and the local distortion structure for the tetragonal VO{sup 2+} in C{sub 6}H{sub 7}KO{sub 7} are theoretically studied based on the crystal-field theory and three-order perturbation formulas of a 3d{sup 1} centre in tetragonal site. The magnitude of orbital reduction factor, core polarisation constant κ, and local structure parameters are obtained by fitting the calculated optical spectra and electron paramagnetic resonance parameters to the experimental values. The theoretical results are in reasonable agreement with the experimental values.

Prediction of peak overlap in NMR spectra

International Nuclear Information System (INIS)

Hefke, Frederik; Schmucki, Roland; Güntert, Peter

2013-01-01

Peak overlap is one of the major factors complicating the analysis of biomolecular NMR spectra. We present a general method for predicting the extent of peak overlap in multidimensional NMR spectra and its validation using both, experimental data sets and Monte Carlo simulation. The method is based on knowledge of the magnetization transfer pathways of the NMR experiments and chemical shift statistics from the Biological Magnetic Resonance Data Bank. Assuming a normal distribution with characteristic mean value and standard deviation for the chemical shift of each observable atom, an analytic expression was derived for the expected overlap probability of the cross peaks. The analytical approach was verified to agree with the average peak overlap in a large number of individual peak lists simulated using the same chemical shift statistics. The method was applied to eight proteins, including an intrinsically disordered one, for which the prediction results could be compared with the actual overlap based on the experimentally measured chemical shifts. The extent of overlap predicted using only statistical chemical shift information was in good agreement with the overlap that was observed when the measured shifts were used in the virtual spectrum, except for the intrinsically disordered protein. Since the spectral complexity of a protein NMR spectrum is a crucial factor for protein structure determination, analytical overlap prediction can be used to identify potentially difficult proteins before conducting NMR experiments. Overlap predictions can be tailored to particular classes of proteins by preparing statistics from corresponding protein databases. The method is also suitable for optimizing recording parameters and labeling schemes for NMR experiments and improving the reliability of automated spectra analysis and protein structure determination.

Measurement of pO2 in a Pre-clinical Model of Rabbit Tumor Using OxyChip, a Paramagnetic Oxygen Sensor.

Science.gov (United States)

Hou, H; Khan, N; Kuppusamy, P

2017-01-01

The objective of this work was to establish a novel and robust technology, based on electron paramagnetic resonance (EPR) oximetry, as a practical tool for measurement of tumor oxygen. Previously, we have reported on the development of oxygen-sensing paramagnetic crystals (LiNc-BuO) encapsulated in a biocompatible polymer, called OxyChip. In this report we present our recent data on the use of OxyChip for pO 2 measurements in the tumor of a pre-clinical, large-animal rabbit model. The results establish that OxyChip is capable of noninvasive and repeated measurement of pO 2 in a large animal model.

Portable, Low-cost NMR with Laser-Lathe Lithography Produced

Energy Technology Data Exchange (ETDEWEB)

Herberg, J L; Demas, V; Malba, V; Bernhardt, A; Evans, L; Harvey, C; Chinn, S; Maxwell, R; Reimer, J; Pines, A

2006-12-21

Nuclear Magnetic Resonance (NMR) is unsurpassed in its ability to non-destructively probe chemical identity. Portable, low-cost NMR sensors would enable on-site identification of potentially hazardous substances, as well as the study of samples in a variety of industrial applications. Recent developments in RF microcoil construction (i.e. coils much smaller than the standard 5 mm NMR RF coils), have dramatically increased NMR sensitivity and decreased the limits-of-detection (LOD). We are using advances in laser pantographic microfabrication techniques, unique to LLNL, to produce RF microcoils for field deployable, high sensitivity NMR-based detectors. This same fabrication technique can be used to produce imaging coils for MRI as well as for standard hardware shimming or 'ex-situ' shimming of field inhomogeneities typically associated with inexpensive magnets. This paper describes a portable NMR system based on a laser-fabricated microcoil and homebuilt probe design. For testing this probe, we used a hand-held 2 kg Halbach magnet that can fit into the palm of a hand, and an RF probe with laser-fabricated microcoils. The focus of the paper is on the evaluation of the microcoils, RF probe, and first generation gradient coils. The setup of this system, initial results, sensitivity measurements, and future plans are discussed. The results, even though preliminary, are promising and provide the foundation for developing a portable, inexpensive NMR system for chemical analysis. Such a system will be ideal for chemical identification of trace substances on site.

CBDS: Constraint-based diagnostic system for malfunction identification in the nuclear power plant

International Nuclear Information System (INIS)

Ha, J.

1992-01-01

Traditional rule-based diagnostic expert systems use the experience of experts in the form of rules that associate symptoms with underlying faults. A commonly recognized failing of such systems is their narrow range of expertise and their inability to recognize problems outside this range of expertise. A model base diagnostic system isolating malfunctioning components-CBDS, the Constraint based Diagnostic System-has been developed. Since the intended behavior of a device is more predictable than unintended behaviors (faults), a model based system using the intended behavior has a potential to diagnose unexpected malfunctions by considering faults as open-quotes anything other than the intended behavior.close quotes As a knowledge base, the CBDS generates and decomposes a constraint network based on the structure and behavior model, which are represented symbolically in algebraic equations. Behaviors of generic components are organized in a component model library. Once the library is available, actual domain knowledge can be represented by declaring component types and their connections. To capture various plant knowledge, the mixed model was developed which allow the use of different parameter types in one equation by defining various operators. The CBDS uses the general idea of model based diagnosis. It detects a discrepancy between observation and prediction using constraint propagation, which carriers and accumulates the assumptions when parameter values are deduced. When measured plant parameters are asserted into a constraint network and are propagated through the network, a discrepancy will be detected if there exists any malfunctioning component. The CBDS was tested in the Recirculation Flow Control System of a BWR, and has been shown to be able to diagnose unexpected events

NMR imaging of the brain: initial impressions

International Nuclear Information System (INIS)

Spencer, D.H.; Bydder, G.M.

1983-01-01

An NMR imaging system designed and built by Thorn-EMI Ltd was installed at Hammersmith Hospital in March 1981. In the first year of operation 180 patients and 40 volunteers have had cranial examinations and initial impressions bases on this experience are presented. Patients with a wide variety of neurological diseases have been studied to provide a basis for diagnostic interpretation, to define distinctive features, and to evaluate different types of scanning sequences. NMR imaging appears to be of considerable value in neurological diagnosis and has a number of advantages over CT. The detailed evaluation of NMR imaging will require much more work but the initial results are very promising

The characterisation of polymers using pulsed NMR

International Nuclear Information System (INIS)

Charlesby, A.

1983-01-01

Broad line pulsed NMR is applied to obtain information on radiation-induced polymer changes and other aspects of polymer science based on the interpretation of spin-spin relaxation curves. Calculations are made to determine the molecular weight, the crosslink density of simple, low molecular weight, flexible polymers. For higher molecular weight polymers, a conclusion can be drawn on the concentrations of entangled and crosslinked units by means of pulsed NMR. Some typical applications of the technique are illustrated by the examples of polyethylenes, rubbers, filled polymeric systems and aqueous polyethylene oxide solutions. The morphology of polymers can be followed by pulsed NMR. (V.N.)

Upcycling: converting waste plastics into paramagnetic, conducting, solid, pure carbon microspheres.

Science.gov (United States)

Pol, Vilas Ganpat

2010-06-15

The recent tremendous increase in the volume of waste plastics (WP) will have a harmful environmental impact on the health of living beings. Hundreds of years are required to degrade WP in atmospheric conditions. Hence, in coming years, in addition to traditional recycling services, innovative "upcycling" processes are necessary. This article presents an environmentally benign, solvent-free autogenic process that converts various WP [low density polyethylene (LDPE), high density polyethylene (HDPE), polyethylene terephthalate (PET), polystyrene (PS), or their mixtures] into carbon microspheres (CMSs), an industrially significant, value-added product. The thermal dissociation of these individual or mixed WP in a closed reactor under autogenic pressure ( approximately 1000 psi) produced dry, pure powder of CMSs. In this paper, the optimization of process parameters such as the effect of mixing of WP with other materials, and the role of reaction temperature and time are reported. Employing advanced analytical techniques, the atomic structure, composition, and morphology of as-obtained CMSs were analyzed. The room-temperature paramagnetism in CMSs prepared from waste LDPE, HDPE, and PS was further studied by electron paramagnetic resonance (EPR). The conducting and paramagnetic nature of CMSs holds promise for their potential applications in toners, printers, paints, batteries, lubricants, and tires.

Potential effect of diaper and cotton ball contamination on NMR- and LC/MS-based metabonomics studies of urine from newborn babies.

Science.gov (United States)

Goodpaster, Aaron M; Ramadas, Eshwar H; Kennedy, Michael A

2011-02-01

Nuclear magnetic resonance (NMR) and liquid chromatography/mass spectrometry (LC/MS) based metabonomics screening of urine has great potential for discovery of biomarkers for diseases that afflict newborn and preterm infants. However, urine collection from newborn infants presents a potential confounding problem due to the possibility that contaminants might leach from materials used for urine collection and influence statistical analysis of metabonomics data. In this manuscript, we have analyzed diaper and cotton ball contamination using synthetic urine to assess its potential to influence the outcome of NMR- and LC/MS-based metabonomics studies of human infant urine. Eight diaper brands were examined using the "diaper plus cotton ball" technique. Data were analyzed using conventional principal components analysis, as well as a statistical significance algorithm developed for, and applied to, NMR data. Results showed most diaper brands had distinct contaminant profiles that could potentially influence NMR- and LC/MS-based metabonomics studies. On the basis of this study, it is recommended that diaper and cotton ball brands be characterized using metabonomics methodologies prior to initiating a metabonomics study to ensure that contaminant profiles are minimal or manageable and that the same diaper and cotton ball brands be used throughout a study to minimize variation.

Reducing constraints on quantum computer design by encoded selective recoupling

International Nuclear Information System (INIS)

Lidar, D.A.; Wu, L.-A.

2002-01-01

The requirement of performing both single-qubit and two-qubit operations in the implementation of universal quantum logic often leads to very demanding constraints on quantum computer design. We show here how to eliminate the need for single-qubit operations in a large subset of quantum computer proposals: those governed by isotropic and XXZ , XY -type anisotropic exchange interactions. Our method employs an encoding of one logical qubit into two physical qubits, while logic operations are performed using an analogue of the NMR selective recoupling method

Risk constraint measures developed for the outcome-based strategy for tank waste management

International Nuclear Information System (INIS)

Harper, B.L.; Gajewski, S.J.; Glantz, C.L.

1996-09-01

This report is one of a series of supporting documents for the outcome-based characterization strategy developed by PNNL. This report presents a set of proposed risk measures with risk constraint (acceptance) levels for use in the Value of Information process used in the NCS. The characterization strategy has developed a risk-based Value of Information (VOI) approach for comparing the cost-effectiveness of characterizing versus mitigating particular waste tanks or tank clusters. The preference between characterizing or mitigating in order to prevent an accident depends on the cost of those activities relative to the cost of the consequences of the accident. The consequences are defined as adverse impacts measured across a broad set of risk categories such as worker dose, public cancers, ecological harm, and sociocultural impacts. Within each risk measure, various open-quotes constraint levelsclose quotes have been identified that reflect regulatory standards or conventionally negotiated thresholds of harm to Hanford resources and values. The cost of consequences includes the open-quotes costs close-quote of exceeding those constraint levels as well as a strictly linear costing per unit of impact within each of the risk measures. In actual application, VOI based-decision making is an iterative process, with a preliminary low-precision screen of potential technical options against the major risk constraints, followed by VOI analysis to determine the cost-effectiveness of gathering additional information and to select a preferred technical option, and finally a posterior screen to determine whether the preferred option meets all relevant risk constraints and acceptability criteria

Fast method of NMR imaging based on trains of spin echoes

International Nuclear Information System (INIS)

Hennel, F.

1993-01-01

A theoretical introduction to Fourier NMR imaging and a discussion of fast methods are presented. Then an application of the method of echo-planar imaging (EPI) with spin echoes in a micro-imaging system is described together with introduced modifications of the sequence. A new technique for the measurement of flow profiles in liquids which results from a modification of x-pulsed EPI is presented. The development of new software for a NMR micro-imaging system is described, too. 51 refs, 29 refs

NMR imaging and pharmaceutical sciences

International Nuclear Information System (INIS)

Beall, P.T.; Good, W.R.

1986-01-01

Described is the technique of NMR-imaging in diagnostic medicine. Proton and phosphorus NMR in diagnosis of abnormal tissue pathology. Discussed is the value of NMR to the pharmaceutical sciences. NMR may play an important role in monitoring the response of tissues to drugs, determining the localization of drugs, performing real time pharmacokinetics and testing the use of NMR contrast pharmaceuticals

Electron paramagnetic resonance of transition ions

CERN Document Server

Abragam, Anatole

1970-01-01

This book is a reissue of a classic Oxford text, and provides a comprehensive treatment of electron paramagnetic resonance of ions of the transition groups. The emphasis is on basic principles, with numerous references to publications containing further experimental results and more detailed developments of the theory. An introductory survey gives a general understanding, and a general survey presents such topics as the classical and quantum resonance equations, thespin-Hamiltonian, Endor, spin-spin and spin-lattice interactions, together with an outline of the known behaviour of ions of each

Paramagnetic susceptibility of the Zr{sub 62}Cu{sub 22}Al{sub 10}Fe{sub 5}Dy{sub 1} metallic glass subjected to high-pressure torsion deformation

Energy Technology Data Exchange (ETDEWEB)

Korolev, A.V., E-mail: korolyov@imp.uran.ru [Institute of Metal Physics of the Ural Branch RAS, Ekaterinburg (Russian Federation); Ural Federal University, Ekaterinburg (Russian Federation); Kourov, N.I. [Institute of Metal Physics of the Ural Branch RAS, Ekaterinburg (Russian Federation); Pushin, V.G. [Institute of Metal Physics of the Ural Branch RAS, Ekaterinburg (Russian Federation); Ural Federal University, Ekaterinburg (Russian Federation); Gunderov, D.V. [Saint-Petersburg State University, Saint-Petersburg (Russian Federation); Ufa State Aviation Technical University, Ufa (Russian Federation); Boltynjuk, E.V.; Ubyivovk, E.V. [Saint-Petersburg State University, Saint-Petersburg (Russian Federation); Valiev, R.Z. [Saint-Petersburg State University, Saint-Petersburg (Russian Federation); Ufa State Aviation Technical University, Ufa (Russian Federation)

2017-09-01

Highlights: • Zr-based BMG was subjected to HPT at temperatures of 20 °C and 150 °C. • Magnetic measurements reveal well recordable changes in paramagnetic susceptibility. • Paramagnetic susceptibility may be an indicator of a change in the structural state. - Abstract: The Zr{sub 62}Cu{sub 22}Al{sub 10}Fe{sub 5}Dy{sub 1} bulk metallic glass is studied in the as-cast state and in the state after processing by high-pressure torsion at temperatures of 20 °C and 150 °C. According to the data from X-ray diffraction and transmission electron microscopy, the structural state of the samples depends weakly on the conducted processing. At the same time, magnetic measurements reveal well recordable changes in paramagnetic susceptibility induced by the processing of the samples. It is assumed that, because of high-pressure torsion deformation, there occurs a noticeable change in the material electronic structure, which leads to a change in the full susceptibility of the samples. The performed studies demonstrate that paramagnetic susceptibility may be an indicator of a change in the structural state of paramagnetic amorphous metallic substances.

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

Directory of Open Access Journals (Sweden)

Monica Scognamiglio

2015-01-01

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

An Efficient Energy Constraint Based UAV Path Planning for Search and Coverage

OpenAIRE

Gramajo, German; Shankar, Praveen

2017-01-01

A path planning strategy for a search and coverage mission for a small UAV that maximizes the area covered based on stored energy and maneuverability constraints is presented. The proposed formulation has a high level of autonomy, without requiring an exact choice of optimization parameters, and is appropriate for real-time implementation. The computed trajectory maximizes spatial coverage while closely satisfying terminal constraints on the position of the vehicle and minimizing the time of ...

Introducing NMR to a General Chemistry Audience: A Structural-Based Instrumental Laboratory Relating Lewis Structures, Molecular Models, and [superscript 13]C NMR Data

Science.gov (United States)

Pulliam, Curtis R.; Pfeiffer, William F.; Thomas, Alyssa C.

2015-01-01

This paper describes a first-year general chemistry laboratory that uses NMR spectroscopy and model building to emphasize molecular shape and structure. It is appropriate for either a traditional or an atoms-first curriculum. Students learn the basis of structure and the use of NMR data through a cooperative learning hands-on laboratory…

Optimization and practical implementation of ultrafast 2D NMR experiments

Energy Technology Data Exchange (ETDEWEB)

Queiroz Junior, Luiz H. K., E-mail: professorkeng@gmail.com [Universidade Federal de Sao Carlos (UFSC), SP (Brazil). Departamento de Quimica; Universidade Federal de Goias (UFGO), Goiania, GO (Brazil). Inst. de Quimica; Ferreira, Antonio G. [Universidade Federal de Sao Carlos (UFSC), SP (Brazil). Departamento de Quimica; Giraudeau, Patrick [Universite de Nantes (France). CNRS, Chimie et Interdisciplinarite: Synthese, Analyse, Modelisation

2013-09-01

Ultrafast 2D NMR is a powerful methodology that allows recording of a 2D NMR spectrum in a fraction of second. However, due to the numerous non-conventional parameters involved in this methodology its implementation is no trivial task. Here, an optimized experimental protocol is carefully described to ensure efficient implementation of ultrafast NMR. The ultrafast spectra resulting from this implementation are presented based on the example of two widely used 2D NMR experiments, COSY and HSQC, obtained in 0.2 s and 41 s, respectively. (author)

ASIC-based design of NMR system health monitor for mission/safety-critical applications.

Science.gov (United States)

Balasubramanian, P

2016-01-01

N-modular redundancy (NMR) is a generic fault tolerance scheme that is widely used in safety-critical circuit/system designs to guarantee the correct operation with enhanced reliability. In passive NMR, at least a majority (N + 1)/2 out of N function modules is expected to operate correctly at any time, where N is odd. Apart from a conventional realization of the NMR system, it would be useful to provide a concurrent indication of the system's health so that an appropriate remedial action may be initiated depending upon an application's safety criticality. In this context, this article presents the novel design of a generic NMR system health monitor which features: (i) early fault warning logic, that is activated upon the production of a conflicting result by even one output of any arbitrary function module, and (ii) error signalling logic, which signals an error when the number of faulty function modules unfortunately attains a majority and the system outputs may no more be reliable. Two sample implementations of NMR systems viz. triple modular redundancy and quintuple modular redundancy with the proposed system health monitoring are presented in this work, with a 4-bit ALU used for the function modules. The simulations are performed using a 32/28 nm CMOS process technology.

Observations of Confinement of a Paramagnetic Liquid in Model Propellant Tanks in Microgravity by the Kelvin Force

Science.gov (United States)

Kuhlman, John; Gray, Donald D.; Barnard, Austin; Hazelton, Jennifer; Lechliter, Matthew; Starn, Andrew; Battleson, Charles; Glaspell, Shannon; Kreitzer, Paul; Leichliter, Michelle

2002-11-01

The magnetic Kelvin force has been proposed as an artificial gravity to control the orientation of paramagnetic liquid propellants such as liquid oxygen in a microgravity environment. This paper reports experiments performed in the NASA "Weightless Wonder" KC-135 aircraft, through the Reduced Gravity Student Flight Opportunities Program. The aircraft flies through a series of parabolic arcs providing about 25 s of microgravity in each arc. The experiment was conceived, designed, constructed, and performed by the undergraduate student team and their two faculty advisors. Two types of tanks were tested: square-base prismatic tanks 5 cm x 5 cm x 8.6 cm and circular cylinders 5 cm in diameter and 8.6 cm tall. The paramagnetic liquid was a 3.3 molar solution of MnCl2 in water. Tests were performed with each type of tank filled to depths of 1 cm and 4 cm. Each test compared a pair of tanks that were identical except that the base of one was a pole face of a 0.6 Tesla permanent magnet. The Kelvin force attracts paramagnetic materials toward regions of higher magnetic field. It was hypothesized that the Kelvin force would hold the liquid in the bottom of the tanks during the periods of microgravity. The tanks were installed in a housing that could slide on rails transverse to the flight direction. By manually shoving the housing, an identical impulse could be provided to each tank at the beginning of each period of microgravity. The resulting fluid motions were videotaped for later analysis.

Detection of Common Problems in Real-Time and Multicore Systems Using Model-Based Constraints

Directory of Open Access Journals (Sweden)

Raphaël Beamonte

2016-01-01

Full Text Available Multicore systems are complex in that multiple processes are running concurrently and can interfere with each other. Real-time systems add on top of that time constraints, making results invalid as soon as a deadline has been missed. Tracing is often the most reliable and accurate tool available to study and understand those systems. However, tracing requires that users understand the kernel events and their meaning. It is therefore not very accessible. Using modeling to generate source code or represent applications’ workflow is handy for developers and has emerged as part of the model-driven development methodology. In this paper, we propose a new approach to system analysis using model-based constraints, on top of userspace and kernel traces. We introduce the constraints representation and how traces can be used to follow the application’s workflow and check the constraints we set on the model. We then present a number of common problems that we encountered in real-time and multicore systems and describe how our model-based constraints could have helped to save time by automatically identifying the unwanted behavior.

WOHLLEBEN EFFECT (PARAMAGNETIC MEISSNER EFFECT) IN HIGH-TEMPERATURE SUPERCONDUCTORS

NARCIS (Netherlands)

KHOMSKII, D

Recently a quite unexpected phenomenon was observed during the study of the magnetic properties of High-T(c) superconductors: In the field-cooled regime the magnetic response of some HTSC at very low fields (less than or similar to 1 Oe), instead of being diamagnetic, becomes paramagnetic. Such

Dynamical magnetic response of paramagnetic CeFe-2

International Nuclear Information System (INIS)

Rainford, B.D.; McK Paul, D.; Warwick Univ., Coventry

1988-01-01

Inelastic neutron scattering has been used to study the energy dependence of the paramagnetic response from CeFe 2 . Our results, when integrated over energy, are in excellent agreement with the polarised neutron experiments of Deportes et al., but the correlation length obtained by fitting the data to a double Lorentzian scattering function is significantly smaller than that derived previously

Theory of NMR probe design