Type I and II β-turns prediction using NMR chemical shifts.

PubMed

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

2014-07-01

A method for predicting type I and II β-turns using nuclear magnetic resonance (NMR) chemical shifts is proposed. Isolated β-turn chemical-shift data were collected from 1,798 protein chains. One-dimensional statistical analyses on chemical-shift data of three classes β-turn (type I, II, and VIII) showed different distributions at four positions, (i) to (i + 3). Considering the central two residues of type I β-turns, the mean values of Cο, Cα, H(N), and N(H) chemical shifts were generally (i + 1) > (i + 2). The mean values of Cβ and Hα chemical shifts were (i + 1) < (i + 2). The distributions of the central two residues in type II and VIII β-turns were also distinguishable by trends of chemical shift values. Two-dimensional cluster analyses on chemical-shift data show positional distributions more clearly. Based on these propensities of chemical shift classified as a function of position, rules were derived using scoring matrices for four consecutive residues to predict type I and II β-turns. The proposed method achieves an overall prediction accuracy of 83.2 and 84.2% with the Matthews correlation coefficient values of 0.317 and 0.632 for type I and II β-turns, indicating that its higher accuracy for type II turn prediction. The results show that it is feasible to use NMR chemical shifts to predict the β-turn types in proteins. The proposed method can be incorporated into other chemical-shift based protein secondary structure prediction methods.

Study of chemical shift in Kα, Kβ1,3 and Kβ// X-ray emission lines of 37Rb compounds with WDXRF

NASA Astrophysics Data System (ADS)

Kainth, Harpreet Singh; Singh, Ranjit; Singh, Tejbir; Mehta, D.; Shahi, J. S.; Kumar, Sanjeev

2018-05-01

The positive and negative chemical shifts in Kα, Kβ1,3 and Kβ// X-ray emission lines of rubidium compounds were measured with high resolution WDXRF spectrometer. The measured energy shifts in Kα emission lines ranges from -2.95 eV to -3.64 eV, Kβ1,3 emission lines ranges from 1.16 eV to 1.32 eV and Kβ// emission lines ranges from 1.31 eV to 4.36 eV respectively. In the present work, it has been found that chemical shift in Kβ// X-ray emission lines were found to be larger than Kα and Kβ1,3 X-ray emission lines. To find the cause of chemical shift, various factors like effective charge, line intensity ratio, bond length and electro-negativity were calculated and correlated with the chemical shift.

Natural Abundance 15 N and 13 C Solid-State NMR Chemical Shifts: High Sensitivity Probes of the Halogen Bond Geometry.

PubMed

Cerreia Vioglio, Paolo; Catalano, Luca; Vasylyeva, Vera; Nervi, Carlo; Chierotti, Michele R; Resnati, Giuseppe; Gobetto, Roberto; Metrangolo, Pierangelo

2016-11-14

Solid-state nuclear magnetic resonance (SSNMR) spectroscopy is a versatile characterization technique that can provide a plethora of information complementary to single crystal X-ray diffraction (SCXRD) analysis. Herein, we present an experimental and computational investigation of the relationship between the geometry of a halogen bond (XB) and the SSNMR chemical shifts of the non-quadrupolar nuclei either directly involved in the interaction ( 15 N) or covalently bonded to the halogen atom ( 13 C). We have prepared two series of X-bonded co-crystals based upon two different dipyridyl modules, and several halobenzenes and diiodoalkanes, as XB-donors. SCXRD structures of three novel co-crystals between 1,2-bis(4-pyridyl)ethane, and 1,4-diiodobenzene, 1,6-diiodododecafluorohexane, and 1,8-diiodohexadecafluorooctane were obtained. For the first time, the change in the 15 N SSNMR chemical shifts upon XB formation is shown to experimentally correlate with the normalized distance parameter of the XB. The same overall trend is confirmed by density functional theory (DFT) calculations of the chemical shifts. 13 C NQS experiments show a positive, linear correlation between the chemical shifts and the C-I elongation, which is an indirect probe of the strength of the XB. These correlations can be of general utility to estimate the strength of the XB occurring in diverse adducts by using affordable SSNMR analysis. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development of 19F-NMR chemical shift detection of DNA B-Z equilibrium using 19F-NMR.

PubMed

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.

Reaction monitoring using hyperpolarized NMR with scaling of heteronuclear couplings by optimal tracking.

PubMed

Zhang, Guannan; Schilling, Franz; Glaser, Steffen J; Hilty, Christian

2016-11-01

Off-resonance decoupling using the method of Scaling of Heteronuclear Couplings by Optimal Tracking (SHOT) enables determination of heteronuclear correlations of chemical shifts in single scan NMR spectra. Through modulation of J-coupling evolution by shaped radio frequency pulses, off resonance decoupling using SHOT pulses causes a user-defined dependence of the observed J-splitting, such as the splitting of 13 C peaks, on the chemical shift offset of coupled nuclei, such as 1 H. Because a decoupling experiment requires only a single scan, this method is suitable for characterizing on-going chemical reactions using hyperpolarization by dissolution dynamic nuclear polarization (D-DNP). We demonstrate the calculation of [ 13 C, 1 H] chemical shift correlations of the carbanionic active sites from hyperpolarized styrene polymerized using sodium naphthalene as an initiator. While off resonance decoupling by SHOT pulses does not enhance the resolution in the same way as a 2D NMR spectrum would, the ability to obtain the correlations in single scans makes this method ideal for determination of chemical shifts in on-going reactions on the second time scale. In addition, we present a novel SHOT pulse that allows to scale J-splittings 50% larger than the respective J-coupling constant. This feature can be used to enhance the resolution of the indirectly detected chemical shift and reduce peak overlap, as demonstrated in a model reaction between p-anisaldehyde and isobutylamine. For both pulses, the accuracy is evaluated under changing signal-to-noise ratios (SNR) of the peaks from reactants and reaction products, with an overall standard deviation of chemical shift differences compared to reference spectra of 0.02ppm when measured on a 400MHz NMR spectrometer. Notably, the appearance of decoupling side-bands, which scale with peak intensity, appears to be of secondary importance. Copyright © 2016 Elsevier Inc. All rights reserved.

Chemical shift-based identification of monosaccharide spin-systems with NMR spectroscopy to complement untargeted glycomics.

PubMed

Klukowski, Piotr; Schubert, Mario

2018-06-15

A better understanding of oligosaccharides and their wide-ranging functions in almost every aspect of biology and medicine promises to uncover hidden layers of biology and will support the development of better therapies. Elucidating the chemical structure of an unknown oligosaccharide is still a challenge. Efficient tools are required for non-targeted glycomics. Chemical shifts are a rich source of information about the topology and configuration of biomolecules, whose potential is however not fully explored for oligosaccharides. We hypothesize that the chemical shifts of each monosaccharide are unique for each saccharide type with a certain linkage pattern, so that correlated data measured by NMR spectroscopy can be used to identify the chemical nature of a carbohydrate. We present here an efficient search algorithm, GlycoNMRSearch, that matches either a subset or the entire set of chemical shifts of an unidentified monosaccharide spin system to all spin systems in an NMR database. The search output is much more precise than earlier search functions and highly similar matches suggest the chemical structure of the spin system within the oligosaccharide. Thus searching for connected chemical shift correlations within all electronically available NMR data of oligosaccharides is a very efficient way of identifying the chemical structure of unknown oligosaccharides. With an improved database in the future, GlycoNMRSearch will be even more efficient deducing chemical structures of oligosaccharides and there is a high chance that it becomes an indispensable technique for glycomics. The search algorithm presented here, together with a graphical user interface, is available at http://glyconmrsearch.santos.pwr.edu.pl. Supplementary data are available at Bioinformatics online.

Correlates to sleepiness on night shift among male workers engaged in three-shift work in a chemical plant: its association with sleep practice and job stress.

PubMed

Kageyama, Takayuki; Kobayashi, Toshio; Abe-Gotoh, Ayano

2011-01-01

The purpose of this study was to examine the correlation of sleepiness during night shift (SNS) in male shiftworkers with nonpharmacological self-management (nPSM) practices to facilitate good day sleep, and also with job stress. Sleepiness on the job and possible correlates to SNS among 157 male shiftworkers in a rotating three-shift schedule at a chemical plant were cross-sectionally investigated using a self-administered questionnaire. Multivariate analyses revealed that SNS was positively associated with drinking alcoholic beverages before day sleep, but inversely associated with subjective health status, being of the evening type, abstaining from caffeine before day sleep, having a bath before day sleep, job control, reward from work, feeling suited to the job, and support from colleagues. SNS correlated with certain nPSM practices and also with possible modifiers of job stress. These findings provide clues to developing countermeasures against SNS among shiftworkers. The effects of nPSM practices and job stress management on their day sleep and SNS should be examined in detail.

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

NASA Astrophysics Data System (ADS)

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

2016-08-01

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

Chemical Shift MR Imaging Methods for the Quantification of Transcatheter Lipiodol Delivery to the Liver: Preclinical Feasibility Studies in a Rodent Model

PubMed Central

Yin, Xiaoming; Guo, Yang; Li, Weiguo; Huo, Eugene; Zhang, Zhuoli; Nicolai, Jodi; Kleps, Robert A.; Hernando, Diego; Katsaggelos, Aggelos K.; Omary, Reed A.

2012-01-01

Purpose: To demonstrate the feasibility of using chemical shift magnetic resonance (MR) imaging fat-water separation methods for quantitative estimation of transcatheter lipiodol delivery to liver tissues. Materials and Methods: Studies were performed in accordance with institutional Animal Care and Use Committee guidelines. Proton nuclear MR spectroscopy was first performed to identify lipiodol spectral peaks and relative amplitudes. Next, phantoms were constructed with increasing lipiodol-water volume fractions. A multiecho chemical shift–based fat-water separation method was used to quantify lipiodol concentration within each phantom. Six rats served as controls; 18 rats underwent catheterization with digital subtraction angiography guidance for intraportal infusion of a 15%, 30%, or 50% by volume lipiodol-saline mixture. MR imaging measurements were used to quantify lipiodol delivery to each rat liver. Lipiodol concentration maps were reconstructed by using both single-peak and multipeak chemical shift models. Intraclass and Spearman correlation coefficients were calculated for statistical comparison of MR imaging–based lipiodol concentration and volume measurements to reference standards (known lipiodol phantom compositions and the infused lipiodol dose during rat studies). Results: Both single-peak and multipeak measurements were well correlated to phantom lipiodol concentrations (r2 > 0.99). Lipiodol volume measurements were progressively and significantly higher when comparing between animals receiving different doses (P < .05 for each comparison). MR imaging–based lipiodol volume measurements strongly correlated with infused dose (intraclass correlation coefficients > 0.93, P < .001) with both single- and multipeak approaches. Conclusion: Chemical shift MR imaging fat-water separation methods can be used for quantitative measurements of lipiodol delivery to liver tissues. © RSNA, 2012 PMID:22623693

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

PubMed

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

2014-01-01

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

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

PubMed

Kanematsu, Yusuke; Tachikawa, Masanori

2014-04-28

We have developed the multicomponent hybrid density functional theory [MC_(HF+DFT)] method with polarizable continuum model (PCM) for the analysis of molecular properties including both nuclear quantum effect and solvent effect. The chemical shifts and H/D isotope shifts of the picolinic acid N-oxide (PANO) molecule in chloroform and acetonitrile solvents are applied by B3LYP electron exchange-correlation functional for our MC_(HF+DFT) method with PCM (MC_B3LYP/PCM). Our MC_B3LYP/PCM results for PANO are in reasonable agreement with the corresponding experimental chemical shifts and isotope shifts. We further investigated the applicability of our method for acetylacetone in several solvents.

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

PubMed Central

Wang, Xianlong; Wang, Chengfei; Zhao, Hui

2012-01-01

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

A theoretical case study of type I and type II beta-turns.

PubMed

Czinki, Eszter; Császár, Attila G; Perczel, András

2003-03-03

NMR chemical shielding anisotropy tensors have been computed by employing a medium size basis set and the GIAO-DFT(B3LYP) formalism of electronic structure theory for all of the atoms of type I and type II beta-turn models. The models contain all possible combinations of the amino acid residues Gly, Ala, Val, and Ser, with all possible side-chain orientations where applicable in a dipeptide. The several hundred structures investigated contain either constrained or optimized phi, psi, and chi dihedral angles. A statistical analysis of the resulting large database was performed and multidimensional (2D and 3D) chemical-shift/chemical-shift plots were generated. The (1)H(alpha-13)C(alpha), (13)C(alpha-1)H(alpha-13)C(beta), and (13)C(alpha-1)H(alpha-13)C' 2D and 3D plots have the notable feature that the conformers clearly cluster in distinct regions. This allows straightforward identification of the backbone and side-chain conformations of the residues forming beta-turns. Chemical shift calculations on larger For-(L-Ala)(n)-NH(2) (n=4, 6, 8) models, containing a single type I or type II beta-turn, prove that the simple models employed are adequate. A limited number of chemical shift calculations performed at the highly correlated CCSD(T) level prove the adequacy of the computational method chosen. For all nuclei, statistically averaged theoretical and experimental shifts taken from the BioMagnetic Resonance Bank (BMRB) exhibit good correlation. These results confirm and extend our previous findings that chemical shift information from selected multiple-pulse NMR experiments could be employed directly to extract folding information for polypeptides and proteins.

(13)C NMR substituent-induced chemical shifts in 4-(substituted phenyl)-3-phenyl-1,2,4-oxadiazol-5(4H)-ones (thiones).

PubMed

Kara, Yesim Saniye

2015-01-01

In the present, study mostly novel ten 4-(substituted phenyl)-3-phenyl-1,2,4-oxadiazol-5(4H)-ones and ten 4-(substituted phenyl)-3-phenyl-1,2,4-oxadiazol-5(4H)-thiones were synthesized. These oxadiazole derivatives were characterized by IR, (1)H NMR, (13)C NMR and elemental analyses. Their (13)C NMR spectra were measured in Deuterochloroform (CDCl3). The correlation analysis for the substituent-induced chemical shift (SCS) with Hammett substituent constants (σ), Brown Okamoto substituent constants (σ(+), σ(-)), inductive substituent constants (σI) and different of resonance substituent constants (σR, σR(o)) were performed using SSP (single substituent parameter), DSP (dual substituent parameter) and DSP-NLR (dual substituent parameter-non-linear resonance) methods, as well as single and multiple regression analysis. Negative ρ values were found for all correlations (reverse substituent effect). The results of all statistical analyses, (13)C NMR chemical shift of CN, CO and CS carbon of oxadiazole rings have shown satisfactory correlation. Copyright © 2015 Elsevier B.V. All rights reserved.

Mechanisms of action of (meth)acrylates in hemolytic activity, in vivo toxicity and dipalmitoylphosphatidylcholine (DPPC) liposomes determined using NMR spectroscopy.

PubMed

Fujisawa, Seiichiro; Kadoma, Yoshinori

2012-01-01

We investigated the quantitative structure-activity relationships between hemolytic activity (log 1/H(50)) or in vivo mouse intraperitoneal (ip) LD(50) using reported data for α,β-unsaturated carbonyl compounds such as (meth)acrylate monomers and their (13)C-NMR β-carbon chemical shift (δ). The log 1/H(50) value for methacrylates was linearly correlated with the δC(β) value. That for (meth)acrylates was linearly correlated with log P, an index of lipophilicity. The ipLD(50) for (meth)acrylates was linearly correlated with δC(β) but not with log P. For (meth)acrylates, the δC(β) value, which is dependent on the π-electron density on the β-carbon, was linearly correlated with PM3-based theoretical parameters (chemical hardness, η; electronegativity, χ; electrophilicity, ω), whereas log P was linearly correlated with heat of formation (HF). Also, the interaction between (meth)acrylates and DPPC liposomes in cell membrane molecular models was investigated using (1)H-NMR spectroscopy and differential scanning calorimetry (DSC). The log 1/H(50) value was related to the difference in chemical shift (ΔδHa) (Ha: H (trans) attached to the β-carbon) between the free monomer and the DPPC liposome-bound monomer. Monomer-induced DSC phase transition properties were related to HF for monomers. NMR chemical shifts may represent a valuable parameter for investigating the biological mechanisms of action of (meth)acrylates.

Mechanisms of Action of (Meth)acrylates in Hemolytic Activity, in Vivo Toxicity and Dipalmitoylphosphatidylcholine (DPPC) Liposomes Determined Using NMR Spectroscopy

PubMed Central

Fujisawa, Seiichiro; Kadoma, Yoshinori

2012-01-01

We investigated the quantitative structure-activity relationships between hemolytic activity (log 1/H50) or in vivo mouse intraperitoneal (ip) LD50 using reported data for α,β-unsaturated carbonyl compounds such as (meth)acrylate monomers and their 13C-NMR β-carbon chemical shift (δ). The log 1/H50 value for methacrylates was linearly correlated with the δCβ value. That for (meth)acrylates was linearly correlated with log P, an index of lipophilicity. The ipLD50 for (meth)acrylates was linearly correlated with δCβ but not with log P. For (meth)acrylates, the δCβ value, which is dependent on the π-electron density on the β-carbon, was linearly correlated with PM3-based theoretical parameters (chemical hardness, η; electronegativity, χ; electrophilicity, ω), whereas log P was linearly correlated with heat of formation (HF). Also, the interaction between (meth)acrylates and DPPC liposomes in cell membrane molecular models was investigated using 1H-NMR spectroscopy and differential scanning calorimetry (DSC). The log 1/H50 value was related to the difference in chemical shift (ΔδHa) (Ha: H (trans) attached to the β-carbon) between the free monomer and the DPPC liposome-bound monomer. Monomer-induced DSC phase transition properties were related to HF for monomers. NMR chemical shifts may represent a valuable parameter for investigating the biological mechanisms of action of (meth)acrylates. PMID:22312284

Modeling {sup 15}N NMR chemical shift changes in protein backbone with pressure

DOE Office of Scientific and Technical Information (OSTI.GOV)

La Penna, Giovanni, E-mail: glapenna@iccom.cnr.it; Mori, Yoshiharu, E-mail: ymori@ims.ac.jp; Kitahara, Ryo, E-mail: ryo@ph.ritsumei.ac.jp

2016-08-28

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

Quantum-mechanics-derived 13Cα chemical shift server (CheShift) for protein structure validation

PubMed Central

Vila, Jorge A.; Arnautova, Yelena A.; Martin, Osvaldo A.; Scheraga, Harold A.

2009-01-01

A server (CheShift) has been developed to predict 13Cα chemical shifts of protein structures. It is based on the generation of 696,916 conformations as a function of the φ, ψ, ω, χ1 and χ2 torsional angles for all 20 naturally occurring amino acids. Their 13Cα chemical shifts were computed at the DFT level of theory with a small basis set and extrapolated, with an empirically-determined linear regression formula, to reproduce the values obtained with a larger basis set. Analysis of the accuracy and sensitivity of the CheShift predictions, in terms of both the correlation coefficient R and the conformational-averaged rmsd between the observed and predicted 13Cα chemical shifts, was carried out for 3 sets of conformations: (i) 36 x-ray-derived protein structures solved at 2.3 Å or better resolution, for which sets of 13Cα chemical shifts were available; (ii) 15 pairs of x-ray and NMR-derived sets of protein conformations; and (iii) a set of decoys for 3 proteins showing an rmsd with respect to the x-ray structure from which they were derived of up to 3 Å. Comparative analysis carried out with 4 popular servers, namely SHIFTS, SHIFTX, SPARTA, and PROSHIFT, for these 3 sets of conformations demonstrated that CheShift is the most sensitive server with which to detect subtle differences between protein models and, hence, to validate protein structures determined by either x-ray or NMR methods, if the observed 13Cα chemical shifts are available. CheShift is available as a web server. PMID:19805131

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

PubMed

Straka, Michal; Lantto, Perttu; Vaara, Juha

2008-03-27

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

Investigation of DOTA-Metal Chelation Effects on the Chemical Shift of 129 Xe

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jeong, Keunhong; Slack, Clancy C.; Vassiliou, Christophoros C.

2015-09-17

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

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

PubMed

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

2016-06-01

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

Calculation of 125Te NMR Chemical Shifts at the Full Four-Component Relativistic Level with Taking into Account Solvent and Vibrational Corrections: A Gateway to Better Agreement with Experiment.

PubMed

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

2017-06-29

Four-component relativistic calculations of 125 Te NMR chemical shifts were performed in the series of 13 organotellurium compounds, potential precursors of the biologically active species, at the density functional theory level under the nonrelativistic and four-component fully relativistic conditions using locally dense basis set scheme derived from relativistic Dyall's basis sets. The relativistic effects in tellurium chemical shifts were found to be of as much as 20-25% of the total calculated values. The vibrational and solvent corrections to 125 Te NMR chemical shifts are about, accordingly, 6 and 8% of their total values. The PBE0 exchange-correlation functional turned out to give the best agreement of calculated tellurium shifts with their experimental values giving the mean absolute percentage error of 4% in the range of ∼1000 ppm, provided all corrections are taken into account.

Theoretical NMR correlations based Structure Discussion.

PubMed

Junker, Jochen

2011-07-28

The constitutional assignment of natural products by NMR spectroscopy is usually based on 2D NMR experiments like COSY, HSQC, and HMBC. The actual difficulty of the structure elucidation problem depends more on the type of the investigated molecule than on its size. The moment HMBC data is involved in the process or a large number of heteroatoms is present, a possibility of multiple solutions fitting the same data set exists. A structure elucidation software can be used to find such alternative constitutional assignments and help in the discussion in order to find the correct solution. But this is rarely done. This article describes the use of theoretical NMR correlation data in the structure elucidation process with WEBCOCON, not for the initial constitutional assignments, but to define how well a suggested molecule could have been described by NMR correlation data. The results of this analysis can be used to decide on further steps needed to assure the correctness of the structural assignment. As first step the analysis of the deviation of carbon chemical shifts is performed, comparing chemical shifts predicted for each possible solution with the experimental data. The application of this technique to three well known compounds is shown. Using NMR correlation data alone for the description of the constitutions is not always enough, even when including 13C chemical shift prediction.

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

PubMed

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

2010-03-17

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

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

PubMed Central

Hong, Mei

2016-01-01

We have determined refined multidimensional chemical shift ranges for intra-residue correlations (13C–13C, 15N–13C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 13C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited “hand-picked” data sets, we show that ~94 % of the 13C NMR data and almost all 15N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6 % of the 13C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. −2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of secondary maxima in the two-dimensional chemical-shift distributions already pre-separated by secondary structure. We demonstrate that some of these correspond to specific regions in the Ramachandran plot, including left-handed helix dihedral angles, reflect unusual hydrogen bonding, or are due to the influence of a following proline residue. With appropriate smoothing, significantly more tightly defined chemical shift ranges are obtained for each amino acid type in the different secondary structures. These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra-residue cross peaks by inspection or by using a provided command-line Python script (PLUQin), which should be useful in protein structure determination. The refined chemical shift distributions are utilized in a simple quality test (SQAT) that should be applied to new protein NMR data before deposition in a databank, and they could benefit many other chemical-shift based tools. PMID:26787537

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

PubMed

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

2016-02-05

Hartree-Fock and density functional theory with the hybrid B3LYP and general gradient KT2 exchange-correlation functionals were used for nonrelativistic and relativistic nuclear magnetic shielding calculations of helium, neon, argon, krypton, and xenon dimers and free atoms. Relativistic corrections were calculated with the scalar and spin-orbit zeroth-order regular approximation Hamiltonian in combination with the large Slater-type basis set QZ4P as well as with the four-component Dirac-Coulomb Hamiltonian using Dyall's acv4z basis sets. The relativistic corrections to the nuclear magnetic shieldings and chemical shifts are combined with nonrelativistic coupled cluster singles and doubles with noniterative triple excitations [CCSD(T)] calculations using the very large polarization-consistent basis sets aug-pcSseg-4 for He, Ne and Ar, aug-pcSseg-3 for Kr, and the AQZP basis set for Xe. For the dimers also, zero-point vibrational (ZPV) corrections are obtained at the CCSD(T) level with the same basis sets were added. Best estimates of the dimer chemical shifts are generated from these nuclear magnetic shieldings and the relative importance of electron correlation, ZPV, and relativistic corrections for the shieldings and chemical shifts is analyzed. © 2015 Wiley Periodicals, Inc.

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

PubMed

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

2017-03-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-05-01

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

Employing NMR Spectroscopy To Evaluate Transmission of Electronic Effects in 4-Substituted Chalcones

NASA Astrophysics Data System (ADS)

Wachter-Jurcsak, Nanette; Zamani, Hossein

1999-05-01

Described is an organic synthesis experiment that demonstrates the electronic transmission by substituents. The effect of substitution at the para-position of the styryl ring of 1,3-diphenyl-2-propenones (chalcones) by typical electron-donating or -accepting groups can be observed by proton and carbon-13 NMR spectroscopy. A linear correlation is observed when the differences in chemical shift measurements for H are plotted against the corresponding Hammett substituent constant values. Good correlation between carbon-13 chemical shifts of the alpha carbon are also observed. The syntheses of the 4-substituted chalcones is presented as well as a brief discussion of the theory.

Nuclear magnetic resonance studies of phosphorus(v) pesticides. Part I. Chemical shifts of protons as a means of identification of pesticides

USGS Publications Warehouse

Babad, H.; Herbert, W.; Goldberg, M.C.

1968-01-01

Correlations of structural and proton chemical-hift data for 40 commercial phosphorus(V) pesticides are reported. Correlations of structure with the phosphorus coupling constants are discussed, and general trends are noted which aid in the use of NMR as a tool for identification and analysis of phosphorus(V) compounds. ?? 1968.

13C and (15)N chemical shift tensors in adenosine, guanosine dihydrate, 2'-deoxythymidine, and cytidine.

PubMed

Stueber, Dirk; Grant, David M

2002-09-04

The (13)C and (15)N chemical shift tensor principal values for adenosine, guanosine dihydrate, 2'-deoxythymidine, and cytidine are measured on natural abundance samples. Additionally, the (13)C and (15)N chemical shielding tensor principal values in these four nucleosides are calculated utilizing various theoretical approaches. Embedded ion method (EIM) calculations improve significantly the precision with which the experimental principal values are reproduced over calculations on the corresponding isolated molecules with proton-optimized geometries. The (13)C and (15)N chemical shift tensor orientations are reliably assigned in the molecular frames of the nucleosides based upon chemical shielding tensor calculations employing the EIM. The differences between principal values obtained in EIM calculations and in calculations on isolated molecules with proton positions optimized inside a point charge array are used to estimate the contributions to chemical shielding arising from intermolecular interactions. Moreover, the (13)C and (15)N chemical shift tensor orientations and principal values correlate with the molecular structure and the crystallographic environment for the nucleosides and agree with data obtained previously for related compounds. The effects of variations in certain EIM parameters on the accuracy of the shielding tensor calculations are investigated.

A theoretical perspective of the nature of hydrogen-bond types - the atoms in molecules approach

NASA Astrophysics Data System (ADS)

Vijaya Pandiyan, B.; Kolandaivel, P.; Deepa, P.

2014-06-01

Hydrogen bonds and their strength were analysed based on their X-H proton-donor bond properties and the parameters of the H-Y distance (Y proton acceptor). Strong, moderate and weak interactions in hydrogen-bond types were verified through the proton affinities of bases (PA), deprotanation enthalpies of acids (DPE) and the chemical shift (σ). The aromaticity and anti-aromaticity were analysed by means of the NICS (0) (nucleus-independent chemical shift), NICS (1) and ΔNICS (0), ΔNICS (1) of hydrogen-bonded molecules. The strength of a hydrogen bond depends on the capacity of hydrogen atom engrossing into the electronegative acceptor atom. The correlation between the above parameters and their relations were discussed through curve fitting. Bader's theory of atoms in molecules has been applied to estimate the occurrence of hydrogen bonds through eight criteria reported by Popelier et al. The lengths and potential energy shifts have been found to have a strong negative linear correlation, whereas the lengths and Laplacian shifts have a strong positive linear correlation. This study illustrates the common factors responsible for strong, moderate and weak interactions in hydrogen-bond types.

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

PubMed

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

2013-01-01

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

NMR Mapping of Protein Conformational Landscapes using Coordinated Behavior of Chemical Shifts upon Ligand Binding

PubMed Central

Cembran, Alessandro; Kim, Jonggul; Gao, Jiali; Veglia, Gianluigi

2014-01-01

Proteins exist as an ensemble of conformers that are distributed on free energy landscapes resembling folding funnels. While the most stable conformers populate low energy basins, protein function is often carried out through low-populated conformational states that occupy high energy basins. Ligand binding shifts the populations of these states, changing the distribution of these conformers. Understanding how the equilibrium among the states is altered upon ligand binding, interaction with other binding partners, and/or mutations and post-translational modifications is of critical importance for explaining allosteric signaling in proteins. Here, we propose a statistical analysis of the chemical shifts (CONCISE, COordiNated ChemIcal Shifts bEhavior) for the interpretation of protein conformational equilibria following linear trajectories of NMR chemical shifts. CONCISE enables one to quantitatively measure the population shifts associated with ligand titrations and estimate the degree of collectiveness of the protein residues’ response to ligand binding, giving a concise view of the structural transitions. The combination of CONCISE with thermocalorimetric and kinetic data allows one to depict a protein’s approximate conformational energy landscape. We tested this method with the catalytic subunit of cAMP-dependent protein kinase A, a ubiquitous enzyme that undergoes conformational transitions upon both nucleotide and pseudo-substrate binding. When complemented with chemical shift covariance analysis (CHESCA), this new method offers both collective response and residue-specific correlations for ligand binding to proteins. PMID:24604024

Experimental and DFT evaluation of the 1H and 13C NMR chemical shifts for calix[4]arenes

NASA Astrophysics Data System (ADS)

Guzzo, Rodrigo N.; Rezende, Michelle Jakeline Cunha; Kartnaller, Vinicius; Carneiro, José Walkimar de M.; Stoyanov, Stanislav R.; Costa, Leonardo Moreira da

2018-04-01

The density functional theory is employed to determine the efficiency of 11 exchange-correlation (XC) functionals to compute the 1H and 13C NMR chemical shifts of p-tert-butylcalix[4]arene (ptcx4, R1 = C(CH3)3) and congeners using the 6-31G(d,p) basis set. The statistical analysis shows that B3LYP, B3PW91 and PBE1PBE are the best XC functionals for the calculation of 1H chemical shifts. Moreover, the best results for the 13C chemical shifts are obtained using the LC-WPBE, M06-2X and wB97X-D functionals. The performance of these XC functionals is tested for three other calix[4]arenes: p-sulfonic acid calix[4]arene (sfxcx4 - R1 = SO3H), p-nitro-calix[4]arene (ncx4, R1 = NO2) and calix[4]arene (cx4 - R1 = H). For 1H chemical shifts B3LYP, B3PW91 and PBE1PBE yield similar results, although B3PW91 shows more consistency in the calculated error for the different structures. For 13C NMR chemical shifts, the XC functional that stood out as best is LC-WPBE. Indeed, the three functionals selected for each of 1H and 13C show good accuracy and can be used in future studies involving the prediction of 1H and 13C chemical shifts for this type of compounds.

17O NMR spectroscopy of substituted methyleneindanones: relationship between chemical shift and oxygen atom electron density

NASA Astrophysics Data System (ADS)

Kumar, Arvind; Boykin, David W.

1993-07-01

17O NMR spectroscopic data for eigth β-substituted methyleneindanones obtained at natural abundance in acetonitrile at 75°C are reported. 17O NMR data for ten para-substituted E-benzalindanones, enriched with 17O, were recorded in acetonitrile at 75°C. The 17O NMR data for the E-benzalindanones gave good correlations with sigma plus values, with literature carbonyl IR stretching frequencies, and with literature 17O NMR carbonyl data of chalcones and 5-aryl-2,3-furandiones. The carbonyl oxygen atom electron density (AM1) gave good correlation with the carbonyl 17O NMR chemical shift of both β-substituted methyleneindanones and the E-benzalindanones.

Identifying guanosine self assembly at natural isotopic abundance by high-resolution 1H and 13C solid-state NMR spectroscopy.

PubMed

Webber, Amy L; Masiero, Stefano; Pieraccini, Silvia; Burley, Jonathan C; Tatton, Andrew S; Iuga, Dinu; Pham, Tran N; Spada, Gian Piero; Brown, Steven P

2011-12-14

By means of the (1)H chemical shifts and the proton-proton proximities as identified in (1)H double-quantum (DQ) combined rotation and multiple-pulse spectroscopy (CRAMPS) solid-state NMR correlation spectra, ribbon-like and quartet-like self-assembly can be identified for guanosine derivatives without isotopic labeling for which it was not possible to obtain single crystals suitable for diffraction. Specifically, characteristic spectral fingerprints are observed for dG(C10)(2) and dG(C3)(2) derivatives, for which quartet-like and ribbon-like self-assembly has been unambiguously identified by (15)N refocused INADEQUATE spectra in a previous study of (15)N-labeled derivatives (Pham, T. N.; et al. J. Am. Chem. Soc.2005, 127, 16018). The NH (1)H chemical shift is observed to be higher (13-15 ppm) for ribbon-like self-assembly as compared to 10-11 ppm for a quartet-like arrangement, corresponding to a change from NH···N to NH···O intermolecular hydrogen bonding. The order of the two NH(2)(1)H chemical shifts is also inverted, with the NH(2) proton closest in space to the NH proton having a higher or lower (1)H chemical shift than that of the other NH(2) proton for ribbon-like as opposed to quartet-like self-assembly. For the dG(C3)(2) derivative for which a single-crystal diffraction structure is available, the distinct resonances and DQ peaks are assigned by means of gauge-including projector-augmented wave (GIPAW) chemical shift calculations. In addition, (14)N-(1)H correlation spectra obtained at 850 MHz under fast (60 kHz) magic-angle spinning (MAS) confirm the assignment of the NH and NH(2) chemical shifts for the dG(C3)(2) derivative and allow longer range through-space N···H proximities to be identified, notably to the N7 nitrogens on the opposite hydrogen-bonding face. © 2011 American Chemical Society

Ab initio 27Al NMR chemical shifts and quadrupolar parameters for Al2O3 phases and their precursors

NASA Astrophysics Data System (ADS)

Ferreira, Ary R.; Küçükbenli, Emine; Leitão, Alexandre A.; de Gironcoli, Stefano

2011-12-01

The gauge-including projector augmented wave (GIPAW) method, within the density functional theory (DFT) generalized gradient approximation (GGA) framework, is applied to compute solid state NMR parameters for 27Al in the α, θ, and κ aluminium oxide phases and their gibbsite and boehmite precursors. The results for well established crystalline phases compare very well with available experimental data and provide confidence in the accuracy of the method. For γ-alumina, four structural models proposed in the literature are discussed in terms of their ability to reproduce the experimental spectra also reported in the literature. Among the considered models, the Fd3¯m structure proposed by Paglia [Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.71.224115 71, 224115 (2005)] shows the best agreement. We attempt to link the theoretical NMR parameters to the local geometry. Chemical shifts depend on coordination number but no further correlation is found with geometrical parameters. Instead, our calculations reveal that, within a given coordination number, a linear correlation exists between chemical shifts and Born effective charges.

Element specificity of ortho-positronium annihilation for alkali-metal loaded SiO2 glasses.

PubMed

Sato, K; Hatta, T

2015-03-07

Momentum distributions associated with ortho-positronium (o-Ps) pick-off annihilation photon are often influenced by light elements, as, e.g., carbon, oxygen, and fluorine. This phenomenon, so-called element specificity of o-Ps pick-off annihilation, has been utilized for studying the elemental environment around the open spaces. To gain an insight into the element specificity of o-Ps pick-off annihilation, the chemical shift of oxygen 1s binding energy and the momentum distributions associated with o-Ps pick-off annihilation were systematically investigated for alkali-metal loaded SiO2 glasses by means of X-ray photoelectron spectroscopy and positron-age-momentum correlation spectroscopy, respectively. Alkali metals introduced into the open spaces surrounded by oxygen atoms cause charge transfer from alkali metals to oxygen atoms, leading to the lower chemical shift for the oxygen 1s binding energy. The momentum distribution of o-Ps localized into the open spaces is found to be closely correlated with the oxygen 1s chemical shift. This correlation with the deepest 1s energy level evidences that the element specificity of o-Ps originates from pick-off annihilation with orbital electrons, i.e., dominantly with oxygen 2p valence electrons and s electrons with lower probability.

Complete (1)H resonance assignment of beta-maltose from (1)H-(1)H DQ-SQ CRAMPS and (1)H (DQ-DUMBO)-(13)C SQ refocused INEPT 2D solid-state NMR spectra and first principles GIPAW calculations.

PubMed

Webber, Amy L; Elena, Bénédicte; Griffin, John M; Yates, Jonathan R; Pham, Tran N; Mauri, Francesco; Pickard, Chris J; Gil, Ana M; Stein, Robin; Lesage, Anne; Emsley, Lyndon; Brown, Steven P

2010-07-14

A disaccharide is a challenging case for high-resolution (1)H solid-state NMR because of the 24 distinct protons (14 aliphatic and 10 OH) having (1)H chemical shifts that all fall within a narrow range of approximately 3 to 7 ppm. High-resolution (1)H (500 MHz) double-quantum (DQ) combined rotation and multiple pulse sequence (CRAMPS) solid-state NMR spectra of beta-maltose monohydrate are presented. (1)H-(1)H DQ-SQ CRAMPS spectra are presented together with (1)H (DQ)-(13)C correlation spectra obtained with a new pulse sequence that correlates a high-resolution (1)H DQ dimension with a (13)C single quantum (SQ) dimension using the refocused INEPT pulse-sequence element to transfer magnetization via one-bond (13)C-(1)H J couplings. Compared to the observation of only a single broad peak in a (1)H DQ spectrum recorded at 30 kHz magic-angle spinning (MAS), the use of DUMBO (1)H homonuclear decoupling in the (1)H DQ CRAMPS experiment allows the resolution of distinct DQ correlation peaks which, in combination with first-principles chemical shift calculations based on the GIPAW (Gauge Including Projector Augmented Waves) plane-wave pseudopotential approach, enables the assignment of the (1)H resonances to the 24 distinct protons. We believe this to be the first experimental solid-state NMR determination of the hydroxyl OH (1)H chemical shifts for a simple sugar. Variable-temperature (1)H-(1)H DQ CRAMPS spectra reveal small increases in the (1)H chemical shifts of the OH resonances upon decreasing the temperature from 348 K to 248 K.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Rongchun; Ramamoorthy, Ayyalusamy, E-mail: ramamoor@umich.edu; Nishiyama, Yusuke

2015-10-28

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

Implementation of the NMR CHEmical Shift Covariance Analysis (CHESCA): A Chemical Biologist's Approach to Allostery.

PubMed

Boulton, Stephen; Selvaratnam, Rajeevan; Ahmed, Rashik; Melacini, Giuseppe

2018-01-01

Mapping allosteric sites is emerging as one of the central challenges in physiology, pathology, and pharmacology. Nuclear Magnetic Resonance (NMR) spectroscopy is ideally suited to map allosteric sites, given its ability to sense at atomic resolution the dynamics underlying allostery. Here, we focus specifically on the NMR CHEmical Shift Covariance Analysis (CHESCA), in which allosteric systems are interrogated through a targeted library of perturbations (e.g., mutations and/or analogs of the allosteric effector ligand). The atomic resolution readout for the response to such perturbation library is provided by NMR chemical shifts. These are then subject to statistical correlation and covariance analyses resulting in clusters of allosterically coupled residues that exhibit concerted responses to the common set of perturbations. This chapter provides a description of how each step in the CHESCA is implemented, starting from the selection of the perturbation library and ending with an overview of different clustering options.

Identification of helix capping and β-turn motifs from NMR chemical shifts

PubMed Central

Shen, Yang; Bax, Ad

2012-01-01

We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and 13Cβ chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of β-turns: I, II, I′, II′ and VIII. Using a database of proteins of known structure, the NMR chemical shifts, together with the PDB-extracted amino acid preference of the helix capping and β-turn motifs are used as input data for training an artificial neural network algorithm, which outputs the statistical probability of finding each motif at any given position in the protein. The trained neural networks, contained in the MICS (motif identification from chemical shifts) program, also provide a confidence level for each of their predictions, and values ranging from ca 0.7–0.9 for the Matthews correlation coefficient of its predictions far exceed that attainable by sequence analysis. MICS is anticipated to be useful both in the conventional NMR structure determination process and for enhancing on-going efforts to determine protein structures solely on the basis of chemical shift information, where it can aid in identifying protein database fragments suitable for use in building such structures. PMID:22314702

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

PubMed

Norquay, Graham; Leung, General; Stewart, Neil J; Wolber, Jan; Wild, Jim M

2017-04-01

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

The temperature dependence of the hydroxyl deuterium quadrupole coupling parameter and the rotational correlation time of the OD internuclear vector in neat ethanol-d

NASA Astrophysics Data System (ADS)

Ferris, Thomas D.; Farrar, Thomas C.

The temperature dependence of the hydroxyl proton chemical shift and deuterium quadrupolar relaxation time of neat ethanol were measured over the temperature range 190-350 K. The proton isotropic chemical shift varies from 6.2 ppm at 190 K to 4.7 ppm at 350 K. The deuterium NMR relaxation time in ethanol- d 1 varies from 6.2 ms to 309 ms over the same range. Ab initio calculations performed on various ethanol clusters ranging in size from monomer to hexamer show a linear correlation ( R 2 = 0.99) between ≤D, the deuterium quadrupole coupling parameter, and δH, the isotropic proton chemical shift in ppm relative to TMS: ≤D(kHz) = 297.60 - 15.28 δH. The temperature dependence of ≤D ranges from 199.5 kHz at 190 K to 221.4 kHz at 350 K. Using the values for ≤D and the relaxation time data, the temperature dependence of the OD rotational correlation time was found to vary from 282 ps at 190 K to 4.5 ps near the boiling point (350 K). Using these correlation times and bulk viscosity data, the Gierer-Wirtz model predicts a supramolecular cluster volume of about 317 A 3 , the approximate volume of a cyclic pentamer cluter of ethanol molecules. The cluster volume was nearly constant from 340 K to about 290 K.

Impact of hydrostatic pressure on an intrinsically disordered protein: a high-pressure NMR study of α-synuclein.

PubMed

Roche, Julien; Ying, Jinfa; Maltsev, Alexander S; Bax, Ad

2013-09-23

The impact of pressure on the backbone (15) N, (1) H and (13) C chemical shifts in N-terminally acetylated α-synuclein has been evaluated over a pressure range 1-2500 bar. Even while the chemical shifts fall very close to random coil values, as expected for an intrinsically disordered protein, substantial deviations in the pressure dependence of the chemical shifts are seen relative to those in short model peptides. In particular, the nonlinear pressure response of the (1) H(N) chemical shifts, which commonly is associated with the presence of low-lying "excited states", is much larger in α-synuclein than in model peptides. The linear pressure response of (1) H(N) chemical shift, commonly linked to H-bond length change, correlates well with those in short model peptides, and is found to be anticorrelated with its temperature dependence. The pressure dependence of (13) C chemical shifts shows remarkably large variations, even when accounting for residue type, and do not point to a clear shift in population between different regions of the Ramachandran map. However, a nearly universal decrease in (3) JHN-Hα by 0.22 ± 0.05 Hz suggests a slight increase in population of the polyproline II region at 2500 bar. The first six residues of N-terminally acetylated synuclein show a transient of approximately 15% population of α-helix, which slightly diminishes at 2500 bar. The backbone dynamics of the protein is not visibly affected beyond the effect of slight increase in water viscosity at 2500 bar. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

NMR parameters in alkali, alkaline earth and rare earth fluorides from first principle calculations.

PubMed

Sadoc, Aymeric; Body, Monique; Legein, Christophe; Biswal, Mamata; Fayon, Franck; Rocquefelte, Xavier; Boucher, Florent

2011-11-07

(19)F isotropic chemical shifts for alkali, alkaline earth and rare earth of column 3 basic fluorides are measured and the corresponding isotropic chemical shieldings are calculated using the GIPAW method. When using the PBE exchange-correlation functional for the treatment of the cationic localized empty orbitals of Ca(2+), Sc(3+) (3d) and La(3+) (4f), a correction is needed to accurately calculate (19)F chemical shieldings. We show that the correlation between experimental isotropic chemical shifts and calculated isotropic chemical shieldings established for the studied compounds allows us to predict (19)F NMR spectra of crystalline compounds with a relatively good accuracy. In addition, we experimentally determine the quadrupolar parameters of (25)Mg in MgF(2) and calculate the electric field gradients of (25)Mg in MgF(2) and (139)La in LaF(3) using both PAW and LAPW methods. The orientation of the EFG components in the crystallographic frame, provided by DFT calculations, is analysed in terms of electron densities. It is shown that consideration of the quadrupolar charge deformation is essential for the analysis of slightly distorted environments or highly irregular polyhedra. This journal is © the Owner Societies 2011

Substituent effect study on experimental ¹³C NMR chemical shifts of (3-(substituted phenyl)-cis-4,5-dihydroisoxazole-4,5-diyl)bis(methylene)diacetate derivatives.

PubMed

Kara, Yesim S

2015-12-05

Eleven novel (3-(substituted phenyl)-cis-4,5-dihydroisoxazole-4,5-diyl)bis(methylene) diacetate derivatives were synthesized in the present study. These dihydroisoxazole derivatives were characterized by IR, (1)H NMR, (13)C NMR and elemental analyses. Their (13)C NMR spectra were measured in Deuterochloroform (CDCl3). The correlation analysis for the substituent-induced chemical shift (SCS) with Hammett substituent constant (σ), inductive substituent constant (σI), different of resonance substituent constants (σR, σR(o)) and Swain-Lupton substituent parameters (F, R) were performed using SSP (single substituent parameter), and DSP (dual substituent parameter) methods, as well as single and multiple regression analysis. From the result of regression analysis, the effect of substituent on the (13)C NMR chemical shifts was explained. Copyright © 2015 Elsevier B.V. All rights reserved.

Understanding the NMR properties and conformational behavior of indole vs. azaindole group in protoberberines: NICS and NCS analysis

NASA Astrophysics Data System (ADS)

Kadam, Shivaji S.; Toušek, Jaromír; Maier, Lukáš; Pipíška, Matej; Sklenář, Vladimír; Marek, Radek

2012-11-01

We report here the preparation and the structural investigation into a series of 8-(indol-1-yl)-7,8-dihydroprotoberberine derivatives derived from berberine, palmatine, and coptisine. Structures of these new compounds were characterized mainly by 2D NMR spectroscopy and the conformational behavior was investigated by using methods of density-functional theory (DFT). PBE0/6-311+G** calculated NMR chemical shifts for selected derivatives correlate excellently with the experimental NMR data and support the structural conclusions drawn from the NMR experiments. An interesting role of the nitrogen atom in position N7' of the indole moiety in 8-(7-azaindol-1-yl)-7,8-dihydroprotoberberines as compared to other 8-indolyl derivatives is investigated in detail. The experimentally observed trends in NMR chemical shifts are rationalized by DFT calculations and analysis based on the nucleus-independent chemical shifts (NICS) and natural localized molecular orbitals (NLMOs).

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

PubMed

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

2011-07-28

We investigate the importance of relativistic effects on NMR shielding constants and chemical shifts of linear HgL(2) (L = Cl, Br, I, CH(3)) compounds using three different relativistic methods: the fully relativistic four-component approach and the two-component approximations, linear response elimination of small component (LR-ESC) and zeroth-order regular approximation (ZORA). LR-ESC reproduces successfully the four-component results for the C shielding constant in Hg(CH(3))(2) within 6 ppm, but fails to reproduce the Hg shielding constants and chemical shifts. The latter is mainly due to an underestimation of the change in spin-orbit contribution. Even though ZORA underestimates the absolute Hg NMR shielding constants by ∼2100 ppm, the differences between Hg chemical shift values obtained using ZORA and the four-component approach without spin-density contribution to the exchange-correlation (XC) kernel are less than 60 ppm for all compounds using three different functionals, BP86, B3LYP, and PBE0. However, larger deviations (up to 366 ppm) occur for Hg chemical shifts in HgBr(2) and HgI(2) when ZORA results are compared with four-component calculations with non-collinear spin-density contribution to the XC kernel. For the ZORA calculations it is necessary to use large basis sets (QZ4P) and the TZ2P basis set may give errors of ∼500 ppm for the Hg chemical shifts, despite deceivingly good agreement with experimental data. A Gaussian nucleus model for the Coulomb potential reduces the Hg shielding constants by ∼100-500 ppm and the Hg chemical shifts by 1-143 ppm compared to the point nucleus model depending on the atomic number Z of the coordinating atom and the level of theory. The effect on the shielding constants of the lighter nuclei (C, Cl, Br, I) is, however, negligible. © 2011 American Institute of Physics

Pressure response of protein backbone structure. Pressure-induced amide 15N chemical shifts in BPTI.

PubMed Central

Akasaka, K.; Li, H.; Yamada, H.; Li, R.; Thoresen, T.; Woodward, C. K.

1999-01-01

The effect of pressure on amide 15N chemical shifts was studied in uniformly 15N-labeled basic pancreatic trypsin inhibitor (BPTI) in 90%1H2O/10%2H2O, pH 4.6, by 1H-15N heteronuclear correlation spectroscopy between 1 and 2,000 bar. Most 15N signals were low field shifted linearly and reversibly with pressure (0.468 +/- 0.285 ppm/2 kbar), indicating that the entire polypeptide backbone structure is sensitive to pressure. A significant variation of shifts among different amide groups (0-1.5 ppm/2 kbar) indicates a heterogeneous response throughout within the three-dimensional structure of the protein. A tendency toward low field shifts is correlated with a decrease in hydrogen bond distance on the order of 0.03 A/2 kbar for the bond between the amide nitrogen atom and the oxygen atom of either carbonyl or water. The variation of 15N shifts is considered to reflect site-specific changes in phi, psi angles. For beta-sheet residues, a decrease in psi angles by 1-2 degrees/2 kbar is estimated. On average, shifts are larger for helical and loop regions (0.553 +/- 0.343 and 0.519 +/- 0.261 ppm/2 kbar, respectively) than for beta-sheet (0.295 +/- 0.195 ppm/2 kbar), suggesting that the pressure-induced structural changes (local compressibilities) are larger in helical and loop regions than in beta-sheet. Because compressibility is correlated with volume fluctuation, the result is taken to indicate that the volume fluctuation is larger in helical and loop regions than in beta-sheet. An important aspect of the volume fluctuation inferred from pressure shifts is that they include motions in slower time ranges (less than milliseconds) in which many biological processes may take place. PMID:10548039

Sesterterpenes from a common marine sponge, Hyrtios erecta.

PubMed

Crews, P; Bescansa, P

1986-01-01

Eleven sesterterpenes have been characterized from the biotoxic extracts of Hyrtios erecta. Their structures and stereochemistry were established by spectral properties or results from chemical interconversions. Especially valuable for establishing stereochemical features were 13C-nmr methyl shift correlations and analysis of 1H-nmr couplings and chemical shifts. The new scalarane sesterterpenes included 2, 3, 7, 9, and 10a (but 9 and 10a might be artifacts), and they were accompanied by five previously described scalaranes, 1, 4, 5a, 6, and 8, along with hyrtial (11), a novel norsesterterpene. Many of these sesterterpenes exhibited interesting biological activity.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

Solid-state 1H magic-angle spinning (MAS) NMR was used to investigate local proton environments in anhydrous [UO 2(OH) 2] (α-UOH) and hydrated uranyl hydroxide [(UO 2) 4O(OH) 6·5H 2O (metaschoepite). For the metaschoepite material, proton resonances of the μ 2-OH hydroxyl and interlayer waters were resolved, with two-dimensional (2D) double-quantum (DQ) 1H– 1H NMR correlation experiments revealing strong dipolar interactions between these different proton species. The experimental NMR results were combined with first-principles CASTEP GIPAW (gauge including projector-augmented wave) chemical shift calculations to develop correlations between hydrogen-bond strength and observed 1H NMR chemical shifts. Furthermore, these NMR correlations allowed characterization ofmore » local hydrogen-bond environments in uranyl U 24 capsules and of changes in hydrogen bonding that occurred during thermal dehydration of metaschoepite.« less

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

DOE PAGES

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

2016-04-27

Solid-state 1H magic-angle spinning (MAS) NMR was used to investigate local proton environments in anhydrous [UO 2(OH) 2] (α-UOH) and hydrated uranyl hydroxide [(UO 2) 4O(OH) 6·5H 2O (metaschoepite). For the metaschoepite material, proton resonances of the μ 2-OH hydroxyl and interlayer waters were resolved, with two-dimensional (2D) double-quantum (DQ) 1H– 1H NMR correlation experiments revealing strong dipolar interactions between these different proton species. The experimental NMR results were combined with first-principles CASTEP GIPAW (gauge including projector-augmented wave) chemical shift calculations to develop correlations between hydrogen-bond strength and observed 1H NMR chemical shifts. Furthermore, these NMR correlations allowed characterization ofmore » local hydrogen-bond environments in uranyl U 24 capsules and of changes in hydrogen bonding that occurred during thermal dehydration of metaschoepite.« less

Plasmonic-Enhanced Catalysis

DTIC Science & Technology

2012-05-30

shifts that cannot be merely explained hydride formation. These unexpected LSPR shifts may be explained by Au/Pd interdiffusion or silicide formation...photocurrent on a chemically modified gold thin film of metal -semiconductor (TiO2) Schottky diodes. • Intrinsic correlation between the hot electron flow...reaction to study catalyst nanoparticles at the single particle level. As hydrogen gas dissociates and intercalates into Pd, Pd changes from a metal to

Relativistic Spin-Orbit Heavy Atom on the Light Atom NMR Chemical Shifts: General Trends Across the Periodic Table Explained.

PubMed

Vícha, Jan; Komorovsky, Stanislav; Repisky, Michal; Marek, Radek; Straka, Michal

2018-06-12

The importance of relativistic effects on the NMR parameters in heavy-atom (HA) compounds, particularly the SO-HALA (Spin-Orbit Heavy Atom on the Light Atom) effect on NMR chemical shifts, has been known for about 40 years. Yet, a general correlation between the electronic structure and SO-HALA effect has been missing. By analyzing 1 H NMR chemical shifts of the sixth-period hydrides (Cs-At), we discovered general electronic-structure principles and mechanisms that dictate the size and sign of the SO-HALA NMR chemical shifts. In brief, partially occupied HA valence shells induce relativistic shielding at the light atom (LA) nuclei, while empty HA valence shells induce relativistic deshielding. In particular, the LA nucleus is relativistically shielded in 5d 2 -5d 8 and 6p 4 HA hydrides and deshielded in 4f 0 , 5d 0 , 6s 0 , and 6p 0 HA hydrides. This general and intuitive concept explains periodic trends in the 1 H NMR chemical shifts along the sixth-period hydrides (Cs-At) studied in this work. We present substantial evidence that the introduced principles have a general validity across the periodic table and can be extended to nonhydride LAs. The decades-old question of why compounds with occupied frontier π molecular orbitals (MOs) cause SO-HALA shielding at the LA nuclei, while the frontier σ MOs cause deshielding is answered. We further derive connection between the SO-HALA NMR chemical shifts and Spin-Orbit-induced Electron Deformation Density (SO-EDD), a property that can be obtained easily from differential electron densities and can be represented graphically. SO-EDD provides an intuitive understanding of the SO-HALA effect in terms of the depletion/concentration of the electron density at LA nuclei caused by spin-orbit coupling due to HA in the presence of a magnetic field. Using an analogy between the SO-EDD concept and arguments from classic NMR theory, the complex question of the SO-HALA NMR chemical shifts becomes easily understandable for a wide chemical audience.

Chemical changes in secondary electron emission during oxidation of nickel /100/ and /111/ crystal surfaces

NASA Technical Reports Server (NTRS)

Holloway, P. H.; Hudson, J. B.

1975-01-01

Changes in the secondary electron spectra (which include chemical shifts of Auger transitions) between 0-70 eV during the oxidation of both (100) and (111) nickel surfaces are reported. The reaction sequence between oxygen and nickel is also briefly described. Emission rate changes are correlated with changes in the work function of the solid.

Hepatic fat quantification using automated six-point Dixon: Comparison with conventional chemical shift based sequences and computed tomography.

PubMed

Shimizu, Kie; Namimoto, Tomohiro; Nakagawa, Masataka; Morita, Kosuke; Oda, Seitaro; Nakaura, Takeshi; Utsunomiya, Daisuke; Yamashita, Yasuyuki

To compare automated six-point Dixon (6-p-Dixon) MRI comparing with dual-echo chemical-shift-imaging (CSI) and CT for hepatic fat fraction in phantoms and clinical study. Phantoms and fifty-nine patients were examined both MRI and CT for quantitative fat measurements. In phantom study, linear regression between fat concentration and 6-p-Dixon showed good agreement. In clinical study, linear regression between 6-p-Dixon and dual-echo CSI showed good agreement. CT attenuation value was strongly correlated with 6-p-Dixon (R 2 =0.852; P<0.001) and dual-echo CSI (R 2 =0.812; P<0.001). Automated 6-p-Dixon and dual-echo CSI were accurate correlation with CT attenuation value of liver parenchyma. 6-p-Dixon has the potential for automated hepatic fat quantification. Copyright © 2017 Elsevier Inc. All rights reserved.

129Xe nuclear magnetic resonance study of pitch-based activated carbon modified by air oxidation/pyrolysis cycles: a new approach to probe the micropore size.

PubMed

Romanenko, Konstantin V; Py, Xavier; d'Espinose de Lacaillerie, Jean-Baptiste; Lapina, Olga B; Fraissard, Jacques

2006-02-23

(129)Xe NMR has been used to study a series of homologous activated carbons obtained from a KOH-activated pitch-based carbon molecular sieve modified by air oxidation/pyrolysis cycles. A clear correlation between the pore size of microporous carbons and the (129)Xe NMR of adsorbed xenon is proposed for the first time. The virial coefficient delta(Xe)(-)(Xe) arising from binary xenon collisions varied linearly with the micropore size and appeared to be a better probe of the microporosity than the chemical shift extrapolated to zero pressure. This correlation was explained by the fact that the xenon collision frequency increases with increasing micropore size. The chemical shift has been shown to vary very little with temperature (less than 9 ppm) for xenon trapped inside narrow and wide micropores. This is indicative of a smooth xenon-surface interaction potential.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cort, John R.; Cho, Herman M.

2009-10-01

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

Correlations between the 1H NMR chemical shieldings and the pKa values of organic acids and amines.

PubMed

Lu, Juanfeng; Lu, Tingting; Zhao, Xinyun; Chen, Xi; Zhan, Chang-Guo

2018-06-01

The acid dissociation constants and 1 H NMR chemical shieldings of organic compounds are important properties that have attracted much research interest. However, few studies have explored the relationship between these two properties. In this work, we theoretically studied the NMR chemical shifts of a series of carboxylic acids and amines in the gas phase and in aqueous solution. It was found that the negative logarithms of the experimental acid dissociation constants (i.e., the pK a values) of the organic acids and amines in aqueous solution correlate almost linearly with the corresponding calculated NMR chemical shieldings. Key factors that affect the theoretically predicted pK a values are discussed in this paper. The present work provides a new way to predict the pK a values of organic/biochemical compounds. Graphical abstract The chemical shielding values of organic acids and amines correlate near linearly with their corresponding pK a values.

13C-13C dipolar recoupling under very fast magic angle spinning in solid-state nuclear magnetic resonance: Applications to distance measurements, spectral assignments, and high-throughput secondary-structure determination

NASA Astrophysics Data System (ADS)

Ishii, Yoshitaka

2001-05-01

A technique is presented to recouple homonuclear dipolar couplings between dilute spin pairs such as 13C-13C systems under very fast magic angle spinning (MAS) in solid-state nuclear magnetic resonance (NMR) spectroscopy. The presented technique, finite pulse rf driven recoupling (fpRFDR), restores homonuclear dipolar interactions based on constructive usage of finite pulse-width effects in a phase- and symmetry-cycled π-pulse train in which a rotor-synchronous π pulse is applied every rotation period. The restored effective dipolar interaction has the form of a zero-quantum dipolar Hamiltonian for static solids, whose symmetry in spin space is different from that obtained by conventional rf driven recoupling (RFDR) techniques. It is demonstrated that the efficiency of recoupling by fpRFDR is not strongly dependent on chemical shift differences or resonance offsets in contrast to previous recoupling methods under very fast MAS. To realize distance measurements without effects of spin relaxation, a constant-time version of fpRFDR (CT-fpRFDR) is introduced, in which the effective evolution period is varied by refocusing dipolar evolution with a rotor-synchronized solid echo while the total recoupling period is kept constant. From CT-fpRFDR experiments at a spinning speed of 30.3 kHz in a field of 17.6 T, the 13C-13C distance of [1-13C]Ala-[1-13C]Gly-Gly was determined to be 3.27 Å, which agrees well with the value of 3.20 Å obtained by x-ray diffraction. Also, two-dimensional (2D) 13C/13C chemical-shift correlation NMR spectrum in a field of 9.4 T was obtained with fpRFDR for fibrils of the segmentally 13C- and 15N-labeled Alzheimer's β-Amyloid fragments, Aβ16-22 (residues 16-22 taken from the 40-residue Aβ peptide) in which Leu-17 through Ala-21 are uniformly 13C- and 15N-labeled. Most 13C resonances for the main chain as well as for the side chains are assigned based on 2D 13C/13C chemical-shift correlation patterns specific to amino-acid types. Examination of the obtained 13C chemical shifts revealed the formation of β-strand across the entire molecule of Aβ16-22. Possibility of high throughput determination of global main-chain structures based on 13C shifts obtained from 2D 13C/13C chemical-shift correlation under very fast MAS is also discussed for uniformly/segmentally 13C-labeled protein/peptide samples.

125Te NMR Probes of Tellurium Oxide Crystals: Shielding-Structure Correlations.

PubMed

Garaga, Mounesha N; Werner-Zwanziger, Ulrike; Zwanziger, Josef W

2018-01-16

The local environments around tellurium atoms in a series of tellurium oxide crystals were probed by 125 Te solid-state NMR spectroscopy. Crystals with distinct TeO n units (n from 3 to 6), including Na 2 TeO 3 , α-TeO 2 and γ-TeO 2 , Te 2 O(PO 4 ) 2 , K 3 LaTe 2 O 9 , BaZnTe 2 O 7 , and CsYTe 3 O 8 were studied. The latter four were synthesized through a solid-state process. X-ray diffraction was used to confirm the successful syntheses. The 125 Te chemical shift was found to exhibit a strong linear correlation with the Te coordination number. The 125 Te chemical-shift components (δ 11 , δ 22 , and δ 33 ) of the TeO 4 units were further correlated to the O-Te-O-bond angles. With the aid of 125 Te NMR, it is likely that these relations can be used to estimate the coordination states of Te atoms in unknown Te crystals and glasses.

Correlations among experimental and theoretical NMR data to determine the absolute stereochemistry of darcyribeirine, a pentacyclic indole alkaloid isolated from Rauvolfia grandiflora

NASA Astrophysics Data System (ADS)

Cancelieri, Náuvia Maria; Ferreira, Thiago Resende; Vieira, Ivo José Curcino; Braz-Filho, Raimundo; Piló-Veloso, Dorila; Alcântara, Antônio Flávio de Carvalho

2015-10-01

Darcyribeirine (1) is a pentacyclic indole alkaloid isolated from Rauvolfia grandiflora. Stereochemistry of 1 was previously proposed based on 1D (coupling constant data) and 2D (NOESY correlations) NMR techniques, having been established a configuration 3R, 15S, and 20R (isomer 1a). Stereoisomers of 1 (i.e., 1a-1h) can be grouped into four sets of enantiomers. Carbon chemical shifts and hydrogen coupling constants were calculated using BLYP/6-31G* theory level for the eight isomers of 1. Calculated NMR data of 1a-1h were correlated with the corresponding experimental data of 1. The best correlations between theoretical and experimental carbon chemical shift data were obtained for the set of enantiomers 1e/1f to structures in the gaseous phase and considering solvent effects (using PCM and explicit models). Similar results were obtained when the same procedure was performed to correlations between theoretical and experimental coupling constant data. Finally, optical rotation calculations indicate 1e as its absolute stereochemistry. Orbital population analysis indicates that the hydrogen bonding between N-H of 1e and DMSO is due to contributions of its frontier unoccupied molecular orbitals, mainly LUMO+1, LUMO+2, and LUMO+3.

Behavior of cesium and thallium cations inside a calixarene cavity as probed by nuclear spin relaxation. Evidence of cation-pi interactions in water.

PubMed

Cuc, Diana; Bouguet-Bonnet, Sabine; Morel-Desrosiers, Nicole; Morel, Jean-Pierre; Mutzenhardt, Pierre; Canet, Daniel

2009-08-06

We have studied the complexes formed between the p-sulfonatocalix[4]arene and cesium or thallium metal cation, first by carbon-13 longitudinal relaxation of the calixarene molecule at two values of the magnetic field B(0). From the longitudinal relaxation times of an aromatic carbon directly bonded to a proton, thus subjected essentially to the dipolar interaction with that proton, we could obtain the correlation time describing the reorientation of the CH bond. The rest of this study has demonstrated that it is also the correlation time describing the tumbling of the whole calixarene assembly. From three non-proton-bearing carbons of the aromatic cycles (thus subjected to the chemical shift anisotropy and dipolar mechanisms), we have been able to determine the variation of the chemical shift anisotropy when going from the free to the complex form of the calixarene. These variations not only provide the location of the cation inside the calixarene cavity but also constitute a direct experimental proof of the cation-pi interactions. These results are complemented by cesium and thallium relaxation measurements performed again at two values of the magnetic field B(0). An estimation of the mean distance between the cation and the calixarene protons could be obtained. These measurements have also revealed an important chemical shift anisotropy of thallium upon complexation.

Tutorial for the structure elucidation of small molecules by means of the LSD software.

PubMed

Nuzillard, Jean-Marc; Plainchont, Bertrand

2018-06-01

Automatic structure elucidation of small molecules by means of the "logic for structure elucidation" (LSD) software is introduced in the context of the automatic exploitation of chemical shift correlation data and with minimal input from chemical shift values. The first step in solving a structural problem by means of LSD is the extraction of pertinent data from the 1D and 2D spectra. This operation requires the labeling of the resonances and of their correlations; its reliability highly depends on the quality of the spectra. The combination of COSY, HSQC, and HMBC spectra results in proximity relationships between nonhydrogen atoms that are associated in order to build the possible solutions of a problem. A simple molecule, camphor, serves as an example for the writing of an LSD input file and to show how solution structures are obtained. An input file for LSD must contain a nonambiguous description of each atom, or atom status, which includes the chemical element symbol, the hybridization state, the number of bound hydrogen atoms and the formal electric charge. In case of atom status ambiguity, the pyLSD program performs clarification by systematically generating the status of the atoms. PyLSD also proposes the use of the nmrshiftdb algorithm in order to rank the solutions of a problem according to the quality of the fit between the experimental carbon-13 chemical shifts, and the ones predicted from the proposed structures. To conclude, some hints toward future uses and developments of computer-assisted structure elucidation by LSD are proposed. Copyright © 2017 John Wiley & Sons, Ltd.

Method And Apparatus For High Resolution Ex-Situ Nmr Spectroscopy

DOEpatents

Pines, Alexander; Meriles, Carlos A.; Heise, Henrike; Sakellariou, Dimitrios; Moule, Adam

2004-01-06

A method and apparatus for ex-situ nuclear magnetic resonance spectroscopy for use on samples outside the physical limits of the magnets in inhomogeneous static and radio-frequency fields. Chemical shift spectra can be resolved with the method using sequences of correlated, composite z-rotation pulses in the presence of spatially matched static and radio frequency field gradients producing nutation echoes. The amplitude of the echoes is modulated by the chemical shift interaction and an inhomogeneity free FID may be recovered by stroboscopically sampling the maxima of the echoes. In an alternative embodiment, full-passage adiabatic pulses are consecutively applied. One embodiment of the apparatus generates a static magnetic field that has a variable saddle point.

Automated Interpretation and Extraction of Topographic Information from Time of Flight Secondary Ion Mass Spectrometry Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ievlev, Anton V.; Belianinov, Alexei; Jesse, Stephen

Time of flight secondary ion mass spectrometry (ToF SIMS) is one of the most powerful characterization tools allowing imaging of the chemical properties of various systems and materials. It allows precise studies of the chemical composition with sub-100-nm lateral and nanometer depth spatial resolution. However, comprehensive interpretation of ToF SIMS results is challengeable, because of the data volume and its multidimensionality. Furthermore, investigation of the samples with pronounced topographical features are complicated by the spectral shift. In this work we developed approach for the comprehensive ToF SIMS data interpretation based on the data analytics and automated extraction of the samplemore » topography based on time of flight shift. We further applied this approach to investigate correlation between biological function and chemical composition in Arabidopsis roots.« less

Automated Interpretation and Extraction of Topographic Information from Time of Flight Secondary Ion Mass Spectrometry Data

DOE PAGES

Ievlev, Anton V.; Belianinov, Alexei; Jesse, Stephen; ...

2017-12-06

Time of flight secondary ion mass spectrometry (ToF SIMS) is one of the most powerful characterization tools allowing imaging of the chemical properties of various systems and materials. It allows precise studies of the chemical composition with sub-100-nm lateral and nanometer depth spatial resolution. However, comprehensive interpretation of ToF SIMS results is challengeable, because of the data volume and its multidimensionality. Furthermore, investigation of the samples with pronounced topographical features are complicated by the spectral shift. In this work we developed approach for the comprehensive ToF SIMS data interpretation based on the data analytics and automated extraction of the samplemore » topography based on time of flight shift. We further applied this approach to investigate correlation between biological function and chemical composition in Arabidopsis roots.« less

On the problem of resonance assignments in solid state NMR of uniformly 15N, 13C-labeled proteins

NASA Astrophysics Data System (ADS)

Tycko, Robert

2015-04-01

Determination of accurate resonance assignments from multidimensional chemical shift correlation spectra is one of the major problems in biomolecular solid state NMR, particularly for relative large proteins with less-than-ideal NMR linewidths. This article investigates the difficulty of resonance assignment, using a computational Monte Carlo/simulated annealing (MCSA) algorithm to search for assignments from artificial three-dimensional spectra that are constructed from the reported isotropic 15N and 13C chemical shifts of two proteins whose structures have been determined by solution NMR methods. The results demonstrate how assignment simulations can provide new insights into factors that affect the assignment process, which can then help guide the design of experimental strategies. Specifically, simulations are performed for the catalytic domain of SrtC (147 residues, primarily β-sheet secondary structure) and the N-terminal domain of MLKL (166 residues, primarily α-helical secondary structure). Assuming unambiguous residue-type assignments and four ideal three-dimensional data sets (NCACX, NCOCX, CONCA, and CANCA), uncertainties in chemical shifts must be less than 0.4 ppm for assignments for SrtC to be unique, and less than 0.2 ppm for MLKL. Eliminating CANCA data has no significant effect, but additionally eliminating CONCA data leads to more stringent requirements for chemical shift precision. Introducing moderate ambiguities in residue-type assignments does not have a significant effect.

3D Double-Quantum/Double-Quantum Exchange Spectroscopy of Protons under 100 kHz Magic Angle Spinning.

PubMed

Zhang, Rongchun; Duong, Nghia Tuan; Nishiyama, Yusuke; Ramamoorthy, Ayyalusamy

2017-06-22

Solid-state 1 H NMR spectroscopy has attracted much attention in the recent years due to the remarkable spectral resolution improvement by ultrafast magic-angle-spinning (MAS) as well as due to the sensitivity enhancement rendered by proton detection. Although these developments have enabled the investigation of a variety of challenging chemical and biological solids, the proton spectral resolution is still poor for many rigid solid systems owing to the presence of conformational heterogeneity and the unsuppressed residual proton-proton dipolar couplings even with the use of the highest currently feasible sample spinning speed of ∼130 kHz. Although a further increase in the spinning speed of the sample could be beneficial to some extent, there is a need for alternate approaches to enhance the spectral resolution. Herein, by fully utilizing the benefits of double-quantum (DQ) coherences, we propose a single radio frequency channel proton-based 3D pulse sequence that correlates double-quantum (DQ), DQ, and single-quantum (SQ) chemical shifts of protons. In addition to the two-spin homonuclear proximity information, the proposed 3D DQ/DQ/SQ experiment also enables the extraction of three-spin and four-spin proximities, which could be beneficial for revealing the dipolar coupled proton network in the solid state. Besides, the 2D DQ/DQ spectrum sliced at different isotropic SQ chemical shift values of the 3D DQ/DQ/SQ spectrum will also facilitate the identification of DQ correlation peaks and improve the spectral resolution, as it only provides the local homonuclear correlation information associated with the specific protons selected by the SQ chemical shift frequency. The 3D pulse sequence and its efficiency are demonstrated experimentally on small molecular compounds in the solid state. We expect that this approach would create avenues for further developments by suitably combining the benefits of partial deuteration of samples, selective excitation/decoupling pulses, heteronuclear spins for spectral editing, and nonuniform sampling.

Correlation of the bond-length change and vibrational frequency shift in model hydrogen-bonded complexes of pyrrole

NASA Astrophysics Data System (ADS)

McDowell, Sean A. C.

2017-04-01

An MP2 computational study of model hydrogen-bonded pyrrole⋯YZ (YZ = NH3, NCH, BF, CO, N2, OC, FB) complexes was undertaken in order to examine the variation of the Nsbnd H bond length change and its associated vibrational frequency shift. The chemical hardness of Y, as well as the YZ dipole moment, were found to be important parameters in modifying the bond length change/frequency shift. The basis set effect on the computed properties was also assessed. A perturbative model, which accurately reproduced the ab initio Nsbnd H bond length changes and frequency shifts, was useful in rationalizing the observed trends.

Access to aliphatic protons as reporters in non-deuterated proteins by solid-state NMR.

PubMed

Vasa, Suresh Kumar; Rovó, Petra; Giller, Karin; Becker, Stefan; Linser, Rasmus

2016-03-28

Interactions within proteins, with their surrounding, and with other molecules are mediated mostly by hydrogen atoms. In fully protonated, inhomogeneous, or larger proteins, however, aliphatic proton shifts tend to show little dispersion despite fast Magic-Angle Spinning. 3D correlations dispersing aliphatic proton shifts by their better resolved amide N/H shifts can alleviate this problem. Using inverse second-order cross-polarization (iSOCP), we here introduce dedicated and improved means to sensitively link site-specific chemical shift information from aliphatic protons with a backbone amide resolution. Thus, even in cases where protein deuteration is impossible, this approach may enable access to various aspects of protein functions that are reported on by protons.

Isolation, spectroscopic and density functional theory studies of 7-(4-methoxyphenyl)-9H-furo[2,3-f]chromen-9-one: a new flavonoid from the bark of Millettia ovalifolia.

PubMed

Taj Ur Rahman; Arfan, Mohammad; Mahmood, Tariq; Liaqat, Wajiha; Gilani, Mazhar Amjad; Uddin, Ghias; Ludwig, Ralf; Zaman, Khair; Choudhary, M Iqbal; Khattak, Khanzadi Fatima; Ayub, Khurshid

2015-07-05

The phytochemical examination of chloroform soluble fraction (FX2) of methanolic extract of bark of Millettia ovalifolia yielded a new flavonoid; 7-(4-methoxyphenyl)-9H-furo [2,3-f]chromen-9-one (1). Compound 1 is characterized by spectroscopic analytical techniques such as UV, IR, 1D, 2D NMR spectroscopy, and mass spectrometry. A theoretical model is also developed for obtaining geometric, electronic and spectroscopic properties of 1. The geometry optimization and harmonic vibration simulations have been carried out at B3LYP/6-31G(d,p). The vibrational spectrum of compound 1 shows nice correlation with the experimental IR spectrum, through a scaling factor of 0.9613. (1)H and (13)C NMR chemical shifts are simulated using Cramer's re-parameterized function WP04 at 6-31G(d,p) basis set, and correlate nicely with the experimental chemical shifts. Copyright © 2015 Elsevier B.V. All rights reserved.

Isolation, spectroscopic and density functional theory studies of 7-(4-methoxyphenyl)-9H-furo[2,3-f]chromen-9-one: A new flavonoid from the bark of Millettia ovalifolia

NASA Astrophysics Data System (ADS)

Rahman, Taj Ur; Arfan, Mohammad; Mahmood, Tariq; Liaqat, Wajiha; Gilani, Mazhar Amjad; Uddin, Ghias; Ludwig, Ralf; Zaman, Khair; Choudhary, M. Iqbal; Khattak, Khanzadi Fatima; Ayub, Khurshid

2015-07-01

The phytochemical examination of chloroform soluble fraction (FX2) of methanolic extract of bark of Millettia ovalifolia yielded a new flavonoid; 7-(4-methoxyphenyl)-9H-furo [2,3-f]chromen-9-one (1). Compound 1 is characterized by spectroscopic analytical techniques such as UV, IR, 1D, 2D NMR spectroscopy, and mass spectrometry. A theoretical model is also developed for obtaining geometric, electronic and spectroscopic properties of 1. The geometry optimization and harmonic vibration simulations have been carried out at B3LYP/6-31G(d,p). The vibrational spectrum of compound 1 shows nice correlation with the experimental IR spectrum, through a scaling factor of 0.9613. 1H and 13C NMR chemical shifts are simulated using Cramer's re-parameterized function WP04 at 6-31G(d,p) basis set, and correlate nicely with the experimental chemical shifts.

Nuclear magnetic resonance spectroscopy in the structure elucidation and biosynthesis of natural products

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meksuriyen, D.

1988-01-01

Examination of a chloroform extract of Dracaena loureiri Gagnep (Agavaceae), a Thia medicinal plant possessing antibacterial activity, has led to the isolation of fifteen flavenoids. The biogenic relationships among these flavenoids isolated were briefly discussed. Definition of the skeleton and the unambiguous assignment of all of the protons of the isolates was achieved through extensive 2D-homonuclear chemical shift correlation, nuclear Overhauser effect (NOE) difference spectroscopy and 2D-NOE experiments. The {sup 1}H and {sup 13}C NMR spectra of staurosporine, a potent biologically active agent from Streptomyces staurosporeus, were unambiguously assigned by using 2D homonuclear chemical shift correlation, NOE, {sup 1}H-detected heteronuclearmore » multiple-quantum coherence via direct coupling and via multiple-bond coupling for resonance assignments of protonated and nonprotonated carbons, respectively. S. Staurosporeus was found to utilize endogenous and exogenous D- and L-isomers of trytophan in the production of staurosporine. The biosynthesis of staurosporine was examined by employing carbon-14, tritium, and carbon-13 labeled precursors.« less

Effects of climate change on bioaccumulation and biomagnification of polycyclic aromatic hydrocarbons in the planktonic food web of a subtropical shallow eutrophic lake in China.

PubMed

Tao, Yuqiang; Xue, Bin; Lei, Guoliang; Liu, Fei; Wang, Zhen

2017-04-01

To date effects of climate change on bioaccumulation and biomagnification of chemical pollutants in planktonic food webs have rarely been studied. Recruitments of plankton have shifted earlier due to global warming. Global warming and precipitation patterns are projected to shift seasonally. Whether and how the shifts in plankton phenology induced by climate change will impact bioaccumulation and biomagnification of chemical pollutants, and how they will respond to climate change are largely unknown. Here, we combine data analysis of the past seven decades, high temporal resolution monitoring and model development to test this hypothesis with nine polycyclic aromatic hydrocarbons (PAHs) in the planktonic food web of a subtropical shallow eutrophic lake in China. We find biphasic correlations between both bioconcentration factors and bioaccumulation factors of the PAHs and the mean temperature, which depend on the recruitment temperatures of cyanobacteria, and copepods and cladocerans. The positive correlations between bioconcentration factors, bioaccumulation factors and the mean temperature will be observed less than approximately 13-18 days by 2050-2060 due to the shifts in plankton phenology. The PAHs and their bioaccumulation and biomagnification will respond seasonally and differently to climate change. Bioaccumulation of most of the PAHs will decrease with global warming, with higher decreasing rates appearing in winter and spring. Biomagnification of most of the PAHs from phytoplankton to zooplankton will increase with global warming, with higher increasing rates appearing in winter and spring. Our study provides novel insights into bioaccumulation and biomagnification of chemical pollutants in eutrophic waters under climate change scenarios. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

1992-03-01

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

New look at the Badger-Bauer rule: Correlations of spectroscopic IR and NMR parameters with hydrogen bond energy and geometry. FHF complexes

NASA Astrophysics Data System (ADS)

Tupikina, E. Yu.; Denisov, G. S.; Melikova, S. M.; Kucherov, S. Yu.; Tolstoy, P. M.

2018-07-01

In this work correlation dependencies between hydrogen bond energy ΔE for complexes with Fsbnd H⋯F hydrogen bond and their spectroscopic characteristics of the IR and NMR spectra are presented. We considered 26 complexes in a wide hydrogen bond energy range 0.2-47 kcal/mol. For each complex we calculated complexation energy (MP2/6-311++G(d,p)), IR spectroscopic parameters (FH stretching frequency ν, FH stretching frequency in local mode approximation νLM at MP2/6-311++G(d,p) level) and NMR parameters (chemical shift of hydrogen δH and fluorine nuclei δF, Nuclear Independent Chemical Shielding and spin-spin coupling constants 1JFH, 1hJH...F, 2hJFF at B3LYP/pcSseg-2 level). It was shown that changes of parameters upon complexation, i.e. changes of the stretching frequency in local mode approximation ΔνLM, change of the proton chemical shift ΔδH and change of the absolute value of spin-spin coupling constant 1JFH could be used for estimation of corresponding hydrogen bond strength. Furthermore, we build correlation dependencies between abovementioned spectroscopic characteristics and geometric ones, such as the asymmetry of bridging proton position q1 = 0.5·(rFH - rH…F).

Automated Processing of Two-Dimensional Correlation Spectra

PubMed

Sengstschmid; Sterk; Freeman

1998-04-01

An automated scheme is described which locates the centers of cross peaks in two-dimensional correlation spectra, even under conditions of severe overlap. Double-quantum-filtered correlation (DQ-COSY) spectra have been investigated, but the method is also applicable to TOCSY and NOESY spectra. The search criterion is the intrinsic symmetry (or antisymmetry) of cross-peak multiplets. An initial global search provides the preliminary information to build up a two-dimensional "chemical shift grid." All genuine cross peaks must be centered at intersections of this grid, a fact that reduces the extent of the subsequent search program enormously. The program recognizes cross peaks by examining the symmetry of signals in a test zone centered at a grid intersection. This "symmetry filter" employs a "lowest value algorithm" to discriminate against overlapping responses from adjacent multiplets. A progressive multiplet subtraction scheme provides further suppression of overlap effects. The processed two-dimensional correlation spectrum represents cross peaks as points at the chemical shift coordinates, with some indication of their relative intensities. Alternatively, the information is presented in the form of a correlation table. The authenticity of a given cross peak is judged by a set of "confidence criteria" expressed as numerical parameters. Experimental results are presented for the 400-MHz double-quantum-filtered COSY spectrum of 4-androsten-3,17-dione, a case where there is severe overlap. Copyright 1998 Academic Press.

Cellulose Structural Polymorphism in Plant Primary Cell Walls Investigated by High-Field 2D Solid-State NMR Spectroscopy and Density Functional Theory Calculations.

PubMed

Wang, Tuo; Yang, Hui; Kubicki, James D; Hong, Mei

2016-06-13

The native cellulose of bacterial, algal, and animal origins has been well studied structurally using X-ray and neutron diffraction and solid-state NMR spectroscopy, and is known to consist of varying proportions of two allomorphs, Iα and Iβ, which differ in hydrogen bonding, chain packing, and local conformation. In comparison, cellulose structure in plant primary cell walls is much less understood because plant cellulose has lower crystallinity and extensive interactions with matrix polysaccharides. Here we have combined two-dimensional magic-angle-spinning (MAS) solid-state nuclear magnetic resonance (solid-state NMR) spectroscopy at high magnetic fields with density functional theory (DFT) calculations to obtain detailed information about the structural polymorphism and spatial distributions of plant primary-wall cellulose. 2D (13)C-(13)C correlation spectra of uniformly (13)C-labeled cell walls of several model plants resolved seven sets of cellulose chemical shifts. Among these, five sets (denoted a-e) belong to cellulose in the interior of the microfibril while two sets (f and g) can be assigned to surface cellulose. Importantly, most of the interior cellulose (13)C chemical shifts differ significantly from the (13)C chemical shifts of the Iα and Iβ allomorphs, indicating that plant primary-wall cellulose has different conformations, packing, and hydrogen bonding from celluloses of other organisms. 2D (13)C-(13)C correlation experiments with long mixing times and with water polarization transfer revealed the spatial distributions and matrix-polysaccharide interactions of these cellulose structures. Celluloses f and g are well mixed chains on the microfibril surface, celluloses a and b are interior chains that are in molecular contact with the surface chains, while cellulose c resides in the core of the microfibril, outside spin diffusion contact with the surface. Interestingly, cellulose d, whose chemical shifts differ most significantly from those of bacterial, algal, and animal cellulose, interacts with hemicellulose, is poorly hydrated, and is targeted by the protein expansin during wall loosening. To obtain information about the C6 hydroxymethyl conformation of these plant celluloses, we carried out DFT calculations of (13)C chemical shifts, using the Iα and Iβ crystal structures as templates and varying the C5-C6 torsion angle. Comparison with the experimental chemical shifts suggests that all interior cellulose favor the tg conformation, but cellulose d also has a similar propensity to adopt the gt conformation. These results indicate that cellulose in plant primary cell walls, due to their interactions with matrix polysaccharides, and has polymorphic structures that are not a simple superposition of the Iα and Iβ allomorphs, thus distinguishing them from bacterial and animal celluloses.

Cellulose Structural Polymorphism in Plant Primary Cell Walls Investigated by High-Field 2D Solid-State NMR Spectroscopy and Density Functional Theory Calculations

PubMed Central

Wang, Tuo; Yang, Hui; Kubicki, James D.; Hong, Mei

2017-01-01

The native cellulose of bacterial, algal, and animal origins has been well studied structurally using X-ray and neutron diffraction and solid-state NMR spectroscopy, and is known to consist of varying proportions of two allomorphs, Iα and Iβ, which differ in hydrogen bonding, chain packing, and local conformation. In comparison, cellulose structure in plant primary cell walls is much less understood because plant cellulose has lower crystallinity and extensive interactions with matrix polysaccharides. Here we have combined two-dimensional magic-angle-spinning (MAS) solid-state nuclear magnetic resonance (solid-state NMR) spectroscopy at high magnetic fields with density functional theory (DFT) calculations to obtain detailed information about the structural polymorphism and spatial distributions of plant primary-wall cellulose. 2D 13C-13C correlation spectra of uniformly 13C-labeled cell walls of several model plants resolved seven sets of cellulose chemical shifts. Among these, five sets (denoted a-e) belong to cellulose in the interior of the microfibril while two sets (f and g) can be assigned to surface cellulose. Importantly, most of the interior cellulose 13C chemical shifts differ significantly from the 13C chemical shifts of the Iα and Iβ allomorphs, indicating that plant primary-wall cellulose has different conformations, packing and hydrogen bonding from celluloses of other organisms. 2D 13C-13C correlation experiments with long mixing times and with water polarization transfer revealed the spatial distributions and matrix-polysaccharide interactions of these cellulose structures. Cellulose f and g are well mixed chains on the microfibril surface, cellulose a and b are interior chains that are in molecular contact with the surface chains, while cellulose c resides in the core of the microfibril, outside spin diffusion contact with the surface. Interestingly, cellulose d, whose chemical shifts differ most significantly from those of bacterial, algal and animal cellulose, interacts with hemicellulose, is poorly hydrated, and is targeted by the protein expansin during wall loosening. To obtain information about the C6 hydroxymethyl conformation of these plant celluloses, we carried out DFT calculations of 13C chemical shifts, using the Iα and Iβ crystal structures as templates and varying the C5-C6 torsion angle. Comparison with the experimental chemical shifts suggests that all interior cellulose favor the tg conformation, but cellulose d also has a similar propensity to adopt the gt conformation. These results indicate that cellulose in plant primary cell walls, due to their interactions with matrix polysaccharides, has polymorphic structures that are not a simple superposition of the Iα and Iβ allomorphs, thus distinguishing them from bacterial and animal celluloses. PMID:27192562

Solution structure of lysine-free (K0) ubiquitin

PubMed Central

Huang, Tao; Li, Jess; Byrd, R Andrew

2014-01-01

Lysine-free ubiquitin (K0-Ub) is commonly used to study the ubiquitin-signaling pathway, where it is assumed to have the same structure and function as wild-type ubiquitin (wt-Ub). However, the K0-Ub 15N heteronuclear single quantum correlation NMR spectrum differs significantly from wt-Ub and the melting temperature is depressed by 19°C, raising the question of the structural integrity and equivalence to wt-Ub. The three-dimensional structure of K0-Ub was determined by solution NMR, using chemical shift and residual dipolar coupling data. K0-Ub adopts the same backbone structure as wt-Ub, and all significant chemical shifts can be related to interactions impacted by the K to R mutations. PMID:24591328

Molecular structure activity on pharmaceutical applications of Phenacetin using spectroscopic investigation

NASA Astrophysics Data System (ADS)

Madanagopal, A.; Periandy, S.; Gayathri, P.; Ramalingam, S.; Xavier, S.

2017-01-01

The pharmaceutical compound; Phenacetin was investigated by analyzing FT-IR, FT-Raman and 1H &13C NMR spectra. The hybrid efficient computational calculations performed for computing physical and chemical parameters. The cause of pharmaceutical activity due to the substitutions; carboxylic, methyl and amine groups in appropriate positions on the pedestal compound was deeply investigated. Moreover, 13C NMR and 1H NMR chemical shifts correlated with TMS standard to explain the truth of compositional ratio of base and ligand groups. The bathochromic shift due to chromophores over the energy levels in UV-Visible region was strongly emphasized the Anti-inflammatory chemical properties. The chemical stability was pronounced by the strong kubo gap which showed the occurring of charge transformation within the molecule. The occurrence of the chemical reaction was feasibly interpreted by Gibbs free energy profile. The standard vibrational analysis stressed the active participation of composed ligand groups for the existence of the analgesic as well as antipyretic properties of the Phenacetin compound. The strong dipole interaction energy utilization for the transition among non-vanishing donor and acceptor for composition of the molecular structure was interpreted.

Updates in MRI characterization of the thymus in myasthenic patients.

PubMed

Popa, G A; Preda, E M; Scheau, C; Vilciu, C; Lupescu, I G

2012-06-12

To evaluate the imaging appearance of the thymus in the myasthenic patients by using chemical shift magnetic resonance imaging, and, to correlate the chemical shift ratio (CSR) with pathologic findings after surgical excision. In the past year, a total of 11 myasthenic patients (4 males, 7 females; age range of 26-65 years), have been investigated by MRI centered at the thymic lodge. Our protocol included a Dual-Echo technique, T1-weighted In-phase/Opposed-phase MR images in all patients. A chemical shift ratio (CSR) was calculated by comparing the signal intensity of the thymus gland with that of the chest wall muscle for quantitative analysis. For this purpose, we have used standard region-of-interest electronic cursors at a slice level of the maximum axial surface of the thymus. We have identified two patients groups: a thymic hyperplasia group and a thymic tumoral group. With the decrease in the signal intensity of the thymus gland at chemical shift, the MR imaging was evident only in the hyperplasia group. The mean CSR in the hyperplasia group was considerably lower than that in the tumor group, 0,4964 ± 0,1841, compared with 1,0398 ± 0,0244. The difference in CSR between the hyperplasia and tumor groups was statistically significant (P=0,0028). MR imaging using T1-weighted In-phase/Opposed-phase images could be a useful diagnostic tool in the preoperative assessment of the thymic lodge and may help differentiate thymic hyperplasia from tumors of the thymus gland.

Differential Dynamic Engagement within 24 SH3 Domain: Peptide Complexes Revealed by Co-Linear Chemical Shift Perturbation Analysis

PubMed Central

Stollar, Elliott J.; Lin, Hong; Davidson, Alan R.; Forman-Kay, Julie D.

2012-01-01

There is increasing evidence for the functional importance of multiple dynamically populated states within single proteins. However, peptide binding by protein-protein interaction domains, such as the SH3 domain, has generally been considered to involve the full engagement of peptide to the binding surface with minimal dynamics and simple methods to determine dynamics at the binding surface for multiple related complexes have not been described. We have used NMR spectroscopy combined with isothermal titration calorimetry to comprehensively examine the extent of engagement to the yeast Abp1p SH3 domain for 24 different peptides. Over one quarter of the domain residues display co-linear chemical shift perturbation (CCSP) behavior, in which the position of a given chemical shift in a complex is co-linear with the same chemical shift in the other complexes, providing evidence that each complex exists as a unique dynamic rapidly inter-converting ensemble. The extent the specificity determining sub-surface of AbpSH3 is engaged as judged by CCSP analysis correlates with structural and thermodynamic measurements as well as with functional data, revealing the basis for significant structural and functional diversity amongst the related complexes. Thus, CCSP analysis can distinguish peptide complexes that may appear identical in terms of general structure and percent peptide occupancy but have significant local binding differences across the interface, affecting their ability to transmit conformational change across the domain and resulting in functional differences. PMID:23251481

Measuring (19)F shift anisotropies and (1)H-(19)F dipolar interactions with ultrafast MAS NMR.

PubMed

Martini, Francesca; Miah, Habeeba K; Iuga, Dinu; Geppi, Marco; Titman, Jeremy J

2015-10-01

A new (19)F anisotropic-isotropic shift correlation experiment is described that operates with ultrafast MAS, resulting in good resolution of isotropic (19)F shifts in the detection dimension. The new experiment makes use of a recoupling sequence designed using symmetry principles that reintroduces the (19)F chemical shift anisotropy in the indirect dimension. The situations in which the new experiment is appropriate are discussed, and the (19)F shift anisotropy parameters in poly(difluoroethylene) (PVDF) are measured. In addition, similar recoupling sequences are shown to be effective for measuring (1)H-(19)F distances via the heteronuclear dipolar interaction. This is demonstrated by application to a recently synthesized zirconium phosphonate material that contains one-dimensional chains linked by H-F hydrogen bonds. Copyright © 2015 Elsevier Inc. All rights reserved.

Proton transfer and hydrogen bonding in the organic solid state: a combined XRD/XPS/ssNMR study of 17 organic acid-base complexes.

PubMed

Stevens, Joanna S; Byard, Stephen J; Seaton, Colin C; Sadiq, Ghazala; Davey, Roger J; Schroeder, Sven L M

2014-01-21

The properties of nitrogen centres acting either as hydrogen-bond or Brønsted acceptors in solid molecular acid-base complexes have been probed by N 1s X-ray photoelectron spectroscopy (XPS) as well as (15)N solid-state nuclear magnetic resonance (ssNMR) spectroscopy and are interpreted with reference to local crystallographic structure information provided by X-ray diffraction (XRD). We have previously shown that the strong chemical shift of the N 1s binding energy associated with the protonation of nitrogen centres unequivocally distinguishes protonated (salt) from hydrogen-bonded (co-crystal) nitrogen species. This result is further supported by significant ssNMR shifts to low frequency, which occur with proton transfer from the acid to the base component. Generally, only minor chemical shifts occur upon co-crystal formation, unless a strong hydrogen bond is formed. CASTEP density functional theory (DFT) calculations of (15)N ssNMR isotropic chemical shifts correlate well with the experimental data, confirming that computational predictions of H-bond strengths and associated ssNMR chemical shifts allow the identification of salt and co-crystal structures (NMR crystallography). The excellent agreement between the conclusions drawn by XPS and the combined CASTEP/ssNMR investigations opens up a reliable avenue for local structure characterization in molecular systems even in the absence of crystal structure information, for example for non-crystalline or amorphous matter. The range of 17 different systems investigated in this study demonstrates the generic nature of this approach, which will be applicable to many other molecular materials in organic, physical, and materials chemistry.

Ab initio/DFT/GIAO-CCSD(T) calculational study of the t-butyl cation: comparison of experimental data with structures, energetics, IR vibrational frequencies, and 13C NMR chemical shifts indicating preferred C(s) conformation.

PubMed

Rasul, Golam; Chen, Jonathan L; Prakash, G K Surya; Olah, George A

2009-06-18

The C(s) conformation of the tert-butyl cation 3 was established to be the preferred global energy minimum using a combination of ab initio, DFT, and CCSD(T) methodology with correlation-consistent basis sets. The potential energy surface of methyl rotation involving the C(3v), C(s), and C(3h) forms, however, in accord with previous studies, is quite flat. The computed IR absorptions of 3 indicate that it has the greatest degree of electron donation from C-H bonds into the C(+)-C bonds. The experimental (13)C NMR chemical shifts also agree very well with the experimental data.

Free variable selection QSPR study to predict 19F chemical shifts of some fluorinated organic compounds using Random Forest and RBF-PLS methods

NASA Astrophysics Data System (ADS)

Goudarzi, Nasser

2016-04-01

In this work, two new and powerful chemometrics methods are applied for the modeling and prediction of the 19F chemical shift values of some fluorinated organic compounds. The radial basis function-partial least square (RBF-PLS) and random forest (RF) are employed to construct the models to predict the 19F chemical shifts. In this study, we didn't used from any variable selection method and RF method can be used as variable selection and modeling technique. Effects of the important parameters affecting the ability of the RF prediction power such as the number of trees (nt) and the number of randomly selected variables to split each node (m) were investigated. The root-mean-square errors of prediction (RMSEP) for the training set and the prediction set for the RBF-PLS and RF models were 44.70, 23.86, 29.77, and 23.69, respectively. Also, the correlation coefficients of the prediction set for the RBF-PLS and RF models were 0.8684 and 0.9313, respectively. The results obtained reveal that the RF model can be used as a powerful chemometrics tool for the quantitative structure-property relationship (QSPR) studies.

Theoretical investigation on the molecular structure, Infrared, Raman and NMR spectra of para-halogen benzenesulfonamides, 4-X-C 6H 4SO 2NH 2 (X = Cl, Br or F)

NASA Astrophysics Data System (ADS)

Karabacak, Mehmet; Çınar, Mehmet; Çoruh, Ali; Kurt, Mustafa

2009-02-01

In the present study, the structural properties of para-halogen benzenesulfonamides, 4-XC 6H 4SO 2NH 2 (4-chlorobenzenesulfonamide (I), 4-bromobenzenesulfonamide (II) and 4-fluorobenzenesulfonamide (III)) have been studied extensively utilizing ab initio Hartree-Fock (HF) and density functional theory (DFT) employing B3LYP exchange correlation. The vibrational frequencies were calculated and scaled values were compared with experimental values. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The effects of the halogen substituent on the characteristic benzenesulfonamides bands in the spectra are discussed. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecules were calculated using the Gauge-Invariant Atomic Orbital (GIAO) method. Finally, geometric parameters, vibrational bands and chemical shifts were compared with available experimental data of the molecules. The fully optimized geometries of the molecules were found to be consistent with the X-ray crystal structures. The observed and calculated frequencies and chemical shifts were found to be in very good agreement.

Single-crystal X-ray diffraction and NMR crystallography of a 1:1 cocrystal of dithianon and pyrimethanil.

PubMed

Pöppler, Ann Christin; Corlett, Emily K; Pearce, Harriet; Seymour, Mark P; Reid, Matthew; Montgomery, Mark G; Brown, Steven P

2017-03-01

A single-crystal X-ray diffraction structure of a 1:1 cocrystal of two fungicides, namely dithianon (DI) and pyrimethanil (PM), is reported [systematic name: 5,10-dioxo-5H,10H-naphtho[2,3-b][1,4]dithiine-2,3-dicarbonitrile-4,6-dimethyl-N-phenylpyrimidin-2-amine (1/1), C 14 H 4 N 2 O 2 S 2 ·C 12 H 13 N 2 ]. Following an NMR crystallography approach, experimental solid-state magic angle spinning (MAS) NMR spectra are presented together with GIPAW (gauge-including projector augmented wave) calculations of NMR chemical shieldings. Specifically, experimental 1 H and 13 C chemical shifts are determined from two-dimensional 1 H- 13 C MAS NMR correlation spectra recorded with short and longer contact times so as to probe one-bond C-H connectivities and longer-range C...H proximities, whereas H...H proximities are identified in a 1 H double-quantum (DQ) MAS NMR spectrum. The performing of separate GIPAW calculations for the full periodic crystal structure and for isolated molecules allows the determination of the change in chemical shift upon going from an isolated molecule to the full crystal structure. For the 1 H NMR chemical shifts, changes of 3.6 and 2.0 ppm correspond to intermolecular N-H...O and C-H...O hydrogen bonding, while changes of -2.7 and -1.5 ppm are due to ring current effects associated with C-H...π interactions. Even though there is a close intermolecular S...O distance of 3.10 Å, it is of note that the molecule-to-crystal chemical shifts for the involved sulfur or oxygen nuclei are small.

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

NASA Astrophysics Data System (ADS)

Zhang, Rongchun; Ramamoorthy, Ayyalusamy

2015-05-01

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

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

PubMed Central

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

2013-01-01

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

Time averaging of NMR chemical shifts in the MLF peptide in the solid state.

PubMed

De Gortari, Itzam; Portella, Guillem; Salvatella, Xavier; Bajaj, Vikram S; van der Wel, Patrick C A; Yates, Jonathan R; Segall, Matthew D; Pickard, Chris J; Payne, Mike C; Vendruscolo, Michele

2010-05-05

Since experimental measurements of NMR chemical shifts provide time and ensemble averaged values, we investigated how these effects should be included when chemical shifts are computed using density functional theory (DFT). We measured the chemical shifts of the N-formyl-L-methionyl-L-leucyl-L-phenylalanine-OMe (MLF) peptide in the solid state, and then used the X-ray structure to calculate the (13)C chemical shifts using the gauge including projector augmented wave (GIPAW) method, which accounts for the periodic nature of the crystal structure, obtaining an overall accuracy of 4.2 ppm. In order to understand the origin of the difference between experimental and calculated chemical shifts, we carried out first-principles molecular dynamics simulations to characterize the molecular motion of the MLF peptide on the picosecond time scale. We found that (13)C chemical shifts experience very rapid fluctuations of more than 20 ppm that are averaged out over less than 200 fs. Taking account of these fluctuations in the calculation of the chemical shifts resulted in an accuracy of 3.3 ppm. To investigate the effects of averaging over longer time scales we sampled the rotameric states populated by the MLF peptides in the solid state by performing a total of 5 micros classical molecular dynamics simulations. By averaging the chemical shifts over these rotameric states, we increased the accuracy of the chemical shift calculations to 3.0 ppm, with less than 1 ppm error in 10 out of 22 cases. These results suggests that better DFT-based predictions of chemical shifts of peptides and proteins will be achieved by developing improved computational strategies capable of taking into account the averaging process up to the millisecond time scale on which the chemical shift measurements report.

Application of unsymmetrical indirect covariance NMR methods to the computation of the (13)C <--> (15)N HSQC-IMPEACH and (13)C <--> (15)N HMBC-IMPEACH correlation spectra.

PubMed

Martin, Gary E; Hilton, Bruce D; Irish, Patrick A; Blinov, Kirill A; Williams, Antony J

2007-10-01

Utilization of long-range (1)H--(15)N heteronuclear chemical shift correlation has continually grown in importance since the first applications were reported in 1995. More recently, indirect covariance NMR methods have been introduced followed by the development of unsymmetrical indirect covariance processing methods. The latter technique has been shown to allow the calculation of hyphenated 2D NMR data matrices from more readily acquired nonhyphenated 2D NMR spectra. We recently reported the use of unsymmetrical indirect covariance processing to combine (1)H--(13)C GHSQC and (1)H--(15)N GHMBC long-range spectra to yield a (13)C--(15)N HSQC-HMBC chemical shift correlation spectrum that could not be acquired in a reasonable period of time without resorting to (15)N-labeled molecules. We now report the unsymmetrical indirect covariance processing of (1)H--(13)C GHMBC and (1)H--(15)N IMPEACH spectra to afford a (13)C--(15)N HMBC-IMPEACH spectrum that has the potential to span as many as six to eight bonds. Correlations for carbon resonances long-range coupled to a protonated carbon in the (1)H--(13)C HMBC spectrum are transferred via the long-range (1)H--(15)N coupling pathway in the (1)H--(15)N IMPEACH spectrum to afford a much broader range of correlation possibilities in the (13)C--(15)N HMBC-IMPEACH correlation spectrum. The indole alkaloid vincamine is used as a model compound to illustrate the application of the method. (c) 2007 John Wiley & Sons, Ltd.

Increased microbial functional diversity under long-term organic and integrated fertilization in a paddy soil.

PubMed

Ding, Long-Jun; Su, Jian-Qiang; Sun, Guo-Xin; Wu, Jin-Shui; Wei, Wen-Xue

2018-02-01

Microbes play key roles in diverse biogeochemical processes including nutrient cycling. However, responses of soil microbial community and functional genes to long-term integrated fertilization (chemical combined with organic fertilization) remain unclear. Here, we used pyrosequencing and a microarray-based GeoChip to explore the shifts of microbial community and functional genes in a paddy soil which received over 21-year fertilization with various regimes, including control (no fertilizer), rice straw (R), rice straw plus chemical fertilizer nitrogen (NR), N and phosphorus (NPR), NP and potassium (NPKR), and reduced rice straw plus reduced NPK (L-NPKR). Significant shifts of the overall soil bacterial composition only occurred in the NPKR and L-NPKR treatments, with enrichment of certain groups including Bradyrhizobiaceae and Rhodospirillaceae families that benefit higher productivity. All fertilization treatments significantly altered the soil microbial functional structure with increased diversity and abundances of genes for carbon and nitrogen cycling, in which NPKR and L-NPKR exhibited the strongest effect, while R exhibited the least. Functional gene structure and abundance were significantly correlated with corresponding soil enzymatic activities and rice yield, respectively, suggesting that the structural shift of the microbial functional community under fertilization might promote soil nutrient turnover and thereby affect yield. Overall, this study indicates that the combined application of rice straw and balanced chemical fertilizers was more pronounced in shifting the bacterial composition and improving the functional diversity toward higher productivity, providing a microbial point of view on applying a cost-effective integrated fertilization regime with rice straw plus reduced chemical fertilizers for sustainable nutrient management.

Burning fire-prone Mediterranean shrublands: immediate changes in soil microbial community structure and ecosystem functions.

PubMed

Goberna, M; García, C; Insam, H; Hernández, M T; Verdú, M

2012-07-01

Wildfires subject soil microbes to extreme temperatures and modify their physical and chemical habitat. This might immediately alter their community structure and ecosystem functions. We burned a fire-prone shrubland under controlled conditions to investigate (1) the fire-induced changes in the community structure of soil archaea, bacteria and fungi by analysing 16S or 18S rRNA gene amplicons separated through denaturing gradient gel electrophoresis; (2) the physical and chemical variables determining the immediate shifts in the microbial community structure; and (3) the microbial drivers of the change in ecosystem functions related to biogeochemical cycling. Prokaryotes and eukaryotes were structured by the local environment in pre-fire soils. Fire caused a significant shift in the microbial community structure, biomass C, respiration and soil hydrolases. One-day changes in bacterial and fungal community structure correlated to the rise in total organic C and NO(3)(-)-N caused by the combustion of plant residues. In the following week, bacterial communities shifted further forced by desiccation and increasing concentrations of macronutrients. Shifts in archaeal community structure were unrelated to any of the 18 environmental variables measured. Fire-induced changes in the community structure of bacteria, rather than archaea or fungi, were correlated to the enhanced microbial biomass, CO(2) production and hydrolysis of C and P organics. This is the first report on the combined effects of fire on the three biological domains in soils. We concluded that immediately after fire the biogeochemical cycling in Mediterranean shrublands becomes less conservative through the increased microbial biomass, activity and changes in the bacterial community structure.

Scalar relativistic computations of nuclear magnetic shielding and g-shifts with the zeroth-order regular approximation and range-separated hybrid density functionals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aquino, Fredy W.; Govind, Niranjan; Autschbach, Jochen

2011-10-01

Density functional theory (DFT) calculations of NMR chemical shifts and molecular g-tensors with Gaussian-type orbitals are implemented via second-order energy derivatives within the scalar relativistic zeroth order regular approximation (ZORA) framework. Nonhybrid functionals, standard (global) hybrids, and range-separated (Coulomb-attenuated, long-range corrected) hybrid functionals are tested. Origin invariance of the results is ensured by use of gauge-including atomic orbital (GIAO) basis functions. The new implementation in the NWChem quantum chemistry package is verified by calculations of nuclear shielding constants for the heavy atoms in HX (X=F, Cl, Br, I, At) and H2X (X = O, S, Se, Te, Po), and Temore » chemical shifts in a number of tellurium compounds. The basis set and functional dependence of g-shifts is investigated for 14 radicals with light and heavy atoms. The problem of accurately predicting F NMR shielding in UF6-nCln, n = 1 to 6, is revisited. The results are sensitive to approximations in the density functionals, indicating a delicate balance of DFT self-interaction vs. correlation. For the uranium halides, the results with the range-separated functionals are mixed.« less

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

PubMed

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

2016-04-01

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

Fully automatic assignment of small molecules' NMR spectra without relying on chemical shift predictions.

PubMed

Castillo, Andrés M; Bernal, Andrés; Patiny, Luc; Wist, Julien

2015-08-01

We present a method for the automatic assignment of small molecules' NMR spectra. The method includes an automatic and novel self-consistent peak-picking routine that validates NMR peaks in each spectrum against peaks in the same or other spectra that are due to the same resonances. The auto-assignment routine used is based on branch-and-bound optimization and relies predominantly on integration and correlation data; chemical shift information may be included when available to fasten the search and shorten the list of viable assignments, but in most cases tested, it is not required in order to find the correct assignment. This automatic assignment method is implemented as a web-based tool that runs without any user input other than the acquired spectra. Copyright © 2015 John Wiley & Sons, Ltd.

Synthesis, spectral studies and antimicrobial activities of some 2-naphthyl pyrazoline derivatives

NASA Astrophysics Data System (ADS)

Sakthinathan, S. P.; Vanangamudi, G.; Thirunarayanan, G.

A series of 2-naphthyl pyrazolines were synthesized by the cyclization of 2-naphthyl chalcones and phenylhydrazine hydrochloride in the presence of sodium acetate. The yields of pyrazoline derivatives are more than 80%. The synthesized pyrazolines were characterized by their physical constants, IR, 1H, 13C and MS spectra. From the IR and NMR spectra the Cdbnd N (cm-1) stretches, the pyrazoline ring proton chemical shifts (ppm) of δ, Hb and Hc and also the carbon chemical shifts (ppm) of δCdbnd N are correlated with Hammett substituent constants, F and R, and Swain-Lupton's parameters using single and multi-regression analyses. From the results of linear regression analysis, the effect of substituents on the group frequencies has been predicted. The antimicrobial activities of all synthesized pyrazolines have been studied.

Chemical shift in Lα, Lβ1, Lβ3,4, Lβ2,15, Lγ1 and Lγ2,3 emission lines of 47Ag, 48Cd and 50Sn compounds

NASA Astrophysics Data System (ADS)

Singh Kainth, Harpreet; Singh, Ranjit; Singh, Gurjot; Mehta, D.

2018-01-01

Positive and negative shifts in L shell emission lines of 47Ag, 48Cd and 50Sn elements in different chemical compounds were determined from their recorded X-ray emission spectra in high resolution wavelength dispersive X-ray fluorescence (WDXRF) spectrometer. In 47Ag compounds, the measured energy shifts in Lα X-ray emission line were in the ranges from (0.12 to 0.40) eV, Lβ1 (0.27 to 0.36) eV, Lβ3,4 (1.10 to 4.89) eV, Lγ1 (-0.09 to 1.13) eV and Lγ2,3 (-2.08 to 0.59) eV. Likewise, for 48Cd compounds, the estimated shifts in Lα X-ray emission lines were in the range (-0.27 to 0.69) eV, Lβ1 (0.50 to 2.06) eV, Lβ2,15 (0.12 to 0.79), Lβ3,4 (-0.62 to 1.79) eV, Lγ1 (0.10 to 1.35) eV and Lγ2,3 (-0.73 to 1.75) eV, while for 50Sn compounds, the measured shifts in Lα X-ray emission lines were in the range of (0.02 to 1.81) eV, Lβ1 (0.11 to 0.78) eV, Lβ2,15 (0.15 to 1.40), Lβ3,4 (0.17 to 2.01) eV, Lγ1 (0.09 to 1.08) eV and Lγ2,3 (0.17 to 1.40) eV respectively. The effective charges (qP, qS, qL and qB) were calculated by four different theoretical methods (Pauling method, Suchet method, Levine method and Batsonav method) and found to be linear dependent with the chemical shift. Further, the measured chemical shifts were correlated with bond length, relative line-width (FWHM), effective charge, electronegativity, number of ligands and Coster-Kronig (CK) transition processes.

Protein structure refinement using a quantum mechanics-based chemical shielding predictor.

PubMed

Bratholm, Lars A; Jensen, Jan H

2017-03-01

The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of a protein backbone and CB chemical shifts (ProCS15, PeerJ , 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1-0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiments that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differ in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural change may be due to force field deficiencies. The overall accuracy of the empirical methods are slightly improved by annealing the CHARMM structure with ProCS15, which may suggest that the minor structural changes introduced by ProCS15-based annealing improves the accuracy of the protein structures. Having established that QM-based chemical shift prediction can deliver the same accuracy as empirical shift predictors we hope this can help increase the accuracy of related approaches such as QM/MM or linear scaling approaches or interpreting protein structural dynamics from QM-derived chemical shift.

Characterization of Non-Innocent Metal Complexes Using Solid-State NMR Spectroscopy: o-Dioxolene Vanadium Complexes

PubMed Central

Chatterjee, Pabitra B.; Goncharov-Zapata, Olga; Quinn, Laurence L.; Hou, Guangjin; Hamaed, Hiyam; Schurko, Robert W.; Polenova, Tatyana; Crans, Debbie C.

2012-01-01

51V solid-state NMR (SSNMR) studies of a series of non-innocent vanadium(V) catechol complexes have been conducted to evaluate the possibility that 51V NMR observables, quadrupolar and chemical shift anisotropies, and electronic structures of such compounds can be used to characterize these compounds. The vanadium(V) catechol complexes described in these studies have relatively small quadrupolar coupling constants, which cover a surprisingly small range from 3.4 to 4.2 MHz. On the other hand, isotropic 51V NMR chemical shifts cover a wide range from −200 ppm to 400 ppm in solution and from −219 to 530 ppm in the solid state. A linear correlation of 51V NMR isotropic solution and solid-state chemical shifts of complexes containing non-innocent ligands is observed. These experimental results provide the information needed for the application of 51V SSNMR spectroscopy in characterizing the electronic properties of a wide variety of vanadium-containing systems, and in particular those containing non-innocent ligands and that have chemical shifts outside the populated range of −300 ppm to −700 ppm. The studies presented in this report demonstrate that the small quadrupolar couplings covering a narrow range of values reflect the symmetric electronic charge distribution, which is also similar across these complexes. These quadrupolar interaction parameters alone are not sufficient to capture the rich electronic structure of these complexes. In contrast, the chemical shift anisotropy tensor elements accessible from 51V SSNMR experiments are a highly sensitive probe of subtle differences in electronic distribution and orbital occupancy in these compounds. Quantum chemical (DFT) calculations of NMR parameters for [VO(hshed)(Cat)] yield 51V CSA tensor in reasonable agreement with the experimental results, but surprisingly, the calculated quadrupolar coupling constant is significantly greater than the experimental value. The studies demonstrate that substitution of the catechol ligand with electron donating groups results in an increase in the HOMO-LUMO gap and can be directly followed by an upfield shift for the vanadium catechol complex. In contrast, substitution of the catechol ligand with electron withdrawing groups results in a decrease in the HOMO-LUMO gap and can directly be followed by a downfield shift for the complex. The vanadium catechol complexes were used in this work because the 51V is a half-integer quadrupolar nucleus whose NMR observables are highly sensitive to the local environment. However, the results are general and could be extended to other redox active complexes that exhibit similar coordination chemistry as the vanadium catechol complexes. PMID:21842875

The 13C nuclear magnetic resonance in graphite intercalation compounds

NASA Technical Reports Server (NTRS)

Tsang, T.; Resing, H. A.

1985-01-01

The (13)C NMR chemical shifts of graphite intercalation compounds were calculated. For acceptor types, the shifts come mainly from the paramagnetic (Ramsey) intra-atomic terms. They are related to the gross features of the two-dimensional band structures. The calculated anisotropy is about -140 ppm and is independent of the finer details such as charge transfer. For donor types, the carbon 2p pi orbitals are spin-polarized because of mixing with metal conduction electrons, thus there is an additional dipolar contribution which may be correlated with the electronic specific heat. The general agreement with experimental data is satisfactory.

C-13 nuclear magnetic resonance in graphite intercalation compounds

NASA Technical Reports Server (NTRS)

Tsang, T.; Resing, H. A.

1985-01-01

The C-13 NMR chemical shifts of graphite intercalation compounds have been calculated. For acceptor types, the shifts come mainly from the paramagnetic (Ramsey) intra-atomic terms. They are related to the gross features of the two-dimensional band structures. The calculated anisotropy is about - 140 ppm and is independent of the finer details such as charge transfer. For donor types, the carbon 2p pi orbitals are spin-polarized because of mixing with metal-conduction electrons, thus there is an additional dipolar contribution which may be correlated with the electronic specific heat. The general agreement with experimental data is satisfactory.

Backbone amide 15N chemical shift tensors report on hydrogen bonding interactions in proteins: A magic angle spinning NMR study.

PubMed

Paramasivam, Sivakumar; Gronenborn, Angela M; Polenova, Tatyana

2018-08-01

Chemical shift tensors (CSTs) are an exquisite probe of local geometric and electronic structure. 15 N CST are very sensitive to hydrogen bonding, yet they have been reported for very few proteins to date. Here we present experimental results and statistical analysis of backbone amide 15 N CSTs for 100 residues of four proteins, two E. coli thioredoxin reassemblies (1-73-(U- 13 C, 15 N)/74-108-(U- 15 N) and 1-73-(U- 15 N)/74-108-(U- 13 C, 15 N)), dynein light chain 8 LC8, and CAP-Gly domain of the mammalian dynactin. The 15 N CSTs were measured by a symmetry-based CSA recoupling method, ROCSA. Our results show that the principal component δ 11 is very sensitive to the presence of hydrogen bonding interactions due to its unique orientation in the molecular frame. The downfield chemical shift change of backbone amide nitrogen nuclei with increasing hydrogen bond strength is manifested in the negative correlation of the principal components with hydrogen bond distance for both α-helical and β-sheet secondary structure elements. Our findings highlight the potential for the use of 15 N CSTs in protein structure refinement. Copyright © 2018 Elsevier Inc. All rights reserved.

Enhanced NMR Discrimination of Pharmaceutically Relevant Molecular Crystal Forms through Fragment-Based Ab Initio Chemical Shift Predictions.

PubMed

Hartman, Joshua D; Day, Graeme M; Beran, Gregory J O

2016-11-02

Chemical shift prediction plays an important role in the determination or validation of crystal structures with solid-state nuclear magnetic resonance (NMR) spectroscopy. One of the fundamental theoretical challenges lies in discriminating variations in chemical shifts resulting from different crystallographic environments. Fragment-based electronic structure methods provide an alternative to the widely used plane wave gauge-including projector augmented wave (GIPAW) density functional technique for chemical shift prediction. Fragment methods allow hybrid density functionals to be employed routinely in chemical shift prediction, and we have recently demonstrated appreciable improvements in the accuracy of the predicted shifts when using the hybrid PBE0 functional instead of generalized gradient approximation (GGA) functionals like PBE. Here, we investigate the solid-state 13 C and 15 N NMR spectra for multiple crystal forms of acetaminophen, phenobarbital, and testosterone. We demonstrate that the use of the hybrid density functional instead of a GGA provides both higher accuracy in the chemical shifts and increased discrimination among the different crystallographic environments. Finally, these results also provide compelling evidence for the transferability of the linear regression parameters mapping predicted chemical shieldings to chemical shifts that were derived in an earlier study.

Enhanced NMR Discrimination of Pharmaceutically Relevant Molecular Crystal Forms through Fragment-Based Ab Initio Chemical Shift Predictions

PubMed Central

2016-01-01

Chemical shift prediction plays an important role in the determination or validation of crystal structures with solid-state nuclear magnetic resonance (NMR) spectroscopy. One of the fundamental theoretical challenges lies in discriminating variations in chemical shifts resulting from different crystallographic environments. Fragment-based electronic structure methods provide an alternative to the widely used plane wave gauge-including projector augmented wave (GIPAW) density functional technique for chemical shift prediction. Fragment methods allow hybrid density functionals to be employed routinely in chemical shift prediction, and we have recently demonstrated appreciable improvements in the accuracy of the predicted shifts when using the hybrid PBE0 functional instead of generalized gradient approximation (GGA) functionals like PBE. Here, we investigate the solid-state 13C and 15N NMR spectra for multiple crystal forms of acetaminophen, phenobarbital, and testosterone. We demonstrate that the use of the hybrid density functional instead of a GGA provides both higher accuracy in the chemical shifts and increased discrimination among the different crystallographic environments. Finally, these results also provide compelling evidence for the transferability of the linear regression parameters mapping predicted chemical shieldings to chemical shifts that were derived in an earlier study. PMID:27829821

Rapid and reliable protein structure determination via chemical shift threading.

PubMed

Hafsa, Noor E; Berjanskii, Mark V; Arndt, David; Wishart, David S

2018-01-01

Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to generate high-resolution 3D protein structures. The key motivations behind using NMR chemical shifts for protein threading lie in the fact that they are easy to measure, they are available prior to 3D structure determination, and they contain vital structural information. The method we have developed uses not only sequence and chemical shift similarity but also chemical shift-derived secondary structure, shift-derived super-secondary structure, and shift-derived accessible surface area to generate a high quality protein structure regardless of the sequence similarity (or lack thereof) to a known structure already in the PDB. The method (called E-Thrifty) was found to be very fast (often < 10 min/structure) and to significantly outperform other shift-based or threading-based structure determination methods (in terms of top template model accuracy)-with an average TM-score performance of 0.68 (vs. 0.50-0.62 for other methods). Coupled with recent developments in chemical shift refinement, these results suggest that protein structure determination, using only NMR chemical shifts, is becoming increasingly practical and reliable. E-Thrifty is available as a web server at http://ethrifty.ca .

Fast Magic-Angle Spinning Three-Dimensional NMR Experiment for Simultaneously Probing H-H and N-H Proximities in Solids.

PubMed

Reddy, G N Manjunatha; Malon, Michal; Marsh, Andrew; Nishiyama, Yusuke; Brown, Steven P

2016-12-06

A fast magic-angle spinning (MAS, 70 kHz) solid-state NMR experiment is presented that combines 1 H Double-Quantum (DQ) and 14 N- 1 H HMQC (Heteronuclear Multiple-Quantum Coherence) pulse-sequence elements, so as to simultaneously probe H-H and N-H proximities in molecular solids. The proposed experiment can be employed in both two-dimensional (2D) and three-dimensional (3D) versions: first, a 2D 14 N HMQC-filtered 1 H-DQ experiment provides specific DQ-SQ correlation peaks for proton pairs that are in close proximities to the nitrogen sites, thereby achieving spectral filtration. Second, a proton-detected three-dimensional (3D) 1 H(DQ)- 14 N(SQ)- 1 H(SQ) experiment correlates 1 H(DQ)- 1 H(SQ) chemical shifts with 14 N shifts such that longer range N···H-H correlations are observed between protons and nitrogen atoms with internuclear NH distances exceeding 3 Å. Both 2D and 3D versions of the proposed experiment are demonstrated for an amino acid hydrochloride salt, l-histidine·HCl·H 2 O, and a DNA nucleoside, guanosine·2H 2 O. In the latter case, the achieved spectral filtration ensures that DQ cross peaks are only observed for guanine NH and CH8 1 H resonances and not ribose and water 1 H resonances, thus providing insight into the changes in the solid-state structure of this hydrate that occur over time; significant changes are observed in the NH and NH 2 1 H chemical shifts as compared to the freshly recrystallized sample previously studied by Reddy et al., Cryst. Growth Des. 2015, 15, 5945.

Synthesis, NMR, FT-IR, X-ray structural characterization, DFT analysis and isomerism aspects of 5-(2,6-dichlorobenzylidene)pyrimidine-2,4,6(1H,3H,5H)-trione.

PubMed

Barakat, Assem; Al-Najjar, Hany J; Al-Majid, Abdullah Mohammed; Soliman, Saied M; Mabkhot, Yahia Nasser; Shaik, Mohammed Rafi; Ghabbour, Hazem A; Fun, Hoong-Kun

2015-08-05

The synthesis and spectral characterization of the 5-(2,6-dichlorobenzylidene)pyrimidine-2,4,6(1H,3H,5H)-trione;3 was reported. The solid state molecular structure of 3 was studied using X-ray crystallography. The relative stabilities of the seven possible isomers of 3 were calculated by DFT/B3LYP method using 6-311 G(d,p) basis set. The calculated total energies and thermodynamic parameters were used to predict the relative stabilities of these isomers. The effect of solvent polarity on the relative stability of these isomers was studied at the same level of theory using PCM. It was found that the keto form, (T0), is the most stable isomer both in the gaseous state and solution. In solution, the calculated total energies of all isomers are decreased indicating that all isomers are stabilized by the solvent effect. The vibrational spectra of the most stable isomer, 3(T0) are calculated using the same level of theory and the results are compared with the experimentally measured FTIR spectra. Good correlation was obtained between the experimental and calculated vibrational frequencies (R(2)=0.9992). The electronic spectra of 3(T0) in gas phase as well as in solutions were calculated using the TD-DFT method. All the predicted electronic transitions showed very little spectral shifts and increase in the intensity of absorption due to solvent effect. Also the (1)H- and (13)C-NMR chemical shifts of the stable isomer were calculated and the results were correlated with the experimental data. Good correlations between the experimental and calculated chemical shifts were obtained. Copyright © 2015 Elsevier B.V. All rights reserved.

Combining multinuclear high-resolution solid-state MAS NMR and computational methods for resonance assignment of glutathione tripeptide.

PubMed

Sardo, Mariana; Siegel, Renée; Santos, Sérgio M; Rocha, João; Gomes, José R B; Mafra, Luis

2012-06-28

We present a complete set of experimental approaches for the NMR assignment of powdered tripeptide glutathione at natural isotopic abundance, based on J-coupling and dipolar NMR techniques combined with (1)H CRAMPS decoupling. To fully assign the spectra, two-dimensional (2D) high-resolution methods, such as (1)H-(13)C INEPT-HSQC/PRESTO heteronuclear correlations (HETCOR), (1)H-(1)H double-quantum (DQ), and (1)H-(14)N D-HMQC correlation experiments, have been used. To support the interpretation of the experimental data, periodic density functional theory calculations together with the GIPAW approach have been used to calculate the (1)H and (13)C chemical shifts. It is found that the shifts calculated with two popular plane wave codes (CASTEP and Quantum ESPRESSO) are in excellent agreement with the experimental results.

Quantitative Chemical Shift-Encoded MRI Is an Accurate Method to Quantify Hepatic Steatosis

PubMed Central

Kühn, Jens-Peter; Hernando, Diego; Mensel, Birger; Krüger, Paul C.; Ittermann, Till; Mayerle, Julia; Hosten, Norbert; Reeder, Scott B.

2014-01-01

Purpose To compare the accuracy of liver fat quantification using a three-echo chemical shift-encoded magnetic resonance imaging (MRI) technique without and with correction for confounders with spectroscopy (MRS) as the reference standard. Materials and Methods Fifty patients (23 women, mean age 56.6 ± 13.2 years) with fatty liver disease were enrolled. Patients underwent T2-corrected single-voxel MRS and a three-echo chemical shift-encoded gradient echo (GRE) sequence at 3.0T. MRI fat fraction (FF) was calculated without and with T2* and T1 correction and multispectral modeling of fat and compared with MRS-FF using linear regression. Results The spectroscopic range of liver fat was 0.11%–38.7%. Excellent correlation between MRS-FF and MRI-FF was observed when using T2* correction (R2=0.96). With use of T2* correction alone, the slope was significantly different from 1 (1.16 ± 0.03, P < 0.001) and the intercept was different from 0 (1.14% ± 0.50%, P < 0.023). This slope was significantly different than 1.0 when no T1 correction was used (P=0.001). When T2*, T1, and spectral complexity of fat were addressed, the results showed equivalence between fat quantification using MRI and MRS (slope: 1.02 ± 0.03, P=0.528; intercept: 0.26% ± 0.46%, P=0.572). Conclusion Complex three-echo chemical shift-encoded MRI is equivalent to MRS for quantifying liver fat, but only with correction for T2* decay and T1 recovery and use of spectral modeling of fat. This is necessary because T2* decay, T1 recovery, and multispectral complexity of fat are processes which may otherwise bias the measurements. PMID:24123655

Chemical shift magnetic resonance imaging is helpful in detecting hepatic steatosis but not fibrosis in patients with nonalcoholic fatty liver disease (NAFLD).

PubMed

Kalra, Naveen; Duseja, Ajay; Das, Ashim; Dhiman, Radha Krishan; Virmani, Vivek; Chawla, Yogesh; Singh, Paramjee; Khandelwal, Niranjan

2009-01-01

Imaging modalities have a role in the diagnosis of patients with nonalcoholic fatty liver disease. Aim of the present study was to evaluate the role of chemical shift magnetic resonance imaging in assessing hepatic steatosis and fibrosis in patients with nonalcoholic fatty liver disease. Chemical shift magnetic resonance imaging was done in 10 biopsy proven patients (7 females, mean age 41 +/- 9.2 years) with nonalcoholic fatty liver disease. Objective measurements of signal intensity (SI) were done and a ratio was calculated (SI out-of- phase liver/ SI out-of- phase kidney)/ (SI in- phase liver/ SI in-phase kidney). A lower ratio indicated a higher signal drop and hence higher fat content. The ratio was correlated with hepatic steatosis on histology (< 33% and > 33%). Patients were classified as having histological NASH or no NASH and MRI was assessed in diagnosing hepatic fibrosis as seen on liver histology. Six patients had > 33% hepatic steatosis on histology. Five patients (50%) had evidence of histological NASH. MRI was not helpful in differentiating patients with and without histological NASH. One patient amongst NASH patients did not have fibrosis, one had stage 1, 2 had stage 2 and one had stage 4 fibrosis. SI ratio ranged between 0.35-0.69 in 6 patients with steatosis > 33% and was in the range of 0.69-1.20 in four patients with steatosis < 33% on histology. Fibrotic changes seen in 4 patients on biopsy were not detected on MRI. Chemical shift MRI provides objective data on fat infiltration in patients with NAFLD without giving information about hepatic fibrosis.

Quantitative chemical shift-encoded MRI is an accurate method to quantify hepatic steatosis.

PubMed

Kühn, Jens-Peter; Hernando, Diego; Mensel, Birger; Krüger, Paul C; Ittermann, Till; Mayerle, Julia; Hosten, Norbert; Reeder, Scott B

2014-06-01

To compare the accuracy of liver fat quantification using a three-echo chemical shift-encoded magnetic resonance imaging (MRI) technique without and with correction for confounders with spectroscopy (MRS) as the reference standard. Fifty patients (23 women, mean age 56.6 ± 13.2 years) with fatty liver disease were enrolled. Patients underwent T2-corrected single-voxel MRS and a three-echo chemical shift-encoded gradient echo (GRE) sequence at 3.0T. MRI fat fraction (FF) was calculated without and with T2* and T1 correction and multispectral modeling of fat and compared with MRS-FF using linear regression. The spectroscopic range of liver fat was 0.11%-38.7%. Excellent correlation between MRS-FF and MRI-FF was observed when using T2* correction (R(2)  = 0.96). With use of T2* correction alone, the slope was significantly different from 1 (1.16 ± 0.03, P < 0.001) and the intercept was different from 0 (1.14% ± 0.50%, P < 0.023). This slope was significantly different than 1.0 when no T1 correction was used (P = 0.001). When T2*, T1, and spectral complexity of fat were addressed, the results showed equivalence between fat quantification using MRI and MRS (slope: 1.02 ± 0.03, P = 0.528; intercept: 0.26% ± 0.46%, P = 0.572). Complex three-echo chemical shift-encoded MRI is equivalent to MRS for quantifying liver fat, but only with correction for T2* decay and T1 recovery and use of spectral modeling of fat. This is necessary because T2* decay, T1 recovery, and multispectral complexity of fat are processes which may otherwise bias the measurements. Copyright © 2013 Wiley Periodicals, Inc.

A Short History of Three Chemical Shifts

ERIC Educational Resources Information Center

Nagaoka, Shin-ichi

2007-01-01

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

Protein structure refinement using a quantum mechanics-based chemical shielding predictor† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc04344e Click here for additional data file.

PubMed Central

2017-01-01

The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of a protein backbone and CB chemical shifts (ProCS15, PeerJ, 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1–0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiments that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differ in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural change may be due to force field deficiencies. The overall accuracy of the empirical methods are slightly improved by annealing the CHARMM structure with ProCS15, which may suggest that the minor structural changes introduced by ProCS15-based annealing improves the accuracy of the protein structures. Having established that QM-based chemical shift prediction can deliver the same accuracy as empirical shift predictors we hope this can help increase the accuracy of related approaches such as QM/MM or linear scaling approaches or interpreting protein structural dynamics from QM-derived chemical shift. PMID:28451325

Linear free energy relationships of the 1H and 13C NMR chemical shifts of 3-methylene-2-substituted-1,4-pentadienes

NASA Astrophysics Data System (ADS)

Valentić, Nataša V.; Vitnik, Željko; Kozhushkov, Sergei I.; de Meijere, Armin; Ušćumlić, Gordana S.; Juranić, Ivan O.

2005-06-01

Linear free energy relationships (LFER) were applied to the 1H and 13C NMR chemical shifts ( δN, N= 1H and 13C, respectively) in the unsaturated backbone of cross-conjugated trienes 3-methylene-2-substituted-1,4-pentadienes. The NMR data were correlated using five different LFER models, based on the mono, the dual and the triple substituent parameter (MSP, DSP and TSP, respectively) treatment. The simple and extended Hammett equations, and the three postulated unconventional LFER models obtained by adaptation of the later, were used. The geometry data, which are needed in Karplus-type and McConnell-type analysis, were obtained using semi-empirical MNDO-PM3 calculations. In correlating the data the TSP approach was more successful than the MSP and DSP approaches. The fact that the calculated molecular geometries allow accurate prediction of the NMR data confirms the validity of unconventional LFER models used. These results suggest the s- cis conformation of the cross-conjugated triene as the preferred one. Postulated unconventional DSP and TSP equations enable the assessment of electronic substituent effects in the presence of other interfering influences.

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

NASA Astrophysics Data System (ADS)

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

2010-07-01

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

Nuclear spin relaxation due to chemical shift anisotropy of gas-phase 129Xe.

PubMed

Hanni, Matti; Lantto, Perttu; Vaara, Juha

2011-08-14

Nuclear spin relaxation provides detailed dynamical information on molecular systems and materials. Here, first-principles modeling of the chemical shift anisotropy (CSA) relaxation time for the prototypic monoatomic (129)Xe gas is carried out, both complementing and predicting the results of NMR measurements. Our approach is based on molecular dynamics simulations combined with pre-parametrized ab initio binary nuclear shielding tensors, an "NMR force field". By using the Redfield relaxation formalism, the simulated CSA time correlation functions lead to spectral density functions that, for the first time, quantitatively determine the experimental spin-lattice relaxation times T(1). The quality requirements on both the Xe-Xe interaction potential and binary shielding tensor are investigated in the context of CSA T(1). Persistent dimers Xe(2) are found to be responsible for the CSA relaxation mechanism in the low-density limit of the gas, completely in line with the earlier experimental findings.

Spin-orbit effects on the (119)Sn magnetic-shielding tensor in solids: a ZORA/DFT investigation.

PubMed

Alkan, Fahri; Holmes, Sean T; Iuliucci, Robbie J; Mueller, Karl T; Dybowski, Cecil

2016-07-28

Periodic-boundary and cluster calculations of the magnetic-shielding tensors of (119)Sn sites in various co-ordination and stereochemical environments are reported. The results indicate a significant difference between the predicted NMR chemical shifts for tin(ii) sites that exhibit stereochemically-active lone pairs and tin(iv) sites that do not have stereochemically-active lone pairs. The predicted magnetic shieldings determined either with the cluster model treated with the ZORA/Scalar Hamiltonian or with the GIPAW formalism are dependent on the oxidation state and the co-ordination geometry of the tin atom. The inclusion of relativistic effects at the spin-orbit level removes systematic differences in computed magnetic-shielding parameters between tin sites of differing stereochemistries, and brings computed NMR shielding parameters into significant agreement with experimentally-determined chemical-shift principal values. Slight improvement in agreement with experiment is noted in calculations using hybrid exchange-correlation functionals.

Solution NMR characterization of magnetic/electronic properties of azide and cyanide-inhibited substrate complexes of human heme oxygenase: implications for steric ligand tilt.

PubMed

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.

Redox-dependent structure change and hyperfine nuclear magnetic resonance shifts in cytochrome c

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng, Yiquing; Roder, H.; Englander, S.W.

1990-04-10

Proton nuclear magnetic resonance assignments for reduced and oxidized equine cytochrome c show that many individual protons exhibit different chemical shifts in the two protein forms, reflecting diamagnetic shift effects due to structure change, and in addition contact and pseudocontact shifts that occur only in the paramagnetic oxidized form. To evaluate the chemical shift differences for structure change, the authors removed the pseudocontact shift contribution by a calculation based on knowledge of the electron spin g tensor. The g-tensor calculation, when repeated using only 12 available C{sub {alpha}}H proton resonances for cytochrom c from tuna, proved to be remarkably stable.more » The derived g tensor was then used together with spatial coordinates for the oxidized form to calculate the pseudocontact shift contribution to proton resonances at 400 identifiable sites throughout the protein, so that the redox-dependent chemical shift discrepancy, could be evaluated. Large residual changes in chemical shift define the Fermi contact shifts, where are found as expected to be limited to the immediate covalent structure of the heme and its ligands and to be asymmetrically distributed over the heme. The chemical shift discrepancies observed appear in the main to reflect structure-dependent diamagnetic shifts rather than hyperfine effects due to displacements in the pseudocontact shift field. Although 51 protons in 29 different residues exhibit significant chemical shift changes, the general impressions one of small structural adjustments to redox-dependent strain rather than sizeable structural displacements or rearrangements.« less

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

PubMed

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

2017-02-01

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

Silicon K-edge XANES spectra of silicate minerals

NASA Astrophysics Data System (ADS)

Li, Dien; Bancroft, G. M.; Fleet, M. E.; Feng, X. H.

1995-03-01

Silicon K-edge x-ray absorption near-edge structure (XANES) spectra of a selection of silicate and aluminosilicate minerals have been measured using synchrotron radiation (SR). The spectra are qualitatively interpreted based on MO calculation of the tetrahedral SiO{4/4-}cluster. The Si K-edge generally shifts to higher energy with increased polymerization of silicates by about 1.3 eV, but with considerable overlap for silicates of different polymerization types. The substitution of Al for Si shifts the Si K-edge to lower energy. The chemical shift of Si K-edge is also sensitive to cations in more distant atom shells; for example, the Si K-edge shifts to lower energy with the substitution of Al for Mg in octahedral sites. The shifts of the Si K-edge show weak correlation with average Si-O bond distance (dSi-O), Si-O bond valence (sSi-O) and distortion of SiO4 tetrahedra, due to the crystal structure complexity of silicate minerals and multiple factors effecting the x-ray absorption processes.

Single-crystal X-ray diffraction and NMR crystallography of a 1:1 cocrystal of di­thia­non and pyrimethanil

PubMed Central

Pöppler, Ann-Christin; Corlett, Emily K.; Pearce, Harriet; Seymour, Mark P.; Reid, Matthew; Montgomery, Mark G.

2017-01-01

A single-crystal X-ray diffraction structure of a 1:1 cocrystal of two fungicides, namely di­thia­non (DI) and pyrimethanil (PM), is reported [systematic name: 5,10-dioxo-5H,10H-naphtho­[2,3-b][1,4]dithiine-2,3-dicarbo­nitrile–4,6-dimethyl-N-phenyl­pyrimidin-2-amine (1/1), C14H4N2O2S2·C12H13N2]. Following an NMR crystallography approach, experimental solid-state magic angle spinning (MAS) NMR spectra are presented together with GIPAW (gauge-including projector augmented wave) calculations of NMR chemical shieldings. Specifically, experimental 1H and 13C chemical shifts are determined from two-dimensional 1H–13C MAS NMR correlation spectra recorded with short and longer contact times so as to probe one-bond C—H connectivities and longer-range C⋯H proximities, whereas H⋯H proximities are identified in a 1H double-quantum (DQ) MAS NMR spectrum. The performing of separate GIPAW calculations for the full periodic crystal structure and for isolated mol­ecules allows the determination of the change in chemical shift upon going from an isolated mol­ecule to the full crystal structure. For the 1H NMR chemical shifts, changes of 3.6 and 2.0 ppm correspond to inter­molecular N—H⋯O and C—H⋯O hydrogen bonding, while changes of −2.7 and −1.5 ppm are due to ring current effects associated with C—H⋯π inter­actions. Even though there is a close inter­molecular S⋯O distance of 3.10 Å, it is of note that the mol­ecule-to-crystal chemical shifts for the involved sulfur or oxygen nuclei are small. PMID:28257008

Theoretical Modeling of 99 Tc NMR Chemical Shifts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hall, Gabriel B.; Andersen, Amity; Washton, Nancy M.

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

Valley-orbit splitting in doped nanocrystalline silicon: k•p calculations

NASA Astrophysics Data System (ADS)

Belyakov, Vladimir A.; Burdov, Vladimir A.

2007-07-01

The valley-orbit splitting in silicon quantum dots with shallow donors has been theoretically studied. In particular, the chemical-shift calculation was carried out within the frames of k•p approximation for single- and many-donor cases. For both cases, the great value of the chemical shift has been obtained compared to its bulk value. Such increase of the chemical shift becomes possible due to the quantum confinement effect in a dot. It is shown for the single-donor case that the level splitting and chemical shift strongly depend on the dot radius and donor position inside the nanocrystal. In the many-donor case, the chemical shift is almost proportional to the number of donors.

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

PubMed

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

2012-03-07

Following the recognition that NMR chemical shifts can be used for protein structure determination, rapid advances have recently been made in methods for extending this strategy for proteins and protein complexes of increasing size and complexity. A remaining major challenge is to develop approaches to exploit the information contained in the chemical shifts about conformational fluctuations in native states of proteins. In this work we show that it is possible to determine an ensemble of conformations representing the free energy surface of RNase A using chemical shifts as replica-averaged restraints in molecular dynamics simulations. Analysis of this surface indicates that chemical shifts can be used to characterize the conformational equilibrium between the two major substates of this protein. © 2012 American Chemical Society

Criteria to average out the chemical shift anisotropy in solid-state NMR when irradiated with BABA I, BABA II, and C7 radiofrequency pulse sequences.

PubMed

Stephane Mananga, Eugene

2013-01-01

Floquet-Magnus expansion is used to study the effect of chemical shift anisotropy in solid-state NMR of rotating solids. The chemical shift interaction is irradiated with two types of radiofrequency pulse sequences: BABA and C7. The criteria for the chemical shift anisotropy to be averaged out in each rotor period are obtained. Copyright © 2013 Elsevier Inc. All rights reserved.

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

PubMed

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

2007-01-24

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

XRD and 29Si MAS-NMR spectroscopy across the β-Lu 2Si 2O 7- β-Y 2Si 2O 7 solid solution

NASA Astrophysics Data System (ADS)

Becerro, Ana I.; Escudero, Alberto

2005-01-01

Samples in the system Lu 2-xY xSi 2O 7 (0⩽ x⩽2) have been synthesized following the sol-gel method and calcined to 1300 °C, a temperature at which the β-polymorph is known to be the stable phase for the end-members Lu 2Si 2O 7 and Y 2Si 2O 7. The XRD patterns of all the compositions studied are compatible with the structure of the β-polymorph. Unit cell parameters are calculated as a function of composition from XRD patterns. They show a linear change with increasing Y content, which indicates a solid solubility of β-Y 2Si 2O 7 in β-Lu 2Si 2O 7 at 1300 °C. 29Si MAS NMR spectra of the different members of the system agree with the XRD results, showing a linear decrease of the 29Si chemical shift with increasing Y content. Finally, a correlation reported in the literature to predict 29Si chemical shifts in silicates is applied here to obtain the theoretical variation in 29Si chemical shift values in the system Lu 2Si 2O 7-Y 2Si 2O 7 and the results compare favorably with the values obtained experimentally.

Optimization of metabolite basis sets prior to quantitation in magnetic resonance spectroscopy: an approach based on quantum mechanics

NASA Astrophysics Data System (ADS)

Lazariev, A.; Allouche, A.-R.; Aubert-Frécon, M.; Fauvelle, F.; Piotto, M.; Elbayed, K.; Namer, I.-J.; van Ormondt, D.; Graveron-Demilly, D.

2011-11-01

High-resolution magic angle spinning (HRMAS) nuclear magnetic resonance (NMR) is playing an increasingly important role for diagnosis. This technique enables setting up metabolite profiles of ex vivo pathological and healthy tissue. The need to monitor diseases and pharmaceutical follow-up requires an automatic quantitation of HRMAS 1H signals. However, for several metabolites, the values of chemical shifts of proton groups may slightly differ according to the micro-environment in the tissue or cells, in particular to its pH. This hampers the accurate estimation of the metabolite concentrations mainly when using quantitation algorithms based on a metabolite basis set: the metabolite fingerprints are not correct anymore. In this work, we propose an accurate method coupling quantum mechanical simulations and quantitation algorithms to handle basis-set changes. The proposed algorithm automatically corrects mismatches between the signals of the simulated basis set and the signal under analysis by maximizing the normalized cross-correlation between the mentioned signals. Optimized chemical shift values of the metabolites are obtained. This method, QM-QUEST, provides more robust fitting while limiting user involvement and respects the correct fingerprints of metabolites. Its efficiency is demonstrated by accurately quantitating 33 signals from tissue samples of human brains with oligodendroglioma, obtained at 11.7 tesla. The corresponding chemical shift changes of several metabolites within the series are also analyzed.

Analysis of the Electronic Structure of the Special Pair of a Bacterial Photosynthetic Reaction Center by 13 C Photochemically Induced Dynamic Nuclear Polarization Magic-Angle Spinning NMR Using a Double-Quantum Axis.

PubMed

Najdanova, Marija; Gräsing, Daniel; Alia, A; Matysik, Jörg

2018-01-01

The origin of the functional symmetry break in bacterial photosynthesis challenges since several decades. Although structurally very similar, the two branches of cofactors in the reaction center (RC) protein complex act very differently. Upon photochemical excitation, an electron is transported along one branch, while the other remains inactive. Photochemically induced dynamic nuclear polarization (photo-CIDNP) magic-angle spinning (MAS) 13 C NMR revealed that the two bacteriochlorophyll cofactors forming the "Special Pair" donor dimer are already well distinguished in the electronic ground state. These previous studies are relying solely on 13 C- 13 C correlation experiments as radio-frequency-driven recoupling (RFDR) and dipolar-assisted rotational resonance (DARR). Obviously, the chemical-shift assignment is difficult in a dimer of tetrapyrrole macrocycles, having eight pyrrole rings of similar chemical shifts. To overcome this problem, an INADEQUATE type of experiment using a POST C7 symmetry-based approach is applied to selectively isotope-labeled bacterial RC of Rhodobacter (R.) sphaeroides wild type (WT). We, therefore, were able to distinguish unresolved sites of the macromolecular dimer. The obtained chemical-shift pattern is in-line with a concentric assembly of negative charge within the common center of the Special Pair supermolecule in the electronic ground state. © 2017 The American Society of Photobiology.

Identification of natural metabolites in mixture: a pattern recognition strategy based on (13)C NMR.

PubMed

Hubert, Jane; Nuzillard, Jean-Marc; Purson, Sylvain; Hamzaoui, Mahmoud; Borie, Nicolas; Reynaud, Romain; Renault, Jean-Hugues

2014-03-18

Because of their highly complex metabolite profile, the chemical characterization of bioactive natural extracts usually requires time-consuming multistep purification procedures to achieve the structural elucidation of pure individual metabolites. The aim of the present work was to develop a dereplication strategy for the identification of natural metabolites directly within mixtures. Exploiting the polarity range of metabolites, the principle was to rapidly fractionate a multigram quantity of a crude extract by centrifugal partition extraction (CPE). The obtained fractions of simplified chemical composition were subsequently analyzed by (13)C NMR. After automatic collection and alignment of (13)C signals across spectra, hierarchical clustering analysis (HCA) was performed for pattern recognition. As a result, strong correlations between (13)C signals of a single structure within the mixtures of the fraction series were visualized as chemical shift clusters. Each cluster was finally assigned to a molecular structure with the help of a locally built (13)C NMR chemical shift database. The proof of principle of this strategy was achieved on a simple model mixture of commercially available plant secondary metabolites and then applied to a bark extract of the African tree Anogeissus leiocarpus Guill. & Perr. (Combretaceae). Starting from 5 g of this genuine extract, the fraction series was generated by CPE in only 95 min. (13)C NMR analyses of all fractions followed by pattern recognition of (13)C chemical shifts resulted in the unambiguous identification of seven major compounds, namely, sericoside, trachelosperogenin E, ellagic acid, an epimer mixture of (+)-gallocatechin and (-)-epigallocatechin, 3,3'-di-O-methylellagic acid 4'-O-xylopyranoside, and 3,4,3'-tri-O-methylflavellagic acid 4'-O-glucopyranoside.

Sum-over-states density functional perturbation theory: Prediction of reliable 13C, 15N, and 17O nuclear magnetic resonance chemical shifts

NASA Astrophysics Data System (ADS)

Olsson, Lars; Cremer, Dieter

1996-11-01

Sum-over-states density functional perturbation theory (SOS-DFPT) has been used to calculate 13C, 15N, and 17O NMR chemical shifts of 20 molecules, for which accurate experimental gas-phase values are available. Compared to Hartree-Fock (HF), SOS-DFPT leads to improved chemical shift values and approaches the degree of accuracy obtained with second order Møller-Plesset perturbation theory (MP2). This is particularly true in the case of 15N chemical shifts where SOS-DFPT performs even better than MP2. Additional improvements of SOS-DFPT chemical shifts can be obtained by empirically correcting diamagnetic and paramagnetic contributions to compensate for deficiencies which are typical of DFT.

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

PubMed

Dumez, Jean-Nicolas; Pickard, Chris J

2009-03-14

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

Relative Configuration of Natural Products Using NMR Chemical Shifts

USDA-ARS?s Scientific Manuscript database

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

Comparison of brown and white adipose tissues in infants and children with chemical-shift-encoded water-fat MRI.

PubMed

Hu, Houchun H; Yin, Larry; Aggabao, Patricia C; Perkins, Thomas G; Chia, Jonathan M; Gilsanz, Vicente

2013-10-01

To compare fat-signal fractions (FFs) and T2* values between brown (BAT) and white (WAT) adipose tissue located within the supraclavicular fossa and subcutaneous depots, respectively. Twelve infants and 39 children were studied. Children were divided into lean and overweight/obese subgroups. Chemical-shift-encoded water-fat magnetic resonance imaging (MRI) was used to quantify FFs and T2* metrics in the supraclavicular and adjacent subcutaneous adipose tissue depots. Linear regression and t-tests were performed. Infants had lower supraclavicular FFs than children (P < 0.01) but T2* values were similar (P = 0.5). Lean children exhibited lower supraclavicular FFs and T2* values than overweight children (P < 0.01). In each individual infant and child, supraclavicular FFs were consistently lower than adjacent subcutaneous FFs. Supraclavicular T2* values were consistently lower than subcutaneous T2* values in children, but not in infants. FFs in both depots were positively correlated with age and weight in infants (P < 0.01). In children, they were correlated with weight and body mass index (BMI) (P < 0.01), but not age. Correlations between T2* and anthropometric variables existed in children (P < 0.01), but were absent in infants. Cross-sectional comparisons suggest variations in FF and T2* values in the supraclavicular and subcutaneous depots of infants and children, which are potentially indicative of physiological differences in adipose tissue fat content, amount, and metabolic activity. Copyright © 2013 Wiley Periodicals, Inc.

The correlation study of temperature distribution with the immunology response under laser radiation

NASA Astrophysics Data System (ADS)

Chen, Yichao; Nordquist, Robert E.; Naylor, Mark F.; Wu, Feng; Liu, Hong; Tesiram, Yasvir A.; Abbott, Andrew; Towner, Rheal A.; Chen, Wei R.

2008-02-01

The 3-D, in vivo temperature distributions within tumor-bearing rats were measured using Magnetic Resonance Imaging (MRI) technique. The in vivo thermal distributions of rats were measured using MRI chemical shift of water proton density. DMBA-4 tumor bearing rats are treated using laser photothermal therapy combined with immunoadjuvant under the observation of MRI. The thermal images and the immunological responses were studied and their relationships were investigated. The study of thermal distribution and correlation with the immunological response under laser treatment provided rich information with potential guidance for thermal-immunological therapy.

Efficient spectroscopic imaging by an optimized encoding of pre-targeted resonances

PubMed Central

Zhang, Zhiyong; Shemesh, Noam; Frydman, Lucio

2016-01-01

A “relaxation-enhanced” (RE) selective-excitation approach to acquire in vivo localized spectra with flat baselines and very good signal-to-noise ratios –particularly at high fields– has been recently proposed. As RE MRS targets a subset of a priori known resonances, new possibilities arise to acquire spectroscopic imaging data in a faster, more efficient manner. Hereby we present one such opportunity based on what we denominate Relaxation-Enhanced Chemical-shift-Encoded Spectroscopically-Separated (RECESS) imaging. RECESS delivers spectral/spatial correlations of various metabolites, by collecting a gradient echo train whose timing is defined by the chemical shifts of the various selectively excited resonances to be disentangled. Different sites thus impart distinct, coherent phase modulations on the images; condition number considerations allow one to disentangle these contributions of the various sites by a simple matrix inversion. The efficiency of the ensuing spectral/spatial correlation method is high enough to enable the examination of additional spatial axes via their phase encoding in CPMG-like spin-echo trains. The ensuing single-shot 1D spectral / 2D spatial RECESS method thus accelerates the acquisition of quality MRSI data by factors that, depending on the sensitivity, range between 2 and 50. This is illustrated with a number of phantom, of ex vivo and of in vivo acquisitions. PMID:26910285

Analysis of the temperature and pressure dependence of the 129Xe NMR chemical shift and signal intensity for the derivation of basic parameters of adsorption as applied to zeolite ZSM-5.

PubMed

Kawata, Yoko; Adachi, Yuko; Haga, Saori; Fukutomi, Junko; Imai, Hirohiko; Kimura, Atsuomi; Fujiwara, Hideaki

2007-12-01

Temperature and pressure dependences of the 129Xe NMR chemical shift and the signal intensity have been investigated using ZSM-5 as an adsorbent under routine conditions without using any high-pressure or especially high-temperature facilities. The use of a rigorously shielded system and a calibration sample for the signal intensity was found to be valuable to obtain reliable data about the chemical shift and the signal intensity. The 129Xe NMR data obtained between 0.05 and 1.5 atm and from 24 to 80 degrees C were analyzed based on the Dubinin-Radushkevich equation as well as the Langmuir type equation. In both analyses, chemical shift data succeeded only partially in providing the profile of adsorption, such as energetic aspects, surface area, saturated amount of Xe adsorption and specific parameters of 129Xe chemical shift. It was shown that the reliable total analysis was achieved when the chemical shift data were used together with the intensity data. Such an analysis of the chemical shift data, aided by the intensity data, will be useful in performing nano-material analysis on 129Xe NMR without invoking the traditional methodology of gravimetric or volumetric adsorption experiments.

Spatial fluorescence cross-correlation spectroscopy between core and ring pinholes

NASA Astrophysics Data System (ADS)

Blancquaert, Yoann; Delon, Antoine; Derouard, Jacques; Jaffiol, Rodolphe

2006-04-01

Fluorescence Correlation Spectroscopy (FCS) is an attractive method to measure molecular concentration, mobility parameters and chemical kinetics. However its ability to descriminate different diffusing species needs to be improved. Recently, we have proposed a simplified spatial Fluorescence cross Correlation Spectroscopy (sFCCS) method, allowing, with only one focused laser beam to obtain two confocal volumes spatially shifted. Now, we present a new sFCCS optical geometry where the two pinholes, a ring and core, are encapsulated one in the other. In this approach all physical and chemical processes that occur in a single volume, like singlet-triplet dynamics and photobleaching, can be eliminated; moreover, this new optical geometry optimises the collection of fluorescence. The first cross Correlation curves for Rhodamine 6G (Rh6G) in Ethanol are presented, in addition to the effect of the size of fluorescent particules (nano-beads, diameters : 20, 100 and 200 nm). The relative simplicity of the method leads us to propose sFCCS as an appropriate method for the determination of diffusion parameters of fluorophores in solution or cells. Nevertheless, progresses in the ingeniering of the optical Molecular Detection Efficiency volumes are highly desirable, in order to improve the descrimination between the cross correlated volumes.

Chemical Shifts of the Carbohydrate Binding Domain of Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum Mechanics/Molecular Mechanics Calculations.

PubMed

Kraus, Jodi; Gupta, Rupal; Yehl, Jenna; Lu, Manman; Case, David A; Gronenborn, Angela M; Akke, Mikael; Polenova, Tatyana

2018-03-22

Magic angle spinning NMR spectroscopy is uniquely suited to probe the structure and dynamics of insoluble proteins and protein assemblies at atomic resolution, with NMR chemical shifts containing rich information about biomolecular structure. Access to this information, however, is problematic, since accurate quantum mechanical calculation of chemical shifts in proteins remains challenging, particularly for 15 N H . Here we report on isotropic chemical shift predictions for the carbohydrate recognition domain of microcrystalline galectin-3, obtained from using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, implemented using an automated fragmentation approach, and using very high resolution (0.86 Å lactose-bound and 1.25 Å apo form) X-ray crystal structures. The resolution of the X-ray crystal structure used as an input into the AF-NMR program did not affect the accuracy of the chemical shift calculations to any significant extent. Excellent agreement between experimental and computed shifts is obtained for 13 C α , while larger scatter is observed for 15 N H chemical shifts, which are influenced to a greater extent by electrostatic interactions, hydrogen bonding, and solvation.

Error assessment in molecular dynamics trajectories using computed NMR chemical shifts.

PubMed

Koes, David R; Vries, John K

2017-01-01

Accurate chemical shifts for the atoms in molecular mechanics (MD) trajectories can be obtained from quantum mechanical (QM) calculations that depend solely on the coordinates of the atoms in the localized regions surrounding atoms of interest. If these coordinates are correct and the sample size is adequate, the ensemble average of these chemical shifts should be equal to the chemical shifts obtained from NMR spectroscopy. If this is not the case, the coordinates must be incorrect. We have utilized this fact to quantify the errors associated with the backbone atoms in MD simulations of proteins. A library of regional conformers containing 169,499 members was constructed from 6 model proteins. The chemical shifts associated with the backbone atoms in each of these conformers was obtained from QM calculations using density functional theory at the B3LYP level with a 6-311+G(2d,p) basis set. Chemical shifts were assigned to each backbone atom in each MD simulation frame using a template matching approach. The ensemble average of these chemical shifts was compared to chemical shifts from NMR spectroscopy. A large systematic error was identified that affected the 1 H atoms of the peptide bonds involved in hydrogen bonding with water molecules or peptide backbone atoms. This error was highly sensitive to changes in electrostatic parameters. Smaller errors affecting the 13 C a and 15 N atoms were also detected. We believe these errors could be useful as metrics for comparing the force-fields and parameter sets used in MD simulation because they are directly tied to errors in atomic coordinates.

Metathesis Activity Encoded in the Metallacyclobutane Carbon-13 NMR Chemical Shift Tensors

PubMed Central

2017-01-01

Metallacyclobutanes are an important class of organometallic intermediates, due to their role in olefin metathesis. They can have either planar or puckered rings associated with characteristic chemical and physical properties. Metathesis active metallacyclobutanes have short M–Cα/α′ and M···Cβ distances, long Cα/α′–Cβ bond length, and isotropic 13C chemical shifts for both early d0 and late d4 transition metal compounds for the α- and β-carbons appearing at ca. 100 and 0 ppm, respectively. Metallacyclobutanes that do not show metathesis activity have 13C chemical shifts of the α- and β-carbons at typically 40 and 30 ppm, respectively, for d0 systems, with upfield shifts to ca. −30 ppm for the α-carbon of metallacycles with higher dn electron counts (n = 2 and 6). Measurements of the chemical shift tensor by solid-state NMR combined with an orbital (natural chemical shift, NCS) analysis of its principal components (δ11 ≥ δ22 ≥ δ33) with two-component calculations show that the specific chemical shift of metathesis active metallacyclobutanes originates from a low-lying empty orbital lying in the plane of the metallacyclobutane with local π*(M–Cα/α′) character. Thus, in the metathesis active metallacyclobutanes, the α-carbons retain some residual alkylidene character, while their β-carbon is shielded, especially in the direction perpendicular to the ring. Overall, the chemical shift tensors directly provide information on the predictive value about the ability of metallacyclobutanes to be olefin metathesis intermediates. PMID:28776018

Novel 2D Triple-Resonance NMR Experiments for Sequential Resonance Assignments of Proteins

NASA Astrophysics Data System (ADS)

Ding, Keyang; Gronenborn, Angela M.

2002-06-01

We present 2D versions of the popular triple resonance HN(CO) CACB, HN(COCA)CACB, HN(CO)CAHA, and HN(COCA) CAHA experiments, commonly used for sequential resonance assignments of proteins. These experiments provide information about correlations between amino proton and nitrogen chemical shifts and the α- and β-carbon and α-proton chemical shifts within and between amino acid residues. Using these 2D spectra, sequential resonance assignments of H N, N, C α, C β, and H α nuclei are easily achieved. The resolution of these spectra is identical to the well-resolved 2D 15N- 1H HSQC and H(NCO)CA spectra, with slightly reduced sensitivity compared to their 3D and 4D versions. These types of spectra are ideally suited for exploitation in automated assignment procedures and thereby constitute a fast and efficient means for NMR structural determination of small and medium-sized proteins in solution in structural genomics programs.

Carbon X-ray absorption spectra of fluoroethenes and acetone: A study at the coupled cluster, density functional, and static-exchange levels of theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fransson, Thomas; Norman, Patrick; Coriani, Sonia

2013-03-28

Near carbon K-edge X-ray absorption fine structure spectra of a series of fluorine-substituted ethenes and acetone have been studied using coupled cluster and density functional theory (DFT) polarization propagator methods, as well as the static-exchange (STEX) approach. With the complex polarization propagator (CPP) implemented in coupled cluster theory, relaxation effects following the excitation of core electrons are accounted for in terms of electron correlation, enabling a systematic convergence of these effects with respect to electron excitations in the cluster operator. Coupled cluster results have been used as benchmarks for the assessment of propagator methods in DFT as well as themore » state-specific static-exchange approach. Calculations on ethene and 1,1-difluoroethene illustrate the possibility of using nonrelativistic coupled cluster singles and doubles (CCSD) with additional effects of electron correlation and relativity added as scalar shifts in energetics. It has been demonstrated that CPP spectra obtained with coupled cluster singles and approximate doubles (CC2), CCSD, and DFT (with a Coulomb attenuated exchange-correlation functional) yield excellent predictions of chemical shifts for vinylfluoride, 1,1-difluoroethene, trifluoroethene, as well as good spectral features for acetone in the case of CCSD and DFT. Following this, CPP-DFT is considered to be a viable option for the calculation of X-ray absorption spectra of larger {pi}-conjugated systems, and CC2 is deemed applicable for chemical shifts but not for studies of fine structure features. The CCSD method as well as the more approximate CC2 method are shown to yield spectral features relating to {pi}*-resonances in good agreement with experiment, not only for the aforementioned molecules but also for ethene, cis-1,2-difluoroethene, and tetrafluoroethene. The STEX approach is shown to underestimate {pi}*-peak separations due to spectral compressions, a characteristic which is inherent to this method.« less

Carbon X-ray absorption spectra of fluoroethenes and acetone: a study at the coupled cluster, density functional, and static-exchange levels of theory.

PubMed

Fransson, Thomas; Coriani, Sonia; Christiansen, Ove; Norman, Patrick

2013-03-28

Near carbon K-edge X-ray absorption fine structure spectra of a series of fluorine-substituted ethenes and acetone have been studied using coupled cluster and density functional theory (DFT) polarization propagator methods, as well as the static-exchange (STEX) approach. With the complex polarization propagator (CPP) implemented in coupled cluster theory, relaxation effects following the excitation of core electrons are accounted for in terms of electron correlation, enabling a systematic convergence of these effects with respect to electron excitations in the cluster operator. Coupled cluster results have been used as benchmarks for the assessment of propagator methods in DFT as well as the state-specific static-exchange approach. Calculations on ethene and 1,1-difluoroethene illustrate the possibility of using nonrelativistic coupled cluster singles and doubles (CCSD) with additional effects of electron correlation and relativity added as scalar shifts in energetics. It has been demonstrated that CPP spectra obtained with coupled cluster singles and approximate doubles (CC2), CCSD, and DFT (with a Coulomb attenuated exchange-correlation functional) yield excellent predictions of chemical shifts for vinylfluoride, 1,1-difluoroethene, trifluoroethene, as well as good spectral features for acetone in the case of CCSD and DFT. Following this, CPP-DFT is considered to be a viable option for the calculation of X-ray absorption spectra of larger π-conjugated systems, and CC2 is deemed applicable for chemical shifts but not for studies of fine structure features. The CCSD method as well as the more approximate CC2 method are shown to yield spectral features relating to π∗-resonances in good agreement with experiment, not only for the aforementioned molecules but also for ethene, cis-1,2-difluoroethene, and tetrafluoroethene. The STEX approach is shown to underestimate π∗-peak separations due to spectral compressions, a characteristic which is inherent to this method.

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

Surface chemical reactivity of ultrathin Pd(111) films on Ru(0001): Importance of orbital symmetry in the application of the d-band model

DOE PAGES

Yin, Xiangshi; Cooper, Valentino R.; Weitering, Hanno H.; ...

2015-09-22

The chemical bonding of adsorbate molecules on transition-metal surfaces is strongly influenced by the hybridization between the molecular orbitals and the metal d-band. The strength of this interaction is often correlated with the location of the metal d-band center relative to the Fermi level. Here, we exploit finite size effects in the electronic structure of ultrathin Pd(111) films grown on Ru(0001) to tune their reactivity by changing the film thickness one atom layer at a time, while keeping all other variables unchanged. Interestingly, while bulk Pd(111) is reactive toward oxygen, Pd(111) films below five monolayers are surprisingly inert. This observationmore » is fully in line with the d-band model prediction when applied to the orbitals involved in the bonding. The shift of the d-band center with film thickness is primarily attributed to shifts in the partial density of states associated with the 4d xz and 4d yz orbitals. This study provides an in-depth look into the orbital specific contributions to the surface chemical reactivity, providing new insights that could be useful in surface catalysis.« less

Characterization of Silicon Nanocrystal Surfaces by Multidimensional Solid-State NMR Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hanrahan, Michael P.; Fought, Ellie L.; Windus, Theresa L.

The chemical and photophysical properties of silicon nanocrystals (Si NCs) are strongly dependent on the chemical composition and structure of their surfaces. Here we use fast magic angle spinning (MAS) and proton detection to enable the rapid acquisition of dipolar and scalar 2D 1H– 29Si heteronuclear correlation (HETCOR) solid-state NMR spectra and reveal a molecular picture of hydride-terminated and alkyl-functionalized surfaces of Si NCs produced in a nonthermal plasma. 2D 1H– 29Si HETCOR and dipolar 2D 1H– 1H multiple-quantum correlation spectra illustrate that resonances from surface mono-, di-, and trihydride groups cannot be resolved, contrary to previous literature assignments. Insteadmore » the 2D NMR spectra illustrate that there is large distribution of 1H and 29Si chemical shifts for the surface hydride species in both the as-synthesized and functionalized Si NCs. However, proton-detected 1H– 29Si refocused INEPT experiments can be used to unambiguously differentiate NMR signals from the different surface hydrides. Varying the 29Si evolution time in refocused INEPT experiments and fitting the oscillation of the NMR signals allows for the relative populations of the different surface hydrides to be estimated. This analysis confirms that monohydride species are the predominant surface species on the as-synthesized Si NCs. A reduction in the populations of the di- and trihydrides is observed upon functionalization with alkyl groups, consistent with our previous hypothesis that the trihydride, or silyl (*SiH 3), group is primarily responsible for initiating surface functionalization reactions. Density functional theory (DFT) calculations were used to obtain quantum chemical structural models of the Si NC surface and reproduce the observed 1H and 29Si chemical shifts. Furthermore, the approaches outlined here will be useful to obtain a more detailed picture of surface structures for Si NCs and other hydride-passivated nanomaterials.« less

Characterization of Silicon Nanocrystal Surfaces by Multidimensional Solid-State NMR Spectroscopy

DOE PAGES

Hanrahan, Michael P.; Fought, Ellie L.; Windus, Theresa L.; ...

2017-11-22

The chemical and photophysical properties of silicon nanocrystals (Si NCs) are strongly dependent on the chemical composition and structure of their surfaces. Here we use fast magic angle spinning (MAS) and proton detection to enable the rapid acquisition of dipolar and scalar 2D 1H– 29Si heteronuclear correlation (HETCOR) solid-state NMR spectra and reveal a molecular picture of hydride-terminated and alkyl-functionalized surfaces of Si NCs produced in a nonthermal plasma. 2D 1H– 29Si HETCOR and dipolar 2D 1H– 1H multiple-quantum correlation spectra illustrate that resonances from surface mono-, di-, and trihydride groups cannot be resolved, contrary to previous literature assignments. Insteadmore » the 2D NMR spectra illustrate that there is large distribution of 1H and 29Si chemical shifts for the surface hydride species in both the as-synthesized and functionalized Si NCs. However, proton-detected 1H– 29Si refocused INEPT experiments can be used to unambiguously differentiate NMR signals from the different surface hydrides. Varying the 29Si evolution time in refocused INEPT experiments and fitting the oscillation of the NMR signals allows for the relative populations of the different surface hydrides to be estimated. This analysis confirms that monohydride species are the predominant surface species on the as-synthesized Si NCs. A reduction in the populations of the di- and trihydrides is observed upon functionalization with alkyl groups, consistent with our previous hypothesis that the trihydride, or silyl (*SiH 3), group is primarily responsible for initiating surface functionalization reactions. Density functional theory (DFT) calculations were used to obtain quantum chemical structural models of the Si NC surface and reproduce the observed 1H and 29Si chemical shifts. Furthermore, the approaches outlined here will be useful to obtain a more detailed picture of surface structures for Si NCs and other hydride-passivated nanomaterials.« less

Unraveling the meaning of chemical shifts in protein NMR.

PubMed

Berjanskii, Mark V; Wishart, David S

2017-11-01

Chemical shifts are among the most informative parameters in protein NMR. They provide wealth of information about protein secondary and tertiary structure, protein flexibility, and protein-ligand binding. In this report, we review the progress in interpreting and utilizing protein chemical shifts that has occurred over the past 25years, with a particular focus on the large body of work arising from our group and other Canadian NMR laboratories. More specifically, this review focuses on describing, assessing, and providing some historical context for various chemical shift-based methods to: (1) determine protein secondary and super-secondary structure; (2) derive protein torsion angles; (3) assess protein flexibility; (4) predict residue accessible surface area; (5) refine 3D protein structures; (6) determine 3D protein structures and (7) characterize intrinsically disordered proteins. This review also briefly covers some of the methods that we previously developed to predict chemical shifts from 3D protein structures and/or protein sequence data. It is hoped that this review will help to increase awareness of the considerable utility of NMR chemical shifts in structural biology and facilitate more widespread adoption of chemical-shift based methods by the NMR spectroscopists, structural biologists, protein biophysicists, and biochemists worldwide. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

Automated and assisted RNA resonance assignment using NMR chemical shift statistics

PubMed Central

Aeschbacher, Thomas; Schmidt, Elena; Blatter, Markus; Maris, Christophe; Duss, Olivier; Allain, Frédéric H.-T.; Güntert, Peter; Schubert, Mario

2013-01-01

The three-dimensional structure determination of RNAs by NMR spectroscopy relies on chemical shift assignment, which still constitutes a bottleneck. In order to develop more efficient assignment strategies, we analysed relationships between sequence and 1H and 13C chemical shifts. Statistics of resonances from regularly Watson–Crick base-paired RNA revealed highly characteristic chemical shift clusters. We developed two approaches using these statistics for chemical shift assignment of double-stranded RNA (dsRNA): a manual approach that yields starting points for resonance assignment and simplifies decision trees and an automated approach based on the recently introduced automated resonance assignment algorithm FLYA. Both strategies require only unlabeled RNAs and three 2D spectra for assigning the H2/C2, H5/C5, H6/C6, H8/C8 and H1′/C1′ chemical shifts. The manual approach proved to be efficient and robust when applied to the experimental data of RNAs with a size between 20 nt and 42 nt. The more advanced automated assignment approach was successfully applied to four stem-loop RNAs and a 42 nt siRNA, assigning 92–100% of the resonances from dsRNA regions correctly. This is the first automated approach for chemical shift assignment of non-exchangeable protons of RNA and their corresponding 13C resonances, which provides an important step toward automated structure determination of RNAs. PMID:23921634

United States Air Force Academy, Department of Chemistry Research: AY 1983-1984.

DTIC Science & Technology

1985-07-01

explored the anticipated relationship between Hammett (T values and chemical shift, and excel- lent correlations have been observed when Brown and Okamoto 0...benzylidene malononitriles. BromiA.ow and Brownlee (12) have suggested the use of benzonitriles for these determinations. The search for Hammett ...Vol. VI, pp. 777-824, Wiley-Interscience, New York, 1974, gives a recent critical review of the various Hammett constants. 10. T.B. Posner and C.D

NMR shielding calculations across the periodic table: diamagnetic uranium compounds. 2. Ligand and metal NMR.

PubMed

Schreckenbach, Georg

2002-12-16

In this and a previous article (J. Phys. Chem. A 2000, 104, 8244), the range of application for relativistic density functional theory (DFT) is extended to the calculation of nuclear magnetic resonance (NMR) shieldings and chemical shifts in diamagnetic actinide compounds. Two relativistic DFT methods are used, ZORA ("zeroth-order regular approximation") and the quasirelativistic (QR) method. In the given second paper, NMR shieldings and chemical shifts are calculated and discussed for a wide range of compounds. The molecules studied comprise uranyl complexes, [UO(2)L(n)](+/-)(q); UF(6); inorganic UF(6) derivatives, UF(6-n)Cl(n), n = 0-6; and organometallic UF(6) derivatives, UF(6-n)(OCH(3))(n), n = 0-5. Uranyl complexes include [UO(2)F(4)](2-), [UO(2)Cl(4)](2-), [UO(2)(OH)(4)](2-), [UO(2)(CO(3))(3)](4-), and [UO(2)(H(2)O)(5)](2+). For the ligand NMR, moderate (e.g., (19)F NMR chemical shifts in UF(6-n)Cl(n)) to excellent agreement [e.g., (19)F chemical shift tensor in UF(6) or (1)H NMR in UF(6-n)(OCH(3))(n)] has been found between theory and experiment. The methods have been used to calculate the experimentally unknown (235)U NMR chemical shifts. A large chemical shift range of at least 21,000 ppm has been predicted for the (235)U nucleus. ZORA spin-orbit appears to be the most accurate method for predicting actinide metal chemical shifts. Trends in the (235)U NMR chemical shifts of UF(6-n)L(n) molecules are analyzed and explained in terms of the calculated electronic structure. It is argued that the energy separation and interaction between occupied and virtual orbitals with f-character are the determining factors.

Visualising crystal packing interactions in solid-state NMR: Concepts and applications

NASA Astrophysics Data System (ADS)

Zilka, Miri; Sturniolo, Simone; Brown, Steven P.; Yates, Jonathan R.

2017-10-01

In this article, we introduce and apply a methodology, based on density functional theory and the gauge-including projector augmented wave approach, to explore the effects of packing interactions on solid-state nuclear magnetic resonance (NMR) parameters. A visual map derived from a so-termed "magnetic shielding contribution field" can be made of the contributions to the magnetic shielding of a specific site—partitioning the chemical shift to specific interactions. The relation to the established approaches of examining the molecule to crystal change in the chemical shift and the nuclear independent chemical shift is established. The results are applied to a large sample of 71 molecular crystals and three further specific examples from supermolecular chemistry and pharmaceuticals. This approach extends the NMR crystallography toolkit and provides insight into the development of both cluster based approaches to the predictions of chemical shifts and for empirical predictions of chemical shifts in solids.

Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins.

PubMed

Tamiola, Kamil; Mulder, Frans A A

2012-10-01

NMR spectroscopy offers the unique possibility to relate the structural propensities of disordered proteins and loop segments of folded peptides to biological function and aggregation behaviour. Backbone chemical shifts are ideally suited for this task, provided that appropriate reference data are available and idiosyncratic sensitivity of backbone chemical shifts to structural information is treated in a sensible manner. In the present paper, we describe methods to detect structural protein changes from chemical shifts, and present an online tool [ncSPC (neighbour-corrected Structural Propensity Calculator)], which unites aspects of several current approaches. Examples of structural propensity calculations are given for two well-characterized systems, namely the binding of α-synuclein to micelles and light activation of photoactive yellow protein. These examples spotlight the great power of NMR chemical shift analysis for the quantitative assessment of protein disorder at the atomic level, and further our understanding of biologically important problems.

Correlated electron-nuclear dynamics in above-threshold multiphoton ionization of asymmetric molecule.

PubMed

Wang, Zhuo; Li, Min; Zhou, Yueming; Lan, Pengfei; Lu, Peixiang

2017-02-20

The partition of the photon energy into the subsystems of molecules determines many photon-induced chemical and physical dynamics in laser-molecule interactions. The electron-nuclear energy sharing from multiphoton ionization of molecules has been used to uncover the correlated dynamics of the electron and fragments. However, most previous studies focus on symmetric molecules. Here we study the electron-nuclear energy sharing in strong-field photoionization of HeH 2+ by solving the one-dimensional time-dependent Schrödinger equation (TDSE). Compared with symmetric molecules, the joint electron-nuclear energy spectrum (JES) of HeH 2+ reveals an anomalous energy shift at certain nuclear energies, while it disappears at higher and lower nuclear energies. Through tracing the time evolution of the wavepacket of bound states, we identify that this energy shift originates from the joint effect of the Stark shift, associated with the permanent dipole, and the Autler-Townes effect due to the coupling of the 2pσ and 2sσ states in strong fields. The energy shift in the JES appears at certain nuclear distances only when both Stark effect and Autler-Townes effect play important roles. We further demonstrate that the electron-nuclei energy sharing can be controlled by varying laser intensity for asymmetric molecules, providing alternative approaches to manipulate photochemical reactions for more complex molecules.

Quantitative and qualitative shifts in defensive metabolites define chemical defense investment during leaf development in Inga, a genus of tropical trees.

PubMed

Wiggins, Natasha L; Forrister, Dale L; Endara, María-José; Coley, Phyllis D; Kursar, Thomas A

2016-01-01

Selective pressures imposed by herbivores are often positively correlated with investments that plants make in defense. Research based on the framework of an evolutionary arms race has improved our understanding of why the amount and types of defenses differ between plant species. However, plant species are exposed to different selective pressures during the life of a leaf, such that expanding leaves suffer more damage from herbivores and pathogens than mature leaves. We hypothesize that this differential selective pressure may result in contrasting quantitative and qualitative defense investment in plants exposed to natural selective pressures in the field. To characterize shifts in chemical defenses, we chose six species of Inga, a speciose Neotropical tree genus. Focal species represent diverse chemical, morphological, and developmental defense traits and were collected from a single site in the Amazonian rainforest. Chemical defenses were measured gravimetrically and by characterizing the metabolome of expanding and mature leaves. Quantitative investment in phenolics plus saponins, the major classes of chemical defenses identified in Inga, was greater for expanding than mature leaves (46% and 24% of dry weight, respectively). This supports the theory that, because expanding leaves are under greater selective pressure from herbivores, they rely more upon chemical defense as an antiherbivore strategy than do mature leaves. Qualitatively, mature and expanding leaves were distinct and mature leaves contained more total and unique metabolites. Intraspecific variation was greater for mature leaves than expanding leaves, suggesting that leaf development is canalized. This study provides a snapshot of chemical defense investment in a speciose genus of tropical trees during the short, few-week period of leaf development. Exploring the metabolome through quantitative and qualitative profiling enables a more comprehensive examination of foliar chemical defense investment.

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

PubMed Central

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

2013-01-01

We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3 JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding. PMID:24391900

Destructive impact of molecular noise on nanoscale electrochemical oscillators

NASA Astrophysics Data System (ADS)

Cosi, Filippo G.; Krischer, Katharina

2017-06-01

We study the loss of coherence of electrochemical oscillations on meso- and nanosized electrodes with numeric simulations of the electrochemical master equation for a prototypical electrochemical oscillator, the hydrogen peroxide reduction on Pt electrodes in the presence of halides. On nanoelectrodes, the electrode potential changes whenever a stochastic electron-transfer event takes place. Electrochemical reaction rate coefficients depend exponentially on the electrode potential and become thus fluctuating quantities as well. Therefore, also the transition rates between system states become time-dependent which constitutes a fundamental difference to purely chemical nanoscale oscillators. Three implications are demonstrated: (a) oscillations and steady states shift in phase space with decreasing system size, thereby also decreasing considerably the oscillating parameter regions; (b) the minimal number of molecules necessary to support correlated oscillations is more than 10 times as large as for nanoscale chemical oscillators; (c) the relation between correlation time and variance of the period of the oscillations predicted for chemical oscillators in the weak noise limit is only fulfilled in a very restricted parameter range for the electrochemical nano-oscillator.

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

PubMed

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

2014-02-01

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

Dual-echo, chemical shift gradient-echo magnetic resonance imaging to quantify hepatic steatosis: Implications for living liver donation.

PubMed

Rinella, Mary E; McCarthy, Richard; Thakrar, Kiran; Finn, John Paul; Rao, Sambasiva M; Koffron, Alan J; Abecassis, Michael; Blei, Andres T

2003-08-01

In living liver donation, a fatty liver poses risks for both recipient and donor. Currently, liver biopsy is the standard for assessing the presence and extent of steatosis. The goals of this study were to correlate a steatosis index derived from magnetic resonance imaging (MRI) to the histologic grade on biopsy as well as to determine the topographic distribution of steatosis within the liver. We examined the ability of dual-echo, chemical shift gradient-echo MRI to predict the degree of steatosis on liver biopsy. A total of 22 subjects received both a liver biopsy and detailed MRI evaluation. These individuals included 15 potential living donors and 7 patients with nonalcoholic fatty liver disease. MRI steatosis index was then compared with histologic grade on liver biopsy. The topographic distribution of hepatic steatosis was determined from those subjects in whom MRI detected hepatic steatosis. The steatosis index had a positive correlation with grade of steatosis on liver biopsy (correlation coefficient, 0.84). There was no significant variation in the degree of steatosis among segments. A steatosis index of >0.2 had good positive and negative predictive value for the presence of significant steatosis (>15%) on biopsy. Our quantitative MRI protocol can predict the degree of hepatic steatosis when it is minimal to moderate, and may obviate the need for liver biopsy for the purpose of quantification of steatosis in living donors. Fat saturation added to the MRI protocol may further improve diagnostic accuracy. This technique may be applicable to the larger population with hepatic steatosis.

Comparison of clinical semi-quantitative assessment of muscle fat infiltration with quantitative assessment using chemical shift-based water/fat separation in MR studies of the calf of post-menopausal women

PubMed Central

Nardo, Lorenzo; Karampinos, Dimitrios C.; Joseph, Gabby B.; Yap, Samuel P.; Baum, Thomas; Krug, Roland; Majumdar, Sharmila; Link, Thomas M.

2013-01-01

Objective The goal of this study was to compare the semi-quantitative Goutallier classification for fat infiltration with quantitative fat-fraction derived from a magnetic resonance imaging (MRI) chemical shift-based water/fat separation technique. Methods Sixty-two women (age 61±6 years), 27 of whom had diabetes, underwent MRI of the calf using a T1-weighted fast spin-echo sequence and a six-echo spoiled gradient-echo sequence at 3 T. Water/fat images and fat fraction maps were reconstructed using the IDEAL algorithm with T2* correction and a multi-peak model for the fat spectrum. Two radiologists scored fat infiltration on the T1-weighted images using the Goutallier classification in six muscle compartments. Spearman correlations between the Goutallier grades and the fat fraction were calculated; in addition, intra-observer and inter-observer agreement were calculated. Results A significant correlation between the clinical grading and the fat fraction values was found for all muscle compartments (P<0.0001, R values ranging from 0.79 to 0.88). Goutallier grades 0–4 had a fat fraction ranging from 3.5 to 19%. Intra-observer and inter-observer agreement values of 0.83 and 0.81 were calculated for the semi-quantitative grading. Conclusion Semi-quantitative grading of intramuscular fat and quantitative fat fraction were significantly correlated and both techniques had excellent reproducibility. However, the clinical grading was found to overestimate muscle fat. PMID:22411305

A sequential assignment procedure for proteins that have intermediate line widths in MAS NMR spectra: amyloid fibrils of human CA150.WW2.

PubMed

Becker, Johanna; Ferguson, Neil; Flinders, Jeremy; van Rossum, Barth-Jan; Fersht, Alan R; Oschkinat, Hartmut

2008-08-11

The second WW domain (WW2) of CA150, a human transcriptional activator, forms amyloid fibrils in vitro under physiological conditions. Based on experimental constraints from MAS NMR spectroscopy experiments, alanine scanning and electron microscopy, a structural model of CA150.WW2 amyloid fibrils was calculated earlier. Here, the assignment strategy is presented and suggested as a general approach for proteins that show intermediate line width. The (13)C,(13)C correlation experiments were recorded on fully or partially (13)C-labelled fibrils. The earlier (13)C assignment (26 residues) was extended to 34 of the 40 residues by direct (13)C-excitation experiments by using a deuterated sample that showed strongly improved line width. A 3D HNC-TEDOR (transferred-echo double-resonance) experiment with deuterated CA150.WW2 fibrils yielded 14 amide nitrogen and proton resonance assignments. The obtained chemical shifts were compared with the chemical shifts determined with the natively folded WW domain. TALOS (Torsion angle likelihood obtained from shift and sequence similarity) predictions confirmed that, under physiological conditions, the fibrillar form of CA150.WW2 adopts a significantly different beta structure than the native WW-domain fold.

Assessment of time to pregnancy and spontaneous abortion status following occupational exposure to organic solvents mixture.

PubMed

Attarchi, Mir Saeed; Ashouri, Monir; Labbafinejad, Yasser; Mohammadi, Saber

2012-04-01

Due to increasing usage of chemicals in various industries, occupational exposure of women with these materials is unavoidable. Nowadays, some studies indicate adverse effects of exposure to these chemicals, especially organic solvents on the reproductive system of females. This study aimed to assess the relationship between spontaneous abortion and occupational exposure to organic solvents mixture in pharmaceutical industry. This study was carried out in a pharmaceutical factory located in the suburb of Tehran in 2010. During the study, married women who were working in the factory laboratory units and had exposure to mixed organic solvents were compared with married women who were working in the packing units of the factory without occupational exposure to organic solvents in terms of spontaneous abortion frequency and duration of pregnancy using statistical methods. In this study, the frequency of spontaneous abortion in employees with and without exposure to organic solvents mixture was 10.7 and 2.9% respectively. This study showed that even after adjustment for confounding factors, there was a significant correlation between spontaneous abortion and occupational exposure to organic solvents mixture and this correlation increased with increasing levels of exposure to organic solvents. Also, a significant correlation was observed between occupational exposure to mixed organic solvents and waiting time to become pregnant (TTP). Furthermore, this study showed that even after adjustment for confounding variables, shift workers were significantly more affected by spontaneous abortion compared to daytime workers (P < 0.001). Also, in our study, synergistic effect between shift working and occupational exposure to organic solvents mixture on spontaneous abortion was seen. According to the results of this study, since there is probability of spontaneous abortion resulting from occupational exposure to various chemicals including organic solvents, recommendation to review the status of occupational exposure of workers can be helpful in improving fertility consultations and reproductive health.

Relativistic effects in the intermolecular interaction-induced nuclear magnetic resonance parameters of xenon dimer.

PubMed

Hanni, Matti; Lantto, Perttu; Ilias, Miroslav; Jensen, Hans Jorgen Aagaard; Vaara, Juha

2007-10-28

Relativistic effects on the (129)Xe nuclear magnetic resonance shielding and (131)Xe nuclear quadrupole coupling (NQC) tensors are examined in the weakly bound Xe(2) system at different levels of theory including the relativistic four-component Dirac-Hartree-Fock (DHF) method. The intermolecular interaction-induced binary chemical shift delta, the anisotropy of the shielding tensor Deltasigma, and the NQC constant along the internuclear axis chi( parallel) are calculated as a function of the internuclear distance. DHF shielding calculations are carried out using gauge-including atomic orbitals. For comparison, the full leading-order one-electron Breit-Pauli perturbation theory (BPPT) is applied using a common gauge origin. Electron correlation effects are studied at the nonrelativistic (NR) coupled-cluster singles and doubles with perturbational triples [CCSD(T)] level of theory. The fully relativistic second-order Moller-Plesset many-body perturbation (DMP2) theory is used to examine the cross coupling between correlation and relativity on NQC. The same is investigated for delta and Deltasigma by BPPT with a density functional theory model. A semiquantitative agreement between the BPPT and DHF binary property curves is obtained for delta and Deltasigma in Xe(2). For these properties, the currently most complete theoretical description is obtained by a piecewise approximation where the uncorrelated relativistic DHF results obtained close to the basis-set limit are corrected, on the one hand, for NR correlation effects and, on the other hand, for the BPPT-based cross coupling of relativity and correlation. For chi( parallel), the fully relativistic DMP2 results obtain a correction for NR correlation effects beyond MP2. The computed temperature dependence of the second virial coefficient of the (129)Xe nuclear shielding is compared to experiment in Xe gas. Our best results, obtained with the piecewise approximation for the binary chemical shift combined with the previously published state of the art theoretical potential energy curve for Xe(2), are in excellent agreement with the experiment for the first time.

Rotational and translational dynamics and their relation to hydrogen bond lifetimes in an ionic liquid by means of NMR relaxation time experiments and molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Strate, Anne; Neumann, Jan; Overbeck, Viviane; Bonsa, Anne-Marie; Michalik, Dirk; Paschek, Dietmar; Ludwig, Ralf

2018-05-01

We report a concerted theoretical and experimental effort to determine the reorientational dynamics as well as hydrogen bond lifetimes for the doubly ionic hydrogen bond +OH⋯O- in the ionic liquid (2-hydroxyethyl)trimethylammonium bis(trifluoromethylsulfonyl)imide [Ch][NTf2] by using a combination of NMR relaxation time experiments, density functional theory (DFT) calculations, and molecular dynamics (MD) simulations. Due to fast proton exchange, the determination of rotational correlation times is challenging. For molecular liquids, 17O-enhanced proton relaxation time experiments have been used to determine the rotational correlation times for the OH vectors in water or alcohols. As an alternative to those expensive isotopic substitution experiments, we employed a recently introduced approach which is providing access to the rotational dynamics from a single NMR deuteron quadrupolar relaxation time experiment. Here, the deuteron quadrupole coupling constants (DQCCs) are obtained from a relation between the DQCC and the δ1H proton chemical shifts determined from a set of DFT calculated clusters in combination with experimentally determined proton chemical shifts. The NMR-obtained rotational correlation times were compared to those obtained from MD simulations and then related to viscosities for testing the applicability of popular hydrodynamic models. In addition, hydrogen bond lifetimes were derived, using hydrogen bond population correlation functions computed from MD simulations. Here, two different time domains were observed: The short-time contributions to the hydrogen lifetimes and the reorientational correlation times have roughly the same size and are located in the picosecond range, whereas the long-time contributions decay with relaxation times in the nanosecond regime and are related to rather slow diffusion processes. The computed average hydrogen bond lifetime is dominated by the long-time process, highlighting the importance and longevity of hydrogen-bonded ion pairs in these ionic liquids.

Citronellal assumes a folded conformation in solution due to dispersion interactions: A joint NMR-DFT analysis

NASA Astrophysics Data System (ADS)

Nardini, Viviani; Dias, Luis Gustavo; Palaretti, Vinicius; da Silva, Gil Valdo José

2018-04-01

Citronellal, an acyclic monoterpenoid, is a small molecule suitable for systematic scanning of its conformational geometric parameters in solution or in the gas phase. We have studied the conformational distribution of citronellal by correlating its structure and theoretical chemical shifts with nuclear magnetic resonance data. Interestingly, folded conformations were the most relevant, as confirmed by NOE experiments. We concluded that the conformational distribution is due to intramolecular dispersion interactions.

Two-site jumps in dimethyl sulfone studied by one- and two-dimensional 17O NMR spectroscopy

NASA Astrophysics Data System (ADS)

Beerwerth, J.; Storek, M.; Greim, D.; Lueg, J.; Siegel, R.; Cetinkaya, B.; Hiller, W.; Zimmermann, H.; Senker, J.; Böhmer, R.

2018-03-01

Polycrystalline dimethyl sulfone is studied using central-transition oxygen-17 exchange NMR. The quadrupolar and chemical shift tensors are determined by combining quantum chemical calculations with line shape analyses of rigid-lattice spectra measured for stationary and rotating samples at several external magnetic fields. Quantum chemical computations predict that the largest principal axes of the chemical shift anisotropy and electrical field gradient tensors enclose an angle of about 73°. This prediction is successfully tested by comparison with absorption spectra recorded at three different external magnetic fields. The experimental one-dimensional motionally narrowed spectra and the two-dimensional exchange spectrum are compatible with model calculations involving jumps of the molecules about their two-fold symmetry axis. This motion is additionally investigated by means of two-time stimulated-echo spectroscopy which allows for a determination of motional correlation functions over a wider temperature range than previously reported using carbon and deuteron NMR. On the basis of suitable second-order quadrupolar frequency distributions, sin-sin stimulated-echo amplitudes are calculated for a two-site model in the limit of vanishing evolution time and compared with experimental findings. The present study thus establishes oxygen-17 NMR as a powerful method that will be particularly useful for the study of solids and liquids devoid of nuclei governed by first-order anisotropies.

Self-energy behavior away from the Fermi surface in doped Mott insulators.

PubMed

Merino, J; Gunnarsson, O; Kotliar, G

2016-02-03

We analyze self-energies of electrons away from the Fermi surface in doped Mott insulators using the dynamical cluster approximation to the Hubbard model. For large onsite repulsion, U, and hole doping, the magnitude of the self-energy for imaginary frequencies at the top of the band ([Formula: see text]) is enhanced with respect to the self-energy magnitude at the bottom of the band ([Formula: see text]). The self-energy behavior at these two [Formula: see text]-points is switched for electron doping. Although the hybridization is much larger for (0, 0) than for [Formula: see text], we demonstrate that this is not the origin of this difference. Isolated clusters under a downward shift of the chemical potential, [Formula: see text], at half-filling reproduce the overall self-energy behavior at (0, 0) and [Formula: see text] found in low hole doped embedded clusters. This happens although there is no change in the electronic structure of the isolated clusters. Our analysis shows that a downward shift of the chemical potential which weakly hole dopes the Mott insulator can lead to a large enhancement of the [Formula: see text] self-energy for imaginary frequencies which is not associated with electronic correlation effects, even in embedded clusters. Interpretations of the strength of electronic correlations based on self-energies for imaginary frequencies are, in general, misleading for states away from the Fermi surface.

Distal and proximal ligand interactions in heme proteins: Correlations between C-O and Fe-C vibrational frequencies, oxygen-17 and carbon-13 nuclear magnetic resonance chemical shifts, and oxygen-17 nuclear quadrupole coupling constants in C sup 17 O- and sup 13 CO-labeled species

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ki Deok Park; Guo, K.; Adebodun, F.

1991-03-05

The authors have obtained the oxygen-17 nuclear magnetic resonance (NMR) spectra of a variety of C{sup 17}O-labeled heme proteins, including sperm whale (Physeter catodon) myoglobin, two synthetic sperm whale myoglobin mutants (His E7 {yields} Val E7; His E7 {yields} Phe E7), adult human hemoglobin, rabbit (Oryctolagus cuniculus) hemoglobin, horseradish (Cochlearia armoracia) peroxidase isoenzymes A and C, and Caldariomyces fumago chloroperoxidase, in some cases as a function of pH, and have determined their isotropic {sup 17}O NMR chemical shifts, {delta}{sub i}, and spin-lattice relaxation times, T{sub 1}. They have also obtained similar results on a picket fence prophyrin. The results showmore » an excellent correlation between the infrared C-O vibrational frequencies, {nu}(C-O), and {delta}{sub i}, between {nu}(C-O) and the {sup 17}O nuclear quadrupole coupling constant, and as expected between e{sup 2}qQ/h and {delta}{sub i}. The results suggest the IR and NMR measurements reflect the same interaction, which is thought to be primarily the degree of {pi}-back-bonding from Fe d to CO {pi}* orbitals, as outlined previously.« less

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

NASA Astrophysics Data System (ADS)

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

2015-09-01

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

Fragment-based (13)C nuclear magnetic resonance chemical shift predictions in molecular crystals: An alternative to planewave methods.

PubMed

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

2015-09-14

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

First-principles calculations of Ti and O NMR chemical shift tensors in ferroelectric perovskites

NASA Astrophysics Data System (ADS)

Pechkis, Daniel; Walter, Eric; Krakauer, Henry

2011-03-01

Complementary chemical shift calculations were carried out with embedded clusters, using quantum chemistry methods, and with periodic boundary conditions, using the GIPAW approach within the Quantum Espresso package. Compared to oxygen chemical shifts, δ̂ (O), cluster calculations for δ̂ (Ti) were found to be more sensitive to size effects, termination, and choice of gaussian-type atomic basis set, while GIPAW results were found to be more sensitive to the pseudopotential construction. The two approaches complemented each other in optimizing these factors. We show that the two approaches yield comparable chemical shifts for suitably converged simulations, and results are compared with available experimental measurements. Supported by ONR.

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

NASA Astrophysics Data System (ADS)

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

1998-11-01

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

Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides.

PubMed

Sumowski, Chris Vanessa; Hanni, Matti; Schweizer, Sabine; Ochsenfeld, Christian

2014-01-14

The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for the example of a prototypical peptide, the 38-residue kaliotoxin KTX comprising 573 atoms. Despite the simplicity of empirical chemical shift prediction programs, the agreement with experimental results is rather good, underlining their usefulness. However, we show in our present work that they are highly insensitive to structural changes, which renders their use for validating predicted structures questionable. In contrast, quantum chemical methods show the expected high sensitivity to structural and electronic changes. This appears to be independent of the quantum chemical approach or the inclusion of solvent effects. For the latter, explicit solvent simulations with increasing number of snapshots were performed for two conformers of an eight amino acid sequence. In conclusion, the empirical approaches neither provide the expected magnitude nor the patterns of NMR chemical shifts determined by the clearly more costly ab initio methods upon structural changes. This restricts the use of empirical prediction programs in studies where peptide and protein structures are utilized for the NMR chemical shift evaluation such as in NMR refinement processes, structural model verifications, or calculations of NMR nuclear spin relaxation rates.

Visible Thermochromism in Vanadium Pentoxide Coatings.

PubMed

Kumar, Sunil; Qadir, Awais; Maury, Francis; Bahlawane, Naoufal

2017-06-28

Although di-vanadium pentoxide (V 2 O 5 ) has been a candidate of extensive research for over half a century, its intrinsic thermochromism has not been reported so far. Films of V 2 O 5 grown on silicon, glass, and metal substrates by metal organic chemical vapor deposition in this study exhibit a thermally induced perceptible color change from bright yellow to deep orange. Temperature-dependent UV-vis spectroscopy and X-ray diffraction allow the correlation between the reversible continuous red shift of the absorption and the anisotropic thermal expansion along the (001) direction, that is, perpendicular to the sheets constituting the layered structure. Furthermore, the possibility of tuning the thermochromic behavior was demonstrated via a chemical doping with chromium.

A high-resolution (13)C 3D CSA-CSA-CSA correlation experiment by means of magic angle turning.

PubMed

Hu, J Z; Ye, C; Pugmire, R J; Grant, D M

2000-08-01

It is shown in this paper that a previously reported 90 degrees sample flipping (13)C 2D CSA-CSA correlation experiment may be carried out alternatively by employing constant slow sample rotation about the magic angle axis and by synchronizing the read pulse to 13 of the rotor cycle. A high-resolution 3D CSA-CSA-CSA correlation experiment based on the magic angle turning technique is reported in which the conventional 90 degrees 2D CSA-CSA powder pattern for each carbon in a system containing a number of inequivalent carbons may be separated according to the isotropic chemical shift value. The technique is demonstrated on 1,2,3-trimethoxybenzene in which all of the overlapping powder patterns that cannot be segregated by the 2D CSA-CSA experiment are resolved successfully by the 3D CSA-CSA-CSA experiment, including even the two methoxy groups (M(1) and M(3)) whose isotropic shifts, confirmed by high-speed MAS, are separated by only 1 ppm. A difference of 4 ppm in the principal value component (delta(33)) between M(1) and M(3) is readily obtained. Copyright 2000 Academic Press.

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

NASA Astrophysics Data System (ADS)

Filatov, Michael; Cremer, Dieter

2003-07-01

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

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

PubMed

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

2014-07-01

The (1)H chemical shifts of 48 amides in DMSO solvent are assigned and presented. The solvent shifts Δδ (DMSO-CDCl3 ) are large (1-2 ppm) for the NH protons but smaller and negative (-0.1 to -0.2 ppm) for close range protons. A selection of the observed solvent shifts is compared with calculated shifts from the present model and from GIAO calculations. Those for the NH protons agree with both calculations, but other solvent shifts such as Δδ(CHO) are not well reproduced by the GIAO calculations. The (1)H chemical shifts of the amides in DMSO were analysed using a functional approach for near ( ≤ 3 bonds removed) protons and the electric field, magnetic anisotropy and steric effect of the amide group for more distant protons. The chemical shifts of the NH protons of acetanilide and benzamide vary linearly with the π density on the αN and βC atoms, respectively. The C=O anisotropy and steric effect are in general little changed from the values in CDCl3. The effects of substituents F, Cl, Me on the NH proton shifts are reproduced. The electric field coefficient for the protons in DMSO is 90% of that in CDCl3. There is no steric effect of the C=O oxygen on the NH proton in an NH…O=C hydrogen bond. The observed deshielding is due to the electric field effect. The calculated chemical shifts agree well with the observed shifts (RMS error of 0.106 ppm for the data set of 257 entries). Copyright © 2014 John Wiley & Sons, Ltd.

Theoretical and experimental NMR study of protopine hydrochloride isomers.

PubMed

Tousek, Jaromír; Malináková, Katerina; Dostál, Jirí; Marek, Radek

2005-07-01

The 1H and 13C NMR chemical shifts of cis- and trans-protopinium salts were measured and calculated. The calculations of the chemical shifts consisted of conformational analysis, geometry optimization (RHF/6-31G** method) and shielding constants calculations (B3LYP/6-31G** method). Based on the results of the quantum chemical calculations, two sets of experimental chemical shifts were assigned to the particular isomers. According to the experimental results, the trans-isomer is more stable and its population is approximately 68%. Copyright 2005 John Wiley & Sons, Ltd

Direct Binding of the Corrector VX-809 to Human CFTR NBD1: Evidence of an Allosteric Coupling between the Binding Site and the NBD1:CL4 Interface.

PubMed

Hudson, Rhea P; Dawson, Jennifer E; Chong, P Andrew; Yang, Zhengrong; Millen, Linda; Thomas, Philip J; Brouillette, Christie G; Forman-Kay, Julie D

2017-08-01

Understanding the mechanism of action of modulator compounds for the cystic fibrosis transmembrane conductance regulator (CFTR) is key for the optimization of therapeutics as well as obtaining insights into the molecular mechanisms of CFTR function. We demonstrate the direct binding of VX-809 to the first nucleotide-binding domain (NBD1) of human CFTR. Disruption of the interaction between C-terminal helices and the NBD1 core upon VX-809 binding is observed from chemical shift changes in the NMR spectra of residues in the helices and on the surface of β -strands S3, S9, and S10. Binding to VX-809 leads to a significant negative shift in NBD1 thermal melting temperature (T m ), pointing to direct VX-809 interaction shifting the NBD1 conformational equilibrium. An inter-residue correlation analysis of the chemical shift changes provides evidence of allosteric coupling between the direct binding site and the NBD1:CL4 interface, thus enabling effects on the interface in the absence of direct binding in that location. These NMR binding data and the negative T m shifts are very similar to those previously reported by us for binding of the dual corrector-potentiator CFFT-001 to NBD1 (Hudson et al., 2012), suggesting that the two compounds may share some aspects of their mechanisms of action. Although previous studies have shown an important role for VX-809 in modulating the conformation of the first membrane spanning domain (Aleksandrov et al., 2012; Ren et al., 2013), this additional mode of VX-809 binding provides insight into conformational dynamics and allostery within CFTR. Copyright © 2017 by The Author(s).

Further conventions for NMR shielding and chemical shifts IUPAC recommendations 2008.

PubMed

Harris, Robin K; Becker, Edwin D; Cabral De Menezes, Sonia M; Granger, Pierre; Hoffman, Roy E; Zilm, Kurt W

2008-03-01

IUPAC has published a number of recommendations regarding the reporting of nuclear magnetic resonance (NMR) data, especially chemical shifts. The most recent publication [Pure Appl. Chem. 73, 1795 (2001)] recommended that tetramethylsilane (TMS) serve as a universal reference for reporting the shifts of all nuclides, but it deferred recommendations for several aspects of this subject. This document first examines the extent to which the (1)H shielding in TMS itself is subject to change by variation in temperature, concentration, and solvent. On the basis of recently published results, it has been established that the shielding of TMS in solution [along with that of sodium-3-(trimethylsilyl)propanesulfonate, DSS, often used as a reference for aqueous solutions] varies only slightly with temperature but is subject to solvent perturbations of a few tenths of a part per million (ppm). Recommendations are given for reporting chemical shifts under most routine experimental conditions and for quantifying effects of temperature and solvent variation, including the use of magnetic susceptibility corrections and of magic-angle spinning (MAS). This document provides the first IUPAC recommendations for referencing and reporting chemical shifts in solids, based on high-resolution MAS studies. Procedures are given for relating (13)C NMR chemical shifts in solids to the scales used for high-resolution studies in the liquid phase. The notation and terminology used for describing chemical shift and shielding tensors in solids are reviewed in some detail, and recommendations are given for best practice.

Further conventions for NMR shielding and chemical shifts (IUPAC Recommendations 2008).

PubMed

Harris, Robin K; Becker, Edwin D; De Menezes, Sonia M Cabral; Granger, Pierre; Hoffman, Roy E; Zilm, Kurt W

2008-06-01

IUPAC has published a number of recommendations regarding the reporting of nuclear magnetic resonance (NMR) data, especially chemical shifts. The most recent publication [Pure Appl. Chem. 73, 1795 (2001)] recommended that tetramethylsilane (TMS) serve as a universal reference for reporting the shifts of all nuclides, but it deferred recommendations for several aspects of this subject. This document first examines the extent to which the (1)H shielding in TMS itself is subject to change by variation in temperature, concentration, and solvent. On the basis of recently published results, it has been established that the shielding of TMS in solution [along with that of sodium-3-(trimethylsilyl)propanesulfonate, DSS, often used as a reference for aqueous solutions] varies only slightly with temperature but is subject to solvent perturbations of a few tenths of a part per million (ppm). Recommendations are given for reporting chemical shifts under most routine experimental conditions and for quantifying effects of temperature and solvent variation, including the use of magnetic susceptibility corrections and of magic-angle spinning (MAS). This document provides the first IUPAC recommendations for referencing and reporting chemical shifts in solids, based on high-resolution MAS studies. Procedures are given for relating (13)C NMR chemical shifts in solids to the scales used for high-resolution studies in the liquid phase. The notation and terminology used for describing chemical shift and shielding tensors in solids are reviewed in some detail, and recommendations are given for best practice. Copyright (c) 2008 John Wiley & Sons, Ltd

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

2013-10-08

Complex tellurides, such as doped PbTe, GeTe, and their alloys, are among the best thermoelectric materials. Knowledge of the change in 125Te NMR chemical shift due to bonding to dopant or “solute” atoms is useful for determination of phase composition, peak assignment, and analysis of local bonding. We have measured the 125Te NMR chemical shifts in PbTe-based alloys, Pb 1-xGe xTe and Pb 1-xSn xTe, which have a rocksalt-like structure, and analyzed their trends. For low x, several peaks are resolved in the 22-kHz MAS 125Te NMR spectra. A simple linear trend in chemical shifts with the number of Pbmore » neighbors is observed. No evidence of a proposed ferroelectric displacement of Ge atoms in a cubic PbTe matrix is detected at low Ge concentrations. The observed chemical shift trends are compared with the results of DFT calculations, which confirm the linear dependence on the composition of the first-neighbor shell. The data enable determination of the composition of various phases in multiphase telluride materials. They also provide estimates of the 125Te chemical shifts of GeTe and SnTe (+970 and +400±150 ppm, respectively, from PbTe), which are otherwise difficult to access due to Knight shifts of many hundreds of ppm in neat GeTe and SnTe.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Metaxas, Athena E.; Cort, John R.

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

The converse approach to NMR chemical shifts from first-principles: application to finite and infinite aromatic compounds

NASA Astrophysics Data System (ADS)

Thonhauser, T.; Ceresoli, D.; Marzari, N.

2009-03-01

We present first-principles, density-functional theory calculations of the NMR chemical shifts for polycyclic aromatic hydrocarbons, starting with benzene and increasing sizes up to the one- and two-dimensional infinite limits of graphene ribbons and sheets. Our calculations are performed using a combination of the recently developed theory of orbital magnetization in solids, and a novel approach to NMR calculations where chemical shifts are obtained from the derivative of the orbital magnetization with respect to a microscopic, localized magnetic dipole. Using these methods we study on equal footing the ^1H and ^13C shifts in benzene, pyrene, coronene, in naphthalene, anthracene, naphthacene, and pentacene, and finally in graphene, graphite, and an infinite graphene ribbon. Our results show very good agreement with experiments and allow us to characterize the trends for the chemical shifts as a function of system size.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nagamura, Naoka, E-mail: NAGAMURA.Naoka@nims.go.jp; Kitada, Yuta; Honma, Itaru

2015-06-22

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

Chemical (knight) shift distortions of quadrupole-split deuteron powder spectra in solids

NASA Astrophysics Data System (ADS)

Torgeson, D. R.; Schoenberger, R. J.; Barnes, R. G.

In strong magnetic fields (e.g., 8 Tesla) anisotropy of the shift tensor (chemical or Knight shift) can alter the spacings of the features of quadrupole-split deuteron spectra of polycrystalline samples. Analysis of powder spectra yields both correct quadrupole coupling and symmetry parameters and all the components of the shift tensor. Synthetic and experimental examples are given to illustrate such behavior.

Indirect detection of infinite-speed MAS solid-state NMR spectra

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perras, Frédéric A.; Venkatesh, Amrit; Hanrahan, Michael P.

Heavy spin-1/2 nuclides are known to possess very large chemical shift anisotropies that can challenge even the most advanced magic-angle-spinning (MAS) techniques. Wide manifolds of overlapping spinning sidebands and insufficient excitation bandwidths often obfuscate meaningful spectral information and force the use of static, low-resolution solid-state (SS)NMR methods for the characterization of materials. In order to address these issues, we have merged fast-magic-angle-turning (MAT) and dipolar heteronuclear multiple-quantum coherence (D-HMQC) experiments to obtain D-HMQC-MAT pulse sequences which enable the rapid acquisition of 2D SSNMR spectra that correlate isotropic 1H chemical shifts to the indirectly detected isotropic “infinite-MAS” spectra of heavy spin-1/2more » nuclides. Furthermore, for these nuclides, the combination of fast MAS and 1H detection provides a high sensitivity, which rivals the DNP-enhanced ultra-wideline SSNMR. The new pulse sequences were used to determine the Pt coordination environments in a complex mixture of decomposition products of transplatin and in a metal-organic framework with Pt ions coordinated to the linker ligands.« less

Indirect detection of infinite-speed MAS solid-state NMR spectra

DOE PAGES

Perras, Frédéric A.; Venkatesh, Amrit; Hanrahan, Michael P.; ...

2017-01-18

Heavy spin-1/2 nuclides are known to possess very large chemical shift anisotropies that can challenge even the most advanced magic-angle-spinning (MAS) techniques. Wide manifolds of overlapping spinning sidebands and insufficient excitation bandwidths often obfuscate meaningful spectral information and force the use of static, low-resolution solid-state (SS)NMR methods for the characterization of materials. In order to address these issues, we have merged fast-magic-angle-turning (MAT) and dipolar heteronuclear multiple-quantum coherence (D-HMQC) experiments to obtain D-HMQC-MAT pulse sequences which enable the rapid acquisition of 2D SSNMR spectra that correlate isotropic 1H chemical shifts to the indirectly detected isotropic “infinite-MAS” spectra of heavy spin-1/2more » nuclides. Furthermore, for these nuclides, the combination of fast MAS and 1H detection provides a high sensitivity, which rivals the DNP-enhanced ultra-wideline SSNMR. The new pulse sequences were used to determine the Pt coordination environments in a complex mixture of decomposition products of transplatin and in a metal-organic framework with Pt ions coordinated to the linker ligands.« less

Distinguishing polymorphs of the semiconducting pigment copper phthalocyanine by solid-state NMR and Raman spectroscopy.

PubMed

Shaibat, Medhat A; Casabianca, Leah B; Siberio-Pérez, Diana Y; Matzger, Adam J; Ishii, Yoshitaka

2010-04-08

Cu(II)(phthalocyanine) (CuPc) is broadly utilized as an archetypal molecular semiconductor and is the most widely used blue printing pigment. CuPc crystallizes in six different forms; the chemical and physical properties are substantially modulated by its molecular packing among these polymorphs. Despite the growing importance of this system, spectroscopic identification of different polymorphs for CuPc has posed difficulties. This study presents the first example of spectroscopic distinction of alpha- and beta-forms of CuPc, the most widely used polymorphs, by solid-state NMR (SSNMR) and Raman spectroscopy. (13)C high-resolution SSNMR spectra of alpha- and beta-CuPc using very-fast magic angle spinning (VFMAS) at 20 kHz show that hyperfine shifts sensitively reflect polymorphs of CuPc. The experimental results were confirmed by ab initio chemical shift calculations. (13)C and (1)H SSNMR relaxation times of alpha- and beta-CuPc under VFMAS also showed marked differences, presumably because of the difference in electronic spin correlation times in the two forms. Raman spectroscopy also provided another reliable method of differentiation between the two polymorphs.

First principles NMR calculations of phenylphosphinic acid C 6H 5HPO(OH): Assignments, orientation of tensors by local field experiments and effect of molecular motion

NASA Astrophysics Data System (ADS)

Gervais, C.; Coelho, C.; Azaı¨s, T.; Maquet, J.; Laurent, G.; Pourpoint, F.; Bonhomme, C.; Florian, P.; Alonso, B.; Guerrero, G.; Mutin, P. H.; Mauri, F.

2007-07-01

The complete set of NMR parameters for 17O enriched phenylphosphinic acid C 6H 5HP ∗O( ∗OH) is calculated from first principles by using the Gauge Including Projected Augmented Wave (GIPAW) approach [C.J. Pickard, F. Mauri, All-electron magnetic response with pseudopotentials: NMR chemical shifts, Phys. Rev. B 63 (2001) 245101/1-245101/13]. The analysis goes beyond the successful assignment of the spectra for all nuclei ( 1H, 13C, 17O, 31P), as: (i) the 1H CSA (chemical shift anisotropy) tensors (magnitude and orientation) have been interpreted in terms of H bonding and internuclear distances. (ii) CSA/dipolar local field correlation experiments have allowed the orientation of the direct P-H bond direction in the 31P CSA tensor to be determined. Experimental and calculated data were compared. (iii) The overestimation of the calculated 31P CSA has been explained by local molecular reorientation and confirmed by low temperature static 1H → 31P CP experiments.

First-principles calculations of finite temperature Sc and O NMR parameters in Pb(Sc2/3W1/3)O3

NASA Astrophysics Data System (ADS)

Krakauer, Henry; Walter, Eric J.; Ellden, Jeremy; Hoatson, Gina L.; Vold, Robert L.

2012-02-01

Understanding the dynamics of complex relaxor ferroelectrics is important to characterizing their large electromechanical coupling. Preliminary NMR measurements of Sc electric-field-gradients (EFG) in Pb(Sc2/3W1/3)O3 (PSW) show a strong temperature dependence in the range T = 250 - 330 K. To understand this behavior, we use the first-principles GIPAWootnotetextC. J. Pickard and F. Mauri, Phys. Rev. B 63, 245101 (2001); method within the Quantum Espresso (QE) packageootnotetextP. Giannozzi et al., Journal of Physics: Condensed Matter 21, 395502 (2009) to calculate ^45Sc and ^17O chemical-shifts and EFG tensors. To study finite temperature effects, we incorporate the thermal expansion of the lattice and sample thermal disorder, using the phonon degrees of freedom. As in our previous studies of perovksites,ootnotetextD. L. Pechkis, E. J. Walter, and H. Krakauer. J. Chem. Phys. 135, 114507 (2011); ibid. 131, 184511 (2009) we show that the ^17O chemical shifts in PSW also exhibit a linear correlation with the nearest-neighbor B-O bond length.

Indirect detection of infinite-speed MAS solid-state NMR spectra

NASA Astrophysics Data System (ADS)

Perras, Frédéric A.; Venkatesh, Amrit; Hanrahan, Michael P.; Goh, Tian Wei; Huang, Wenyu; Rossini, Aaron J.; Pruski, Marek

2017-03-01

Heavy spin-1/2 nuclides are known to possess very large chemical shift anisotropies that can challenge even the most advanced magic-angle-spinning (MAS) techniques. Wide manifolds of overlapping spinning sidebands and insufficient excitation bandwidths often obfuscate meaningful spectral information and force the use of static, low-resolution solid-state (SS)NMR methods for the characterization of materials. To address these issues, we have merged fast-magic-angle-turning (MAT) and dipolar heteronuclear multiple-quantum coherence (D-HMQC) experiments to obtain D-HMQC-MAT pulse sequences which enable the rapid acquisition of 2D SSNMR spectra that correlate isotropic 1H chemical shifts to the indirectly detected isotropic "infinite-MAS" spectra of heavy spin-1/2 nuclides. For these nuclides, the combination of fast MAS and 1H detection provides a high sensitivity, which rivals the DNP-enhanced ultra-wideline SSNMR. The new pulse sequences were used to determine the Pt coordination environments in a complex mixture of decomposition products of transplatin and in a metal-organic framework with Pt ions coordinated to the linker ligands.

Design and chemical synthesis of iodine-containing molecules for application to solar-pumped I* lasers

NASA Technical Reports Server (NTRS)

Shiner, C. S.

1986-01-01

The design and chemical synthesis of new media for solar pumped iodine molecule lasers are explored. In an effort to prepare an iodo fluorocarbon compound absorbing strongly at 300 nm or above, the synthesis of perfluoro allylic iodides was investigated. These compounds furnish especially stable allylic radicals upon photodissociation. The desired red shift is anticipated in the absorption maximum could correlate with increasing radical stability. This expectation was based upon the analysis, previously reported, of the structures and absorption maxima of compounds studied earlier. A previously unknown substance was prepared, a prototypical target molecule, perfluoro-3-iodocyclopent-1-ene. It was obtained by reaction of perfluorocyclopentene with sulfur trioxide under the influence of antimony pentafluoride catalyst, followed by treatment of the resulting allylic fluorosulfonate with sodium iodide in sulfoland solvent. Preliminary data indicate that the absorption maximum for the iodo fluorocarbon is not shifted significantly to longer wavelength. It is not certain whether this result reflects an unexpected influence of the cyclic structure upon the position of the absorption maximum.

Measurements of relative chemical shift tensor orientations in solid-state NMR: new slow magic angle spinning dipolar recoupling experiments.

PubMed

Jurd, Andrew P S; Titman, Jeremy J

2009-08-28

Solid-state NMR experiments can be used to determine conformational parameters, such as interatomic distances and torsion angles. The latter can be obtained from measurements of the relative orientation of two chemical shift tensors, if the orientation of these with respect to the surrounding bonds is known. In this paper, a new rotor-synchronized magic angle spinning (MAS) dipolar correlation experiment is described which can be used in this way. Because the experiment requires slow MAS rates, a novel recoupling sequence, designed using symmetry principles, is incorporated into the mixing period. This recoupling sequence is based in turn on a new composite cyclic pulse referred to as COAST (for combined offset and anisotropy stabilization). The new COAST-C7(2)(1) sequence is shown to give good theoretical and experimental recoupling efficiency, even when the CSA far exceeds the MAS rate. In this regime, previous recoupling sequences, such as POST-C7(2)(1), exhibit poor recoupling performance. The effectiveness of the new method has been explored by a study of the dipeptide L-phenylalanyl-L-phenylalanine.

IR and NMR spectral studies of 4-bromo-1-naphthyl chalcones-assessment of substituent effects

NASA Astrophysics Data System (ADS)

Thirunarayanan, G.; Gopalakrishnan, M.; Vanangamudi, G.

2007-07-01

Infrared νCO (cm -1) of s-cis and s-trans frequencies and nuclear magnetic resonance chemical shifts δ1H (ppm) of H-α and H-β, δ13C (ppm) of C-α and C-β data were assigned from their respective spectra of a series of various substituted styryl 4-bromo-1-naphthyl chalcones. These values are correlated with various Hammett substituent constants. From the results of statistical analysis, the effect of substituents can be explained.

Quantification of Absolute Fat Mass by Magnetic Resonance Imaging: a Validation Study against Chemical Analysis

PubMed Central

Hu, Houchun H.; Li, Yan; Nagy, Tim R.; Goran, Michael I.; Nayak, Krishna S.

2011-01-01

Objective To develop a magnetic resonance imaging (MRI)-based approach for quantifying absolute fat mass in organs, muscles, and adipose tissues, and to validate its accuracy against reference chemical analysis (CA). Methods Chemical-shift imaging can accurately decompose water and fat signals from the acquired MRI data. A proton density fat fraction (PDFF) can be computed from the separated images, and reflects the relative fat content on a voxel-by-voxel basis. The PDFF is mathematically closely related to the fat mass fraction and can be converted to absolute fat mass in grams by multiplying by the voxel volume and the mass density of fat. In this validation study, 97 freshly excised and unique samples from four pigs, comprising of organs, muscles, and adipose and lean tissues were imaged by MRI and then analyzed independently by CA. Linear regression was used to assess correlation, agreement, and measurement differences between MRI and CA. Results Considering all 97 samples, a strong correlation and agreement was obtained between MRI and CA-derived fat mass (slope = 1.01, intercept = 1.99g, r2 = 0.98, p < 0.01). The mean difference d between MRI and CA was 2.17±3.40g. MRI did not exhibit any tendency to under or overestimate CA (p > 0.05). When considering samples from each pig separately, the results were (slope = 1.05, intercept = 1.11g, r2 = 0.98, d = 2.66±4.36g), (slope = 0.99, intercept = 2.33g, r2 = 0.99, d = 1.88±2.68g), (slope = 1.07, intercept = 1.52g, r2 = 0.96, d = 2.73±2.50g), and (slope=0.92, intercept=2.84g, r2 = 0.97, d = 1.18±3.90g), respectively. Conclusion Chemical-shift MRI and PDFF provides an accurate means of determining absolute fat mass in organs, muscles, and adipose and lean tissues. PMID:23204926

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hartman, Joshua D.; Beran, Gregory J. O., E-mail: gregory.beran@ucr.edu; Monaco, Stephen

2015-09-14

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

A unique, fast-forwards rotating schedule with 12-h long shifts prevents chronic sleep debt.

PubMed

Fischer, Dorothee; Vetter, Céline; Oberlinner, Christoph; Wegener, Sven; Roenneberg, Till

2016-01-01

Sleep debt--together with circadian misalignment--is considered a central factor for adverse health outcomes associated with shift work. Here, we describe in detail sleep-wake behavior in a fast-forward rotating 12-h shift schedule, which involves at least 24 hours off after each shift and thus allows examining the role of immediate recovery after shift-specific sleep debt. Thirty-five participants at two chemical plants in Germany were chronotyped using the Munich ChronoType Questionnaire for Shift-Workers (MCTQ(Shift)) and wore actimeters throughout the two-week study period. From these actimetry recordings, we computed sleep and nap duration, social jetlag (a measure of circadian misalignment), and the daily timing of activity and sleep (center of gravity and mid-sleep, respectively). We observed that the long off-work periods between each shift create a fast alternation between shortened (mean ± standard deviation, 5h 17min ± 56min) and extended (8h 25min ± 72min) sleep episodes resulting in immanent reductions of sleep debt. Additionally, extensive napping of early chronotypes (up to 3 hours before the night shift) statistically compensated short sleep durations after the night shift. Partial rank correlations showed chronotype-dependent patterns of sleep and activity that were similar to those previously described in 8-h schedules; however, sleep before the day shift did not differ between chronotypes. Our findings indicate that schedules preventing a build-up of chronic sleep debt may reduce detrimental effects of shift work irrespective of shift duration. Prospective studies are needed to further elucidate the relationship between sleep, the circadian system, and health and safety hazards.

Computational and spectroscopic data correlation study of N,N'-bisarylmalonamides (Part II).

PubMed

Arsovski, Violeta M; Božić, Bojan Đ; Mirković, Jelena M; Vitnik, Vesna D; Vitnik, Željko J; Petrović, Slobodan D; Ušćumlić, Gordana S; Mijin, Dušan Ž

2015-09-01

To complement a previous UV study, we present a quantitative evaluation of substituent effects on spectroscopic data ((1)H and (13)C NMR chemical shifts as well as FT-IR absorption frequency) applied to N,N'-bisarylmalonamides, using simple and extended Hammett equations as well as the Swain-Lupton equation. Furthermore, the DFT CAM-B3LYP/6-311+G(d,p) method was applied to study the impact of different solvents on the geometry of the molecules and their spectral data. Additionally, experimental data are correlated with theoretical results; excellent linear dependence was obtained. The overall results presented in this paper show that N,N'-bisarylmalonamides are prominent candidates for model molecules.

Gray matter correlates of set-shifting among neurodegenerative disease, mild cognitive impairment, and healthy older adults

PubMed Central

PA, JUDY; POSSIN, KATHERINE L.; WILSON, STEPHEN M.; QUITANIA, LOVINGLY C.; KRAMER, JOEL H.; BOXER, ADAM L.; WEINER, MICHAEL W.; JOHNSON, JULENE K.

2010-01-01

There is increasing recognition that set-shifting, a form of cognitive control, is mediated by different neural structures. However, these regions have not yet been carefully identified as many studies do not account for the influence of component processes (e.g., motor speed). We investigated gray matter correlates of set-shifting while controlling for component processes. Using the Design Fluency (DF), Trail Making Test (TMT), and Color Word Interference (CWI) subtests from the Delis-Kaplan Executive Function System (D-KEFS), we investigated the correlation between set-shifting performance and gray matter volume in 160 subjects with neurodegenerative disease, mild cognitive impairment, and healthy older adults using voxel-based morphometry. All three set-shifting tasks correlated with multiple, widespread gray matter regions. After controlling for the component processes, set-shifting performance correlated with focal regions in prefrontal and posterior parietal cortices. We also identified bilateral prefrontal cortex and the right posterior parietal lobe as common sites for set-shifting across the three tasks. There was a high degree of multicollinearity between the set-shifting conditions and the component processes of TMT and CWI, suggesting DF may better isolate set-shifting regions. Overall, these findings highlight the neuroanatomical correlates of set-shifting and the importance of controlling for component processes when investigating complex cognitive tasks. PMID:20374676

Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds

PubMed Central

Geng, Haifeng; Tran-Gyamfi, Mary B.; Lane, Todd W.; Sale, Kenneth L.; Yu, Eizadora T.

2016-01-01

Open microalgae cultures host a myriad of bacteria, creating a complex system of interacting species that influence algal growth and health. Many algal microbiota studies have been conducted to determine the relative importance of bacterial taxa to algal culture health and physiological states, but these studies have not characterized the interspecies relationships in the microbial communities. We subjected Nanochroloropsis salina cultures to multiple chemical treatments (antibiotics and quorum sensing compounds) and obtained dense time-series data on changes to the microbial community using 16S gene amplicon metagenomic sequencing (21,029,577 reads for 23 samples) to measure microbial taxa-taxa abundance correlations. Short-term treatment with antibiotics resulted in substantially larger shifts in the microbiota structure compared to changes observed following treatment with signaling compounds and glucose. We also calculated operational taxonomic unit (OTU) associations and generated OTU correlation networks to provide an overview of possible bacterial OTU interactions. This analysis identified five major cohesive modules of microbiota with similar co-abundance profiles across different chemical treatments. The Eigengenes of OTU modules were examined for correlation with different external treatment factors. This correlation-based analysis revealed that culture age (time) and treatment types have primary effects on forming network modules and shaping the community structure. Additional network analysis detected Alteromonadeles and Alphaproteobacteria as having the highest centrality, suggesting these species are “keystone” OTUs in the microbial community. Furthermore, we illustrated that the chemical tropodithietic acid, which is secreted by several species in the Alphaproteobacteria taxon, is able to drastically change the structure of the microbiota within 3 h. Taken together, these results provide valuable insights into the structure of the microbiota associated with N. salina cultures and how these structures change in response to chemical perturbations. PMID:27507966

Molecular dynamics averaging of Xe chemical shifts in liquids.

PubMed

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

2004-11-15

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Basse, Kristoffer; Shankar, Ravi; Bjerring, Morten

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

Density functional study of the 13C NMR chemical shifts in small-to-medium-diameter infinite single-walled carbon nanotubes.

PubMed

Zurek, Eva; Pickard, Chris J; Walczak, Brian; Autschbach, Jochen

2006-11-02

NMR chemical shifts were calculated for semiconducting (n,0) single-walled carbon nanotubes (SWNTs) with n ranging from 7 to 17. Infinite isolated SWNTs were calculated using a gauge-including projector-augmented plane-wave (GIPAW) approach with periodic boundary conditions and density functional theory (DFT). In order to minimize intertube interactions in the GIPAW computations, an intertube distance of 8 A was chosen. For the infinite tubes, we found a chemical shift range of over 20 ppm for the systems considered here. The SWNT family with lambda = mod(n, 3) = 0 has much smaller chemical shifts compared to the other two families with lambda = 1 and lambda = 2. For all three families, the chemical shifts decrease roughly inversely proportional to the tube's diameter. The results were compared to calculations of finite capped SWNT fragments using a gauge-including atomic orbital (GIAO) basis. Direct comparison of the two types of calculations could be made if benzene was used as the internal (computational) reference. The NMR chemical shifts of finite SWNTs were found to converge very slowly, if at all, to the infinite limit, indicating that capping has a strong effect (at least for the (9,0) tubes) on the calculated properties. Our results suggest that (13)C NMR has the potential for becoming a useful tool in characterizing SWNT samples.

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

PubMed

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

2014-09-14

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

Comparison of clinical semi-quantitative assessment of muscle fat infiltration with quantitative assessment using chemical shift-based water/fat separation in MR studies of the calf of post-menopausal women.

PubMed

Alizai, Hamza; Nardo, Lorenzo; Karampinos, Dimitrios C; Joseph, Gabby B; Yap, Samuel P; Baum, Thomas; Krug, Roland; Majumdar, Sharmila; Link, Thomas M

2012-07-01

The goal of this study was to compare the semi-quantitative Goutallier classification for fat infiltration with quantitative fat-fraction derived from a magnetic resonance imaging (MRI) chemical shift-based water/fat separation technique. Sixty-two women (age 61 ± 6 years), 27 of whom had diabetes, underwent MRI of the calf using a T1-weighted fast spin-echo sequence and a six-echo spoiled gradient-echo sequence at 3 T. Water/fat images and fat fraction maps were reconstructed using the IDEAL algorithm with T2* correction and a multi-peak model for the fat spectrum. Two radiologists scored fat infiltration on the T1-weighted images using the Goutallier classification in six muscle compartments. Spearman correlations between the Goutallier grades and the fat fraction were calculated; in addition, intra-observer and inter-observer agreement were calculated. A significant correlation between the clinical grading and the fat fraction values was found for all muscle compartments (P < 0.0001, R values ranging from 0.79 to 0.88). Goutallier grades 0-4 had a fat fraction ranging from 3.5 to 19%. Intra-observer and inter-observer agreement values of 0.83 and 0.81 were calculated for the semi-quantitative grading. Semi-quantitative grading of intramuscular fat and quantitative fat fraction were significantly correlated and both techniques had excellent reproducibility. However, the clinical grading was found to overestimate muscle fat. Fat infiltration of muscle commonly occurs in many metabolic and neuromuscular diseases. • Image-based semi-quantitative classifications for assessing fat infiltration are not well validated. • Quantitative MRI techniques provide an accurate assessment of muscle fat.

Factors affecting the use of 13Cα chemical shifts to determine, refine, and validate protein structures

PubMed Central

Vila, Jorge A.; Scheraga, Harold A.

2008-01-01

Interest centers here on the analysis of two different, but related, phenomena that affect side-chain conformations and consequently 13Cα chemical shifts and their applications to determine, refine, and validate protein structures. The first is whether 13Cα chemical shifts, computed at the DFT level of approximation with charged residues is a better approximation of observed 13Cα chemical shifts than those computed with neutral residues for proteins in solution. Accurate computation of 13Cα chemical shifts requires a proper representation of the charges, which might not take on integral values. For this analysis, the charges for 139 conformations of the protein ubiquitin were determined by explicit consideration of protein binding equilibria, at a given pH, that is, by exploring the 2ξ possible ionization states of the whole molecule, with ξ being the number of ionizable groups. The results of this analysis, as revealed by the shielding/deshield-ing of the 13Cα nucleus, indicated that: (i) there is a significant difference in the computed 13Cα chemical shifts, between basic and acidic groups, as a function of the degree of charge of the side chain; (ii) this difference is attributed to the distance between the ionizable groups and the 13Cα nucleus, which is shorter for the acidic Asp and Glu groups as compared with that for the basic Lys and Arg groups; and (iii) the use of neutral, rather than charged, basic and acidic groups is a better approximation of the observed 13Cα chemical shifts of a protein in solution. The second is how side-chain flexibility influences computed 13Cα chemical shifts in an additional set of ubiquitin conformations, in which the side chains are generated from an NMR-derived structure with the backbone conformation assumed to be fixed. The 13Cα chemical shift of a given amino acid residue in a protein is determined, mainly, by its own backbone and side-chain torsional angles, independent of the neighboring residues; the conformation of a given residue itself, however, depends on the environment of this residue and, hence, on the whole protein structure. As a consequence, this analysis reveals the role and impact of an accurate side-chain computation in the determination and refinement of protein conformation. The results of this analysis are: (i) a lower error between computed and observed 13Cα chemical shifts (by up to 3.7 ppm), was found for ~68% and ~63% of all ionizable residues and all non-Ala/Pro/Gly residues, respectively, in the additional set of conformations, compared with results for the model from which the set was derived; and (ii) all the additional conformations exhibit a lower root-mean-square-deviation (1.97 ppm ≤ rmsd ≤ 2.13 ppm), between computed and observed 13Cα chemical shifts, than the rmsd (2.32 ppm) computed for the starting conformation from which this additional set was derived. As a validation test, an analysis of the additional set of ubiquitin conformations, comparing computed and observed values of both 13Cα chemical shifts and χ1 torsional angles (given by the vicinal coupling constants, 3JN–Cγ and 3JC′–Cγ, is discussed. PMID:17975838

Dynamic XPS measurements of ultrathin polyelectrolyte films containing antibacterial Ag–Cu nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taner-Camcı, Merve; Suzer, Sefik, E-mail: suzer@fen.bilkent.edu.tr

Ultrathin films consisting of polyelectrolyte layers prepared by layer-by-layer deposition technique and containing also Ag and Cu nanoparticles exhibit superior antibacterial activity toward Escherichia coli. These films have been investigated with XPS measurements under square wave excitation at two different frequencies, in order to further our understanding about the chemical/physical nature of the nanoparticles. Dubbed as dynamical XPS, such measurements bring out similarities and differences among the surface structures by correlating the binding energy shifts of the corresponding XPS peaks. Accordingly, it is observed that the Cu2p, Ag3d of the metal nanoparticles, and S2p of cysteine, the stabilizer and themore » capping agent, exhibit similar shifts. On the other hand, the C1s, N1s, and S2p peaks of the polyelectrolyte layers shift differently. This finding leads us the claim that the Ag and Cu atoms are in a nanoalloy structure, capped with cystein, as opposed to phase separated entities.« less

Synthetic, Infrared, 1Hand 13CNMR Spectral Studies on N-(p-Substituted Phenyl)-p-Substituted Benzenesulphonamides, p-X'C6H4SO2NH- (p-XC6H4), where X' or X = H, CH3, C2H5, F, Cl or Br

NASA Astrophysics Data System (ADS)

Gowda, B. Thimme; Jayalakshmi, K. L.; Shetty, Mahesha

2004-05-01

Thirty N-(p-substituted phenyl)-p-substituted benzenesulphonamides of the general formula, p-X'C6H4SO2NH(p-XC6H4), where X' or X = H, CH3, C2H5, F, Cl or Br, are synthesised and their infrared spectra in the solid state and 1H and 13C NMR spectra in solution are measured. The N-H stretching vibrational frequencies, νN-H vary in the range 3334 - 3219 cm-1, while the asymmetric and symmetric SO2 vibrations appear in the ranges 1377 - 1311 cm-1 and 1182 - 1151 cm-1, respectively. The compounds exhibit S-N and C-N stretching vibrational absorptions in the ranges 937 - 898 cm-1 and 1310 - 1180 cm-1, respectively. There are no particular trends in the variation of these frequencies on substitution with either electron withdrawing or electron donating groups. The 1H and 13C chemical shifts of N-(p-substituted phenyl)-p-substituted benzenesulphonamides, are assigned to various protons and carbons of the two benzene rings. Further, incremental shifts of the ring protons and carbons due to -SO2NH(p-XC6H4) groups in the compounds of the formula, C6H5SO2NH(p-XC6H4), and p-X'C6H4SO2- and p-X'C6H4SO2NH- groups in the compounds of the formula, p-X'C6H4SO2NH(C6H5) are computed and used to calculate the 1H and 13C chemical shifts of the parallely substituted compounds of the general formula p-X'C6H4SO2NH(p-XC6H4). The computed values agree well with the observed chemical shifts. The above incremental shifts are found to correlate with the Hammett substituent parameters.

Organometallic benzylidene anilines: donor-acceptor features in NCN-pincer Pt(ii) complexes with a 4-(E)-[(4-R-phenyl)imino]methyl substituent.

PubMed

Batema, Guido D; Lutz, Martin; Spek, Anthony L; van Walree, Cornelis A; van Klink, Gerard P M; van Koten, Gerard

2014-08-28

A series of organometallic 4,4'-substituted benzylidene aniline complexes 4-ClPt-3,5-(CH2NMe2)2C6H2CH[double bond, length as m-dash]NC6H4R'-4', abbreviated as PtCl[NCN(CH[double bond, length as m-dash]NC6H4R'-4')-4], with R' = NMe2, Me, H, Cl, CN (, respectively), was synthesized via a Schiff-base condensation reaction involving reaction of PtCl[NCN(CH[double bond, length as m-dash]O)-4] () with the appropriate 4-R'-substituted aniline derivative () in toluene. The resulting arylplatinum(ii) products were obtained in 75-88% yield. Notably, product was also obtained in 68% yield from a reaction in the solid state by grinding solid with aniline . The structures of , , and in the solid state (single crystal X-ray diffraction) showed a non-planar geometry, in particular for compound . The electronic interaction between the donor benzylidene fragment PtCl(NCN-CH) and the para-R' aniline substituent through the azomethine bridge was studied with NMR and UV/Vis spectroscopy. Linear correlations were found between the azomethine (1)H, the (195)Pt NMR and various (13)C NMR chemical shifts, and the substituent parameters σF and σR of R' at the aniline site. In common with organic benzylidene anilines, the azomethine (1)H NMR chemical shift showed anomalous substituent behavior. The (195)Pt NMR chemical shift of the platinum center can be used as a probe for the electronic properties of the delocalized π-system of the benzylidene aniline framework, to which it is connected. The dual substituent parameter treatment of the azomethine (13)C NMR shift gave important insight into the unique behaviour of the Pt-pincer group as a substituent. Inductively, it is a very strong electron-withdrawing group, whereas mesomerically it behaves like a very strong electron donating group.

pH-Dependent spin state population and 19F NMR chemical shift via remote ligand protonation in an iron(ii) complex.

PubMed

Gaudette, Alexandra I; Thorarinsdottir, Agnes E; Harris, T David

2017-11-30

An Fe II complex that features a pH-dependent spin state population, by virtue of a variable ligand protonation state, is described. This behavior leads to a highly pH-dependent 19 F NMR chemical shift with a sensitivity of 13.9(5) ppm per pH unit at 37 °C, thereby demonstrating the potential utility of the complex as a 19 F chemical shift-based pH sensor.

Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil.

PubMed

Su, Jian-Qiang; Ding, Long-Jun; Xue, Kai; Yao, Huai-Ying; Quensen, John; Bai, Shi-Jie; Wei, Wen-Xue; Wu, Jin-Shui; Zhou, Jizhong; Tiedje, James M; Zhu, Yong-Guan

2015-01-01

The influence of long-term chemical fertilization on soil microbial communities has been one of the frontier topics of agricultural and environmental sciences and is critical for linking soil microbial flora with soil functions. In this study, 16S rRNA gene pyrosequencing and a functional gene array, geochip 4.0, were used to investigate the shifts in microbial composition and functional gene structure in paddy soils with different fertilization treatments over a 22-year period. These included a control without fertilizers; chemical nitrogen fertilizer (N); N and phosphate (NP); N and potassium (NK); and N, P and K (NPK). Based on 16S rRNA gene data, both species evenness and key genera were affected by P fertilization. Functional gene array-based analysis revealed that long-term fertilization significantly changed the overall microbial functional structures. Chemical fertilization significantly increased the diversity and abundance of most genes involved in C, N, P and S cycling, especially for the treatments NK and NPK. Significant correlations were found among functional gene structure and abundance, related soil enzymatic activities and rice yield, suggesting that a fertilizer-induced shift in the microbial community may accelerate the nutrient turnover in soil, which in turn influenced rice growth. The effect of N fertilization on soil microbial functional genes was mitigated by the addition of P fertilizer in this P-limited paddy soil, suggesting that balanced chemical fertilization is beneficial to the soil microbial community and its functions. © 2014 John Wiley & Sons Ltd.

VITAL NMR: Using Chemical Shift Derived Secondary Structure Information for a Limited Set of Amino Acids to Assess Homology Model Accuracy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brothers, Michael C; Nesbitt, Anna E; Hallock, Michael J

2011-01-01

Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR (SSNMR) data. Such data is obtainable in a rapid manner by simple SSNMR experiments (e.g., (13)C-(13)C 2D correlation spectra). To test our homology model scoring procedure for various amino acid labeling schemes, we generated a library ofmore » 7,474 homology models for 22 protein targets culled from the TALOS+/SPARTA+ training set of protein structures. Using subsets of amino acids that are plausibly assigned by SSNMR, we discovered that pairs of the residues Val, Ile, Thr, Ala and Leu (VITAL) emulate an ideal dataset where all residues are site specifically assigned. Scoring the models with a predicted VITAL site-specific dataset and calculating secondary structure with the Chemical Shift Index resulted in a Pearson correlation coefficient (-0.75) commensurate to the control (-0.77), where secondary structure was scored site specifically for all amino acids (ALL 20) using STRIDE. This method promises to accelerate structure procurement by SSNMR for proteins with unknown folds through guiding the selection of remotely homologous protein templates and assessing model quality.« less

Energy decomposition analysis of single bonds within Kohn-Sham density functional theory.

PubMed

Levine, Daniel S; Head-Gordon, Martin

2017-11-28

An energy decomposition analysis (EDA) for single chemical bonds is presented within the framework of Kohn-Sham density functional theory based on spin projection equations that are exact within wave function theory. Chemical bond energies can then be understood in terms of stabilization caused by spin-coupling augmented by dispersion, polarization, and charge transfer in competition with destabilizing Pauli repulsions. The EDA reveals distinguishing features of chemical bonds ranging across nonpolar, polar, ionic, and charge-shift bonds. The effect of electron correlation is assessed by comparison with Hartree-Fock results. Substituent effects are illustrated by comparing the C-C bond in ethane against that in bis(diamantane), and dispersion stabilization in the latter is quantified. Finally, three metal-metal bonds in experimentally characterized compounds are examined: a [Formula: see text]-[Formula: see text] dimer, the [Formula: see text]-[Formula: see text] bond in dizincocene, and the Mn-Mn bond in dimanganese decacarbonyl.

Protein Structural Information Derived from NMR Chemical Shift with the Neural Network Program TALOS-N

PubMed Central

Shen, Yang; Bax, Ad

2015-01-01

Summary Chemical shifts are obtained at the first stage of any protein structural study by NMR spectroscopy. Chemical shifts are known to be impacted by a wide range of structural factors and the artificial neural network based TALOS-N program has been trained to extract backbone and sidechain torsion angles from 1H, 15N and 13C shifts. The program is quite robust, and typically yields backbone torsion angles for more than 90% of the residues, and sidechain χ1 rotamer information for about half of these, in addition to reliably predicting secondary structure. The use of TALOS-N is illustrated for the protein DinI, and torsion angles obtained by TALOS-N analysis from the measured chemical shifts of its backbone and 13Cβ nuclei are compared to those seen in a prior, experimentally determined structure. The program is also particularly useful for generating torsion angle restraints, which then can be used during standard NMR protein structure calculations. PMID:25502373

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

PubMed

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

2014-09-23

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

Ab initio/GIAO-CCSD(T) (13)C NMR study of the rearrangement and dynamic aspects of rapidly equilibrating tertiary carbocations, C6H13(+) and C7H15(+).

PubMed

Olah, George A; Prakash, G K Surya; Rasul, Golam

2016-01-05

The rearrangement pathways of the equilibrating tertiary carbocations, 2,3-dimethyl-2-butyl cation (C6H13(+), 1), 2,3,3-trimethyl-2-butyl cation (C7H15(+), 5) and 2,3-dimethyl-2-pentyl cation (C7H15(+), 8 and 9) were investigated using the ab initio/GIAO-CCSD(T) (13)C NMR method. Comparing the calculated and experimental (13)C NMR chemical shifts of a series of carbocations indicates that excellent prediction of δ(13)C could be achieved through scaling. In the case of symmetrical equilibrating cations (1 and 5) the Wagner-Meerwein 1,2-hydride and 1,2-methide shifts, respectively, produce the same structure. This indicates that the overall (13)C NMR chemical shifts are conserved and independent of temperature. However, in the case of unsymmetrical equilibrating cations (8 and 9) the Wagner-Meerwein shift produces different tertiary structures, which have slightly different thermodynamic stabilities and, thus, different spectra. At the MP4(SDTQ)/cc-pVTZ//MP2/cc-pVTZ + ZPE level structure 8 is only 90 calories/mol more stable than structure 9. Based on computed (13)C NMR chemical shift calculations, mole fractions of these isomers were determined by assuming the observed chemical shifts are due to the weighted average of the chemical shifts of the static ions. © 2015 Wiley Periodicals, Inc.

Saturated amine oxides: Part 8. Hydroacridines: Part 27. Effects of N-oxidation and of N-quaternization on the 15N NMR chemical shifts of N-methylpiperidine-derived mono-, bi-, and tricycloaliphatic tertiary amines.

PubMed

Potmischil, Francisc; Duddeck, Helmut; Nicolescu, Alina; Deleanu, Calin

2007-03-01

The (15)N chemical shifts of 13 N-methylpiperidine-derived mono-, bi- and tricycloaliphatic tertiary amines, their methiodides and their N-epimeric pairs of N-oxides were measured, and the contributions of specific structural parameters to the chemical shifts were determined by multilinear regression analysis. Within the examined compounds, the effects of N-oxidation upon the (15)N chemical shifts of the amines vary from +56 ppm to +90 ppm (deshielding), of which approx. +67.7 ppm is due to the inductive effect of the incoming N(+)--O(-) oxygen atom, whereas the rest is due to the additive shift effects of the various C-alkyl substituents of the piperidine ring. The effects of quaternization vary from -3.1 ppm to +29.3 ppm, of which approx. +8.9 ppm is due to the inductive effect of the incoming N(+)--CH(3) methyl group, and the rest is due to the additive shift effects of the various C-alkyl substituents of the piperidine ring. The shift effects of the C-alkyl substituents in the amines, the N-oxides and the methiodides are discussed. Copyright (c) 2007 John Wiley & Sons, Ltd.

Mechanism of Protein Denaturation: Partial Unfolding of the P22 Coat Protein I-Domain by Urea Binding

PubMed Central

Newcomer, Rebecca L.; Fraser, LaTasha C.R.; Teschke, Carolyn M.; Alexandrescu, Andrei T.

2015-01-01

The I-domain is an insertion domain of the bacteriophage P22 coat protein that drives rapid folding and accounts for over half of the stability of the full-length protein. We sought to determine the role of hydrogen bonds (H-bonds) in the unfolding of the I-domain by examining 3JNC’ couplings transmitted through H-bonds, the temperature and urea-concentration dependence of 1HN and 15N chemical shifts, and native-state hydrogen exchange at urea concentrations where the domain is predominantly folded. The native-state hydrogen-exchange data suggest that the six-stranded β-barrel core of the I-domain is more stable against unfolding than a smaller subdomain comprised of a short α-helix and three-stranded β-sheet. H-bonds, separately determined from solvent protection and 3JNC’ H-bond couplings, are identified with an accuracy of 90% by 1HN temperature coefficients. The accuracy is improved to 95% when 15N temperature coefficients are also included. In contrast, the urea dependence of 1HN and 15N chemical shifts is unrelated to H-bonding. The protein segments with the largest chemical-shift changes in the presence of urea show curved or sigmoidal titration curves suggestive of direct urea binding. Nuclear Overhauser effects to urea for these segments are also consistent with specific urea-binding sites in the I-domain. Taken together, the results support a mechanism of urea unfolding in which denaturant binds to distinct sites in the I-domain. Disordered segments bind urea more readily than regions in stable secondary structure. The locations of the putative urea-binding sites correlate with the lower stability of the structure against solvent exchange, suggesting that partial unfolding of the structure is related to urea accessibility. PMID:26682823

Interplay between membrane curvature and protein conformational equilibrium investigated by solid-state NMR.

PubMed

Liao, Shu Y; Lee, Myungwoon; Hong, Mei

2018-03-01

Many membrane proteins sense and induce membrane curvature for function, but structural information about how proteins modulate their structures to cause membrane curvature is sparse. We review our recent solid-state NMR studies of two virus membrane proteins whose conformational equilibrium is tightly coupled to membrane curvature. The influenza M2 proton channel has a drug-binding site in the transmembrane (TM) pore. Previous chemical shift data indicated that this pore-binding site is lost in an M2 construct that contains the TM domain and a curvature-inducing amphipathic helix. We have now obtained chemical shift perturbation, protein-drug proximity, and drug orientation data that indicate that the pore-binding site is restored when the full cytoplasmic domain is present. This finding indicates that the curvature-inducing amphipathic helix distorts the TM structure to interfere with drug binding, while the cytoplasmic tail attenuates this effect. In the second example, we review our studies of a parainfluenza virus fusion protein that merges the cell membrane and the virus envelope during virus entry. Chemical shifts of two hydrophobic domains of the protein indicate that both domains have membrane-dependent backbone conformations, with the β-strand structure dominating in negative-curvature phosphatidylethanolamine (PE) membranes. 31 P NMR spectra and 1 H- 31 P correlation spectra indicate that the β-strand-rich conformation induces saddle-splay curvature to PE membranes and dehydrates them, thus stabilizing the hemifusion state. These results highlight the indispensable role of solid-state NMR to simultaneously determine membrane protein structures and characterize the membrane curvature in which these protein structures exist. Copyright © 2018 Elsevier Inc. All rights reserved.

Tuning the electronic hybridization in the heavy fermion cage compound YbFe2Zn20 with Cd doping

NASA Astrophysics Data System (ADS)

Cabrera-Baez, M.; Ribeiro, R. A.; Avila, M. A.

2016-09-01

The tuning of the electronic properties of heavy fermion compounds by chemical substitution provides excellent opportunities for further understanding the physics of hybridized ions in crystal lattices. Here we present an investigation on the effects of Cd doping in flux-grown single crystals of the complex intermetallic cage compound YbFe2Zn20, which has been described as a heavy fermion with a Sommerfeld coefficient of 535 mJ mol-1 · K-2. The substitution of Cd for Zn disturbs the system by expanding the unit cell and, in this case, the size of the Zn cages that surround the Yb and Fe. With an increasing amount of Cd, the hybridization between the Yb 4f electrons and the conduction electrons is weakened, as shown by a decrease in the Sommerfeld coefficient, which should be accompanied by a valence shift of the Yb3+ due to the negative chemical pressure effect. This scenario is also supported by the low temperature DC magnetic susceptibility, which is gradually suppressed and shows an increment of the Kondo temperature, based on a shift to higher temperatures of the characteristic broad susceptibility peak. Furthermore, the DC resistivity decreases with the isoelectronic substitution of Cd for Zn, contrary to expectations in an increasingly disordered system, and implying that the valence shift is not related to charge carrier doping. The combined results demonstrate the excellent complementarity between positive physical pressure and negative chemical pressure, and point to a rich playground for exploring the physics and chemistry of strongly correlated electron systems in the general family of Zn20 compounds, despite their structural complexity.

Environmental epigenomics: Current approaches to assess epigenetic effects of endocrine disrupting compounds (EDC's) on human health.

PubMed

Tapia-Orozco, Natalia; Santiago-Toledo, Gerardo; Barrón, Valeria; Espinosa-García, Ana María; García-García, José Antonio; García-Arrazola, Roeb

2017-04-01

Environmental Epigenomics is a developing field to study the epigenetic effect on human health from exposure to environmental factors. Endocrine disrupting chemicals have been detected primarily in pharmaceutical drugs, personal care products, food additives, and food containers. Exposure to endocrine-disrupting chemicals (EDCs) has been associated with a high incidence and prevalence of many endocrine-related disorders in humans. Nevertheless, further evidence is needed to establish a correlation between exposure to EDC and human disorders. Conventional detection of EDCs is based on chemical structure and concentration sample analysis. However, substantial evidence has emerged, suggesting that cell exposure to EDCs leads to epigenetic changes, independently of its chemical structure with non-monotonic low-dose responses. Consequently, a paradigm shift in toxicology assessment of EDCs is proposed based on a comprehensive review of analytical techniques used to evaluate the epigenetic effects. Fundamental insights reported elsewhere are compared in order to establish DNA methylation analysis as a viable method for assessing endocrine disruptors beyond the conventional study approach of chemical structure and concentration analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

Solution and solid-state effects on NMR chemical shifts in sesquiterpene lactones: NMR, X-ray, and theoretical methods.

PubMed

Dračínský, Martin; Buděšínský, Miloš; Warżajtis, Beata; Rychlewska, Urszula

2012-01-12

Selected guaianolide type sesquiterpene lactones were studied combining solution and solid-state NMR spectroscopy with theoretical calculations of the chemical shifts in both environments and with the X-ray data. The experimental (1)H and (13)C chemical shifts in solution were successfully reproduced by theoretical calculations (with the GIAO method and DFT B3LYP 6-31++G**) after geometry optimization (DFT B3LYP 6-31 G**) in vacuum. The GIPAW method was used for calculations of solid-state (13)C chemical shifts. The studied cases involved two polymorphs of helenalin, two pseudopolymorphs of 6α-hydroxydihydro-aromaticin and two cases of multiple asymmetric units in crystals: one in which the symmetry-independent molecules were connected by a series of hydrogen bonds (geigerinin) and the other in which the symmetry-independent molecules, deprived of any specific intermolecular interactions, differed in the conformation of the side chain (badkhysin). Geometrically different molecules present in the crystal lattices could be easily distinguished in the solid-state NMR spectra. Moreover, the experimental differences in the (13)C chemical shifts corresponding to nuclei in different polymorphs or in geometrically different molecules were nicely reproduced with the GIPAW calculations.

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

PubMed

Sahakyan, Aleksandr B; Vendruscolo, Michele

2013-02-21

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

NMR shifts for polycyclic aromatic hydrocarbons from first-principles

NASA Astrophysics Data System (ADS)

Thonhauser, T.; Ceresoli, Davide; Marzari, Nicola

We present first-principles, density-functional theory calculations of the NMR chemical shifts for polycyclic aromatic hydrocarbons, starting with benzene and increasing sizes up to the one- and two-dimensional infinite limits of graphene ribbons and sheets. Our calculations are performed using a combination of the recently developed theory of orbital magnetization in solids, and a novel approach to NMR calculations where chemical shifts are obtained from the derivative of the orbital magnetization with respect to a microscopic, localized magnetic dipole. Using these methods we study on equal footing the 1H and 13 shifts in benzene, pyrene, coronene, in naphthalene, anthracene, naphthacene, and pentacene, and finally in graphene, graphite, and an infinite graphene ribbon. Our results show very good agreement with experiments and allow us to characterize the trends for the chemical shifts as a function of system size.

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

PubMed

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.

Correlation of interface states/border traps and threshold voltage shift on AlGaN/GaN metal-insulator-semiconductor high-electron-mobility transistors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Tian-Li, E-mail: Tian-Li.Wu@imec.be; Groeseneken, Guido; Department of Electrical Engineering, KU Leuven, Leuven

2015-08-31

In this paper, three electrical techniques (frequency dependent conductance analysis, AC transconductance (AC-g{sub m}), and positive gate bias stress) were used to evaluate three different gate dielectrics (Plasma-Enhanced Atomic Layer Deposition Si{sub 3}N{sub 4}, Rapid Thermal Chemical Vapor Deposition Si{sub 3}N{sub 4}, and Atomic Layer Deposition (ALD) Al{sub 2}O{sub 3}) for AlGaN/GaN Metal-Insulator-Semiconductor High-Electron-Mobility Transistors. From these measurements, the interface state density (D{sub it}), the amount of border traps, and the threshold voltage (V{sub TH}) shift during a positive gate bias stress can be obtained. The results show that the V{sub TH} shift during a positive gate bias stress ismore » highly correlated to not only interface states but also border traps in the dielectric. A physical model is proposed describing that electrons can be trapped by both interface states and border traps. Therefore, in order to minimize the V{sub TH} shift during a positive gate bias stress, the gate dielectric needs to have a lower interface state density and less border traps. However, the results also show that the commonly used frequency dependent conductance analysis technique to extract D{sub it} needs to be cautiously used since the resulting value might be influenced by the border traps and, vice versa, i.e., the g{sub m} dispersion commonly attributed to border traps might be influenced by interface states.« less

A Chemical View on X-ray Photoelectron Spectroscopy: the ESCA Molecule and Surface-to-Bulk XPS Shifts.

PubMed

Delesma, Francisco A; Van den Bossche, Maxime; Grönbeck, Henrik; Calaminici, Patrizia; Köster, Andreas M; Pettersson, Lars G M

2018-01-19

In this paper we remind the reader of a simple, intuitive picture of chemical shifts in X-ray photoelectron spectroscopy (XPS) as the difference in chemical bonding between the probed atom and its neighbor to the right in the periodic table, the so called Z+1 approximation. We use the classical ESCA molecule, ethyl trifluoroacetate, and 4d-transition metals to explicitly demonstrate agreement between core-level shifts computed as differences between final core-hole states and the approach where each core-ionized atom is replaced by a Z+1 atom. In this final state, or total energy picture, the XPS shift arises due to the more or less unfavorable chemical bonding of the effective nitrogen in the carbon geometry for the ESCA molecule. Surface core level shifts in metals are determined by whether the Z+1 atom as an alloy segregates to the surface or is more soluble in the bulk. As further illustration of this more chemical picture, we compare the geometry of C 1s and O 1s core-ionized CO with that of, respectively, NO + and CF + . The scope is not to propose a new method to compute XPS shifts but rather to stress the validity of this simple interpretation. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lowery, Thomas J.; Doucleff, Michealeen; Ruiz, E. Janette

2005-02-01

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

Comparative NMR Analysis of an 80-Residue G Protein-Coupled Receptor Fragment in Two Membrane Mimetic Environments

PubMed Central

LS, Cohen; B, Arshava; A, Neumoin; JM, Becker; P, Güntert; O, Zerbe; Naider, F

2011-01-01

Fragments of integral membrane proteins have been used to study the physical chemical properties of regions of transporters and receptors. Ste2p(G31-T110) is an 80-residue polypeptide which contains a portion of the N-terminal domain, transmembrane domain 1 (TM1), intracellular loop 1, TM2 and part of extracellular loop 2 of the α-factor receptor (Ste2p) from Saccharomyces cerevisiae. The structure of this peptide was previously determined to form a helical hairpin in lyso-palmitoylphosphatidyl-glycerol micelles (LPPG)[1]. Herein, we perform a systematic comparison of the structure of this protein fragment in micelles and trifluoroethanol(TFE):water in order to understand whether spectra recorded in organic:aqueous medium can facilitate the structure determination in a micellar environment. Using uniformly labeled peptide and peptide selectively protonated on Ile, Val and Leu methyl groups in a perdeuterated background and a broad set of 3D NMR experiments we assigned 89% of the observable atoms. NOEs and chemical shift analysis were used to define the helical regions of the fragment. Together with constraints from paramagnetic spin labeling, NOEs were used to calculate a transiently folded helical hairpin structure for this peptide in TFE:water. Correlation of chemical shifts was insufficient to transfer assignments from TFE:water to LPPG spectra in the absence of further information. PMID:21791199

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

ERIC Educational Resources Information Center

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

2015-01-01

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

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

PubMed Central

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

2011-01-01

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

Ab initio/GIAO-CCSD(T) study of structures, energies, and 13C NMR chemical shifts of C4H7(+) and C5H9(+) ions: relative stability and dynamic aspects of the cyclopropylcarbinyl vs bicyclobutonium ions.

PubMed

Olah, George A; Surya Prakash, G K; Rasul, Golam

2008-07-16

The structures and energies of the carbocations C 4H 7 (+) and C 5H 9 (+) were calculated using the ab initio method. The (13)C NMR chemical shifts of the carbocations were calculated using the GIAO-CCSD(T) method. The pisigma-delocalized bisected cyclopropylcarbinyl cation, 1 and nonclassical bicyclobutonium ion, 2 were found to be the minima for C 4H 7 (+) at the MP2/cc-pVTZ level. At the MP4(SDTQ)/cc-pVTZ//MP2/cc-pVTZ + ZPE level the structure 2 is 0.4 kcal/mol more stable than the structure 1. The (13)C NMR chemical shifts of 1 and 2 were calculated by the GIAO-CCSD(T) method. Based on relative energies and (13)C NMR chemical shift calculations, an equilibrium involving the 1 and 2 in superacid solutions is most likely responsible for the experimentally observed (13)C NMR chemical shifts, with the latter as the predominant equilibrating species. The alpha-methylcyclopropylcarbinyl cation, 4, and nonclassical bicyclobutonium ion, 5, were found to be the minima for C 5H 9 (+) at the MP2/cc-pVTZ level. At the MP4(SDTQ)/cc-pVTZ//MP2/cc-pVTZ + ZPE level ion 5 is 5.9 kcal/mol more stable than the structure 4. The calculated (13)C NMR chemical shifts of 5 agree rather well with the experimental values of C 5H 9 (+).

Investigating the Vanadium Environments in Hydroxylamido V(V) Dipicolinate Complexes Using 51V NMR Spectroscopy and Density Functional Theory

PubMed Central

Ooms, Kristopher J.; Bolte, Stephanie E.; Smee, Jason J.; Baruah, Bharat; Crans, Debbie C.; Polenova, Tatyana

2014-01-01

Using 51V magic angle spinning solid-state NMR, SSNMR, spectroscopy and quantum chemical DFT calculations we have characterized the chemical shift and quadrupolar coupling parameters of a series of 8 hydroxylamido vanadium(V) dipicolinate complexes of the general formula VO(dipic)(ONR1R2)(H2O) where R1 and R2 can be H, CH3, or CH2CH3. This class of vanadium compounds was chosen for investigation because of their seven coordinate vanadium atom, a geometry for which there is limited 51V SSNMR data. Furthermore, a systematic series of compounds with different electronic properties are available and allows for the effects of ligand substitution on the NMR parameters to be studied. The quadrupolar coupling constants, CQ, are small, 3.0 to 3.9 MHz, but exhibit variations as a function of the ligand substitution. The chemical shift tensors in the solid state are sensitive to changes in both the hydroxylamide substituent and the dipic ligand, a sensitivity which is not observed for isotropic chemical shifts in solution. The chemical shift tensors span approximately 1000 ppm, and are nearly axially symmetric. Based on DFT calculations of the chemical shift tensors, one of the largest contributors to the magnetic shielding anisotropy is an occupied molecular orbital with significant vanadium dz2 character along the V=O bond. PMID:17902653

Improved Electrostatic Embedding for Fragment-Based Chemical Shift Calculations in Molecular Crystals.

PubMed

Hartman, Joshua D; Balaji, Ashwin; Beran, Gregory J O

2017-12-12

Fragment-based methods predict nuclear magnetic resonance (NMR) chemical shielding tensors in molecular crystals with high accuracy and computational efficiency. Such methods typically employ electrostatic embedding to mimic the crystalline environment, and the quality of the results can be sensitive to the embedding treatment. To improve the quality of this embedding environment for fragment-based molecular crystal property calculations, we borrow ideas from the embedded ion method to incorporate self-consistently polarized Madelung field effects. The self-consistent reproduction of the Madelung potential (SCRMP) model developed here constructs an array of point charges that incorporates self-consistent lattice polarization and which reproduces the Madelung potential at all atomic sites involved in the quantum mechanical region of the system. The performance of fragment- and cluster-based 1 H, 13 C, 14 N, and 17 O chemical shift predictions using SCRMP and density functionals like PBE and PBE0 are assessed. The improved embedding model results in substantial improvements in the predicted 17 O chemical shifts and modest improvements in the 15 N ones. Finally, the performance of the model is demonstrated by examining the assignment of the two oxygen chemical shifts in the challenging γ-polymorph of glycine. Overall, the SCRMP-embedded NMR chemical shift predictions are on par with or more accurate than those obtained with the widely used gauge-including projector augmented wave (GIPAW) model.

The relativistic theory of the chemical shift

NASA Astrophysics Data System (ADS)

Pyper, N. C.

1983-04-01

A relativistic theory of the NMR chemical shift for a closed-shell system is presented. The final expression for the shielding, derived by, applying two Gordon decompositions to the Dirac current operator, closely parallels the Ramsey non-relativistic result.

Exploiting the Synergy of Powder X-ray Diffraction and Solid-State NMR Spectroscopy in Structure Determination of Organic Molecular Solids

PubMed Central

2013-01-01

We report a strategy for structure determination of organic materials in which complete solid-state nuclear magnetic resonance (NMR) spectral data is utilized within the context of structure determination from powder X-ray diffraction (XRD) data. Following determination of the crystal structure from powder XRD data, first-principles density functional theory-based techniques within the GIPAW approach are exploited to calculate the solid-state NMR data for the structure, followed by careful scrutiny of the agreement with experimental solid-state NMR data. The successful application of this approach is demonstrated by structure determination of the 1:1 cocrystal of indomethacin and nicotinamide. The 1H and 13C chemical shifts calculated for the crystal structure determined from the powder XRD data are in excellent agreement with those measured experimentally, notably including the two-dimensional correlation of 1H and 13C chemical shifts for directly bonded 13C–1H moieties. The key feature of this combined approach is that the quality of the structure determined is assessed both against experimental powder XRD data and against experimental solid-state NMR data, thus providing a very robust validation of the veracity of the structure. PMID:24386493

Distinguishing Polymorphs of the Semiconducting Pigment Copper Phthalocyanine by Solid-state NMR and Raman Spectroscopy

PubMed Central

Shaibat, Medhat A.; Casabianca, Leah B.; Siberio-Pérez, Diana Y.; Matzger, Adam J; Ishii, Yoshitaka

2010-01-01

Cu(II)(phthalocyanine) (CuPc) is broadly utilized as an archetypal molecular semiconductor and is the most widely used blue printing pigment. CuPc crystallizes in six different forms; the chemical and physical properties are substantially modulated by its molecular packing among these polymorphs. Despite the growing importance of this system, spectroscopic identification of different polymorphs for CuPc has posed difficulties. This study presents the first example of spectroscopic distinction of α- and β-forms of CuPc, the most widely used polymorphs, by solid-state NMR (SSNMR) and Raman spectroscopy. 13C high-resolution SSNMR spectra of α- and β-CuPc using very-fast magic angle spinning (VFMAS) at 20 kHz show that hyperfine shifts sensitively reflect polymorphs of CuPc. The experimental results were confirmed by ab initio chemical shift calculations. 13C and 1H SSNMR relaxation times of α- and β-CuPc under VFMAS also showed marked differences, presumably because of the difference in electronic spin correlation times in the two forms. Raman spectroscopy also provided another reliable method of differentiation between the two polymorphs. PMID:20225842

Exploiting the Synergy of Powder X-ray Diffraction and Solid-State NMR Spectroscopy in Structure Determination of Organic Molecular Solids.

PubMed

Dudenko, Dmytro V; Williams, P Andrew; Hughes, Colan E; Antzutkin, Oleg N; Velaga, Sitaram P; Brown, Steven P; Harris, Kenneth D M

2013-06-13

We report a strategy for structure determination of organic materials in which complete solid-state nuclear magnetic resonance (NMR) spectral data is utilized within the context of structure determination from powder X-ray diffraction (XRD) data. Following determination of the crystal structure from powder XRD data, first-principles density functional theory-based techniques within the GIPAW approach are exploited to calculate the solid-state NMR data for the structure, followed by careful scrutiny of the agreement with experimental solid-state NMR data. The successful application of this approach is demonstrated by structure determination of the 1:1 cocrystal of indomethacin and nicotinamide. The 1 H and 13 C chemical shifts calculated for the crystal structure determined from the powder XRD data are in excellent agreement with those measured experimentally, notably including the two-dimensional correlation of 1 H and 13 C chemical shifts for directly bonded 13 C- 1 H moieties. The key feature of this combined approach is that the quality of the structure determined is assessed both against experimental powder XRD data and against experimental solid-state NMR data, thus providing a very robust validation of the veracity of the structure.

Repeatability of two-dimensional chemical shift imaging multivoxel proton magnetic resonance spectroscopy for measuring human cerebral choline-containing compounds.

PubMed

Puri, Basant K; Egan, Mary; Wallis, Fintan; Jakeman, Philip

2018-03-22

To investigate the repeatability of proton magnetic resonance spectroscopy in the in vivo measurement of human cerebral levels of choline-containing compounds (Cho). Two consecutive scans were carried out in six healthy resting subjects at a magnetic field strength of 1.5 T. On each occasion, neurospectroscopy data were collected from 64 voxels using the same 2D chemical shift imaging (CSI) sequence. The data were analyzed in the same way, using the same software, to obtain the values for each voxel of the ratio of Cho to creatine. The Wilcoxon related-samples signed-rank test, coefficient of variation (CV), repeatability coefficient (RC), and intraclass correlation coefficient (ICC) were used to assess the repeatability. The CV ranged from 2.75% to 33.99%, while the minimum RC was 5.68%. There was excellent reproducibility, as judged by significant ICC values, in 26 voxels. Just three voxels showed significant differences according to the Wilcoxon related-samples signed-rank test. It is therefore concluded that when CSI multivoxel proton neurospectroscopy is used to measure cerebral choline-containing compounds at 1.5 T, the reproducibility is highly acceptable.

CCR5 RNA Pseudoknots: Residue and Site-Specific Labeling correlate Internal Motions with microRNA Binding.

PubMed

Chen, Bin; Longhini, Andrew P; Nußbaumer, Felix; Kreutz, Christoph; Dinman, Jonathan D; Dayie, T Kwaku

2018-04-11

Conformational dynamics of RNA molecules play a critical role in governing their biological functions. Measurements of RNA dynamic behavior sheds important light on sites that interact with their binding partners or cellular stimulators. However, such measurements using solution-state NMR are difficult for large RNA molecules (>70 nt; nt=nucleotides) owing to severe spectral overlap, homonuclear 13 C scalar couplings, and line broadening. Herein, a strategic combination of solid-phase synthesis, site-specific isotopic labeled phosphoramidites, and enzymatic ligation is introduced. This approach allowed the position-specific insertion of isotopic probes into a 96 nt CCR5 RNA fragment. Accurate measurements of functional dynamics using the Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion (RD) experiments enabled extraction of the exchange rates and populations of this RNA. NMR chemical shift perturbation analysis of the RNA/microRNA-1224 complex indicated that A90-C1' of the pseudoknot exhibits similar changes in chemical shift observed in the excited state. This work demonstrates the general applicability of a NMR-labeling strategy to probe functional RNA structural dynamics. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative two-dimensional HSQC experiment for high magnetic field NMR spectrometers

NASA Astrophysics Data System (ADS)

Koskela, Harri; Heikkilä, Outi; Kilpeläinen, Ilkka; Heikkinen, Sami

2010-01-01

The finite RF power available on carbon channel in proton-carbon correlation experiments leads to non-uniform cross peak intensity response across carbon chemical shift range. Several classes of broadband pulses are available that alleviate this problem. Adiabatic pulses provide an excellent magnetization inversion over a large bandwidth, and very recently, novel phase-modulated pulses have been proposed that perform 90° and 180° magnetization rotations with good offset tolerance. Here, we present a study how these broadband pulses (adiabatic and phase-modulated) can improve quantitative application of the heteronuclear single quantum coherence (HSQC) experiment on high magnetic field strength NMR spectrometers. Theoretical and experimental examinations of the quantitative, offset-compensated, CPMG-adjusted HSQC (Q-OCCAHSQC) experiment are presented. The proposed experiment offers a formidable improvement to the offset performance; 13C offset-dependent standard deviation of the peak intensity was below 6% in range of ±20 kHz. This covers the carbon chemical shift range of 150 ppm, which contains the protonated carbons excluding the aldehydes, for 22.3 T NMR magnets. A demonstration of the quantitative analysis of a fasting blood plasma sample obtained from a healthy volunteer is given.

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

ERIC Educational Resources Information Center

Boggess, Robert K.

1988-01-01

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

Pauling Electronegativity On/Off Effects Assessed by 13 C and 29 Si NMR Spectroscopic Analysis.

PubMed

Benedetti, Michele; De Castro, Federica; Fanizzi, Francesco P

2017-11-27

In carbon and silicon tetrahalide compounds, the experimental 13 C and 29 Si NMR chemical-shift values are known to increase or decrease on increasing the overall sum of the ionic radii of the bonded halides Σ(r h ) (normal and inverse halogen dependence (NHD and IHD, respectively)). Herein, we extrapolate the main factors responsible for such NMR chemical shifts. Intriguingly, we found a characteristic value for the overall sum of the Pauling electronegativities of the bonded halides Σ(χ h ), which works as a triggering factor to determine the transition from the NHD to IHD. Below this Σ(χ h ) value, the chemical shift of the central atom was strictly related to only the Σ(r h ) value, thus producing a NHD trend. Conversely, above this value, the chemical shift of the central atom was dependent on both the Σ(r h ) and Σ(χ h ) values, thus producing a IHD trend. A simple model, in which the effect of the Σ(χ h ) value on 13 C and 29 Si NMR chemical shifts is related to an apparent increase in the Σ(r h ) value, is deduced. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Visual attention shifting in autism spectrum disorders.

PubMed

Richard, Annette E; Lajiness-O'Neill, Renee

2015-01-01

Abnormal visual attention has been frequently observed in autism spectrum disorders (ASD). Abnormal shifting of visual attention is related to abnormal development of social cognition and has been identified as a key neuropsychological finding in ASD. Better characterizing attention shifting in ASD and its relationship with social functioning may help to identify new targets for intervention and improving social communication in these disorders. Thus, the current study investigated deficits in attention shifting in ASD as well as relationships between attention shifting and social communication in ASD and neurotypicals (NT). To investigate deficits in visual attention shifting in ASD, 20 ASD and 20 age- and gender-matched NT completed visual search (VS) and Navon tasks with attention-shifting demands as well as a set-shifting task. VS was a feature search task with targets defined in one of two dimensions; Navon required identification of a target letter presented at the global or local level. Psychomotor and processing speed were entered as covariates. Relationships between visual attention shifting, set shifting, and social functioning were also examined. ASD and NT showed comparable costs of shifting attention. However, psychomotor and processing speed were slower in ASD than in NT, and psychomotor and processing speed were positively correlated with attention-shifting costs on Navon and VS, respectively, for both groups. Attention shifting on VS and Navon were correlated among NT, while attention shifting on Navon was correlated with set shifting among ASD. Attention-shifting costs on Navon were positively correlated with restricted and repetitive behaviors among ASD. Relationships between attention shifting and psychomotor and processing speed, as well as relationships between measures of different aspects of visual attention shifting, suggest inefficient top-down influences over preattentive visual processing in ASD. Inefficient attention shifting may be related to restricted and repetitive behaviors in these disorders.

The unexpected roles of σ and π orbitals in electron donor and acceptor group effects on the 13C NMR chemical shifts in substituted benzenes† †Electronic supplementary information (ESI) available: Experimental 13C NMR chemical shifts, individual components of the 13C NMR shielding tensor, lists and graphics of NLMO contributions, and tables of NLMO properties. See DOI: 10.1039/c7sc02163a Click here for additional data file.

PubMed Central

Viesser, Renan V.

2017-01-01

Effects of electron-donating (R = NH2) and electron-withdrawing (R = NO2) groups on 13C NMR chemical shifts in R-substituted benzene are investigated by molecular orbital analyses. The 13C shift substituent effect in ortho, meta, and para position is determined by the σ bonding orbitals in the aryl ring. The π orbitals do not explain the substituent effects in the NMR spectrum as conventionally suggested in textbooks. The familiar electron donating and withdrawing effects on the π system by NH2 and NO2 substituents induce changes in the σ orbital framework, and the 13C chemical shifts follow the trends induced in the σ orbitals. There is an implicit dependence of the σ orbital NMR shift contributions on the π framework, via unoccupied π* orbitals, due to the fact that the nuclear shielding is a response property. PMID:28989684

Computation provides chemical insight into the diverse hydride NMR chemical shifts of [Ru(NHC)4(L)H]0/+ species (NHC = N-heterocyclic carbene; L = vacant, H2, N2, CO, MeCN, O2, P4, SO2, H-, F- and Cl-) and their [Ru(R2PCH2CH2PR2)2(L)H]+ congeners.

PubMed

Häller, L Jonas L; Mas-Marzá, Elena; Cybulski, Mateusz K; Sanguramath, Rajashekharayya A; Macgregor, Stuart A; Mahon, Mary F; Raynaud, Christophe; Russell, Christopher A; Whittlesey, Michael K

2017-02-28

Relativistic density functional theory calculations, both with and without the effects of spin-orbit coupling, have been employed to model hydride NMR chemical shifts for a series of [Ru(NHC) 4 (L)H] 0/+ species (NHC = N-heterocyclic carbene; L = vacant, H 2 , N 2 , CO, MeCN, O 2 , P 4 , SO 2 , H - , F - and Cl - ), as well as selected phosphine analogues [Ru(R 2 PCH 2 CH 2 PR 2 ) 2 (L)H] + (R = i Pr, Cy; L = vacant, O 2 ). Inclusion of spin-orbit coupling provides good agreement with the experimental data. For the NHC systems large variations in hydride chemical shift are shown to arise from the paramagnetic term, with high net shielding (L = vacant, Cl - , F - ) being reinforced by the contribution from spin-orbit coupling. Natural chemical shift analysis highlights the major orbital contributions to the paramagnetic term and rationalizes trends via changes in the energies of the occupied Ru d π orbitals and the unoccupied σ* Ru-H orbital. In [Ru(NHC) 4 (η 2 -O 2 )H] + a δ-interaction with the O 2 ligand results in a low-lying LUMO of d π character. As a result this orbital can no longer contribute to the paramagnetic shielding, but instead provides additional deshielding via overlap with the remaining (occupied) d π orbital under the L z angular momentum operator. These two effects account for the unusual hydride chemical shift of +4.8 ppm observed experimentally for this species. Calculations reproduce hydride chemical shift data observed for [Ru( i Pr 2 PCH 2 CH 2 P i Pr 2 ) 2 (η 2 -O 2 )H] + (δ = -6.2 ppm) and [Ru(R 2 PCH 2 CH 2 PR 2 ) 2 H] + (ca. -32 ppm, R = i Pr, Cy). For the latter, the presence of a weak agostic interaction trans to the hydride ligand is significant, as in its absence (R = Me) calculations predict a chemical shift of -41 ppm, similar to the [Ru(NHC) 4 H] + analogues. Depending on the strength of the agostic interaction a variation of up to 18 ppm in hydride chemical shift is possible and this factor (that is not necessarily readily detected experimentally) can aid in the interpretation of hydride chemical shift data for nominally unsaturated hydride-containing species. The synthesis and crystallographic characterization of the BAr F 4 - salts of [Ru(IMe 4 ) 4 (L)H] + (IMe 4 = 1,3,4,5-tetramethylimidazol-2-ylidene; L = P 4 , SO 2 ; Ar F = 3,5-(CF 3 ) 2 C 6 H 3 ) and [Ru(IMe 4 ) 4 (Cl)H] are also reported.

Multinuclear NMR studies of relaxor ferroelectrics

NASA Astrophysics Data System (ADS)

Zhou, Donghua

Multinuclear NMR of 93Nb, 45Sc, and 207Pb has been carried out to study the structure, disorder, and dynamics of a series of important solid solutions: perovskite relaxor ferroelectric materials (1-x) Pb(Mg1/3Nb 2/3)O3-x Pb(Sc1/2Nb1/2)O 3 (PMN-PSN). 93Nb NMR investigations of the local structure and cation order/disorder are presented as a function of PSN concentration, x. The superb fidelity and accuracy of 3QMAS allows us to make clear and consistent assignments of spectral intensities to the 28 possible nearest B-site neighbor (nBn) configurations, (NMg, NSc, NNb), where each number ranges from 0 to 6 and their sum is 6. For most of the 28 possible nBn configurations, isotropic chemical shifts and quadrupole product constants have been extracted from the data. The seven configurations with only larger cations, Mg 2+ and Sc3+ (and no Nb5+) are assigned to the seven observed narrow peaks, whose deconvoluted intensities facilitate quantitative evaluation of, and differentiation between, different models of B-site (chemical) disorder. The "completely random" model is ruled out and the "random site" model is shown to be in qualitative agreement with the NMR experiments. To obtain quantitative agreement with observed NMR intensities, the random site model is slightly modified by including unlike-pair interaction energies. To date, 45Sc studies have not been as fruitful as 93Nb NMR because the resolution is lower in the 45Sc spectra. The lower resolution of 45Sc spectra is due to a smaller span of isotropic chemical shift (40 ppm for 45Sc vs. 82 ppm for 93Nb) and to the lack of a fortuitous mechanism that simplifies the 93Nb spectra; for 93Nb the overlap of the isotropic chemical shifts of 6-Sc and 6-Nb configurations results in the alignment of all the 28 configurations along only seven quadrupole distribution axes. Finally we present variable temperature 207Pb static, MAS, and 2D-PASS NMR studies. Strong linear correlations between isotropic and anisotropic chemical shifts show that Pb-O bonds vary from more ionic to more covalent environments. Distributions of Pb-O bond lengthes are also quantitatively described. Such distributions are used to examine two competing models of Pb displacements; the shell model and the unique direction model. Only the latter model is able to reproduce the observed Pb-O distance distribution.

Measurement of residual chemical shift anisotropies in compressed polymethylmethacrylate gels. Automatic compensation of gel isotropic shift contribution.

PubMed

Hallwass, Fernando; Teles, Rubens R; Hellemann, Erich; Griesinger, Christian; Gil, Roberto R; Navarro-Vázquez, Armando

2018-05-01

Mechanical compression of polymer gels provides a simple way for the measurement of residual chemical shift anisotropies, which then can be employed, on its own, or in combination with residual dipolar couplings, for structural elucidation purposes. Residual chemical shift anisotropies measured using compression devices needed a posteriori correction to account for the increase of the polymer to solvent ratio inside the swollen gel. This correction has been cast before in terms of a single-free parameter which, as shown here, can be simultaneously optimized along with the components of the alignment tensor while still retaining discriminating power of the different relative configurations as illustrated in the stereochemical analysis of α-santonin and 10-epi-8-deoxycumambrin B. Copyright © 2018 John Wiley & Sons, Ltd.

Intramolecular interactions of L-phenylalanine revealed by inner shell chemical shift

NASA Astrophysics Data System (ADS)

Ganesan, Aravindhan; Wang, Feng

2009-07-01

Intramolecular interactions of the functional groups, carboxylic acid, amino, and phenyl in L-phenylalanine have been revealed through inner shell chemical shift. The chemical shift and electronic structures are studied using its derivatives, 2-phenethylamine (PEA) and 3-phenylpropionic acid (PPA), through substitutions of the functional groups on the chiral carbon Cα, i.e., carboxylic acid (-COOH) and amino (-NH2) groups. Inner shell ionization spectra of L-phenylalanine are simulated using density functional theory based B3LYP/TZVP and LB94/et-pVQZ models, which achieve excellent agreement with the most recently available synchrotron sourced x-ray photoemission spectroscopy of L-phenylalanine (Elettra, Italy). The present study reveals insight into behavior of the peptide bond (CO-NH) through chemical shift of the C1-Cα-Cβ(-Cγ) chain and intramolecular interactions with phenyl. It is found that the chemical shift of the carbonyl C1(=O) site exhibits an apparently redshift (smaller energy) when interacting with the phenyl aromatic group. Removal of the amino group (-NH2) from L-phenylalanine (which forms PPA) brings this energy on C1 close to that in L-alanine (δ <0.01 eV). Chemical environment of Cα and Cβ exhibits more significant differences in L-alanine than in the aromatic species, indicating that the phenyl group indeed affects the peptide bond in the amino acid fragment. No direct evidences are found that the carbonyl acid and amino group interact with the phenyl ring through conventional hydrogen bonds.

Tissue specific resonance frequencies of water and metabolites within the human brain

NASA Astrophysics Data System (ADS)

Chadzynski, Grzegorz L.; Bender, Benjamin; Groeger, Adriane; Erb, Michael; Klose, Uwe

2011-09-01

Chemical shift imaging (CSI) without water suppression was used to examine tissue-specific resonance frequencies of water and metabolites within the human brain. The aim was to verify if there are any regional differences in those frequencies and to determine the influence of chemical shift displacement in slice-selection direction. Unsuppressed spectra were acquired at 3 T from nine subjects. Resonance frequencies of water and after water signal removal of total choline, total creatine and NAA were estimated. Furthermore, frequency distances between the water and those resonances were calculated. Results were corrected for chemical shift displacement. Frequency distances between water and metabolites were consistent and greater for GM than for WM. The highest value of WM to GM difference (14 ppb) was observed for water to NAA frequency distance. This study demonstrates that there are tissue-specific differences between frequency distances of water and metabolites. Moreover, the influence of chemical shift displacement in slice-selection direction is showed to be negligible.

Tissue specific resonance frequencies of water and metabolites within the human brain.

PubMed

Chadzynski, Grzegorz L; Bender, Benjamin; Groeger, Adriane; Erb, Michael; Klose, Uwe

2011-09-01

Chemical shift imaging (CSI) without water suppression was used to examine tissue-specific resonance frequencies of water and metabolites within the human brain. The aim was to verify if there are any regional differences in those frequencies and to determine the influence of chemical shift displacement in slice-selection direction. Unsuppressed spectra were acquired at 3T from nine subjects. Resonance frequencies of water and after water signal removal of total choline, total creatine and NAA were estimated. Furthermore, frequency distances between the water and those resonances were calculated. Results were corrected for chemical shift displacement. Frequency distances between water and metabolites were consistent and greater for GM than for WM. The highest value of WM to GM difference (14ppb) was observed for water to NAA frequency distance. This study demonstrates that there are tissue-specific differences between frequency distances of water and metabolites. Moreover, the influence of chemical shift displacement in slice-selection direction is showed to be negligible. Copyright © 2011 Elsevier Inc. All rights reserved.

Characterization and prediction of monomer-based dose rate effects in electron-beam polymerization

NASA Astrophysics Data System (ADS)

Schissel, Sage M.; Lapin, Stephen C.; Jessop, Julie L. P.

2017-12-01

Properties of some materials produced by electron-beam (EB) induced polymerization appear dependent upon the rate at which the initiating dose was delivered. However, the magnitude of these dose rate effects (DREs) can vary greatly with different monomer formulations, suggesting DREs are dependent on chemical structure. The relationship among dose, dose rate, conversion, and the glass transition temperature (Tg) of the cured material was explored for an acrylate monomer series. A strong correlation was determined between the DRE magnitude and monomer size, and this correlation may be attributed to chain transfer. Using the Tg shift caused by changes in dose, a preliminary predictive relationship was developed to estimate the magnitude of the Tg DRE, enabling scale-up of process variables for polymers prone to dose rate effects.

Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds

DOE PAGES

Geng, Haifeng; Tran-Gyamfi, Mary B.; Lane, Todd W.; ...

2016-07-26

Open microalgae cultures host a myriad of bacteria, creating a complex system of interacting species that influence algal growth and health. Many algal microbiota studies have been conducted to determine the relative importance of bacterial taxa to algal culture health and physiological states, but these studies have not characterized the interspecies relationships in the microbial communities. Here we subjected Nanochroloropsis salina cultures to multiple chemical treatments (antibiotics and quorum sensing compounds) and obtained dense time-series data on changes to the microbial community using 16S gene amplicon metagenomic sequencing (21,029,577 reads for 23 samples) to measure microbial taxa-taxa abundance correlations. Short-termmore » treatment with antibiotics resulted in substantially larger shifts in the microbiota structure compared to changes observed following treatment with signaling compounds and glucose. We also calculated operational taxonomic unit (OTU) associations and generated OTU correlation networks to provide an overview of possible bacterial OTU interactions. This analysis identified five major cohesive modules of microbiota with similar co-abundance profiles across different chemical treatments. The Eigengenes of OTU modules were examined for correlation with different external treatment factors. This correlation-based analysis revealed that culture age (time) and treatment types have primary effects on forming network modules and shaping the community structure. Additional network analysis detected Alteromonadeles and Alphaproteobacteria as having the highest centrality, suggesting these species are “keystone” OTUs in the microbial community. Furthermore, we illustrated that the chemical tropodithietic acid, which is secreted by several species in the Alphaproteobacteria taxon, is able to drastically change the structure of the microbiota within 3 h. Lastly, taken together, these results provide valuable insights into the structure of the microbiota associated with N. salina cultures and how these structures change in response to chemical perturbations.« less

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

PubMed

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

2008-04-15

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

Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Geng, Haifeng; Tran-Gyamfi, Mary B.; Lane, Todd W.

Open microalgae cultures host a myriad of bacteria, creating a complex system of interacting species that influence algal growth and health. Many algal microbiota studies have been conducted to determine the relative importance of bacterial taxa to algal culture health and physiological states, but these studies have not characterized the interspecies relationships in the microbial communities. Here we subjected Nanochroloropsis salina cultures to multiple chemical treatments (antibiotics and quorum sensing compounds) and obtained dense time-series data on changes to the microbial community using 16S gene amplicon metagenomic sequencing (21,029,577 reads for 23 samples) to measure microbial taxa-taxa abundance correlations. Short-termmore » treatment with antibiotics resulted in substantially larger shifts in the microbiota structure compared to changes observed following treatment with signaling compounds and glucose. We also calculated operational taxonomic unit (OTU) associations and generated OTU correlation networks to provide an overview of possible bacterial OTU interactions. This analysis identified five major cohesive modules of microbiota with similar co-abundance profiles across different chemical treatments. The Eigengenes of OTU modules were examined for correlation with different external treatment factors. This correlation-based analysis revealed that culture age (time) and treatment types have primary effects on forming network modules and shaping the community structure. Additional network analysis detected Alteromonadeles and Alphaproteobacteria as having the highest centrality, suggesting these species are “keystone” OTUs in the microbial community. Furthermore, we illustrated that the chemical tropodithietic acid, which is secreted by several species in the Alphaproteobacteria taxon, is able to drastically change the structure of the microbiota within 3 h. Lastly, taken together, these results provide valuable insights into the structure of the microbiota associated with N. salina cultures and how these structures change in response to chemical perturbations.« less

Intermolecular shielding contributions studied by modeling the 13C chemical-shift tensors of organic single crystals with plane waves

PubMed Central

Johnston, Jessica C.; Iuliucci, Robbie J.; Facelli, Julio C.; Fitzgerald, George; Mueller, Karl T.

2009-01-01

In order to predict accurately the chemical shift of NMR-active nuclei in solid phase systems, magnetic shielding calculations must be capable of considering the complete lattice structure. Here we assess the accuracy of the density functional theory gauge-including projector augmented wave method, which uses pseudopotentials to approximate the nodal structure of the core electrons, to determine the magnetic properties of crystals by predicting the full chemical-shift tensors of all 13C nuclides in 14 organic single crystals from which experimental tensors have previously been reported. Plane-wave methods use periodic boundary conditions to incorporate the lattice structure, providing a substantial improvement for modeling the chemical shifts in hydrogen-bonded systems. Principal tensor components can now be predicted to an accuracy that approaches the typical experimental uncertainty. Moreover, methods that include the full solid-phase structure enable geometry optimizations to be performed on the input structures prior to calculation of the shielding. Improvement after optimization is noted here even when neutron diffraction data are used for determining the initial structures. After geometry optimization, the isotropic shift can be predicted to within 1 ppm. PMID:19831448

Computation of deuterium isotope perturbation of 13C NMR chemical shifts of alkanes: a local mode zero-point level approach.

PubMed

Yang, Kin S; Hudson, Bruce

2010-11-25

Replacement of H by D perturbs the (13)C NMR chemical shifts of an alkane molecule. This effect is largest for the carbon to which the D is attached, diminishing rapidly with intervening bonds. The effect is sensitive to stereochemistry and is large enough to be measured reliably. A simple model based on the ground (zero point) vibrational level and treating only the C-H(D) degrees of freedom (local mode approach) is presented. The change in CH bond length with H/D substitution as well as the reduction in the range of the zero-point level probability distribution for the stretch and both bend degrees of freedom are computed. The (13)C NMR chemical shifts are computed with variation in these three degrees of freedom, and the results are averaged with respect to the H and D distribution functions. The resulting differences in the zero-point averaged chemical shifts are compared with experimental values of the H/D shifts for a series of cycloalkanes, norbornane, adamantane, and protoadamantane. Agreement is generally very good. The remaining differences are discussed. The proton spectrum of cyclohexane- is revisited and updated with improved agreement with experiment.

Structure and electronic properties of azadirachtin.

PubMed

de Castro, Elton A S; de Oliveira, Daniel A B; Farias, Sergio A S; Gargano, Ricardo; Martins, João B L

2014-02-01

We performed a combined DFT and Monte Carlo (13)C NMR chemical-shift study of azadirachtin A, a triterpenoid that acts as a natural insect antifeedant. A conformational search using a Monte Carlo technique based on the RM1 semiempirical method was carried out in order to establish its preferred structure. The B3LYP/6-311++G(d,p), wB97XD/6-311++G(d,p), M06/6-311++G(d,p), M06-2X/6-311++G(d,p), and CAM-B3LYP/6-311++G(d,p) levels of theory were used to predict NMR chemical shifts. A Monte Carlo population-weighted average spectrum was produced based on the predicted Boltzmann contributions. In general, good agreement between experimental and theoretical data was obtained using both methods, and the (13)C NMR chemical shifts were predicted highly accurately. The geometry was optimized at the semiempirical level and used to calculate the NMR chemical shifts at the DFT level, and these shifts showed only minor deviations from those obtained following structural optimization at the DFT level, and incurred a much lower computational cost. The theoretical ultraviolet spectrum showed a maximum absorption peak that was mainly contributed by the tiglate group.

Tautomerism and spectroscopic properties of the immunosuppressant azathioprine.

PubMed

Makhyoun, Mohamed A; Massoud, Raghdaa A; Soliman, Saied M

2013-10-01

The molecular structure and the relative stabilities of the four possible tautomers of the immunosuppressant azathioprine (AZA) are calculated by DFT/B3LYP method using different basis sets. The results of the energy analysis and thermodynamic treatment of the obtained data are used to predict the relative stabilities of the AZA tautomers. The effect of solvents such as DMSO and water on the stability of the AZA tautomers was studied using the polarized continuum method (PCM) at the same level of theory. The calculation predicted that, the total energies of all tautomers are decreased indicating that all tautomers are more or less stabilized by the solvent effect. The vibrational spectra of AZA are calculated using the same level of theory and the results are compared with the experimentally measured FTIR spectra. Good correlation is obtained between the experimental and calculated vibrational frequencies (R(2)=0.997). The electronic spectra of AZA in gas phase and in methanol as solvent are calculated using the TD-DFT method. The calculations predicted bathochromic shift in all the spectral bands in presence of solvent compared to the gas phase. Also the NMR spectra of all tautomers are calculated and the results are correlated with the experimental NMR chemical shifts where the most stable tautomer gives the best correlation coefficient (R(2)=0.996). Copyright © 2013 Elsevier B.V. All rights reserved.

Regime shifts driven by dynamic correlations in gene expression noise

NASA Astrophysics Data System (ADS)

Sharma, Yogita; Dutta, Partha Sharathi

2017-08-01

Gene expression is a noisy process that leads to regime shifts between alternative steady states among individual living cells, inducing phenotypic variability. The effects of white noise on the regime shift in bistable systems have been well characterized, however little is known about such effects of colored noise (noise with nonzero correlation time). Here, we show that noise correlation time, by considering a genetic circuit of autoactivation, can have a significant effect on the regime shift between distinct phenotypic states in gene expression. We demonstrate this theoretically, using stochastic potential, stationary probability density function, and first-passage time based on the Fokker-Planck description, where the Ornstein-Uhlenbeck process is used to model colored noise. We find that an increase in noise correlation time in the degradation rate can induce a regime shift from a low to a high protein concentration state and enhance the bistable regime, while an increase in noise correlation time in the basal rate retains the bimodal distribution. We then show how cross-correlated colored noises in basal and degradation rates can induce regime shifts from a low to a high protein concentration state, but reduce the bistable regime. We also validate these results through direct numerical simulations of the stochastic differential equation. In gene expression understanding the causes of regime shift to a harmful phenotype could improve early therapeutic intervention in complex human diseases.

Phosphorus-31, sup 15 N, and sup 13 C NMR of glyphosate: Comparison of pH titrations to the herbicidal dead-end complex with 5-enolpyruvoylshikimate-3-phosphate synthase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castellino, S.; Leo, G.C.; Sammons, R.D.

1989-05-02

The herbicidal dead-end ternary complex (E{sup S3P}{sub Glyph}) of glyphosate (N-(phosphonomethyl)glycine) with 5-enolpyruvoylshikimate-3-phosphate synthase (EPSPS) and the substrate shikimate 3-phosphate (S3P) has been characterized by {sup 31}P, {sup 15}N, and {sup 13}C NMR. The NMR spectra of EPSPS-bound glyphosate show unique chemical shifts ({delta}) for each of the three nuclei. By {sup 31}P NMR, glyphosate in the dead-end complex is a distinct species 3.5 ppm downfield from free glyphosate. The {sup 13}C signal of glyphosate in the dead-end complex is shifted 4 ppm downfield from that of free glyphosate. The {sup 15}N signal for glyphosate (99%) in the dead-end complexmore » is 5 ppm further downfield than that of any free zwitterionic species and 10 ppm downfield from that of the average free species at pH 10.1. The structures of each ionic state of glyphosate are modeled with force field calculations by using MacroModel. A correlation is made for the {sup 31}P {delta} and the C-P-O bond angle, and the {sup 13}C and {sup 15}N {delta} values are postulated to be related to C-C-O and C-N-C bond angles, respectively. The downfield {sup 31}P chemical shift perturbation for S3P in the EPSPS binary complex is consistent with ionization of the 3-phosphate of S3P upon binding. Comparison with the S3P {sup 31}P {delta} vs pH titration curve specifies predominantly the dianion of the 3-phosphate in the E{sup S3P} binary complex, while the E{sup S3P}{sub Glyph} complex indicates net protonation at the 3-phosphate. Chemical shift perturbations of this latter type may be explained by changes in the O-P-O bond angle.« less

Use of 13Cα Chemical-Shifts in Protein Structure Determination

PubMed Central

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

2008-01-01

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

Protein Structure Determination from Pseudocontact Shifts Using ROSETTA

PubMed Central

Schmitz, Christophe; Vernon, Robert; Otting, Gottfried; Baker, David; Huber, Thomas

2013-01-01

Paramagnetic metal ions generate pseudocontact shifts (PCSs) in nuclear magnetic resonance spectra that are manifested as easily measurable changes in chemical shifts. Metals can be incorporated into proteins through metal binding tags, and PCS data constitute powerful long-range restraints on the positions of nuclear spins relative to the coordinate system of the magnetic susceptibility anisotropy tensor (Δχ-tensor) of the metal ion. We show that three-dimensional structures of proteins can reliably be determined using PCS data from a single metal binding site combined with backbone chemical shifts. The program PCS-ROSETTA automatically determines the Δχ-tensor and metal position from the PCS data during the structure calculations, without any prior knowledge of the protein structure. The program can determine structures accurately for proteins of up to 150 residues, offering a powerful new approach to protein structure determination that relies exclusively on readily measurable backbone chemical shifts and easily discriminates between correctly and incorrectly folded conformations. PMID:22285518

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-08-21

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

Design and chemical synthesis of iodine-containing molecules for application to solar-pumped I* lasers

NASA Technical Reports Server (NTRS)

Shiner, C. S.

1985-01-01

This work is directed toward the design and chemical synthesis of new media for solar-pumped I* lasers. In view of the desirability of preparing a perfluoroalkyl iodide absorbing strongly at 300 nm, the relationship betwen perfluoroalkyl iodide structure and the corresponding absorption wavelength was reexamined. Analysis of existing data suggests that, in this family of compounds, the absorption maximum shifts to longer wavelength, as desired, as the C-I bond in the lasant is progressively weakened. Weakening of the C-I bond correlates, in turn, with increasing stability of the perfluoroalkyl radical formed upon photodissociation of the iodide. The extremely promising absorption characteristics of perfluoro-tert-butyl iodide can be accounted for on this basis. A new technique of diode laser probing to obtain precise yields of I* atoms in photodissociation was also developed.

Relativistic effects on the NMR parameters of Si, Ge, Sn, and Pb alkynyl compounds: Scalar versus spin-orbit effects

NASA Astrophysics Data System (ADS)

Demissie, Taye B.

2017-11-01

The NMR chemical shifts and indirect spin-spin coupling constants of 12 molecules containing 29Si, 73Ge, 119Sn, and 207Pb [X(CCMe)4, Me2X(CCMe)2, and Me3XCCH] are presented. The results are obtained from non-relativistic as well as two- and four-component relativistic density functional theory (DFT) calculations. The scalar and spin-orbit relativistic contributions as well as the total relativistic corrections are determined. The main relativistic effect in these molecules is not due to spin-orbit coupling but rather to the scalar relativistic contraction of the s-shells. The correlation between the calculated and experimental indirect spin-spin coupling constants showed that the four-component relativistic density functional theory (DFT) approach using the Perdew's hybrid scheme exchange-correlation functional (PBE0; using the Perdew-Burke-Ernzerhof exchange and correlation functionals) gives results in good agreement with experimental values. The indirect spin-spin coupling constants calculated using the spin-orbit zeroth order regular approximation together with the hybrid PBE0 functional and the specially designed J-coupling (JCPL) basis sets are in good agreement with the results obtained from the four-component relativistic calculations. For the coupling constants involving the heavy atoms, the relativistic corrections are of the same order of magnitude compared to the non-relativistically calculated results. Based on the comparisons of the calculated results with available experimental values, the best results for all the chemical shifts and non-existing indirect spin-spin coupling constants for all the molecules are reported, hoping that these accurate results will be used to benchmark future DFT calculations. The present study also demonstrates that the four-component relativistic DFT method has reached a level of maturity that makes it a convenient and accurate tool to calculate indirect spin-spin coupling constants of "large" molecular systems involving heavy atoms.

Solid-state (185/187)Re NMR and GIPAW DFT study of perrhenates and Re2(CO)10: chemical shift anisotropy, NMR crystallography, and a metal-metal bond.

PubMed

Widdifield, Cory M; Perras, Frédéric A; Bryce, David L

2015-04-21

Advances in solid-state nuclear magnetic resonance (SSNMR) methods, such as dynamic nuclear polarization (DNP), intricate pulse sequences, and increased applied magnetic fields, allow for the study of systems which even very recently would be impractical. However, SSNMR methods using certain quadrupolar probe nuclei (i.e., I > 1/2), such as (185/187)Re remain far from fully developed due to the exceedingly strong interaction between the quadrupole moment of these nuclei and local electric field gradients (EFGs). We present a detailed high-field (B0 = 21.1 T) experimental SSNMR study on several perrhenates (KReO4, AgReO4, Ca(ReO4)2·2H2O), as well as ReO3 and Re2(CO)10. We propose solid ReO3 as a new rhenium SSNMR chemical shift standard due to its reproducible and sharp (185/187)Re NMR resonances. We show that for KReO4, previously poorly understood high-order quadrupole-induced effects (HOQIE) on the satellite transitions can be used to measure the EFG tensor asymmetry (i.e., ηQ) to nearly an order-of-magnitude greater precision than competing SSNMR and nuclear quadrupole resonance (NQR) approaches. Samples of AgReO4 and Ca(ReO4)2·2H2O enable us to comment on the effects of counter-ions and hydration upon Re(vii) chemical shifts. Calcium-43 and (185/187)Re NMR tensor parameters allow us to conclude that two proposed crystal structures for Ca(ReO4)2·2H2O, which would be considered as distinct, are in fact the same structure. Study of Re2(CO)10 provides insights into the effects of Re-Re bonding on the rhenium NMR tensor parameters and rhenium oxidation state on the Re chemical shift value. As overtone NQR experiments allowed us to precisely measure the (185/187)Re EFG tensor of Re2(CO)10, we were able to measure rhenium chemical shift anisotropy (CSA) for the first time in a powdered sample. Experimental observations are supported by gauge-including projector augmented-wave (GIPAW) density functional theory (DFT) calculations, with NMR tensor calculations also provided for NH4ReO4, NaReO4 and RbReO4. These calculations are able to reproduce many of the experimental trends in rhenium δiso values and EFG tensor magnitudes. Using KReO4 as a prototypical perrhenate-containing system, we establish a correlation between the tetrahedral shear strain parameter (|ψ|) and the nuclear electric quadrupolar coupling constant (CQ), which enables the refinement of the structure of ND4ReO4. Shortcomings in traditional DFT approaches, even when including relativistic effects via the zeroth-order regular approximation (ZORA), for calculating rhenium NMR tensor parameters are identified for Re2(CO)10.

Unusually large chemical potential shift in a degenerate semiconductor: Angle-resolved photoemission study of SnSe and Na-doped SnSe

NASA Astrophysics Data System (ADS)

Maeda, M.; Yamamoto, K.; Mizokawa, T.; Saini, N. L.; Arita, M.; Namatame, H.; Taniguchi, M.; Tan, G.; Zhao, L. D.; Kanatzidis, M. G.

2018-03-01

We have studied the electronic structure of SnSe and Na-doped SnSe by means of angle-resolved photoemission spectroscopy. The valence-band top reaches the Fermi level by the Na doping, indicating that Na-doped SnSe can be viewed as a degenerate semiconductor. However, in the Na-doped system, the chemical potential shift with temperature is unexpectedly large and is apparently inconsistent with the degenerate semiconductor picture. The large chemical potential shift and anomalous spectral shape are key ingredients for an understanding of the novel metallic state with the large thermoelectric performance in Na-doped SnSe.

Unusually large chemical potential shift in a degenerate semiconductor: Angle-resolved photoemission study of SnSe and Na-doped SnSe

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maeda, M.; Yamamoto, K.; Mizokawa, T.

In this work, we have studied the electronic structure of SnSe and Na-doped SnSe by means of angle-resolved photoemission spectroscopy. The valence-band top reaches the Fermi level by the Na doping, indicating that Na-doped SnSe can be viewed as a degenerate semiconductor. However, in the Na-doped system, the chemical potential shift with temperature is unexpectedly large and is apparently inconsistent with the degenerate semiconductor picture. Lastly, the large chemical potential shift and anomalous spectral shape are key ingredients for an understanding of the novel metallic state with the large thermoelectric performance in Na-doped SnSe.

Unusually large chemical potential shift in a degenerate semiconductor: Angle-resolved photoemission study of SnSe and Na-doped SnSe

DOE PAGES

Maeda, M.; Yamamoto, K.; Mizokawa, T.; ...

2018-03-23

In this work, we have studied the electronic structure of SnSe and Na-doped SnSe by means of angle-resolved photoemission spectroscopy. The valence-band top reaches the Fermi level by the Na doping, indicating that Na-doped SnSe can be viewed as a degenerate semiconductor. However, in the Na-doped system, the chemical potential shift with temperature is unexpectedly large and is apparently inconsistent with the degenerate semiconductor picture. Lastly, the large chemical potential shift and anomalous spectral shape are key ingredients for an understanding of the novel metallic state with the large thermoelectric performance in Na-doped SnSe.

Calculation of binary magnetic properties and potential energy curve in xenon dimer: second virial coefficient of (129)Xe nuclear shielding.

PubMed

Hanni, Matti; Lantto, Perttu; Runeberg, Nino; Jokisaari, Jukka; Vaara, Juha

2004-09-22

Quantum chemical calculations of the nuclear shielding tensor, the nuclear quadrupole coupling tensor, and the spin-rotation tensor are reported for the Xe dimer using ab initio quantum chemical methods. The binary chemical shift delta, the anisotropy of the shielding tensor Delta sigma, the nuclear quadrupole coupling tensor component along the internuclear axis chi( parallel ), and the spin-rotation constant C( perpendicular ) are presented as a function of internuclear distance. The basis set superposition error is approximately corrected for by using the counterpoise correction (CP) method. Electron correlation effects are systematically studied via the Hartree-Fock, complete active space self-consistent field, second-order Møller-Plesset many-body perturbation, and coupled-cluster singles and doubles (CCSD) theories, the last one without and with noniterative triples, at the nonrelativistic all-electron level. We also report a high-quality theoretical interatomic potential for the Xe dimer, gained using the relativistic effective potential/core polarization potential scheme. These calculations used valence basis set of cc-pVQZ quality supplemented with a set of midbond functions. The second virial coefficient of Xe nuclear shielding, which is probably the experimentally best-characterized intermolecular interaction effect in nuclear magnetic resonance spectroscopy, is computed as a function of temperature, and compared to experiment and earlier theoretical results. The best results for the second virial coefficient, obtained using the CCSD(CP) binary chemical shift curve and either our best theoretical potential or the empirical potentials from the literature, are in good agreement with experiment. Zero-point vibrational corrections of delta, Delta sigma, chi (parallel), and C (perpendicular) in the nu=0, J=0 rovibrational ground state of the xenon dimer are also reported.

Soil biota and agriculture production in conventional and organic farming

NASA Astrophysics Data System (ADS)

Schrama, Maarten; de Haan, Joj; Carvalho, Sabrina; Kroonen, Mark; Verstegen, Harry; Van der Putten, Wim

2015-04-01

Sustainable food production for a growing world population requires a healthy soil that can buffer environmental extremes and minimize its losses. There are currently two views on how to achieve this: by intensifying conventional agriculture or by developing organically based agriculture. It has been established that yields of conventional agriculture can be 20% higher than of organic agriculture. However, high yields of intensified conventional agriculture trade off with loss of soil biodiversity, leaching of nutrients, and other unwanted ecosystem dis-services. One of the key explanations for the loss of nutrients and GHG from intensive agriculture is that it results in high dynamics of nutrient losses, and policy has aimed at reducing temporal variation. However, little is known about how different agricultural practices affect spatial variation, and it is unknown how soil fauna acts this. In this study we compare the spatial and temporal variation of physical, chemical and biological parameters in a long term (13-year) field experiment with two conventional farming systems (low and medium organic matter input) and one organic farming system (high organic matter input) and we evaluate the impact on ecosystem services that these farming systems provide. Soil chemical (N availability, N mineralization, pH) and soil biological parameters (nematode abundance, bacterial and fungal biomass) show considerably higher spatial variation under conventional farming than under organic farming. Higher variation in soil chemical and biological parameters coincides with the presence of 'leaky' spots (high nitrate leaching) in conventional farming systems, which shift unpredictably over the course of one season. Although variation in soil physical factors (soil organic matter, soil aggregation, soil moisture) was similar between treatments, but averages were higher under organic farming, indicating more buffered conditions for nutrient cycling. All these changes coincide with pronounced shifts in soil fauna composition (nematodes, earthworms) and an increase in earthworm activity. Hence, more buffered conditions and shifts in soil fauna composition under organic farming may underlie the observed reduction in spatial variation of soil chemical and biological parameters, which in turn correlates positively with a long-term increase in yield. Our study highlights the need for both policymakers and farmers alike to support spatial stability-increasing farming.

A canonical correlation analysis based EMG classification algorithm for eliminating electrode shift effect.

PubMed

Zhe Fan; Zhong Wang; Guanglin Li; Ruomei Wang

2016-08-01

Motion classification system based on surface Electromyography (sEMG) pattern recognition has achieved good results in experimental condition. But it is still a challenge for clinical implement and practical application. Many factors contribute to the difficulty of clinical use of the EMG based dexterous control. The most obvious and important is the noise in the EMG signal caused by electrode shift, muscle fatigue, motion artifact, inherent instability of signal and biological signals such as Electrocardiogram. In this paper, a novel method based on Canonical Correlation Analysis (CCA) was developed to eliminate the reduction of classification accuracy caused by electrode shift. The average classification accuracy of our method were above 95% for the healthy subjects. In the process, we validated the influence of electrode shift on motion classification accuracy and discovered the strong correlation with correlation coefficient of >0.9 between shift position data and normal position data.

Structure of dimethylphenyl betaine hydrochloride studied by X-ray diffraction, DFT calculation, NMR and FTIR spectra

NASA Astrophysics Data System (ADS)

Szafran, M.; Katrusiak, A.; Dega-Szafran, Z.; Kowalczyk, I.

2013-01-01

The structure of dimethylphenyl betaine hydrochloride (1) has been studied by X-ray diffraction, DFT calculations, NMR and FTIR spectra. The crystals are monoclinic, space group P21/c. In the crystal, the Cl- anion is connected with protonated betaine through the O-H⋯Cl- hydrogen bond of 2.943(2) Å. The structures in the gas phase (2) and water solution (3) have been optimized by the B3LYP/6-311++G(d,p) approach and the geometrical results have been compared with the X-ray data of 1. The FTIR spectrum of the solid compound is consistent with the X-ray results. The probable assignments of the anharmonic experimental vibrational frequencies of the investigated chloride (1) based on the calculated harmonic frequencies in water solution (3) are proposed. The correlations between the experimental 1H and 13C NMR chemical shifts (δexp) of 1 in D2O and the magnetic isotropic shielding constants (σcalc) calculated by the GIAO/B3LYP/6-311G++(d,p) approach, using the screening solvation model (COSMO), δexp = a + b σcalc, for optimized molecule 3 in water solution are linear and correctly reproduce the experimental chemical shifts.

Physicochemical characterization and structural evaluation of a specific 2:1 cocrystal of naproxen-nicotinamide.

PubMed

Ando, Shigeru; Kikuchi, Junko; Fujimura, Yuko; Ida, Yasuo; Higashi, Kenjirou; Moribe, Kunikazu; Yamamoto, Keiji

2012-09-01

Physicochemical characterization and structural evaluation of a 2:1 naproxen-nicotinamide cocrystal were performed. The 2:1 cocrystal showed rapid naproxen dissolution and less water vapor adsorption, indicating better pharmaceutical properties of naproxen. The unique 2:1 cocrystal formation was evaluated by solid-state nuclear magnetic resonance (NMR). The assignments of all H and (13) C peaks for naproxen and the cocrystal were performed using dipolar-insensitive nuclei enhanced by polarization transfer and (1) H-(13) C cross-polarization (CP)-heteronuclear correlation (HETCOR) NMR measurements. The (13) C chemical shift revealed that two naproxen molecules and one nicotinamide molecule existed in the asymmetric unit of the cocrystal. The (1) H chemical shifts indicated that the carboxylic group of the naproxen in the cocrystal was nonionized, and the CH-π interaction between naproxens was very strong. From the (1) H-(13) C CP-HETCOR NMR spectrum with contact time of 5 ms, two different synthons, carboxylic acid-amide and carboxylic acid-pyridine ring, were found between naproxen and nicotinamide. Single-crystal X-ray analysis, which supported the solid-state NMR results, clarified the geometry and intermolecular interactions in more detail. The structure is unique among pharmaceutical cocrystals because each carboxyl group of the two naproxens formed different intermolecular synthons. Copyright © 2012 Wiley Periodicals, Inc.

Fragment Screening of Human Aquaporin 1

PubMed Central

To, Janet; Torres, Jaume

2016-01-01

Aquaporins (AQPs) are membrane proteins that enable water transport across cellular plasma membranes in response to osmotic gradients. Phenotypic analyses have revealed important physiological roles for AQPs, and the potential for AQP water channel modulators in various disease states has been proposed. For example, AQP1 is overexpressed in tumor microvessels, and this correlates with higher metastatic potential and aggressiveness of the malignancy. Chemical modulators would help in identifying the precise contribution of water channel activity in these disease states. These inhibitors would also be important therapeutically, e.g., in anti-cancer treatment. This perceived importance contrasts with the lack of success of high-throughput screens (HTS) to identify effective and specific inhibitors of aquaporins. In this paper, we have screened a library of 1500 “fragments”, i.e., smaller than molecules used in HTS, against human aquaporin (hAQP1) using a thermal shift assay and surface plasmon resonance. Although these fragments may not inhibit their protein target, they bound to and stabilized hAQP1 (sub mM binding affinities (KD), with an temperature of aggregation shift ΔTagg of +4 to +50 °C) in a concentration-dependent fashion. Chemically expanded versions of these fragments should follow the determination of their binding site on the aquaporin surface. PMID:27023529

Solution conformation of a peptide fragment representing a proposed RNA-binding site of a viral coat protein studied by two-dimensional NMR

DOE Office of Scientific and Technical Information (OSTI.GOV)

van der Graaf, M.; van Mierlo, C.P.M.; Hemminga, M.A.

1991-06-11

The first 25 amino acids of the coat protein of cowpea chlorotic mottle virus are essential for binding the encapsidated RNA. Although an {alpha}-helical conformation has been predicted for this highly positively charged N-terminal region. No experimental evidence for this conformation has been presented so far. In this study, two-dimensional proton NMR experiments were performed on a chemically synthesized pentacosapeptide containing the first 25 amino acids of this coat protein. All resonances could be assigned by a combined use of two-dimensional correlated spectroscopy and nuclear Overhauser enhancement spectroscopy carried out at four different temperatures. Various NMR parameters indicate the presencemore » of a conformational ensemble consisting of helical structures rapidly converting into more extended states. Differences in chemical shifts and nuclear Overhauser effects indicate that lowering the temperature induces a shift of the dynamic equilibrium toward more helical structures. At 10{degrees}C, a perceptible fraction of the conformational ensemble consists of structures with an {alpha}-helical conformation between residues 9 and 17, likely starting with a turnlike structure around Thr9 and Arg10. Both the conformation and the position of this helical region agree well with the secondary structure predictions mentioned above.« less

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

ERIC Educational Resources Information Center

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

2014-01-01

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

Revisiting HgCl 2: A solution- and solid-state 199Hg NMR and ZORA-DFT computational study

NASA Astrophysics Data System (ADS)

Taylor, R. E.; Carver, Colin T.; Larsen, Ross E.; Dmitrenko, Olga; Bai, Shi; Dybowski, C.

2009-07-01

The 199Hg chemical-shift tensor of solid HgCl 2 was determined from spectra of polycrystalline materials, using static and magic-angle spinning (MAS) techniques at multiple spinning frequencies and field strengths. The chemical-shift tensor of solid HgCl 2 is axially symmetric ( η = 0) within experimental error. The 199Hg chemical-shift anisotropy (CSA) of HgCl 2 in a frozen solution in dimethylsulfoxide (DMSO) is significantly smaller than that of the solid, implying that the local electronic structure in the solid is different from that of the material in solution. The experimental chemical-shift results (solution and solid state) are compared with those predicted by density functional theory (DFT) calculations using the zeroth-order regular approximation (ZORA) to account for relativistic effects. 199Hg spin-lattice relaxation of HgCl 2 dissolved in DMSO is dominated by a CSA mechanism, but a second contribution to relaxation arises from ligand exchange. Relaxation in the solid state is independent of temperature, suggesting relaxation by paramagnetic impurities or defects.

Predictive Quantum Chemistry: A Step Toward ``Chemistry Without Test Tubes''

NASA Astrophysics Data System (ADS)

Perera, Ajith

2007-12-01

The merits of the claims made in two recent papers entitled "First generation of pentazole (HN5, pentazolic acid), the final azole, and a zinc pentazolate salt in solution: A new N-dearylation of 1-(p-methoxyphenyl) pyrazoles, a 2-(p-methoxyphenyl) tetrazole and application of the methodology to 1-(p-methoxyphenyl) pentazole" (R. N. Butler, J. C. Stephan and L. A. Burke, J. Chem. Commun. 2003, 1016-1017) and "First generation of the pentazolate anion is solution is far from over" (T. Schroer, R. Haiges, S. Schneider and K. O. Christe, Chem. Commun. 2005, 1607-1609) are verified by predictive quality theoretical methods. Knowing whether the CF3OH in HF solution undergoes protonation to form CF3[OH2]+ is critical to the success of the recently proposed synthetic route to form the prototype perfluorinated alcohol, CF3OH. Chirstie and co-workers first considered the 13C and 19F shielding constants to distinguish CF3OH and CF3[OH2]+, but it turns out that they both have similar chemical shifts. Furthermore, they noted that the computed 13C chemical shifts differ by 11 ppm from the measured ones and claimed that "These findings presented a dilemma because either experimental or the calculated shifts has to be seriously flawed and, therefore chemical shifts alone it was impossible to decide whether CF3OH in liquid HF is protonated or not". Instead of chemical shifts, they propose to use 13C-19F NMR spin-spin coupling constants and argue that the observed 20 Hz difference of 1J(13C-19F) to the increase in the covalent character upon protonation. The reported discrepancy in computed and measured chemical shifts is reexamined and the spin-spin coupling constants results are verified by the predicative-level calculations.

Usefulness of chemical-shift MRI in discriminating increased liver echogenicity in glycogenosis.

PubMed

Pozzato, C; Dall'asta, C; Radaelli, G; Torcoletti, M; Formenti, A; Riva, E; Cornalba, G; Pontiroli, A E

2007-11-01

Glycogen storage diseases are inherited defects which cause accumulation of glycogen in the tissues. Hepatic steatosis is defined as accumulation of fat within hepatocytes. On sonography, liver shows increased echogenicity both in glycogen storage diseases and steatosis. Liver hyperechogenicity in glycogen storage diseases may depend on accumulation of glycogen and/or fat. Chemical-shift magnetic resonance imaging can discriminate tissues only containing water from those containing both fat and water. The primary aim of the present study was to evaluate the usefulness of liver chemical-shift magnetic resonance imaging for detecting liver steatosis in patients with metabolic impairment due to glycogen storage diseases. Twelve patients with type I (n=8) or type III (n=4) glycogen storage diseases were studied and compared to 12 obese-overweight subjects with known liver steatosis. As control group 12 lean normal voluntary subjects were recruited. Liver was evaluated by sonography and chemical-shift magnetic resonance imaging to calculate hepatic fat fraction. A significant difference in echogenicity between patients with glycogen storage diseases and normal subjects was observed (p<0.05), while this difference was not present between overweight-obese and glycogen storage diseases patients. On the contrary, fat fraction was similar between glycogen storage diseases patients and normal subjects and different between glycogen storage diseases patients and overweight-obese (p<0.05). The present data suggest that chemical-shift magnetic resonance imaging may exclude fat deposition as a cause of liver hyperechogenicity in subjects with glycogen storage diseases.

Using 1H and 13C NMR chemical shifts to determine cyclic peptide conformations: a combined molecular dynamics and quantum mechanics approach.

PubMed

Nguyen, Q Nhu N; Schwochert, Joshua; Tantillo, Dean J; Lokey, R Scott

2018-05-10

Solving conformations of cyclic peptides can provide insight into structure-activity and structure-property relationships, which can help in the design of compounds with improved bioactivity and/or ADME characteristics. The most common approaches for determining the structures of cyclic peptides are based on NMR-derived distance restraints obtained from NOESY or ROESY cross-peak intensities, and 3J-based dihedral restraints using the Karplus relationship. Unfortunately, these observables are often too weak, sparse, or degenerate to provide unequivocal, high-confidence solution structures, prompting us to investigate an alternative approach that relies only on 1H and 13C chemical shifts as experimental observables. This method, which we call conformational analysis from NMR and density-functional prediction of low-energy ensembles (CANDLE), uses molecular dynamics (MD) simulations to generate conformer families and density functional theory (DFT) calculations to predict their 1H and 13C chemical shifts. Iterative conformer searches and DFT energy calculations on a cyclic peptide-peptoid hybrid yielded Boltzmann ensembles whose predicted chemical shifts matched the experimental values better than any single conformer. For these compounds, CANDLE outperformed the classic NOE- and 3J-coupling-based approach by disambiguating similar β-turn types and also enabled the structural elucidation of the minor conformer. Through the use of chemical shifts, in conjunction with DFT and MD calculations, CANDLE can help illuminate conformational ensembles of cyclic peptides in solution.

In vivo single-shot 13C spectroscopic imaging of hyperpolarized metabolites by spatiotemporal encoding

NASA Astrophysics Data System (ADS)

Schmidt, Rita; Laustsen, Christoffer; Dumez, Jean-Nicolas; Kettunen, Mikko I.; Serrao, Eva M.; Marco-Rius, Irene; Brindle, Kevin M.; Ardenkjaer-Larsen, Jan Henrik; Frydman, Lucio

2014-03-01

Hyperpolarized metabolic imaging is a growing field that has provided a new tool for analyzing metabolism, particularly in cancer. Given the short life times of the hyperpolarized signal, fast and effective spectroscopic imaging methods compatible with dynamic metabolic characterizations are necessary. Several approaches have been customized for hyperpolarized 13C MRI, including CSI with a center-out k-space encoding, EPSI, and spectrally selective pulses in combination with spiral EPI acquisitions. Recent studies have described the potential of single-shot alternatives based on spatiotemporal encoding (SPEN) principles, to derive chemical-shift images within a sub-second period. By contrast to EPSI, SPEN does not require oscillating acquisition gradients to deliver chemical-shift information: its signal encodes both spatial as well as chemical shift information, at no extra cost in experimental complexity. SPEN MRI sequences with slice-selection and arbitrary excitation pulses can also be devised, endowing SPEN with the potential to deliver single-shot multi-slice chemical shift images, with a temporal resolution required for hyperpolarized dynamic metabolic imaging. The present work demonstrates this with initial in vivo results obtained from SPEN-based imaging of pyruvate and its metabolic products, after injection of hyperpolarized [1-13C]pyruvate. Multi-slice chemical-shift images of healthy rats were obtained at 4.7 T in the region of the kidney, and 4D (2D spatial, 1D spectral, 1D temporal) data sets were obtained at 7 T from a murine lymphoma tumor model.

In vivo single-shot 13C spectroscopic imaging of hyperpolarized metabolites by spatiotemporal encoding

PubMed Central

Schmidt, Rita; Laustsen, Christoffer; Dumez, Jean-Nicolas; Kettunen, Mikko I.; Serrao, Eva M.; Marco-Rius, Irene; Brindle, Kevin M.; Ardenkjaer-Larsen, Jan Henrik; Frydman, Lucio

2016-01-01

Hyperpolarized metabolic imaging is a growing field that has provided a tool for analyzing metabolism, particularly in cancer. Given the short life times of the hyperpolarized signal, fast and effective spectroscopic imaging methods compatible with dynamic metabolic characterizations are necessary. Several approaches have been customized for hyperpolarized 13C MRI, including CSI with a center-out k-space encoding, EPSI, and spectrally selective pulses in combination with spiral EPI acquisitions. Recent studies have described the potential of single-shot alternatives based on spatiotemporal encoding (SPEN) principles, to derive chemical-shift images within a sub-second period. By contrast to EPSI, SPEN does not require oscillating acquisition gradients to deliver chemical-shift information: its signal encodes both spatial as well as chemical shift information, at no extra cost in experimental complexity. SPEN MRI sequences with slice-selection and arbitrary excitation pulses can also be devised, endowing SPEN with the potential to deliver single-shot multi-slice chemical shift images, with a temporal resolution required for hyperpolarized dynamic metabolic imaging. The present work demonstrates this with initial in vivo results obtained from SPEN-based imaging of pyruvate and its metabolic products, after injection of hyperpolarized [1-13C]pyruvate. Multi-slice chemical-shift images of healthy rats were obtained at 4.7 T in the region of the kidney, and 4D (2D spatial, 1D spectral, 1D temporal) data sets were obtained at 7 T from a murine lymphoma tumor model. PMID:24486720

Diffusion-weighted imaging of the liver at 3 T using section-selection gradient reversal: emphasis on chemical shift artefacts and lesion conspicuity.

PubMed

Lee, J S; Kim, Y K; Jeong, W K; Choi, D; Lee, W J

2015-04-01

To assess the value of section-selection gradient reversal (SSGR) in liver diffusion-weighted imaging (DWI) by comparing it to conventional DWI with an emphasis on chemical shift artefacts and lesion conspicuity. Forty-eight patients (29 men and 19 women; age range 33-80 years) with 48 liver lesions underwent two DWI examinations using spectral presaturation with inversion recovery fat suppression with and without SSGR at 3 T. Two reviewers evaluated each DWI (b = 100 and b = 800 image) with respect to chemical shift artefacts and liver lesion conspicuity using five-point scales and performed pairwise comparisons between the two DWIs. The signal-to-noise ratio (SNR) of the liver and the lesion and the lesion-liver contrast-to-noise ratio (CNR) were also calculated. SSGR-DWI was significantly better than conventional DWI with respect to chemical shift artefacts and lesion conspicuity in both separate reviews and pairwise comparisons (p < 0.05). There were significant differences in the SNR of the liver (b = 100 and b = 800 images) and lesion (b = 800) between SSGR-DWI and conventional DWI (p < 0.05). Applying the SSGR method to DWI using SPIR fat suppression at 3 T could significantly reduce chemical shift artefacts without incurring additional acquisition time or SNR penalties, which leads to increased conspicuity of focal liver lesions. Copyright © 2014 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

Accurate determination of chemical shift tensor orientations of single-crystals by solid-state magic angle spinning NMR

NASA Astrophysics Data System (ADS)

Avadhut, Yamini S.; Weber, Johannes; Schmedt auf der Günne, Jörn

2017-09-01

An improved implementation of single-crystal magic-angle-spinning (MAS) NMR is presented which gives access to chemical shift tensors both in orientation (relative to the crystal axis system) and principal axis values. For mounting arbitrary crystals inside ordinary MAS rotors, a mounting tool is described which allows to relate the crystal orientation determined by diffraction techniques to the rotor coordinate system. The crystal is finally mounted into a MAS rotor equipped with a special insert which allows a defined reorientation of the single-crystal by 90°. The approach is based on the idea that the dispersive spectra, which are obtained when applying read-pulses at specific rotor-phases, not only yield the size of the eigenvalues but also encode the orientation of the different chemical shift (rank-2) tensors. For this purpose two 2D-data sets with orthogonal crystal orientation are fitted simultaneously. The presented analysis for chemical shift tensors is supported by an analytical formula which allows fast calculation of phase and amplitude of individual spinning side-bands and by a protocol which solves the problem of finding the correct reference phase of the spectrum. Different rotor-synchronized pulse-sequences are introduced for the same reason. Experiments are performed on L-alanine and O-phosphorylethanolamine and the observed errors are analyzed in detail. The experimental data are opposed to DFT-computed chemical shift tensors which have been obtained by the extended embedded ion method.

Hypothalamic digoxin, hemispheric chemical dominance, and the tridosha theory.

PubMed

Kurup, Ravi Kumar; Kurup, Parameswara Achutha

2003-05-01

Ayurveda, the traditional Indian System of Medicine, deals with the theory of the three tridosha states (both physical and psychological): Vata, Pitta, and Kapha. They are the three major human constitutional types that both depend on psychological and physical characteristics. The Pitta state is described as a critical, discriminative, and rational psychological state of mind, while the Kapha state is described as being dominant for emotional stimuli. The Vata state is an intermediate unstable shifting state. The Pitta types are of average height and built with well developed musculature. The Vata types are thin individuals with low body mass index. The Kapha types are short stocky individuals that tend toward obesity, and who are sedentary. The study assessed the biochemical differences between right hemispheric dominant, bihemispheric dominant, and left hemispheric dominant individuals, and then compared this with the patterns obtained in the Vata, Pitta, and Kapha states. The isoprenoid metabolites (digoxin, dolichol, and ubiquinone), glycoconjugate metabolism, free radical metabolism, and the RBC membrane composition were studied. The hemispheric chemical dominance in various systemic diseases and psychological states was also investigated. The results showed that right hemispheric chemically dominant/Kapha state had elevated digoxin levels, increased free radical production and reduced scavenging, increased tryptophan catabolites and reduced tyrosine catabolites, increased glycoconjugate levels and increased cholesterol: phospholipid ratio of RBC membranes. Left hemispheric chemically dominant/Pitta states had the opposite biochemical patterns. The patterns were normal or intermediate in the bihemispheric chemically dominant/Vata state. This pattern could be correlated with various systemic and neuropsychiatric diseases and personality traits. Right hemispheric chemical dominance/Kapha state represents a hyperdigoxinemic state with membrane sodium-potassium ATPase inhibition. Left hemispheric chemical dominance/Pitta state represents the reverse pattern with hypodigoxinemia and membrane sodium-potassium ATPase stimulation. The Vata state is the intermediate bihemispheric chemical dominant state. Ninety-five percent of the patients/individuals in the tridosha, pathological, and psychological groups were right-handed/left hemispheric dominant, however, their biochemical patterns were different--either left hemispheric chemical dominant or right hemispheric chemical dominant. Hemispheric chemical dominance/tridosha states had no correlation with cerebral dominance detected by handedness/dichotic listening test.

Frequency-Modulation Correlation Spectrometer

NASA Technical Reports Server (NTRS)

Margolis, J. S.; Martonchik, J. V.

1985-01-01

New type of correlation spectrometer eliminates need to shift between two cells, one empty and one containing reference gas. Electrooptical phase modulator sinusoidally shift frequencies of sample transmission spectrum.

Mechanism of Protein Denaturation: Partial Unfolding of the P22 Coat Protein I-Domain by Urea Binding.

PubMed

Newcomer, Rebecca L; Fraser, LaTasha C R; Teschke, Carolyn M; Alexandrescu, Andrei T

2015-12-15

The I-domain is an insertion domain of the bacteriophage P22 coat protein that drives rapid folding and accounts for over half of the stability of the full-length protein. We sought to determine the role of hydrogen bonds (H-bonds) in the unfolding of the I-domain by examining (3)JNC' couplings transmitted through H-bonds, the temperature and urea-concentration dependence of (1)HN and (15)N chemical shifts, and native-state hydrogen exchange at urea concentrations where the domain is predominantly folded. The native-state hydrogen-exchange data suggest that the six-stranded β-barrel core of the I-domain is more stable against unfolding than a smaller subdomain comprised of a short α-helix and three-stranded β-sheet. H-bonds, separately determined from solvent protection and (3)JNC' H-bond couplings, are identified with an accuracy of 90% by (1)HN temperature coefficients. The accuracy is improved to 95% when (15)N temperature coefficients are also included. In contrast, the urea dependence of (1)HN and (15)N chemical shifts is unrelated to H-bonding. The protein segments with the largest chemical-shift changes in the presence of urea show curved or sigmoidal titration curves suggestive of direct urea binding. Nuclear Overhauser effects to urea for these segments are also consistent with specific urea-binding sites in the I-domain. Taken together, the results support a mechanism of urea unfolding in which denaturant binds to distinct sites in the I-domain. Disordered segments bind urea more readily than regions in stable secondary structure. The locations of the putative urea-binding sites correlate with the lower stability of the structure against solvent exchange, suggesting that partial unfolding of the structure is related to urea accessibility. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Reduced dimensionality tailored HN(C)N experiments for facile backbone resonance assignment of proteins through unambiguous identification of sequential HSQC peaks

NASA Astrophysics Data System (ADS)

Kumar, Dinesh

2013-12-01

Two novel reduced dimensionality (RD) tailored HN(C)N [S.C. Panchal, N.S. Bhavesh, R.V. Hosur, Improved 3D triple resonance experiments, HNN and HN(C)N, for HN and 15N sequential correlations in (13C, 15N) labeled proteins: application to unfolded proteins, J. Biomol. NMR 20 (2001) 135-147] experiments are proposed to facilitate the backbone resonance assignment of proteins both in terms of its accuracy and speed. These experiments - referred here as (4,3)D-hNCOcaNH and (4,3)D-hNcoCANH - exploit the linear combination of backbone 15N and 13C‧/13Cα chemical shifts simultaneously to achieve higher peak dispersion and randomness along their respective F1 dimensions. Simply, this has been achieved by modulating the backbone 15N(i) chemical shifts with that of 13C‧ (i - 1)/13Cα (i - 1) spins following the established reduced dimensionality NMR approach [T. Szyperski, D.C. Yeh, D.K. Sukumaran, H.N. Moseley, G.T. Montelione, Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment, Proc. Natl. Acad. Sci. USA 99 (2002) 8009-8014]. Though the modification is simple it has resulted an ingenious improvement of HN(C)N both in terms of peak dispersion and easiness of establishing the sequential connectivities. The increased dispersion along F1 dimension solves two purposes here: (i) resolves the ambiguities arising because of degenerate 15N chemical shifts and (ii) reduces the signal overlap in F2(15N)-F3(1H) planes (an important requisite in HN(C)N based assignment protocol for facile and unambiguous identification of sequentially connected HSQC peaks). The performance of both these experiments and the assignment protocol has been demonstrated using bovine apo Calbindin-d9k (75 aa) and urea denatured UNC60B (a 152 amino acid ADF/cofilin family protein of Caenorhabditis elegans), as representatives of folded and unfolded protein systems, respectively.

Calcium-43 chemical shift tensors as probes of calcium binding environments. Insight into the structure of the vaterite CaCO3 polymorph by 43Ca solid-state NMR spectroscopy.

PubMed

Bryce, David L; Bultz, Elijah B; Aebi, Dominic

2008-07-23

Natural-abundance (43)Ca solid-state NMR spectroscopy at 21.1 T and gauge-including projector-augmented-wave (GIPAW) DFT calculations are developed as tools to provide insight into calcium binding environments, with special emphasis on the calcium chemical shift (CS) tensor. The first complete analysis of a (43)Ca solid-state NMR spectrum, including the relative orientation of the CS and electric field gradient (EFG) tensors, is reported for calcite. GIPAW calculations of the (43)Ca CS and EFG tensors for a series of small molecules are shown to reproduce experimental trends; for example, the trend in available solid-state chemical shifts is reproduced with a correlation coefficient of 0.983. The results strongly suggest the utility of the calcium CS tensor as a novel probe of calcium binding environments in a range of calcium-containing materials. For example, for three polymorphs of CaCO3 the CS tensor span ranges from 8 to 70 ppm and the symmetry around calcium is manifested differently in the CS tensor as compared with the EFG tensor. The advantages of characterizing the CS tensor are particularly evident in very high magnetic fields where the effect of calcium CS anisotropy is augmented in hertz while the effect of second-order quadrupolar broadening is often obscured for (43)Ca because of its small quadrupole moment. Finally, as an application of the combined experimental-theoretical approach, the solid-state structure of the vaterite polymorph of calcium carbonate is probed and we conclude that the hexagonal P6(3)/mmc space group provides a better representation of the structure than does the orthorhombic Pbnm space group, thereby demonstrating the utility of (43)Ca solid-state NMR as a complementary tool to X-ray crystallographic methods.

High SNR Acquisitions Improve the Repeatability of Liver Fat Quantification Using Confounder-corrected Chemical Shift-encoded MR Imaging

PubMed Central

Motosugi, Utaroh; Hernando, Diego; Wiens, Curtis; Bannas, Peter; Reeder, Scott. B

2017-01-01

Purpose: To determine whether high signal-to-noise ratio (SNR) acquisitions improve the repeatability of liver proton density fat fraction (PDFF) measurements using confounder-corrected chemical shift-encoded magnetic resonance (MR) imaging (CSE-MRI). Materials and Methods: Eleven fat-water phantoms were scanned with 8 different protocols with varying SNR. After repositioning the phantoms, the same scans were repeated to evaluate the test-retest repeatability. Next, an in vivo study was performed with 20 volunteers and 28 patients scheduled for liver magnetic resonance imaging (MRI). Two CSE-MRI protocols with standard- and high-SNR were repeated to assess test-retest repeatability. MR spectroscopy (MRS)-based PDFF was acquired as a standard of reference. The standard deviation (SD) of the difference (Δ) of PDFF measured in the two repeated scans was defined to ascertain repeatability. The correlation between PDFF of CSE-MRI and MRS was calculated to assess accuracy. The SD of Δ and correlation coefficients of the two protocols (standard- and high-SNR) were compared using F-test and t-test, respectively. Two reconstruction algorithms (complex-based and magnitude-based) were used for both the phantom and in vivo experiments. Results: The phantom study demonstrated that higher SNR improved the repeatability for both complex- and magnitude-based reconstruction. Similarly, the in vivo study demonstrated that the repeatability of the high-SNR protocol (SD of Δ = 0.53 for complex- and = 0.85 for magnitude-based fit) was significantly higher than using the standard-SNR protocol (0.77 for complex, P < 0.001; and 0.94 for magnitude-based fit, P = 0.003). No significant difference was observed in the accuracy between standard- and high-SNR protocols. Conclusion: Higher SNR improves the repeatability of fat quantification using confounder-corrected CSE-MRI. PMID:28190853

Backbone dynamics of the antifungal Psd1 pea defensin and its correlation with membrane interaction by NMR spectroscopy.

PubMed

de Medeiros, Luciano Neves; Angeli, Renata; Sarzedas, Carolina G; Barreto-Bergter, Eliana; Valente, Ana Paula; Kurtenbach, Eleonora; Almeida, Fabio C L

2010-02-01

Plant defensins are cysteine-rich cationic peptides, components of the innate immune system. The antifungal sensitivity of certain exemplars was correlated to the level of complex glycosphingolipids in the membrane of fungi strains. Psd1 is a 46 amino acid residue defensin isolated from pea seeds which exhibit antifungal activity. Its structure is characterized by the so-called cysteine-stabilized alpha/beta motif linked by three loops as determined by two-dimensional NMR. In the present work we explored the measurement of heteronuclear Nuclear Overhauser Effects, R1 and R2 (15)N relaxation ratios, and chemical shift to probe the backbone dynamics of Psd1 and its interaction with membrane mimetic systems with phosphatidylcholine (PC) or dodecylphosphocholine (DPC) with glucosylceramide (CMH) isolated from Fusarium solani. The calculated R2 values predicted a slow motion around the highly conserved among Gly12 residue and also in the region of the Turn3 His36-Trp38. The results showed that Psd1 interacts with vesicles of PC or PC:CMH in slightly different forms. The interaction was monitored by chemical shift perturbation and relaxation properties. Using this approach we could map the loops as the binding site of Psd1 with the membrane. The major binding epitope showed conformation exchange properties in the mus-ms timescale supporting the conformation selection as the binding mechanism. Moreover, the peptide corresponding to part of Loop1 (pepLoop1: Gly12 to Ser19) is also able to interact with DPC micelles acquiring a stable structure and in the presence of DPC:CMH the peptide changes to an extended conformation, exhibiting NOE mainly with the carbohydrate and ceramide parts of CMH. Copyright 2009 Elsevier B.V. All rights reserved.

NMR Determination of Protein Partitioning into Membrane Domains with Different Curvatures and Application to the Influenza M2 Peptide

PubMed Central

Wang, Tuo; Cady, Sarah D.; Hong, Mei

2012-01-01

The M2 protein of the influenza A virus acts both as a drug-sensitive proton channel and mediates virus budding through membrane scission. The segment responsible for causing membrane curvature is an amphipathic helix in the cytoplasmic domain of the protein. Here, we use 31P and 13C solid-state NMR to examine M2-induced membrane curvature. M2(22–46), which includes only the transmembrane (TM) helix, and M2(21–61), which contains an additional amphipathic helix, are studied. 31P chemical shift lineshapes indicate that M2(21–61) causes a high-curvature isotropic phase to both cholesterol-rich virus-mimetic membranes and 1,2-dimyristoyl-sn-glycero-3-phosphocholine bilayers, whereas M2(22–46) has minimal effect. The lamellar and isotropic domains have distinct 31P isotropic chemical shifts, indicating perturbation of the lipid headgroup conformation by the amphipathic helix. 31P- and 13C-detected 1H T2 relaxation and two-dimensional peptide-lipid correlation spectra show that M2(21–61) preferentially binds to the high-curvature domain. 31P linewidths indicate that the isotropic vesicles induced by M2(21–61) are 10–35 nm in diameter, and the virus-mimetic vesicles are smaller than the 1,2-dimyristoyl-sn-glycero-3-phosphocholine vesicles. A strong correlation is found between high membrane curvature and weak drug-binding ability of the TM helix. Thus, the M2 amphipathic helix causes membrane curvature, which in turn perturbs the TM helix conformation, abolishing drug binding. These NMR experiments are applicable to other curvature-inducing membrane proteins such as fusion proteins and antimicrobial peptides. PMID:22385849

Robust alignment of chromatograms by statistically analyzing the shifts matrix generated by moving window fast Fourier transform cross-correlation.

PubMed

Zhang, Mingjing; Wen, Ming; Zhang, Zhi-Min; Lu, Hongmei; Liang, Yizeng; Zhan, Dejian

2015-03-01

Retention time shift is one of the most challenging problems during the preprocessing of massive chromatographic datasets. Here, an improved version of the moving window fast Fourier transform cross-correlation algorithm is presented to perform nonlinear and robust alignment of chromatograms by analyzing the shifts matrix generated by moving window procedure. The shifts matrix in retention time can be estimated by fast Fourier transform cross-correlation with a moving window procedure. The refined shift of each scan point can be obtained by calculating the mode of corresponding column of the shifts matrix. This version is simple, but more effective and robust than the previously published moving window fast Fourier transform cross-correlation method. It can handle nonlinear retention time shift robustly if proper window size has been selected. The window size is the only one parameter needed to adjust and optimize. The properties of the proposed method are investigated by comparison with the previous moving window fast Fourier transform cross-correlation and recursive alignment by fast Fourier transform using chromatographic datasets. The pattern recognition results of a gas chromatography mass spectrometry dataset of metabolic syndrome can be improved significantly after preprocessing by this method. Furthermore, the proposed method is available as an open source package at https://github.com/zmzhang/MWFFT2. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Validation of goose liver fat measurement by QCT and CSE-MRI with biochemical extraction and pathology as reference.

PubMed

Xu, Li; Duanmu, Yangyang; Blake, Glen M; Zhang, Chenxin; Zhang, Yong; Brown, Keenan; Wang, Xiaoqi; Wang, Peng; Zhou, Xingang; Zhang, Manling; Wang, Chao; Guo, Zhe; Guglielmi, Giuseppe; Cheng, Xiaoguang

2018-05-01

This study aimed to validate the accuracy and reliability of quantitative computed tomography (QCT) and chemical shift encoded magnetic resonance imaging (CSE-MRI) to assess hepatic steatosis. Twenty-two geese with a wide range of hepatic steatosis were collected. After QCT and CSE-MRI examinations, the liver of each goose was removed and samples were taken from the left lobe, upper and lower half of the right lobe for biochemical measurement and histology. Fat percentages by QCT and proton density fat fraction by MRI (MRI-PDFF) were measured within the sample regions of biochemical measurement and histology. The accuracy of QCT and MR measurements were assessed through Spearman correlation coefficients (r) and Passing and Bablok regression equations using biochemical measurement as the "gold standard". Both QCT and MRI correlated highly with chemical extraction [r = 0.922 (p < 0.001) and r = 0.949 (p < 0.001) respectively]. Chemically extracted triglyceride was accurately predicted by both QCT liver fat percentages (Y = 0.6 + 0.866 × X) and by MRI-PDFF (Y = -1.8 + 0.773 × X). QCT and CSE-MRI measurements of goose liver fat were accurate and reliable compared with biochemical measurement. • QCT and CSE-MRI can measure liver fat content accurately and reliably • Histological grading of hepatic steatosis has larger sampling variability • QCT and CSE-MRI have potential in the clinical setting.

Large Scale Patterns of Antimicrofouling Defenses in the Hard Coral Pocillopora verrucosa in an Environmental Gradient along the Saudi Arabian Coast of the Red Sea

PubMed Central

Wahl, Martin; Al Sofyani, Abdulmohsin; Saha, Mahasweta; Kruse, Inken; Lenz, Mark; Sawall, Yvonne

2014-01-01

Large scale patterns of ecologically relevant traits may help identify drivers of their variability and conditions beneficial or adverse to the expression of these traits. Antimicrofouling defenses in scleractinian corals regulate the establishment of the associated biofilm as well as the risks of infection. The Saudi Arabian Red Sea coast features a pronounced thermal and nutritional gradient including regions and seasons with potentially stressful conditions to corals. Assessing the patterns of antimicrofouling defenses across the Red Sea may hint at the susceptibility of corals to global change. We investigated microfouling pressure as well as the relative strength of 2 alternative antimicrofouling defenses (chemical antisettlement activity, mucus release) along the pronounced environmental gradient along the Saudi Arabian Red Sea coast in 2 successive years. Microfouling pressure was exceptionally low along most of the coast but sharply increased at the southernmost sites. Mucus release correlated with temperature. Chemical defense tended to anti-correlate with mucus release. As a result, the combined action of mucus release and chemical antimicrofouling defense seemed to warrant sufficient defense against microbes along the entire coast. In the future, however, we expect enhanced energetic strain on corals when warming and/or eutrophication lead to higher bacterial fouling pressure and a shift towards putatively more costly defense by mucus release. PMID:25485603

Osmotically shrunken LIPOCEST agents: an innovative class of magnetic resonance imaging contrast media based on chemical exchange saturation transfer.

PubMed

Terreno, Enzo; Delli Castelli, Daniela; Violante, Elisabetta; Sanders, Honorius M H F; Sommerdijk, Nico A J M; Aime, Silvio

2009-01-01

The peculiar properties of osmotically shrunken liposomes acting as magnetic resonance imaging-chemical exchange saturation transfer (MRI-CEST) contrast agents have been investigated. Attention has been primarily devoted to assessing the contribution arising from encapsulated and incorporated paramagnetic lanthanide(III)-based shift reagents in determining the chemical shift of the intraliposomal water protons, which is a relevant factor for generating the CEST contrast. It is demonstrated that a highly shifted resonance for the encapsulated water can be attained by increasing the percentage of the amphiphilic shift reagent incorporated in the liposome bilayer. It is also demonstrated that the shift contribution arising from the bulk magnetic susceptibility can be optimized through the modulation of the osmotic shrinkage. In terms of sensitivity, it is shown that the saturation transfer efficiency can be significantly improved by increasing the size of the vesicle, thus allowing a high number of exchangeable protons to be saturated. In addition, the role played by the intensity of the saturating radiofrequency field has also been highlighted.

Metal alkyls programmed to generate metal alkylidenes by α-H abstraction: prognosis from NMR chemical shift† †Electronic supplementary information (ESI) available: Experimental and computational details, NMR spectra, results of NMR calculations and NCS analysis, graphical representation of shielding tensors, molecular orbital diagrams of selected compounds, optimized structures for all calculated species. See DOI: 10.1039/c7sc05039a

PubMed Central

Gordon, Christopher P.; Yamamoto, Keishi; Searles, Keith; Shirase, Satoru

2018-01-01

Metal alkylidenes, which are key organometallic intermediates in reactions such as olefination or alkene and alkane metathesis, are typically generated from metal dialkyl compounds [M](CH2R)2 that show distinctively deshielded chemical shifts for their α-carbons. Experimental solid-state NMR measurements combined with DFT/ZORA calculations and a chemical shift tensor analysis reveal that this remarkable deshielding originates from an empty metal d-orbital oriented in the M–Cα–Cα′ plane, interacting with the Cα p-orbital lying in the same plane. This π-type interaction inscribes some alkylidene character into Cα that favors alkylidene generation via α-H abstraction. The extent of the deshielding and the anisotropy of the alkyl chemical shift tensors distinguishes [M](CH2R)2 compounds that form alkylidenes from those that do not, relating the reactivity to molecular orbitals of the respective molecules. The α-carbon chemical shifts and tensor orientations thus predict the reactivity of metal alkyl compounds towards alkylidene generation. PMID:29675237

Hydrogen Atomic Positions of O-H···O Hydrogen Bonds in Solution and in the Solid State: The Synergy of Quantum Chemical Calculations with ¹H-NMR Chemical Shifts and X-ray Diffraction Methods.

PubMed

Siskos, Michael G; Choudhary, M Iqbal; Gerothanassis, Ioannis P

2017-03-07

The exact knowledge of hydrogen atomic positions of O-H···O hydrogen bonds in solution and in the solid state has been a major challenge in structural and physical organic chemistry. The objective of this review article is to summarize recent developments in the refinement of labile hydrogen positions with the use of: (i) density functional theory (DFT) calculations after a structure has been determined by X-ray from single crystals or from powders; (ii) ¹H-NMR chemical shifts as constraints in DFT calculations, and (iii) use of root-mean-square deviation between experimentally determined and DFT calculated ¹H-NMR chemical shifts considering the great sensitivity of ¹H-NMR shielding to hydrogen bonding properties.

Effect of a Perturbation on the Chemical Equilibrium: Comparison with Le Chatelier's Principle

ERIC Educational Resources Information Center

Torres, Emilio Martinez

2007-01-01

This article develops a general thermodynamic treatment to predict the direction of shift in a chemical equilibrium when it is subjected to a stress. This treatment gives an inequality that relates the change in the perturbed variable and the change that the equilibrium shift produces in the conjugated variable. To illustrate the generality of…

Analyzing neural responses with vector fields.

PubMed

Buneo, Christopher A

2011-04-15

Analyzing changes in the shape and scale of single cell response fields is a key component of many neurophysiological studies. Typical analyses of shape change involve correlating firing rates between experimental conditions or "cross-correlating" single cell tuning curves by shifting them with respect to one another and correlating the overlapping data. Such shifting results in a loss of data, making interpretation of the resulting correlation coefficients problematic. The problem is particularly acute for two dimensional response fields, which require shifting along two axes. Here, an alternative method for quantifying response field shape and scale based on correlation of vector field representations is introduced. The merits and limitations of the methods are illustrated using both simulated and experimental data. It is shown that vector correlation provides more information on response field changes than scalar correlation without requiring field shifting and concomitant data loss. An extension of this vector field approach is also demonstrated which can be used to identify the manner in which experimental variables are encoded in studies of neural reference frames. Copyright © 2011 Elsevier B.V. All rights reserved.

A Selective-Echo Method for Chemical-Shift Imaging of Two-Component Systems

NASA Astrophysics Data System (ADS)

Gerald, Rex E., II; Krasavin, Anatoly O.; Botto, Robert E.

A simple and effective method for selectively imaging either one of two chemical species in a two-component system is presented and demonstrated experimentally. The pulse sequence employed, selective- echo chemical- shift imaging (SECSI), is a hybrid (frequency-selective/ T1-contrast) technique that is executed in a short period of time, utilizes the full Boltzmann magnetization of each chemical species to form the corresponding image, and requires only hard pulses of quadrature phase. This approach provides a direct and unambiguous representation of the spatial distribution of the two chemical species. In addition, the performance characteristics and the advantages of the SECSI sequence are compared on a common basis to those of other pulse sequences.

Chemical Behavior of Sulfur in Minerals and Silicate Glasses Studied Using Inner Shell Spectroscopy

NASA Astrophysics Data System (ADS)

Alonso Mori, R.; Paris, E.; Glatzel, P.; Giuli, G.; Scaillet, B.

2008-12-01

Understanding the chemical behaviour of sulfur is of fundamental importance in explaining different geological mechanisms ranging from volcano-climatic interactions to the genesis of ore deposits. Understanding how sulphur behaves is also of great economic importance in industrial activities including glass-forming processes and the treatment of vitreous waste material from refuse incineration. The chemical behaviour of sulfur in minerals and glasses has been widely studied via X-ray absorption near edge structure (XANES) spectroscopy, which probes the unoccupied density of states and thus provides information on the oxidation state and local structure of the species under study. However, the XANES spectral shape is influenced by various effects, namely the local symmetry, the ligand type, even up to high coordination spheres, and the valence electron occupation, making it difficult to systematically analyze the different spectral contributions. We use X-ray emission spectroscopy (XES) as a complementary technique to avoid some of the inherent difficulties of XANES analysis, and to extract additional information on the electronic structure. The Kb lines, close to the K-edge, directly yield the p-density of occupied valence states, giving valuable information on the local coordination. We have compared XANES and Kb XES experimental data on sulfur- bearing minerals with ab initio quantum-chemical calculations based on density functional theory (DFT), in order to visualize the molecular orbitals and to extract information about the chemical bonding in these compounds. The S Ka emission lines, which arise from 2p to 1s transitions, are expected to be mostly free from chemical bond effects except for small energy shifts that reflect the valence orbital electron population via screening effects. S Ka shifts can be readily used to determine the speciation of sulfur in silicate glasses. The electronic configuration of the sulfur atoms is obtained by calculating the effective charge around the sulfur atom based on the Mulliken population analysis generated by DFT calculations, and then successfully correlated with the observed experimental shifts. In order to check these results using a theoretical framework other than DFT, we also performed calculations using a multiple scattering approach (FEFF8.4). X-ray absorption and emission spectroscopy has been applied to three series of peralkaline rhyolitic obsidians each with different alkali/alumina ratios ((Na2O + K2O)/Al2O3). The occurrence of sulfur was accurately determined by using the energy shift of the S Ka emission lines to make a quantitative analysis. We observe that we can follow the evolution of sulfur as a function of controlled formation conditions with respect to pressure, temperature or oxygen fugacity, and determine whether it is present as sulfate or sulfide. XANES and Kb emission lines also yield detailed information on the local chemistry and structure, and thus help us to understand the geochemical role of S in these systems.

On the correlation between bond-length change and vibrational frequency shift in halogen-bonded complexes

NASA Astrophysics Data System (ADS)

Wang, Weizhou; Zhang, Yu; Ji, Baoming; Tian, Anmin

2011-06-01

The C-Hal (Hal = Cl, Br, or I) bond-length change and the corresponding vibrational frequency shift of the C-Hal stretch upon the C-Hal ⋯Y (Y is the electron donor) halogen bond formation have been determined by using density functional theory computations. Plots of the C-Hal bond-length change versus the corresponding vibrational frequency shift of the C-Hal stretch all give straight lines. The coefficients of determination range from 0.94366 to 0.99219, showing that the correlation between the C-Hal bond-length change and the corresponding frequency shift is very good in the halogen-bonded complexes. The possible effects of vibrational coupling, computational method, and anharmonicity on the bond-length change-frequency shift correlation are discussed in detail.

Accelerating two-dimensional nuclear magnetic resonance correlation spectroscopy via selective coherence transfer

NASA Astrophysics Data System (ADS)

Ye, Qimiao; Chen, Lin; Qiu, Wenqi; Lin, Liangjie; Sun, Huijun; Cai, Shuhui; Wei, Zhiliang; Chen, Zhong

2017-01-01

Nuclear magnetic resonance (NMR) spectroscopy serves as an important tool for both qualitative and quantitative analyses of various systems in chemistry, biology, and medicine. However, applications of one-dimensional 1H NMR are often restrained by the presence of severe overlap among different resonances. The advent of two-dimensional (2D) 1H NMR constitutes a promising alternative by extending the crowded resonances into a plane and thereby alleviating the spectral congestions. However, the enhanced ability in discriminating resonances is achieved at the cost of extended experimental duration due to necessity of various scans with progressive delays to construct the indirect dimension. Therefore, in this study, we propose a selective coherence transfer (SECOT) method to accelerate acquisitions of 2D correlation spectroscopy by converting chemical shifts into spatial positions within the effective sample length and then performing an echo planar spectroscopic imaging module to record the spatial and spectral information, which generates 2D correlation spectrum after 2D Fourier transformation. The feasibility and effectiveness of SECOT have been verified by a set of experiments under both homogeneous and inhomogeneous magnetic fields. Moreover, evaluations of SECOT for quantitative analyses are carried out on samples with a series of different concentrations. Based on these experimental results, the SECOT may open important perspectives for fast, accurate, and stable investigations of various chemical systems both qualitatively and quantitatively.

A heteronuclear zero quantum coherence Nz-exchange experiment that resolves resonance overlap and its application to measure the rates of heme binding to the IsdC protein.

PubMed

Robson, Scott A; Peterson, Robert; Bouchard, Louis-S; Villareal, Valerie A; Clubb, Robert T

2010-07-21

Chemical exchange phenomena in NMR spectra can be quantitatively interpreted to measure the rates of ligand binding, as well as conformational and chemical rearrangements. In macromolecules, processes that occur slowly on the chemical shift time scale are frequently studied using 2D heteronuclear ZZ or N(z)-exchange spectroscopy. However, to successfully apply this method, peaks arising from each exchanging species must have unique chemical shifts in both dimensions, a condition that is often not satisfied in protein-ligand binding equilibria for (15)N nuclei. To overcome the problem of (15)N chemical shift degeneracy we developed a heteronuclear zero-quantum (and double-quantum) coherence N(z)-exchange experiment that resolves (15)N chemical shift degeneracy in the indirect dimension. We demonstrate the utility of this new experiment by measuring the heme binding kinetics of the IsdC protein from Staphylococcus aureus. Because of peak overlap, we could not reliably analyze binding kinetics using conventional methods. However, our new experiment resulted in six well-resolved systems that yielded interpretable data. We measured a relatively slow k(off) rate of heme from IsdC (<10 s(-1)), which we interpret as necessary so heme loaded IsdC has time to encounter downstream binding partners to which it passes the heme. The utility of using this new exchange experiment can be easily expanded to (13)C nuclei. We expect our heteronuclear zero-quantum coherence N(z)-exchange experiment will expand the usefulness of exchange spectroscopy to slow chemical exchange events that involve ligand binding.

A structural study of fentanyl by DFT calculations, NMR and IR spectroscopy

NASA Astrophysics Data System (ADS)

Asadi, Zahra; Esrafili, Mehdi D.; Vessally, Esmail; Asnaashariisfahani, Manzarbanou; Yahyaei, Saeideh; Khani, Ali

2017-01-01

N-(1-(2-phenethyl)-4-piperidinyl-N-phenyl-propanamide (fentanyl) is synthesized and characterized by FT-IR, 1H NMR, 13C NMR, mass spectroscopy and elemental analyses. The geometry optimization is performed using the B3LYP and M06 density functionals with 6-311 + G(d) and 6-311++G(d,p) basis sets. The complete assignments are performed on the basis of the potential energy distribution (PED) of the all vibrational modes. Almost a nice correlation is found between the calculated 13C chemical shifts and experimental data. The frontier molecular orbitals and molecular electrostatic potential of fentanyl are also obtained.

Hypothesis testing for differentially correlated features.

PubMed

Sheng, Elisa; Witten, Daniela; Zhou, Xiao-Hua

2016-10-01

In a multivariate setting, we consider the task of identifying features whose correlations with the other features differ across conditions. Such correlation shifts may occur independently of mean shifts, or differences in the means of the individual features across conditions. Previous approaches for detecting correlation shifts consider features simultaneously, by computing a correlation-based test statistic for each feature. However, since correlations involve two features, such approaches do not lend themselves to identifying which feature is the culprit. In this article, we instead consider a serial testing approach, by comparing columns of the sample correlation matrix across two conditions, and removing one feature at a time. Our method provides a novel perspective and favorable empirical results compared with competing approaches. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Conformational analysis of the chemical shifts for molecules containing diastereotopic methylene protons

NASA Astrophysics Data System (ADS)

Borowski, Piotr

2012-01-01

Quantum chemistry SCF/GIAO calculations were carried out on a set of compounds containing diastereotopic protons. Five molecules, including recently synthesized 1,3-di(2,3-epoxypropoxy)benzene, containing the chiral or pro-chiral center and the neighboring methylene group, were chosen. The rotational averages (i.e. normalized averages with respect to the rotation about the torsional angle τ with the exponential energy weight at temperature T) calculated individually for each of the methylene protons in 1,3-di(2,3-epoxypropoxy)benzene differ by ca. 0.6 ppm, which is significantly less than the value calculated for the lowest energy conformer. This value turned out to be low enough to guarantee the proper ordering of theoretical chemical shifts, supporting the interpretation of the 1H NMR spectrum of this important compound. The rotational averages of chemical shifts for methylene protons for a given type of conformer are shown to be essentially equal to the Boltzmann averages (here, the population-weighted averages for the individual conformers representing minima on the E( τ) cross-section). The calculated Boltzmann averages in the representative conformational space may exhibit completely different ordering as compared to the chemical shifts calculated for the lowest-energy conformer. This is especially true in the case of molecules, for which no significant steric effects are present. In this case, only Boltzmann averages account for the experimental pattern of proton signals. In addition, better overall agreement with experiment (lower value of the root-mean-square deviation between calculated and measured chemical shifts) is typically obtained when Boltzmann averages are used.

Solvent and H/D isotope effects on the proton transfer pathways in heteroconjugated hydrogen-bonded phenol-carboxylic acid anions observed by combined UV-vis and NMR spectroscopy.

PubMed

Koeppe, Benjamin; Guo, Jing; Tolstoy, Peter M; Denisov, Gleb S; Limbach, Hans-Heinrich

2013-05-22

Heteroconjugated hydrogen-bonded anions A···H···X(-) of phenols (AH) and carboxylic/inorganic acids (HX) dissolved in CD2Cl2 and CDF3/CDF2Cl have been studied by combined low-temperature UV-vis and (1)H/(13)C NMR spectroscopy (UVNMR). The systems constitute small molecular models of hydrogen-bonded cofactors in proteins such as the photoactive yellow protein (PYP). Thus, the phenols studied include the PYP cofactor 4-hydroxycinnamic acid methyl thioester, and the more acidic 4-nitrophenol and 2-chloro-4-nitrophenol which mimic electronically excited cofactor states. It is shown that the (13)C chemical shifts of the phenolic residues of A···H···X(-), referenced to the corresponding values of A···H···A(-), constitute excellent probes for the average proton positions. These shifts correlate with those of the H-bonded protons, as well as with the H/D isotope effects on the (13)C chemical shifts. A combined analysis of UV-vis and NMR data was employed to elucidate the proton transfer pathways in a qualitative way. Dual absorption bands of the phenolic moiety indicate a double-well situation for the shortest OHO hydrogen bonds studied. Surprisingly, when the solvent polarity is low the carboxylates are protonated whereas the proton shifts toward the phenolic oxygens when the polarity is increased. This finding indicates that because of stronger ion-dipole interactions small anions are stabilized at high solvent polarity and large anions exhibiting delocalized charges at low solvent polarities. It also explains the large acidity difference of phenols and carboxylic acids in water, and the observation that this difference is strongly reduced in the interior of proteins when both partners form mutual hydrogen bonds.

High-resolution magnetic resonance spectroscopy using a solid-state spin sensor

NASA Astrophysics Data System (ADS)

Glenn, David R.; Bucher, Dominik B.; Lee, Junghyun; Lukin, Mikhail D.; Park, Hongkun; Walsworth, Ronald L.

2018-03-01

Quantum systems that consist of solid-state electronic spins can be sensitive detectors of nuclear magnetic resonance (NMR) signals, particularly from very small samples. For example, nitrogen–vacancy centres in diamond have been used to record NMR signals from nanometre-scale samples, with sensitivity sufficient to detect the magnetic field produced by a single protein. However, the best reported spectral resolution for NMR of molecules using nitrogen–vacancy centres is about 100 hertz. This is insufficient to resolve the key spectral identifiers of molecular structure that are critical to NMR applications in chemistry, structural biology and materials research, such as scalar couplings (which require a resolution of less than ten hertz) and small chemical shifts (which require a resolution of around one part per million of the nuclear Larmor frequency). Conventional, inductively detected NMR can provide the necessary high spectral resolution, but its limited sensitivity typically requires millimetre-scale samples, precluding applications that involve smaller samples, such as picolitre-volume chemical analysis or correlated optical and NMR microscopy. Here we demonstrate a measurement technique that uses a solid-state spin sensor (a magnetometer) consisting of an ensemble of nitrogen–vacancy centres in combination with a narrowband synchronized readout protocol to obtain NMR spectral resolution of about one hertz. We use this technique to observe NMR scalar couplings in a micrometre-scale sample volume of approximately ten picolitres. We also use the ensemble of nitrogen–vacancy centres to apply NMR to thermally polarized nuclear spins and resolve chemical-shift spectra from small molecules. Our technique enables analytical NMR spectroscopy at the scale of single cells.

Efficiency enhancement of ZnO nanostructure assisted Si solar cell based on fill factor enlargement and UV-blue spectral down-shifting

NASA Astrophysics Data System (ADS)

Gholizadeh, A.; Reyhani, A.; Parvin, P.; Mortazavi, S. Z.

2017-05-01

ZnO nanostructures (including nano-plates and nano-rods (NRs)) are grown in various temperatures and Ar/O2 flow rates using thermal chemical vapor deposition, which affect the structure, nano-plate/NR population, and the quality of ZnO nanostructures. X-ray diffraction (XRD) attests that the peak intensity of the crystallographic plane (1 0 0) is correlated to nano-plate abundance. Moreover, optical properties elucidate that the population of nano-plates in samples strongly affect the band gap, binding energy of the exciton, and UV-visible (UV-vis) absorption and spectral luminescence emissions. In fact, the exciton binding energy reduces from ~100 to 80 meV when the population of nano-plates increases in samples. Photovoltaic characteristics based on the drop-casting on Si solar cells reveals three dominant factors, namely, the equivalent series resistance, decreasing reflectance, and down-shifting, in order to scale up the absolute efficiency by 3%. As a consequence, the oxygen vacancies in ZnO nanostructures give rise to the down-shifting and increase of free-carriers, leading to a reduction in the equivalent series resistance and an enlargement of fill factor. To obtain a larger I sc, reduction of spectral reflectance is essential; however, the down-shifting process is shown to be dominant by lessening the surface electron-hole recombination rate over the UV-blue spectral range.

Effect of a Perturbation on the Chemical Equilibrium: Comparison with Le Châtelier's Principle

NASA Astrophysics Data System (ADS)

Martínez Torres, Emilio

2007-03-01

This article develops a general thermodynamic treatment to predict the direction of shift in a chemical equilibrium when it is subjected to a stress. This treatment gives an inequality that relates the change in the perturbed variable and the change that the equilibrium shift produces in the conjugated variable. To illustrate the generality of this approach, it has been applied to predict the direction of shift caused by changes of pressure, volume, and amount of substance. In this last case, the well-known unexpected shift in the ammonia synthesis equilibrium upon addition of nitrogen is easily explained. From the above referred inequality and the stability criteria of thermodynamics some conclusions have been obtained about the direction of shift in terms of extensive and extensive variables. This article is suitable for physical chemistry courses.

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

PubMed

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

2016-07-18

High-pressure (HP) NMR spectroscopy is an important method for detecting rare functional states of proteins by analyzing the pressure response of chemical shifts. However, for the analysis of the shifts it is mandatory to understand the origin of the observed pressure dependence. Here we present experimental HP NMR data on the (15) N-enriched peptide bond model, N-methylacetamide (NMA), in water, combined with quantum-chemical computations of the magnetic parameters using a pressure-sensitive solvation model. Theoretical analysis of NMA and the experimentally used internal reference standard 4,4-dimethyl-4-silapentane-1-sulfonic (DSS) reveal that a substantial part of observed shifts can be attributed to purely solvent-induced electronic polarization of the backbone. DSS is only marginally responsive to pressure changes and is therefore a reliable sensor for variations in the local magnetic field caused by pressure-induced changes of the magnetic susceptibility of the solvent. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

PubMed

Hartman, Joshua D; Beran, Gregory J O

2014-11-11

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

Functional Similarity of Medial Superior Parietal Areas for Shift-Selective Attention Signals in Humans and Monkeys.

PubMed

Caspari, Natalie; Arsenault, John T; Vandenberghe, Rik; Vanduffel, Wim

2018-06-01

We continually shift our attention between items in the visual environment. These attention shifts are usually based on task relevance (top-down) or the saliency of a sudden, unexpected stimulus (bottom-up), and are typically followed by goal-directed actions. It could be argued that any species that can covertly shift its focus of attention will rely on similar, evolutionarily conserved neural substrates for processing such shift-signals. To address this possibility, we performed comparative fMRI experiments in humans and monkeys, combining traditional, and novel, data-driven analytical approaches. Specifically, we examined correspondences between monkey and human brain areas activated during covert attention shifts. When "shift" events were compared with "stay" events, the medial (superior) parietal lobe (mSPL) and inferior parietal lobes showed similar shift sensitivities across species, whereas frontal activations were stronger in monkeys. To identify, in a data-driven manner, monkey regions that corresponded with human shift-selective SPL, we used a novel interspecies beta-correlation strategy whereby task-related beta-values were correlated across voxels or regions-of-interest in the 2 species. Monkey medial parietal areas V6/V6A most consistently correlated with shift-selective human mSPL. Our results indicate that both species recruit corresponding, evolutionarily conserved regions within the medial superior parietal lobe for shifting spatial attention.

Endocrine Disrupting Chemical Induced "Pollution of Metabolic Pathways": A Case of Shifting Paradigms With Implications for Vascular Diseases.

PubMed

Janardhanan, Rajiv

2018-05-14

The latter half of the twentieth century has witnessed a humongous spurt in the use of synthetic chemicals in a wide variety of industrial and agricultural applications are leading to niche specific perturbations affecting every trophic level of the ecosystems due to unmitigated environmental contamination. Despite the incremental usefulness of endocrine disrupting chemicals (EDCs) such as pesticides and plasticizers, their statutory impact on environmental health is assuming worrisome proportions. The EDCs can disrupt physiological homeostasis resulting in developmental and reproductive abnormalities. Both preclinical animal experiments, as well as epidemiological studies, have correlated EDC exposure with metabolic disorders such as metabolic syndrome, type 2 diabetes as well as cardiovascular health. Here we briefly review the statutory impact of EDCs on metabolic disruption as well as their impact on environmental health. Finally, difficulties pertaining to the categorization of EDC induced metabolic diseases as risk factors for global disease burden have been addressed taking into account the complexity of such interactions. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

The P K-near edge absorption spectra of phosphates

NASA Astrophysics Data System (ADS)

Franke, R.; Hormes, J.

1995-12-01

The X-ray absorption near edge structure (XANES) at the P K-edge in several orthophosphates with various cations, in condensed, and in substituted sodium phosphates have been measured using synchrotron radiation from the ELSA storage ring at the University of Bonn. The measured spectra demonstrate that chemical changes beyond the PO 4- tetrahedra are reflected by energy shifts of the pre-edge and continuum resonances, by the presence of characteristic shoulders and new peaks and by differences in the intensity of the white line. We discuss the energy differences between the white line positions and the corresponding P ls binding energies as a measure of half of the energy gap. The corresponding values correlate with the valence of the cations and the intensity of the white lines. The energy positions of the continuum resonances are discussed on the basis of an empirical bond-length correlation supporting a 1/ r2 - dependence.

HN(α/β-COCA-J) Experiment for Measurement of 1JC‧Cα Couplings from Two-Dimensional [15N, 1H] Correlation Spectrum

NASA Astrophysics Data System (ADS)

Permi, Perttu; Sorsa, Tia; Kilpeläinen, Ilkka; Annila, Arto

1999-11-01

Anew method for measurement of one-bond 13C‧-13Cα scalar and dipolar couplings from a two-dimensional [15N, 1H] correlation spectrum is presented. The experiment is based on multiple-quantum coherence, which is created between nitrogen and carbonyl carbon for simultaneous evolution of 15N chemical shift and coupling between 13C‧ and 13Cα. Optional subspectral editing is provided by the spin-state-selective filters. The residual dipolar dipolar contribution to the 13C‧-13Cα coupling can be measured from these simplified [15N, 1H]-HSQC-like spectra. In this way, without explicit knowledge of carbon assignments, conformational changes of proteins dissolved in dilute liquid crystals can be probed conveniently, e.g., in structure activity relationship by NMR studies. The method is demonstrated with human cardiac troponin C.

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

PubMed

Markin, Craig J; Spyracopoulos, Leo

2012-12-01

NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K ( D )) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K ( D ) value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of (1)H-(15)N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k ( off )). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k ( off ) ~ 3,000 s(-1) in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k ( off ) from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k ( off ) values over a wide range, from 100 to 15,000 s(-1). The validity of line shape analysis for k ( off ) values approaching intermediate exchange (~100 s(-1)), may be facilitated by more accurate K ( D ) measurements from NMR-monitored chemical shift titrations, for which the dependence of K ( D ) on the chemical shift difference (Δω) between free and bound states is extrapolated to Δω = 0. The demonstrated accuracy and precision for k ( off ) will be valuable for the interpretation of biological kinetics in weakly interacting protein-protein networks, where a small change in the magnitude of the underlying kinetics of a given pathway may lead to large changes in the associated downstream signaling cascade.

Chemical shifts of diamagnetic azafullerenes: (C 59N) 2 and C 59HN

NASA Astrophysics Data System (ADS)

Bühl, Michael; Curioni, Alessandro; Andreoni, Wanda

1997-08-01

13C and 15N chemical shifts have been calculated for the azafullerenes (C 59N) 2 and C 59HN using the GIAO (gauge including atomic orbitals)-SCF method based on the geometry obtained with the density functional theory BLYP scheme Our results are in good agreement with experimental data, in particular, for the "anomalous" shift of the saturated carbon. Combined with previous calculations of the structural stability and electronic as well as vibrational properties, the present findings confirm the calculated structures for both molecules and establish the [6,6]-closed configuration for the dimer.

Photoinduced intramolecular charge transfer (ICT) reaction in trans-methyl p-(dimethylamino) cinnamate: A combined fluorescence measurement and quantum chemical calculations

NASA Astrophysics Data System (ADS)

Chakraborty, Amrita; Kar, Samiran; Guchhait, Nikhil

2006-01-01

The photophysical behaviour of trans-methyl p-(dimethylamino) cinnamate ( t-MDMAC) donor-acceptor system has been investigated by steady-state absorption and emission spectroscopy and quantum chemical calculations. The molecule t-MDMAC shows an emission from the locally excited state in non-polar solvents. In addition to weak local emission, a strong solvent dependent red shifted fluorescence in polar aprotic solvents is attributed to highly polar intramolecular charge transfer state. However, the formation of hydrogen-bonded clusters with polar protic solvents has been suggested from a linear correlation between the observed red shifted fluorescence band maxima with hydrogen bonding parameters ( α). Calculations by ab initio and density functional theory show that the lone pair electron at nitrogen center is out of plane of the benzene ring in the global minimum ground state structure. In the gas phase, a potential energy surface along the twist coordinate at the donor (-NMe 2) and acceptor (-CH = CHCOOMe) sites shows stabilization of S 1 state and destabilization S 2 and S 0 states. A similar potential energy calculation along the twist coordinate in acetonitrile solvent using non-equilibrium polarized continuum model also shows more stabilization of S 1 state relative to other states and supports solvent dependent red shifted emission properties. In all types of calculations it is found that the nitrogen lone pair is delocalized over the benzene ring in the global minimum ground state and is localized on the nitrogen centre at the 90° twisted configuration. The S 1 energy state stabilization along the twist coordinate at the donor site and localized nitrogen lone pair at the perpendicular configuration support well the observed dual fluorescence in terms of proposed twisted intramolecular charge transfer (TICT) model.

Determination of accurate 1H positions of an alanine tripeptide with anti-parallel and parallel β-sheet structures by high resolution 1H solid state NMR and GIPAW chemical shift calculation.

PubMed

Yazawa, Koji; Suzuki, Furitsu; Nishiyama, Yusuke; Ohata, Takuya; Aoki, Akihiro; Nishimura, Katsuyuki; Kaji, Hironori; Shimizu, Tadashi; Asakura, Tetsuo

2012-11-25

The accurate (1)H positions of alanine tripeptide, A(3), with anti-parallel and parallel β-sheet structures could be determined by highly resolved (1)H DQMAS solid-state NMR spectra and (1)H chemical shift calculation with gauge-including projector augmented wave calculations.

A Three-Dimensional DOSY HMQC Experiment for the High-Resolution Analysis of Complex Mixtures

NASA Astrophysics Data System (ADS)

Barjat, Hervé; Morris, Gareth A.; Swanson, Alistair G.

1998-03-01

A three-dimensional experiment is described in which NMR signals are separated according to their proton chemical shift,13C chemical shift, and diffusion coefficient. The sequence is built up from a stimulated echo sequence with bipolar field gradient pulses and a conventional decoupled HMQC sequence. Results are presented for a model mixture of quinine, camphene, and geraniol in deuteriomethanol.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sevelsted, Tine F.; Herfort, Duncan; Skibsted, Jørgen, E-mail: jskib@chem.au.dk

2013-10-15

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

Red-Shifting versus Blue-Shifting Hydrogen Bonds: Perspective from Ab Initio Valence Bond Theory.

PubMed

Chang, Xin; Zhang, Yang; Weng, Xinzhen; Su, Peifeng; Wu, Wei; Mo, Yirong

2016-05-05

Both proper, red-shifting and improper, blue-shifting hydrogen bonds have been well-recognized with enormous experimental and computational studies. The current consensus is that there is no difference in nature between these two kinds of hydrogen bonds, where the electrostatic interaction dominates. Since most if not all the computational studies are based on molecular orbital theory, it would be interesting to gain insight into the hydrogen bonds with modern valence bond (VB) theory. In this work, we performed ab initio VBSCF computations on a series of hydrogen-bonding systems, where the sole hydrogen bond donor CF3H interacts with ten hydrogen bond acceptors Y (═NH2CH3, NH3, NH2Cl, OH(-), H2O, CH3OH, (CH3)2O, F(-), HF, or CH3F). This series includes four red-shifting and six blue-shifting hydrogen bonds. Consistent with existing findings in literature, VB-based energy decomposition analyses show that electrostatic interaction plays the dominating role and polarization plays the secondary role in all these hydrogen-bonding systems, and the charge transfer interaction, which denotes the hyperconjugation effect, contributes only slightly to the total interaction energy. As VB theory describes any real chemical bond in terms of pure covalent and ionic structures, our fragment interaction analysis reveals that with the approaching of a hydrogen bond acceptor Y, the covalent state of the F3C-H bond tends to blue-shift, due to the strong repulsion between the hydrogen atom and Y. In contrast, the ionic state F3C(-) H(+) leads to the red-shifting of the C-H vibrational frequency, owing to the attraction between the proton and Y. Thus, the relative weights of the covalent and ionic structures essentially determine the direction of frequency change. Indeed, we find the correlation between the structural weights and vibrational frequency changes.

Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental 129Xe NMR Spectroscopy

PubMed Central

Selent, Marcin; Nyman, Jonas; Roukala, Juho; Ilczyszyn, Marek; Oilunkaniemi, Raija; Bygrave, Peter J.; Laitinen, Risto; Jokisaari, Jukka

2017-01-01

Abstract An approach is presented for the structure determination of clathrates using NMR spectroscopy of enclathrated xenon to select from a set of predicted crystal structures. Crystal structure prediction methods have been used to generate an ensemble of putative structures of o‐ and m‐fluorophenol, whose previously unknown clathrate structures have been studied by 129Xe NMR spectroscopy. The high sensitivity of the 129Xe chemical shift tensor to the chemical environment and shape of the crystalline cavity makes it ideal as a probe for porous materials. The experimental powder NMR spectra can be used to directly confirm or reject hypothetical crystal structures generated by computational prediction, whose chemical shift tensors have been simulated using density functional theory. For each fluorophenol isomer one predicted crystal structure was found, whose measured and computed chemical shift tensors agree within experimental and computational error margins and these are thus proposed as the true fluorophenol xenon clathrate structures. PMID:28111848

Tracking changes in the optical properties and molecular composition of dissolved organic matter during drinking water production.

PubMed

Lavonen, E E; Kothawala, D N; Tranvik, L J; Gonsior, M; Schmitt-Kopplin, P; Köhler, S J

2015-11-15

Absorbance, 3D fluorescence and ultrahigh resolution electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS) were used to explain patterns in the removal of chromophoric and fluorescent dissolved organic matter (CDOM and FDOM) at the molecular level during drinking water production at four large drinking water treatment plants in Sweden. When dissolved organic carbon (DOC) removal was low, shifts in the dissolved organic matter (DOM) composition could not be detected with commonly used DOC-normalized parameters (e.g. specific UV254 absorbance - SUVA), but was clearly observed by using differential absorbance and fluorescence or ESI-FT-ICR-MS. In addition, we took a novel approach by identifying how optical parameters were correlated to the elemental composition of DOM by using rank correlation to connect optical properties to chemical formulas assigned to mass peaks from FT-ICR-MS analyses. Coagulation treatment selectively removed FDOM at longer emission wavelengths (450-600 nm), which significantly correlated with chemical formulas containing oxidized carbon (average carbon oxidation state ≥ 0), low hydrogen to carbon ratios (H/C: average ± SD = 0.83 ± 0.13), and abundant oxygen-containing functional groups (O/C = 0.62 ± 0.10). Slow sand filtration was less efficient in removing DOM, yet selectively targeted FDOM at shorter emission wavelengths (between 300 and 450 nm), which commonly represents algal rather than terrestrial sources. This shorter wavelength FDOM correlated with chemical formulas containing reduced carbon (average carbon oxidation state ≤ 0), with relatively few carbon-carbon double bonds (H/C = 1.32 ± 0.16) and less oxygen per carbon (O/C = 0.43 ± 0.10) than those removed during coagulation. By coupling optical approaches with FT-ICR-MS to characterize DOM, we were for the first time able to confirm the molecular composition of absorbing and fluorescing DOM selectively targeted during drinking water treatment. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

First Steps in Eukaryogenesis: Physical Phenomena in the Origin and Evolution of Chromosome Structure

NASA Astrophysics Data System (ADS)

Chela-Flores, Julian

1998-04-01

Our present understanding of the origin and evolution of chromosomes differs considerably from current understanding of the origin and evolution of the cell itself. Chromosome origins have been less prominent in research, as the emphasis has not shifted so far appreciably from the phenomenon of primeval nucleic acid encapsulation to that of the origin of gene organization, expression, and regulation. In this work we discuss some reasons why preliminary steps in this direction are being taken. We have been led to examine properties that have contributed to raise the ancestral prokaryotic programmes to a level where we can appreciate in eukaryotes a clear departure from earlier themes in the evolution of the cell from the last common ancestor. We shift our point of view from evolution of cell morphology to the point of view of the genes. In particular, we focus attention on possible physical bases for the way transmission of information has evolved in eukaryotes, namely, the inactivation of whole chromosomes. The special case of the inactivation of the X chromosome in mammals is discussed, paying particular attention to the physical process of the spread of X inactivation in monotremes (platypus and echidna). When experimental data is unavailable some theoretical analysis is possible based on the idea that in certain cases collective phenomena in genetics, rather than chemical detail, are better correlates of complex chemical processes.

Characterization of the phosphatic mineral of the barnacle Ibla cumingi at atomic level by solid-state nuclear magnetic resonance: comparison with other phosphatic biominerals

PubMed Central

Reid, David G.; Mason, Matthew J.; Chan, Benny K. K.; Duer, Melinda J.

2012-01-01

Ibliform barnacles are among the few invertebrate animals harnessing calcium phosphate to construct hard tissue. The 31P solid-state NMR (SSNMR) signal from the shell plates of Ibla cumingi (Iblidae) is broader than that of bone, and shifted by ca 1 ppm to low frequency. 1H–31P heteronuclear correlation (HETCOR) experiments show a continuum of different phosphorus/phosphate atomic environments, close to hydrogen populations with resonance frequencies between ca 10 and 20 ppm. Associated 1H and 31P chemical shifts argue the coexistence of weakly (high 31P frequency, low 1H frequency) to more strongly (lower 31P frequency, higher 1H frequency) hydrogen-bonded hydrogen phosphate-like molecular/ionic species. There is no resolved signal from discrete OH− ions. 13C SSNMR shows chitin, protein and other organic biomolecules but, unlike bone, there are no significant atomic scale organic matrix–mineral contacts. The poorly ordered hydrogen phosphate-like iblid mineral is strikingly different, structurally and compositionally, from both vertebrate bone mineral and the more crystalline fluoroapatite of the linguliform brachiopods. It probably represents a previously poorly characterized calcium phosphate biomineral, the evolution of which may have reflected either the chemical conditions of ancestral seas or the mechanical advantages of phosphatic biomineralization over a calcium carbonate equivalent. PMID:22298816

Critical Analysis of Cluster Models and Exchange-Correlation Functionals for Calculating Magnetic Shielding in Molecular Solids.

PubMed

Holmes, Sean T; Iuliucci, Robbie J; Mueller, Karl T; Dybowski, Cecil

2015-11-10

Calculations of the principal components of magnetic-shielding tensors in crystalline solids require the inclusion of the effects of lattice structure on the local electronic environment to obtain significant agreement with experimental NMR measurements. We assess periodic (GIPAW) and GIAO/symmetry-adapted cluster (SAC) models for computing magnetic-shielding tensors by calculations on a test set containing 72 insulating molecular solids, with a total of 393 principal components of chemical-shift tensors from 13C, 15N, 19F, and 31P sites. When clusters are carefully designed to represent the local solid-state environment and when periodic calculations include sufficient variability, both methods predict magnetic-shielding tensors that agree well with experimental chemical-shift values, demonstrating the correspondence of the two computational techniques. At the basis-set limit, we find that the small differences in the computed values have no statistical significance for three of the four nuclides considered. Subsequently, we explore the effects of additional DFT methods available only with the GIAO/cluster approach, particularly the use of hybrid-GGA functionals, meta-GGA functionals, and hybrid meta-GGA functionals that demonstrate improved agreement in calculations on symmetry-adapted clusters. We demonstrate that meta-GGA functionals improve computed NMR parameters over those obtained by GGA functionals in all cases, and that hybrid functionals improve computed results over the respective pure DFT functional for all nuclides except 15N.

The Correlation Between Cognitive and Movement Shifting and Brain Activity in Children With ADHD.

PubMed

Kang, Kyoung Doo; Han, Doug Hyun; Kim, Sun Mi; Bae, Sujin; Renshaw, Perry F

2018-05-01

We assessed the correlation between the deficits of cognition, movement, and brain activity in children with Attention Deficit Hyperactvity Disorder (ADHD). We recruited 15 children with ADHD and 15 age- and sex-matched healthy control participants. Clinical symptoms, cognitive shifting, movement shifting, and brain activity were assessed using the Korean ADHD Rating Scale, the Wisconsin Card Sorting Test (WCST), the 7- and 14-ring drill test with hop jumps (7 HJ and 14 HJ), and 3.0 Tesla functional magnetic resonance imaging scanner, respectively. ADHD children showed an increased distance traveled and decreased speed on the 14 HJ task. In response to the WCST task, ADHD children showed decreased activation within right gyrus. Total distance on the 14 HJ task was negatively correlated with the mean β value of Cluster 2 in ADHD children. These results suggested that children with ADHD showed difficulty with attention shifting as well as with movement shifting.

Correlations between the resonant frequency shifts and the thermodynamic quantities for the α-β transition in quartz

NASA Astrophysics Data System (ADS)

Lider, M. C.; Yurtseven, H.

2018-05-01

The resonant frequency shifts are related to the thermodynamic quantities (compressibility, order parameter and susceptibility) for the α-β transition in quartz. The experimental data for the resonant frequencies and the bulk modulus from the literature are used for those correlations. By calculating the order parameter from the mean field theory, correlation between the resonant frequencies of various modes and the order parameter is examined according to the quasi-harmonic phonon theory for the α-β transition in quartz. Also, correlation between the bulk modulus in relation to the resonant frequency shifts and the order parameter susceptibility is constructed for the α-β transition in this crystalline system.

New perspectives in the PAW/GIPAW approach: J(P-O-Si) coupling constants, antisymmetric parts of shift tensors and NQR predictions.

PubMed

Bonhomme, Christian; Gervais, Christel; Coelho, Cristina; Pourpoint, Frédérique; Azaïs, Thierry; Bonhomme-Coury, Laure; Babonneau, Florence; Jacob, Guy; Ferrari, Maude; Canet, Daniel; Yates, Jonathan R; Pickard, Chris J; Joyce, Siân A; Mauri, Francesco; Massiot, Dominique

2010-12-01

In 2001, Pickard and Mauri implemented the gauge including projected augmented wave (GIPAW) protocol for first-principles calculations of NMR parameters using periodic boundary conditions (chemical shift anisotropy and electric field gradient tensors). In this paper, three potentially interesting perspectives in connection with PAW/GIPAW in solid-state NMR and pure nuclear quadrupole resonance (NQR) are presented: (i) the calculation of J coupling tensors in inorganic solids; (ii) the calculation of the antisymmetric part of chemical shift tensors and (iii) the prediction of (14)N and (35)Cl pure NQR resonances including dynamics. We believe that these topics should open new insights in the combination of GIPAW, NMR/NQR crystallography, temperature effects and dynamics. Points (i), (ii) and (iii) will be illustrated by selected examples: (i) chemical shift tensors and heteronuclear (2)J(P-O-Si) coupling constants in the case of silicophosphates and calcium phosphates [Si(5)O(PO(4))(6), SiP(2)O(7) polymorphs and α-Ca(PO(3))(2)]; (ii) antisymmetric chemical shift tensors in cyclopropene derivatives, C(3)X(4) (X = H, Cl, F) and (iii) (14)N and (35)Cl NQR predictions in the case of RDX (C(3)H(6)N(6)O(6)), β-HMX (C(4)H(8)N(8)O(8)), α-NTO (C(2)H(2)N(4)O(3)) and AlOPCl(6). RDX, β-HMX and α-NTO are explosive compounds. Copyright © 2010 John Wiley & Sons, Ltd.

2J, 3J-HMBC: A New Long-Range Heteronuclear Shift Correlation Technique Capable of Differentiating 2JCH from 3JCH Correlations to Protonated Carbons

NASA Astrophysics Data System (ADS)

Krishnamurthy, V. V.; Russell, David J.; Hadden, Chad E.; Martin, Gary E.

2000-09-01

The development of a series of new, accordion-optimized long-range heteronuclear shift correlation techniques has been reported. A further derivative of the constant time variable delay introduced in the IMPEACH-MBC experiment, a STAR (Selectively Tailored Accordion F1 Refocusing) operator is described in the present report. Incorporation of the STAR operator with the capability of user-selected homonuclear modulation scaling as in the CIGAR-HMBC experiment, into a long-range heteronuclear shift correlation pulse sequence, 2J,3J-HMBC, affords for the first time in a proton-detected experiment the means of unequivocally differentiating two-bond (2JCH) from three-bond (3JCH) long-range correlations to protonated carbons.

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

PubMed

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

1994-08-01

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

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

PubMed

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

2012-10-01

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

Assessment of Thematic Mapper Band-to-band Registration by the Block Correlation Method

NASA Technical Reports Server (NTRS)

Card, D. H.; Wrigley, R. C.; Mertz, F. C.; Hall, J. R.

1984-01-01

The design of the Thematic Mapper (TM) multispectral radiometer makes it susceptible to band-to-band misregistration. To estimate band-to-band misregistration a block correlation method is employed. This method is chosen over other possible techniques (band differencing and flickering) because quantitative results are produced. The method correlates rectangular blocks of pixels from one band against blocks centered on identical pixels from a second band. The block pairs are shifted in pixel increments both vertically and horizontally with respect to each other and the correlation coefficient for each shift position is computed. The displacement corresponding to the maximum correlation is taken as the best estimate of registration error for each block pair. Subpixel shifts are estimated by a bi-quadratic interpolation of the correlation values surrounding the maximum correlation. To obtain statistical summaries for each band combination post processing of the block correlation results performed. The method results in estimates of registration error that are consistent with expectations.

Hydroxy protons as structural probes to reveal hydrogen bonding properties of polyols in aqueous solution by NMR spectroscopy

NASA Astrophysics Data System (ADS)

Oruc, Gizem; Varnali, Tereza; Bekiroglu, Somer

2018-05-01

The solution properties of ethylene glycol (ethane-1,2-diol), glycerol (propane-1,2,3-triol), erythritol ((2R,3S)-butane-1,2,3,4-tetraol), D-xylitol ((2R,3r,4S)-pentane-1,2,3,4,5-pentaol), D-mannitol ((2R,3R,4R,5R)-hexane-1,2,3,4,5,6-hexaol), and D-sorbitol ((2S,3R,4R,5R)-hexane-1,2,3,4,5,6-hexaol), constituting a subgroup of polyalcohols/polyols of maximum six carbon atoms have been investigated using 1H NMR chemical shifts, coupling constants, temperature coefficients, and chemical exchange rates of hydroxy protons in aqueous medium. Relative within a molecule, minimum two-fold difference in rate of exchange values and higher temperature dependence of chemical shifts of the hydroxy protons on terminal carbon atoms confirm that sustainable hydrogen bonding interactions is accentuated for the hydroxyl groups on secondary carbons. Compared to the primary carbons i.e. terminal ones, the hydroxy protons on second and third carbon atoms exhibit much lower rate of exchange and smaller temperature coefficients, indicating that they are further involved in transient hydrogen bonding interactions. Scalar 3JOH,CH-couplings ranging between 3.9 and 7.2 Hz imply that the hydroxyl groups are practically in free rotation regime. Examination of the chemical shift differences with respect to the shift of glycol hydroxy proton reveals that the disparity between terminal and inner hydroxyl groups disclosed by the exchange rates and temperature coefficients is sustained with the exception of 0.003 and 0.053 ppm for O(3)H of mannitol and O(5)H of sorbitol respectively. The experimental findings have been augmented by quantum chemical calculations targeting theoretical NMR chemical shifts, as well as the conformational analysis of the structures.

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

PubMed

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.

How well do Radiologic Assessments of Truncal and Shoulder Balance Correlate With Cosmetic Assessment Indices in Lenke 1C Adolescent Idiopathic Scoliosis?

PubMed

Sharma, Shallu; Andersen, Thomas; Wu, Chunsen; Sun, Haolin; Wang, Yu; Hansen, Ebbe S; Bünger, Cody E

2016-10-01

A correlation study. The primary objective was to determine the correlation between radiologic and cosmetic indices of trunk and shoulder balance before and after scoliosis surgery in Lenke 1C adolescent idiopathic scoliosis and to determine whether postoperative trunk shift is affiliated with worsening of the patients' cosmesis. Achieving a symmetrical appearance with truncal and shoulder balance is of prime importance to adolescent idiopathic scoliosis patients and their surgeons. However, surgeons prefer radiographic indices rather than measures of patients' clinical appearance. If radiographic indices are to be considered accurate depictions of the patient's cosmesis, radiologic and cosmetic indices must necessarily exhibit high association. Radiographic and cosmetic indices of trunk and shoulder balance, along with posterior trunk symmetry index, were measured preoperatively and 3 months postoperatively in 33 Lenke 1C scoliosis patients. Pearson correlation analysis was performed. Paired t test was used to determine significant changes in radiographic and cosmetic indices after surgery. Independent-sample t test was used for all intergroup analyses in trunk shift and no-trunk-shift groups. Correlation coefficients between radiologic and cosmetic indices ranged between -0.63 and 0.70 with thoracic apical vertebra-central sacral vertical line (AV-CSVL) distance and first rib angle showing consistent correlations with cosmetic trunk and cosmetic shoulder balance indices. Trunk shift, a postoperative iatrogenic phenomenon, was seen in 19 (58%) patients. These patients had higher preoperative thoracic AV-CSVL translation, thoracic apical vertebra-first thoracic vertebra (AV-T1) translation, thoracic deformity correction rate, AV-T1 correction rates, and shorter fusions compared with the no-trunk-shift group. Posterior trunk symmetry index worsened in trunk shift group and improved significantly (-7.94 vs. 16.53) in no-trunk-shift group. Significant association (P=0.004) was seen between radiographic and cosmetic trunk shift. Radiographic indices can only minisculely (r≤0.7) reflect cosmetic deformity in Lenke 1C scoliosis, which emphasizes not only the vulnerability of overreliance on radiographic indices but also the vital importance of clinical cosmetic evaluations. In particular, cosmetic shoulder height and angle are not represented by radiographic indices. However, radiograph trunk shift was significantly associated with cosmetic trunk shift in cosmetic pictures.

Phylogeny-based comparative methods question the adaptive nature of sporophytic specializations in mosses.

PubMed

Huttunen, Sanna; Olsson, Sanna; Buchbender, Volker; Enroth, Johannes; Hedenäs, Lars; Quandt, Dietmar

2012-01-01

Adaptive evolution has often been proposed to explain correlations between habitats and certain phenotypes. In mosses, a high frequency of species with specialized sporophytic traits in exposed or epiphytic habitats was, already 100 years ago, suggested as due to adaptation. We tested this hypothesis by contrasting phylogenetic and morphological data from two moss families, Neckeraceae and Lembophyllaceae, both of which show parallel shifts to a specialized morphology and to exposed epiphytic or epilithic habitats. Phylogeny-based tests for correlated evolution revealed that evolution of four sporophytic traits is correlated with a habitat shift. For three of them, evolutionary rates of dual character-state changes suggest that habitat shifts appear prior to changes in morphology. This suggests that they could have evolved as adaptations to new habitats. Regarding the fourth correlated trait the specialized morphology had already evolved before the habitat shift. In addition, several other specialized "epiphytic" traits show no correlation with a habitat shift. Besides adaptive diversification, other processes thus also affect the match between phenotype and environment. Several potential factors such as complex genetic and developmental pathways yielding the same phenotypes, differences in strength of selection, or constraints in phenotypic evolution may lead to an inability of phylogeny-based comparative methods to detect potential adaptations.

Theoretical study of the hyperfine-interaction constants and the isotope-shift factors for the 3 s21S0-3 s 3 p 3,1P1o transitions in Al+

NASA Astrophysics Data System (ADS)

Zhang, Tingxian; Xie, Luyou; Li, Jiguang; Lu, Zehuang

2017-07-01

We calculated the magnetic dipole and the electric quadrupole hyperfine interaction constants of 3 s 3 p 3,1P1o states and the isotope shift, including mass and field shift, factors for transitions from these two states to the ground state 3 s 2 1S0 in Al+ ions using the multiconfiguration Dirac-Hartree-Fock method. The effects of the electron correlations and the Breit interaction on these physical quantities were investigated in detail based on the active space approach. It is found that the core-core and the higher order correlations are considerable for evaluating the uncertainties of the atomic parameters concerned. The uncertainties of the hyperfine interaction constants in this work are less than 1.6%. Although the isotope shift factors are highly sensitive to the electron correlations, reasonable uncertainties were obtained by exploring the effects of the electron correlations. Moreover, we found that the relativistic nuclear recoil corrections to the mass shift factors are very small and insensitive to the electron correlations for Al+. These atomic parameters present in this work are valuable for extracting the nuclear electric quadrupole moments and the mean-square charge radii of Al isotopes.

pH Dependent Spin State Population and 19F NMR Chemical Shift via Remote Ligand Protonation in an Iron(II) Complex (Postprint)

DTIC Science & Technology

2017-12-11

AFRL-RX-WP-JA-2017-0501 pH- DEPENDENT SPIN STATE POPULATION AND 19F NMR CHEMICAL SHIFT VIA REMOTE LIGAND PROTONATION IN AN IRON(II...From - To) 16 November 2017 Interim 24 January 2014 – 16 October 2017 4. TITLE AND SUBTITLE PH- DEPENDENT SPIN STATE POPULATION AND 19F NMR CHEMICAL...dx.doi.org/10.1039/C7CC08099A 14. ABSTRACT (Maximum 200 words) An FeII complex that features a pH- dependent spin state population, by virtue of a

An extrapolation scheme for solid-state NMR chemical shift calculations

NASA Astrophysics Data System (ADS)

Nakajima, Takahito

2017-06-01

Conventional quantum chemical and solid-state physical approaches include several problems to accurately calculate solid-state nuclear magnetic resonance (NMR) properties. We propose a reliable computational scheme for solid-state NMR chemical shifts using an extrapolation scheme that retains the advantages of these approaches but reduces their disadvantages. Our scheme can satisfactorily yield solid-state NMR magnetic shielding constants. The estimated values have only a small dependence on the low-level density functional theory calculation with the extrapolation scheme. Thus, our approach is efficient because the rough calculation can be performed in the extrapolation scheme.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xing, Y; Macq, B; Bondar, L

Purpose: To quantify the accuracy in predicting the Bragg peak position using simulated in-room measurements of prompt gamma (PG) emissions for realistic treatment error scenarios that combine several sources of errors. Methods: Prompt gamma measurements by a knife-edge slit camera were simulated using an experimentally validated analytical simulation tool. Simulations were performed, for 143 treatment error scenarios, on an anthropomorphic phantom and a pencil beam scanning plan for nasal cavity. Three types of errors were considered: translation along each axis, rotation around each axis, and CT-calibration errors with magnitude ranging respectively, between −3 and 3 mm, −5 and 5 degrees,more » and between −5 and +5%. We investigated the correlation between the Bragg peak (BP) shift and the horizontal shift of PG profiles. The shifts were calculated between the planned (reference) position and the position by the error scenario. The prediction error for one spot was calculated as the absolute difference between the PG profile shift and the BP shift. Results: The PG shift was significantly and strongly correlated with the BP shift for 92% of the cases (p<0.0001, Pearson correlation coefficient R>0.8). Moderate but significant correlations were obtained for all cases that considered only CT-calibration errors and for 1 case that combined translation and CT-errors (p<0.0001, R ranged between 0.61 and 0.8). The average prediction errors for the simulated scenarios ranged between 0.08±0.07 and 1.67±1.3 mm (grand mean 0.66±0.76 mm). The prediction error was moderately correlated with the value of the BP shift (p=0, R=0.64). For the simulated scenarios the average BP shift ranged between −8±6.5 mm and 3±1.1 mm. Scenarios that considered combinations of the largest treatment errors were associated with large BP shifts. Conclusion: Simulations of in-room measurements demonstrate that prompt gamma profiles provide reliable estimation of the Bragg peak position for complex error scenarios. Yafei Xing and Luiza Bondar are funded by BEWARE grants from the Walloon Region. The work presents simulations results for a prompt gamma camera prototype developed by IBA.« less

Palladium complexes with simple iminopyridines as catalysts for polyketone synthesis.

PubMed

Rosar, V; Dedeic, D; Nobile, T; Fini, F; Balducci, G; Alessio, E; Carfagna, C; Milani, B

2016-10-07

Four iminopyridines (N-N') differing in the nature of the substituents on the iminic carbon and on the ortho positions of the aryl ring (H or CH3) on the iminic nitrogen were used for the synthesis of neutral and monocationic palladium(ii) complexes of general formulae [Pd(CH3)Cl(N-N')] and [Pd(CH3)(NCCH3)(N-N')][PF6]. The detailed NMR characterization in solution highlighted that: (i) for both series of complexes, the Pd-CH3 signal is progressively shifted to a lower frequency on increasing the number of methyl groups on the ligand skeleton; (ii) for the neutral derivatives, the chemical shift of the (15)N NMR signals, determined through {(1)H,(15)N}-HMBC spectra, is significantly affected by the coordination to palladium; (iii) the coordination induced shift (CIS) of the nitrogen atom trans to the CH3 ligand is smaller than the other. The structure in the solid state for the neutral derivatives with all the four ligands was solved, pointing out that: (iv) the Pd-C bond distance increases with the basicity of the nitrogen-donor ligand; (v) the Pd-N bond distance correlates well with the CIS value. The combining of the solution and solid state structural features allows stating that: (vi) the Pd-CH3 singlet is a good probe for the electron donor capability of the ligand; (vii) the CIS value might be used as a probe for the strength of the Pd-N bond. All monocationic complexes generated active catalysts for the CO/vinyl arene copolymerization, leading to prevailingly syndiotactic polyketones. The catalyst performances, both in terms of catalyst productivity and polymer molecular weight, correlate well with the precatalyst structural features.

Study of mutual influence of hydrogen bonds in complicated complexes by low-temperature 1H NMR spectroscopy

NASA Astrophysics Data System (ADS)

Golubev, N. S.; Denisov, G. S.

1992-07-01

1H NMR spectra of various acid-base complexes of different stoichiometry at 100-120K in freon mixtures have been obtained. The separate signals of non-equivalent OH-protons, involved in different H-bonds, have allowed us to consider the problem of the mutual influence of these bonds, using a correlation between the δ OH chemical shift and the AΔ H H-bond enthalpy. The mutual strengthening of H-bonds in complexes of the AH⋯AH⋯B type and their weakening in AH⋯B⋯HA complexes have been found, the value of the effect being about 10-30%

XPS Investigation on Changes in UO 2 Speciation following Exposure to Humidity

DOE PAGES

Donald, Scott B.; Davisson, M. Lee; Nelson, Art J.

2016-04-27

High purity UO 2powder samples were subjected to accelerated aging under controlled conditions with relative humidity ranging from 34% to 98%. Characterization of the chemical speciation of the products was accomplished using X-ray photoelectron spectroscopy (XPS). A shift to higher uranium oxidation states was found to be directly correlated to increased relative humidity exposure. In addition, the relative abundance of O 2-, OH -, and H 2O was found to vary with exposure time. Therefore, it is expected that uranium oxide materials exposed to high relative humidity conditions during processing and storage would display a similar increase in average uraniummore » valence.« less

Magnetic susceptibility as a direct measure of oxidation state in LiFePO4 batteries and cyclic water gas shift reactors.

PubMed

Kadyk, Thomas; Eikerling, Michael

2015-08-14

The possibility of correlating the magnetic susceptibility to the oxidation state of the porous active mass in a chemical or electrochemical reactor was analyzed. The magnetic permeability was calculated using a hierarchical model of the reactor. This model was applied to two practical examples: LiFePO4 batteries, in which the oxidation state corresponds with the state-of-charge, and cyclic water gas shift reactors, in which the oxidation state corresponds to the depletion of the catalyst. In LiFePO4 batteries phase separation of the lithiated and delithiated phases in the LiFePO4 particles in the positive electrode gives rise to a hysteresis effect, i.e. the magnetic permeability depends on the history of the electrode. During fast charge or discharge, non-uniform lithium distributionin the electrode decreases the hysteresis effect. However, the overall sensitivity of the magnetic response to the state-of-charge lies in the range of 0.03%, which makes practical measurement challenging. In cyclic water gas shift reactors, the sensitivity is 4 orders of magnitude higher and without phase separation, no hysteresis occurs. This shows that the method is suitable for such reactors, in which large changes of the magnetic permeability of the active material occurs.

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

PubMed

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

1981-01-01

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

Ligand Binding Analysis and Screening by Chemical Denaturation Shift

PubMed Central

Sch n, Arne; Brown, Richard K.; Hutchins, Burleigh M.; Freire, Ernesto

2013-01-01

The identification of small molecule ligands is an important first step in drug development, especially drugs that target proteins with no intrinsic activity. Towards this goal, it is important to have access to technologies that are able to measure binding affinities for a large number of potential ligands in a fast and accurate way. Since ligand binding stabilizes the protein structure in a manner dependent on concentration and binding affinity, the magnitude of the protein stabilization effect elicited by binding can be used to identify and characterize ligands. For example, the shift in protein denaturation temperature (Tm shift) has become a popular approach to identify potential ligands. However, Tm shifts cannot be readily transformed into binding affinities and the ligand rank order obtained at denaturation temperatures (60°C or higher) does not necessarily coincide with the rank order at physiological temperature. An alternative approach is the use of chemical denaturation, which can be implemented at any temperature. Chemical denaturation shifts allow accurate determination of binding affinities with a surprisingly wide dynamic range (high micromolar to sub nanomolar) and in situations in which binding changes the cooperativity of the unfolding transition. In this paper we develop the basic analytical equations and provide several experimental examples. PMID:23994566

Ligand binding analysis and screening by chemical denaturation shift.

PubMed

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

2013-12-01

The identification of small molecule ligands is an important first step in drug development, especially drugs that target proteins with no intrinsic activity. Toward this goal, it is important to have access to technologies that are able to measure binding affinities for a large number of potential ligands in a fast and accurate way. Because ligand binding stabilizes the protein structure in a manner dependent on concentration and binding affinity, the magnitude of the protein stabilization effect elicited by binding can be used to identify and characterize ligands. For example, the shift in protein denaturation temperature (Tm shift) has become a popular approach to identify potential ligands. However, Tm shifts cannot be readily transformed into binding affinities, and the ligand rank order obtained at denaturation temperatures (≥60°C) does not necessarily coincide with the rank order at physiological temperature. An alternative approach is the use of chemical denaturation, which can be implemented at any temperature. Chemical denaturation shifts allow accurate determination of binding affinities with a surprisingly wide dynamic range (high micromolar to sub nanomolar) and in situations where binding changes the cooperativity of the unfolding transition. In this article, we develop the basic analytical equations and provide several experimental examples. Copyright © 2013 Elsevier Inc. All rights reserved.

Evidence of chemical-potential shift with hole doping in Bi2Sr2CaCu2O8+δ

NASA Astrophysics Data System (ADS)

Shen, Z.-X.; Dessau, D. S.; Wells, B. O.; Olson, C. G.; Mitzi, D. B.; Lombado, Lou; List, R. S.; Arko, A. J.

1991-12-01

We have performed photoemission studies on high-quality Bi2Sr2CaCu2O8+δ samples with various δ. Our results show a clear chemical-potential shift (0.15-0.2 eV) as a function of doping. This result and the existing angle-resolved-photoemission data give a rather standard doping behavior of this compound in its highly doped regime.

13C nuclear magnetic resonance data of lanosterol derivatives—Profiling the steric topology of the steroid skeleton via substituent effects on its 13C NMR

NASA Astrophysics Data System (ADS)

Dias, Jerry Ray; Gao, Hongwu

2009-12-01

The 13C NMR spectra of over 24 tetracyclic triterpenoid derivatives have been structurally analyzed. The 13C NMR chemical shifts allow one to probe the steric topology of the rigid steroid skeleton and inductive effects of its substituents. Use of deuterium labeling in chemical shift assignment and B-ring aromatic terpenoids are also featured.

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

PubMed Central

Shen, Yang; Bax, Ad

2013-01-01

A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, ≥ 90% fraction of the residues, with an error rate smaller than ca 3.5%, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed (φ,ψ) torsion angles of ca 12°. TALOS-N also reports sidechain χ1 rotameric states for about 50% of the residues, and a consistency with reference structures of 89%. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts. PMID:23728592

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

PubMed Central

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

2017-01-01

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

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

PubMed Central

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo

2012-01-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu. PMID:22903636

NMR spectroscopic studies of a TAT-derived model peptide in imidazolium-based ILs: influence on chemical shifts and the cis/trans equilibrium state.

PubMed

Wiedemann, Christoph; Ohlenschläger, Oliver; Mrestani-Klaus, Carmen; Bordusa, Frank

2017-09-13

NMR spectroscopy was used to study systematically the impact of imidazolium-based ionic liquid (IL) solutions on a TAT-derived model peptide containing Xaa-Pro peptide bonds. The selected IL anions cover a wide range of the Hofmeister series of ions. Based on highly resolved one- and two-dimensional NMR spectra individual 1 H and 13 C peptide chemical shift differences were analysed and a classification of IL anions according to the Hofmeister series was derived. The observed chemical shift changes indicate significant interactions between the peptide and the ILs. In addition, we examined the impact of different ILs towards the cis/trans equilibrium state of the Xaa-Pro peptide bonds. In this context, the IL cations appear to be of exceptional importance for inducing an alteration of the native cis/trans equilibrium state of Xaa-Pro bonds in favour of the trans-isomers.

A Critical Assessment of the Performance of Protein-ligand Scoring Functions Based on NMR Chemical Shift Perturbations

PubMed Central

Wang, Bing; Westerhoff, Lance M.; Merz, Kenneth M.

2008-01-01

We have generated docking poses for the FKBP-GPI complex using eight docking programs, and compared their scoring functions with scoring based on NMR chemical shift perturbations (NMRScore). Because the chemical shift perturbation (CSP) is exquisitely sensitive on the orientation of ligand inside the binding pocket, NMRScore offers an accurate and straightforward approach to score different poses. All scoring functions were inspected by their abilities to highly rank the native-like structures and separate them from decoy poses generated for a protein-ligand complex. The overall performance of NMRScore is much better than that of energy-based scoring functions associated with docking programs in both aspects. In summary, we find that the combination of docking programs with NMRScore results in an approach that can robustly determine the binding site structure for a protein-ligand complex, thereby, providing a new tool facilitating the structure-based drug discovery process. PMID:17867664

Nuclear magnetic resonance spectral analysis and molecular properties of berberine

NASA Astrophysics Data System (ADS)

Huang, Ming-Ju; Lee, Ken S.; Hurley, Sharon J.

An extensive theoretical study of berberine has been performed at the ab initio HF/6-31G**, HF/6-311G**, and B3LYP/6-311G** levels with and without solvent effects. The optimized structures are compared with X-ray data. We found that the optimized structures with solvent effects are in slightly better agreement with X-ray data than those without solvent effects. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of berberine were calculated by using the gauge-independent atomic orbital (GIAO) (with and without solvent effects), CSGT, and IGAIM methods. The calculated chemical shifts were compared with the two-dimensional NMR experimental data. Overall, the calculated chemical shifts show very good agreement with the experimental results. The harmonic vibrational frequencies for berberine were calculated at the B3LYP/6-311G** level.

Hydride ions in oxide hosts hidden by hydroxide ions

PubMed Central

Hayashi, Katsuro; Sushko, Peter V.; Hashimoto, Yasuhiro; Shluger, Alexander L.; Hosono, Hideo

2014-01-01

The true oxidation state of formally ‘H−’ ions incorporated in an oxide host is frequently discussed in connection with chemical shifts of 1H nuclear magnetic resonance spectroscopy, as they can exhibit values typically attributed to H+. Here we systematically investigate the link between geometrical structure and chemical shift of H− ions in an oxide host, mayenite, with a combination of experimental and ab initio approaches, in an attempt to resolve this issue. We demonstrate that the electron density near the hydrogen nucleus in an OH− ion (formally H+ state) exceeds that in an H− ion. This behaviour is the opposite to that expected from formal valences. We deduce a relationship between the chemical shift of H− and the distance from the H− ion to the coordinating electropositive cation. This relationship is pivotal for resolving H− species that are masked by various states of H+ ions. PMID:24662678

Crystal structures, spectroscopic and theoretical study of novel Schiff bases of 2-(methylthiomethyl)anilines.

PubMed

Olalekan, Temitope E; Adejoro, Isaiah A; VanBrecht, Bernardus; Watkins, Gareth M

2015-03-15

New Schiff bases derived from p-methoxysalicylaldehyde and 2-(methylthiomethyl)anilines (substituted with methyl, methoxy, nitro) were synthesized and characterized by elemental analyses, FT-IR, NMR, electronic spectra and quantum chemical calculations. X-ray crystallography of two compounds showed the solid structures are stabilized by intramolecular and intermolecular H-bonds. The effect of OH⋯N interaction between the phenolic hydrogen and imine nitrogen on the proton and carbon NMR shifts, and the role of CH⋯O and CH⋯S contacts are discussed. The bond lengths and angles, (1)H and (13)C NMR data, E(LUMO-HOMO), dipole moments and polarizability of the compounds were predicted by density functional theory, DFT (B3LYP/6-31G∗∗) method. The experimental geometric parameters and the NMR shifts were compared with the calculated values, which gave good correlations. The electronic effects of aryl ring substituents (methyl, methoxy and nitro) on the properties of the resulting compounds, such as the color, NMR shifts, electronic spectra and the calculated energy band gaps, dipole moments and polarizability are discussed. Increase in electron density shifted the phenolic proton resonance to lower fields. The methoxy-substituted compound has a small dipole moment and subsequent large polarizability value. Highest polarity was indicated by the nitro compound which also showed high polarizability due to its larger size. The energy gaps obtained from E(LUMO-HOMO) calculations suggest these compounds may have applications as organic semiconducting materials. Copyright © 2014 Elsevier B.V. All rights reserved.

NMR Crystallography of Enzyme Active Sites: Probing Chemically-Detailed, Three-Dimensional Structure in Tryptophan Synthase

PubMed Central

Dunn, Michael F.

2013-01-01

Conspectus NMR crystallography – the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry – offers unprecedented insight into three-dimensional, chemically-detailed structure. From its initial role in refining diffraction data of organic and inorganic solids, NMR crystallography is now being developed for application to active sites in biomolecules, where it reveals chemically-rich detail concerning the interactions between enzyme site residues and the reacting substrate that is not achievable when X-ray, NMR, or computational methodologies are applied in isolation. For example, typical X-ray crystal structures (1.5 to 2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate, but do not directly identify the protonation state of either. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them, only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but rely on chemical details that must be specified. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which models of the active site can be developed using computational chemistry; these models can be distinguished by comparison of their calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at highest resolution. In this Account, we detail our first steps in the development of NMR crystallography for application to enzyme catalysis. We begin with a brief introduction to NMR crystallography and then define the process that we have employed to probe the active site in the β-subunit of tryptophan synthase with unprecedented atomic-level resolution. This approach has resulted in a novel structural hypothesis for the protonation state of the quinonoid intermediate in tryptophan synthase and its surprising role in directing the next step in the catalysis of L-Trp formation. PMID:23537227

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

PubMed

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

2014-07-14

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

Repeatability of chemical-shift-encoded water-fat MRI and diffusion-tensor imaging in lower extremity muscles in children.

PubMed

Ponrartana, Skorn; Andrade, Kristine E; Wren, Tishya A L; Ramos-Platt, Leigh; Hu, Houchun H; Bluml, Stefan; Gilsanz, Vicente

2014-06-01

The purpose of this study was to assess the repeatability of water-fat MRI and diffusion-tensor imaging (DTI) as quantitative biomarkers of pediatric lower extremity skeletal muscle. MRI at 3 T of a randomly selected thigh and lower leg of seven healthy children was studied using water-fat separation and DTI techniques. Muscle-fat fraction, apparent diffusion coefficient (ADC), and fractional anisotropy (FA) values were calculated. Test-retest and interrater repeatability were assessed by calculating the Pearson correlation coefficient, intraclass correlation coefficient, and Bland-Altman analysis. Bland-Altman plots show that the mean difference between test-retest and interrater measurements of muscle-fat fraction, ADC, and FA was near 0. The correlation coefficients and intraclass correlation coefficients were all between 0.88 and 0.99 (p < 0.05), suggesting excellent reliability of the measurements. Muscle-fat fraction measurements from water-fat MRI exhibited the highest intraclass correlation coefficient. Interrater agreement was consistently better than test-retest comparisons. Water-fat MRI and DTI measurements in lower extremity skeletal muscles are objective repeatable biomarkers in children. This knowledge should aid in the understanding of the number of participants needed in clinical trials when using these determinations as an outcome measure to noninvasively monitor neuromuscular disease.

Calculation of correlation times for the. gamma. -alumina-supported molybdenum subcarbonyl, Mo(CO) sub 3 (ads)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wagner, G.W.; Hanson, B.E.

1989-07-05

The theory of carbon-13 NMR line widths in the solid state for molecules with large chemical shift anisotropies is applied to the adsorbed molybdenum subcarbonyls Mo(CO){sub 3}(ads) and Mo(CO){sub 5}(ads). Correlation times for the rotation of the molybdenum subcarbonyl groups Mo(CO){sub 3}(ads) and Mo(CO){sub 5}(ads) on partially dehydroxylated alumina are calculated. Good agreement is obtained between data reported at observation frequencies of 15 to 75.5 MHz for carbon-13 for Mo(CO){sub 3}(ads). The correlation time for this adsorbed species is calculated to have a lower limit of 4.6 {plus minus} 0.5 ms. The presence of broad lines in the room temperaturemore » spectra for Mo(CO){sub 3}(ads) is thus explained by a slow molecular motion. Data for Mo(CO){sub 5}(ads) are available at observation frequencies of 15 to 90.5 MHz. A good fit to the experimental data is obtained assuming either long or short correlation times for this species. Thus literature estimates of <10{sup {minus}6}s for the correlation time for this species cannot be confirmed with certainty from the analysis presented here.« less

Physics-based method to validate and repair flaws in protein structures

PubMed Central

Martin, Osvaldo A.; Arnautova, Yelena A.; Icazatti, Alejandro A.; Scheraga, Harold A.; Vila, Jorge A.

2013-01-01

A method that makes use of information provided by the combination of 13Cα and 13Cβ chemical shifts, computed at the density functional level of theory, enables one to (i) validate, at the residue level, conformations of proteins and detect backbone or side-chain flaws by taking into account an ensemble average of chemical shifts over all of the conformations used to represent a protein, with a sensitivity of ∼90%; and (ii) provide a set of (χ1/χ2) torsional angles that leads to optimal agreement between the observed and computed 13Cα and 13Cβ chemical shifts. The method has been incorporated into the CheShift-2 protein validation Web server. To test the reliability of the provided set of (χ1/χ2) torsional angles, the side chains of all reported conformations of five NMR-determined protein models were refined by a simple routine, without using NOE-based distance restraints. The refinement of each of these five proteins leads to optimal agreement between the observed and computed 13Cα and 13Cβ chemical shifts for ∼94% of the flaws, on average, without introducing a significantly large number of violations of the NOE-based distance restraints for a distance range ≤ 0.5 Ǻ, in which the largest number of distance violations occurs. The results of this work suggest that use of the provided set of (χ1/χ2) torsional angles together with other observables, such as NOEs, should lead to a fast and accurate refinement of the side-chain conformations of protein models. PMID:24082119

Physics-based method to validate and repair flaws in protein structures.

PubMed

Martin, Osvaldo A; Arnautova, Yelena A; Icazatti, Alejandro A; Scheraga, Harold A; Vila, Jorge A

2013-10-15

A method that makes use of information provided by the combination of (13)C(α) and (13)C(β) chemical shifts, computed at the density functional level of theory, enables one to (i) validate, at the residue level, conformations of proteins and detect backbone or side-chain flaws by taking into account an ensemble average of chemical shifts over all of the conformations used to represent a protein, with a sensitivity of ∼90%; and (ii) provide a set of (χ1/χ2) torsional angles that leads to optimal agreement between the observed and computed (13)C(α) and (13)C(β) chemical shifts. The method has been incorporated into the CheShift-2 protein validation Web server. To test the reliability of the provided set of (χ1/χ2) torsional angles, the side chains of all reported conformations of five NMR-determined protein models were refined by a simple routine, without using NOE-based distance restraints. The refinement of each of these five proteins leads to optimal agreement between the observed and computed (13)C(α) and (13)C(β) chemical shifts for ∼94% of the flaws, on average, without introducing a significantly large number of violations of the NOE-based distance restraints for a distance range ≤ 0.5 , in which the largest number of distance violations occurs. The results of this work suggest that use of the provided set of (χ1/χ2) torsional angles together with other observables, such as NOEs, should lead to a fast and accurate refinement of the side-chain conformations of protein models.

Nuclear magnetic resonance, vibrational spectroscopic studies, physico-chemical properties and computational calculations on (nitrophenyl) octahydroquinolindiones by DFT method.

PubMed

Pasha, M A; Siddekha, Aisha; Mishra, Soni; Azzam, Sadeq Hamood Saleh; Umapathy, S

2015-02-05

In the present study, 2'-nitrophenyloctahydroquinolinedione and its 3'-nitrophenyl isomer were synthesized and characterized by FT-IR, FT-Raman, (1)H NMR and (13)C NMR spectroscopy. The molecular geometry, vibrational frequencies, (1)H and (13)C NMR chemical shift values of the synthesized compounds in the ground state have been calculated by using the density functional theory (DFT) method with the 6-311++G (d,p) basis set and compared with the experimental data. The complete vibrational assignments of wave numbers were made on the basis of potential energy distribution using GAR2PED programme. Isotropic chemical shifts for (1)H and (13)C NMR were calculated using gauge-invariant atomic orbital (GIAO) method. The experimental vibrational frequencies, (1)H and (13)C NMR chemical shift values were found to be in good agreement with the theoretical values. On the basis of vibrational analysis, molecular electrostatic potential and the standard thermodynamic functions have been investigated. Copyright © 2014 Elsevier B.V. All rights reserved.

Generation and structural validation of a library of diverse xyloglucan-derived oligosaccharides, including an update on xyloglucan nomenclature.

PubMed

Tuomivaara, Sami T; Yaoi, Katsuro; O'Neill, Malcolm A; York, William S

2015-01-30

Xyloglucans are structurally complex plant cell wall polysaccharides that are involved in cell growth and expansion, energy metabolism, and signaling. Determining the structure-function relationships of xyloglucans would benefit from the availability of a comprehensive and structurally diverse collection of rigorously characterized xyloglucan oligosaccharides. Here, we present a workflow for the semi-preparative scale generation and purification of neutral and acidic xyloglucan oligosaccharides using a combination of enzymatic and chemical treatments and size-exclusion chromatography. Twenty-six of these oligosaccharides were purified to near homogeneity and their structures validated using a combination of matrix-assisted laser desorption/ionization mass spectrometry, high-performance anion exchange chromatography, and 1H nuclear magnetic resonance spectroscopy. Mass spectrometry and analytical chromatography were compared as methods for xyloglucan oligosaccharide quantification. 1H chemical shifts were assigned using two-dimensional correlation spectroscopy. A comprehensive update of the nomenclature describing xyloglucan side-chain structures is provided for reference. Copyright © 2014 Elsevier Ltd. All rights reserved.

FACILITATED CHEMICAL SYNTHESIS UNDER ALTERNATE REACTION CONDITIONS

EPA Science Inventory

The chemical research in the late 1990's witnessed a paradigm shift towards "environmentally-friendly chemistry" more popularly known as "green chemistry" due to the increasing environmental concerns and legislative requirements to curb the release of chemical waste into the atmo...

CHEMICAL SYNTHESIS USING 'GREENER' ALTERNATIVE REACTION CONDITIONS AND MEDIA

EPA Science Inventory

The chemical research during the last decade has witnessed a paradigm shift towards "environmentally-friendly chemistry" more popularly known as "green chemistry" due to the increasing environmental concerns and legislative requirements to curb the release of chemical waste into ...

¹H, ¹³C, ¹⁵N and ³¹P chemical shift assignments of a human Xist RNA A-repeat tetraloop hairpin essential for X-chromosome inactivation.

PubMed

Duszczyk, Malgorzata M; Sattler, Michael

2012-04-01

Initiation of X-chromosome inactivation in female mammals depends on the non-coding RNA Xist. We have solved the NMR structure of a 14-nucleotide hairpin with a novel AUCG tetraloop fold from a Xist A-repeat that is essential for silencing. The (1)H, (13)C, (15)N and (31)P chemical shift assignments are reported.

Dynamic metabolic imaging of hyperpolarized [2-(13) C]pyruvate using spiral chemical shift imaging with alternating spectral band excitation.

PubMed

Josan, Sonal; Hurd, Ralph; Park, Jae Mo; Yen, Yi-Fen; Watkins, Ron; Pfefferbaum, Adolf; Spielman, Daniel; Mayer, Dirk

2014-06-01

In contrast to [1-(13) C]pyruvate, hyperpolarized [2-(13) C]pyruvate permits the ability to follow the (13) C label beyond flux through pyruvate dehydrogenase complex and investigate the incorporation of acetyl-coenzyme A into different metabolic pathways. However, chemical shift imaging (CSI) with [2-(13) C]pyruvate is challenging owing to the large spectral dispersion of the resonances, which also leads to severe chemical shift displacement artifacts for slice-selective acquisitions. This study introduces a sequence for three-dimensional CSI of [2-(13) C]pyruvate using spectrally selective excitation of limited frequency bands containing a subset of metabolites. Dynamic CSI data were acquired alternately from multiple frequency bands in phantoms for sequence testing and in vivo in rat heart. Phantom experiments verified the radiofrequency pulse design and demonstrated that the signal behavior of each group of resonances was unaffected by excitation of the other frequency bands. Dynamic three-dimensional (13) C CSI data demonstrated the sequence capability to image pyruvate, lactate, acetylcarnitine, glutamate, and acetoacetate, enabling the analysis of organ-specific spectra and metabolite time courses. The presented method allows CSI of widely separated resonances without chemical shift displacement artifact, acquiring multiple frequency bands alternately to obtain dynamic time-course information. This approach enables robust imaging of downstream metabolic products of acetyl-coenzyme A with hyperpolarized [2-(13) C]pyruvate. Copyright © 2013 Wiley Periodicals, Inc.

Inclusion compound of vitamin B6 in β-CD. Physico-chemical and structural investigations

NASA Astrophysics Data System (ADS)

Borodi, Gheorghe; Kacso, Irina; Farcaş, Sorin I.; Bratu, Ioan

2009-08-01

Structural and physico-chemical characterization of supramolecular assembly of vitamin B6 with β-cyclodextrin (β-CD) prepared by different methods (kneading, co-precipitation and freeze-drying) has been performed by using several spectroscopic techniques (FTIR, 1H NMR, UV-Vis), powder X-ray diffraction and DSC in order to evidence the inclusion compound formation. An analysis of the chemical shifts observed in the 1H-NMR spectra and of the vibrational frequency shifts led to the tentative conclusion that the vitamin B6 probably enters the cyclodextrin torus when forming the β-CD-vitamin B6 inclusion complex.

Density functional theory study on aqueous aluminum-fluoride complexes: exploration of the intrinsic relationship between water-exchange rate constants and structural parameters for monomer aluminum complexes.

PubMed

Jin, Xiaoyan; Qian, Zhaosheng; Lu, Bangmei; Yang, Wenjing; Bi, Shuping

2011-01-01

Density functional theory (DFT) calculation is carried out to investigate the structures, (19)F and (27)Al NMR chemical shifts of aqueous Al-F complexes and their water-exchange reactions. The following investigations are performed in this paper: (1) the microscopic properties of typical aqueous Al-F complexes are obtained at the level of B3LYP/6-311+G**. Al-OH(2) bond lengths increase with F(-) replacing inner-sphere H(2)O progressively, indicating labilizing effect of F(-) ligand. The Al-OH(2) distance trans to fluoride is longer than other Al-OH(2) distance, accounting for trans effect of F(-) ligand. (19)F and (27)Al NMR chemical shifts are calculated using GIAO method at the HF/6-311+G** level relative to F(H(2)O)(6)(-) and Al(H(2)O)(6)(3+) references, respectively. The results are consistent with available experimental values; (2) the dissociative (D) activated mechanism is observed by modeling water-exchange reaction for [Al(H(2)O)(6-i)F(i)]((3-i)+) (i = 1-4). The activation energy barriers are found to decrease with increasing F(-) substitution, which is in line with experimental rate constants (k(ex)). The log k(ex) of AlF(3)(H(2)O)(3)(0) and AlF(4)(H(2)O)(2)(-) are predicted by three ways. The results indicate that the correlation between log k(ex) and Al-O bond length as well as the given transmission coefficient allows experimental rate constants to be predicted, whereas the correlation between log k(ex) and activation free energy is poor; (3) the environmental significance of this work is elucidated by the extension toward three fields, that is, polyaluminum system, monomer Al-organic system and other metal ions system with high charge-to-radius ratio.

Progress in high temperature speckle-shift strain measurement system

NASA Technical Reports Server (NTRS)

Lant, Christian T.; Barranger, John P.

1990-01-01

A fast, easy to use speckle tracking system is under development for the speckle-shift strain measurement technique. Preliminary correlation tests on wire specimens show strong correlations of well-developed speckle patterns. Stable cross-correlations were obtained from a tungsten filament at 2480 C. An analysis of the optical system determines the minimum required sampling frequency of the speckle pattern to be 2.55 pixels per speckle.

Digital Holographic Interferometry and Speckle Correlation

NASA Astrophysics Data System (ADS)

Yamaguchi, Ichirou

2010-04-01

Relations and combinations between holographic interferometry and speckle correlation in contouring by phase-shifting digital holography are discussed. Three-dimensional distributions of correlations of the complex amplitudes and intensities before and after the laser wavelength shift are calculated in numerical simulations where a rough surface is modeled with random numbers. Fringe localization related to speckle displacement as well as speckle suppression in phase analysis are demonstrated for general surface shape and recording conditions.

Exploring Initiative as a Signal of Knowledge Co-Construction During Collaborative Problem Solving.

PubMed

Howard, Cynthia; Di Eugenio, Barbara; Jordan, Pamela; Katz, Sandra

2017-08-01

Peer interaction has been found to be conducive to learning in many settings. Knowledge co-construction (KCC) has been proposed as one explanatory mechanism. However, KCC is a theoretical construct that is too abstract to guide the development of instructional software that can support peer interaction. In this study, we present an extensive analysis of a corpus of peer dialogs that we collected in the domain of introductory Computer Science. We show that the notion of task initiative shifts correlates with both KCC and learning. Speakers take task initiative when they contribute new content that advances problem solving and that is not invited by their partner; if initiative shifts between the partners, it indicates they both contribute to problem solving. We found that task initiative shifts occur more frequently within KCC episodes than outside. In addition, task initiative shifts within KCC episodes correlate with learning for low pre-testers, and total task initiative shifts correlate with learning for high pre-testers. As recognizing task initiative shifts does not require as much deep knowledge as recognizing KCC, task initiative shifts as an indicator of productive collaboration are potentially easier to model in instructional software that simulates a peer. Copyright © 2016 Cognitive Science Society, Inc.

Effect of an invasive ant and its chemical control on a threatened endemic Seychelles millipede.

PubMed

Lawrence, James M; Samways, Michael J; Henwood, Jock; Kelly, Janine

2011-06-01

The impact of invasive species on island faunas can be of major local consequence, while their control is an important part of island ecosystem restoration. Among these invasive species are ants, of which some have a disruptive impact on indigenous arthropod populations. Here, we study the impact of the invasive African big-headed ant, Pheidole megacephala, on a small Seychelles island, Cousine, and assess the impact of this ant, and its chemical control, using the commercially available hydramethylnon-based bait, Siege, on the endemic keystone Seychelles giant millipede species, Sechelleptus seychellarum. We found no significant correlations in landscape-scale spatial overlap and abundance between the ant and the millipede. Furthermore, the ant did not attack healthy millipedes, but fed only on dying and dead individuals. The chemical defences of the millipede protected it from ant predation. Ingestion of the bait at standard concentration had no obvious impact on the millipede. The most significant threat to the Seychelles giant millipede in terms of P. megacephala invasion is from possible catastrophic shifts in ecosystem function through ant hemipteran mutualisms which can lead to tree mortality, resulting in alteration of the millipede's habitat.

Causal Correlation Functions and Fourier Transforms: Application in Calculating Pressure Induced Shifts

NASA Technical Reports Server (NTRS)

Ma, Q.; Tipping, R. H.; Lavrentieva, N. N.

2012-01-01

By adopting a concept from signal processing, instead of starting from the correlation functions which are even, one considers the causal correlation functions whose Fourier transforms become complex. Their real and imaginary parts multiplied by 2 are the Fourier transforms of the original correlations and the subsequent Hilbert transforms, respectively. Thus, by taking this step one can complete the two previously needed transforms. However, to obviate performing the Cauchy principal integrations required in the Hilbert transforms is the greatest advantage. Meanwhile, because the causal correlations are well-bounded within the time domain and band limited in the frequency domain, one can replace their Fourier transforms by the discrete Fourier transforms and the latter can be carried out with the FFT algorithm. This replacement is justified by sampling theory because the Fourier transforms can be derived from the discrete Fourier transforms with the Nyquis rate without any distortions. We apply this method in calculating pressure induced shifts of H2O lines and obtain more reliable values. By comparing the calculated shifts with those in HITRAN 2008 and by screening both of them with the pair identity and the smooth variation rules, one can conclude many of shift values in HITRAN are not correct.

Highly active Pt/MoC and Pt/TiC catalysts for the low-temperature water-gas shift reaction: Effects of the carbide metal/carbon ratio on the catalyst performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rodriguez, José A.; Ramírez, Pedro J.; Gutierrez, Ramón A.

We present that Pt/MoC and Pt/TiC(001) are excellent catalysts for the low-temperature water-gas shift (WGS, CO + H 2O → H 2 + CO 2) reaction. They exhibit high-activity, stability and selectivity. The highest catalytic activities are seen for small coverages of Pt on the carbide substrates. Synergistic effects at the metal-carbide interface produce an enhancement in chemical activity with respect to pure Pt, MoC and TiC. A clear correlation is found between the ability of the Pt/MoC and Pt/TiC(001) surfaces to partially dissociate water and their catalytic activity for the WGS reaction. Finally, an overall comparison of the resultsmore » for Pt/MoC and Pt/Mo 2C(001) indicates that the metal/carbon ratio in the carbide support can have a strong influence in the stability and selectivity of WGS catalysts and is a parameter that must be taken into consideration when designing these systems.« less

Isotopically Enriched C-13 Diamond Anvil as a Stress Sensor in High Pressure Experiments

NASA Astrophysics Data System (ADS)

Vohra, Yogesh; Qiu, Wei; Kondratyev, Andreiy; Velisavljevic, Nenad; Baker, Paul

2004-03-01

The conventional high pressure diamond anvils were modified by growing an isotopically pure C-13 diamond layer by microwave plasma chemical vapor deposition using methane/hydrogen/oxygen chemistry. The isotopically pure C-13 nature of the culet of the diamond anvil was confirmed by the Raman spectroscopy measurements. This isotopically engineered diamond anvil was used against a natural abundance diamond anvil for high pressure experiments in a diamond anvil cell. Spatial resolved Raman spectroscopy was used to measure the stress induced shift in the C-13 layer as well as the undelying C-12 layer to ultra high pressures. The observed shift and splitiing of the diamond first order Raman spectrum was correlated with the stress distribution in the diamond anvil cell. The experimental results will be compared with the finite element modeling results using NIKE-2D software in order to create a mathematical relationship between sets of the following parameters: vertical (z axis) distance; horizontal (r axis) distance; max shear stress, and pressure. The isotopically enriched diamond anvils offer unique opportunities to measure stress distribution in the diamond anvil cell devices.

Modeling the absorption spectrum of the permanganate ion in vacuum and in aqueous solution

NASA Astrophysics Data System (ADS)

Olsen, Jógvan Magnus Haugaard; Hedegård, Erik Donovan

The absorption spectrum of the MnO$_{4}$$^{-}$ ion has been a test-bed for quantum-chemical methods over the last decades. Its correct description requires highly-correlated multiconfigurational methods, which are incompatible with the inclusion of finite-temperature and solvent effects due to their high computational demands. Therefore, implicit solvent models are usually employed. Here we show that implicit solvent models are not sufficiently accurate to model the solvent shift of MnO$_{4}$$^{-}$, and we analyze the origins of their failure. We obtain the correct solvent shift for MnO$_{4}$$^{-}$ in aqueous solution by employing the polarizable embedding (PE) model combined with a range-separated complete active space short-range density functional theory method (CAS-srDFT). Finite-temperature effects are taken into account by averaging over structures obtained from ab initio molecular dynamics simulations. The explicit treatment of finite-temperature and solvent effects facilitates the interpretation of the bands in the low-energy region of the MnO$_{4}$$^{-}$ absorption spectrum, whose assignment has been elusive.

Interresidue carbonyl-carbonyl polarization transfer experiments in uniformly 13C, 15N-labeled peptides and proteins

NASA Astrophysics Data System (ADS)

Janik, Rafal; Ritz, Emily; Gravelle, Andrew; Shi, Lichi; Peng, Xiaohu; Ladizhansky, Vladimir

2010-03-01

In this work, we demonstrate that Homonuclear Rotary Resonance Recoupling (HORROR) can be used to reintroduce carbonyl-carbonyl interresidue dipolar interactions and to achieve efficient polarization transfer between carbonyl atoms in uniformly 13C, 15N-labeled peptides and proteins. We show that the HORROR condition is anisotropically broadened and overall shifted to higher radio frequency intensities because of the CSA effects. These effects are analyzed theoretically using Average Hamiltonian Theory. At spinning frequencies used in this study, 22 kHz, this broadening is experimentally found to be on the order of a kilohertz at a proton field of 600 MHz. To match HORROR condition over all powder orientations, variable amplitude radio frequency (RF) fields are required, and efficient direct transfers on the order of 20-30% can be straightforwardly established. Two- and three-dimensional chemical shift correlation experiments establishing long-range interresidue connectivities (e.g., (N[i]-CO[i - 2])) are demonstrated on the model peptide N-acetyl-valine-leucine, and on the third immunoglobulin binding domain of protein G. Possible future developments are discussed.

Highly active Pt/MoC and Pt/TiC catalysts for the low-temperature water-gas shift reaction: Effects of the carbide metal/carbon ratio on the catalyst performance

DOE PAGES

Rodriguez, José A.; Ramírez, Pedro J.; Gutierrez, Ramón A.

2016-09-20

We present that Pt/MoC and Pt/TiC(001) are excellent catalysts for the low-temperature water-gas shift (WGS, CO + H 2O → H 2 + CO 2) reaction. They exhibit high-activity, stability and selectivity. The highest catalytic activities are seen for small coverages of Pt on the carbide substrates. Synergistic effects at the metal-carbide interface produce an enhancement in chemical activity with respect to pure Pt, MoC and TiC. A clear correlation is found between the ability of the Pt/MoC and Pt/TiC(001) surfaces to partially dissociate water and their catalytic activity for the WGS reaction. Finally, an overall comparison of the resultsmore » for Pt/MoC and Pt/Mo 2C(001) indicates that the metal/carbon ratio in the carbide support can have a strong influence in the stability and selectivity of WGS catalysts and is a parameter that must be taken into consideration when designing these systems.« less

Lanthanide ion (III) complexes of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate (DOTA-4AmP8−) for dual biosensing of pH with CEST (chemical exchange saturation transfer) and BIRDS (biosensor imaging of redundant deviation in shifts)

PubMed Central

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

2014-01-01

Relaxivity based magnetic resonance of phosphonated ligands chelated with gadolinium (Gd3+) shows promise for pH imaging. However instead of monitoring the paramagnetic effect of lanthanide complexes on the relaxivity of water protons, biosensor (or molecular) imaging with magnetic resonance is also possible by detecting either the non-exchangeable or the exchangeable protons on the lanthanide complexes themselves. The non-exchangeable protons (e.g., –CHx, where 3≥x≥1) are detected using a three-dimensional chemical shift imaging method called Biosensor Imaging of Redundant Deviation in Shifts (BIRDS), whereas the exchangeable protons (e.g., –OH or –NHy, where 2≥y≥1) are measured with Chemical Exchange Saturation Transfer (CEST) contrast. Here we tested the feasibility of BIRDS and CEST for pH imaging of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate (DOTA-4AmP8−) chelated with thulium (Tm3+) and ytterbium (Yb3+). BIRDS and CEST experiments show that both complexes are responsive to pH and temperature changes. Higher pH and temperature sensitivities are obtained with BIRDS for either complex when using the chemical shift difference between two proton resonances vs. using the chemical shift of a single proton resonance, thereby eliminating the need to use water resonance as reference. While CEST contrast for both agents is linearly dependent on pH within a relatively large range (i.e., 6.3-7.9), much stronger CEST contrast is obtained with YbDOTA-4AmP5− than with TmDOTA-4AmP5−. In addition, we demonstrate the prospect of using BIRDS to calibrate CEST as new platform for quantitative pH imaging. PMID:24801742

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

PubMed

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

2015-01-01

Relaxivity-based magnetic resonance of phosphonated ligands chelated with gadolinium (Gd(3+)) shows promise for pH imaging. However instead of monitoring the paramagnetic effect of lanthanide complexes on the relaxivity of water protons, biosensor (or molecular) imaging with magnetic resonance is also possible by detecting either the nonexchangeable or the exchangeable protons on the lanthanide complexes themselves. The nonexchangeable protons (e.g. -CHx, where 3 ≥ x ≥ 1) are detected using a three-dimensional chemical shift imaging method called biosensor imaging of redundant deviation in shifts (BIRDS), whereas the exchangeable protons (e.g. -OH or -NHy , where 2 ≥ y ≥ 1) are measured with chemical exchange saturation transfer (CEST) contrast. Here we tested the feasibility of BIRDS and CEST for pH imaging of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate (DOTA-4AmP(8-)) chelated with thulium (Tm(3+) ) and ytterbium (Yb(3+)). BIRDS and CEST experiments show that both complexes are responsive to pH and temperature changes. Higher pH and temperature sensitivities are obtained with BIRDS for either complex when using the chemical shift difference between two proton resonances vs using the chemical shift of a single proton resonance, thereby eliminating the need to use water resonance as reference. While CEST contrast for both agents is linearly dependent on pH within a relatively large range (i.e. 6.3-7.9), much stronger CEST contrast is obtained with YbDOTA-4AmP(5-) than with TmDOTA-4AmP(5-). In addition, we demonstrate the prospect of using BIRDS to calibrate CEST as new platform for quantitative pH imaging. Copyright © 2014 John Wiley & Sons, Ltd.

An NMR study of microvoids in polymers

NASA Technical Reports Server (NTRS)

Toy, James; Mattix, Larry

1995-01-01

An understanding of polymer defect structures, like microvoids in polymeric matrices, is crucial to their fabrication and application potential. In this project guest atoms are introduced into the microvoids in PMR-15 and NMR is used to determine microvoid sizes and locations. Xenon is a relatively inert probe that would normally be found naturally in polymer or in NMR probe materials. There are two NMR active xenon isotopes, Xe-129 and Xe-131. The Xe atom has a very high polarizability, which makes it sensitive to the intracrystalline environment of polymers. Interactions between the Xe atoms and the host matrix perturb the Xe electron cloud, deshielding the nuclei, and thereby expanding the range of the observed NMR chemical shifts. This chemical shift range which may be as large as 5000 ppm, permits subtle structural and chemical effects to be studied with high sensitivity. The Xe(129)-NMR line shape has been found to vary in response to changes in the pore symmetry of the framework hosts line Zeolites and Clathrasil compounds. Before exposure to Xe gas, the PMR-15 samples were dried in a vacuum oven at 150 C for 48 hours. The samples were then exposed to Xe gas at 30 psi for 72 hours and sealed in glass tubes with 1 atmosphere of xenon gas. Xenon gas at 1 atmosphere was used to tune up the spectrometer and to set up the appropriate NMR parameters. A single Xe-129 line at 83.003498 Mhz (with protons at 300 Mhz) was observed for the gas. With the xenon charged PMR-15 samples, a second broader line is observed 190 ppm downfield from the gas line (also observed). The width of the NMR line from the Xe-129 absorbed in the polymer is at least partially due to the distribution of microvoid sizes. From the chemical shift (relative to the gas line) and the line width, we estimate the average void sizes to be 2.74 +/- 0.20 angstroms. Since Xe-129 has such a large chemical shift range (approximately 5000 ppm), we expect the chemical shift anisotropy to contribute to the line width (delta upsilon = 2.5 kHz).

31P NMR Chemical Shifts of Solvents and Products Impurities in Biomass Pretreatments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Mi; Yoo, Chang Geun; Pu, Yunqiao

The identification of chemical impurities is crucial in elucidating the structures of biorefinery products using nuclear magnetic resonance (NMR) spectroscopic analysis. In the current biorefinery platform, contaminants derived from pretreatment solvents and decomposition byproducts may lead to misassignment of the NMR spectra of biorefinery products (e.g, lignin and bio-oils). Therefore, we investigated in this paper 54 commonly reported compounds including alcohols, carbohydrates, organic acids, aromatics, aldehydes, and ionic liquids associated with biomass pretreatment using 31P NMR. The chemical shifts of these chemicals after derivatizing with 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane (TMDP) were provided. Finally, the 31P NMR signals of these derivatives could serve asmore » valuable and informative spectral data in characterizing lignocellulose-based compounds.« less

31P NMR Chemical Shifts of Solvents and Products Impurities in Biomass Pretreatments

DOE PAGES

Li, Mi; Yoo, Chang Geun; Pu, Yunqiao; ...

2017-12-05

The identification of chemical impurities is crucial in elucidating the structures of biorefinery products using nuclear magnetic resonance (NMR) spectroscopic analysis. In the current biorefinery platform, contaminants derived from pretreatment solvents and decomposition byproducts may lead to misassignment of the NMR spectra of biorefinery products (e.g, lignin and bio-oils). Therefore, we investigated in this paper 54 commonly reported compounds including alcohols, carbohydrates, organic acids, aromatics, aldehydes, and ionic liquids associated with biomass pretreatment using 31P NMR. The chemical shifts of these chemicals after derivatizing with 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane (TMDP) were provided. Finally, the 31P NMR signals of these derivatives could serve asmore » valuable and informative spectral data in characterizing lignocellulose-based compounds.« less

A meta-analysis including dose-response relationship between night shift work and the risk of colorectal cancer.

PubMed

Wang, Xiao; Ji, Alin; Zhu, Yi; Liang, Zhen; Wu, Jian; Li, Shiqi; Meng, Shuai; Zheng, Xiangyi; Xie, Liping

2015-09-22

A meta-analysis was conducted to quantitatively evaluate the correlation between night shift work and the risk of colorectal cancer. We searched for publications up to March 2015 using PubMed, Web of Science, Cochrane Library, EMBASE and the Chinese National Knowledge Infrastructure databases, and the references of the retrieved articles and relevant reviews were also checked. OR and 95% CI were used to assess the degree of the correlation between night shift work and risk of colorectal cancer via fixed- or random-effect models. A dose-response meta-analysis was performed as well. The pooled OR estimates of the included studies illustrated that night shift work was correlated with an increased risk of colorectal cancer (OR = 1.318, 95% CI 1.121-1.551). No evidence of publication bias was detected. In the dose-response analysis, the rate of colorectal cancer increased by 11% for every 5 years increased in night shift work (OR = 1.11, 95% CI 1.03-1.20). In conclusion, this meta-analysis indicated that night shift work was associated with an increased risk of colorectal cancer. Further researches should be conducted to confirm our findings and clarify the potential biological mechanisms.

Spectral and structural studies of dimethylphenyl betaine hydrate

NASA Astrophysics Data System (ADS)

Szafran, M.; Ostrowska, K.; Katrusiak, A.; Dega-Szafran, Z.

2014-07-01

Hydrates of betaines can be divided into four groups depending on the interactions of their water molecules with the carboxylate group. Dimethylphenyl betaine crystallizes as monohydrate (1), in which water molecules mediate in hydrogen bonds between the carboxylate groups. The water molecules are H-bonded only to one oxygen atom of the dimethylphenyl betaine molecules and link them into a chain via two O(1 W)sbnd H⋯O hydrogen bonds of the lengths 2.779(2) and 2.846(2) Å. The structures of monomer (2) and dimer (4) hydrates in vacuum, and the structure of monomer (3) in an aqueous environment have been optimized by the B3LYP/6-311++G(d,p) approach and the geometrical results have been compared with the X-ray diffraction data of 1. The calculated IR frequencies for the optimized structure have been used for the assignments of FTIR bands, the broad absorption band in the range 3415-3230 cm-1 has been assigned to the O(1w)sbnd H⋯O hydrogen bonds. The correlations between the experimental 1H and 13C NMR chemical shifts (δexp) of 1 in D2O and the magnetic isotropic shielding constants (σcalc) calculated by the GIAO/B3LYP/6-311G++(d,p) approach, using the screening solvation model (COSMO), δexp = a + b σcalc, for optimized molecule 3 in water solution are linear and well reproduce the experimental chemical shifts.

Synthesis, spectroscopic characterization, X-ray structure and DFT studies on 2,6-bis(1-benzyl-1H-benzo[d]imidazol-2-yl)pyridine

NASA Astrophysics Data System (ADS)

İnkaya, Ersin; Günnaz, Salih; Özdemir, Namık; Dayan, Osman; Dinçer, Muharrem; Çetinkaya, Bekir

2013-02-01

The title molecule, 2,6-bis(1-benzyl-1H-benzo[d]imidazol-2-yl)pyridine (C33H25N5), was synthesized and characterized by elemental analysis, FT-IR spectroscopy, one- and two-dimensional NMR spectroscopies, and single-crystal X-ray diffraction. In addition, the molecular geometry, vibrational frequencies and gauge-independent atomic orbital (GIAO) 1H and 13C NMR chemical shift values of the title compound in the ground state have been calculated using the density functional theory at the B3LYP/6-311G(d,p) level, and compared with the experimental data. The complete assignments of all vibrational modes were performed by potential energy distributions using VEDA 4 program. The geometrical parameters of the optimized structure are in good agreement with the X-ray crystallographic data, and the theoretical vibrational frequencies and GIAO 1H and 13C NMR chemical shifts show good agreement with experimental values. Besides, molecular electrostatic potential (MEP) distribution, frontier molecular orbitals (FMO) and non-linear optical properties of the title compound were investigated by theoretical calculations at the B3LYP/6-311G(d,p) level. The linear polarizabilities and first hyper polarizabilities of the molecule indicate that the compound is a good candidate of nonlinear optical materials. The thermodynamic properties of the compound at different temperatures were calculated, revealing the correlations between standard heat capacity, standard entropy, standard enthalpy changes and temperatures.

Dynamical patterns and regime shifts in the nonlinear model of soil microorganisms growth

NASA Astrophysics Data System (ADS)

Zaitseva, Maria; Vladimirov, Artem; Winter, Anna-Marie; Vasilyeva, Nadezda

2017-04-01

Dynamical model of soil microorganisms growth and turnover is formulated as a system of nonlinear partial differential equations of reaction-diffusion type. We consider spatial distributions of concentrations of several substrates and microorganisms. Biochemical reactions are modelled by chemical kinetic equations. Transport is modelled by simple linear diffusion for all chemical substances, while for microorganisms we use different transport functions, e.g. some of them can actively move along gradient of substrate concentration, while others cannot move. We solve our model in two dimensions, starting from uniform state with small initial perturbations for various parameters and find parameter range, where small initial perturbations grow and evolve. We search for bifurcation points and critical regime shifts in our model and analyze time-space profile and phase portraits of these solutions approaching critical regime shifts in the system, exploring possibility to detect such shifts in advance. This work is supported by NordForsk, project #81513.

Phosphorus Imaging as a Tool for Studying the pH Metabolism in Living Insects

NASA Astrophysics Data System (ADS)

Skibbe, U.; Christeller, J. T.; Eccles, C. D.; Laing, W. A.; Callaghan, P. T.

1995-09-01

Comparative 31P NMR and 1H NMR imaging experiments at submillimeter pixel resolution were carried out, using a specially constructed solenoidal RF coil. Chemical-shift imaging is used to provide pH maps from the midgut of a Lepidopteran larvae and to demonstrate physiological dependence in the resulting images, The titration curve of pH versus chemical shift for inorganic phosphate is extended beyond the "normal" biological range to the strong alkaline limit.

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

PubMed Central

Mananga, Eugene Stephane

2013-01-01

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

An Evaluation of the Relationship among Urine, Air, and Hand Measures of Exposure to Bisphenol A (BPA) in US Manufacturing Workers.

PubMed

Hines, Cynthia J; Christianson, Annette L; Jackson, Matthew V; Ye, Xiaoyun; Pretty, Jack R; Arnold, James E; Calafat, Antonia M

2018-06-13

Exposure to bisphenol A (BPA) can be assessed using external and internal exposure measures. We examined the relationship between two measures of external BPA exposure (air and hand-wipe samples) and one of internal exposure (total BPA in urine) for a group of US manufacturing workers. During 2013-2014, we recruited 78 workers from six US companies that made BPA or made products with BPA. We quantified BPA in seven urine samples, two full-shift air samples and in pre- and end-shift hand-wipe samples collected from workers over 2 consecutive days. We examined correlations between creatinine-corrected urinary concentrations of total BPA (total BPACR) and BPA levels in air and hand wipes using Pearson's correlation coefficient. We also applied mixed-effects regression models to examine the relationship between total BPACR with BPA in air (urine~air model) and with BPA in end-shift hand wipes (urine~hand model), separately and together (urine~air+hand model), after adjusting for covariates. End-shift total BPACR strongly correlated with BPA in air (rp = 0.79, P < 0.0001) and nearly as strongly with BPA in end-shift hand wipes (rp = 0.75, P < 0.0001). In mixed-effect models, BPA air concentration and end-shift hand-wipe BPA level were significantly and positively associated with end-shift total BPACR (P < 0.0001 each). We found a significant effect of the Day 1 BPA air concentration on Day 2 total BPACR (P = 0.0104). When BPA air concentration and end-shift hand-wipe BPA level were in the same model, the air concentration (P < 0.0001) was more significant than the hand-wipe level (P = 0.0106). BPA levels in air and end-shift hand wipes strongly correlated with total BPACR, suggesting that both inhalation and dermal contract were likely exposure routes; however, inhalation, on average, appeared to be a more dominant exposure route than dermal contact for these manufacturing workers.

Job Relocation is High in Chemical Industry.

ERIC Educational Resources Information Center

Chemical and Engineering News, 1979

1979-01-01

The chances of an employee being relocated are higher in the chemical and plastics industries than in U.S. business as a whole. But the benefits provided by chemical and plastics companies to employees shifted to other locations are generally better than average. (Author/BB)

Velocity encoding with the slice select refocusing gradient for faster imaging and reduced chemical shift-induced phase errors.

PubMed

Middione, Matthew J; Thompson, Richard B; Ennis, Daniel B

2014-06-01

To investigate a novel phase-contrast MRI velocity-encoding technique for faster imaging and reduced chemical shift-induced phase errors. Velocity encoding with the slice select refocusing gradient achieves the target gradient moment by time shifting the refocusing gradient, which enables the use of the minimum in-phase echo time (TE) for faster imaging and reduced chemical shift-induced phase errors. Net forward flow was compared in 10 healthy subjects (N = 10) within the ascending aorta (aAo), main pulmonary artery (PA), and right/left pulmonary arteries (RPA/LPA) using conventional flow compensated and flow encoded (401 Hz/px and TE = 3.08 ms) and slice select refocused gradient velocity encoding (814 Hz/px and TE = 2.46 ms) at 3 T. Improved net forward flow agreement was measured across all vessels for slice select refocused gradient compared to flow compensated and flow encoded: aAo vs. PA (1.7% ± 1.9% vs. 5.8% ± 2.8%, P = 0.002), aAo vs. RPA + LPA (2.1% ± 1.7% vs. 6.0% ± 4.3%, P = 0.03), and PA vs. RPA + LPA (2.9% ± 2.1% vs. 6.1% ± 6.3%, P = 0.04), while increasing temporal resolution (35%) and signal-to-noise ratio (33%). Slice select refocused gradient phase-contrast MRI with a high receiver bandwidth and minimum in-phase TE provides more accurate and less variable flow measurements through the reduction of chemical shift-induced phase errors and a reduced TE/repetition time, which can be used to increase the temporal/spatial resolution and/or reduce breath hold durations. Copyright © 2013 Wiley Periodicals, Inc.

Shifting covariability of North American summer monsoon precipitation with antecedent winter precipitation

USGS Publications Warehouse

McCabe, G.J.; Clark, M.P.

2006-01-01

Previous research has suggested that a general inverse relation exists between winter precipitation in the southwestern United states (US) and summer monsoon precipitation. In addition, it has been suggested that this inverse relation between winter precipitation and the magnitude of the southwestern US monsoon breaks down under certain climatic conditions that override the regional winter/monsoon precipitation relations. Results from this new study indicate that the winter/monsoon precipitation relations do not break down, but rather shift location through time. The strength of winter/monsoon precipitation relations, as indexed by 20-year moving correlations between winter precipitation and monsoon precipitation, decreased in Arizona after about 1970, but increased in New Mexico. The changes in these correlations appear to be related to an eastward shift in the location of monsoon precipitation in the southwestern US. This eastward shift in monsoon precipitation and the changes in correlations with winter precipitation also appear to be related to an eastward shift in July/August atmospheric circulation over the southwestern US that resulted in increased monsoon precipitation in New Mexico. Results also indicate that decreases in sea-surface temperatures (SSTs) in the central North Pacific Ocean also may be associated with th changes in correlations between winter and monsoon precipitation. Copyright ?? 2006 Royal Meteorological Society.

Incubation rhythm in the Fulmar Fulmarus glacialis: Annual variation and sex roles

USGS Publications Warehouse

Hatch, Scott A.

1990-01-01

I monitored the incubation schedules of Fulmars Fulmarus glacialis in an Alaskan colony by observing nests where the male and female were of different colour phases. Complete shifts of up to 16 days were recorded; the average shift in mid-incubation was 4–6 days. Mean shift length was inversely correlated with hatching success in 5 years, suggesting that Fulmars adjusted their foraging patterns to annual differences in food availability. Males assumed the larger share (55%) of incubation on average, and a larger share in years with lower hatching success. Serial correlation in the length of incubation shifts had two components - the influence of prior shift lengths on time spent foraging and individual variation. Failure of the male to relieve the female soon after laying resulted in a few breeding failures and egg losses were associated with exceptionally long shifts throughout incubation.

Evaluation of portal venous velocity with Doppler ultrasound in patients with nonalcoholic fatty liver disease.

PubMed

Ulusan, Serife; Yakar, Tolga; Koc, Zafer

2011-01-01

We examined the relationship between portal venous velocity and hepatic-abdominal fat in patients with nonalcoholic fatty liver disease (NAFLD), using spectral Doppler ultrasonography (US) and magnetic resonance imaging (MRI). In this prospective study, 35 patients with NAFLD and 29 normal healthy adults (control group) underwent portal Doppler US. The severity of hepatic steatosis in patients with NAFLD was assessed by MRI through chemical shift imaging, using a modification of the Dixon method. Abdominal (intra-abdominal and subcutaneous) fat was measured by MRI. The difference in portal venous velocity between the patients with NAFLD and the control group was significant (p < 0.0001). There was no correlation between the degree of abdominal or hepatic fat and portal venous velocity (p > 0.05). There were strong correlations between the hepatic fat fraction and subcutaneous adiposity (p < 0.0001), intraperitoneal fat accumulation (p = 0.017), and retroperitoneal fat accumulation (p < 0.0001). Our findings suggest that patients with NAFLD have lower portal venous velocities than normal healthy subjects.

Détermination assistée par ordinateur de la structure des molécules organiques

NASA Astrophysics Data System (ADS)

Nuzillard, J.-M.

1998-02-01

Nuclear Magnetic Resonance spectroscopy offers the unique possibility of accessing proximity relationships between atoms by means of chemical shift correlation experiments. Structure determination of small molecules has become thus much simpler. Computer programs can use directly correlation information for structure analysis. The use and operation mechanism of such a program, LSD (Logic for Structure Determination) are presented. The example compound is gibberellic acid, a natural product. La spectroscopie de Résonance Magnétique Nucléaire offre un moyen unique de déterminer des relations de proximité entre atomes par le biais des expériences de corrélation. L'analyse structurale de petites molécules organiques s'en trouve extrêmement facilitée. Des programmes informatiques peuvent utiliser directement les informations de corrélation pour déduire des structures. Le fonctionnement et l'usage d'un tel programme, LSD (Logic for Structure Determination), sont détaillés sur un exemple, l'acide gibberellique.

Cognitive Inflexibility and Frontal-Cortical Activation in Pediatric Obsessive-Compulsive Disorder

PubMed Central

Britton, Jennifer C.; Rauch, Scott L.; Rosso, Isabelle M.; Killgore, William D.S.; Price, Lauren M.; Ragan, Jennifer; Chosak, Anne; Hezel, Dianne M.; Pine, Daniel S.; Leibenluft, Ellen; Pauls, David L.; Jenike, Michael A.; Stewart, S. Evelyn

2014-01-01

Objective Deficits in cognitive flexibility and response inhibition have been linked to perturbations in cortico-striatal-thalamic circuitry in adult obsessive-compulsive disorder (OCD). Although similar cognitive deficits have been identified in pediatric OCD, few neuroimaging studies have been conducted to examine its neural correlates in the developing brain. In this study, we tested hypotheses regarding group differences in the behavioral and neural correlates of cognitive flexibility in a pediatric OCD and a healthy comparison (HC) sample. Method In this functional magnetic resonance imaging (fMRI) study, a pediatric sample of 10- to 17-year-old subjects, 15 with OCD and 20 HC, completed a set-shifting task. The task, requiring an extradimensional shift to identify a target, examines cognitive flexibility. Within each block, the dimension (color or shape) that identified the target either alternated (i.e., mixed) or remained unchanged (i.e., repeated). Results Compared with the HC group, the OCD group tended to be slower to respond to trials within mixed blocks. Compared with the HC group, the OCD group exhibited less left inferior frontal gyrus/BA47 activation in the set-shifting contrast (i.e., HC > OCD, mixed versus repeated); only the HC group exhibited significant activation in this region. The correlation between set shifting-induced right caudate activation and shift cost (i.e., reaction time differential in response to mixed versus repeated trials) was significantly different between HC and OCD groups, in that we found a positive correlation in HC and a negative correlation in OCD. Conclusions In pediatric OCD, less fronto-striatal activation may explain previously identified deficits in shifting cognitive sets. PMID:20732630

Molecular dynamics in aluminum layered double hydroxides as studied by 1H T1ρ NMR measurements

NASA Astrophysics Data System (ADS)

Vyalikh, Anastasia; Wang, De-Yi; Wagenknecht, Udo; Heinrich, Gert; Scheler, Ulrich

2011-06-01

Proton dynamics in pristine and organically-modified layered double hydroxide has been studied by 1H T1ρ. Inverse Laplace transform with spectral resolution results in a correlation of T1ρ and chemical shift. In LDH two contributions are resolved. They are assigned to the metal hydroxides, forming the LDH sheets (4-8 ms), and mobile interlayer water (2 ms). Apparent T1ρ values of OH-protons in surfactant-modified LDH are different in dodecylbenzenesulfonate- (SDBS) and sodium octasulfonate- (C8) modified LDH. This difference is explained by the presence of water in LDH-SDBS. The effects of spin diffusion have been studied by performing 2D 1H RFDR in the LDH-SDBS.

High Level ab initio Predictions of the Energetics of mCO2•(H2O)n (n = 1-3, m = 1-12) Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thanthiriwatte, Sahan; Duke, Jessica R.; Jackson, Virgil E.

Electronic structure calculations at the correlated molecular orbital theory and density functional theory levels have been used to generate a reliable set of clustering energies for up to three water molecules in carbon dioxide clusters up to n = 12. The structures and energetics are dominated by Lewis acid-base interactions with hydrogen bonding interactions playing a lesser energetic role. The actual binding energies are somewhat larger than might be expected. The correlated molecular orbital MP2 method and density functional theory with the ωB97X exchange-correlation functional provide good results for the energetics of the clusters but the B3LYP and ωB97X-D functionalsmore » do not. Seven CO2 molecules form the first solvent shell about a single H2O with four CO2 molecules interacting with the H2O via Lewis acid-base interactions, two CO2 interacting with the H2O by hydrogen bonds, and the seventh CO2 completing the shell. The Lewis acid-base and weak hydrogen bond interactions between the water molecules and the CO2 molecules are strong enough to disrupt the trimer ring configuration for as few as seven CO2 molecules. Calculated 13C NMR chemical shifts for mCO2•(H2O)n show little change with respect to the number of H2O or CO2 molecules in the cluster. The O-H stretching frequencies do exhibit shifts that can provide information about the interactions between water and CO2 molecules.« less

Overnight fluid shifts in subjects with and without obstructive sleep apnea

PubMed Central

Ding, Ning; Lin, Wei; Zhang, Xi-Long; Ding, Wen-Xiao; Gu, Bing; Ni, Bu-Qing; Zhang, Wei; Zhang, Shi-Jiang

2014-01-01

Objective To investigate the characteristics of baseline body fluid content and overnight fluid shifts between non-obstructive sleep apnea (non-OSA) and obstructive sleep apnea (OSA) subjects. Methods A case-controlled study was performed between February 2013 and January 2014, with 36 (18 OSA and 18 non-OSA) outpatients enrolled in this study. Polysomnographic parameters and results of body fluid were compared between the two groups. Results There were no differences in age, weight, and body mass index (BMI) between groups. Compared with the non-OSA group, OSA group had significantly higher neck circumference (NC) and fluid volume shift in the legs. OSA patients had higher left and right leg fluid indices than non-OSA subjects. There were significant correlations between apnoea-hypopnoea index and baseline fluid indices in both legs as well as the reduction in overnight change in both legs fluid volume. The increase in NC was also significantly correlated with the reduction in overnight change in both legs fluid volume, but not with the change in head and neck fluid volume. There were significant correlations between change in NC and increased fluid shifts in head and neck volume. Conclusions OSA patients had a higher baseline fluid content in both legs as compared with non-OSA subjects, which may be the basic factor with regards to fluid shifts in OSA patients. The increase in head and neck fluid shift volume did not directly correlate with the severity of OSA. PMID:25589967

Potential for Higher Treatment Failure in Obese Patients: Correlation of Elevated Body Mass Index and Increased Daily Prostate Deviations From the Radiation Beam Isocenters in an Analysis of 1,465 Computed Tomographic Images

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wong, James R.; Gao Zhanrong; Merrick, Scott

2009-09-01

Purpose: Recent clinical outcome studies on prostate cancer have reported the influence of patient's obesity on the biochemical failure rates after various treatment modalities. In this study, we investigated the effect of patient's physical characteristics on prostate shift in external beam radiotherapy (EBRT) and hypothesized that there maybe a correlation between patient physique and tumor shift. Methods and Materials: A retrospective analysis was performed using data for 117 patients who received image-guided radiation therapy (IGRT) for prostate cancer between January 2005 and April 2007. A total of 1,465 CT scans were analyzed. The standard deviations (SDs) of prostate shifts formore » all patients, along with patient weight, body mass index (BMI), and subcutaneous adipose-tissue thickness (SAT), were determined. Spearman rank correlation analysis was performed. Results: Of the 117 patients, 26.5% were considered normal weight, 48.7% were overweight, 17.9% were mildly obese, and 6.9% were moderately to severely obese. Notably 1.3%, 1.5%, 2.0%, and 21.2% of the respective shifts were greater than 10 mm in the left-right (LR) direction for the four patient groups, whereas in the anterior-posterior direction the shifts are 18.2%, 12.6%, 6.7%, and 21.0%, respectively. Strong correlations were observed between SAT, BMI, patient weight, and SDs of daily shifts in the LR direction (p < 0.01). Conclusions: The strong correlation between obesity and shift indicates that without image-guided radiation therapy, the target volume (prostate with or without seminal vesicles) may not receive the intended dose for patients who are moderate to severely obese. This may explain the higher recurrence rate with conventional external beam radiation therapy.« less

Neural correlates of set-shifting in children with autism

PubMed Central

Yerys, Benjamin E.; Antezana, Ligia; Weinblatt, Rachel; Jankowski, Kathryn F.; Strang, John; Vaidya, Chandan J.; Schultz, Robert T.; Gaillard, William D.; Kenworthy, Lauren

2015-01-01

Autism spectrum disorder (ASD) is often associated with high levels of inflexible thinking and rigid behavior. The neural correlates of these behaviors have been investigated in adults and older adolescents, but not children. Prior studies utilized set-shifting tasks that engaged multiple levels of shifting, and depended on learning abstract rules and establishing a strong prepotent bias. These additional demands complicate simple interpretations of the results. We used functional magnetic resonance imaging (fMRI) to investigate the neural correlates of set-shifting in 20 children (ages 7-14) with ASD and 19 typically developing, matched, control children. Participants completed a set-shifting task that minimized non-shifting task demands through the use of concrete instructions that provide spatial mapping of stimuli-responses. The shift/stay sets were given an equal number of trials to limit the prepotent bias. Both groups showed an equivalent ‘switch cost’, responding less accurately and slower to Switch stimuli than Stay stimuli, although the ASD group was less accurate overall. Both groups showed activation in prefrontal, striatal, parietal, and cerebellum regions known to govern effective set-shifts. Compared to controls, children with ASD demonstrated decreased activation of the right middle temporal gyrus across all trials, but increased activation in the mid-dorsal cingulate cortex/superior frontal gyrus, left middle frontal and right inferior frontal gyri during the Switch vs. Stay contrast. The successful behavioral switching performance of children with ASD comes at the cost of requiring greater engagement of frontal regions, suggesting less efficiency at this lowest level of shifting. PMID:25599972

Mutual orientation of three magnetic tensors in a polycrystalline dipeptide by dipole-modulated 15N chemical shift spectroscopy

NASA Astrophysics Data System (ADS)

Hartzell, C. J.; Pratum, T. K.; Drobny, G.

1987-10-01

This study demonstrates the mutual orientation of three tensor interactions in a single NMR experiment. The orientation of the 15N chemical shift tensor relative to the molecular frame has thus been determined in polycrystalline L-[1-13C] alanyl-L-[15N] alanine. The 13C-15N and 15N-1H dipole interactions are determined using the 1H dipole-modulated, 13C dipole-coupled 15N spectrum obtained as a transform of the data in t2. From simulations of the experimental spectra, two sets of polar angles have been determined relating the 13C-15N and 15N-1H dipoles to the 15N chemical shift tensor. The values determined are βCN =106°, αCN =5° and βNH =-19°, αNH =12°. The experiment verifies, without reference to single crystal data, that σ33 lies in the peptide plane and σ22 is nearly perpendicular to the plane.

Arginine Interactions with Anatase TiO2 (100) Surface and the Perturbation of 49Ti NMR Chemical Shifts - A DFT Investigation: Relevance to Renu-Seeram Bio Solar Cell

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koch, Rainer; Lipton, Andrew S.; Filipek, S.

2011-06-01

Density functional theoretical calculations have been utilized to investigate the interaction of the amino acid arginine with the (100) surface of anatase and the reproduction of experimentally measured 49Ti NMR chemical shifts of anatase. Significant binding of arginine through electrostatic interaction and hydrogen bonds of the arginine guanidinium protons to the TiO2 surface oxygen atoms is observed, allowing attachment of proteins to titania surfaces in the construction of bio-sensitized solar cells. GIAO-B3LYP/6-31G(d) NMR calculation of a three-layer model based on the experimental structure of this TiO2 modification gives an excellent reproduction of the experimental value (-927 ppm) within +/- 7more » ppm, however, the change in relative chemical shifts, EFGs and CSA suggest that the effect of the electrostatic arginine binding might be too small for experimental detection.« less

Identifying stereoisomers by ab-initio calculation of secondary isotope shifts on NMR chemical shieldings.

PubMed

Böhm, Karl-Heinz; Banert, Klaus; Auer, Alexander A

2014-04-23

We present ab-initio calculations of secondary isotope effects on NMR chemical shieldings. The change of the NMR chemical shift of a certain nucleus that is observed if another nucleus is replaced by a different isotope can be calculated by computing vibrational corrections on the NMR parameters using electronic structure methods. We demonstrate that the accuracy of the computational results is sufficient to even distinguish different conformers. For this purpose, benchmark calculations for fluoro(2-2H)ethane in gauche and antiperiplanar conformation are carried out at the HF, MP2 and CCSD(T) level of theory using basis sets ranging from double- to quadruple-zeta quality. The methodology is applied to the secondary isotope shifts for 2-fluoronorbornane in order to resolve an ambiguity in the literature on the assignment of endo- and exo-2-fluoronorbornanes with deuterium substituents in endo-3 and exo-3 positions, also yielding insight into mechanistic details of the corresponding synthesis.

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

NASA Astrophysics Data System (ADS)

Durbeej, Bo; Eriksson, Leif A.

2003-06-01

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

Experience and limited lighting may affect sleepiness of tunnel workers

PubMed Central

2014-01-01

Background Working on shifts, especially on a night shift, influences the endogenous sleep regulation system leading to diminished sleep time and increased somnolence. We attempted to evaluate the impact of shifts on sleepiness and correlate the sleepiness score to the experience in a shift schedule. Materials and methods This cross-sectional study consists of 42 male and 2 female workers involved in a tunnel construction. They underwent spirometry, pulse oximetry and were asked to complete the Epworth Sleepiness Scale questionnaire. Results Statistical analysis revealed that workers of lower Epworth had a mean age of 43.6 years, compared to the mean age of 36.4 years of workers with higher Epworth. Furthermore, workers of lower Epworth were characterized by a mean number of shift years equal to 14.8, while those of higher Epworth possessed a mean number of shift years equal to 8. The shift schedule did not reveal any statistically significant correlation. Conclusions Workers employed for a longer time had diminished sleepiness. However, there is no relationship between night shifts and sleepiness, possibly because of exposure to artificial lighting in the construction site. PMID:24993796

Experience and limited lighting may affect sleepiness of tunnel workers.

PubMed

Lykouras, Dimosthenis; Karkoulias, Kiriakos; Patouchas, Dimitrios; Lakoumentas, John; Sampsonas, Fotis; Tranou, Magdalini-Konstantina; Faliagka, Evanthia; Tsakalidis, Athanasios; Spiropoulos, Kostas

2014-07-03

Working on shifts, especially on a night shift, influences the endogenous sleep regulation system leading to diminished sleep time and increased somnolence. We attempted to evaluate the impact of shifts on sleepiness and correlate the sleepiness score to the experience in a shift schedule. This cross-sectional study consists of 42 male and 2 female workers involved in a tunnel construction. They underwent spirometry, pulse oximetry and were asked to complete the Epworth Sleepiness Scale questionnaire. Statistical analysis revealed that workers of lower Epworth had a mean age of 43.6 years, compared to the mean age of 36.4 years of workers with higher Epworth. Furthermore, workers of lower Epworth were characterized by a mean number of shift years equal to 14.8, while those of higher Epworth possessed a mean number of shift years equal to 8. The shift schedule did not reveal any statistically significant correlation. Workers employed for a longer time had diminished sleepiness. However, there is no relationship between night shifts and sleepiness, possibly because of exposure to artificial lighting in the construction site.

125Te NMR shielding and optoelectronic spectra in XTe3O8 (X = Ti, Zr, Sn and Hf) compounds: Ab initio calculations

NASA Astrophysics Data System (ADS)

Bashi, M.; Rahnamaye Aliabad, H. A.; Mowlavi, A. A.; Ahmad, Iftikhar

2017-11-01

We have calculated the NMR shielding, structural properties and optoelectronic spectra of XTe3O8 (X = Ti, Zr, Sn and Hf) compounds. The full potential linearized augmented plane wave (FP-LAPW) method and the modified Becke-Johnson (mBJ) are used by density functional theory schemes. The calculated shielding and measured shifts are arranged in a straight line and the tensors of magnetic shielding have a low symmetry and the shielding along the x direction is greater than the y and z directions. Obtained results show that the X ions have the most important influence on the 125Te chemical shift. Calculated chemical shielding components (σii) decrease from Ti to Sn then increases from Sn to Hf so that these behaviors are vice versa for 125Te isotropic chemical shift (δiso). Density of states spectra show that the X-p and d states play key role in the optical and NMR calculations. Optical results illustrate that there is a direct relation between the chemical shielding components for Te atom and the static dielectric function, refractive index and Plasmon energies.

Genetically encoded pH-indicators reveal activity-dependent cytosolic acidification of Drosophila motor nerve termini in vivo

PubMed Central

Rossano, Adam J; Chouhan, Amit K; Macleod, Gregory T

2013-01-01

All biochemical processes, including those underlying synaptic function and plasticity, are pH sensitive. Cytosolic pH (pHcyto) shifts are known to accompany nerve activity in situ, but technological limitations have prevented characterization of such shifts in vivo. Genetically encoded pH-indicators (GEpHIs) allow for tissue-specific in vivo measurement of pH. We expressed three different GEpHIs in the cytosol of Drosophila larval motor neurons and observed substantial presynaptic acidification in nerve termini during nerve stimulation in situ. SuperEcliptic pHluorin was the most useful GEpHI for studying pHcyto shifts in this model system. We determined the resting pH of the nerve terminal cytosol to be 7.30 ± 0.02, and observed a decrease of 0.16 ± 0.01 pH units when the axon was stimulated at 40 Hz for 4 s. Realkalinization occurred upon cessation of stimulation with a time course of 20.54 ± 1.05 s (τ). The chemical pH-indicator 2′,7′-bis-(2-carboxyethyl)-5-(and-6)-carboxyfluorescein corroborated these changes in pHcyto. Bicarbonate-derived buffering did not contribute to buffering of acid loads from short (≤4 s) trains of action potentials but did buffer slow (∼60 s) acid loads. The magnitude of cytosolic acid transients correlated with cytosolic Ca2+ increase upon stimulation, and partial inhibition of the plasma membrane Ca2+-ATPase, a Ca2+/H+ exchanger, attenuated pHcyto shifts. Repeated stimulus trains mimicking motor patterns generated greater cytosolic acidification (∼0.30 pH units). Imaging through the cuticle of intact larvae revealed spontaneous pHcyto shifts in presynaptic termini in vivo, similar to those seen in situ during fictive locomotion, indicating that presynaptic pHcyto shifts cannot be dismissed as artifacts of ex vivo preparations. PMID:23401611

Characterization of human brown adipose tissue by chemical-shift water-fat MRI.

PubMed

Hu, Houchun H; Perkins, Thomas G; Chia, Jonathan M; Gilsanz, Vicente

2013-01-01

The purpose of this study was to characterize human brown adipose tissue (BAT) with chemical-shift water-fat MRI and to determine whether trends and differences in fat-signal fractions and T2(*) relaxation times between BAT and white adipose tissue (WAT) are consistently observed postmortem and in vivo in infants, adolescents, and adults. A postmortem body and eight patients were studied. A six-echo spoiled gradient-echo chemical-shift water-fat MRI sequence was performed at 3 T to jointly quantify fat-signal fraction and T2(*) in interscapular-supraclavicular BAT and subcutaneous WAT. To confirm BAT identity, biopsy and histology served as the reference in the postmortem study and PET/CT was used in five of the eight patients who required examination for medical care. Fat-signal fractions and T2(*) times were lower in BAT than in WAT in the postmortem example and in seven of eight patients. With the exception of one case, nominal comparisons between brown and white adipose tissues were statistically significant (p < 0.05). Between subjects, a large range of fat-signal fraction values was observed in BAT but not in WAT. We have shown that fat-signal fractions and T2(*) values jointly derived from chemical-shift water-fat MRI are lower in BAT than in WAT likely because of differences in cellular structures, triglyceride content, and vascularization. The two metrics can serve as complementary biomarkers in the detection of BAT.

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2014-03-01

Complexation of tetrakis(μ2-N,N'-diphenylformamidinato-N,N')-di-rhodium(II) with ligands containing nitrile, isonitrile, amine, hydroxyl, sulfhydryl, isocyanate, and isothiocyanate functional groups has been studied in liquid and solid phases using (1)H, (13)C and (15)N NMR, (13)C and (15)N cross polarisation-magic angle spinning NMR, and absorption spectroscopy in the visible range. The complexation was monitored using various NMR physicochemical parameters, such as chemical shifts, longitudinal relaxation times T1 , and NOE enhancements. Rhodium(II) tetraformamidinate selectively bonded only unbranched amine (propan-1-amine), pentanenitrile, and (1-isocyanoethyl)benzene. No complexation occurred in the case of ligands having hydroxyl, sulfhydryl, isocyanate, and isothiocyanate functional groups, and more expanded amine molecules such as butan-2-amine and 1-azabicyclo[2.2.2]octane. Such features were opposite to those observed in rhodium(II) tetracarboxylates, forming adducts with all kind of ligands. Special attention was focused on the analysis of Δδ parameters, defined as a chemical shift difference between signal in adduct and corresponding signal in free ligand. In the case of (1)H NMR, Δδ values were either negative in adducts of rhodium(II) tetraformamidinate or positive in adducts of rhodium(II) tetracarboxylates. Experimental findings were supported by density functional theory molecular modelling and gauge independent atomic orbitals chemical shift calculations. The calculation of chemical shifts combined with scaling procedure allowed to reproduce qualitatively Δδ parameters. Copyright © 2013 John Wiley & Sons, Ltd.

Development of a Simulink Library for the Design, Testing and Simulation of Software Defined GPS Radios. With Application to the Development of Parallel Correlator Structures

DTIC Science & Technology

2014-05-01

function Value = Select_Element(Index,Signal) %# eml Value = Signal(Index); Code Listing 1 Code for Selector Block 12 | P a g e 4.3...code for the Simulink function shiftedSignal = fcn(signal,Shift) %# eml shiftedSignal = circshift(signal,Shift); Code Listing 2 Code for CircShift

Biological monitoring of smoke exposure among wildland firefighters: A pilot study comparing urinary methoxyphenols with personal exposures to carbon monoxide, particulate matter, and levoglucosan.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neitzel, R.; Naeher, L., P.; Paulsen, M.

2009-04-01

Urinary methoxyphenols (MPs) have been proposed as biomarkers of woodsmoke exposure. However, few field studies have been undertaken to evaluate the relationship between woodsmoke exposure and urinary MP concentrations. We conducted a pilot study at the US Forest ServiceFSavannah River Site, in which carbon monoxide (CO), levoglucosan (LG), and particulate matter (PM2.5) exposures were measured in wildland firefighters on prescribedburn days. Pre- and post-shift urine samples were collected from each subject, and cross-shift changes in creatinine-corrected urinary MP concentrations were calculated. Correlations between exposure measures and creatine-adjusted urinary MP concentrations were explored, and regression models were developed relating changes inmore » urinary MP concentrations to measured exposure levels. Full-shift measurements were made on 13 firefighters over 20 work shifts in winter 2004 at the US Forest Service Savannah River site, a National Environmental Research Park. The average workshift length across the 20 measured shifts was 701±95 min. LG and CO exposures were significantly correlated for samples where the filter measurement captured at least 60% of the work shift (16 samples), as well as for the smaller set of full-shift exposure samples (n¼9). PM2.5 and CO exposures were not significantly correlated, and LG and PM2.5 exposures were only significantly correlated for samples representing at least 60% of the work shift. Creatinine-corrected urinary concentrations for 20 of the 22 MPs showed cross-shift increases, with 14 of these changes showing statistical significance. Individual and summed creatinine-adjusted guaiacol urinary MPs were highly associated with CO (and, to a lesser degree, LG) exposure levels, and random-effects regression models including CO and LG exposure levels explained up to 80% of the variance in cross-shift changes in summed creatinine-adjusted guaiacol urinary MP concentrations. Although limited by the small sample size, this pilot study demonstrates that urinary MP concentrations may be effective biomarkers of occupational exposure to wood smoke among wildland firefighters.« less

Biological monitoring of smoke exposure among wildland firefighters: Apilot study comparing urinary methoxyphenols with personal exposures to carbon monoxide, particulate matter, and levoglucosan.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neitzel, R.; Naeher, L., P.; Paulsen, M.

2009-04-01

Urinary methoxyphenols (MPs) have been proposed as biomarkers of woodsmoke exposure. However, few field studies have been undertaken to evaluate the relationship between woodsmoke exposure and urinary MP concentrations. We conducted a pilot study at the US Forest Service Savannah River Site, in which carbon monoxide (CO), levoglucosan (LG), and particulate matter (PM2.5) exposures were measured in wildland firefighters on prescribed burn days. Pre- and post-shift urine samples were collected from each subject, and cross-shift changes in creatinine-corrected urinary MP concentrations were calculated. Correlations between exposure measures and creatine-adjusted urinary MP concentrations were explored, and regression models were developed relatingmore » changes in urinary MP concentrations to measured exposure levels. Full-shift measurements were made on 13 firefighters over 20 work shifts in winter 2004 at the US Forest Service Savannah River site, a National Environmental Research Park. The average workshift length across the 20 measured shifts was 701±95 min. LG and CO exposures were significantly correlated for samples where the filter measurement captured at least 60% of the work shift (16 samples), as well as for the smaller set of full-shift exposure samples (n¼9). PM2.5 and CO exposures were not significantly correlated, and LG and PM2.5 exposures were only significantly correlated for samples representing at least 60% of the work shift. Creatinine-corrected urinary concentrations for 20 of the 22 MPs showed cross-shift increases, with 14 of these changes showing statistical significance. Individual and summed creatinine-adjusted guaiacol urinary MPs were highly associated with CO (and, to a lesser degree, LG) exposure levels, and random-effects regression models including CO and LG exposure levels explained up to 80% of the variance in cross-shift changes in summed creatinine-adjusted guaiacol urinary MP concentrations. Although limited by the small sample size, this pilot study demonstrates that urinary MP concentrations may be effective biomarkers of occupational exposure to wood smoke among wildland firefighters.« less

Biological monitoring of smoke exposure among wildland firefighters: A pilot study comparing urinary methoxyphenols with personal exposures to carbon monoxide, particulate matter, and levoglucosan.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neitzel, R.; Naeher, L., P.; Paulsen, M.

2009-04-01

Urinary methoxyphenols (MPs) have been proposed as biomarkers of woodsmoke exposure. However, few field studies have been undertaken to evaluate the relationship between woodsmoke exposure and urinary MP concentrations. We conducted a pilot study at the US Forest Service Savannah River Site, in which carbon monoxide (CO), levoglucosan (LG), and particulate matter (PM2.5) exposures were measured in wildland firefighters on prescribed burn days. Pre- and post-shift urine samples were collected from each subject, and cross-shift changes in creatinine-corrected urinary MP concentrations were calculated. Correlations between exposure measures and creatine-adjusted urinary MP concentrations were explored, and regression models were developed relatingmore » changes in urinary MP concentrations to measured exposure levels. Full-shift measurements were made on 13 firefighters over 20 work shifts in winter 2004 at the US Forest Service Savannah River site, a National Environmental Research Park. The average workshift length across the 20 measured shifts was 701±95 min. LG and CO exposures were significantly correlated for samples where the filter measurement captured at least 60% of the work shift (16 samples), as well as for the smaller set of full-shift exposure samples (n¼9). PM2.5 and CO exposures were not significantly correlated, and LG and PM2.5 exposures were only significantly correlated for samples representing at least 60% of the work shift. Creatinine-corrected urinary concentrations for 20 of the 22 MPs showed cross-shift increases, with 14 of these changes showing statistical significance. Individual and summed creatinine-adjusted guaiacol urinary MPs were highly associated with CO (and, to a lesser degree, LG) exposure levels, and random-effects regression models including CO and LG exposure levels explained up to 80% of the variance in cross-shift changes in summed creatinine-adjusted guaiacol urinary MP concentrations. Although limited by the small sample size, this pilot study demonstrates that urinary MP concentrations may be effective biomarkers of occupational exposure to wood smoke among wildland firefighters.« less

Biological monitoring of smoke exposure among wildland firefighters: Apilot study comparing urinary methoxyphenols with personal exposures to carbon monoxide, particulate matter, and levoglucosan.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neitzel, R.; Naeher, L., P.; Paulsen, M.

2009-04-01

Urinary methoxyphenols (MPs) have been proposed as biomarkers of woodsmoke exposure. However, few field studies have been undertaken to evaluate the relationship between woodsmoke exposure and urinary MP concentrations. We conducted a pilot study at the US Forest ServiceFSavannah River Site, in which carbon monoxide (CO), levoglucosan (LG), and particulate matter (PM2.5) exposures were measured in wildland firefighters on prescribed burn days. Pre- and post-shift urine samples were collected from each subject, and cross-shift changes in creatinine-corrected urinary MP concentrations were calculated. Correlations between exposure measures and creatine-adjusted urinary MP concentrations were explored, and regression models were developed relating changesmore » in urinary MP concentrations to measured exposure levels. Full-shift measurements were made on 13 firefighters over 20 work shifts in winter 2004 at the US Forest Service Savannah River site, a National Environmental Research Park. The average workshift length across the 20 measured shifts was 701±95 min. LG and CO exposures were significantly correlated for samples where the filter measurement captured at least 60% of the work shift (16 samples), as well as for the smaller set of full-shift exposure samples (n¼9). PM2.5 and CO exposures were not significantly correlated, and LG and PM2.5 exposures were only significantly correlated for samples representing at least 60% of the work shift. Creatinine-corrected urinary concentrations for 20 of the 22 MPs showed cross-shift increases, with 14 of these changes showing statistical significance. Individual and summed creatinine-adjusted guaiacol urinary MPs were highly associated with CO (and, to a lesser degree, LG) exposure levels, and random-effects regression models including CO and LG exposure levels explained up to 80% of the variance in cross-shift changes in summed creatinine-adjusted guaiacol urinary MP concentrations. Although limited by the small sample size, this pilot study demonstrates that urinary MP concentrations may be effective biomarkers of occupational exposure to wood smoke among wildland firefighters.« less

Biological monitoring of smoke exposure among wildland firefighters: Apilot study comparing urinary methoxyphenols with personal exposures to carbon monoxide, particulate matter, and levoglucosan.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neitzel, R.; Naeher, L., P.; Paulsen, M.

2008-04-01

Urinary methoxyphenols (MPs) have been proposed as biomarkers of woodsmoke exposure. However, few field studies have been undertaken to evaluate the relationship between woodsmoke exposure and urinary MP concentrations. We conducted a pilot study at the US Forest Service Savannah River Site, in which carbon monoxide (CO), levoglucosan (LG), and particulate matter (PM2.5) exposures were measured in wildland firefighters on prescribed burn days. Pre- and post-shift urine samples were collected from each subject, and cross-shift changes in creatinine-corrected urinary MP concentrations were calculated. Correlations between exposure measures and creatine-adjusted urinary MP concentrations were explored, and regression models were developed relatingmore » changes in urinary MP concentrations to measured exposure levels. Full-shift measurements were made on 13 firefighters over 20 work shifts in winter 2004 at the US Forest Service Savannah River site, a National Environmental Research Park. The average workshift length across the 20 measured shifts was 701±95 min. LG and CO exposures were significantly correlated for samples where the filter measurement captured at least 60% of the work shift (16 samples), as well as for the smaller set of full-shift exposure samples (n¼9). PM2.5 and CO exposures were not significantly correlated, and LG and PM2.5 exposures were only significantly correlated for samples representing at least 60% of the work shift. Creatinine-corrected urinary concentrations for 20 of the 22 MPs showed cross-shift increases, with 14 of these changes showing statistical significance. Individual and summed creatinine-adjusted guaiacol urinary MPs were highly associated with CO (and, to a lesser degree, LG) exposure levels, and random-effects regression models including CO and LG exposure levels explained up to 80% of the variance in cross-shift changes in summed creatinine-adjusted guaiacol urinary MP concentrations. Although limited by the small sample size, this pilot study demonstrates that urinary MP concentrations may be effective biomarkers of occupational exposure to wood smoke among wildland firefighters.« less

Coronary artery atherosclerosis associated with shift work in chemical plant workers by using coronary CT angiography.

PubMed

Kang, WonYang; Park, Won-Ju; Jang, Keun-Ho; Kim, Soo-Hyeon; Gwon, Do-Hyeong; Lim, Hyeong-Min; Ahn, Ji-Sung; Moon, Jai-Dong

2016-08-01

The aim of this study was to investigate whether shift work is related to elevated risk of coronary artery disease (CAD) by determining the coronary artery calcium (CAC) score and the presence of coronary artery stenosis by using coronary artery CT angiography (CCTA). In this study, 110 male workers participated and underwent a CCTA examination for CAC scoring, which represents coronary artery plaque, and were evaluated for luminal stenosis. All of the participants were working in the same chemical plant, of whom 70 worked day shifts and 40 worked rotating shifts. In a multivariate logistic regression analysis, including age, smoking status, alcohol consumption, regular exercise and waist circumference, shift work was associated with a 2.89-fold increase in the odds of developing coronary plaque compared with day work (OR, 2.89; 95% CI 1.07 to 7.82). The association between shift work and coronary plaque was strong after adjustment for age, low-density lipoprotein cholesterol, hypertension and diabetes mellitus (OR, 2.92; 95% CI 1.02 to 8.33). In addition, the number of years of shift work employment was associated with coronary plaque. However, no association was found between shift work and coronary artery stenosis. Shift work could induce CAD onset via the atherosclerotic process, and shift work employment duration was associated with an increased risk of atherosclerosis in male workers. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Benchmarking Hydrogen and Carbon NMR Chemical Shifts at HF, DFT, and MP2 Levels.

PubMed

Flaig, Denis; Maurer, Marina; Hanni, Matti; Braunger, Katharina; Kick, Leonhard; Thubauville, Matthias; Ochsenfeld, Christian

2014-02-11

An extensive study of error distributions for calculating hydrogen and carbon NMR chemical shifts at Hartree-Fock (HF), density functional theory (DFT), and Møller-Plesset second-order perturbation theory (MP2) levels is presented. Our investigation employs accurate CCSD(T)/cc-pVQZ calculations for providing reference data for 48 hydrogen and 40 carbon nuclei within an extended set of chemical compounds covering a broad range of the NMR scale with high relevance to chemical applications, especially in organic chemistry. Besides the approximations of HF, a variety of DFT functionals, and conventional MP2, we also present results with respect to a spin component-scaled MP2 (GIAO-SCS-MP2) approach. For each method, the accuracy is analyzed in detail for various basis sets, allowing identification of efficient combinations of method and basis set approximations.

Enhancing Thai Students' Learning of Chemical Kinetics

ERIC Educational Resources Information Center

Chairam, Sanoe; Somsook, Ekasith; Coll, Richard K.

2009-01-01

Chemical kinetics is an extremely important concept for introductory chemistry courses. The literature suggests that instruction in chemical kinetics is often teacher-dominated at both the secondary school and tertiary levels, and this is the case in Thailand--the educational context for this inquiry. The work reported here seeks to shift students…

Hydrodynamic fluctuations, nonequilibrium equations of state, and the shift of the spinodal line in polymer solutions under flow

DOE Office of Scientific and Technical Information (OSTI.GOV)

Criado-Sancho, M.; Casas-Vazquez, J.; Jou, D.

1997-08-01

In the literature, the shift of the spinodal line of polymer solutions under flow is attributed either to an actual shift of the spinodal due to a nonequilibrium modification of the equation of state for the chemical potential, or to an apparent shift due to an increase of hydrodynamic fluctuations owing to the flow. Here we see that both approaches are compatible and that both effects add up. {copyright} {ital 1997} {ital The American Physical Society}

Wavelet filtered shifted phase-encoded joint transform correlation for face recognition

NASA Astrophysics Data System (ADS)

Moniruzzaman, Md.; Alam, Mohammad S.

2017-05-01

A new wavelet-filtered-based Shifted- phase-encoded Joint Transform Correlation (WPJTC) technique has been proposed for efficient face recognition. The proposed technique uses discrete wavelet decomposition for preprocessing and can effectively accommodate various 3D facial distortions, effects of noise, and illumination variations. After analyzing different forms of wavelet basis functions, an optimal method has been proposed by considering the discrimination capability and processing speed as performance trade-offs. The proposed technique yields better correlation discrimination compared to alternate pattern recognition techniques such as phase-shifted phase-encoded fringe-adjusted joint transform correlator. The performance of the proposed WPJTC has been tested using the Yale facial database and extended Yale facial database under different environments such as illumination variation, noise, and 3D changes in facial expressions. Test results show that the proposed WPJTC yields better performance compared to alternate JTC based face recognition techniques.

A meta-analysis including dose-response relationship between night shift work and the risk of colorectal cancer

PubMed Central

Wang, Xiao; Ji, Alin; Zhu, Yi; Liang, Zhen; Wu, Jian; Li, Shiqi; Meng, Shuai; Zheng, Xiangyi; Xie, Liping

2015-01-01

A meta-analysis was conducted to quantitatively evaluate the correlation between night shift work and the risk of colorectal cancer. We searched for publications up to March 2015 using PubMed, Web of Science, Cochrane Library, EMBASE and the Chinese National Knowledge Infrastructure databases, and the references of the retrieved articles and relevant reviews were also checked. OR and 95% CI were used to assess the degree of the correlation between night shift work and risk of colorectal cancer via fixed- or random-effect models. A dose-response meta-analysis was performed as well. The pooled OR estimates of the included studies illustrated that night shift work was correlated with an increased risk of colorectal cancer (OR = 1.318, 95% CI 1.121–1.551). No evidence of publication bias was detected. In the dose-response analysis, the rate of colorectal cancer increased by 11% for every 5 years increased in night shift work (OR = 1.11, 95% CI 1.03–1.20). In conclusion, this meta-analysis indicated that night shift work was associated with an increased risk of colorectal cancer. Further researches should be conducted to confirm our findings and clarify the potential biological mechanisms. PMID:26208480

Estimation bias from using nonlinear Fourier plane correlators for sub-pixel image shift measurement and implications for the binary joint transform correlator

NASA Astrophysics Data System (ADS)

Grycewicz, Thomas J.; Florio, Christopher J.; Franz, Geoffrey A.; Robinson, Ross E.

2007-09-01

When using Fourier plane digital algorithms or an optical correlator to measure the correlation between digital images, interpolation by center-of-mass or quadratic estimation techniques can be used to estimate image displacement to the sub-pixel level. However, this can lead to a bias in the correlation measurement. This bias shifts the sub-pixel output measurement to be closer to the nearest pixel center than the actual location. The paper investigates the bias in the outputs of both digital and optical correlators, and proposes methods to minimize this effect. We use digital studies and optical implementations of the joint transform correlator to demonstrate optical registration with accuracies better than 0.1 pixels. We use both simulations of image shift and movies of a moving target as inputs. We demonstrate bias error for both center-of-mass and quadratic interpolation, and discuss the reasons that this bias is present. Finally, we suggest measures to reduce or eliminate the bias effects. We show that when sub-pixel bias is present, it can be eliminated by modifying the interpolation method. By removing the bias error, we improve registration accuracy by thirty percent.

Contribution of the frontal eye field to gaze shifts in the head-unrestrained rhesus monkey: neuronal activity.

PubMed

Knight, T A

2012-12-06

The frontal eye field (FEF) has a strong influence on saccadic eye movements with the head restrained. With the head unrestrained, eye saccades combine with head movements to produce large gaze shifts, and microstimulation of the FEF evokes both eye and head movements. To test whether the dorsomedial FEF provides commands for the entire gaze shift or its separate eye and head components, we recorded extracellular single-unit activity in monkeys trained to make large head-unrestrained gaze shifts. We recorded 80 units active during gaze shifts, and closely examined 26 of these that discharged a burst of action potentials that preceded horizontal gaze movements. These units were movement or visuomovement related and most exhibited open movement fields with respect to amplitude. To reveal the relations of burst parameters to gaze, eye, and/or head movement metrics, we used behavioral dissociations of gaze, eye, and head movements and linear regression analyses. The burst number of spikes (NOS) was strongly correlated with movement amplitude and burst temporal parameters were strongly correlated with movement temporal metrics for eight gaze-related burst neurons and five saccade-related burst neurons. For the remaining 13 neurons, the NOS was strongly correlated with the head movement amplitude, but burst temporal parameters were most strongly correlated with eye movement temporal metrics (head-eye-related burst neurons, HEBNs). These results suggest that FEF units do not encode a command for the unified gaze shift only; instead, different units may carry signals related to the overall gaze shift or its eye and/or head components. Moreover, the HEBNs exhibit bursts whose magnitude and timing may encode a head displacement signal and a signal that influences the timing of the eye saccade, thereby serving as a mechanism for coordinating the eye and head movements of a gaze shift. Copyright © 2012 IBRO. Published by Elsevier Ltd. All rights reserved.

Optical-Correlator Neural Network Based On Neocognitron

NASA Technical Reports Server (NTRS)

Chao, Tien-Hsin; Stoner, William W.

1994-01-01

Multichannel optical correlator implements shift-invariant, high-discrimination pattern-recognizing neural network based on paradigm of neocognitron. Selected as basic building block of this neural network because invariance under shifts is inherent advantage of Fourier optics included in optical correlators in general. Neocognitron is conceptual electronic neural-network model for recognition of visual patterns. Multilayer processing achieved by iteratively feeding back output of feature correlator to input spatial light modulator and updating Fourier filters. Neural network trained by use of characteristic features extracted from target images. Multichannel implementation enables parallel processing of large number of selected features.

Integrative Network-based Analysis of Magnetic Resonance Spectroscopy and Genome Wide Expression in Glioblastoma multiforme

PubMed Central

Heiland, Dieter Henrik; Mader, Irina; Schlosser, Pascal; Pfeifer, Dietmar; Carro, Maria Stella; Lange, Thomas; Schwarzwald, Ralf; Vasilikos, Ioannis; Urbach, Horst; Weyerbrock, Astrid

2016-01-01

The goal of this study was to identify correlations between metabolites from proton MR spectroscopy and genetic pathway activity in glioblastoma multiforme (GBM). Twenty patients with primary GBM were analysed by short echo-time chemical shift imaging and genome-wide expression analyses. Weighed Gene Co-Expression Analysis was used for an integrative analysis of imaging and genetic data. N-acetylaspartate, normalised to the contralateral healthy side (nNAA), was significantly correlated to oligodendrocytic and neural development. For normalised creatine (nCr), a group with low nCr was linked to the mesenchymal subtype, while high nCr could be assigned to the proneural subtype. Moreover, clustering of normalised glutamine and glutamate (nGlx) revealed two groups, one with high nGlx being attributed to the neural subtype, and one with low nGlx associated with the classical subtype. Hence, the metabolites nNAA, nCr, and nGlx correlate with a specific gene expression pattern reflecting the previously described subtypes of GBM. Moreover high nNAA was associated with better clinical prognosis, whereas patients with lower nNAA revealed a shorter progression-free survival (PFS). PMID:27350391

Simultaneous acquisition of 2D and 3D solid-state NMR experiments for sequential assignment of oriented membrane protein samples.

PubMed

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

2015-05-01

We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins reconstituted in mechanically or magnetically aligned lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living (15)N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through (15)N-(15)N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish (15)N-(15)N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI-HETCOR and 3D PISEMAI-HETCOR-mixing experiments.

Backbone and sidechain methyl Ile (δ1), Leu and Val chemical shift assignments of RDE-4 (1-243), an RNA interference initiation protein in C. elegans.

PubMed

Chiliveri, Sai Chaitanya; Kumar, Sonu; Marelli, Udaya Kiran; Deshmukh, Mandar V

2012-10-01

The RNAi pathway of several organisms requires presence of double stranded RNA binding proteins for functioning of Dicer in gene regulation. In C. elegans, a double stranded RNA binding protein, RDE-4 (385 aa, 44 kDa) recognizes long exogenous dsRNA and initiates the RNAi pathway. We have achieved complete backbone and stereospecific methyl sidechain Ile (δ1), Leu and Val chemical shifts of first 243 amino acids of RDE-4, namely RDE-4ΔC.

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

NASA Technical Reports Server (NTRS)

Grodzka, P.; Facemire, B.

1977-01-01

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

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

NASA Astrophysics Data System (ADS)

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

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, S.B.; Cohen, M.L.; Louie, S.G.

1991-04-15

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

Cortico-pontine theta carrier frequency phase shift across sleep/wake states following monoaminergic lesion in rat.

PubMed

Kalauzi, Aleksandar; Spasic, Sladjana; Petrovic, Jelena; Ciric, Jelena; Saponjic, Jelena

2012-06-01

This study was aimed to explore the sleep/wake states related cortico-pontine theta carrier frequency phase shift following a systemically induced chemical axotomy of the monoaminergic afferents within a brain of the freely moving rats. Our experiments were performed in 14 adult, male Sprague Dawley rats, chronically implanted for sleep recording. We recorded sleep during baseline condition, following sham injection (saline i.p. 1 ml/kg), and every week for 5 weeks following injection of the systemic neurotoxins (DSP-4 or PCA; 1 ml/kg, i.p.) for chemical axotomy of the locus coeruleus (LC) and dorsal raphe (DR) axon terminals. After sleep/wake states identification, FFT analysis was performed on 5 s epochs. Theta carrier frequency phase shift (∆Φ) was calculated for each epoch by averaging theta Fourier component phase shifts, and the ∆Φ values were plotted for each rat in control condition and 28 days following the monoaminergic lesions, as a time for permanently established DR or LC chemical axotomy. Calculated group averages have shown that ∆Φ increased between pons and cortex significantly in all sleep/wake states (Wake, NREM and REM) following the monoaminergic lesions, with respect to controls. Monoaminergic lesions established the pontine leading role in the brain theta oscillations during all sleep/wake states.

Circadian type, chronic fatigue, and serum IgM in the shift workers of an industrial organization

PubMed Central

Khaleghipour, Shahnaz; Masjedi, Mohsen; Kelishadi, Roya

2015-01-01

Background: Night shift workers are more vulnerable to immune-related diseases. Immunoglobulin M (IgM) is a potent activator of complement, and complement has a crucial role in defense against bacterial infections. Circadian type is known as an effective agent on vulnerability and adaptation with shift work due to non-compliance with shift stress. The objective of this study was to investigate the correlation of circadian type and chronic fatigue with the serum concentration of IgM in a group of shift workers. Materials and Methods: This cross-sectional study was performed in an industrial organization in Isfahan, Iran. The study population consisted of 221 male employees working at night shifts who were selected by random cluster sampling. The following questionnaires were used: composite morningness (Torsvall and Akerstedt), circadian type (Folkard), and chronic fatigue (Barton and colleagues). The serum concentration of IgM was measured by the nephelometric method. The data were analyzed with the Pearson coefficient correlation and the path analysis for finding the pattern of the structural equations to evaluate the direct and indirect relationships between variables, using the SPSS 15 and LISREL 8.5 statistical software. Results: Significant correlation was documented between morningness, flexibility, languidness, and chronic fatigue with the serum concentration of IgM (P < 0.01). Conclusion: The results showed that the shift workers with morningness and languidness experienced more problems during the working hours due to more tiredness, and had decreased serum concentration of IgM. Correct management of shift work may attenuate fatigue in workers and also improve many health issues experienced by the shift workers. PMID:25802830

Relationships between the center of pressure and the movements of the ankle and knee joints during the stance phase in patients with severe medial knee osteoarthritis.

PubMed

Fukaya, Takashi; Mutsuzaki, Hirotaka; Okubo, Tomoyuki; Mori, Koichi; Wadano, Yasuyoshi

2016-08-01

The knee joint movement during the stance phase is affected by altered ankle movement and the center of pressure (COP). However the relationships between changes in the center of pressure (COP) and the altered kinematics and kinetics of the ankle and knee joints in patients with osteoarthritis (OA) of the knee are not well understood. The purpose of this study was to determine the relationships between changes in the COP and the altered kinematic and kinetic variables in ankle and knee joints during the stance phase in patients with medial knee OA. Fourteen patients with knee OA (21 knees) and healthy subjects were assessed by gait analysis using an eight-camera motion analysis system to record forward and lateral shifts in the COP and the angle and net internal moments of the knee and ankle joint. Spearman rank-correlation coefficients were used to determine the relationship between these results. In knees with medial OA, lateral shifts in the COP were correlated with knee flexion angle. Lateral shifts in the COP were correlated with the second peak of the knee extensor moment and correlated with the knee abductor moment. In patients with medial knee OA, lateral shifts in the COP were negatively correlated with the kinematic and kinetic variables in the sagittal plane of the knee joints. Controlling such lateral shifts in the COP may thus be an effective intervention for mechanical loads on the knee during the stance phase in patients with knee OA. Copyright © 2016 Elsevier B.V. All rights reserved.

A multi-standard approach for GIAO (13)C NMR calculations.

PubMed

Sarotti, Ariel M; Pellegrinet, Silvina C

2009-10-02

The influence of the reference standard employed in the calculation of (13)C NMR chemical shifts was investigated over a large variety of known organic compounds, using different quantum chemistry methods and basis sets. After detailed analysis of the collected data, we found that methanol and benzene are excellent reference standards for computing NMR shifts of sp(3)- and sp-sp(2)-hybridized carbon atoms, respectively. This multi-standard approach (MSTD) performs better than TMS in terms of accuracy and precision and also displays much lower dependence on the level of theory employed. The use of mPW1PW91/6-31G(d)//mPW1PW91/6-31G(d) level is recommended for accurate (13)C NMR chemical shift prediction at low computational cost.

Neural Correlates of Set-Shifting in Children With Autism.

PubMed

Yerys, Benjamin E; Antezana, Ligia; Weinblatt, Rachel; Jankowski, Kathryn F; Strang, John; Vaidya, Chandan J; Schultz, Robert T; Gaillard, William D; Kenworthy, Lauren

2015-08-01

Autism spectrum disorder (ASD) is often associated with high levels of inflexible thinking and rigid behavior. The neural correlates of these behaviors have been investigated in adults and older adolescents, but not children. Prior studies utilized set-shifting tasks that engaged multiple levels of shifting, and depended on learning abstract rules and establishing a strong prepotent bias. These additional demands complicate simple interpretations of the results. We used functional magnetic resonance imaging (fMRI) to investigate the neural correlates of set-shifting in 20 children (ages 7-14) with ASD and 19 typically developing, matched, control children. Participants completed a set-shifting task that minimized nonshifting task demands through the use of concrete instructions that provide spatial mapping of stimuli-responses. The shift/stay sets were given an equal number of trials to limit the prepotent bias. Both groups showed an equivalent "switch cost," responding less accurately and slower to Switch stimuli than Stay stimuli, although the ASD group was less accurate overall. Both groups showed activation in prefrontal, striatal, parietal, and cerebellum regions known to govern effective set-shifts. Compared to controls, children with ASD demonstrated decreased activation of the right middle temporal gyrus across all trials, but increased activation in the mid-dorsal cingulate cortex/superior frontal gyrus, left middle frontal, and right inferior frontal gyri during the Switch vs. Stay contrast. The successful behavioral switching performance of children with ASD comes at the cost of requiring greater engagement of frontal regions, suggesting less efficiency at this lowest level of shifting. © 2015 International Society for Autism Research, Wiley Periodicals, Inc.

Hybrid Theory of P-Wave Electron-Hydrogen Elastic Scattering

NASA Technical Reports Server (NTRS)

Bhatia, Anand

2012-01-01

We report on a study of electron-hydrogen scattering, using a combination of a modified method of polarized orbitals and the optical potential formalism. The calculation is restricted to P waves in the elastic region, where the correlation functions are of Hylleraas type. It is found that the phase shifts are not significantly affected by the modification of the target function by a method similar to the method of polarized orbitals and they are close to the phase shifts calculated earlier by Bhatia. This indicates that the correlation function is general enough to include the target distortion (polarization) in the presence of the incident electron. The important fact is that in the present calculation, to obtain similar results only 35-term correlation function is needed in the wave function compared to the 220-term wave function required in the above-mentioned previous calculation. Results for the phase shifts, obtained in the present hybrid formalism, are rigorous lower bounds to the exact phase shifts.

Approximating the Shifted Hartree-Exchange-Correlation Potential in Direct Energy Kohn-Sham Theory.

PubMed

Sharpe, Daniel J; Levy, Mel; Tozer, David J

2018-02-13

Levy and Zahariev [Phys. Rev. Lett. 113 113002 (2014)] have proposed a new approach for performing density functional theory calculations, termed direct energy Kohn-Sham (DEKS) theory. In this approach, the electronic energy equals the sum of orbital energies, obtained from Kohn-Sham-like orbital equations involving a shifted Hartree-exchange-correlation potential, which must be approximated. In the present study, density scaling homogeneity considerations are used to facilitate DEKS calculations on a series of atoms and molecules, leading to three nonlocal approximations to the shifted potential. The first two rely on preliminary Kohn-Sham calculations using a standard generalized gradient approximation (GGA) exchange-correlation functional and the results illustrate the benefit of describing the dominant Hartree component of the shift exactly. A uniform electron gas analysis is used to eliminate the need for these preliminary Kohn-Sham calculations, leading to a potential with an unconventional form that yields encouraging results, providing strong motivation for further research in DEKS theory.

Distribution of mean Doppler shift, spectral width, and skewness of coherent 50-MHz auroral radar backscatter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Watermann, J.; McNamara, A.G.; Sofko, G.J.

Some 7,700 radio aurora spectra obtained from a six link 50-MHz CW radar network set up on the Canadian prairies were analyzed with respect to the distributions of mean Doppler shift, spectral width and skewness. A comparison with recently published SABRE results obtained at 153 MHz shows substantial differences in the distributions which are probably due to different experimental and geophysical conditions. The spectra are mostly broad with mean Doppler shifts close to zero (type II spectra). The typical groupings of type I and type III spectra are clearly identified. All types appear to be in general much more symmetricmore » than those recorded with SABRE, and the skewness is only weakly dependent on the sign of the mean Doppler shift. Its distribution peaks near zero and shows a weak positive correlation with the type II Doppler shifts while the mostly positive type I Doppler shifts are slightly negatively correlated with the skewness.« less

Potentiation of Chemical Ototoxicity by Noise

PubMed Central

Steyger, Peter S.

2010-01-01

High-intensity and/or prolonged exposure to noise causes temporary or permanent threshold shifts in auditory perception. Occupational exposure to solvents or administration of clinically important drugs, such as aminoglycoside antibiotics and cisplatin, also can induce permanent hearing loss. The mechanisms by which these ototoxic insults cause auditory dysfunction are still being unraveled, yet they share common sequelae, particularly generation of reactive oxygen species, that ultimately lead to hearing loss and deafness. Individuals are frequently exposed to ototoxic chemical contaminants (e.g., fuel) and noise simultaneously in a variety of work and recreational environments. Does simultaneous exposure to chemical ototoxins and noise potentiate auditory dysfunction? Exposure to solvent vapor in noisy environments potentiates the permanent threshold shifts induced by noise alone. Moderate noise levels potentiate both aminoglycoside- and cisplatin-induced ototoxicity in both rate of onset and in severity of auditory dysfunction. Thus, simultaneous exposure to chemical ototoxins and moderate levels of noise can potentiate auditory dysfunction. Preventing the ototoxic synergy of noise and chemical ototoxins requires removing exposure to ototoxins and/or attenuating noise exposure levels when chemical ototoxins are present. PMID:20523755

Characterization of Cleaning and Disinfecting Tasks and Product Use Among Hospital Occupations

PubMed Central

Saito, Rena; Virji, M. Abbas; Henneberger, Paul K.; Humann, Michael J.; LeBouf, Ryan F.; Stanton, Marcia L.; Liang, Xiaoming; Stefaniak, Aleksandr B.

2016-01-01

Background Healthcare workers have an elevated prevalence of asthma and related symptoms associated with the use of cleaning/disinfecting products. The objective of this study was to identify and characterize cleaning/disinfecting tasks and products used among hospital occupations. Methods Workers from 14 occupations at five hospitals were monitored for 216 shifts, and work tasks and products used were recorded at five-minute intervals. The major chemical constituents of each product were identified from safety data sheets. Results Cleaning and disinfecting tasks were performed with a high frequency at least once per shift in many occupations. Medical equipment preparers, housekeepers, floor strippers/waxers, and endoscopy technicians spent on average 108–177 min/shift performing cleaning/disinfecting tasks. Many occupations used products containing amines and quaternary ammonium compounds for > 100 min/shift. Conclusions This analysis demonstrates that many occupations besides housekeeping incur exposures to cleaning/disinfecting products, albeit for different durations and using products containing different chemicals. PMID:25351791

30 CFR 47.54 - Availability of an MSDS.

Code of Federal Regulations, 2010 CFR

2010-07-01

... make MSDSs accessible to miners during each work shift for each hazardous chemical to which they may be exposed either— (a) At each work area where the hazardous chemical is produced or used, or (b) At an...

Interspecies chemical communication in bacterial development.

PubMed

Straight, Paul D; Kolter, Roberto

2009-01-01

Our view of bacteria, from the earliest observations through the heyday of antibiotic discovery, has shifted dramatically. We recognize communities of bacteria as integral and functionally important components of diverse habitats, ranging from soil collectives to the human microbiome. To function as productive communities, bacteria coordinate metabolic functions, often requiring shifts in growth and development. The hallmark of cellular development, which we characterize as physiological change in response to environmental stimuli, is a defining feature of many bacterial interspecies interactions. Bacterial communities rely on chemical exchanges to provide the cues for developmental change. Traditional methods in microbiology focus on isolation and characterization of bacteria in monoculture, separating the organisms from the surroundings in which interspecies chemical communication has relevance. Developing multispecies experimental systems that incorporate knowledge of bacterial physiology and metabolism with insights from biodiversity and metagenomics shows great promise for understanding interspecies chemical communication in the microbial world.

A Novel Multiple-Access Correlation-Delay-Shift-Keying

NASA Astrophysics Data System (ADS)

Duan, J. Y.; Jiang, G. P.; Yang, H.

In Correlation-Delay-Shift-Keying (CDSK), the reference signal and the information-bearing signal are added together during a certain time delay. Because the reference signal is not strictly orthogonal to the information-bearing signal, the cross-correlation between the adjacent chaotic signal (Intra-signal Interference, ISI) will be introduced into the demodulation at the receiver. Therefore, the Bit-Error Ratio (BER) of CDSK is higher than that of Differential-Chaos-Shift-Keying (DCSK). To avoid the ISI component and enhance the BER performance of CDSK in multiuser scenario, Multiple-Access CDSK with No Intra-signal Interference (MA-CDSK-NII) is proposed. By constructing the repeated chaotic generator and applying the Walsh code sequence to modulate the reference signal, in MA-CDSK-NII, the ISI component will be eliminated during the demodulation. Gaussian approximation method is adopted here to obtain the exact performance analysis of MA-CDSK-NII over additive white Gaussian noise (AWGN) channel and Rayleigh multipath fading channels. Results show that, due to no ISI component and lower transmitting power, the BER performance of MA-CDSK-NII can be better than that of multiple-access CDSK and Code-Shifted Differential-Chaos-Shift-Keying (CS-DCSK).

The effects of state anxiety and thermal comfort on sleep quality and eye fatigue in shift work nurses.

PubMed

Dehghan, Habibollah; Azmoon, Hiva; Souri, Shiva; Akbari, Jafar

2014-01-01

Psychological problems as state anxiety (SA) in the work environment has negative effect on the employees life especially shift work nurses, i.e. negative effect on mental and physical health (sleep quality, eye fatigue and comfort thermal). The purpose of this study was determination of effects of state anxiety and thermal comfort on sleep quality and eye fatigue in shift work nurses. This cross-sectional research conducted on 82 shift-work personnel of 18 nursing workstations of Isfahan hospitals in 2012. To measure the SA, sleep quality, visual fatigue and thermal comfort, Spielberger state-trait anxiety inventory, Pittsburg sleep quality index, eye fatigue questionnaire and thermal comfort questionnaire were used respectively. The data were analyzed with descriptive statistics, student test and correlation analysis. Correlation between SA and sleep quality was -0.664(P < 0001), Pearson correlation between SA and thermal comfort was -0.276(P = 0.016) and between SA and eye fatigue was 0.57 (P < 0001). Based on these results, it can be concluded that improvement of thermal conditions and reduce state anxiety level can be reduce eye fatigue and increase the sleep quality in shift work nurses.

The effects of state anxiety and thermal comfort on sleep quality and eye fatigue in shift work nurses

PubMed Central

Dehghan, Habibollah; Azmoon, Hiva; Souri, Shiva; Akbari, Jafar

2014-01-01

Psychological problems as state anxiety (SA) in the work environment has negative effect on the employees life especially shift work nurses, i.e. negative effect on mental and physical health (sleep quality, eye fatigue and comfort thermal). The purpose of this study was determination of effects of state anxiety and thermal comfort on sleep quality and eye fatigue in shift work nurses. Methods: This cross-sectional research conducted on 82 shift-work personnel of 18 nursing workstations of Isfahan hospitals in 2012. To measure the SA, sleep quality, visual fatigue and thermal comfort, Spielberger state-trait anxiety inventory, Pittsburg sleep quality index, eye fatigue questionnaire and thermal comfort questionnaire were used respectively. The data were analyzed with descriptive statistics, student test and correlation analysis. Results: Correlation between SA and sleep quality was −0.664(P < 0001), Pearson correlation between SA and thermal comfort was −0.276(P = 0.016) and between SA and eye fatigue was 0.57 (P < 0001). Conclusion: Based on these results, it can be concluded that improvement of thermal conditions and reduce state anxiety level can be reduce eye fatigue and increase the sleep quality in shift work nurses. PMID:25077165

[Shiftwork and health--experience from a chemical company].

PubMed

Oberlinner, C; Lang, S; Nasterlack, M; Yong, M

2013-03-01

Shiftwork is an essential part of our society. At the same time scientific evaluations demonstrate possible negative effects of shiftwork on the health status of the employees. Against this background we performed different studies to evaluate these effects within the specific shift system in a large chemical site in Germany. METHODS AND STUDY GROUP: To evaluate the impact of the different working times on job-related stress perception and work-life-balance we performed a cross-sectional study with 1494 blue collar workers (825 shift- and 669 day workers). Employees working in the rotating shift system reported lower frequencies of perceived time pressure (p = 0.008), and lower stress levels (p = 0.01), compared to the day workers. No significant difference was found with regard to work-life-balance and other aspects of job-related stress perception within both groups. Against the general opinion and study-results in the past we did not find a negative effect of our shift-system on self-reported stress. These results are in accordance with results of other cohort-studies on the specific shift system within the company demonstrating no difference in the health status of our shift workers compared to day workers. © Georg Thieme Verlag KG Stuttgart · New York.

Accurate and fiducial-marker-free correction for three-dimensional chromatic shift in biological fluorescence microscopy.

PubMed

Matsuda, Atsushi; Schermelleh, Lothar; Hirano, Yasuhiro; Haraguchi, Tokuko; Hiraoka, Yasushi

2018-05-15

Correction of chromatic shift is necessary for precise registration of multicolor fluorescence images of biological specimens. New emerging technologies in fluorescence microscopy with increasing spatial resolution and penetration depth have prompted the need for more accurate methods to correct chromatic aberration. However, the amount of chromatic shift of the region of interest in biological samples often deviates from the theoretical prediction because of unknown dispersion in the biological samples. To measure and correct chromatic shift in biological samples, we developed a quadrisection phase correlation approach to computationally calculate translation, rotation, and magnification from reference images. Furthermore, to account for local chromatic shifts, images are split into smaller elements, for which the phase correlation between channels is measured individually and corrected accordingly. We implemented this method in an easy-to-use open-source software package, called Chromagnon, that is able to correct shifts with a 3D accuracy of approximately 15 nm. Applying this software, we quantified the level of uncertainty in chromatic shift correction, depending on the imaging modality used, and for different existing calibration methods, along with the proposed one. Finally, we provide guidelines to choose the optimal chromatic shift registration method for any given situation.

Structure elucidation of the designer drug N-(1-amino-3,3-dimethyl-1-oxobutan-2-yl)-1-(5-fluoropentyl)-3-(4-fluorophenyl)-pyrazole-5-carboxamide and the relevance of predicted (13) C NMR shifts - a case study.

PubMed

Girreser, Ulrich; Rösner, Peter; Vasilev, Andrej

2016-07-01

The detailed structure elucidation process of the new cannabimimetic designer drug, N-(1-amino-3,3-dimethyl-1-oxobutan-2-yl)-1-(5-fluoropentyl)-3-(4-fluorophenyl)-pyrazole-5-carboxamide, with a highly substituted pyrazole skeleton, using nuclear magnetic resonance (NMR) spectroscopic and mass spectrometric (MS) techniques is described. After a first analysis of the NMR spectra and comparison with 48 possible pyrazole and imidazole structures, a subset of six positional isomeric pyrazoles and six imidazoles remained conceivable. Four substituents of the heterocyclic skeleton were identified: a proton bound to a pyrazole ring carbon atom; a 5-fluoropentyl group; a 4-fluorophenyl substituent; and a carbamoyl group, which is N-substituted with a methyl residue carrying a tert.-butyl and a carbamoyl substituent. The 5-fluoropentyl residue is situated at the nitrogen ring atom. Additional NMR experiments like the (1) H,(13) C HMBC were performed, but due to the small number of signals based on long-range couplings, the comparison of predicted and observed (13) C chemical shifts became necessary. The open access Internet shift prediction programs NMRDB, NMRSHIFTDB2, and CSEARCH were employed for the prediction of (13) C shift values which allowed an efficient and unambiguous structure determination. For the identified N-(1-amino-3,3-dimethyl-1-oxobutan-2-yl)-1-(5-fluoropentyl)-3-(4-fluorophenyl)-pyrazole-5-carboxamide, the best agreement between predicted (13) C shifts and the observed chemical shifts and long-range couplings for the pyrazole ring carbon atoms, with a standard error of about 2 ppm, was found with each of the predictions. For the comparison of measured and predicted chemical shifts model compounds with simple substituents proved helpful. The identified compound is a homologue of AZ-037 which is offered by Internet suppliers. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Relating the Chemical Composition of Dissolved Organic Matter Draining Permafrost Soils to its Photochemical Degradation in Arctic Surface Waters.

NASA Astrophysics Data System (ADS)

Ward, C.; Cory, R. M.

2015-12-01

Thawing permafrost soils are expected to shift the chemical composition of DOM exported to and degraded in arctic surface waters. While DOM photo-degradation is an important component of the freshwater C cycle in the Arctic, the molecular controls on DOM photo-degradation remain poorly understood, making it difficult to predict how shifting chemical composition may alter DOM photo-degradation in arctic surface waters. To address this knowledge gap, we quantified the susceptibility of DOM draining the shallow organic mat and the deeper permafrost layer to complete photo-oxidation to CO₂ and partial photo-oxidation to compounds that remain in the DOM pool, and investigated changes in DOM chemical composition following sunlight exposure. DOM leached from the organic mat contained higher molecular weight, more oxidized and unsaturated aromatic species compared to permafrost DOM. Despite significant differences in initial chemical composition, permafrost and organic mat DOM had similar susceptibilities to complete photo-oxidation to CO₂. Concurrent losses of carboxyl moieties and shifts in chemical composition during photo-degradation indicated that carboxyl-rich tannin-like compounds in both DOM sources were likely photo-decarboxylated to CO₂. Permafrost DOM had a higher susceptibility to partial photo-oxidation compared to organic mat DOM, potentially due to a lower abundance of phenolic compounds that act as "antioxidants" and slow the oxidation of DOM. These results demonstrated how chemical composition controls the photo-degradation of DOM in arctic surface waters, and that DOM photo-degradation will likely remain an important component of the freshwater C budget in the Arctic with increased export of permafrost DOM to surface waters.

Alternate binding modes for a ubiquitin-SH3 domain interaction studied by NMR spectroscopy.

PubMed

Korzhnev, Dmitry M; Bezsonova, Irina; Lee, Soyoung; Chalikian, Tigran V; Kay, Lewis E

2009-02-20

Surfaces of many binding domains are plastic, enabling them to interact with multiple targets. An understanding of how they bind and recognize their partners is therefore predicated on characterizing such dynamic interfaces. Yet, these interfaces are difficult to study by standard biophysical techniques that often 'freeze' out conformations or that produce data averaged over an ensemble of conformers. In this study, we used NMR spectroscopy to study the interaction between the C-terminal SH3 domain of CIN85 and ubiquitin that involves the 'classical' binding sites of these proteins. Notably, chemical shift titration data of one target with another and relaxation dispersion data that report on millisecond time scale exchange processes are both well fit to a simple binding model in which free protein is in equilibrium with a single bound conformation. However, dissociation constants and chemical shift differences between free and bound states measured from both classes of experiment are in disagreement. It is shown that the data can be reconciled by considering three-state binding models involving two distinct bound conformations. By combining titration and dispersion data, kinetic and thermodynamic parameters of the three-state binding reaction are obtained along with chemical shifts for each state. A picture emerges in which one bound conformer has increased entropy and enthalpy relative to the second and chemical shifts similar to that of the free state, suggesting a less packed interface. This study provides an example of the interplay between entropy and enthalpy to fine-tune molecular interactions involving the same binding surfaces.

"Ask Ernö": a self-learning tool for assignment and prediction of nuclear magnetic resonance spectra.

PubMed

Castillo, Andrés M; Bernal, Andrés; Dieden, Reiner; Patiny, Luc; Wist, Julien

2016-01-01

We present "Ask Ernö", a self-learning system for the automatic analysis of NMR spectra, consisting of integrated chemical shift assignment and prediction tools. The output of the automatic assignment component initializes and improves a database of assigned protons that is used by the chemical shift predictor. In turn, the predictions provided by the latter facilitate improvement of the assignment process. Iteration on these steps allows Ask Ernö to improve its ability to assign and predict spectra without any prior knowledge or assistance from human experts. This concept was tested by training such a system with a dataset of 2341 molecules and their (1)H-NMR spectra, and evaluating the accuracy of chemical shift predictions on a test set of 298 partially assigned molecules (2007 assigned protons). After 10 iterations, Ask Ernö was able to decrease its prediction error by 17 %, reaching an average error of 0.265 ppm. Over 60 % of the test chemical shifts were predicted within 0.2 ppm, while only 5 % still presented a prediction error of more than 1 ppm. Ask Ernö introduces an innovative approach to automatic NMR analysis that constantly learns and improves when provided with new data. Furthermore, it completely avoids the need for manually assigned spectra. This system has the potential to be turned into a fully autonomous tool able to compete with the best alternatives currently available.Graphical abstractSelf-learning loop. Any progress in the prediction (forward problem) will improve the assignment ability (reverse problem) and vice versa.

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

PubMed

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

2015-07-01

The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

13C chemical-shift anisotropy of alkyl-substituted aromatic carbon in anthracene derivatives.

PubMed

Hoop, Cody L; Iuliucci, Robbie J

2013-06-01

The (13)C chemical-shift anisotropy in anthracene derivatives (9,10-dimethylanthracene, 9,10-dihydroanthracene, dianthracene, and triptycene) has been measured by the 2D FIREMAT timed pulse sequence and the corresponding set of principal values has been determined by the TIGER processing method. These molecules expand the data base of (13)C CSA measurements of fused aromatic rings some bridged by sp(3) carbon resulting in an unusual bonding configuration, which leads to distinctive aromatic (13)C CSA values. Crystal lattice distortions to the CSA were observed to change the isotropic shift by 2.5 to 3.3 ppm and changes as large as 8.3 ppm in principal components. Modeling of the CSA data by GIPAW DFT (GGA-PBE/ultrafine) shielding calculations resulted in an rms chemical-shift distance of 2.8 ppm after lattice including geometry optimization of the diffraction structures by the GIPAW method at GGA-PBE/ultrafine level. Attention is given to the substituted aromatic carbon in the phenyl groups (here forth referred to as the α-carbon) with respect to CSA modeling with electronic methods. The (13)C CSA of this position is accurately determined due to its spectral isolation of the isotropic shift that limits overlap in the FIREMAT spectrum. In cases where the bridging ring is sp(3) carbon, the current density is reduced from extending beyond the peripheral phenyl groups; this plays a significant role in the magnetic shielding of the α-position. Nuclear independent chemical-shift calculations based on GIAO DFT (B3LYP/6-31G(d)) shielding calculations were used to model the intramolecular π-interactions in dianthracene and triptycene. These NICS results estimate the isotropic shift of the α-position in dianthracene to be insignificantly affected by the presence of the neighboring aromatic rings. However, a notable change in isotropic shielding, Δσ(iso)=-2.1 ppm, is predicted for the α- position of triptycene. Experimentally, the δ22 principal component at the α-position for both dianthracene and triptycene increases by at least 12 ppm compared to 9,10-dihydroanthracene. To rationalize this change, shielding calculations in idealized structures are explored. The spatial position of the bicyclic scaffolding of the bridging ring plays a key role in the large increase in δ22 for the α-carbon. Copyright © 2013 Elsevier Inc. All rights reserved.

An image analysis of TLC patterns for quality control of saffron based on soil salinity effect: A strategy for data (pre)-processing.

PubMed

Sereshti, Hassan; Poursorkh, Zahra; Aliakbarzadeh, Ghazaleh; Zarre, Shahin; Ataolahi, Sahar

2018-01-15

Quality of saffron, a valuable food additive, could considerably affect the consumers' health. In this work, a novel preprocessing strategy for image analysis of saffron thin layer chromatographic (TLC) patterns was introduced. This includes performing a series of image pre-processing techniques on TLC images such as compression, inversion, elimination of general baseline (using asymmetric least squares (AsLS)), removing spots shift and concavity (by correlation optimization warping (COW)), and finally conversion to RGB chromatograms. Subsequently, an unsupervised multivariate data analysis including principal component analysis (PCA) and k-means clustering was utilized to investigate the soil salinity effect, as a cultivation parameter, on saffron TLC patterns. This method was used as a rapid and simple technique to obtain the chemical fingerprints of saffron TLC images. Finally, the separated TLC spots were chemically identified using high-performance liquid chromatography-diode array detection (HPLC-DAD). Accordingly, the saffron quality from different areas of Iran was evaluated and classified. Copyright © 2017 Elsevier Ltd. All rights reserved.

Magneto-optical contrast in liquid-state optically detected NMR spectroscopy

PubMed Central

Pagliero, Daniela; Meriles, Carlos A.

2011-01-01

We use optical Faraday rotation (OFR) to probe nuclear spins in real time at high-magnetic field in a range of diamagnetic sample fluids. Comparison of OFR-detected NMR spectra reveals a correlation between the relative signal amplitude and the fluid Verdet constant, which we interpret as a manifestation of the variable detuning between the probe beam and the sample optical transitions. The analysis of chemical-shift-resolved, optically detected spectra allows us to set constraints on the relative amplitudes of hyperfine coupling constants, both for protons at chemically distinct sites and other lower-gyromagnetic-ratio nuclei including carbon, fluorine, and phosphorous. By considering a model binary mixture we observe a complex dependence of the optical response on the relative concentration, suggesting that the present approach is sensitive to the solvent-solute dynamics in ways complementary to those known in inductive NMR. Extension of these experiments may find application in solvent suppression protocols, sensitivity-enhanced NMR of metalloproteins in solution, the investigation of solvent-solute interactions, or the characterization of molecular orbitals in diamagnetic systems. PMID:22100736

NMReDATA, a standard to report the NMR assignment and parameters of organic compounds.

PubMed

Pupier, Marion; Nuzillard, Jean-Marc; Wist, Julien; Schlörer, Nils E; Kuhn, Stefan; Erdelyi, Mate; Steinbeck, Christoph; Williams, Antony J; Butts, Craig; Claridge, Tim D W; Mikhova, Bozhana; Robien, Wolfgang; Dashti, Hesam; Eghbalnia, Hamid R; Farès, Christophe; Adam, Christian; Kessler, Pavel; Moriaud, Fabrice; Elyashberg, Mikhail; Argyropoulos, Dimitris; Pérez, Manuel; Giraudeau, Patrick; Gil, Roberto R; Trevorrow, Paul; Jeannerat, Damien

2018-04-14

Even though NMR has found countless applications in the field of small molecule characterization, there is no standard file format available for the NMR data relevant to structure characterization of small molecules. A new format is therefore introduced to associate the NMR parameters extracted from 1D and 2D spectra of organic compounds to the proposed chemical structure. These NMR parameters, which we shall call NMReDATA (for nuclear magnetic resonance extracted data), include chemical shift values, signal integrals, intensities, multiplicities, scalar coupling constants, lists of 2D correlations, relaxation times, and diffusion rates. The file format is an extension of the existing Structure Data Format, which is compatible with the commonly used MOL format. The association of an NMReDATA file with the raw and spectral data from which it originates constitutes an NMR record. This format is easily readable by humans and computers and provides a simple and efficient way for disseminating results of structural chemistry investigations, allowing automatic verification of published results, and for assisting the constitution of highly needed open-source structural databases. Copyright © 2018 John Wiley & Sons, Ltd.