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Sample records for 2d chemical shift

  1. Chemical Shifts to Metabolic Pathways: Identifying Metabolic Pathways Directly from a Single 2D NMR Spectrum.

    PubMed

    Dubey, Abhinav; Rangarajan, Annapoorni; Pal, Debnath; Atreya, Hanudatta S

    2015-12-15

    Identifying cellular processes in terms of metabolic pathways is one of the avowed goals of metabolomics studies. Currently, this is done after relevant metabolites are identified to allow their mapping onto specific pathways. This task is daunting due to the complex nature of cellular processes and the difficulty in establishing the identity of individual metabolites. We propose here a new method: ChemSMP (Chemical Shifts to Metabolic Pathways), which facilitates rapid analysis by identifying the active metabolic pathways directly from chemical shifts obtained from a single two-dimensional (2D) [(13)C-(1)H] correlation NMR spectrum without the need for identification and assignment of individual metabolites. ChemSMP uses a novel indexing and scoring system comprised of a "uniqueness score" and a "coverage score". Our method is demonstrated on metabolic pathways data from the Small Molecule Pathway Database (SMPDB) and chemical shifts from the Human Metabolome Database (HMDB). Benchmarks show that ChemSMP has a positive prediction rate of >90% in the presence of decluttered data and can sustain the same at 60-70% even in the presence of noise, such as deletions of peaks and chemical shift deviations. The method tested on NMR data acquired for a mixture of 20 amino acids shows a success rate of 93% in correct recovery of pathways. When used on data obtained from the cell lysate of an unexplored oncogenic cell line, it revealed active metabolic pathways responsible for regulating energy homeostasis of cancer cells. Our unique tool is thus expected to significantly enhance analysis of NMR-based metabolomics data by reducing existing impediments.

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

    PubMed

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

    2013-05-01

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

  3. 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.

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

    SciTech Connect

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy

    2015-05-28

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

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

    PubMed

    Ramírez-Gualito, Karla; Jeannerat, Damien

    2015-11-01

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

  6. Chemical Approaches to 2D Materials.

    PubMed

    Samorì, Paolo; Palermo, Vincenzo; Feng, Xinliang

    2016-08-01

    Chemistry plays an ever-increasing role in the production, functionalization, processing and applications of graphene and other 2D materials. This special issue highlights a selection of enlightening chemical approaches to 2D materials, which nicely reflect the breadth of the field and convey the excitement of the individuals involved in it, who are trying to translate graphene and related materials from the laboratory into a real, high-impact technology.

  7. Understanding NMR Chemical Shifts

    NASA Astrophysics Data System (ADS)

    Jameson, Cynthia J.

    1996-10-01

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

  8. Knight shifts around vacancies in the 2D Heisenberg model.

    PubMed

    Anfuso, Fabrizio; Eggert, Sebastian

    2006-01-13

    The local response to a uniform field around vacancies in the two-dimensional spin-1/2 Heisenberg antiferromagnet is determined by numerical quantum Monte Carlo simulations as a function of temperature. It is possible to separate the Knight shifts into uniform and staggered contributions on the lattice which are analyzed and understood in detail. The contributions show interesting long- and short-range behavior that may be of relevance in NMR and susceptibility measurements. For more than one impurity, remarkable nonlinear enhancement and cancellation effects take place. We predict that the Curie impurity susceptibility will be observable for a random impurity concentration even in the thermodynamic limit.

  9. Chemical vapour deposition: Transition metal carbides go 2D

    DOE PAGES

    Gogotsi, Yury

    2015-08-17

    Here, the research community has been steadily expanding the family of few-atom-thick crystals beyond graphene, discovering new materials or producing known materials in a 2D state and demonstrating their unique properties1, 2. Recently, nanometre-thin 2D transition metal carbides have also joined this family3. Writing in Nature Materials, Chuan Xu and colleagues now report a significant advance in the field, showing the synthesis of large-area, high-quality, nanometre-thin crystals of molybdenum carbide that demonstrate low-temperature 2D superconductivity4. Moreover, they also show that other ultrathin carbide crystals, such as tungsten and tantalum carbides, can be grown by chemical vapour deposition with a highmore » crystallinity and very low defect concentration.« less

  10. Chemical vapour deposition: Transition metal carbides go 2D

    SciTech Connect

    Gogotsi, Yury

    2015-08-17

    Here, the research community has been steadily expanding the family of few-atom-thick crystals beyond graphene, discovering new materials or producing known materials in a 2D state and demonstrating their unique properties1, 2. Recently, nanometre-thin 2D transition metal carbides have also joined this family3. Writing in Nature Materials, Chuan Xu and colleagues now report a significant advance in the field, showing the synthesis of large-area, high-quality, nanometre-thin crystals of molybdenum carbide that demonstrate low-temperature 2D superconductivity4. Moreover, they also show that other ultrathin carbide crystals, such as tungsten and tantalum carbides, can be grown by chemical vapour deposition with a high crystallinity and very low defect concentration.

  11. Single-shot and phase-shifting digital holographic microscopy using a 2-D grating.

    PubMed

    Yang, Taeseok Daniel; Kim, Hyung-Jin; Lee, Kyoung J; Kim, Beop-Min; Choi, Youngwoon

    2016-05-02

    We demonstrate digital holographic microscopy that, while being based on phase-shifting interferometry, is capable of single-shot measurements. A two-dimensional (2-D) diffraction grating placed in a Fourier plane of a standard in-line holographic phase microscope generates multiple copies of a sample image on a camera sensor. The identical image copies are spatially separated with different overall phase shifts according to the diffraction orders. The overall phase shifts are adjusted by controlling the lateral position of the grating. These phase shifts are then set to be multiples of π/2. Interferograms composed of four image copies combined with a parallel reference beam are acquired in a single shot. The interferograms are processed through a phase-shifting algorithm to produce a single complex image. By taking advantage of the higher sampling capacity of the in-line holography, we can increase the imaging information density by a factor of 3 without compromising the imaging acquisition speed.

  12. Chemical Shift Anisotropy Selective Inversion*

    PubMed Central

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

    2009-01-01

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

  13. 2D-3D MIGRATION AND CONFORMATIONAL MULTIPLICATION OF CHEMICALS IN LARGE CHEMICAL INVENTORIES

    EPA Science Inventory

    Chemical interactions are three-dimensional (3D) in nature and require modeling chemicals as 3D entities. In turn, using 3D models of chemicals leads to the realization that a single 2D structure can have hundreds of different conformations, and the electronic properties of these...

  14. 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…

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

    PubMed

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

    2009-05-01

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

  16. Construction and repair of highly ordered 2D covalent networks by chemical equilibrium regulation.

    PubMed

    Guan, Cui-Zhong; Wang, Dong; Wan, Li-Jun

    2012-03-21

    The construction of well-ordered 2D covalent networks via the dehydration of di-borate aromatic molecules was successfully realized through introducing a small amount of water into a closed reaction system to regulate the chemical equilibrium.

  17. Chemical shift prediction for denatured proteins.

    PubMed

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

    2013-02-01

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

  18. Protein structure determination from NMR chemical shifts.

    PubMed

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

    2007-06-05

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

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

    PubMed

    Kono, Hiroyuki; Hashimoto, Hisaho; Shimizu, Yuuichi

    2015-03-15

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

  20. Assessing the shift of radiobiological metrics in lung radiotherapy plans using 2D gamma index

    PubMed Central

    Balosso, Jacques

    2016-01-01

    Background The purpose of this work is to investigate the 2D gamma (γ) maps to illustrate the change of radiobiological outcomes for lung radiotherapy plans and evaluate the correlation between tumor control probability (TCP), normal tissue complication probability (NTCP) with γ passing rates (γ-rates). Methods Nine patients with lung cancer were used. The doses were calculated using Modified Batho method integrated with pencil beam convolution (MB-PBC) and anisotropic analytical algorithm (AAA) using the same beam arrangements and prescription dose. The TCP and NTCP were estimated, respectively, using equivalent uniform dose (EUD) model and Lyman-Kutcher-Burman (LKB) model. The correlation between ΔTCP or ΔNTCP with γ-rates, from 2%/2 and 3%/3 mm, were tested to explore the best correlation predicting the relevant γ criteria using Spearman’s rank test (ρ). Wilcoxon paired test was used to calculate P value. Results TCP value was significantly lower in the recalculated AAA plans as compared to MB plans. However, AAA predicted more NTCP on lung pneumonitis according to the LKB model and using relevant radiobiological parameters (n, m and TD50) for MB-PBC and AAA, with P=0.03. The data showed a weak correlation between radiobiological metrics with γ-rates or γ-mean, ρ<0.3. Conclusions AAA and MB yield different TCP values as well as NTCP for lung pneumonitis based on the LKB model parameters. Therefore, 2D γ-maps, generated with 2%/2 or 3%/3 mm, could illustrate visual information about the radiobiological changes. The information is useful to evaluate the clinical outcome of a radiotherapy treatment and to approve the treatment plan of the patient if the dose constraints are respected. On the other hand, the γ-maps tool can be used as quality assurance (QA) process to check the predicted TCP and NTCP from radiobiological models. PMID:27413708

  1. Band Gap Engineering in a 2D Material for Solar-to-Chemical Energy Conversion.

    PubMed

    Hu, Jun; Guo, Zhenkun; Mcwilliams, Peter E; Darges, John E; Druffel, Daniel L; Moran, Andrew M; Warren, Scott C

    2016-01-13

    The electronic structure of 2D semiconductors depends on their thickness, providing new opportunities to engineer semiconductors for energy conversion, electronics, and catalysis. Here we show how a 3D semiconductor, black phosphorus, becomes active for solar-to-chemical energy conversion when it is thinned to a 2D material. The increase in its band gap, from 0.3 eV (3D) to 2.1 eV (2D monolayer), is accompanied by a 40-fold enhancement in the formation of chemical products. Despite this enhancement, smaller flakes also have shorter excited state lifetimes. We deduce a mechanism in which recombination occurs at flake edges, while the "van der Waals" surface of black phosphorus bonds to chemical intermediates and facilitates electron transfer. The unique properties of black phosphorus highlight its potential as a customizable material for solar energy conversion and catalysis, while also allowing us to identify design rules for 2D photocatalysts that will enable further improvements in these materials.

  2. The red-shift of surface plasmon absorption of 2D nanogold arrangement from disordered to ordered.

    PubMed

    Tang, Junke; Li, Jinru; Rong, Huiling; Zou, Bingsuo; Jiang, Long

    2008-01-01

    In this article, the changing of surface plasmon resonance (SPR) absorption of 2D arrangement of Au (3 nm) nanoparticles coated with 1-dodecanethiol (C12H25SH), obtained at different desolvation extents, had been investigated. It has been found that an obvious red-shifted happened when these arrays changed from loose, disordered to close-packed and ordered. Both transmission electron microscopy pictures and variation of SPR absorption of these arrays showed that the formation of long range two-dimension (2D) arrangement of nanoparticles coated with C12H25SH might be involved in two stages: At the first stage the particles can move freely and random patterns from loose to close package was driven by the Brownian Movement of solvated particles and as a result the voids were eliminated. The red shift of SPR absorption with the coverage (d lamda/d theta) is relative low. At the second stage, where the particles cannot move freely because of lack of solvent and a long-range two-dimension crystal was formed, the SPR shift to a longer wavelength with a larger d lamda/d theta. It is mainly attributed to the strong increase of the orientation and dipolar moment of the absorbed C12H25SH molecule on nanoparticles.

  3. Lipophilic chemical exposure as a cause of type 2 diabetes (T2D).

    PubMed

    Zeliger, Harold I

    2013-01-01

    The prevalence of type 2 diabetes (T2D) is increasing worldwide in pandemic-like numbers. It is considered, at least in part, to be an environmental illness. Recent research has shown that diabetes can be caused by exposure to persistent organic pollutants (POPs), exudates from common plastics, air pollution, primary and secondary tobacco smoke, and some pharmaceuticals. These chemicals vary widely in structure, chemical properties, and composition and are not currently believed to induce a similar effect. A unifying explanation for the induction of T2D by this diversified group of chemicals is proposed here. These toxicants have one thing in common. All are lipophilic species that permeate lipophilic body membranes, thereby promoting the absorption of toxic hydrophilic species that would otherwise not penetrate lipophilic membranes. It is further proposed that exposure to the lipophilic and hydrophilic species need not occur simultaneously but can occur sequentially, with the lipophile absorbed first and retained in body serum, followed by a subsequent exposure to the hydrophile. The lipophilic chemical can be one of the POPs (including dioxins, furans, polychlorinated biphenyls, polybrominated biphenyls, polybrominated diphenyl ethers, or organochlorine pesticides); a more rapidly metabolized or eliminated species including plastic exudates like phthalate esters and bisphenol A; air pollutants and tobacco smoke components including aliphatic, aromatic, or polynuclear aromatic hydrocarbons; or pharmaceuticals like some statins and second-generation antipsychotic drugs. This hypothesis suggests that the T2D pandemic as well as the rapid increase of other environmental disease prevalence is, at least in part, due to sequential exposure to levels of lipophilic and hydrophilic environmental pollutants that are much lower than those currently believed to be toxic. As a consequence of this hypothesis, the allowable levels of exposure to these pollutants should be

  4. Mapping of protein structural ensembles by chemical shifts.

    PubMed

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

    2010-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Alderman, D. W.

    1998-12-01

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

  6. 29Si NMR Chemical Shift Calculation for Silicate Species by Gaussian Software

    NASA Astrophysics Data System (ADS)

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

    2005-05-01

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

  7. D2d(23)-C84 versus Sc2C2@D2d(23)-C84: Impact of Endohedral Sc2C2 Doping on Chemical Reactivity in the Photolysis of Diazirine.

    PubMed

    Yamada, Michio; Tanabe, Yukiko; Dang, Jing-Shuang; Sato, Satoru; Mizorogi, Naomi; Hachiya, Makoto; Suzuki, Mitsuaki; Abe, Tsuneyuki; Kurihara, Hiroki; Maeda, Yutaka; Zhao, Xiang; Lian, Yongfu; Nagase, Shigeru; Akasaka, Takeshi

    2016-12-21

    We compared the chemical reactivity of D2d(23)-C84 and that of Sc2C2@D2d(23)-C84, both having the same carbon cage geometry, in the photolysis of 2-adamantane-2,3'-[3H]-diazirine, to clarify metal-atom doping effects on the chemical reactivity of the carbon cage. Experimental and computational studies have revealed that the chemical reactivity of the D2d(23)-C84 carbon cage is altered drastically by endohedral Sc2C2 doping. The reaction of empty D2d(23)-C84 with the diazirine under photoirradiation yields two adamantylidene (Ad) adducts. NMR spectroscopic studies revealed that the major Ad monoadduct (C84(Ad)-A) has a fulleroid structure and that the minor Ad monoadduct (C84(Ad)-B) has a methanofullerene structure. The latter was also characterized using X-ray crystallography. C84(Ad)-A is stable under photoirradiation, but it interconverted to C84(Ad)-B by heating at 80 °C. In contrast, the reaction of endohedral Sc2C2@D2d(23)-C84 with diazirine under photoirradiation affords four Ad monoadducts (Sc2C2@C84(Ad)-A, Sc2C2@C84(Ad)-B, Sc2C2@C84(Ad)-C, and Sc2C2@C84(Ad)-D). The structure of Sc2C2@C84(Ad)-C was characterized using X-ray crystallography. Thermal interconversion of Sc2C2@C84(Ad)-A and Sc2C2@C84(Ad)-B to Sc2C2@C84(Ad)-C was also observed. The reaction mechanisms of the Ad addition and thermal interconversion were elucidated from theoretical calculations. Calculation results suggest that C84(Ad)-B and Sc2C2@C84(Ad)-C are thermodynamically favorable products. Their different chemical reactivities derive from Sc2C2 doping, which raises the HOMO and LUMO levels of the D2d(23)-C84 carbon cage.

  8. Using chemical shift perturbation to characterise ligand binding.

    PubMed

    Williamson, Mike P

    2013-08-01

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

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

    ERIC Educational Resources Information Center

    Friedrich, Edwin C.; Runkle, Katherine Gates

    1984-01-01

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

  10. Relative Configuration of Natural Products Using NMR Chemical Shifts

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  11. A 2-D Self-Consistent DSMC Model for Chemically Reacting Low Pressure Plasma Reactors

    SciTech Connect

    Bartel, Timothy J.; Economou, Demetre; Johannes, Justine E.

    1999-06-17

    This paper will focus on the methodology of using a 2D plasma Direct Simulation Monte Carlo technique to simulate the species transport in an inductively coupled, low pressure, chemically reacting plasma system. The pressure in these systems is typically less than 20 mtorr with plasma densities of approximately 10{sup 17} {number_sign}/m{sup 3} and an ionization level of only 0.1%. This low ionization level tightly couples the neutral, ion, and electron chemistries and interactions in a system where the flow is subsonic. We present our strategy and compare simulation results to experimental data for Cl{sub 2} in a Gaseous Electronics Conference (GEC) reference cell modified with an inductive coil.

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

    PubMed

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

    2012-02-01

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

  13. CHEM2D: a two-dimensional, three-phase, nine-component chemical flood simulator. Volume I. CHEM2D technical description and FORTRAN code

    SciTech Connect

    Fanchi, J.R.

    1985-04-01

    Under the sponsorship of the US Department of Energy, a publicly available chemical simulator has been evaluated and substantially enhanced to serve as a useful tool for projecting polymer or chemical flood performance. The program, CHEM2D, is a two-dimensional, three-phase, nine-component finite-difference numerical simulator. It can model primary depletion, waterfloods, polymer floods, and micellar/polymer floods using heterogeneous linear, areal, or cross-sectional reservoir descriptions. The user may specify well performance as either pressure or rate constrained. Both a constant time step size and a variable time step size based on extrapolation of concentration changes are available as options. A solution technique which is implicit in pressure and explicit in saturations and concentrations is used. The major physical mechanisms that are modeled include adsorption, capillary trapping, cation exchange, dilution, dispersion, interfacial tension, binary or ternary phase behavior, non-Newtonian polymer rheology, and two-phase or three-phase relative permeability. Typical components include water, oil, surfactant, polymer, and three ions (chloride, calcium, and sodium). Components may partition amongst the aqueous, oleic, and microemulsion phases. Volume I of this report provides a discussion of the formulation and algorithms used within CHEM2D. Included in Volume I are a number of validation and illustrative examples, as well as the FORTRAN code. The CHEM2D user's manual, Volume II, contains both the input data sets for the examples presented in Volume I and an example output. All appendices and a phase behavior calculation program are collected in Volume III. 20 references.

  14. 2D-Visualization of metabolic activity with planar optical chemical sensors (optodes)

    NASA Astrophysics Data System (ADS)

    Meier, R. J.; Liebsch, G.

    2015-12-01

    Microbia plays an outstandingly important role in many hydrologic compartments, such as e.g. the benthic community in sediments, or biologically active microorganisms in the capillary fringe, in ground water, or soil. Oxygen, pH, and CO2 are key factors and indicators for microbial activity. They can be measured using optical chemical sensors. These sensors record changing fluorescence properties of specific indicator dyes. The signals can be measured in a non-contact mode, even through transparent walls, which is important for many lab-experiments. They can measure in closed (transparent) systems, without sampling or intruding into the sample. They do not consume the analytes while measuring, are fully reversible and able to measure in non-stirred solutions. These sensors can be applied as high precision fiberoptic sensors (for profiling), robust sensor spots, or as planar sensors for 2D visualization (imaging). Imaging enables to detect thousands of measurement spots at the same time and generate 2D analyte maps over a region of interest. It allows for comparing different regions within one recorded image, visualizing spatial analyte gradients, or more important to identify hot spots of metabolic activity. We present ready-to-use portable imaging systems for the analytes oxygen, pH, and CO2. They consist of a detector unit, planar sensor foils and a software for easy data recording and evaluation. Sensors foils for various analytes and measurement ranges enable visualizing metabolic activity or analyte changes in the desired range. Dynamics of metabolic activity can be detected in one shot or over long time periods. We demonstrate the potential of this analytical technique by presenting experiments on benthic disturbance-recovery dynamics in sediments and microbial degradation of organic material in the capillary fringe. We think this technique is a new tool to further understand how microbial and geochemical processes are linked in (not solely) hydrologic

  15. Is the Lamb shift chemically significant?

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

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

  16. Initial results with the LLNL 2-D chemical-radiative-transport model of the troposphere and stratosphere

    SciTech Connect

    Wuebbles, D.J.; Connell, P.S.; Grant, K.E.; Tarp, R.; Taylor, K.E.

    1987-09-01

    Significant progress has been made at LLNL in the development of a zonally averaged (two-dimensional) chemical-radiative-transport model of the troposphere and stratosphere. Although further model development and refinement is being planned the LLNL 2-D model is currently ready to be applied to appropriately designed research studies of stratospheric chemical processes and interactions. Several such studies are now underway. This paper provides a description of the existing 2-D model and discusses some of the pertinent results for evaluating the capabilities of the model. Special attempts at improving the timing of the model are also discussed. 6 figs.

  17. Proton chemical shift tensors determined by 3D ultrafast MAS double-quantum NMR spectroscopy

    SciTech Connect

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

    2015-10-14

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

  18. Proton chemical shift tensors determined by 3D ultrafast MAS double-quantum NMR spectroscopy.

    PubMed

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

    2015-10-14

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

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

    PubMed

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

    2015-01-01

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

  20. Counterion influence on chemical shifts in strychnine salts

    SciTech Connect

    Metaxas, Athena E.; Cort, John R.

    2013-05-01

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

  1. Generalized Mechanistic Model for the Chemical Vapor Deposition of 2D Transition Metal Dichalcogenide Monolayers.

    PubMed

    Govind Rajan, Ananth; Warner, Jamie H; Blankschtein, Daniel; Strano, Michael S

    2016-04-26

    Transition metal dichalcogenides (TMDs) like molybdenum disulfide (MoS2) and tungsten disulfide (WS2) are layered materials capable of growth to one monolayer thickness via chemical vapor deposition (CVD). Such CVD methods, while powerful, are notoriously difficult to extend across different reactor types and conditions, with subtle variations often confounding reproducibility, particularly for 2D TMD growth. In this work, we formulate the first generalized TMD synthetic theory by constructing a thermodynamic and kinetic growth mechanism linked to CVD reactor parameters that is predictive of specific geometric shape, size, and aspect ratio from triangular to hexagonal growth, depending on specific CVD reactor conditions. We validate our model using experimental data from Wang et al. (Chem. Mater. 2014, 26, 6371-6379) that demonstrate the systemic evolution of MoS2 morphology down the length of a flow CVD reactor where variations in gas phase concentrations can be accurately estimated using a transport model (CSulfur = 9-965 μmol/m(3); CMoO3 = 15-16 mmol/m(3)) under otherwise isothermal conditions (700 °C). A stochastic model which utilizes a site-dependent activation energy barrier based on the intrinsic TMD bond energies and a series of Evans-Polanyi relations leads to remarkable, quantitative agreement with both shape and size evolution along the reactor. The model is shown to extend to the growth of WS2 at 800 °C and MoS2 under varied process conditions. Finally, a simplified theory is developed to translate the model into a "kinetic phase diagram" of the growth process. The predictive capability of this model and its extension to other TMD systems promise to significantly increase the controlled synthesis of such materials.

  2. 15N chemical shift referencing in solid state NMR.

    PubMed

    Bertani, Philippe; Raya, Jésus; Bechinger, Burkhard

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1999-05-01

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

  4. NMR Chemical Shifts in Hard Carbon Nitride Compounds

    SciTech Connect

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

    1998-04-01

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

  5. Protein Structure Refinement Using 13Cα Chemical Shift Tensors

    PubMed Central

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

    2009-01-01

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

  6. Molecular dynamics averaging of Xe chemical shifts in liquids

    NASA Astrophysics Data System (ADS)

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

    2004-11-01

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

  7. Chemical shift and coupling constant analysis of dibenzyloxy disulfides

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1997-06-01

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

  9. Hierarchical alignment and full resolution pattern recognition of 2D NMR spectra: application to nematode chemical ecology.

    PubMed

    Robinette, Steven L; Ajredini, Ramadan; Rasheed, Hasan; Zeinomar, Abdulrahman; Schroeder, Frank C; Dossey, Aaron T; Edison, Arthur S

    2011-03-01

    Nuclear magnetic resonance (NMR) is the most widely used nondestructive technique in analytical chemistry. In recent years, it has been applied to metabolic profiling due to its high reproducibility, capacity for relative and absolute quantification, atomic resolution, and ability to detect a broad range of compounds in an untargeted manner. While one-dimensional (1D) (1)H NMR experiments are popular in metabolic profiling due to their simplicity and fast acquisition times, two-dimensional (2D) NMR spectra offer increased spectral resolution as well as atomic correlations, which aid in the assignment of known small molecules and the structural elucidation of novel compounds. Given the small number of statistical analysis methods for 2D NMR spectra, we developed a new approach for the analysis, information recovery, and display of 2D NMR spectral data. We present a native 2D peak alignment algorithm we term HATS, for hierarchical alignment of two-dimensional spectra, enabling pattern recognition (PR) using full-resolution spectra. Principle component analysis (PCA) and partial least squares (PLS) regression of full resolution total correlation spectroscopy (TOCSY) spectra greatly aid the assignment and interpretation of statistical pattern recognition results by producing back-scaled loading plots that look like traditional TOCSY spectra but incorporate qualitative and quantitative biological information of the resonances. The HATS-PR methodology is demonstrated here using multiple 2D TOCSY spectra of the exudates from two nematode species: Pristionchus pacificus and Panagrellus redivivus. We show the utility of this integrated approach with the rapid, semiautomated assignment of small molecules differentiating the two species and the identification of spectral regions suggesting the presence of species-specific compounds. These results demonstrate that the combination of 2D NMR spectra with full-resolution statistical analysis provides a platform for chemical and

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  11. Shifted Landau ladders and low field magneto-oscillations in high-mobility GaAs 2D hole systems

    NASA Astrophysics Data System (ADS)

    Zhang, Po; Wang, Jianli; Zhang, Chi; Du, Rui-Rui; Pfeiffer, L. N.; West, K. W.

    2017-03-01

    We present well-developed low-field magneto-resistance oscillations originating from zero-field spin splitting (ZFSS) of heavy holes in high mobility GaAs/AlGaAs quantum wells. This low field oscillation is 1/B-periodic and emerges before the onset of Shubnikov-de Haas oscillations. The effect can be explained by resonant scattering between two Landau ladders shifted by the ZFSS gap, which in turn can be measured by comparing with the hole cyclotron energy. A front gate is fabricated to tune the ZFSS and hence the oscillation period.

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

    PubMed

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

    2005-02-01

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

  13. Frequency shifts of vibrational and rotational states of dilute H2, D2, and HD impurities in solid Ar under pressure

    NASA Astrophysics Data System (ADS)

    Silvi, B.; Chandrasekharan, V.; Chergui, M.; Etters, R. D.

    1986-02-01

    The frequency shifts of the vibrational and rotational transitions of H2, D2, and HD molecules trapped in solid Ar are calculated at zero temperature and at pressures 0<=P<=373 kbar. It is found that the pure vibrational and rotational-vibrational transition frequencies are strongly red-shifted in the solid at P=0, compared to gas-phase values, and the agreement with Raman scattering measurements is generally good. The calculated pure rotational transitions also show a small red shift at P=0 in the solid and are in generally good agreement with the measurements of Jodl and Bier, but less so with those of Prochaska and Andrews, who, except for D2(Ar), measure small blue shifts. The calculated local-mode frequencies of the impurity molecules in the solid at P=0 are also in good agreement with experiment, especially when thermal corrections are considered. With increasing pressure all transition frequencies and the local-mode frequencies are strongly blue-shifted with respect to P=0 solid values.

  14. In situ 2D maps of pH shifts across brass-lead galvanic joints using microelectrodes

    NASA Astrophysics Data System (ADS)

    Ma, Xiangmeng; Lee, Woo Hyoung; Lytle, Darren A.

    2017-02-01

    Galvanic corrosion in drinking water distribution systems, such as conditions following partial lead service line replacement, can be a significant source of lead in tap water. The objective of this work was to measure the pH directly near metal surfaces using a novel experimental tool in order to understand the water chemistry at a lead-containing galvanic couple in drinking water. Specifically, pH microprofiles in the proximity of corroding metal surfaces were measured using a microelectrode to construct detailed in situ 2D spatial maps of the pH across a galvanic couple at 100 µm above the metal’s surface under flowing and stagnation conditions. The opposite pH trend was directly observed across the galvanic couple under flow and stagnation conditions. Water stagnation resulted in a pH at the anode (leaded solder) of 1.5 pH units lower than the bulk water pH (9.0) and as much as 2.5 pH units lower than the cathode (brass). These conditions can enhance lead release at the anode, which reflects different anodic-cathodic relationships of coupled metals primarily controlled by water flow. Most importantly, this work has demonstrated the ability to make real pH measurement at the surface of corroding metals using a novel microelectrode approach.

  15. 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.

  16. Chemical-shift MRI of exogenous lipoid pneumonia

    SciTech Connect

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

    1996-05-01

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

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

    NASA Astrophysics Data System (ADS)

    Adrian, Frank J.

    2004-05-01

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

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

    PubMed

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

    2011-08-16

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

  19. Thermal Shock Properties of a 2D-C/SiC Composite Prepared by Chemical Vapor Infiltration

    NASA Astrophysics Data System (ADS)

    Zhang, Chengyu; Wang, Xuanwei; Wang, Bo; Liu, Yongsheng; Han, Dong; Qiao, Shengru; Guo, Yong

    2013-06-01

    The thermal shock properties of a two-dimensional carbon fiber-reinforced silicon carbide composite with a multilayered self-healing coating (2D-C/SiC) were investigated in air. The composite was prepared by low-pressure chemical vapor infiltration. 2D-C/SiC specimens were thermally shocked for different cycles between 900 and 300 °C. The thermal shock resistance was characterized by residual tensile properties and mass variation. The change of the surface morphology and microstructural evolution of the composite were examined by a scanning electron microscope. In addition, the phase evolution on the surfaces was identified using an X-ray diffractometer. It is found that the composite retains its tensile strength within 20 thermal shock cycles. However, the modulus of 2D-C/SiC decreases gradually with increasing thermal shock cycles. Extensive pullout of fibers on the fractured surface and peeling off of the coating suggest that the damage caused by the thermal shock involves weakening of the bonding strength of coating/composite and fiber/matrix. In addition, the carbon fibers in the near-surface zone were oxidized through the matrix cracks, and the fiber/matrix interfaces delaminated when the composite was subjected to a larger number of thermal shock cycles.

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

    NASA Astrophysics Data System (ADS)

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

    1997-01-01

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

  1. Versatile Method for Producing 2D and 3D Conductive Biomaterial Composites Using Sequential Chemical and Electrochemical Polymerization.

    PubMed

    Severt, Sean Y; Ostrovsky-Snider, Nicholas A; Leger, Janelle M; Murphy, Amanda R

    2015-11-18

    Flexible and conductive biocompatible materials are attractive candidates for a wide range of biomedical applications including implantable electrodes, tissue engineering, and controlled drug delivery. Here, we demonstrate that chemical and electrochemical polymerization techniques can be combined to create highly versatile silk-conducting polymer (silk-CP) composites with enhanced conductivity and electrochemical stability. Interpenetrating silk-CP composites were first generated via in situ deposition of polypyrrole during chemical polymerization of pyrrole. These composites were sufficiently conductive to serve as working electrodes for electropolymerization, which allowed an additional layer of CP to be deposited on the surface. This sequential method was applied to both 2D films and 3D sponge-like silk scaffolds, producing conductive materials with biomimetic architectures. Overall, this two-step technique expanded the range of available polymers and dopants suitable for the synthesis of mechanically robust, biocompatible, and highly conductive silk-based materials.

  2. Ultrahigh resolution protein structures using NMR chemical shift tensors

    PubMed Central

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

    2011-01-01

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

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

    SciTech Connect

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

    1990-07-01

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

  4. NMR chemical shifts in amino acids: Effects of environments, electric field, and amine group rotation

    SciTech Connect

    Yoon, Young-Gui; Pfrommer, Bernd G.; Louie, Steven G.; Canning, Andrew

    2002-03-03

    The authors present calculations of NMR chemical shifts in crystalline phases of some representative amino acids such as glycine, alanine, and alanyl-alanine. To get an insight on how different environments affect the chemical shifts, they study the transition from the crystalline phase to completely isolated molecules of glycine. In the crystalline limit, the shifts are dominated by intermolecular hydrogen-bonds. In the molecular limit, however, dipole electric field effects dominate the behavior of the chemical shifts. They show that it is necessary to average the chemical shifts in glycine over geometries. Tensor components are analyzed to get the angle dependent proton chemical shifts, which is a more refined characterization method.

  5. Instabilities of propagating quasi-2D gaseous flames and chemical fronts in narrow channels

    NASA Astrophysics Data System (ADS)

    Abid, Mohamed

    1999-12-01

    In order to examine systematically the effects of buoyancy and thermal expansion on propagating fronts, two types of fronts, one having small thermal expansion and one having large thermal expansion, were studied in two- dimensional Hele-Shaw cells (a narrow gap between two flat parallel plates). These cells were used because it is probably the simplest flow apparatus capable of exhibiting buoyancy effects. The small-expansion fronts employed were aqueous Autocatalytic Chemical Reaction fronts that produce propagating fronts, similar to premixed gas flame fronts. The aqueous systems have numerous advantages over gaseous fronts for obtaining fundamental data on the interaction between propagating fronts and buoyancy. These advantages include nearly constant density, nearly constant thermodynamic and transport properties, negligible influence of heat losses, and a high Schmidt number. Only upward propagating fronts exhibited wrinkling, indicating that buoyancy effects induced wrinkling. A well-defined characteristic wrinkle wavelength was found that was practically independent of the cell thickness and the laminar propagation rate but inversely proportional to the square root of the cosine angle between gravity and the propagating front. The only mechanism consistent with these observations is the presence of an effective surface tension at the interface between product and reactant, which, according to the Saffman-Taylor analysis, will produce a wavelength selection mechanism for buoyantly unstable flows. Correlation between a buoyancy parameter and the wrinkled front speed matched the Yakhot model for the effect of turbulence intensity on turbulent flame speed reasonably well even with no adjustable parameters. Experiments using gaseous flame fronts were also performed in order to compare with aqueous fronts to assess thermal expansion effects and heat losses. The gaseous flames were composed of CH4 or C3H 8 as fuel, O2 as oxidizer and N2 or CO2 as diluent

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

    PubMed

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

    2008-10-15

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

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed

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

    2011-08-04

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

  9. Determination of amyloid core structure using chemical shifts.

    PubMed

    Skora, Lukasz; Zweckstetter, Markus

    2012-12-01

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

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

    PubMed Central

    2014-01-01

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

  11. Theoretical Modeling of 99 Tc NMR Chemical Shifts

    SciTech Connect

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

    2016-09-06

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

  12. Quantum chemical analysis of thermodynamics of 2D cluster formation of alkanes at the water/vapor interface in the presence of aliphatic alcohols.

    PubMed

    Vysotsky, Yu B; Kartashynska, E S; Belyaeva, E A; Fainerman, V B; Vollhardt, D; Miller, R

    2015-11-21

    Using the quantum chemical semi-empirical PM3 method it is shown that aliphatic alcohols favor the spontaneous clusterization of vaporous alkanes at the water surface due to the change of adsorption from the barrier to non-barrier mechanism. A theoretical model of the non-barrier mechanism for monolayer formation is developed. In the framework of this model alcohols (or any other surfactants) act as 'floats', which interact with alkane molecules of the vapor phase using their hydrophobic part, whereas the hydrophilic part is immersed into the water phase. This results in a significant increase of contact effectiveness of alkanes with the interface during the adsorption and film formation. The obtained results are in good agreement with the existing experimental data. To test the model the thermodynamic and structural parameters of formation and clusterization are calculated for vaporous alkanes C(n)H(2n+2) (n(CH3) = 6-16) at the water surface in the presence of aliphatic alcohols C(n)H(2n+1)OH (n(OH) = 8-16) at 298 K. It is shown that the values of clusterization enthalpy, entropy and Gibbs' energy per one monomer of the cluster depend on the chain lengths of corresponding alcohols and alkanes, the alcohol molar fraction in the monolayers formed, and the shift of the alkane molecules with respect to the alcohol molecules Δn. Two possible competitive structures of mixed 2D film alkane-alcohol are considered: 2D films 1 with single alcohol molecules enclosed by alkane molecules (the alcohols do not form domains) and 2D films 2 that contain alcohol domains enclosed by alkane molecules. The formation of the alkane films of the first type is nearly independent of the surfactant type present at the interface, but depends on their molar fraction in the monolayer formed and the chain length of the compounds participating in the clusterization, whereas for the formation of the films of the second type the interaction between the hydrophilic parts of the surfactant is

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

    PubMed Central

    Bashir, Adil; Yablonskiy, Dmitriy A.

    2007-01-01

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

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

    PubMed

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

    2017-03-01

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

  15. Applications of Chemical Shift Imaging to Marine Sciences

    PubMed Central

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

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Kumari, Amrita; Dorai, Kavita

    2013-06-01

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

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

    PubMed Central

    Lebedev, A V; Rezvukhin, A I

    1984-01-01

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

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

    SciTech Connect

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

    1991-01-01

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

  19. Isotope-Labeled Amyloids via Synthesis, Expression, and Chemical Ligation for Use in FTIR, 2D IR, and NMR Studies.

    PubMed

    Zhang, Tianqi O; Grechko, Maksim; Moran, Sean D; Zanni, Martin T

    2016-01-01

    This chapter provides protocols for isotope-labeling the human islet amyloid polypeptide (hIAPP or amylin) involved in type II diabetes and γD-crystallin involved in cataract formation. Because isotope labeling improves the structural resolution, these protocols are useful for experiments using Fourier transform infrared (FTIR), two-dimensional infrared (2D IR), and NMR spectroscopies. Our research group specializes in using 2D IR spectroscopy and isotope labeling. 2D IR spectroscopy provides structural information by measuring solvation from 2D diagonal lineshapes and vibrational couplings from cross peaks. Infrared spectroscopy can be used to study kinetics, membrane proteins, and aggregated proteins. Isotope labeling provides greater certainty in the spectral assignment, which enables new structural insights that are difficult to obtain with other methods. For amylin, we provide a protocol for (13)C/(18)O labeling backbone carbonyls at one or more desired amino acids in order to obtain residue-specific structural resolution. We also provide a protocol for expressing and purifying amylin from E. coli, which enables uniform (13)C or (13)C/(15)N labeling. Uniform labeling is useful for measuring the monomer infrared spectrum in an amyloid oligomer or fiber as well as amyloid protein bound to another polypeptide or protein, such as a chaperone or an inhibitor. In addition, our expression protocol results in 2-2.5 mg of amylin peptide per 1 L cell culture, which is a high enough yield to straightforwardly obtain the 2-10 mg needed for high resolution and solid-state NMR experiments. Finally, we provide a protocol to isotope-label either of the two domains of γD-crystallin using expressed protein ligation. Domain labeling makes it possible to resolve the structures of the two halves of the protein in FTIR and 2D IR spectra. With modifications, these strategies and protocols for isotope labeling can be applied to other amyloid polypeptides and proteins.

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

    PubMed

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

    2015-11-01

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

  1. Atmospheric Nitrogen Trifluoride: Optimized emission estimates using 2-D and 3-D Chemical Transport Models from 1973-2008

    NASA Astrophysics Data System (ADS)

    Ivy, D. J.; Rigby, M. L.; Prinn, R. G.; Muhle, J.; Weiss, R. F.

    2009-12-01

    We present optimized annual global emissions from 1973-2008 of nitrogen trifluoride (NF3), a powerful greenhouse gas which is not currently regulated by the Kyoto Protocol. In the past few decades, NF3 production has dramatically increased due to its usage in the semiconductor industry. Emissions were estimated through the 'pulse-method' discrete Kalman filter using both a simple, flexible 2-D 12-box model used in the Advanced Global Atmospheric Gases Experiment (AGAGE) network and the Model for Ozone and Related Tracers (MOZART v4.5), a full 3-D atmospheric chemistry model. No official audited reports of industrial NF3 emissions are available, and with limited information on production, a priori emissions were estimated using both a bottom-up and top-down approach with two different spatial patterns based on semiconductor perfluorocarbon (PFC) emissions from the Emission Database for Global Atmospheric Research (EDGAR v3.2) and Semiconductor Industry Association sales information. Both spatial patterns used in the models gave consistent results, showing the robustness of the estimated global emissions. Differences between estimates using the 2-D and 3-D models can be attributed to transport rates and resolution differences. Additionally, new NF3 industry production and market information is presented. Emission estimates from both the 2-D and 3-D models suggest that either the assumed industry release rate of NF3 or industry production information is still underestimated.

  2. 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.

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

    ERIC Educational Resources Information Center

    Boggess, Robert K.

    1988-01-01

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

  4. 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.

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

    PubMed

    Shahab, Yosif A; Khalil, Rabah A

    2006-10-01

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

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

    PubMed

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

    2015-10-01

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

  7. 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

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

    PubMed

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

    2012-02-16

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

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

    SciTech Connect

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

    1985-06-01

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

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

    PubMed

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

    2012-01-01

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

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

    PubMed

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

    2015-10-13

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

  12. 1H, 13C and 15N chemical shift assignments of the thioredoxin from the obligate anaerobe Desulfovibrio vulgaris Hildenborough.

    PubMed

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

    2011-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Jouini, N.

    1986-07-01

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

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

    SciTech Connect

    Jouini, N.

    1986-07-15

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

  15. Status of the solar and infrared radiation submodels in the LLNL 1-D and 2-D chemical-transport models

    SciTech Connect

    Grant, K.E.; Taylor, K.E.; Ellis, J.S.; Wuebbles, D.J.

    1987-07-01

    The authors have implemented a series of state of the art radiation transport submodels in previously developed one dimensional and two dimensional chemical transport models of the troposphere and stratosphere. These submodels provide the capability of calculating accurate solar and infrared heating rates. They are a firm basis for further radiation submodel development as well as for studying interactions between radiation and model dynamics under varying conditions of clear sky, clouds, and aerosols. 37 refs., 3 figs.

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

    PubMed

    Frank, Aaron T

    2016-02-22

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

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

    PubMed

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

    2003-01-01

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

  18. 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.

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

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  1. Isotope shifts of the 6d{sup 2} D{sub 3/2}-7 p{sup 2} P{sub 1/2} transition in trapped short-lived {sup 209-214}Ra{sup +}

    SciTech Connect

    Giri, G. S.; Versolato, O. O.; Berg, J. E. van den; Boell, O.; Dammalapati, U.; Hoek, D. J. van der; Jungmann, K.; Kruithof, W. L.; Mueller, S.; Nunez Portela, M.; Onderwater, C. J. G.; Santra, B.; Timmermans, R. G. E.; Wansbeek, L. W.; Willmann, L.; Wilschut, H. W.

    2011-08-15

    Laser spectroscopy of short-lived radium isotopes in a linear Paul trap has been performed. The isotope shifts of the 6d{sup 2} D{sub 3/2} -7 p{sup 2} P{sub 1/2} transition in {sup 209-214}Ra{sup +}, which are sensitive to the short-range part of the atomic wave functions, were measured. The results are essential experimental input for improving the precision of atomic structure calculations. This is indispensable for parity violation in Ra{sup +} aiming at the determination of the weak mixing angle.

  2. 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.

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

    PubMed

    Hansen, Poul Erik

    2015-01-30

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

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

    PubMed

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

    2016-08-28

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

  5. Three-Dimensional Mapping of Soil Chemical Characteristics at Micrometric Scale by Combining 2D SEM-EDX Data and 3D X-Ray CT Images

    PubMed Central

    Hapca, Simona; Baveye, Philippe C.; Wilson, Clare; Lark, Richard Murray; Otten, Wilfred

    2015-01-01

    There is currently a significant need to improve our understanding of the factors that control a number of critical soil processes by integrating physical, chemical and biological measurements on soils at microscopic scales to help produce 3D maps of the related properties. Because of technological limitations, most chemical and biological measurements can be carried out only on exposed soil surfaces or 2-dimensional cuts through soil samples. Methods need to be developed to produce 3D maps of soil properties based on spatial sequences of 2D maps. In this general context, the objective of the research described here was to develop a method to generate 3D maps of soil chemical properties at the microscale by combining 2D SEM-EDX data with 3D X-ray computed tomography images. A statistical approach using the regression tree method and ordinary kriging applied to the residuals was developed and applied to predict the 3D spatial distribution of carbon, silicon, iron, and oxygen at the microscale. The spatial correlation between the X-ray grayscale intensities and the chemical maps made it possible to use a regression-tree model as an initial step to predict the 3D chemical composition. For chemical elements, e.g., iron, that are sparsely distributed in a soil sample, the regression-tree model provides a good prediction, explaining as much as 90% of the variability in some of the data. However, for chemical elements that are more homogenously distributed, such as carbon, silicon, or oxygen, the additional kriging of the regression tree residuals improved significantly the prediction with an increase in the R2 value from 0.221 to 0.324 for carbon, 0.312 to 0.423 for silicon, and 0.218 to 0.374 for oxygen, respectively. The present research develops for the first time an integrated experimental and theoretical framework, which combines geostatistical methods with imaging techniques to unveil the 3-D chemical structure of soil at very fine scales. The methodology presented

  6. Three-Dimensional Mapping of Soil Chemical Characteristics at Micrometric Scale by Combining 2D SEM-EDX Data and 3D X-Ray CT Images.

    PubMed

    Hapca, Simona; Baveye, Philippe C; Wilson, Clare; Lark, Richard Murray; Otten, Wilfred

    2015-01-01

    There is currently a significant need to improve our understanding of the factors that control a number of critical soil processes by integrating physical, chemical and biological measurements on soils at microscopic scales to help produce 3D maps of the related properties. Because of technological limitations, most chemical and biological measurements can be carried out only on exposed soil surfaces or 2-dimensional cuts through soil samples. Methods need to be developed to produce 3D maps of soil properties based on spatial sequences of 2D maps. In this general context, the objective of the research described here was to develop a method to generate 3D maps of soil chemical properties at the microscale by combining 2D SEM-EDX data with 3D X-ray computed tomography images. A statistical approach using the regression tree method and ordinary kriging applied to the residuals was developed and applied to predict the 3D spatial distribution of carbon, silicon, iron, and oxygen at the microscale. The spatial correlation between the X-ray grayscale intensities and the chemical maps made it possible to use a regression-tree model as an initial step to predict the 3D chemical composition. For chemical elements, e.g., iron, that are sparsely distributed in a soil sample, the regression-tree model provides a good prediction, explaining as much as 90% of the variability in some of the data. However, for chemical elements that are more homogenously distributed, such as carbon, silicon, or oxygen, the additional kriging of the regression tree residuals improved significantly the prediction with an increase in the R2 value from 0.221 to 0.324 for carbon, 0.312 to 0.423 for silicon, and 0.218 to 0.374 for oxygen, respectively. The present research develops for the first time an integrated experimental and theoretical framework, which combines geostatistical methods with imaging techniques to unveil the 3-D chemical structure of soil at very fine scales. The methodology presented

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

    PubMed

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

    2010-04-28

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

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

    PubMed

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

    2015-02-21

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2012-05-21

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

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

    NASA Astrophysics Data System (ADS)

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

    1994-04-01

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

  12. The chemical composition of animal cells reconstructed from 2D and 3D ToF-SIMS analysis

    NASA Astrophysics Data System (ADS)

    Breitenstein, D.; Rommel, C. E.; Stolwijk, J.; Wegener, J.; Hagenhoff, B.

    2008-12-01

    This paper gives an overview on the progress achieved in our lab within the last two years in the analysis of single cells and tissue-like cell layers by time-of-flight secondary ion mass spectrometry (ToF-SIMS). Basically two types of investigations were performed: on the one hand a two-dimensional imaging and on the other hand a three-dimensional microarea analysis. In both cases chemical fixation in combination with slow air-drying were used as easy sample preparation method. It was the goal of both approaches to identify the distribution of natural components as well as the localisation of xenobiotic fluorophors. In our experimental set-ups the distribution of phophatidylcholine and amino-acid signals were in line with the expectation. In contrast, the distribution of the fluorophor ethidiumhomodimer could only be detected within the two-dimensional imaging, whereas it was not detected in the three-dimensional analysis. Also four other fluorophors failed in the latter approach. Thus, in our hands the three-dimensional detection is to date limited to certain molecules with a comparably low mass and/or an intrinsical charge.

  13. Multi-GPU unsteady 2D flow simulation coupled with a state-to-state chemical kinetics

    NASA Astrophysics Data System (ADS)

    Tuttafesta, Michele; Pascazio, Giuseppe; Colonna, Gianpiero

    2016-10-01

    In this work we are presenting a GPU version of a CFD code for high enthalpy reacting flow, using the state-to-state approach. In supersonic and hypersonic flows, thermal and chemical non-equilibrium is one of the fundamental aspects that must be taken into account for the accurate characterization of the plasma and state-to-state kinetics is the most accurate approach used for this kind of problems. This model consists in writing a continuity equation for the population of each vibrational level of the molecules in the mixture, determining at the same time the species densities and the distribution of the population in internal levels. An explicit scheme is employed here to integrate the governing equations, so as to exploit the GPU structure and obtain an efficient algorithm. The best performances are obtained for reacting flows in state-to-state approach, reaching speedups of the order of 100, thanks to the use of an operator splitting scheme for the kinetics equations.

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

    PubMed

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

    2010-09-01

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

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

    PubMed Central

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

    2015-01-01

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

  16. 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…

  17. Chemical profiling and adulteration screening of Aquilariae Lignum Resinatum by Fourier transform infrared (FT-IR) spectroscopy and two-dimensional correlation infrared (2D-IR) spectroscopy.

    PubMed

    Qu, Lei; Chen, Jian-Bo; Zhang, Gui-Jun; Sun, Su-Qin; Zheng, Jing

    2017-03-05

    As a kind of expensive perfume and valuable herb, Aquilariae Lignum Resinatum (ALR) is often adulterated for economic motivations. In this research, Fourier transform infrared (FT-IR) spectroscopy is employed to establish a simple and quick method for the adulteration screening of ALR. First, the principal chemical constituents of ALR are characterized by FT-IR spectroscopy at room temperature and two-dimensional correlation infrared (2D-IR) spectroscopy with thermal perturbation. Besides the common cellulose and lignin compounds, a certain amount of resin is the characteristic constituent of ALR. Synchronous and asynchronous 2D-IR spectra indicate that the resin (an unstable secondary metabolite) is more sensitive than cellulose and lignin (stable structural constituents) to the thermal perturbation. Using a certified ALR sample as the reference, the infrared spectral correlation threshold is determined by 30 authentic samples and 6 adulterated samples. The spectral correlation coefficient of an authentic ALR sample to the standard reference should be not less than 0.9886 (p=0.01). Three commercial adulterated ALR samples are identified by the correlation threshold. Further interpretation of the infrared spectra of the adulterated samples indicates the common adulterating methods - counterfeiting with other kind of wood, adding ingredient such as sand to increase the weight, and adding the cheap resin such as rosin to increase the content of resin compounds. Results of this research prove that FT-IR spectroscopy can be used as a simple and accurate quality control method of ALR.

  18. Chemical profiling and adulteration screening of Aquilariae Lignum Resinatum by Fourier transform infrared (FT-IR) spectroscopy and two-dimensional correlation infrared (2D-IR) spectroscopy

    NASA Astrophysics Data System (ADS)

    Qu, Lei; Chen, Jian-bo; Zhang, Gui-Jun; Sun, Su-qin; Zheng, Jing

    2017-03-01

    As a kind of expensive perfume and valuable herb, Aquilariae Lignum Resinatum (ALR) is often adulterated for economic motivations. In this research, Fourier transform infrared (FT-IR) spectroscopy is employed to establish a simple and quick method for the adulteration screening of ALR. First, the principal chemical constituents of ALR are characterized by FT-IR spectroscopy at room temperature and two-dimensional correlation infrared (2D-IR) spectroscopy with thermal perturbation. Besides the common cellulose and lignin compounds, a certain amount of resin is the characteristic constituent of ALR. Synchronous and asynchronous 2D-IR spectra indicate that the resin (an unstable secondary metabolite) is more sensitive than cellulose and lignin (stable structural constituents) to the thermal perturbation. Using a certified ALR sample as the reference, the infrared spectral correlation threshold is determined by 30 authentic samples and 6 adulterated samples. The spectral correlation coefficient of an authentic ALR sample to the standard reference should be not less than 0.9886 (p = 0.01). Three commercial adulterated ALR samples are identified by the correlation threshold. Further interpretation of the infrared spectra of the adulterated samples indicates the common adulterating methods - counterfeiting with other kind of wood, adding ingredient such as sand to increase the weight, and adding the cheap resin such as rosin to increase the content of resin compounds. Results of this research prove that FT-IR spectroscopy can be used as a simple and accurate quality control method of ALR.

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

    NASA Astrophysics Data System (ADS)

    Fukushima, Kenji; Hidaka, Yoshimasa

    2016-09-01

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

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

    PubMed

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

    2004-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

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

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

    SciTech Connect

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

    1992-04-08

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

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

    NASA Astrophysics Data System (ADS)

    Zurek, Eva; Autschbach, Jochen

    2007-12-01

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

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

    PubMed

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

    2016-01-01

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

  5. Pilot Study on the Detection of Simulated Lesions Using a 2D and 3D Digital Full-Field Mammography System with a Newly Developed High Resolution Detector Based on Two Shifts of a-Se.

    PubMed

    Schulz-Wendtland, R; Bani, M; Lux, M P; Schwab, S; Loehberg, C R; Jud, S M; Rauh, C; Bayer, C M; Beckmann, M W; Uder, M; Fasching, P A; Adamietz, B; Meier-Meitinger, M

    2012-05-01

    Purpose: Experimental study of a new system for digital 2D and 3D full-field mammography (FFDM) using a high resolution detector based on two shifts of a-Se. Material and Methods: Images were acquired using the new FFDM system Amulet® (FujiFilm, Tokio, Japan), an a-Se detector (receptor 24 × 30 cm(2), pixel size 50 µm, memory depth 12 bit, spatial resolution 10 lp/mm, DQE > 0.50). Integrated in the detector is a new method for data transfer, based on optical switch technology. The object of investigation was the Wisconsin Mammographic Random Phantom, Model 152A (Radiation Measurement Inc., Middleton, WI, USA) and the same parameters and exposure data (Tungsten, 100 mAs, 30 kV) were consistently used. We acquired 3 different pairs of images in the c-c and ml planes (2D) and in the c-c and c-c planes with an angle of 4 degrees (3D). Five radiologists experienced in mammography (experience ranging from 3 months to more than 5 years) analyzed the images (monitoring) which had been randomly encoded (random generator) with regard to the recognition of details such as specks of aluminum oxide (200-740 µm), nylon fibers (0.4-1.6 mm) and round lesions/masses (diameters 5-14 mm), using special linear glasses for 3D visualization, and compared the results. Results: A total of 225 correct positive decisions could be detected: we found 222 (98.7 %) correct positive results for 2D and 3D visualization in each case. Conclusion: The results of this phantom study showed the same detection rates for both 2D and 3D imaging using full field digital mammography. Our results must be confirmed in further clinical trials.

  6. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

  8. 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

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

    PubMed

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

    2013-06-04

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

  10. 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

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

    PubMed

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

    2015-08-21

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

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

    PubMed

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

    2007-10-01

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

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

    PubMed

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

    2011-04-07

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

  14. Large-Size 2D β-Cu2 S Nanosheets with Giant Phase Transition Temperature Lowering (120 K) Synthesized by a Novel Method of Super-Cooling Chemical-Vapor-Deposition.

    PubMed

    Li, Bo; Huang, Le; Zhao, Guangyao; Wei, Zhongming; Dong, Huanli; Hu, Wenping; Wang, Lin-Wang; Li, Jingbo

    2016-10-01

    2D triangular β-Cu2 S nanosheets with large size and high quality are synthesized by a novel method of super-cooling chemical-vapor-deposition. The phase transition of this 2D material from β-Cu2 S to γ-Cu2 S occurs at 258 K (-15 °C), and such transition temperature is 120 K lower than that of its bulk counterpart (about 378 K).

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

    SciTech Connect

    Martin, Bob; Autschbach, Jochen

    2015-02-07

    Using a recently proposed equation for NMR nuclear magnetic shielding for molecules with unpaired electrons [A. Soncini and W. Van den Heuvel, J. Chem. Phys. 138, 021103 (2013)], equations for the temperature (T) dependent isotropic shielding for multiplets with an effective spin S equal to 1/2, 1, 3/2, 2, and 5/2 in terms of electron paramagnetic resonance spin Hamiltonian parameters are derived and then expanded in powers of 1/T. One simplifying assumption used is that a matrix derived from the zero-field splitting (ZFS) tensor and the Zeeman coupling matrix (g-tensor) share the same principal axis system. The influence of the rhombic ZFS parameter E is only investigated for S = 1. Expressions for paramagnetic contact shielding (from the isotropic part of the hyperfine coupling matrix) and pseudo-contact or dipolar shielding (from the anisotropic part of the hyperfine coupling matrix) are considered separately. The leading order is always 1/T. A temperature dependence of the contact shielding as 1/T and of the dipolar shielding as 1/T{sup 2}, which is sometimes assumed in the assignment of paramagnetic chemical shifts, is shown to arise only if S ≥ 1 and zero-field splitting is appreciable, and only if the Zeeman coupling matrix is nearly isotropic (Δg = 0). In such situations, an assignment of contact versus dipolar shifts may be possible based only on linear and quadratic fits of measured variable-temperature chemical shifts versus 1/T. Numerical data are provided for nickelocene (S = 1). Even under the assumption of Δg = 0, a different leading order of contact and dipolar shifts in powers of 1/T is not obtained for S = 3/2. When Δg is not very small, dipolar and contact shifts both depend in leading order in 1/T in all cases, with sizable contributions in order 1/T{sup n} with n = 2 and higher.

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

    PubMed

    Martin, Bob; Autschbach, Jochen

    2015-02-07

    Using a recently proposed equation for NMR nuclear magnetic shielding for molecules with unpaired electrons [A. Soncini and W. Van den Heuvel, J. Chem. Phys. 138, 021103 (2013)], equations for the temperature (T) dependent isotropic shielding for multiplets with an effective spin S equal to 1/2, 1, 3/2, 2, and 5/2 in terms of electron paramagnetic resonance spin Hamiltonian parameters are derived and then expanded in powers of 1/T. One simplifying assumption used is that a matrix derived from the zero-field splitting (ZFS) tensor and the Zeeman coupling matrix (g-tensor) share the same principal axis system. The influence of the rhombic ZFS parameter E is only investigated for S = 1. Expressions for paramagnetic contact shielding (from the isotropic part of the hyperfine coupling matrix) and pseudo-contact or dipolar shielding (from the anisotropic part of the hyperfine coupling matrix) are considered separately. The leading order is always 1/T. A temperature dependence of the contact shielding as 1/T and of the dipolar shielding as 1/T(2), which is sometimes assumed in the assignment of paramagnetic chemical shifts, is shown to arise only if S ≥ 1 and zero-field splitting is appreciable, and only if the Zeeman coupling matrix is nearly isotropic (Δg = 0). In such situations, an assignment of contact versus dipolar shifts may be possible based only on linear and quadratic fits of measured variable-temperature chemical shifts versus 1/T. Numerical data are provided for nickelocene (S = 1). Even under the assumption of Δg = 0, a different leading order of contact and dipolar shifts in powers of 1/T is not obtained for S = 3/2. When Δg is not very small, dipolar and contact shifts both depend in leading order in 1/T in all cases, with sizable contributions in order 1/T(n) with n = 2 and higher.

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

    PubMed

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

    2017-04-13

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

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

    PubMed

    Kjaergaard, Magnus; Poulsen, Flemming M

    2011-06-01

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

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

    PubMed

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

    2016-02-01

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

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

    PubMed

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

    2008-08-14

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

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

    PubMed

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

    1993-07-01

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

  2. 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.

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

    PubMed Central

    Görling, Benjamin; Bräse, Stefan; Luy, Burkhard

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

    Görling, Benjamin; Bräse, Stefan; Luy, Burkhard

    2016-09-02

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

  6. Calculation of NMR chemical shifts. 7. Gauge-invariant INDO method

    NASA Astrophysics Data System (ADS)

    Fukui, H.; Miura, K.; Hirai, A.

    A gauge-invariant INDO method based on the coupled Hartree-Fuck perturbation theory is presented and applied to the calculation of 1H and 13C chemical shifts of hydrocarbons including ring compounds. Invariance of the diamagnetic and paramagnetic shieldings with respect to displacement of the coordinate origin is discussed. Comparison between calculated and experimental results exhibits fairly good agreement, provided that the INDO parameters of Ellis et al. (J. Am. Chem. Soc.94, 4069 (1972)) are used with the inclusion of all multicenter one-electron integrals.

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

    PubMed

    Rozwadowski, Z

    2006-09-01

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

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

    PubMed

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

    2009-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2007-11-01

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

  10. 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.

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

    PubMed

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

    2010-05-01

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

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

    PubMed

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

    2009-09-10

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

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

    PubMed

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

    2016-10-05

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

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

    PubMed

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

    2012-03-20

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

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

    PubMed

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

    2013-01-21

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

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

    NASA Astrophysics Data System (ADS)

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

    2002-08-01

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

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

    PubMed

    Frach, Roland; Kast, Stefan M

    2014-12-11

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

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

    PubMed Central

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

    2013-01-01

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

  19. Chemical analysis of solid materials by a LIMS instrument designed for space research: 2D elemental imaging, sub-nm depth profiling and molecular surface analysis

    NASA Astrophysics Data System (ADS)

    Moreno-García, Pavel; Grimaudo, Valentine; Riedo, Andreas; Neuland, Maike B.; Tulej, Marek; Broekmann, Peter; Wurz, Peter

    2016-04-01

    Direct quantitative chemical analysis with high lateral and vertical resolution of solid materials is of prime importance for the development of a wide variety of research fields, including e.g., astrobiology, archeology, mineralogy, electronics, among many others. Nowadays, studies carried out by complementary state-of-the-art analytical techniques such as Auger Electron Spectroscopy (AES), X-ray Photoelectron Spectroscopy (XPS), Secondary Ion Mass Spectrometry (SIMS), Glow Discharge Time-of-Flight Mass Spectrometry (GD-TOF-MS) or Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) provide extensive insight into the chemical composition and allow for a deep understanding of processes that might have fashioned the outmost layers of an analyte due to its interaction with the surrounding environment. Nonetheless, these investigations typically employ equipment that is not suitable for implementation on spacecraft, where requirements concerning weight, size and power consumption are very strict. In recent years Laser Ablation/Ionization Mass Spectrometry (LIMS) has re-emerged as a powerful analytical technique suitable not only for laboratory but also for space applications.[1-3] Its improved performance and measurement capabilities result from the use of cutting edge ultra-short femtosecond laser sources, improved vacuum technology and fast electronics. Because of its ultimate compactness, simplicity and robustness it has already proven to be a very suitable analytical tool for elemental and isotope investigations in space research.[4] In this contribution we demonstrate extended capabilities of our LMS instrument by means of three case studies: i) 2D chemical imaging performed on an Allende meteorite sample,[5] ii) depth profiling with unprecedented sub-nm vertical resolution on Cu electrodeposited interconnects[6,7] and iii) preliminary molecular desorption of polymers without assistance of matrix or functionalized substrates.[8] On the whole

  20. Detection of Anisotropic Hyperfine Components of Chemically Prepared Carotenoid Radical Cations:1D and 2D ESEEM and Pulsed ENDOR Study

    SciTech Connect

    Konovalova, Tatyana A.; Dikanov, Sergei A.; Bowman, Michael K.; Kispert, Lowell D.

    2001-09-06

    Canthaxanthin and 8'-apo-B-caroten-8'-al radical cations chemically prepared on activated silica-alumina and in CH2CI2 solution containing A1C13 were studied by pulsed EPR and ENDOR spectroscopies. Both the 1D three-pulse ESEEM and the 2D HYSCORE spectra of the carotenoid-A1C13 mixtures exhibited the 27 A1 nuclei peak at 3.75 MHz. This indicates electron-transfer interactions between carotenoids and A1III ions resulting in the formation and stabilization of carotenoid radical cations. Davies ENDOR measurements of the canthaxanthin radical cation on silica-alumina determined the hyperfine couplings of B protons belonging to three different methyl groups with ahI=2.6 MHz, aH2=8.6MHz, and ah3 ca. 13 MHz. The principal components of the proton hyperfine tensors were obtained from HYSCORE spectra in A1C13 solutions and on the solid support. Identification of the protons was made on the basis of isotropic hyperfine couplings determined by RHF-INDO/SP molecular orbital calculations. In frozen A1C13 solution, the C(7, 7')Ha and C(14, 14')-Ha a protons were observed for Canthaxanthin and the C(8 or 14')-Ha, C(15')-Ha were observed for 8'-apo-B-caroten-8'-al. On the silica-alumina support, the C(10, 10')-Ha, C(11, 11')-Ha, and C(15,15')-Ha a protons were measured for Canthaxanthin and the C(12)-Ha and C(15')-Ha were measured for 8' apo-B-caroten-8'-al. Some protons with large isotropic couplings (>10 MHz) determined from HYSCORE analysis could be assigned to B protons, but the principal components of their hyperfine tensors are much more anisotropic than those reported previously for B protons. We suggest that cis/trans isomerization of carotenoids on silica-alumina results in stabilization of di-cis isomers with large isotropic couplings for some a protons which are comparable to those of B protons.

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

    SciTech Connect

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

    2015-06-22

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

  2. 125Te NMR chemical-shift trends in PbTe-GeTe and PbTe-SnTe alloys.

    PubMed

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

    2013-01-01

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

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

    PubMed

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

    2014-05-29

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

  4. 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…

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

    PubMed

    Kou, Gaoshan; Feng, Yonge

    2015-09-07

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

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

    PubMed

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

    2016-09-01

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

  7. 129Xe chemical shift in human blood and pulmonary blood oxygenation measurement in humans using hyperpolarized 129Xe NMR

    PubMed Central

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

    2016-01-01

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

  8. Experimental study of resolution of proton chemical shifts in solids: Combined multiple pulse NMR and magic-angle spinning

    SciTech Connect

    Ryan, L.M.; Taylor, R.E.; Paff, A.J.; Gerstein, B.C.

    1980-01-01

    High-resolution nuclear magnetic resonance spectra of protons in rigid, randomly oriented solids have been measured using combined homonuclear dipolar decoupling (via multiple pulse techniques) and attenuation of chemical shift anisotropies (via magic-angle sample spinning). Under those conditions, isotropic proton chemical shifts were recorded for a variety of chemical species, with individual linewidths varying from about 55 to 110 Hz (1--2 ppm). Residual line broadening was due predominately to (i) magnetic-field instability and inhomogeneity, (ii) unresolved proton--proton spin couplings, (iii) chemical shift dispersion, (iv) residual dipolar broadening, and (v) lifetime broadening under the multiple pulse sequences used. The magnitudes of those effects and the current limits of resolution for this experiment in our spectrometer have been investigated. The compounds studied included organic solids (4, 4'-dimethylbenzophenone, 2, 6-dimethylbenzoic acid, and aspirin), polymers (polystyrene and polymethylmethacrylate), and the vitrain portion of a bituminous coal.

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

    PubMed

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

    2016-04-01

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

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

    PubMed

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

    2012-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    SciTech Connect

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

    1989-02-07

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

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

    SciTech Connect

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

    2011-09-21

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

  15. Three-dimensional mapping of soil chemical characteristics at micrometric scale: Statistical prediction by combining 2D SEM-EDX data and 3D X-ray computed micro-tomographic images

    NASA Astrophysics Data System (ADS)

    Hapca, Simona

    2015-04-01

    Many soil properties and functions emerge from interactions of physical, chemical and biological processes at microscopic scales, which can be understood only by integrating techniques that traditionally are developed within separate disciplines. While recent advances in imaging techniques, such as X-ray computed tomography (X-ray CT), offer the possibility to reconstruct the 3D physical structure at fine resolutions, for the distribution of chemicals in soil, existing methods, based on scanning electron microscope (SEM) and energy dispersive X-ray detection (EDX), allow for characterization of the chemical composition only on 2D surfaces. At present, direct 3D measurement techniques are still lacking, sequential sectioning of soils, followed by 2D mapping of chemical elements and interpolation to 3D, being an alternative which is explored in this study. Specifically, we develop an integrated experimental and theoretical framework which combines 3D X-ray CT imaging technique with 2D SEM-EDX and use spatial statistics methods to map the chemical composition of soil in 3D. The procedure involves three stages 1) scanning a resin impregnated soil cube by X-ray CT, followed by precision cutting to produce parallel thin slices, the surfaces of which are scanned by SEM-EDX, 2) alignment of the 2D chemical maps within the internal 3D structure of the soil cube, and 3) development, of spatial statistics methods to predict the chemical composition of 3D soil based on the observed 2D chemical and 3D physical data. Specifically, three statistical models consisting of a regression tree, a regression tree kriging and cokriging model were used to predict the 3D spatial distribution of carbon, silicon, iron and oxygen in soil, these chemical elements showing a good spatial agreement between the X-ray grayscale intensities and the corresponding 2D SEM-EDX data. Due to the spatial correlation between the physical and chemical data, the regression-tree model showed a great potential

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

    PubMed

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

    2012-08-21

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-06-01

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

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

    PubMed

    Wood, Ezra C; Charest, John R

    2014-10-21

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

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

    PubMed

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

    2007-03-15

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

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

    SciTech Connect

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

    2015-09-14

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-10-01

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

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

    PubMed

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

    2013-01-24

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

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

    PubMed

    Burke, James R.; Frey, Perry A.

    1996-01-26

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

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

    PubMed Central

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

    2013-01-01

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

  6. 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.

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

    PubMed Central

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

    2014-01-01

    NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very limited statistical data basis, such methods are still in their infancy in the field of nucleic acids, especially when non-canonical structures and nucleic acid complexes are considered. Here, we present an ab initio approach for predicting proton chemical shifts of arbitrary nucleic acid structures based on state-of-the-art fragment-based quantum chemical calculations. We tested our prediction method on a diverse set of nucleic acid structures including double-stranded DNA, hairpins, DNA/protein complexes and chemically-modified DNA. Overall, our quantum chemical calculations yield highly/very accurate predictions with mean absolute deviations of 0.3–0.6 ppm and correlation coefficients (r2) usually above 0.9. This will allow for identifying misassignments and validating 3D structures. Furthermore, our calculations reveal that chemical shifts of protons involved in hydrogen bonding are predicted significantly less accurately. This is in part caused by insufficient inclusion of solvation effects. However, it also points toward shortcomings of current force fields used for structure determination of nucleic acids. Our quantum chemical calculations could therefore provide input for force field optimization. PMID:25404135

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

    PubMed

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

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

    DTIC Science & Technology

    2011-07-26

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

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

    NASA Astrophysics Data System (ADS)

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

    2002-01-01

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

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

    PubMed

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

    2017-04-01

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

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

    PubMed

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

    2002-08-01

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

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

    PubMed

    Ying, Jinfa; Grishaev, Alexander; Bax, Ad

    2006-03-01

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

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

    PubMed

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

    2007-02-01

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

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

    PubMed

    Sahakyan, Aleksandr B; Vendruscolo, Michele

    2013-02-21

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

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

    PubMed

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

    2008-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1995-04-01

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

  20. Modeling chemical interaction profiles: I. Spectral data-activity relationship and structure-activity relationship models for inhibitors and non-inhibitors of cytochrome P450 CYP3A4 and CYP2D6 isozymes.

    PubMed

    McPhail, Brooks; Tie, Yunfeng; Hong, Huixiao; Pearce, Bruce A; Schnackenberg, Laura K; Ge, Weigong; Valerio, Luis G; Fuscoe, James C; Tong, Weida; Buzatu, Dan A; Wilkes, Jon G; Fowler, Bruce A; Demchuk, Eugene; Beger, Richard D

    2012-03-15

    An interagency collaboration was established to model chemical interactions that may cause adverse health effects when an exposure to a mixture of chemicals occurs. Many of these chemicals--drugs, pesticides, and environmental pollutants--interact at the level of metabolic biotransformations mediated by cytochrome P450 (CYP) enzymes. In the present work, spectral data-activity relationship (SDAR) and structure-activity relationship (SAR) approaches were used to develop machine-learning classifiers of inhibitors and non-inhibitors of the CYP3A4 and CYP2D6 isozymes. The models were built upon 602 reference pharmaceutical compounds whose interactions have been deduced from clinical data, and 100 additional chemicals that were used to evaluate model performance in an external validation (EV) test. SDAR is an innovative modeling approach that relies on discriminant analysis applied to binned nuclear magnetic resonance (NMR) spectral descriptors. In the present work, both 1D ¹³C and 1D ¹⁵N-NMR spectra were used together in a novel implementation of the SDAR technique. It was found that increasing the binning size of 1D ¹³C-NMR and ¹⁵N-NMR spectra caused an increase in the tenfold cross-validation (CV) performance in terms of both the rate of correct classification and sensitivity. The results of SDAR modeling were verified using SAR. For SAR modeling, a decision forest approach involving from 6 to 17 Mold2 descriptors in a tree was used. Average rates of correct classification of SDAR and SAR models in a hundred CV tests were 60% and 61% for CYP3A4, and 62% and 70% for CYP2D6, respectively. The rates of correct classification of SDAR and SAR models in the EV test were 73% and 86% for CYP3A4, and 76% and 90% for CYP2D6, respectively. Thus, both SDAR and SAR methods demonstrated a comparable performance in modeling a large set of structurally diverse data. Based on unique NMR structural descriptors, the new SDAR modeling method complements the existing SAR

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

    PubMed

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1992-07-01

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

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

    NASA Astrophysics Data System (ADS)

    Jameson, Cynthia J.; Lim, Hyung-Mi

    1995-09-01

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

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

    PubMed

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

    2015-09-03

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

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

    PubMed

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

    2016-11-07

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

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

    USGS Publications Warehouse

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Nanba, Tokuro; Nishimura, Mitsunori; Miura, Yoshinari

    2004-12-01

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

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

    PubMed

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

    2012-06-21

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

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

    NASA Astrophysics Data System (ADS)

    Jameson, Cynthia J.; Lim, Hyung-Mi

    1997-09-01

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

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

    PubMed

    Fujisawa, Seiichiro; Ishihara, Mariko; Kadoma, Yoshinori

    2005-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

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

  12. Vertical 2D Heterostructures

    NASA Astrophysics Data System (ADS)

    Lotsch, Bettina V.

    2015-07-01

    Graphene's legacy has become an integral part of today's condensed matter science and has equipped a whole generation of scientists with an armory of concepts and techniques that open up new perspectives for the postgraphene area. In particular, the judicious combination of 2D building blocks into vertical heterostructures has recently been identified as a promising route to rationally engineer complex multilayer systems and artificial solids with intriguing properties. The present review highlights recent developments in the rapidly emerging field of 2D nanoarchitectonics from a materials chemistry perspective, with a focus on the types of heterostructures available, their assembly strategies, and their emerging properties. This overview is intended to bridge the gap between two major—yet largely disjunct—developments in 2D heterostructures, which are firmly rooted in solid-state chemistry or physics. Although the underlying types of heterostructures differ with respect to their dimensions, layer alignment, and interfacial quality, there is common ground, and future synergies between the various assembly strategies are to be expected.

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

    PubMed

    Vila, Jorge A; Scheraga, Harold A

    2009-10-20

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

  14. Comparison of Brachionus calyciflorus 2-d and Microtox{reg{underscore}sign} chronic 22-H tests with Daphnia magna 21-d test for the chronic toxicity assessment of chemicals

    SciTech Connect

    Radix, P.; Leonard, M.; Papantoniou, C.; Roman, G.; Saouter, E.; Gallotti-Schmitt, S.; Thiebaud, H.; Vasseur, P.

    1999-10-01

    The Daphnia magna 21-d test may be required by European authorities as a criterion for the assessment of aquatic chronic toxicity for the notification of new substances. However, this test has several drawbacks. It is labor-intensive, relatively expensive, and requires the breeding of test organisms. The Brachionous calyciflorus 2-d test and Microtox chronic 22-h test do not suffer from these disadvantages and could be used as substitutes for the Daphnia 21-d test for screening assays. During this study, the toxicity of 25 chemicals was measured using both the microtox chronic toxicity and B. calyciflorus 2-d tests, and the no-observed-effect concentrations (NOECs) were compared to the D. magna 21-d test. The Brachionus test was slightly less sensitive than the Daphnia test, but the correlation between the two tests was relatively good (r{sup 2} = 0.54). The B. calyciflorus 2-d test, and to a lesser extent the Microtox chronic 22-h test, were able to predict the chronic toxicity values of the Daphnia 21-d test. They constitute promising cost-effective tools for chronic toxicity screening.

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

    PubMed

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

    2006-11-01

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

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

    PubMed

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

    2012-10-01

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

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

    PubMed

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

    2014-12-01

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

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

    PubMed

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

    2010-06-09

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  20. Determination of chemical changes in Isatis indigotica seeds carried after Chinese first spaceship with FTIR and 2D-IR correlation spectroscopy.

    PubMed

    Chen, Xiangdong; Keong, Choong Yew; Mei, Xiling; Lan, Jin

    2014-04-24

    Spaceflight represents a complex environmental condition. Space mutagenesis breeding has achieved and marked certain results over the years. This method was employed in our previous studies in order to obtain improved germplasm of Isatis indigotica. This study is to determine the chemical changes in I. indigotica seeds carried after Chinese first spaceship (Shenzhou I). Fourier transform infrared (FTIR), second derivative and two-dimensional infrared (2DIR) correlation spectroscopy were used in analysis. Not much differences between the two spectra were found except the peaks in the range of 1500-1200 cm(-)(1) which was about 7 cm(-)(1) different and indicated the absorption could be initialed from different bonds. SP4 showed different derivative compared with C4 in the second derivative spectra of 1200-800 cm(-)(1). The stronger signal of 2DIR in SP4 indicated the protein content of the seed was changed after spaceflight. It is concluded that spaceflight provided an extreme condition that caused changes of chemical properties in I. indigotica.

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

    PubMed

    Konstantinov, Ivan A; Broadbelt, Linda J

    2011-11-10

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

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

    PubMed

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

    2014-11-01

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

  3. 2D semiconductor optoelectronics

    NASA Astrophysics Data System (ADS)

    Novoselov, Kostya

    The advent of graphene and related 2D materials has recently led to a new technology: heterostructures based on these atomically thin crystals. The paradigm proved itself extremely versatile and led to rapid demonstration of tunnelling diodes with negative differential resistance, tunnelling transistors, photovoltaic devices, etc. By taking the complexity and functionality of such van der Waals heterostructures to the next level we introduce quantum wells engineered with one atomic plane precision. Light emission from such quantum wells, quantum dots and polaritonic effects will be discussed.

  4. In situ observation of reduction kinetics and 2D mapping of chemical state for heterogeneous reduction in iron-ore sinters

    NASA Astrophysics Data System (ADS)

    Kimura, M.; Murao, R.; Ohta, N.; Noami, K.; Uemura, Y.; Niwa, Y.; Kimijima, K.; Takeichi, Y.; Nitani, H.

    2016-05-01

    Iron-ore sinters constitute the major component of the iron-bearing burden in blast furnaces, and the mechanism of their reduction is one of the key processes in iron making. The heterogeneous reduction of sintered oxides was investigated by the combination of X-ray fluorescence and absorption fine structure, X-ray diffraction, and computed tomography. Two - dimensional mapping of the chemical states (CSs) was performed. The iron CSs FeIII, FeII, and Fe0 exhibited a heterogeneous distribution in a reduced sinter. The reduction started near micro pores, at iron-oxide grains rather than calcium-ferrite ones. The heterogeneous reduction among grains in a sinter may cause the formation of micro cracks. These results provide fundamental insights into heterogeneous reduction schemes for iron-ore sinters.

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

    PubMed

    Engtrakul, Chaiwat; Irurzun, Veronica M; Gjersing, Erica L; Holt, Josh M; Larsen, Brian A; Resasco, Daniel E; Blackburn, Jeffrey L

    2012-03-14

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

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

    PubMed

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

    2015-10-01

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

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

    PubMed Central

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

    2015-01-01

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

  8. 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

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

    SciTech Connect

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

    2011-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  11. Assessing 2D electrophoretic mobility spectroscopy (2D MOSY) for analytical applications.

    PubMed

    Fang, Yuan; Yushmanov, Pavel V; Furó, István

    2016-12-08

    Electrophoretic displacement of charged entity phase modulates the spectrum acquired in electrophoretic NMR experiments, and this modulation can be presented via 2D FT as 2D mobility spectroscopy (MOSY) spectra. We compare in various mixed solutions the chemical selectivity provided by 2D MOSY spectra with that provided by 2D diffusion-ordered spectroscopy (DOSY) spectra and demonstrate, under the conditions explored, a superior performance of the former method. 2D MOSY compares also favourably with closely related LC-NMR methods. The shape of 2D MOSY spectra in complex mixtures is strongly modulated by the pH of the sample, a feature that has potential for areas such as in drug discovery and metabolomics. Copyright © 2016 The Authors. Magnetic Resonance in Chemistry published by John Wiley & Sons Ltd. StartCopTextCopyright © 2016 The Authors. Magnetic Resonance in Chemistry published by John Wiley & Sons Ltd.

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

    PubMed

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

    2008-04-01

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

  13. The IDOL–UBE2D complex mediates sterol-dependent degradation of the LDL receptor

    PubMed Central

    Zhang, Li; Fairall, Louise; Goult, Benjamin T.; Calkin, Anna C.; Hong, Cynthia; Millard, Christopher J.; Tontonoz, Peter; Schwabe, John W.R.

    2011-01-01

    We previously identified the E3 ubiquitin ligase IDOL as a sterol-dependent regulator of the LDL receptor (LDLR). The molecular pathway underlying IDOL action, however, remains to be determined. Here we report the identification and biochemical and structural characterization of an E2–E3 ubiquitin ligase complex for LDLR degradation. We identified the UBE2D family (UBE2D1–4) as E2 partners for IDOL that support both autoubiquitination and IDOL-dependent ubiquitination of the LDLR in a cell-free system. NMR chemical shift mapping and a 2.1 Å crystal structure of the IDOL RING domain–UBE2D1 complex revealed key interactions between the dimeric IDOL protein and the E2 enzyme. Analysis of the IDOL–UBE2D1 interface also defined the stereochemical basis for the selectivity of IDOL for UBE2Ds over other E2 ligases. Structure-based mutations that inhibit IDOL dimerization or IDOL–UBE2D interaction block IDOL-dependent LDLR ubiquitination and degradation. Furthermore, expression of a dominant-negative UBE2D enzyme inhibits the ability of IDOL to degrade the LDLR in cells. These results identify the IDOL–UBE2D complex as an important determinant of LDLR activity, and provide insight into molecular mechanisms underlying the regulation of cholesterol uptake. PMID:21685362

  14. Indirectly detected chemical shift correlation NMR spectroscopy in solids under fast magic angle spinning

    SciTech Connect

    Mao, Kanmi

    2011-01-01

    The development of fast magic angle spinning (MAS) opened up an opportunity for the indirect detection of insensitive low-γ nuclei (e.g., 13C and 15N) via the sensitive high-{gamma} nuclei (e.g., 1H and 19F) in solid-state NMR, with advanced sensitivity and resolution. In this thesis, new methodology utilizing fast MAS is presented, including through-bond indirectly detected heteronuclear correlation (HETCOR) spectroscopy, which is assisted by multiple RF pulse sequences for 1H-1H homonuclear decoupling. Also presented is a simple new strategy for optimization of 1H-1H homonuclear decoupling. As applications, various classes of materials, such as catalytic nanoscale materials, biomolecules, and organic complexes, are studied by combining indirect detection and other one-dimensional (1D) and two-dimensional (2D) NMR techniques. Indirectly detected through-bond HETCOR spectroscopy utilizing refocused INEPT (INEPTR) mixing was developed under fast MAS (Chapter 2). The time performance of this approach in 1H detected 2D 1H{l_brace}13C{r_brace} spectra was significantly improved, by a factor of almost 10, compared to the traditional 13C detected experiments, as demonstrated by measuring naturally abundant organic-inorganic mesoporous hybrid materials. The through-bond scheme was demonstrated as a new analytical tool, which provides complementary structural information in solid-state systems in addition to through-space correlation. To further benefit the sensitivity of the INEPT transfer in rigid solids, the combined rotation and multiple-pulse spectroscopy (CRAMPS) was implemented for homonuclear 1H decoupling under fast MAS (Chapter 3). Several decoupling schemes (PMLG5m$\\bar{x}$, PMLG5mm$\\bar{x}$x and SAM3) were analyzed to maximize the performance of through-bond transfer based

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

    PubMed

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

    2015-01-01

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

  16. 2-d Finite Element Code Postprocessor

    SciTech Connect

    Sanford, L. A.; Hallquist, J. O.

    1996-07-15

    ORION is an interactive program that serves as a postprocessor for the analysis programs NIKE2D, DYNA2D, TOPAZ2D, and CHEMICAL TOPAZ2D. ORION reads binary plot files generated by the two-dimensional finite element codes currently used by the Methods Development Group at LLNL. Contour and color fringe plots of a large number of quantities may be displayed on meshes consisting of triangular and quadrilateral elements. ORION can compute strain measures, interface pressures along slide lines, reaction forces along constrained boundaries, and momentum. ORION has been applied to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

  17. 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.

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

    PubMed

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

    2014-06-14

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

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

    PubMed

    Dimock, Abigail N; Spriet, Mathieu

    2010-01-01

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

  20. 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.

  1. Generates 2D Input for DYNA NIKE & TOPAZ

    SciTech Connect

    Hallquist, J. O.; Sanford, Larry

    1996-07-15

    MAZE is an interactive program that serves as an input and two-dimensional mesh generator for DYNA2D, NIKE2D, TOPAZ2D, and CHEMICAL TOPAZ2D. MAZE also generates a basic template for ISLAND input. MAZE has been applied to the generation of input data to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

  2. MAZE96. Generates 2D Input for DYNA NIKE & TOPAZ

    SciTech Connect

    Sanford, L.; Hallquist, J.O.

    1992-02-24

    MAZE is an interactive program that serves as an input and two-dimensional mesh generator for DYNA2D, NIKE2D, TOPAZ2D, and CHEMICAL TOPAZ2D. MAZE also generates a basic template for ISLAND input. MAZE has been applied to the generation of input data to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

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

    PubMed

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

    2016-04-14

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

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

    PubMed

    Van den Heuvel, Willem; Soncini, Alessandro

    2013-02-07

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

  5. Parallel Stitching of 2D Materials.

    PubMed

    Ling, Xi; Lin, Yuxuan; Ma, Qiong; Wang, Ziqiang; Song, Yi; Yu, Lili; Huang, Shengxi; Fang, Wenjing; Zhang, Xu; Hsu, Allen L; Bie, Yaqing; Lee, Yi-Hsien; Zhu, Yimei; Wu, Lijun; Li, Ju; Jarillo-Herrero, Pablo; Dresselhaus, Mildred; Palacios, Tomás; Kong, Jing

    2016-03-23

    Diverse parallel stitched 2D heterostructures, including metal-semiconductor, semiconductor-semiconductor, and insulator-semiconductor, are synthesized directly through selective "sowing" of aromatic molecules as the seeds in the chemical vapor deposition (CVD) method. The methodology enables the large-scale fabrication of lateral heterostructures, which offers tremendous potential for its application in integrated circuits.

  6. Parallel stitching of 2D materials

    DOE PAGES

    Ling, Xi; Wu, Lijun; Lin, Yuxuan; ...

    2016-01-27

    Diverse parallel stitched 2D heterostructures, including metal–semiconductor, semiconductor–semiconductor, and insulator–semiconductor, are synthesized directly through selective “sowing” of aromatic molecules as the seeds in the chemical vapor deposition (CVD) method. Lastly, the methodology enables the large-scale fabrication of lateral heterostructures, which offers tremendous potential for its application in integrated circuits.

  7. Radiofrequency Spectroscopy and Thermodynamics of Fermi Gases in the 2D to Quasi-2D Dimensional Crossover

    NASA Astrophysics Data System (ADS)

    Cheng, Chingyun; Kangara, Jayampathi; Arakelyan, Ilya; Thomas, John

    2016-05-01

    We tune the dimensionality of a strongly interacting degenerate 6 Li Fermi gas from 2D to quasi-2D, by adjusting the radial confinement of pancake-shaped clouds to control the radial chemical potential. In the 2D regime with weak radial confinement, the measured pair binding energies are in agreement with 2D-BCS mean field theory, which predicts dimer pairing energies in the many-body regime. In the qausi-2D regime obtained with increased radial confinement, the measured pairing energy deviates significantly from 2D-BCS theory. In contrast to the pairing energy, the measured radii of the cloud profiles are not fit by 2D-BCS theory in either the 2D or quasi-2D regimes, but are fit in both regimes by a beyond mean field polaron-model of the free energy. Supported by DOE, ARO, NSF, and AFOSR.

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

    PubMed Central

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

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

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

    PubMed

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

    2015-11-17

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

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

    SciTech Connect

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

    2010-01-01

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

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

    PubMed

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

    2016-07-13

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

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

    NASA Astrophysics Data System (ADS)

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

    1992-12-01

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

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

    PubMed

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

    2015-11-11

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

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

    PubMed Central

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

    1997-01-01

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

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

    PubMed Central

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

    2004-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

  18. E-2D Advanced Hawkeye Aircraft (E-2D AHE)

    DTIC Science & Technology

    2015-12-01

    Selected Acquisition Report (SAR) RCS: DD-A&T(Q&A)823-364 E-2D Advanced Hawkeye Aircraft (E-2D AHE) As of FY 2017 President’s Budget Defense...Office Estimate RDT&E - Research, Development, Test, and Evaluation SAR - Selected Acquisition Report SCP - Service Cost Position TBD - To Be Determined

  19. Orthotropic Piezoelectricity in 2D Nanocellulose

    NASA Astrophysics Data System (ADS)

    García, Y.; Ruiz-Blanco, Yasser B.; Marrero-Ponce, Yovani; Sotomayor-Torres, C. M.

    2016-10-01

    The control of electromechanical responses within bonding regions is essential to face frontier challenges in nanotechnologies, such as molecular electronics and biotechnology. Here, we present Iβ-nanocellulose as a potentially new orthotropic 2D piezoelectric crystal. The predicted in-layer piezoelectricity is originated on a sui-generis hydrogen bonds pattern. Upon this fact and by using a combination of ab-initio and ad-hoc models, we introduce a description of electrical profiles along chemical bonds. Such developments lead to obtain a rationale for modelling the extended piezoelectric effect originated within bond scales. The order of magnitude estimated for the 2D Iβ-nanocellulose piezoelectric response, ~pm V‑1, ranks this material at the level of currently used piezoelectric energy generators and new artificial 2D designs. Such finding would be crucial for developing alternative materials to drive emerging nanotechnologies.

  20. Orthotropic Piezoelectricity in 2D Nanocellulose

    PubMed Central

    García, Y.; Ruiz-Blanco, Yasser B.; Marrero-Ponce, Yovani; Sotomayor-Torres, C. M.

    2016-01-01

    The control of electromechanical responses within bonding regions is essential to face frontier challenges in nanotechnologies, such as molecular electronics and biotechnology. Here, we present Iβ-nanocellulose as a potentially new orthotropic 2D piezoelectric crystal. The predicted in-layer piezoelectricity is originated on a sui-generis hydrogen bonds pattern. Upon this fact and by using a combination of ab-initio and ad-hoc models, we introduce a description of electrical profiles along chemical bonds. Such developments lead to obtain a rationale for modelling the extended piezoelectric effect originated within bond scales. The order of magnitude estimated for the 2D Iβ-nanocellulose piezoelectric response, ~pm V−1, ranks this material at the level of currently used piezoelectric energy generators and new artificial 2D designs. Such finding would be crucial for developing alternative materials to drive emerging nanotechnologies. PMID:27708364

  1. Orthotropic Piezoelectricity in 2D Nanocellulose.

    PubMed

    García, Y; Ruiz-Blanco, Yasser B; Marrero-Ponce, Yovani; Sotomayor-Torres, C M

    2016-10-06

    The control of electromechanical responses within bonding regions is essential to face frontier challenges in nanotechnologies, such as molecular electronics and biotechnology. Here, we present Iβ-nanocellulose as a potentially new orthotropic 2D piezoelectric crystal. The predicted in-layer piezoelectricity is originated on a sui-generis hydrogen bonds pattern. Upon this fact and by using a combination of ab-initio and ad-hoc models, we introduce a description of electrical profiles along chemical bonds. Such developments lead to obtain a rationale for modelling the extended piezoelectric effect originated within bond scales. The order of magnitude estimated for the 2D Iβ-nanocellulose piezoelectric response, ~pm V(-1), ranks this material at the level of currently used piezoelectric energy generators and new artificial 2D designs. Such finding would be crucial for developing alternative materials to drive emerging nanotechnologies.

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

    PubMed

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

    2014-04-28

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

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

    PubMed

    Raya, Jésus; Perrone, Barbara; Hirschinger, Jérôme

    2013-02-01

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

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

    NASA Astrophysics Data System (ADS)

    Raya, Jésus; Perrone, Barbara; Hirschinger, Jérôme

    2013-02-01

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

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

    PubMed

    Gersbach, P V; Reddy, N

    2002-08-01

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

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

    PubMed

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

    2016-08-07

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

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

    PubMed

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

    2008-09-15

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

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

    PubMed

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

    2016-08-31

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

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

    PubMed Central

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-08-01

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

  11. 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.

  12. Theoretical study of the C{sup -} {sup 4}S{sub 3/2}{sup o} and {sup 2}D{sub 3/2,5/2}{sup o} bound states and C ground configuration: Fine and hyperfine structures, isotope shifts, and transition probabilities

    SciTech Connect

    Carette, T.; Godefroid, M. R.

    2011-06-15

    This work is an ab initio study of the 2p{sup 3} {sup 4}S{sub 3/2}{sup o}, and {sup 2}D{sub 3/2,5/2}{sup o} states of C{sup -} and 2p{sup 2} {sup 3}P{sub 0,1,2}, {sup 1}D{sub 2}, and {sup 1}S{sub 0} states of neutral carbon. We use the multiconfiguration Hartree-Fock approach, focusing on the accuracy of the wave function itself. We obtain all C{sup -} detachment thresholds, including correlation effects to about 0.5%. Isotope shifts and hyperfine structures are calculated. The achieved accuracy of the latter is of the order of 0.1 MHz. Intraconfiguration transition probabilities are also estimated.

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

    PubMed

    Vícha, Jan; Marek, Radek; Straka, Michal

    2016-10-17

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

  14. 2D Metals by Repeated Size Reduction.

    PubMed

    Liu, Hanwen; Tang, Hao; Fang, Minghao; Si, Wenjie; Zhang, Qinghua; Huang, Zhaohui; Gu, Lin; Pan, Wei; Yao, Jie; Nan, Cewen; Wu, Hui

    2016-10-01

    A general and convenient strategy for manufacturing freestanding metal nanolayers is developed on large scale. By the simple process of repeatedly folding and calendering stacked metal sheets followed by chemical etching, free-standing 2D metal (e.g., Ag, Au, Fe, Cu, and Ni) nanosheets are obtained with thicknesses as small as 1 nm and with sizes of the order of several micrometers.

  15. WE-AB-BRA-07: Quantitative Evaluation of 2D-2D and 2D-3D Image Guided Radiation Therapy for Clinical Trial Credentialing, NRG Oncology/RTOG

    SciTech Connect

    Giaddui, T; Yu, J; Xiao, Y; Jacobs, P; Manfredi, D; Linnemann, N

    2015-06-15

    Purpose: 2D-2D kV image guided radiation therapy (IGRT) credentialing evaluation for clinical trial qualification was historically qualitative through submitting screen captures of the fusion process. However, as quantitative DICOM 2D-2D and 2D-3D image registration tools are implemented in clinical practice for better precision, especially in centers that treat patients with protons, better IGRT credentialing techniques are needed. The aim of this work is to establish methodologies for quantitatively reviewing IGRT submissions based on DICOM 2D-2D and 2D-3D image registration and to test the methodologies in reviewing 2D-2D and 2D-3D IGRT submissions for RTOG/NRG Oncology clinical trials qualifications. Methods: DICOM 2D-2D and 2D-3D automated and manual image registration have been tested using the Harmony tool in MIM software. 2D kV orthogonal portal images are fused with the reference digital reconstructed radiographs (DRR) in the 2D-2D registration while the 2D portal images are fused with DICOM planning CT image in the 2D-3D registration. The Harmony tool allows alignment of the two images used in the registration process and also calculates the required shifts. Shifts calculated using MIM are compared with those submitted by institutions for IGRT credentialing. Reported shifts are considered to be acceptable if differences are less than 3mm. Results: Several tests have been performed on the 2D-2D and 2D-3D registration. The results indicated good agreement between submitted and calculated shifts. A workflow for reviewing these IGRT submissions has been developed and will eventually be used to review IGRT submissions. Conclusion: The IROC Philadelphia RTQA center has developed and tested a new workflow for reviewing DICOM 2D-2D and 2D-3D IGRT credentialing submissions made by different cancer clinical centers, especially proton centers. NRG Center for Innovation in Radiation Oncology (CIRO) and IROC RTQA center continue their collaborative efforts to enhance

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

    SciTech Connect

    Kanematsu, Yusuke; Tachikawa, Masanori

    2014-04-28

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

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

    PubMed

    Kiralj, Rudolf; Ferreira, Márcia M C

    2008-07-10

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

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

    PubMed

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

    2010-10-14

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

  19. A constraint-based assignment system for automating long side chain assignments in protein 2D NMR spectra

    SciTech Connect

    Leishman, S.; Gray, P.; Fothergill, J.E.

    1995-12-31

    The sequential assignment of protein 2D NMR data has been tackled by many automated and semi-automated systems. One area that these systems have not tackled is the searching of the TOCSY spectrum looking for cross peaks and chemical shift values for hydrogen nuclei that are at the end of long side chains. This paper describes our system for solving this problem using constraint logic programming and compares our constraint satisfaction algorithm to a standard backtracking version.

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

    PubMed

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

    2009-02-01

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

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

    PubMed

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

    2005-02-15

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

  2. 1H and 13C NMR chemical shift assignments of spiro-cycloalkylidenehomo- and methanofullerenes by the DFT-GIAO method.

    PubMed

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

    2011-06-01

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

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

    PubMed

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

    2016-02-01

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

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

    USGS Publications Warehouse

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1996-09-01

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

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

    PubMed

    Toy, Mehmet; Tanak, Hasan

    2016-01-05

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

  7. 13C-detected NMR experiments for measuring chemical shifts and coupling constants in nucleic acid bases.

    PubMed

    Fiala, Radovan; Sklenár, Vladimír

    2007-10-01

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

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

    PubMed

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

    2007-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    PubMed

    Jose, K V Jovan; Raghavachari, Krishnan

    2017-03-14

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

  11. Optoelectronics with 2D semiconductors

    NASA Astrophysics Data System (ADS)

    Mueller, Thomas

    2015-03-01

    Two-dimensional (2D) atomic crystals, such as graphene and layered transition-metal dichalcogenides, are currently receiving a lot of attention for applications in electronics and optoelectronics. In this talk, I will review our research activities on electrically driven light emission, photovoltaic energy conversion and photodetection in 2D semiconductors. In particular, WSe2 monolayer p-n junctions formed by electrostatic doping using a pair of split gate electrodes, type-II heterojunctions based on MoS2/WSe2 and MoS2/phosphorene van der Waals stacks, 2D multi-junction solar cells, and 3D/2D semiconductor interfaces will be presented. Upon optical illumination, conversion of light into electrical energy occurs in these devices. If an electrical current is driven, efficient electroluminescence is obtained. I will present measurements of the electrical characteristics, the optical properties, and the gate voltage dependence of the device response. In the second part of my talk, I will discuss photoconductivity studies of MoS2 field-effect transistors. We identify photovoltaic and photoconductive effects, which both show strong photoconductive gain. A model will be presented that reproduces our experimental findings, such as the dependence on optical power and gate voltage. We envision that the efficient photon conversion and light emission, combined with the advantages of 2D semiconductors, such as flexibility, high mechanical stability and low costs of production, could lead to new optoelectronic technologies.

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

    PubMed Central

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Yamaki, Daisuke; Hada, Masahiko

    2012-12-01

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

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

    PubMed

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

    2016-01-11

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

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

    PubMed

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

    2016-02-01

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

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

    PubMed

    Kuo, M C; Gibbons, W A

    1979-12-25

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

  17. Recent advances in 2D materials for photocatalysis.

    PubMed

    Luo, Bin; Liu, Gang; Wang, Lianzhou

    2016-04-07

    Two-dimensional (2D) materials have attracted increasing attention for photocatalytic applications because of their unique thickness dependent physical and chemical properties. This review gives a brief overview of the recent developments concerning the chemical synthesis and structural design of 2D materials at the nanoscale and their applications in photocatalytic areas. In particular, recent progress on the emerging strategies for tailoring 2D material-based photocatalysts to improve their photo-activity including elemental doping, heterostructure design and functional architecture assembly is discussed.

  18. Noninvasive deep Raman detection with 2D correlation analysis

    NASA Astrophysics Data System (ADS)

    Kim, Hyung Min; Park, Hyo Sun; Cho, Youngho; Jin, Seung Min; Lee, Kang Taek; Jung, Young Mee; Suh, Yung Doug

    2014-07-01

    The detection of poisonous chemicals enclosed in daily necessaries is prerequisite essential for homeland security with the increasing threat of terrorism. For the detection of toxic chemicals, we combined a sensitive deep Raman spectroscopic method with 2D correlation analysis. We obtained the Raman spectra from concealed chemicals employing spatially offset Raman spectroscopy in which incident line-shaped light experiences multiple scatterings before being delivered to inner component and yielding deep Raman signal. Furthermore, we restored the pure Raman spectrum of each component using 2D correlation spectroscopic analysis with chemical inspection. Using this method, we could elucidate subsurface component under thick powder and packed contents in a bottle.

  19. Highly crystalline 2D superconductors

    NASA Astrophysics Data System (ADS)

    Saito, Yu; Nojima, Tsutomu; Iwasa, Yoshihiro

    2016-12-01

    Recent advances in materials fabrication have enabled the manufacturing of ordered 2D electron systems, such as heterogeneous interfaces, atomic layers grown by molecular beam epitaxy, exfoliated thin flakes and field-effect devices. These 2D electron systems are highly crystalline, and some of them, despite their single-layer thickness, exhibit a sheet resistance more than an order of magnitude lower than that of conventional amorphous or granular thin films. In this Review, we explore recent developments in the field of highly crystalline 2D superconductors and highlight the unprecedented physical properties of these systems. In particular, we explore the quantum metallic state (or possible metallic ground state), the quantum Griffiths phase observed in out-of-plane magnetic fields and the superconducting state maintained in anomalously large in-plane magnetic fields. These phenomena are examined in the context of weakened disorder and/or broken spatial inversion symmetry. We conclude with a discussion of how these unconventional properties make highly crystalline 2D systems promising platforms for the exploration of new quantum physics and high-temperature superconductors.

  20. Extensions of 2D gravity

    SciTech Connect

    Sevrin, A.

    1993-06-01

    After reviewing some aspects of gravity in two dimensions, I show that non-trivial embeddings of sl(2) in a semi-simple (super) Lie algebra give rise to a very large class of extensions of 2D gravity. The induced action is constructed as a gauged WZW model and an exact expression for the effective action is given.

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

    PubMed

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

    2011-06-09

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

  2. Exploring the use of Generalized Indirect Covariance to reconstruct pure shift NMR spectra: Current Pros and Cons

    NASA Astrophysics Data System (ADS)

    Fredi, André; Nolis, Pau; Cobas, Carlos; Martin, Gary E.; Parella, Teodor

    2016-05-01

    The current Pros and Cons of a processing protocol to generate pure chemical shift NMR spectra using Generalized Indirect Covariance are presented and discussed. The transformation of any standard 2D homonuclear and heteronuclear spectrum to its pure shift counterpart by using a reference DIAG spectrum is described. Reconstructed pure shift NMR spectra of NOESY, HSQC, HSQC-TOCSY and HSQMBC experiments are reported for the target molecule strychnine.

  3. Exploring the use of Generalized Indirect Covariance to reconstruct pure shift NMR spectra: Current Pros and Cons.

    PubMed

    Fredi, André; Nolis, Pau; Cobas, Carlos; Martin, Gary E; Parella, Teodor

    2016-05-01

    The current Pros and Cons of a processing protocol to generate pure chemical shift NMR spectra using Generalized Indirect Covariance are presented and discussed. The transformation of any standard 2D homonuclear and heteronuclear spectrum to its pure shift counterpart by using a reference DIAG spectrum is described. Reconstructed pure shift NMR spectra of NOESY, HSQC, HSQC-TOCSY and HSQMBC experiments are reported for the target molecule strychnine.

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

    PubMed

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

    2014-04-21

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

  5. Metrology for graphene and 2D materials

    NASA Astrophysics Data System (ADS)

    Pollard, Andrew J.

    2016-09-01

    The application of graphene, a one atom-thick honeycomb lattice of carbon atoms with superlative properties, such as electrical conductivity, thermal conductivity and strength, has already shown that it can be used to benefit metrology itself as a new quantum standard for resistance. However, there are many application areas where graphene and other 2D materials, such as molybdenum disulphide (MoS2) and hexagonal boron nitride (h-BN), may be disruptive, areas such as flexible electronics, nanocomposites, sensing and energy storage. Applying metrology to the area of graphene is now critical to enable the new, emerging global graphene commercial world and bridge the gap between academia and industry. Measurement capabilities and expertise in a wide range of scientific areas are required to address this challenge. The combined and complementary approach of varied characterisation methods for structural, chemical, electrical and other properties, will allow the real-world issues of commercialising graphene and other 2D materials to be addressed. Here, examples of metrology challenges that have been overcome through a multi-technique or new approach are discussed. Firstly, the structural characterisation of defects in both graphene and MoS2 via Raman spectroscopy is described, and how nanoscale mapping of vacancy defects in graphene is also possible using tip-enhanced Raman spectroscopy (TERS). Furthermore, the chemical characterisation and removal of polymer residue on chemical vapour deposition (CVD) grown graphene via secondary ion mass spectrometry (SIMS) is detailed, as well as the chemical characterisation of iron films used to grow large domain single-layer h-BN through CVD growth, revealing how contamination of the substrate itself plays a role in the resulting h-BN layer. In addition, the role of international standardisation in this area is described, outlining the current work ongoing in both the International Organization of Standardization (ISO) and the

  6. 1H NMR spectra of alcohols and diols in chloroform: DFT/GIAO calculation of chemical shifts.

    PubMed

    Lomas, John S

    2014-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Kleinpeter, Erich; Klaumünzer, Ute

    2014-09-01

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

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

    PubMed Central

    Grayev, Allison; Reeder, Scott; Hanna, Amgad

    2016-01-01

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

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

    SciTech Connect

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

    1991-08-01

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

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

    NASA Astrophysics Data System (ADS)

    Czernek, Jiří; Brus, Jiří

    2014-07-01

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

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

    PubMed

    Smith, David C

    2005-08-01

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

  13. Recent developments in 2D layered inorganic nanomaterials for sensing

    NASA Astrophysics Data System (ADS)

    Kannan, Padmanathan Karthick; Late, Dattatray J.; Morgan, Hywel; Rout, Chandra Sekhar

    2015-08-01

    Two dimensional layered inorganic nanomaterials (2D-LINs) have recently attracted huge interest because of their unique thickness dependent physical and chemical properties and potential technological applications. The properties of these layered materials can be tuned via both physical and chemical processes. Some 2D layered inorganic nanomaterials like MoS2, WS2 and SnS2 have been recently developed and employed in various applications, including new sensors because of their layer-dependent electrical properties. This article presents a comprehensive overview of recent developments in the application of 2D layered inorganic nanomaterials as sensors. Some of the salient features of 2D materials for different sensing applications are discussed, including gas sensing, electrochemical sensing, SERS and biosensing, SERS sensing and photodetection. The working principles of the sensors are also discussed together with examples.

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

    PubMed

    Mananga, Eugene Stephane

    2013-01-01

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

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

    PubMed

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

    2015-10-14

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

  16. 1H, 15N, and 13C chemical shift assignments of cyanobacteriochrome NpR6012g4 in the red-absorbing dark state.

    PubMed

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

    2016-04-01

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

  17. 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

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

    PubMed

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

    2015-08-07

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

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

    PubMed

    Lomas, John S

    2016-01-01

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

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

    PubMed

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

    2010-12-01

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

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

    PubMed

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

    2016-02-01

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

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

    PubMed Central

    Liu, Yizhou

    2010-01-01

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

  3. Aristoxazole analogues. Conversion of 8-nitro-1-naphthoic acid to 2-methylnaphtho[1,2-d]oxazole-9-carboxylic acid: comments on the chemical mechanism of formation of DNA adducts by the aristolochic acids.

    PubMed

    Priestap, Horacio A; Barbieri, Manuel A; Johnson, Francis

    2012-07-27

    2-Methylnaphtho[1,2-d]oxazole-9-carboxylic acid was obtained by reduction of 8-nitro-1-naphthoic acid with zinc-acetic acid. This naphthoxazole is a condensation product between an 8-nitro-1-naphthoic acid reduction intermediate and acetic acid and is a lower homologue of aristoxazole, a similar condensation product of aristolochic acid I with acetic acid that was previously reported. Both oxazoles are believed to arise via a common nitrenium/carbocation ion mechanism that is likely related to that which leads to aristolochic acid-DNA-adducts.

  4. Analysis of pyruvylated beta-carrageenan by 2D NMR spectroscopy and reductive partial hydrolysis.

    PubMed

    Falshaw, Ruth; Furneaux, Richard H; Wong, Herbert

    2003-06-23

    A polysaccharide rich in 4',6'-O-(1-carboxyethylidene)-substituted (i.e., pyruvylated) beta-carrageenan has been prepared by solvolytic desulfation of a polysaccharide containing predominantly pyruvylated alpha-carrageenan, which was extracted from the red seaweed, Callophycus tridentifer. The 13C and 1H NMR chemical shifts of pyruvylated beta-carrageenan have been fully assigned using 2D NMR spectroscopic techniques. The 4',6'-O-(1-methoxycarbonylethylidene) group, generated during chemical methylation of the polysaccharide, has been shown to survive under the conditions of acidic hydrolysis that cleave the 3,6-anhydro-alpha-D-galactosidic bonds in permethylated samples of both pyruvylated beta- and pyruvylated alpha-carrageenans. As a result, two novel pyruvylated carrabiitol derivatives have been prepared.

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

    NASA Astrophysics Data System (ADS)

    Kozawa, Takahiro

    2015-01-01

    In chemically amplified resists used for high-volume production of semiconductor devices, the control of acid catalytic reaction is essential for fine patterning. A basic compound, called a quencher, plays an important role in the control of acid catalytic reaction. In particular, the photodecomposable quencher is effective for the enhancement of the chemical gradient. In this study, the effects of photodecomposable quenchers on the dose shift (the deviation from the sizing dose) dependences of line width, line edge roughness (LER), and stochastic defect generation were investigated, assuming line-and-space patterns with 11 nm half-pitch. The exposure latitude of line width in a chemically amplified resist with photodecomposable quenchers was larger than that in a chemically amplified resist with conventional non-photodecomposable quenchers at sizing doses >20 mJ cm-2. By using photodecomposable quenchers, LER and the probability of stochastic defect generation were decreased, while the dose shift dependences of LER and stochastic defect generation did not significantly differ, compared with those observed using conventional non-photodecomposable quenchers.

  6. Calculation of the {sup 13}C NMR chemical shift of ether linkages in lignin derived geopolymers: Constraints on the preservation of lignin primary structure with diagenesis

    SciTech Connect

    Cody, G.D.; Saghi-Szabo, G.

    1999-01-01

    Methodology for the calculation of {sup 13}C NMR shielding on molecular organic fragments, representative of monomers in a type 3 kerogen, is presented. Geometry optimization of each molecular fragment was carried out using Density Functional Theory employing the generalized gradient approximation. NMR shieldings were calculated using the Individual Gauge for Localized orbital Method. Convincing agreement was obtained between calculated and experimentally derived isotropic chemical shielding values over a broad frequency range. Shielding calculations employing the localized orbitals/local origin method resulted in nearly identical results. NMR chemical shift static powder patterns also exhibit excellent agreement with experimental values. These quantum mechanical calculations were applied to determine the extent of lignin primary structure preservation with diagenesis. Specifically, the calculations were used to assess whether inhomogeneous spectral broadening due to both functional group variation and local configurational variability may inhibit the detection of otherwise significant quantities of alkyl-aryl ethers in lignin derived geopolymers. Determination of the chemical-shielding tensor principle axis values reveals a strong correlation between anisotropy and asymmetry with local configuration effects such as dihedral rotation, phenyl group rotation, and bond angle variation. These results indicate that a range of 9 ppm in the isotropic chemical shift can be ascribed to local configuration. Consequently, an upper limit of 5% alkyl-aryl-linkages may go undetected using NMR spectroscopy on lignin-derived geopolymers at the liginite-sub-bituminous transition. It is concluded that the primary structure of lignin does not persist in kerogens even at relatively low thermal maturities.

  7. Calculation of the 13C NMR chemical shift of ether linkages in lignin derived geopolymers: . Constraints on the preservation of lignin primary structure with diagenesis

    NASA Astrophysics Data System (ADS)

    Cody, G. D.; Sághi-Szabó, G.

    1999-01-01

    Methodology for the calculation of 13C NMR shieldings on molecular organic fragments, representative of monomers in a type III kerogen, is presented. Geometry optimization of each molecular fragment was carried out using Density Functional Theory employing the generalized gradient approximation. NMR shieldings were calculated using the Individual Gauge for Localized Orbital Method. Convincing agreement was obtained between calculated and experimentally derived isotropic chemical shielding values over a broad frequency range. Shielding calculations employing the localized orbitals/local origin method resulted in nearly identical results. NMR chemical shift static powder patterns also exhibit excellent agreement with experimental values. These quantum mechanical calculations were applied to determine the extent of lignin primary structure preservation with diagenesis. Specifically, the calculations were used to assess whether inhomogeneous spectral broadening due to both functional group variation and local configurational variability may inhibit the detection of otherwise significant quantities of alkyl-aryl ethers in lignin derived geopolymers. Determination of the chemical-shielding tensor principle axis values reveals a strong correlation between anisotropy and asymmetry with local configuration effects such as dihedral rotation, phenyl group rotation, and bond angle variation. These results indicate that a range of 9 ppm in the isotropic chemical shift can be ascribed to local configuration. Consequently, an upper limit of 5% alkyl-aryl-linkages may go undetected using NMR spectroscopy on lignin-derived geopolymers at the liginite-sub-bituminous transition. It is concluded that the primary structure of lignin does not persist in kerogens even at relatively low thermal maturities.

  8. 2D quasiperiodic plasmonic crystals

    PubMed Central

    Bauer, Christina; Kobiela, Georg; Giessen, Harald

    2012-01-01

    Nanophotonic structures with irregular symmetry, such as quasiperiodic plasmonic crystals, have gained an increasing amount of attention, in particular as potential candidates to enhance the absorption of solar cells in an angular insensitive fashion. To examine the photonic bandstructure of such systems that determines their optical properties, it is necessary to measure and model normal and oblique light interaction with plasmonic crystals. We determine the different propagation vectors and consider the interaction of all possible waveguide modes and particle plasmons in a 2D metallic photonic quasicrystal, in conjunction with the dispersion relations of a slab waveguide. Using a Fano model, we calculate the optical properties for normal and inclined light incidence. Comparing measurements of a quasiperiodic lattice to the modelled spectra for angle of incidence variation in both azimuthal and polar direction of the sample gives excellent agreement and confirms the predictive power of our model. PMID:23209871

  9. Valleytronics in 2D materials

    NASA Astrophysics Data System (ADS)

    Schaibley, John R.; Yu, Hongyi; Clark, Genevieve; Rivera, Pasqual; Ross, Jason S.; Seyler, Kyle L.; Yao, Wang; Xu, Xiaodong

    2016-11-01

    Semiconductor technology is currently based on the manipulation of electronic charge; however, electrons have additional degrees of freedom, such as spin and valley, that can be used to encode and process information. Over the past several decades, there has been significant progress in manipulating electron spin for semiconductor spintronic devices, motivated by potential spin-based information processing and storage applications. However, experimental progress towards manipulating the valley degree of freedom for potential valleytronic devices has been limited until very recently. We review the latest advances in valleytronics, which have largely been enabled by the isolation of 2D materials (such as graphene and semiconducting transition metal dichalcogenides) that host an easily accessible electronic valley degree of freedom, allowing for dynamic control.

  10. Unparticle example in 2D.

    PubMed

    Georgi, Howard; Kats, Yevgeny

    2008-09-26

    We discuss what can be learned about unparticle physics by studying simple quantum field theories in one space and one time dimension. We argue that the exactly soluble 2D theory of a massless fermion coupled to a massive vector boson, the Sommerfield model, is an interesting analog of a Banks-Zaks model, approaching a free theory at high energies and a scale-invariant theory with nontrivial anomalous dimensions at low energies. We construct a toy standard model coupling to the fermions in the Sommerfield model and study how the transition from unparticle behavior at low energies to free particle behavior at high energies manifests itself in interactions with the toy standard model particles.

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

    PubMed

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

    2015-08-03

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

  12. In Situ Solid-State Reactions Monitored by X-ray Absorption Spectroscopy: Temperature-Induced Proton Transfer Leads to Chemical Shifts.

    PubMed

    Stevens, Joanna S; Walczak, Monika; Jaye, Cherno; Fischer, Daniel A

    2016-10-24

    The dramatic colour and phase alteration with the solid-state, temperature-dependent reaction between squaric acid and 4,4'-bipyridine has been probed in situ with X-ray absorption spectroscopy. The electronic and chemical sensitivity to the local atomic environment through chemical shifts in the near-edge X-ray absorption fine structure (NEXAFS) revealed proton transfer from the acid to the bipyridine base through the change in nitrogen protonation state in the high-temperature form. Direct detection of proton transfer coupled with structural analysis elucidates the nature of the solid-state process, with intermolecular proton transfer occurring along an acid-base chain followed by a domino effect to the subsequent acid-base chains, leading to the rapid migration along the length of the crystal. NEXAFS thereby conveys the ability to monitor the nature of solid-state chemical reactions in situ, without the need for a priori information or long-range order.

  13. Quantum coherence selective 2D Raman–2D electronic spectroscopy

    PubMed Central

    Spencer, Austin P.; Hutson, William O.; Harel, Elad

    2017-01-01

    Electronic and vibrational correlations report on the dynamics and structure of molecular species, yet revealing these correlations experimentally has proved extremely challenging. Here, we demonstrate a method that probes correlations between states within the vibrational and electronic manifold with quantum coherence selectivity. Specifically, we measure a fully coherent four-dimensional spectrum which simultaneously encodes vibrational–vibrational, electronic–vibrational and electronic–electronic interactions. By combining near-impulsive resonant and non-resonant excitation, the desired fifth-order signal of a complex organic molecule in solution is measured free of unwanted lower-order contamination. A critical feature of this method is electronic and vibrational frequency resolution, enabling isolation and assignment of individual quantum coherence pathways. The vibronic structure of the system is then revealed within an otherwise broad and featureless 2D electronic spectrum. This method is suited for studying elusive quantum effects in which electronic transitions strongly couple to phonons and vibrations, such as energy transfer in photosynthetic pigment–protein complexes. PMID:28281541

  14. Quantum coherence selective 2D Raman-2D electronic spectroscopy

    NASA Astrophysics Data System (ADS)

    Spencer, Austin P.; Hutson, William O.; Harel, Elad

    2017-03-01

    Electronic and vibrational correlations report on the dynamics and structure of molecular species, yet revealing these correlations experimentally has proved extremely challenging. Here, we demonstrate a method that probes correlations between states within the vibrational and electronic manifold with quantum coherence selectivity. Specifically, we measure a fully coherent four-dimensional spectrum which simultaneously encodes vibrational-vibrational, electronic-vibrational and electronic-electronic interactions. By combining near-impulsive resonant and non-resonant excitation, the desired fifth-order signal of a complex organic molecule in solution is measured free of unwanted lower-order contamination. A critical feature of this method is electronic and vibrational frequency resolution, enabling isolation and assignment of individual quantum coherence pathways. The vibronic structure of the system is then revealed within an otherwise broad and featureless 2D electronic spectrum. This method is suited for studying elusive quantum effects in which electronic transitions strongly couple to phonons and vibrations, such as energy transfer in photosynthetic pigment-protein complexes.

  15. Quantum coherence selective 2D Raman-2D electronic spectroscopy.

    PubMed

    Spencer, Austin P; Hutson, William O; Harel, Elad

    2017-03-10

    Electronic and vibrational correlations report on the dynamics and structure of molecular species, yet revealing these correlations experimentally has proved extremely challenging. Here, we demonstrate a method that probes correlations between states within the vibrational and electronic manifold with quantum coherence selectivity. Specifically, we measure a fully coherent four-dimensional spectrum which simultaneously encodes vibrational-vibrational, electronic-vibrational and electronic-electronic interactions. By combining near-impulsive resonant and non-resonant excitation, the desired fifth-order signal of a complex organic molecule in solution is measured free of unwanted lower-order contamination. A critical feature of this method is electronic and vibrational frequency resolution, enabling isolation and assignment of individual quantum coherence pathways. The vibronic structure of the system is then revealed within an otherwise broad and featureless 2D electronic spectrum. This method is suited for studying elusive quantum effects in which electronic transitions strongly couple to phonons and vibrations, such as energy transfer in photosynthetic pigment-protein complexes.

  16. An Alternative Scheme for 13C Chemical-Shift Imaging via Inverse Detection of Protons through an MILS (or Inverse SLIM) Technique

    PubMed

    Lee; Tzou; Chiou; Yeung

    1998-01-01

    An alternative scheme in acquiring 13C spectroscopic images using inverse detection via polarization transfer through protons was proposed and experimentally verified by a phantom using a heteronuclear multiple-quantum coherence technique. This scheme has some features that, in special circumstances, can be exploited to one's advantages. These features are: (1) signal enhancement, a feat realizable under favorable conditions; (2) spectroscopic encoding via constant time; and (3) improvement of the time efficiency of the constant-time method via optimization by singular-value decomposition analysis. Features (1) and (2) can, in some cases, yield better sensitivity than the conventional 3DFT technique without sacrificing the most important attribute of 13C, the enormity of the chemical shifts. Such is the case because spectroscopic images acquired by the technique proposed are based on the chemical shifts of carbon, in contrast to the other more prevalent inverse-detection schemes. Feature (2) can also offer higher spatial resolution by shifting the emphasis of signal encoding from a spectral-resolution-first viewpoint to one that favors spatial resolution. Feature (3) was adopted from a method previously known as MILS (metabolite imaging of lines in a spectrum), or the inverse of SLIM, an economical scheme originally proposed by Hu et al. (1988, Magn. Reson. Med. 8, 314) for obtaining a compartmentalized NMR spectrum. Copyright 1998 Academic Press. Copyright 1998 Academic Press

  17. Experimental validation of equations for 2D DIC uncertainty quantification.

    SciTech Connect

    Reu, Phillip L.; Miller, Timothy J.

    2010-03-01

    Uncertainty quantification (UQ) equations have been derived for predicting matching uncertainty in two-dimensional image correlation a priori. These equations include terms that represent the image noise and image contrast. Researchers at the University of South Carolina have extended previous 1D work to calculate matching errors in 2D. These 2D equations have been coded into a Sandia National Laboratories UQ software package to predict the uncertainty for DIC images. This paper presents those equations and the resulting error surfaces for trial speckle images. Comparison of the UQ results with experimentally subpixel-shifted images is also discussed.

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

  19. Transport-induced shifts in condensate dew-point and composition in multicomponent systems with chemical reaction

    NASA Technical Reports Server (NTRS)

    Rosner, D. E.; Nagarajan, R.

    1985-01-01

    Partial heterogeneous condensation phenomena in multicomponent reacting systems are analyzed taking into consideration the chemical element transport phenomena. It is demonstrated that the dew-point surface temperature in chemically reactive systems is not a purely thermodynamic quantity, but is influenced by the multicomponent diffusion and Soret-mass diffusion phenomena. Several distinct dew-points are shown to exist in such systems and, as a result of transport constraints, the 'sharp' locus between two chemically distinct condensates is systematically moved to a difference mainstream composition.

  20. 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.

  1. Shift of optical absorption edge in SnO2 films with high concentrations of nitrogen grown by chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Jiang, Jie; Lu, Yinmei; Meyer, Bruno K.; Hofmann, Detlev M.; Eickhoff, Martin

    2016-06-01

    The optical and electrical properties of n-type SnO2 films with high concentrations of nitrogen (SnO2:N) grown by chemical vapor deposition are studied. The carrier concentration increases from 4.1 × 1018 to 3.9 × 1019 cm-3 and the absorption edge shifts from 4.26 to 4.08 eV with increasing NH3 flow rate. Typical Urbach tails were observed from the absorption spectra and the Urbach energy increases from 0.321 to 0.526 eV with increasing NH3 flow rate. An "effective" absorption edge of about 4.61 eV was obtained for all investigated samples from fitting the extrapolations of the Urbach tails. Burstein-Moss effect, electron-impurity, and electron-electron interactions are shown to play a minor role for the shift of the absorption edges in SnO2:N thin films.

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

    PubMed Central

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

    2009-01-01

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

  3. ORION96. 2-d Finite Element Code Postprocessor

    SciTech Connect

    Sanford, L.A.; Hallquist, J.O.

    1992-02-02

    ORION is an interactive program that serves as a postprocessor for the analysis programs NIKE2D, DYNA2D, TOPAZ2D, and CHEMICAL TOPAZ2D. ORION reads binary plot files generated by the two-dimensional finite element codes currently used by the Methods Development Group at LLNL. Contour and color fringe plots of a large number of quantities may be displayed on meshes consisting of triangular and quadrilateral elements. ORION can compute strain measures, interface pressures along slide lines, reaction forces along constrained boundaries, and momentum. ORION has been applied to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

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

    NASA Astrophysics Data System (ADS)

    Smith, David C.

    2005-08-01

    The "RAMANITA ©" method, for semi-quantitative chemical analysis of mineral solid-solutions by multidimensional calibration of Raman wavenumber shifts and mathematical calculation by simultaneous equations, is published here in detail in English for the first time. It was conceived by the present writer 20 years ago for binary and ternary pyroxene and garnet systems. The mathematical description was set out in 1989, but in an abstract in an obscure French special publication. Detailed "step-by-step" calibration of two garnet ternaries, followed by their linking, by M. Pinet and D.C. Smith in the early 1990s provided a hexary garnet database. Much later, using this garnet database, which forms part of his personal database called RAMANITA ©, the present writer began to develop the method by improving the terminology, automating the calculations, discussing problems and experimenting with different real chemical problems in archaeometry. Although this RAMANITA © method has been very briefly mentioned in two recent books, the necessary full mathematical explanation is given only here. The method will find application in any study which requires obtaining a non-destructive semi-quantitative chemical analysis from mineral solid solutions that cannot be analysed by any destructive analytical method, in particular for archaeological, geological or extraterrestrial research projects, e.g. from gemstones or other crystalline artworks of the cultural heritage (especially by Mobile Raman Microscopy (MRM)) in situ in museums or at archaeological sites, including under water for subaquatic archaeometry; from scientifically precious mineral microinclusions (such as garnet or pyroxene within diamond); from minerals in rocks analysed in situ on planetary bodies by a rover (especially "at distance" by telescopy). Recently some other workers have begun deducing chemical compositions from Raman wavenumber shifts in multivariate chemical space, but the philosophical approach is

  5. Collisions of slow polyatomic ions with surfaces: dissociation and chemical reactions of C2H2+*, C2H3+, C2H4+*, C2H5+, and their deuterated variants C2D2+* and C2D4+* on room-temperature and heated carbon surfaces.

    PubMed

    Jasík, Juraj; Zabka, Jan; Feketeova, Linda; Ipolyi, Imre; Märk, Tilmann D; Herman, Zdenek

    2005-11-17

    Interaction of C2Hn+ (n = 2-5) hydrocarbon ions and some of their isotopic variants with room-temperature and heated (600 degrees C) highly oriented pyrolytic graphite (HOPG) surfaces was investigated over the range of incident energies 11-46 eV and an incident angle of 60 degrees with respect to the surface normal. The work is an extension of our earlier research on surface interactions of CHn+ (n = 3-5) ions. Mass spectra, translational energy distributions, and angular distributions of product ions were measured. Collisions with the HOPG surface heated to 600 degrees C showed only partial or substantial dissociation of the projectile ions; translational energy distributions of the product ions peaked at about 50% of the incident energy. Interactions with the HOPG surface at room temperature showed both surface-induced dissociation of the projectiles and, in the case of radical cation projectiles C2H2+* and C2H4+*, chemical reactions with the hydrocarbons on the surface. These reactions were (i) H-atom transfer to the projectile, formation of protonated projectiles, and their subsequent fragmentation and (ii) formation of a carbon chain build-up product in reactions of the projectile ion with a terminal CH3-group of the surface hydrocarbons and subsequent fragmentation of the product ion to C3H3+. The product ions were formed in inelastic collisions in which the translational energy of the surface-excited projectile peaked at about 32% of the incident energy. Angular distributions of reaction products showed peaking at subspecular angles close to 68 degrees (heated surfaces) and 72 degrees (room-temperature surfaces). The absolute survival probability at the incident angle of 60 degrees was about 0.1% for C2H2+*, close to 1% for C2H4+* and C2H5+, and about 3-6% for C2H3+.

  6. 1H and 13C NMR Chemical Shift Assignments and Conformational Analysis for the Two Diastereomers of the Vitamin K Epoxide Reductase Inhibitor Brodifacoum

    SciTech Connect

    Cort, John R.; Cho, Herman M.

    2009-10-01

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

  7. Available information in 2D motional Stark effect imaging.

    PubMed

    Creese, Mathew; Howard, John

    2010-10-01

    Recent advances in imaging techniques have allowed the extension of the standard polarimetric 1D motional Stark effect (MSE) diagnostic to 2D imaging of the internal magnetic field of fusion devices [J. Howard, Plasma Phys. Controlled Fusion 50, 125003 (2008)]. This development is met with the challenge of identifying and extracting the new information, which can then be used to increase the accuracy of plasma equilibrium and current density profile determinations. This paper develops a 2D analysis of the projected MSE polarization orientation and Doppler phase shift. It is found that, for a standard viewing position, the 2D MSE imaging system captures sufficient information to allow imaging of the internal vertical magnetic field component B(Z)(r,z) in a tokamak.

  8. 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.

  9. Solvatochromic shift of donor-acceptor substituted bithiophene in solvents of different polarity: quantum chemical and molecular dynamics simulations.

    PubMed

    Meng, Suci; Ma, Jing

    2008-04-10

    The dependence of excitation energies of the solvatochromic dye, 5-dimethylamino-5'-nitro-2,2'-bithiophene (Me(2)N-2T-NO(2)) on the solvent polarity is demonstrated by time-dependent density functional theory (TD-DFT) calculations in combination with molecular dynamics (MD) simulations. Three kinds of solvation models, namely, the continuum dielectric model, the discrete approach, and the combined discrete/continuum strategy, are employed to calculate the lowest dipole-allowed excitation energies of Me(2)N-2T-NO(2) in seven solvents with the dielectric constant, epsilon, ranging from 2.23 to 111.00. Our calculations demonstrate the limitations of the continuum dielectric model in predicting the solvatochromic shift of Me(2)N-2T-NO(2) in very polar solvents with epsilon > 35. The accuracy of the explicit solvent model is largely limited by the size of supermolecular cluster. The combined discrete/continuum solvent model gives a satisfactory description of the bathochromic shift of Me(2)N-2T-NO(2) with increasing solvent polarity, in agreement with the experimental observations.

  10. 2D Hybrid Nanostructured Dirac Materials for Broadband Transparent Electrodes.

    PubMed

    Guo, Yunfan; Lin, Li; Zhao, Shuli; Deng, Bing; Chen, Hongliang; Ma, Bangjun; Wu, Jinxiong; Yin, Jianbo; Liu, Zhongfan; Peng, Hailin

    2015-08-05

    Broadband transparent electrodes based on 2D hybrid nanostructured Dirac materials between Bi2 Se3 and graphene are synthesized using a chemical vapor deposition (CVD) method. Bi2 Se3 nanoplates are preferentially grown along graphene grain boundaries as "smart" conductive patches to bridge the graphene boundary. These hybrid films increase by one- to threefold in conductivity while remaining highly transparent over broadband wavelength. They also display outstanding chemical stability and mechanical flexibility.

  11. Preliminary results of determination of chemical changes on Lingzhi or Reishi medicinal mushroom, Ganoderma lucidum (W.Curt.:Fr.)P. Karst. (higher Basidiomycetes) carried by Shenzhou I spaceship with FTIR and 2D-IR correlation spectroscopy.

    PubMed

    Choong, Yew Keong; Chen, Xiangdong; Jamal, Jamia Azdina; Wang, Qiuying; Lan, Jin

    2012-01-01

    Spaceflight represents a complex environmental condition. Space mutagenesis breeding has achieved marked results over the years. The objective of this study is to determine the chemical changes in medicinal mushroom Ganoderma lucidum cultivated after spaceflight in 1999. Fourier transform infrared (FTIR) and two-dimensional infrared (2DIR) correlation spectroscopy were used in analysis. The sample Sx and its control Cx showed the least dissimilarities in one-dimensional FTIR spectra, but absorbance of Sx is twice as high as Cx. Sx presented a clear peak at 1648 cm in 2nd derivative spectra, which could not be detected in the Cx. The 2DIR spectra showed the intensity of Sx in the range 1800-1400 cm-1 for protein is higher than the control. The sample Sx produced some carbohydrate peaks in the area of 889 cm-1 compared with the Cx. The spaceflight set up an extreme condition and caused changes of chemical properties in G. lucidum strain.

  12. Evaluation of a rabbit model for osteomyelitis by high field, high resolution imaging using the chemical-shift-specific-slice-selection technique.

    PubMed

    Volk, A; Crémieux, A C; Belmatoug, N; Vallois, J M; Pocidalo, J J; Carbon, C

    1994-01-01

    The rabbit model of osteomyelitis introduced by C.W. Norden, based on injection of an infecting solution (Staphylococcus aureus, sodium morrhuate) into the tibia, was studied at 4.7 Tesla with a time-efficient chemical shift selective imaging technique, Chemical Shift Specific Slice Selection (C4S). The evolution of the disease over several weeks was followed on water-selective, fat-selective, and sum images obtained simultaneously with this imaging sequence. Experiments were performed either on different groups of rabbits at different times after infection with subsequent sacrifice of the animal and microbiological analysis of the infected tibia or on the same group of animals imaged several times after infection. Associated analysis of the water and fat selective images revealed marrow modifications very early (Day 5 after inoculation) demonstrating the high sensitivity of the employed imaging technique. Later on, bone modifications were best identified on the sum images. Additional experiments performed on animals injected with a noninfecting solution containing only sodium morrhuate showed however that the sclerosing agent alone can yield images similar to those produced by infection at early stages after inoculation. Therefore, the Norden model would not be suitable for monitoring quantitatively outcome of therapy by magnetic resonance imaging. It is however well adapted for the evaluation and optimization of MRI techniques or protocols intended to detect early changes of bone marrow produced by septic or aseptic infarct.

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

    PubMed

    Goudarzi, Nasser

    2016-04-05

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

  14. Triosephosphate isomerase: 15N and 13C chemical shift assignments and conformational change upon ligand binding by magic-angle spinning solid-state NMR spectroscopy.

    PubMed

    Xu, Yimin; Lorieau, Justin; McDermott, Ann E

    2010-03-19

    Microcrystalline uniformly (13)C,(15)N-enriched yeast triosephosphate isomerase (TIM) is sequentially assigned by high-resolution solid-state NMR (SSNMR). Assignments are based on intraresidue and interresidue correlations, using dipolar polarization transfer methods, and guided by solution NMR assignments of the same protein. We obtained information on most of the active-site residues involved in chemistry, including some that were not reported in a previous solution NMR study, such as the side-chain carbons of His95. Chemical shift differences comparing the microcrystalline environment to the aqueous environment appear to be mainly due to crystal packing interactions. Site-specific perturbations of the enzyme's chemical shifts upon ligand binding are studied by SSNMR for the first time. These changes monitor proteinwide conformational adjustment upon ligand binding, including many of the sites probed by solution NMR and X-ray studies. Changes in Gln119, Ala163, and Gly210 were observed in our SSNMR studies, but were not reported in solution NMR studies (chicken or yeast). These studies identify a number of new sites with particularly clear markers for ligand binding, paving the way for future studies of triosephosphate isomerase dynamics and mechanism.

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

    PubMed

    Torii, Hajime

    2016-09-15

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

  16. Understanding Chemical versus Electrostatic Shifts in X-ray Photoelectron Spectra of Organic Self-Assembled Monolayers

    PubMed Central

    2016-01-01

    The focus of the present article is on understanding the insight that X-ray photoelectron spectroscopy (XPS) measurements can provide when studying self-assembled monolayers. Comparing density functional theory calculations to experimental data on deliberately chosen model systems, we show that both the chemical environment and electrostatic effects arising from a superposition of molecular dipoles influence the measured core-level binding energies to a significant degree. The crucial role of the often overlooked electrostatic effects in polar self-assembled monolayers (SAMs) is unambiguously demonstrated by changing the dipole density through varying the SAM coverage. As a consequence of this effect, care has to be taken when extracting chemical information from the XP spectra of ordered organic adsorbate layers. Our results, furthermore, imply that XPS is a powerful tool for probing local variations in the electrostatic energy in nanoscopic systems, especially in SAMs. PMID:26937264

  17. Final Technical Report: A Paradigm Shift in Chemical Processing: New Sustainable Chemistries for Low-VOC Coatings

    SciTech Connect

    Smith, Kenneth F.

    2006-07-26

    The project employed new processes to make emulsion polymers from reduced levels of petroleum-derived chemical feedstocks. Most waterborne paints contain spherical, emulsion polymer particles that serve as the film-forming binder phase. Our goal was to make emulsion polymer particles containing 30 percent feedstock that would function as effectively as commercial emulsions made from higher level feedstock. The processes developed yielded particles maintained their film formation capability and binding capacity while preserving the structural integrity of the particles after film formation. Rohm and Haas Company (ROH) and Archer Daniels Midland Company (ADM) worked together to employ novel polymer binders (ROH) and new, non-volatile, biomass-derived coalescing agents (ADM). The University of Minnesota Department of Chemical Engineering and Material Science utilized its unique microscopy capabilities to characterize films made from the New Emulsion Polymers (NEP).

  18. NKG2D ligands as therapeutic targets

    PubMed Central

    Spear, Paul; Wu, Ming-Ru; Sentman, Marie-Louise; Sentman, Charles L.

    2013-01-01

    The Natural Killer Group 2D (NKG2D) receptor plays an important role in protecting the host from infections and cancer. By recognizing ligands induced on infected or tumor cells, NKG2D modulates lymphocyte activation and promotes immunity to eliminate ligand-expressing cells. Because these ligands are not widely expressed on healthy adult tissue, NKG2D ligands may present a useful target for immunotherapeutic approaches in cancer. Novel therapies targeting NKG2D ligands for the treatment of cancer have shown preclinical success and are poised to enter into clinical trials. In this review, the NKG2D receptor and its ligands are discussed in the context of cancer, infection, and autoimmunity. In addition, therapies targeting NKG2D ligands in cancer are also reviewed. PMID:23833565

  19. Theoretical investigations of the γ- gauche effect on the 13C chemical shifts produced by oxygen atoms at the γ position by quantum chemistry calculations

    NASA Astrophysics Data System (ADS)

    Suzuki, Shinji; Horii, Fumitaka; Kurosu, Hiromichi

    2009-02-01

    The γ- gauche effect on 13C chemical shifts that is produced by the O atoms located at the γ positions has been evaluated by quantum chemistry calculations based on the GAIO-CHF procedure. The γ- gauche effects produced by the O and Cl atoms in n-propanol and n-propyl chloride are found to be, respectively, +1.4 and -0.7 ppm, whereas that due to the C atom in n-butane is -3.0 ppm in good agreement of the values previously calculated. The apparent cause of such a difference in the γ- gauche effect is mainly relatively higher shielding of the CH 3 carbon in the trans conformation for the n-propanol and n-propyl chloride. Extending the n-propanol chain at both ends causes no significant change in the γ- gauche effect produced by the O atom. In 2-butanol and 2-methyl-2-butanol as examples of secondarily and tertiarily substituted compounds, the γ- gauche effects produced by the γ-OH groups are estimated to be -7 to -9 ppm. In addition, the γ- gauche effect due to the C atom is found to increase in n-butane, secondary, and tertiary butanols in this order. The γ- gauche effect produced by the O atom in hydroxyethylcyclohexane is as negligibly small as -0.7 ppm, whereas that produced by the C atom in ethylcyclohexane is about -5 ppm. These results suggest that the γ- gauche effect, including downfield shift, produced by the O atom in a compound greatly depends on its chemical structure, whereas upfield shifts of -3 to -7 ppm are induced in all examined compounds as the γ- gauche effect due to the C atom.

  20. Sculpting 3D spatial selectivity with pairs of 2D pulses: A comparison of methods

    NASA Astrophysics Data System (ADS)

    Farkash, Gil; Dumez, Jean-Nicolas; Frydman, Lucio

    2016-12-01

    Enhancing the specificity of the spins' excitation can improve the capabilities of magnetic resonance. Exciting voxels with tailored 3D shapes reduces partial volume effects and enhances contrast, particularly in cases where cubic voxels or other simple geometries do not provide an optimal localization. Spatial excitation profiles of arbitrary shapes can be implemented using so-called multidimensional RF pulses, which are often limited in practice to 2D implementations owing to their sensitivity to field inhomogeneities. Recent work has shown the potential of spatio-temporally encoded (SPEN) pulses towards alleviating these constraints. In particular, 2D pulses operating in a so-called hybrid scheme where the "low-bandwidth" spatial dimension is sculpted by a SPEN strategy while an orthogonal axis is shaped by regular k-space encoding, have been shown resilient to chemical shift and B0 field inhomogeneities. In this work we explore the use of pairs of 2D pulses, with one of these addressing geometries in the x-y plane and the other in the x-z dimension, to sculpt complex 3D volumes in phantoms and in vivo. To overcome limitations caused by the RF discretization demanded by these 2D pulses, a number of "unfolding" techniques yielding images from the centerband RF excitation while deleting sideband contributions - even in cases where center- and side-bands severely overlap - were developed. Thus it was possible to increase the gradient strengths applied along the low bandwidth dimensions, significantly improving the robustness of this kind of 3D sculpting pulses. Comparisons against conventional pulses designed on the basis of pure k-space trajectories, are presented.

  1. An open canvas--2D materials with defects, disorder, and functionality.

    PubMed

    Zou, Xiaolong; Yakobson, Boris I

    2015-01-20

    CONSPECTUS: While some exceptional properties are unique to graphene only (its signature Dirac-cone gapless dispersion, carrier mobility, record strength), other features are common to other two-dimensional materials. The broader family "beyond graphene" offers greater choices to be explored and tailored for various applications. Transition metal dichalcogenides (TMDCs), hexagonal boron nitride (h-BN), and 2D layers of pure elements, like phosphorus or boron, can complement or even surpass graphene in many ways and uses, ranging from electronics and optoelectronics to catalysis and energy storage. Their availability greatly relies on chemical vapor deposition growth of large samples, which are highly polycrystalline and include interfaces such as edges, heterostructures, and grain boundaries, as well as dislocations and point defects. These imperfections do not always degrade the material properties, but they often bring new physics and even useful functionality. It turns particularly interesting in combination with the sheer openness of all 2D sheets, fully exposed to the environment, which, as we show herein, can change and tune the defect structures and consequently all their qualities, from electronic levels, conductivity, magnetism, and optics to structural mobility of dislocations and catalytic activities. In this Account, we review our progress in understanding of various defects. We begin by expressing the energy of an arbitrary graphene edge analytically, so that the environment is regarded by "chemical phase shift". This has profound implications for graphene and carbon nanotube growth. Generalization of this equation to heteroelemental BN gives a method to determine the energy for arbitrary edges of BN, depending on the partial chemical potentials. This facilitates the tuning of the morphology and electronic and magnetic properties of pure BN or hybrid BN|C systems. Applying a similar method to three-atomic-layer TMDCs reveals more diverse edge

  2. In vivo 1D and 2D correlation MR spectroscopy of the soleus muscle at 7T

    NASA Astrophysics Data System (ADS)

    Ramadan, Saadallah; Ratai, Eva-Maria; Wald, Lawrence L.; Mountford, Carolyn E.

    2010-05-01

    AimThis study aims to (1) undertake and analyse 1D and 2D MR correlation spectroscopy from human soleus muscle in vivo at 7T, and (2) determine T1 and T2 relaxation time constants at 7T field strength due to their importance in sequence design and spectral quantitation. MethodSix healthy, male volunteers were consented and scanned on a 7T whole-body scanner (Siemens AG, Erlangen, Germany). Experiments were undertaken using a 28 cm diameter detunable birdcage coil for signal excitation and an 8.5 cm diameter surface coil for signal reception. The relaxation time constants, T1 and T2 were recorded using a STEAM sequence, using the 'progressive saturation' method for the T1 and multiple echo times for T2. The 2D L-Correlated SpectroscopY (L-COSY) method was employed with 64 increments (0.4 ms increment size) and eight averages per scan, with a total time of 17 min. ResultsT1 and T2 values for the metabolites of interest were determined. The L-COSY spectra obtained from the soleus muscle provided information on lipid content and chemical structure not available, in vivo, at lower field strengths. All molecular fragments within multiple lipid compartments were chemically shifted by 0.20-0.26 ppm at this field strength. 1D and 2D L-COSY spectra were assigned and proton connectivities were confirmed with the 2D method. ConclusionIn vivo 1D and 2D spectroscopic examination of muscle can be successfully recorded at 7T and is now available to assess lipid alterations as well as other metabolites present with disease. T1 and T2 values were also determined in soleus muscle of male healthy volunteers.

  3. Chemical potential shift and gap-state formation in SrTiO{sub 3−δ} revealed by photoemission spectroscopy

    SciTech Connect

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

    2014-08-07

    In this study, we report on investigations of the electronic structure of SrTiO{sub 3} annealed at temperature ranging between 550 and 840 °C in an ultrahigh vacuum. Annealing induced oxygen vacancies (O{sub vac}) impart considerable changes in the electronic structure of SrTiO{sub 3}. Using core-level photoemission spectroscopy, we have studied the chemical potential shift (Δμ) as a function of annealing temperature. The result shows that the chemical potential monotonously increases with electron doping in SrTiO{sub 3−δ}. The monotonous increase of the chemical potential rules out the existence of electronic phase separation in the sample. Using valence band photoemission, we have demonstrated the formation of a low density of states at the near Fermi level electronic spectrum of SrTiO{sub 3−δ}. The gap-states were observed by spectral weight transfer over a large energy scale of the stoichiometric band gap of SrTiO{sub 3} system leading finally to an insulator-metal transition. We have interpreted our results from the point of structural distortions induced by oxygen vacancies.

  4. Mapping of the C3d ligand binding site on complement receptor 2 (CR2/CD21) using nuclear magnetic resonance and chemical shift analysis.

    PubMed

    Kovacs, James M; Hannan, Jonathan P; Eisenmesser, Elan Z; Holers, V Michael

    2009-04-03

    Complement receptor 2 (CR2, CD21) is a cell membrane protein, with 15 or 16 extracellular short consensus repeats (SCRs), that promotes B lymphocyte responses and bridges innate and acquired immunity. The most distally located SCRs (SCR1-2) mediate the interaction of CR2 with its four known ligands (C3d, Epstein-Barr virus gp350, interferon-alpha, and CD23). Inhibitory monoclonal antibodies against SCR1-2 block binding of all ligands. To develop ligand-specific inhibitors that would also assist in identifying residues unique to each receptor-ligand interaction, phage were selected from randomly generated libraries by panning with recombinant SCR1-2, followed by specific ligand-driven elution. Derived peptides were tested by competition ELISA. One peptide, C3dp1 (APQHLSSQYSRT) exhibited ligand-specific inhibition at midmicromolar IC(50). C3d was titrated into (15)N-labeled SCR1-2, which revealed chemical shift changes indicative of specific intermolecular interactions. With backbone assignments made, the chemical shift changes were mapped onto the crystal structure of SCR1-2. With regard to C3d, the binding surface includes regions of SCR1, SCR2, and the inter-SCR linker, specifically residues Arg(13), Tyr(16), Arg(28), Tyr(29), Ser(32), Thr(34), Lys(48), Asp(56), Lys(57), Tyr(68), Arg(83), Gly(84), Asn(101), Asn(105), and Ser(109). SCR1 and SCR2 demonstrated distinct binding modes. The CR2 binding surface incorporating SCR1 is inconsistent with a previous x-ray CR2-C3d co-crystal analysis but consistent with mutagenesis, x-ray neutron scattering, and inhibitory monoclonal antibody epitope mapping. Titration with C3dp1 yielded chemical shift changes (Arg(13), Tyr(16), Thr(34), Lys(48), Asp(56), Lys(57), Tyr(68), Arg(83), Gly(84), Asn(105), and Ser(109)) overlapping with C3d, indicating that C3dp1 interacts at the same CR2 site as C3d.

  5. Quantitative 2D liquid-state NMR.

    PubMed

    Giraudeau, Patrick

    2014-06-01

    Two-dimensional (2D) liquid-state NMR has a very high potential to simultaneously determine the absolute concentration of small molecules in complex mixtures, thanks to its capacity to separate overlapping resonances. However, it suffers from two main drawbacks that probably explain its relatively late development. First, the 2D NMR signal is strongly molecule-dependent and site-dependent; second, the long duration of 2D NMR experiments prevents its general use for high-throughput quantitative applications and affects its quantitative performance. Fortunately, the last 10 years has witnessed an increasing number of contributions where quantitative approaches based on 2D NMR were developed and applied to solve real analytical issues. This review aims at presenting these recent efforts to reach a high trueness and precision in quantitative measurements by 2D NMR. After highlighting the interest of 2D NMR for quantitative analysis, the different strategies to determine the absolute concentrations from 2D NMR spectra are described and illustrated by recent applications. The last part of the manuscript concerns the recent development of fast quantitative 2D NMR approaches, aiming at reducing the experiment duration while preserving - or even increasing - the analytical performance. We hope that this comprehensive review will help readers to apprehend the current landscape of quantitative 2D NMR, as well as the perspectives that may arise from it.

  6. IUPAP Award: Ion transport in 2D materials

    NASA Astrophysics Data System (ADS)

    Bao, Wenzhong

    Intercalation in 2D materials drastically influences both physical and chemical properties, which leads to a new degree of freedom for fundamental studies and expands the potential applications of 2D materials. In this talk, I will discuss our work in the past two years related to ion intercalation of 2D materials, including insertion of Li and Na ions in graphene and MoS2. We focused on both fundamental mechanism and potential application, e.g. we measured in-situ optical transmittance spectra and electrical transport properties of few-layer graphene (FLG) nanostructures upon electrochemical lithiation/delithiation. By observing a simultaneous increase of both optical transmittance and DC conductivity, strikingly different from other materials, we proposed its application as a next generation transparent electrode.

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

    PubMed

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

    2006-06-01

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

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

    PubMed

    Dracínský, Martin; Kaminský, Jakub; Bour, Petr

    2009-03-07

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

  9. 1H chemical shift imaging of the brain in guanidino methyltransferase deficiency, a creatine deficiency syndrome; guanidinoacetate accumulation in the gray matter.

    PubMed

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

    2005-09-01

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

  10. Structural elucidation of dioxa-cage compounds from tetrahydroisobenzofuran-1(3H)-one: analysis of NMR data and GIAO chemical shifts calculations.

    PubMed

    da Costa Resende, Gabriela; Alvarenga, Elson Santiago

    2016-12-01

    The polycyclic compounds, especially the dioxa-cages, have attracted considerable attention in recent years. In our work, a series of 9β-substituted 3-oxo-4,11-dioxatetracyclo[5.2.1.1(5,8) .0(2,6) ]undecane compounds were unexpectedly isolated during bromination, chlorination and epoxidation reactions of the 3-hydroxy-3a,4,7,7a-tetrahydro-4,7-methanoisobenzofuran-1(3H)-one. After careful analysis of the NMR data, the chemical shifts of the isolated and the expected products were predicted by theoretical calculations using density functional theory and gauge including atomic orbitals. The best correlation between calculated and experimental data was evaluated by comparing mean absolute errors and applying DP4 probability methodology. Results from both approaches indicated a correct structural elucidation. Copyright © 2016 John Wiley & Sons, Ltd.

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

    PubMed

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

    2015-09-21

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

  12. Constant-time 2D and 3D through-bond correlation NMR spectroscopy of solids under 60 kHz MAS

    SciTech Connect

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy

    2016-01-21

    Establishing connectivity and proximity of nuclei is an important step in elucidating the structure and dynamics of molecules in solids using magic angle spinning (MAS) NMR spectroscopy. Although recent studies have successfully demonstrated the feasibility of proton-detected multidimensional solid-state NMR experiments under ultrafast-MAS frequencies and obtaining high-resolution spectral lines of protons, assignment of proton resonances is a major challenge. In this study, we first re-visit and demonstrate the feasibility of 2D constant-time uniform-sign cross-peak correlation (CTUC-COSY) NMR experiment on rigid solids under ultrafast-MAS conditions, where the sensitivity of the experiment is enhanced by the reduced spin-spin relaxation rate and the use of low radio-frequency power for heteronuclear decoupling during the evolution intervals of the pulse sequence. In addition, we experimentally demonstrate the performance of a proton-detected pulse sequence to obtain a 3D {sup 1}H/{sup 13}C/{sup 1}H chemical shift correlation spectrum by incorporating an additional cross-polarization period in the CTUC-COSY pulse sequence to enable proton chemical shift evolution and proton detection in the incrementable t{sub 1} and t{sub 3} periods, respectively. In addition to through-space and through-bond {sup 13}C/{sup 1}H and {sup 13}C/{sup 13}C chemical shift correlations, the 3D {sup 1}H/{sup 13}C/{sup 1}H experiment also provides a COSY-type {sup 1}H/{sup 1}H chemical shift correlation spectrum, where only the chemical shifts of those protons, which are bonded to two neighboring carbons, are correlated. By extracting 2D F1/F3 slices ({sup 1}H/{sup 1}H chemical shift correlation spectrum) at different {sup 13}C chemical shift frequencies from the 3D {sup 1}H/{sup 13}C/{sup 1}H spectrum, resonances of proton atoms located close to a specific carbon atom can be identified. Overall, the through-bond and through-space homonuclear/heteronuclear proximities determined from the

  13. Constant-time 2D and 3D through-bond correlation NMR spectroscopy of solids under 60 kHz MAS

    PubMed Central

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy

    2016-01-01

    Establishing connectivity and proximity of nuclei is an important step in elucidating the structure and dynamics of molecules in solids using magic angle spinning (MAS) NMR spectroscopy. Although recent studies have successfully demonstrated the feasibility of proton-detected multidimensional solid-state NMR experiments under ultrafast-MAS frequencies and obtaining high-resolution spectral lines of protons, assignment of proton resonances is a major challenge. In this study, we first re-visit and demonstrate the feasibility of 2D constant-time uniform-sign cross-peak correlation (CTUC-COSY) NMR experiment on rigid solids under ultrafast-MAS conditions, where the sensitivity of the experiment is enhanced by the reduced spin-spin relaxation rate and the use of low radio-frequency power for heteronuclear decoupling during the evolution intervals of the pulse sequence. In addition, we experimentally demonstrate the performance of a proton-detected pulse sequence to obtain a 3D 1H/13C/1H chemical shift correlation spectrum by incorporating an additional cross-polarization period in the CTUC-COSY pulse sequence to enable proton chemical shift evolution and proton detection in the incrementable t1 and t3 periods, respectively. In addition to through-space and through-bond 13C/1H and 13C/13C chemical shift correlations, the 3D 1H/13C/1H experiment also provides a COSY-type 1H/1H chemical shift correlation spectrum, where only the chemical shifts of those protons, which are bonded to two neighboring carbons, are correlated. By extracting 2D F1/F3 slices (1H/1H chemical shift correlation spectrum) at different 13C chemical shift frequencies from the 3D 1H/13C/1H spectrum, resonances of proton atoms located close to a specific carbon atom can be identified. Overall, the through-bond and through-space homonuclear/heteronuclear proximities determined from the 3D 1H/13C/1H experiment would be useful to study the structure and dynamics of a variety of chemical and biological

  14. Annotated Bibliography of EDGE2D Use

    SciTech Connect

    J.D. Strachan and G. Corrigan

    2005-06-24

    This annotated bibliography is intended to help EDGE2D users, and particularly new users, find existing published literature that has used EDGE2D. Our idea is that a person can find existing studies which may relate to his intended use, as well as gain ideas about other possible applications by scanning the attached tables.

  15. Staring 2-D hadamard transform spectral imager

    DOEpatents

    Gentry, Stephen M.; Wehlburg, Christine M.; Wehlburg, Joseph C.; Smith, Mark W.; Smith, Jody L.

    2006-02-07

    A staring imaging system inputs a 2D spatial image containing multi-frequency spectral information. This image is encoded in one dimension of the image with a cyclic Hadamarid S-matrix. The resulting image is detecting with a spatial 2D detector; and a computer applies a Hadamard transform to recover the encoded image.

  16. 2D nanomaterials based electrochemical biosensors for cancer diagnosis.

    PubMed

    Wang, Lu; Xiong, Qirong; Xiao, Fei; Duan, Hongwei

    2017-03-15

    Cancer is a leading cause of death in the world. Increasing evidence has demonstrated that early diagnosis holds the key towards effective treatment outcome. Cancer biomarkers are extensively used in oncology for cancer diagnosis and prognosis. Electrochemical sensors play key roles in current laboratory and clinical analysis of diverse chemical and biological targets. Recent development of functional nanomaterials offers new possibilities of improving the performance of electrochemical sensors. In particular, 2D nanomaterials have stimulated intense research due to their unique array of structural and chemical properties. The 2D materials of interest cover broadly across graphene, graphene derivatives (i.e., graphene oxide and reduced graphene oxide), and graphene-like nanomaterials (i.e., 2D layered transition metal dichalcogenides, graphite carbon nitride and boron nitride nanomaterials). In this review, we summarize recent advances in the synthesis of 2D nanomaterials and their applications in electrochemical biosensing of cancer biomarkers (nucleic acids, proteins and some small molecules), and present a personal perspective on the future direction of this area.

  17. 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.

  18. An unequal cross-over event within the CYP2D gene cluster generates a chimeric CYP2D7/CYP2D6 gene which is associated with the poor metabolizer phenotype.

    PubMed Central

    Panserat, S; Mura, C; Gérard, N; Vincent-Viry, M; Galteau, M M; Jacoz-Aigrain, E; Krishnamoorthy, R

    1995-01-01

    1. The study of the CYP2D genotype and phenotype of a Caucasian family revealed that a XbaI-9 kb allele was associated with the poor metabolizer phenotype. 2. A Polymerase Chain Reaction (PCR)-based assay showed that the previously described mutations D6A and D6B are not associated with the XbaI-9 kb allele. 3. To explore the molecular basis of the poor metabolizer phenotype associated with the XbaI-9 kb allele, complete sequencing of the nine exons and intron-exon boundaries of the CYP2D6 gene was undertaken after amplification by PCR. 4. All the exons were successfully amplified using CYP2D6 gene-specific primers except exon 1 which required a combination of CYP2D7 gene-specific 5' primer and a CYP2D6 gene-specific 3' primer. 5. Sequence data derived from this amplified product revealed that the XbaI-9 kb allele corresponds to a novel rearrangement of the locus. This involved a deletion of an approximately 20 kilobase (kb) DNA segment generating a hybrid 5' CYP2D7/CYP2D6 3' gene. 6. The chimeric gene is non-functional presumably due to an insertion in exon 1 (characteristic of the exon 1 of the CYP2D7 gene) which causes a shift in the reading frame with premature termination of translation. Images Figure 1 Figure 2 Figure 4 PMID:8554938

  19. An Intercomparison of 2-D Models Within a Common Framework

    NASA Technical Reports Server (NTRS)

    Weisenstein, Debra K.; Ko, Malcolm K. W.; Scott, Courtney J.; Jackman, Charles H.; Fleming, Eric L.; Considine, David B.; Kinnison, Douglas E.; Connell, Peter S.; Rotman, Douglas A.; Bhartia, P. K. (Technical Monitor)

    2002-01-01

    A model intercomparison among the Atmospheric and Environmental Research (AER) 2-D model, the Goddard Space Flight Center (GSFC) 2-D model, and the Lawrence Livermore National Laboratory 2-D model allows us to separate differences due to model transport from those due to the model's chemical formulation. This is accomplished by constructing two hybrid models incorporating the transport parameters of the GSFC and LLNL models within the AER model framework. By comparing the results from the native models (AER and e.g. GSFC) with those from the hybrid model (e.g. AER chemistry with GSFC transport), differences due to chemistry and transport can be identified. For the analysis, we examined an inert tracer whose emission pattern is based on emission from a High Speed Civil Transport (HSCT) fleet; distributions of trace species in the 2015 atmosphere; and the response of stratospheric ozone to an HSCT fleet. Differences in NO(y) in the upper stratosphere are found between models with identical transport, implying different model representations of atmospheric chemical processes. The response of O3 concentration to HSCT aircraft emissions differs in the models from both transport-dominated differences in the HSCT-induced perturbations of H2O and NO(y) as well as from differences in the model represent at ions of O3 chemical processes. The model formulations of cold polar processes are found to be the most significant factor in creating large differences in the calculated ozone perturbations

  20. Experimental validation of 2-D generalized geometric super resolved approach

    NASA Astrophysics Data System (ADS)

    Borkowski, Amikam; Zalevsky, Zeev; Cohen, Nadav; Hadas, Zadok; Marom, Emanuel; Javidi, Bahram

    2014-01-01

    In this paper, we generalize the method of using a 2-D moving binary random mask to overcome the geometrical resolution limitation of an imaging sensor. The spatial blurring is caused by the size of the imaging sensor pixels which yield insufficient spatial sampling. The mask is placed in an intermediate image plane and can be shifted in any direction while keeping the sensor as well as all other optical components fixed. Out of the set of images that are captured and registered, a high resolution image can be composed. In addition, this proposed approach reduces the amount of required computations and it has an improved robustness to spatial noise.

  1. Towards functional assembly of 3D and 2D nanomaterials

    NASA Astrophysics Data System (ADS)

    Jacobs, Christopher B.; Wang, Kai; Ievlev, Anton V.; Muckley, Eric S.; Ivanov, Ilia N.

    2016-09-01

    Functional assemblies of materials can be realized by tuning the work function and band gap of nanomaterials by rational material selection and design. Here we demonstrate the structural assembly of 2D and 3D nanomaterials and show that layering a 2D material monolayer on a 3D metal oxide leads to substantial alteration of both the surface potential and optical properties of the 3D material. A 40 nm thick film of polycrystalline NiO was produced by room temperature rf-sputtering, resulting in a 3D nanoparticle assembly. Chemical vapor deposition (CVD) grown 10-30 μm WS2 flakes (2D material) were placed on the NiO surface using a PDMS stamp transfer technique. The 2D/3D WS2/NiO assembly was characterized using confocal micro Raman spectroscopy to evaluate the vibrational properties and using Kelvin probe force microscopy (KPFM) to evaluate the surface potential. Raman maps of the 2D/3D assembly show spatial non-uniformity of the A1g mode ( 418 cm-1) and the disorder-enhanced longitudinal acoustic mode, 2LA(M) ( 350 cm-1), suggesting that the WS2 exists in a strained condition on when transferred onto 3D polycrystalline NiO. KPFM measurements show that single layer WS2 on SiO2 has a surface potential 75 mV lower than that of SiO2, whereas the surface potential of WS2 on NiO is 15 mV higher than NiO, indicating that WS2 could act as electron donor or acceptor depending on the 3D material it is interfaced with. Thus 2D and 3D materials can be organized into functional assemblies with electron flow controlled by the WS2 either as the electron donor or acceptor.

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

    NASA Astrophysics Data System (ADS)

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

    2000-12-01

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

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

    PubMed

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

    2011-12-01

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

  4. Matrix models of 2d gravity

    SciTech Connect

    Ginsparg, P.

    1991-01-01

    These are introductory lectures for a general audience that give an overview of the subject of matrix models and their application to random surfaces, 2d gravity, and string theory. They are intentionally 1.5 years out of date.

  5. Matrix models of 2d gravity

    SciTech Connect

    Ginsparg, P.

    1991-12-31

    These are introductory lectures for a general audience that give an overview of the subject of matrix models and their application to random surfaces, 2d gravity, and string theory. They are intentionally 1.5 years out of date.

  6. Brittle damage models in DYNA2D

    SciTech Connect

    Faux, D.R.

    1997-09-01

    DYNA2D is an explicit Lagrangian finite element code used to model dynamic events where stress wave interactions influence the overall response of the system. DYNA2D is often used to model penetration problems involving ductile-to-ductile impacts; however, with the advent of the use of ceramics in the armor-anti-armor community and the need to model damage to laser optics components, good brittle damage models are now needed in DYNA2D. This report will detail the implementation of four brittle damage models in DYNA2D, three scalar damage models and one tensor damage model. These new brittle damage models are then used to predict experimental results from three distinctly different glass damage problems.

  7. 2D/3D switchable displays

    NASA Astrophysics Data System (ADS)

    Dekker, T.; de Zwart, S. T.; Willemsen, O. H.; Hiddink, M. G. H.; IJzerman, W. L.

    2006-02-01

    A prerequisite for a wide market acceptance of 3D displays is the ability to switch between 3D and full resolution 2D. In this paper we present a robust and cost effective concept for an auto-stereoscopic switchable 2D/3D display. The display is based on an LCD panel, equipped with switchable LC-filled lenticular lenses. We will discuss 3D image quality, with the focus on display uniformity. We show that slanting the lenticulars in combination with a good lens design can minimize non-uniformities in our 20" 2D/3D monitors. Furthermore, we introduce fractional viewing systems as a very robust concept to further improve uniformity in the case slanting the lenticulars and optimizing the lens design are not sufficient. We will discuss measurements and numerical simulations of the key optical characteristics of this display. Finally, we discuss 2D image quality, the switching characteristics and the residual lens effect.

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

    PubMed

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

    2011-04-30

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

  9. High resolution spectroscopy and chemical shift imaging of hyperpolarized 129Xe dissolved in the human brain in vivo at 1.5 tesla

    PubMed Central

    Rao, Madhwesha; Stewart, Neil J.; Norquay, Graham; Griffiths, Paul D.

    2016-01-01

    Purpose Upon inhalation, xenon diffuses into the bloodstream and is transported to the brain, where it dissolves in various compartments of the brain. Although up to five chemically distinct peaks have been previously observed in 129Xe rat head spectra, to date only three peaks have been reported in the human head. This study demonstrates high resolution spectroscopy and chemical shift imaging (CSI) of 129Xe dissolved in the human head at 1.5 Tesla. Methods A 129Xe radiofrequency coil was built in‐house and 129Xe gas was polarized using spin‐exchange optical pumping. Following the inhalation of 129Xe gas, NMR spectroscopy was performed with spectral resolution of 0.033 ppm. Two‐dimensional CSI in all three anatomical planes was performed with spectral resolution of 2.1 ppm and voxel size 20 mm × 20 mm. Results Spectra of hyperpolarized 129Xe dissolved in the human head showed five distinct peaks at 188 ppm, 192 ppm, 196 ppm, 200 ppm, and 217 ppm. Assignment of these peaks was consistent with earlier studies. Conclusion High resolution spectroscopy and CSI of hyperpolarized 129Xe dissolved in the human head has been demonstrated. For the first time, five distinct NMR peaks have been observed in 129Xe spectra from the human head in vivo. Magn Reson Med 75:2227–2234, 2016. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. PMID:27080441

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

    PubMed

    Hashemi, Majid

    2015-12-05

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

  11. Accurate Measurements of Multiple-Bond 13C- 1H Coupling Constants from Phase-Sensitive 2D INEPT Spectra

    NASA Astrophysics Data System (ADS)

    Ding, Keyang

    1999-10-01

    Measurements of multiple-bond 13C-1H coupling constants are of great interest for the assignment of nonprotonated 13C resonances and the elucidation of molecular conformation in solution. Usually, the heteronuclear multiple-bond coupling constants were measured either by the JCH splittings mostly in selective 2D spectra or in 3D spectra, which are time consuming, or by the cross peak intensity analysis in 2D quantitative heteronuclear J correlation spectra (1994, G. Zhu, A. Renwick, and A. Bax, J. Magn. Reson. A 110, 257; 1994, A. Bax, G. W. Vuister, S. Grzesiek, F. Delaglio, A. C. Wang, R. Tschudin, and G. Zhu, Methods Enzymol. 239, 79.), which suffer from the accuracy problem caused by the signal-to-noise ratio and the nonpure absorptive peak patterns. Concerted incrementation of the duration for developing proton antiphase magnetization with respect to carbon-13 and the evolution time for proton chemical shift in different steps in a modified INEPT pulse sequence provides a new method for accurate measurements of heteronuclear multiple-bond coupling constants in a single 2D experiment.

  12. 129Xe NMR chemical shift in Xe@C60 calculated at experimental conditions: essential role of the relativity, dynamics, and explicit solvent.

    PubMed

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

    2013-08-15

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

  13. ¹³C solid-state NMR analysis of the most common pharmaceutical excipients used in solid drug formulations, Part I: Chemical shifts assignment.

    PubMed

    Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika Agnieszka; Szeleszczuk, Łukasz; Wawer, Iwona

    2016-04-15

    Solid-state NMR is an excellent and useful method for analyzing solid-state forms of drugs. In the (13)C CP/MAS NMR spectra of the solid dosage forms many of the signals originate from the excipients and should be distinguished from those of active pharmaceutical ingredient (API). In this work the most common pharmaceutical excipients used in the solid drug formulations: anhydrous α-lactose, α-lactose monohydrate, mannitol, sucrose, sorbitol, sodium starch glycolate type A and B, starch of different origin, microcrystalline cellulose, hypromellose, ethylcellulose, methylcellulose, hydroxyethylcellulose, sodium alginate, magnesium stearate, sodium laurilsulfate and Kollidon(®) were analyzed. Their (13)C CP/MAS NMR spectra were recorded and the signals were assigned, employing the results (R(2): 0.948-0.998) of GIPAW calculations and theoretical chemical shifts. The (13)C ssNMR spectra for some of the studied excipients have not been published before while for the other signals in the spectra they were not properly assigned or the assignments were not correct. The results summarize and complement the data on the (13)C ssNMR analysis of the most common pharmaceutical excipients and are essential for further NMR studies of API-excipient interactions in the pharmaceutical formulations.

  14. Linear-scaling method for calculating nuclear magnetic resonance chemical shifts using gauge-including atomic orbitals within Hartree-Fock and density-functional theory.

    PubMed

    Kussmann, Jörg; Ochsenfeld, Christian

    2007-08-07

    Details of a new density matrix-based formulation for calculating nuclear magnetic resonance chemical shifts at both Hartree-Fock and density functional theory levels are presented. For systems with a nonvanishing highest occupied molecular orbital-lowest unoccupied molecular orbital gap, the method allows us to reduce the asymptotic scaling order of the computational effort from cubic to linear, so that molecular systems with 1000 and more atoms can be tackled with today's computers. The key feature is a reformulation of the coupled-perturbed self-consistent field (CPSCF) theory in terms of the one-particle density matrix (D-CPSCF), which avoids entirely the use of canonical MOs. By means of a direct solution for the required perturbed density matrices and the adaptation of linear-scaling integral contraction schemes, the overall scaling of the computational effort is reduced to linear. A particular focus of our formulation is to ensure numerical stability when sparse-algebra routines are used to obtain an overall linear-scaling behavior.

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

    PubMed

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

    2017-03-11

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

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

    PubMed

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

    2012-11-26

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

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

    PubMed Central

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

    2005-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Pandey, Manoj Kumar; Nishiyama, Yusuke

    2015-12-01

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

  19. Chemical-shift X-ray standing wavefield determination of the local structure of methanethiolate phases on Ni( 1 1 1 )

    NASA Astrophysics Data System (ADS)

    Fisher, C. J.; Woodruff, D. P.; Jones, R. G.; Cowie, B. C. C.; Formoso, V.

    2002-01-01

    By monitoring the X-ray absorption through the chemically-shifted components of the S 1s photoemission signal, normal-incidence X-ray standing wavefield absorption at the (1 1 1) and ( 1¯ 1 1) scatterer planes has been used to determine the local adsorption geometry of the two distinct methanethiolate (CH 3S-) species which occur on Ni(1 1 1) following exposure to methanethiol. The species which is favoured at low temperatures is found to occupy either mixed hollow or bridge sites on a non-reconstructed Ni(1 1 1) surface, whereas that seen at higher temperatures is shown to involve Ni surface layer reconstruction and the data are consistent with hollow site adsorption on a reduced density outermost Ni layer. The relative merits of alternative reconstruction models based on that which occurs due to methanethiolate adsorption on Cu(1 1 1), or the (5√3×2)rect. phase formed by atomic S on Ni(1 1 1), are discussed. Both of these models are based on local square or `pseudo-(1 0 0)' outermost Ni layers. Co-adsorbed atomic sulphur, to which the methanethiolate species decompose at higher temperatures, appears to occupy mainly fcc hollow sites at low temperatures, but is partially converted to the local geometry of the ordered reconstructed (5√3×2)rect.-S phase after higher temperature annealing.

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

    NASA Astrophysics Data System (ADS)

    Thurber, Kent R.; Tycko, Robert

    2009-01-01

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

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

    PubMed

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

    2016-04-01

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

  2. How to turn your pump–probe instrument into a multidimensional spectrometer: 2D IR and Vis spectroscopies via pulse shaping

    PubMed Central

    Shim, Sang-Hee; Zanni, Martin T.

    2010-01-01

    We have recently developed a new and simple way of collecting 2D infrared and visible spectra that utilizes a pulse shaper and a partly collinear beam geometry. 2D IR and Vis spectroscopies are powerful tools for studying molecular structures and their dynamics. They can be used to correlate vibrational or electronic eigenstates, measure energy transfer rates, and quantify the dynamics of lineshapes, for instance, all with femtosecond time-resolution. As a result, they are finding use in systems that exhibit fast dynamics, such as sub-millisecond chemical and biological dynamics, and in hard-to-study environments, such as in membranes. While powerful, these techniques have been difficult to implement because they require a series of femtosecond pulses to be spatially and temporally overlapped with precise time-resolution and interferometric phase stability. However, many of the difficulties associated with implementing 2D spectroscopies are eliminated by using a pulse shaper and a simple beam geometry, which substantially lowers the technical barriers required for researchers to enter this exciting field while simultaneously providing many new capabilities. The aim of this paper is to provide an overview of the methods for collecting 2D spectra so that an outsider considering using 2D spectroscopy in their own research can judge which approach would be most suitable for their research aims. This paper focuses primarily on 2D IR spectroscopy, but also includes our recent work on adapting this technology to collecting 2D Vis spectra. We review work that has already been published as well as cover several topics that we have not reported previously, including phase cycling methods to remove background signals, eliminate unwanted scatter, and shift data collection into the rotating frame. PMID:19290321

  3. Krüppel-like factor 9 promotes hepatic cytochrome P450 2D6 expression during pregnancy in CYP2D6-humanized mice.

    PubMed

    Koh, Kwi Hye; Pan, Xian; Zhang, Wei; McLachlan, Alan; Urrutia, Raul; Jeong, Hyunyoung

    2014-12-01

    Cytochrome P450 2D6 (CYP2D6), a major drug-metabolizing enzyme, is responsible for metabolism of approximately 25% of marketed drugs. Clinical evidence indicates that metabolism of CYP2D6 substrates is increased during pregnancy, but the underlying mechanisms remain unclear. To identify transcription factors potentially responsible for CYP2D6 induction during pregnancy, a panel of genes differentially expressed in the livers of pregnant versus nonpregnant CYP2D6-humanized (tg-CYP2D6) mice was compiled via microarray experiments followed by real-time quantitative reverse-transcription polymerase chain reaction(qRT-PCR) verification. As a result, seven transcription factors-activating transcription factor 5 (ATF5), early growth response 1 (EGR1), forkhead box protein A3 (FOXA3), JUNB, Krüppel-like factor 9 (KLF9), KLF10, and REV-ERBα-were found to be up-regulated in liver during pregnancy. Results from transient transfection and promoter reporter gene assays indicate that KLF9 itself is a weak transactivator of CYP2D6 promoter but significantly enhances CYP2D6 promoter transactivation by hepatocyte nuclear factor 4 (HNF4α), a known transcriptional activator of CYP2D6 expression. The results from deletion and mutation analysis of CYP2D6 promoter activity identified a KLF9 putative binding motif at -22/-14 region to be critical in the potentiation of HNF4α-induced transactivation of CYP2D6. Electrophoretic mobility shift assays revealed a direct binding of KLF9 to the putative KLF binding motif. Results from chromatin immunoprecipitation assay showed increased recruitment of KLF9 to CYP2D6 promoter in the livers of tg-CYP2D6 mice during pregnancy. Taken together, our data suggest that increased KLF9 expression is in part responsible for CYP2D6 induction during pregnancy via the potentiation of HNF4α transactivation of CYP2D6.

  4. Spectroscopic properties of multilayered gold nanoparticle 2D sheets.

    PubMed

    Yoshida, Akihito; Imazu, Keisuke; Li, Xinheng; Okamoto, Koichi; Tamada, Kaoru

    2012-12-11

    We report the fabrication technique and optical properties of multilayered two-dimensional (2D) gold nanoparticle sheets ("Au nanosheet"). The 2D crystalline monolayer sheet composed of Au nanoparticles shows an absorption peak originating from a localized surface plasmon resonance (LSPR). It was found that the absorption spectra dramatically change when the monolayers are assembled into the multilayers on different substrates (quartz or Au). In the case of the multilayers on Au thin film (d = 200 nm), the LSPR peak is shifted to longer wavelength at the near-IR region by increasing the number of layers. The absorbance also depends on the layer number and shows the nonlinear behavior. On the other hand, the multilayers on quartz substrate show neither such LSPR peak shift nor nonlinear response of absorbance. The layer number dependence on metal surfaces can be interpreted as the combined effects between the near-field coupling of the LSPR and the far-field optics of the stratified metamaterial films, as proposed in our previous study. We also report the spectroscopic properties of hybrid multilayers composed of two kinds of monolayers, i.e., Au nanosheet and Ag nanosheet. The combination of the different metal nanoparticle sheets realizes more flexible plasmonic color tuning.

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

    PubMed

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

    2014-11-01

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

  6. Photo-and Electro-Switchable 1/2D Diffractive Structures Exploiting Soft-Matter

    DTIC Science & Technology

    2013-05-01

    again, a linear red-shift is observed, which clearly confirms that the behavior reported in Figure 4a is due to a photo - thermal mechanism; furthermore...AFRL-AFOSR-UK-TR-2013-0022 Photo -and Electro-Switchable 1/2D Diffractive Structures Exploiting Soft-Matter Luciano De Sio...TYPE Final Report 3. DATES COVERED (From – To) 14 November 2011 – 13 November 2012 4. TITLE AND SUBTITLE Photo -and Electro-Switchable 1/2D

  7. 2D Crystal Semiconductors New Materials for GHz-THz Devices

    DTIC Science & Technology

    2015-10-02

    frequency operation. 4) Identify methods to improve carrier transport in 2D Crystal semiconductors. 5) Compare FETs made from naturally occuring and... chemically synthesized 2D Crystal semic???ductors. 6) Elucidate the effect of contact resistance, and gauge the challenges for GHz-THz electronics by... chemical doping, which involved replac- ing a small number of atoms of the 3-D semiconductor by those with higher or lower valence. The next advance

  8. Hard and Soft Physics with 2D Materials

    NASA Astrophysics Data System (ADS)

    McEuen, Paul

    With their remarkable structural, thermal, mechanical, optical, chemical, and electronic properties, 2D materials are truly special. For example, a graphene sheet can be made into a high-performance transistor, but it is also the ultimate realization of a thin mechanical sheet. Such sheets, first studied in detail by August Föppl over a hundred years ago, are notoriously complex, since they can bend, buckle, and crumple in a variety of ways. In this talk, I will discuss a number of experiments to probe these unusual materials, from the effects of ripples on the mechanical properties of a graphene sheet, to folding with atomically thin bimorphs, to the electronic properties of bilayer graphene solitons. Finally, I discuss how the Japanese paper art of kirigami (kiru = `to cut', kami = `paper') applied to 2D materials offers a route to mechanical metamaterials and the construction of nanoscale machines.

  9. 2D FEM Heat Transfer & E&M Field Code

    SciTech Connect

    1992-04-02

    TOPAZ and TOPAZ2D are two-dimensional implicit finite element computer codes for heat transfer analysis. TOPAZ2D can also be used to solve electrostatic and magnetostatic problems. The programs solve for the steady-state or transient temperature or electrostatic and magnetostatic potential field on two-dimensional planar or axisymmetric geometries. Material properties may be temperature or potential-dependent and either isotropic or orthotropic. A variety of time and temperature-dependent boundary conditions can be specified including temperature, flux, convection, and radiation. By implementing the user subroutine feature, users can model chemical reaction kinetics and allow for any type of functional representation of boundary conditions and internal heat generation. The programs can solve problems of diffuse and specular band radiation in an enclosure coupled with conduction in the material surrounding the enclosure. Additional features include thermal contact resistance across an interface, bulk fluids, phase change, and energy balances.

  10. 2D microwave imaging reflectometer electronics

    SciTech Connect

    Spear, A. G.; Domier, C. W. Hu, X.; Muscatello, C. M.; Ren, X.; Luhmann, N. C.; Tobias, B. J.

    2014-11-15

    A 2D microwave imaging reflectometer system has been developed to visualize electron density fluctuations on the DIII-D tokamak. Simultaneously illuminated at four probe frequencies, large aperture optics image reflections from four density-dependent cutoff surfaces in the plasma over an extended region of the DIII-D plasma. Localized density fluctuations in the vicinity of the plasma cutoff surfaces modulate the plasma reflections, yielding a 2D image of electron density fluctuations. Details are presented of the receiver down conversion electronics that generate the in-phase (I) and quadrature (Q) reflectometer signals from which 2D density fluctuation data are obtained. Also presented are details on the control system and backplane used to manage the electronics as well as an introduction to the computer based control program.

  11. Large Area Synthesis of 2D Materials

    NASA Astrophysics Data System (ADS)

    Vogel, Eric

    Transition metal dichalcogenides (TMDs) have generated significant interest for numerous applications including sensors, flexible electronics, heterostructures and optoelectronics due to their interesting, thickness-dependent properties. Despite recent progress, the synthesis of high-quality and highly uniform TMDs on a large scale is still a challenge. In this talk, synthesis routes for WSe2 and MoS2 that achieve monolayer thickness uniformity across large area substrates with electrical properties equivalent to geological crystals will be described. Controlled doping of 2D semiconductors is also critically required. However, methods established for conventional semiconductors, such as ion implantation, are not easily applicable to 2D materials because of their atomically thin structure. Redox-active molecular dopants will be demonstrated which provide large changes in carrier density and workfunction through the choice of dopant, treatment time, and the solution concentration. Finally, several applications of these large-area, uniform 2D materials will be described including heterostructures, biosensors and strain sensors.

  12. 2D microwave imaging reflectometer electronics.

    PubMed

    Spear, A G; Domier, C W; Hu, X; Muscatello, C M; Ren, X; Tobias, B J; Luhmann, N C

    2014-11-01

    A 2D microwave imaging reflectometer system has been developed to visualize electron density fluctuations on the DIII-D tokamak. Simultaneously illuminated at four probe frequencies, large aperture optics image reflections from four density-dependent cutoff surfaces in the plasma over an extended region of the DIII-D plasma. Localized density fluctuations in the vicinity of the plasma cutoff surfaces modulate the plasma reflections, yielding a 2D image of electron density fluctuations. Details are presented of the receiver down conversion electronics that generate the in-phase (I) and quadrature (Q) reflectometer signals from which 2D density fluctuation data are obtained. Also presented are details on the control system and backplane used to manage the electronics as well as an introduction to the computer based control program.

  13. Shifting Attention

    ERIC Educational Resources Information Center

    Ingram, Jenni

    2014-01-01

    This article examines the shifts in attention and focus as one teacher introduces and explains an image that represents the processes involved in a numeric problem that his students have been working on. This paper takes a micro-analytic approach to examine how the focus of attention shifts through what the teacher and students do and say in the…

  14. 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

  15. 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

  16. 2D Distributed Sensing Via TDR

    DTIC Science & Technology

    2007-11-02

    plate VEGF CompositeSensor Experimental Setup Air 279 mm 61 78 VARTM profile: slope RTM profile: rectangle 22 1 Jul 2003© 2003 University of Delaware...2003 University of Delaware All rights reserved Vision: Non-contact 2D sensing ü VARTM setup constructed within TL can be sensed by its EM field: 2D...300.0 mm/ns. 1 2 1 Jul 2003© 2003 University of Delaware All rights reserved Model Validation “ RTM Flow” TDR Response to 139 mm VEGC

  17. Inkjet printing of 2D layered materials.

    PubMed

    Li, Jiantong; Lemme, Max C; Östling, Mikael

    2014-11-10

    Inkjet printing of 2D layered materials, such as graphene and MoS2, has attracted great interests for emerging electronics. However, incompatible rheology, low concentration, severe aggregation and toxicity of solvents constitute critical challenges which hamper the manufacturing efficiency and product quality. Here, we introduce a simple and general technology concept (distillation-assisted solvent exchange) to efficiently overcome these challenges. By implementing the concept, we have demonstrated excellent jetting performance, ideal printing patterns and a variety of promising applications for inkjet printing of 2D layered materials.

  18. The basics of 2D DIGE.

    PubMed

    Beckett, Phil

    2012-01-01

    The technique of two-dimensional (2D) gel electrophoresis is a powerful tool for separating complex mixtures of proteins, but since its inception in the mid 1970s, it acquired the stigma of being a very difficult application to master and was generally used to its best effect by experts. The introduction of commercially available immobilized pH gradients in the early 1990s provided enhanced reproducibility and easier protocols, leading to a pronounced increase in popularity of the technique. However gel-to-gel variation was still difficult to control without the use of technical replicates. In the mid 1990s (at the same time as the birth of "proteomics"), the concept of multiplexing fluorescently labeled proteins for 2D gel separation was realized by Jon Minden's group and has led to the ability to design experiments to virtually eliminate gel-to-gel variation, resulting in biological replicates being used for statistical analysis with the ability to detect very small changes in relative protein abundance. This technology is referred to as 2D difference gel electrophoresis (2D DIGE).

  19. Muscle metabolism and activation heterogeneity by combined 31P chemical shift and T2 imaging, and pulmonary O2 uptake during incremental knee-extensor exercise.

    PubMed

    Cannon, Daniel T; Howe, Franklyn A; Whipp, Brian J; Ward, Susan A; McIntyre, Dominick J; Ladroue, Christophe; Griffiths, John R; Kemp, Graham J; Rossiter, Harry B

    2013-09-01

    The integration of skeletal muscle substrate depletion, metabolite accumulation, and fatigue during large muscle-mass exercise is not well understood. Measurement of intramuscular energy store degradation and metabolite accumulation is confounded by muscle heterogeneity. Therefore, to characterize regional metabolic distribution in the locomotor muscles, we combined 31P magnetic resonance spectroscopy, chemical shift imaging, and T2-weighted imaging with pulmonary oxygen uptake during bilateral knee-extension exercise to intolerance. Six men completed incremental tests for the following: (1) unlocalized 31P magnetic resonance spectroscopy; and (2) spatial determination of 31P metabolism and activation. The relationship of pulmonary oxygen uptake to whole quadriceps phosphocreatine concentration ([PCr]) was inversely linear, and three of four knee-extensor muscles showed activation as assessed by change in T2. The largest changes in [PCr], [inorganic phosphate] ([Pi]) and pH occurred in rectus femoris, but no voxel (72 cm3) showed complete PCr depletion at exercise cessation. The most metabolically active voxel reached 11 ± 9 mM [PCr] (resting, 29 ± 1 mM), 23 ± 11 mM [Pi] (resting, 7 ± 1 mM), and a pH of 6.64 ± 0.29 (resting, 7.08 ± 0.03). However, the distribution of 31P metabolites and pH varied widely between voxels, and the intervoxel coefficient of variation increased between rest (∼10%) and exercise intolerance (∼30-60%). Therefore, the limit of tolerance was attained with wide heterogeneity in substrate depletion and fatigue-related metabolite accumulation, with extreme metabolic perturbation isolated to only a small volume of active muscle (<5%). Regional intramuscular disturbances are thus likely an important requisite for exercise intolerance. How these signals integrate to limit muscle power production, while regional "recruitable muscle" energy stores are presumably still available, remains uncertain.

  20. An optimized method for NMR-based plant seed metabolomic analysis with maximized polar metabolite extraction efficiency, signal-to-noise ratio, and chemical shift consistency.

    PubMed

    Wu, Xiangyu; Li, Ning; Li, Hongde; Tang, Huiru

    2014-04-07

    Plant metabolomic analysis has become an essential part of functional genomics and systems biology and requires effective extraction of both primary and secondary metabolites from plant cells. To establish an optimized extraction method for the NMR-based analysis, we used the seeds of mungbean (Vigna radiata cv. Elü no. 1) as a model and systematically investigated the dependence of the metabolite composition in plant extracts on various extraction parameters including cell-breaking methods, extraction solvents, number of extraction repeats, tissue-to-solvent ratio, and extract-to-buffer ratio (for final NMR analysis). We also compared two NMR approaches for quantitative metabolomic analysis from completely relaxed spectra directly and from partially relaxed spectra calculated with T1. By maximizing the extraction efficiency and signal-to-noise ratio but minimizing inter-sample chemical-shift variations and metabolite degradations, we established a parameter-optimized protocol for NMR-based plant seed metabolomic analysis. We concluded that aqueous methanol was the best extraction solvent with an optimal tissue-to-solvent ratio of about 1 : 10-1 : 15 (mg per μL). The combination of tissuelyser homogenization with ultrasonication was the choice of cell-breaking method with three repeated extractions being necessary. For NMR analysis, the optimal extract-to-solvent was around 5-8 mg mL(-1) and completely relaxed spectra were ideal for intrinsically quantitative metabolomic analysis although partially relaxed spectra were employable for comparative metabolomics. This optimized method will offer ensured data quality for high-throughput and reliable plant metabolomics studies.

  1. Comparison of accelerated 3-D spiral chemical shift imaging and single-voxel spectroscopy at 3T in the pediatric age group.

    PubMed

    Yazbek, Sandrine; Prabhu, Sanjay P; Connaughton, Pauline; Grant, Patricia E; Gagoski, Borjan

    2015-08-01

    Single-voxel spectroscopy (SVS) is usually used in the pediatric population when a short acquisition time is crucial. To overcome the long acquisition time of 3-D phase-encoded chemical shift imaging (CSI) and lack of spatial coverage of single-voxel spectroscopy, efficient encoding schemes using spiral k-space trajectories have been successfully deployed, enabling acquisition of volumetric CSI in <5 min. We assessed feasibility of using 3-D spiral CSI sequence routinely in pediatric clinical settings by comparing its reconstructed spectra against SVS spectra. Volumetric spiral CSI obtained spectra from 2-cc isotropic voxels over a 16×16×10-cm region. SVS acquisition encoded a 3.4-cc (1.5-mm) isotropic voxel. Acquisition time was 3 min for every technique. Data were gathered prospectively from 11 random pediatric patients. Spectra from left basal ganglia were obtained using both techniques and were processed with post-processing software. The following metabolite ratios were calculated: N-acetylaspartate/creatine (NAA/Cr), choline/creatine (Cho/Cr), lactate/creatine (Lac/Cr) and N-acetylapartate/choline (NAA/Cho). We collected data on 11 children ages 4 days to 10 years. In 10/11 cases, spectral quality of both methods was acceptable. Considering 10/11 cases, we found a statistically significant difference between SVS and 3-D spiral CSI for all three ratios. However, this difference was fixed and was probably caused by a fixed bias. This means that 3-D spiral CSI can be used instead of SVS by removing the mean difference between the methods for each ratio. Accelerated 3-D CSI is feasible in pediatric patients and can potentially substitute for SVS.

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

    PubMed

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

    2012-04-01

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

  3. Application of 2D Non-Graphene Materials and 2D Oxide Nanostructures for Biosensing Technology

    PubMed Central

    Shavanova, Kateryna; Bakakina, Yulia; Burkova, Inna; Shtepliuk, Ivan; Viter, Roman; Ubelis, Arnolds; Beni, Valerio; Starodub, Nickolaj; Yakimova, Rositsa; Khranovskyy, Volodymyr

    2016-01-01

    The discovery of graphene and its unique properties has inspired researchers to try to invent other two-dimensional (2D) materials. After considerable research effort, a distinct “beyond graphene” domain has been established, comprising the library of non-graphene 2D materials. It is significant that some 2D non-graphene materials possess solid advantages over their predecessor, such as having a direct band gap, and therefore are highly promising for a number of applications. These applications are not limited to nano- and opto-electronics, but have a strong potential in biosensing technologies, as one example. However, since most of the 2D non-graphene materials have been newly discovered, most of the research efforts are concentrated on material synthesis and the investigation of the properties of the material. Applications of 2D non-graphene materials are still at the embryonic stage, and the integration of 2D non-graphene materials into devices is scarcely reported. However, in recent years, numerous reports have blossomed about 2D material-based biosensors, evidencing the growing potential of 2D non-graphene materials for biosensing applications. This review highlights the recent progress in research on the potential of using 2D non-graphene materials and similar oxide nanostructures for different types of biosensors (optical and electrochemical). A wide range of biological targets, such as glucose, dopamine, cortisol, DNA, IgG, bisphenol, ascorbic acid, cytochrome and estradiol, has been reported to be successfully detected by biosensors with transducers made of 2D non-graphene materials. PMID:26861346

  4. Application of 2D Non-Graphene Materials and 2D Oxide Nanostructures for Biosensing Technology.

    PubMed

    Shavanova, Kateryna; Bakakina, Yulia; Burkova, Inna; Shtepliuk, Ivan; Viter, Roman; Ubelis, Arnolds; Beni, Valerio; Starodub, Nickolaj; Yakimova, Rositsa; Khranovskyy, Volodymyr

    2016-02-06

    The discovery of graphene and its unique properties has inspired researchers to try to invent other two-dimensional (2D) materials. After considerable research effort, a distinct "beyond graphene" domain has been established, comprising the library of non-graphene 2D materials. It is significant that some 2D non-graphene materials possess solid advantages over their predecessor, such as having a direct band gap, and therefore are highly promising for a number of applications. These applications are not limited to nano- and opto-electronics, but have a strong potential in biosensing technologies, as one example. However, since most of the 2D non-graphene materials have been newly discovered, most of the research efforts are concentrated on material synthesis and the investigation of the properties of the material. Applications of 2D non-graphene materials are still at the embryonic stage, and the integration of 2D non-graphene materials into devices is scarcely reported. However, in recent years, numerous reports have blossomed about 2D material-based biosensors, evidencing the growing potential of 2D non-graphene materials for biosensing applications. This review highlights the recent progress in research on the potential of using 2D non-graphene materials and similar oxide nanostructures for different types of biosensors (optical and electrochemical). A wide range of biological targets, such as glucose, dopamine, cortisol, DNA, IgG, bisphenol, ascorbic acid, cytochrome and estradiol, has been reported to be successfully detected by biosensors with transducers made of 2D non-graphene materials.

  5. Eluding catastrophic shifts.

    PubMed

    Villa Martín, Paula; Bonachela, Juan A; Levin, Simon A; Muñoz, Miguel A

    2015-04-14

    Transitions between regimes with radically different properties are ubiquitous in nature. Such transitions can occur either smoothly or in an abrupt and catastrophic fashion. Important examples of the latter can be found in ecology, climate sciences, and economics, to name a few, where regime shifts have catastrophic consequences that are mostly irreversible (e.g., desertification, coral reef collapses, and market crashes). Predicting and preventing these abrupt transitions remains a challenging and important task. Usually, simple deterministic equations are used to model and rationalize these complex situations. However, stochastic effects might have a profound effect. Here we use 1D and 2D spatially explicit models to show that intrinsic (demographic) stochasticity can alter deterministic predictions dramatically, especially in the presence of other realistic features such as limited mobility or spatial heterogeneity. In particular, these ingredients can alter the possibility of catastrophic shifts by giving rise to much smoother and easily reversible continuous ones. The ideas presented here can help further understand catastrophic shifts and contribute to the discussion about the possibility of preventing such shifts to minimize their disruptive ecological, economic, and societal consequences.

  6. Eluding catastrophic shifts

    PubMed Central

    Villa Martín, Paula; Bonachela, Juan A.; Levin, Simon A.; Muñoz, Miguel A.

    2015-01-01

    Transitions between regimes with radically different properties are ubiquitous in nature. Such transitions can occur either smoothly or in an abrupt and catastrophic fashion. Important examples of the latter can be found in ecology, climate sciences, and economics, to name a few, where regime shifts have catastrophic consequences that are mostly irreversible (e.g., desertification, coral reef collapses, and market crashes). Predicting and preventing these abrupt transitions remains a challenging and important task. Usually, simple deterministic equations are used to model and rationalize these complex situations. However, stochastic effects might have a profound effect. Here we use 1D and 2D spatially explicit models to show that intrinsic (demographic) stochasticity can alter deterministic predictions dramatically, especially in the presence of other realistic features such as limited mobility or spatial heterogeneity. In particular, these ingredients can alter the possibility of catastrophic shifts by giving rise to much smoother and easily reversible continuous ones. The ideas presented here can help further understand catastrophic shifts and contribute to the discussion about the possibility of preventing such shifts to minimize their disruptive ecological, economic, and societal consequences. PMID:25825772

  7. 2-D linear motion system. Innovative technology summary report

    SciTech Connect

    1998-11-01

    The US Department of Energy's (DOE's) nuclear facility decontamination and decommissioning (D and D) program requires buildings to be decontaminated, decommissioned, and surveyed for radiological contamination in an expeditious and cost-effective manner. Simultaneously, the health and safety of personnel involved in the D and D activities is of primary concern. D and D workers must perform duties high off the ground, requiring the use of manlifts or scaffolding, often, in radiologically or chemically contaminated areas or in areas with limited access. Survey and decontamination instruments that are used are sometimes heavy or awkward to use, particularly when the worker is operating from a manlift or scaffolding. Finding alternative methods of performing such work on manlifts or scaffolding is important. The 2-D Linear Motion System (2-D LMS), also known as the Wall Walker{trademark}, is designed to remotely position tools and instruments on walls for use in such activities as radiation surveys, decontamination, and painting. Traditional (baseline) methods for operating equipment for these tasks require workers to perform duties on elevated platforms, sometimes several meters above the ground surface and near potential sources of contamination. The Wall Walker 2-D LMS significantly improves health and safety conditions by facilitating remote operation of equipment. The Wall Walker 2-D LMS performed well in a demonstration of its precision, accuracy, maneuverability, payload capacity, and ease of use. Thus, this innovative technology is demonstrated to be a viable alternative to standard methods of performing work on large, high walls, especially those that have potential contamination concerns. The Wall Walker was used to perform a final release radiological survey on over 167 m{sup 2} of walls. In this application, surveying using a traditional (baseline) method that employs an aerial lift for manual access was 64% of the total cost of the improved technology

  8. Compatible embedding for 2D shape animation.

    PubMed

    Baxter, William V; Barla, Pascal; Anjyo, Ken-Ichi

    2009-01-01

    We present new algorithms for the compatible embedding of 2D shapes. Such embeddings offer a convenient way to interpolate shapes having complex, detailed features. Compared to existing techniques, our approach requires less user input, and is faster, more robust, and simpler to implement, making it ideal for interactive use in practical applications. Our new approach consists of three parts. First, our boundary matching algorithm locates salient features using the perceptually motivated principles of scale-space and uses these as automatic correspondences to guide an elastic curve matching algorithm. Second, we simplify boundaries while maintaining their parametric correspondence and the embedding of the original shapes. Finally, we extend the mapping to shapes' interiors via a new compatible triangulation algorithm. The combination of our algorithms allows us to demonstrate 2D shape interpolation with instant feedback. The proposed algorithms exhibit a combination of simplicity, speed, and accuracy that has not been achieved in previous work.

  9. Schottky diodes from 2D germanane

    NASA Astrophysics Data System (ADS)

    Sahoo, Nanda Gopal; Esteves, Richard J.; Punetha, Vinay Deep; Pestov, Dmitry; Arachchige, Indika U.; McLeskey, James T.

    2016-07-01

    We report on the fabrication and characterization of a Schottky diode made using 2D germanane (hydrogenated germanene). When compared to germanium, the 2D structure has higher electron mobility, an optimal band-gap, and exceptional stability making germanane an outstanding candidate for a variety of opto-electronic devices. One-atom-thick sheets of hydrogenated puckered germanium atoms have been synthesized from a CaGe2 framework via intercalation and characterized by XRD, Raman, and FTIR techniques. The material was then used to fabricate Schottky diodes by suspending the germanane in benzonitrile and drop-casting it onto interdigitated metal electrodes. The devices demonstrate significant rectifying behavior and the outstanding potential of this material.

  10. Extrinsic Cation Selectivity of 2D Membranes

    PubMed Central

    2017-01-01

    From a systematic study of the concentration driven diffusion of positive and negative ions across porous 2D membranes of graphene and hexagonal boron nitride (h-BN), we prove their cation selectivity. Using the current–voltage characteristics of graphene and h-BN monolayers separating reservoirs of different salt concentrations, we calculate the reversal potential as a measure of selectivity. We tune the Debye screening length by exchanging the salt concentrations and demonstrate that negative surface charge gives rise to cation selectivity. Surprisingly, h-BN and graphene membranes show similar characteristics, strongly suggesting a common origin of selectivity in aqueous solvents. For the first time, we demonstrate that the cation flux can be increased by using ozone to create additional pores in graphene while maintaining excellent selectivity. We discuss opportunities to exploit our scalable method to use 2D membranes for applications including osmotic power conversion. PMID:28157333

  11. Static & Dynamic Response of 2D Solids

    SciTech Connect

    Lin, Jerry

    1996-07-15

    NIKE2D is an implicit finite-element code for analyzing the finite deformation, static and dynamic response of two-dimensional, axisymmetric, plane strain, and plane stress solids. The code is fully vectorized and available on several computing platforms. A number of material models are incorporated to simulate a wide range of material behavior including elasto-placicity, anisotropy, creep, thermal effects, and rate dependence. Slideline algorithms model gaps and sliding along material interfaces, including interface friction, penetration and single surface contact. Interactive-graphics and rezoning is included for analyses with large mesh distortions. In addition to quasi-Newton and arc-length procedures, adaptive algorithms can be defined to solve the implicit equations using the solution language ISLAND. Each of these capabilities and more make NIKE2D a robust analysis tool.

  12. Explicit 2-D Hydrodynamic FEM Program

    SciTech Connect

    Lin, Jerry

    1996-08-07

    DYNA2D* is a vectorized, explicit, two-dimensional, axisymmetric and plane strain finite element program for analyzing the large deformation dynamic and hydrodynamic response of inelastic solids. DYNA2D* contains 13 material models and 9 equations of state (EOS) to cover a wide range of material behavior. The material models implemented in all machine versions are: elastic, orthotropic elastic, kinematic/isotropic elastic plasticity, thermoelastoplastic, soil and crushable foam, linear viscoelastic, rubber, high explosive burn, isotropic elastic-plastic, temperature-dependent elastic-plastic. The isotropic and temperature-dependent elastic-plastic models determine only the deviatoric stresses. Pressure is determined by one of 9 equations of state including linear polynomial, JWL high explosive, Sack Tuesday high explosive, Gruneisen, ratio of polynomials, linear polynomial with energy deposition, ignition and growth of reaction in HE, tabulated compaction, and tabulated.

  13. Quasiparticle interference in unconventional 2D systems

    NASA Astrophysics Data System (ADS)

    Chen, Lan; Cheng, Peng; Wu, Kehui

    2017-03-01

    At present, research of 2D systems mainly focuses on two kinds of materials: graphene-like materials and transition-metal dichalcogenides (TMDs). Both of them host unconventional 2D electronic properties: pseudospin and the associated chirality of electrons in graphene-like materials, and spin-valley-coupled electronic structures in the TMDs. These exotic electronic properties have attracted tremendous interest for possible applications in nanodevices in the future. Investigation on the quasiparticle interference (QPI) in 2D systems is an effective way to uncover these properties. In this review, we will begin with a brief introduction to 2D systems, including their atomic structures and electronic bands. Then, we will discuss the formation of Friedel oscillation due to QPI in constant energy contours of electron bands, and show the basic concept of Fourier-transform scanning tunneling microscopy/spectroscopy (FT-STM/STS), which can resolve Friedel oscillation patterns in real space and consequently obtain the QPI patterns in reciprocal space. In the next two parts, we will summarize some pivotal results in the investigation of QPI in graphene and silicene, in which systems the low-energy quasiparticles are described by the massless Dirac equation. The FT-STM experiments show there are two different interference channels (intervalley and intravalley scattering) and backscattering suppression, which associate with the Dirac cones and the chirality of quasiparticles. The monolayer and bilayer graphene on different substrates (SiC and metal surfaces), and the monolayer and multilayer silicene on a Ag(1 1 1) surface will be addressed. The fifth part will introduce the FT-STM research on QPI in TMDs (monolayer and bilayer of WSe2), which allow us to infer the spin texture of both conduction and valence bands, and present spin-valley coupling by tracking allowed and forbidden scattering channels.

  14. Compact 2-D graphical representation of DNA

    NASA Astrophysics Data System (ADS)

    Randić, Milan; Vračko, Marjan; Zupan, Jure; Novič, Marjana

    2003-05-01

    We present a novel 2-D graphical representation for DNA sequences which has an important advantage over the existing graphical representations of DNA in being very compact. It is based on: (1) use of binary labels for the four nucleic acid bases, and (2) use of the 'worm' curve as template on which binary codes are placed. The approach is illustrated on DNA sequences of the first exon of human β-globin and gorilla β-globin.

  15. Realistic and efficient 2D crack simulation

    NASA Astrophysics Data System (ADS)

    Yadegar, Jacob; Liu, Xiaoqing; Singh, Abhishek

    2010-04-01

    Although numerical algorithms for 2D crack simulation have been studied in Modeling and Simulation (M&S) and computer graphics for decades, realism and computational efficiency are still major challenges. In this paper, we introduce a high-fidelity, scalable, adaptive and efficient/runtime 2D crack/fracture simulation system by applying the mathematically elegant Peano-Cesaro triangular meshing/remeshing technique to model the generation of shards/fragments. The recursive fractal sweep associated with the Peano-Cesaro triangulation provides efficient local multi-resolution refinement to any level-of-detail. The generated binary decomposition tree also provides efficient neighbor retrieval mechanism used for mesh element splitting and merging with minimal memory requirements essential for realistic 2D fragment formation. Upon load impact/contact/penetration, a number of factors including impact angle, impact energy, and material properties are all taken into account to produce the criteria of crack initialization, propagation, and termination leading to realistic fractal-like rubble/fragments formation. The aforementioned parameters are used as variables of probabilistic models of cracks/shards formation, making the proposed solution highly adaptive by allowing machine learning mechanisms learn the optimal values for the variables/parameters based on prior benchmark data generated by off-line physics based simulation solutions that produce accurate fractures/shards though at highly non-real time paste. Crack/fracture simulation has been conducted on various load impacts with different initial locations at various impulse scales. The simulation results demonstrate that the proposed system has the capability to realistically and efficiently simulate 2D crack phenomena (such as window shattering and shards generation) with diverse potentials in military and civil M&S applications such as training and mission planning.

  16. Engineering light outcoupling in 2D materials.

    PubMed

    Lien, Der-Hsien; Kang, Jeong Seuk; Amani, Matin; Chen, Kevin; Tosun, Mahmut; Wang, Hsin-Ping; Roy, Tania; Eggleston, Michael S; Wu, Ming C; Dubey, Madan; Lee, Si-Chen; He, Jr-Hau; Javey, Ali

    2015-02-11

    When light is incident on 2D transition metal dichalcogenides (TMDCs), it engages in multiple reflections within underlying substrates, producing interferences that lead to enhancement or attenuation of the incoming and outgoing strength of light. Here, we report a simple method to engineer the light outcoupling in semiconducting TMDCs by modulating their dielectric surroundings. We show that by modulating the thicknesses of underlying substrates and capping layers, the interference caused by substrate can significantly enhance the light absorption and emission of WSe2, resulting in a ∼11 times increase in Raman signal and a ∼30 times increase in the photoluminescence (PL) intensity of WSe2. On the basis of the interference model, we also propose a strategy to control the photonic and optoelectronic properties of thin-layer WSe2. This work demonstrates the utilization of outcoupling engineering in 2D materials and offers a new route toward the realization of novel optoelectronic devices, such as 2D LEDs and solar cells.

  17. Irreversibility-inversions in 2D turbulence

    NASA Astrophysics Data System (ADS)

    Bragg, Andrew; de Lillo, Filippo; Boffetta, Guido

    2016-11-01

    We consider a recent theoretical prediction that for inertial particles in 2D turbulence, the nature of the irreversibility of their pair dispersion inverts when the particle inertia exceeds a certain value. In particular, when the particle Stokes number, St , is below a certain value, the forward-in-time (FIT) dispersion should be faster than the backward-in-time (BIT) dispersion, but for St above this value, this should invert so that BIT becomes faster than FIT dispersion. This non-trivial behavior arises because of the competition between two physically distinct irreversibility mechanisms that operate in different regimes of St . In 3D turbulence, both mechanisms act to produce faster BIT than FIT dispersion, but in 2D, the two mechanisms have opposite effects because of the inverse energy cascade in the turbulent velocity field. We supplement the qualitative argument given by Bragg et al. by deriving quantitative predictions of this effect in the short-time dispersion limit. These predictions are then confirmed by results of inertial particle dispersion in a direct numerical simulation of 2D turbulence.

  18. Kinetic parameter estimation in N. europaea biofilms using a 2-D reactive transport model.

    PubMed

    Lauchnor, Ellen G; Semprini, Lewis; Wood, Brian D

    2015-06-01

    Biofilms of the ammonia oxidizing bacterium Nitrosomonas europaea were cultivated to study microbial processes associated with ammonia oxidation in pure culture. We explored the hypothesis that the kinetic parameters of ammonia oxidation in N. europaea biofilms were in the range of those determined with batch suspended cells. Oxygen and pH microelectrodes were used to measure dissolved oxygen (DO) concentrations and pH above and inside biofilms and reactive transport modeling was performed to simulate the measured DO and pH profiles. A two dimensional (2-D) model was used to simulate advection parallel to the biofilm surface and diffusion through the overlying fluid while reaction and diffusion were simulated in the biofilm. Three experimental studies of microsensor measurements were performed with biofilms: i) NH3 concentrations near the Ksn value of 40 μM determined in suspended cell tests ii) Limited buffering capacity which resulted in a pH gradient within the biofilms and iii) NH3 concentrations well below the Ksn value. Very good fits to the DO concentration profiles both in the fluid above and in the biofilms were achieved using the 2-D model. The modeling study revealed that the half-saturation coefficient for NH3 in N. europaea biofilms was close to the value measured in suspended cells. However, the third study of biofilms with low availability of NH3 deviated from the model prediction. The model also predicted shifts in the DO profiles and the gradient in pH that resulted for the case of limited buffering capacity. The results illustrate the importance of incorporating both key transport and chemical processes in a biofilm reactive transport model.

  19. Dephosphorylation of MAP2D enhances its binding to vimentin in preovulatory ovarian granulosa cells.

    PubMed

    Flynn, Maxfield P; Fiedler, Sarah E; Karlsson, Amelia B; Carr, Daniel W; Maizels, Evelyn T; Hunzicker-Dunn, Mary

    2016-08-01

    Preovulatory granulosa cells express the low-molecular-mass MAP2D variant of microtubule-associated protein 2 (MAP2). Activation of the luteinizing hormone choriogonadotropin receptor by human choriogonadotropin (hCG) promotes dephosphorylation of MAP2D on Thr256 and Thr259. We sought to evaluate the association of MAP2D with the cytoskeleton, and the effect of hCG on this association. MAP2D partially colocalized, as assessed by confocal immunofluorescence microscopy, with the vimentin intermediate filament and microtubule cytoskeletons in naive cells. In vitro binding studies showed that MAP2D bound directly to vimentin and β-tubulin. Phosphorylation of recombinant MAP2D on Thr256 and Thr259, which mimics the phosphorylation status of MAP2D in naive cells, reduces binding of MAP2D to vimentin and tubulin by two- and three-fold, respectively. PKA-dependent phosphorylation of vimentin (Ser32 and Ser38) promoted binding of vimentin to MAP2D and increased contraction of granulosa cells with reorganization of vimentin filaments and MAP2D from the periphery into a thickened layer surrounding the nucleus and into prominent cellular extensions. Chemical disruption of vimentin filament organization increased progesterone production. Taken together, these results suggest that hCG-stimulated dephosphorylation of MAP2D at Thr256 and Thr259, phosphorylation of vimentin at Ser38 and Ser72, and the resulting enhanced binding of MAP2D to vimentin might contribute to the progesterone synthetic response required for ovulation.

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

    PubMed

    Ling, M; Brauer, M

    1992-01-01

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

  1. 2D superconductivity by ionic gating

    NASA Astrophysics Data System (ADS)

    Iwasa, Yoshi

    2D superconductivity is attracting a renewed interest due to the discoveries of new highly crystalline 2D superconductors in the past decade. Superconductivity at the oxide interfaces triggered by LaAlO3/SrTiO3 has become one of the promising routes for creation of new 2D superconductors. Also, the MBE grown metallic monolayers including FeSe are also offering a new platform of 2D superconductors. In the last two years, there appear a variety of monolayer/bilayer superconductors fabricated by CVD or mechanical exfoliation. Among these, electric field induced superconductivity by electric double layer transistor (EDLT) is a unique platform of 2D superconductivity, because of its ability of high density charge accumulation, and also because of the versatility in terms of materials, stemming from oxides to organics and layered chalcogenides. In this presentation, the following issues of electric filed induced superconductivity will be addressed; (1) Tunable carrier density, (2) Weak pinning, (3) Absence of inversion symmetry. (1) Since the sheet carrier density is quasi-continuously tunable from 0 to the order of 1014 cm-2, one is able to establish an electronic phase diagram of superconductivity, which will be compared with that of bulk superconductors. (2) The thickness of superconductivity can be estimated as 2 - 10 nm, dependent on materials, and is much smaller than the in-plane coherence length. Such a thin but low resistance at normal state results in extremely weak pinning beyond the dirty Boson model in the amorphous metallic films. (3) Due to the electric filed, the inversion symmetry is inherently broken in EDLT. This feature appears in the enhancement of Pauli limit of the upper critical field for the in-plane magnetic fields. In transition metal dichalcogenide with a substantial spin-orbit interactions, we were able to confirm the stabilization of Cooper pair due to its spin-valley locking. This work has been supported by Grant-in-Aid for Specially

  2. The Anatomy of High-Performance 2D Similarity Calculations

    PubMed Central

    Haque, Imran S.; Pande, Vijay S.

    2011-01-01

    Similarity measures based on the comparison of dense bit-vectors of two-dimensional chemical features are a dominant method in chemical informatics. For large-scale problems, including compound selection and machine learning, computing the intersection between two dense bit-vectors is the overwhelming bottleneck. We describe efficient implementations of this primitive, as well as example applications, using features of modern CPUs that allow 20-40x performance increases relative to typical code. Specifically, we describe fast methods for population count on modern x86 processors and cache-efficient matrix traversal and leader clustering algorithms that alleviate memory bandwidth bottlenecks in similarity matrix construction and clustering. The speed of our 2D comparison primitives is within a small factor of that obtained on GPUs, and does not require specialized hardware. PMID:21854053

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

    PubMed

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

    2013-05-01

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

  4. Fluid Shifts

    NASA Technical Reports Server (NTRS)

    Stenger, M. B.; Hargens, A.; Dulchavsky, S.; Ebert, D.; Lee, S.; Laurie, S.; Garcia, K.; Sargsyan, A.; Martin, D.; Lui, J.; Macias, B.; Arbeille, P.; Danielson, R.; Chang, D.; Gunga, H.; Johnston, S.; Westby, C.; Ribeiro, L.; Ploutz-Snyder, R.; Smith, S.

    2015-01-01

    INTRODUCTION: Mechanisms responsible for the ocular structural and functional changes that characterize the visual impairment and intracranial pressure (ICP) syndrome (VIIP) are unclear, but hypothesized to be secondary to the cephalad fluid shift experienced in spaceflight. This study will relate the fluid distribution and compartmentalization associated with long-duration spaceflight with VIIP symptoms. We also seek to determine whether the magnitude of fluid shifts during spaceflight, as well as the VIIP-related effects of those shifts, can be predicted preflight with acute hemodynamic manipulations, and also if lower body negative pressure (LBNP) can reverse the VIIP effects. METHODS: Physiologic variables will be examined pre-, in- and post-flight in 10 International Space Station crewmembers including: fluid compartmentalization (D2O and NaBr dilution); interstitial tissue thickness (ultrasound); vascular dimensions and dynamics (ultrasound and MRI (including cerebrospinal fluid pulsatility)); ocular measures (optical coherence tomography, intraocular pressure, ultrasound); and ICP measures (tympanic membrane displacement, otoacoustic emissions). Pre- and post-flight measures will be assessed while upright, supine and during 15 deg head-down tilt (HDT). In-flight measures will occur early and late during 6 or 12 month missions. LBNP will be evaluated as a countermeasure during HDT and during spaceflight. RESULTS: The first two crewmembers are in the preflight testing phase. Preliminary results characterize the acute fluid shifts experienced from upright, to supine and HDT postures (increased stroke volume, jugular dimensions and measures of ICP) which are reversed with 25 millimeters Hg LBNP. DISCUSSION: Initial results indicate that acute cephalad fluid shifts may be related to VIIP symptoms, but also may be reversible by LBNP. The effect of a chronic fluid shift has yet to be evaluated. Learning Objectives: Current spaceflight VIIP research is described

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

    PubMed

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

    2009-12-15

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

  6. Arginine Interactions with Anatase TiO2 (100) Surface and the Perturbation of 49Ti NMR Chemical Shifts - A DFT Investigation: Relevance to Renu-Seeram Bio Solar Cell

    SciTech Connect

    Koch, Rainer; Lipton, Andrew S.; Filipek, S.; Renugopalakrishnan, Venkatesan M.

    2011-06-01

    Density functional theoretical calculations have been utilized to investigate the interaction of the amino acid arginine with the (100) surface of anatase and the reproduction of experimentally measured 49Ti NMR chemical shifts of anatase. Significant binding of arginine through electrostatic interaction and hydrogen bonds of the arginine guanidinium protons to the TiO2 surface oxygen atoms is observed, allowing attachment of proteins to titania surfaces in the construction of bio-sensitized solar cells. GIAO-B3LYP/6-31G(d) NMR calculation of a three-layer model based on the experimental structure of this TiO2 modification gives an excellent reproduction of the experimental value (-927 ppm) within +/- 7 ppm, however, the change in relative chemical shifts, EFGs and CSA suggest that the effect of the electrostatic arginine binding might be too small for experimental detection.

  7. Application of ChemDraw NMR Tool: Correlation of Program-Generated (Super 13)C Chemical Shifts and pK[subscript a] Values of Para-Substituted Benzoic Acids

    ERIC Educational Resources Information Center

    Hongyi Wang

    2005-01-01

    A study uses the ChemDraw nuclear magnetic resonance spectroscopy (NMR) tool to process 15 para-substituted benzoic acids and generate (super 13)C NMR chemical shifts of C1 through C5. The data were plotted against their pK[subscript a] value and a fairly good linear fit was found for pK[subscript a] versus delta[subscript c1].

  8. Proton Resonance Frequency Chemical Shift Thermometry: Experimental Design and Validation Towards High-Resolution Non-Invasive Temperature Monitoring, and in vivo Experience in a Non-human Primate Model of Acute Ischemic Stroke

    PubMed Central

    Dehkharghani, Seena; Mao, Hui; Howell, Leonard; Zhang, Xiaodong; Pate, K S; Magrath, P R; Tong, Frank; Wei, L; Qiu, D; Fleischer, C; Oshinski, J N

    2016-01-01

    BACKGROUND AND PURPOSE Applications for non-invasive biological temperature monitoring are widespread in biomedicine, and of particular interest in the context of brain temperature regulation, where traditionally costly and invasive monitoring schemes limit their applicability in many settings. Brain thermal regulation therefore remains controversial, motivating the development of non-invasive approaches such as temperature-sensitive NMR phenomena. The purpose of this work was to compare the utility of competing approaches to MR thermometry (MRT) employing proton resonance frequency chemical shift. Three methodologies were tested, hypothesizing the feasibility of a fast and accurate approach to chemical shift thermometry, in a phantom study at 3.0 Tesla. MATERIALS AND METHODS A conventional, paired approach (DIFF-1), an accelerated single-scan approach (DIFF-2), and a new, further accelerated strategy (DIFF-3) were tested. Phantom temperatures were modulated during real-time fiber optic temperature monitoring, with MRT derived simultaneously from temperature-sensitive changes in the water proton chemical shift (~0.01 ppm/°C). MRT was subsequently performed in a series of in vivo non-human primate experiments under physiologic and ischemic conditions testing its reproducibility and overall performance. RESULTS Chemical shift thermometry demonstrated excellent agreement with phantom temperatures for all three approaches (DIFF-1 linear regression R2=0.994, p<0.001, acquisition time 4 min 40 s; DIFF-2 R2=0.996, p<0.001, acquisition time 4 min; DIFF-3 R2=0.998, p<0.001, acquisition time 40 s). CONCLUSION These findings confirm the comparability in performance of three competing approaches MRT, and present in vivo applications under physiologic and ischemic conditions in a primate stroke model. PMID:25655874

  9. 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.

  10. Fluid Shifts

    NASA Technical Reports Server (NTRS)

    Stenger, M.; Hargens, A.; Dulchavsky, S.; Ebert, D.; Lee, S.; Lauriie, S.; Garcia, K.; Sargsyan, A.; Martin, D.; Ribeiro, L.; Lui, J.; Macias, B.; Arbeille, P.; Danielson, R.; Chang, D.; Johnston, S.; Ploutz-Snyder, R.; Smith, S.

    2016-01-01

    NASA is focusing on long-duration missions on the International Space Station (ISS) and future exploration-class missions beyond low-Earth orbit. Visual acuity changes observed after short-duration missions were largely transient, but more than 50% of ISS astronauts experienced more profound, chronic changes with objective structural and functional findings such as papilledema and choroidal folds. Globe flattening, optic nerve sheath dilation, and optic nerve tortuosity also are apparent. This pattern is referred to as the visual impairment and intracranial pressure (VIIP) syndrome. VIIP signs and symptoms, as well as postflight lumbar puncture data, suggest that elevated intracranial pressure (ICP) may be associated with the spaceflight-induced cephalad fluid shifts, but this hypothesis has not been tested. The purpose of this study is to characterize fluid distribution and compartmentalization associated with long-duration spaceflight, and to correlate these findings with vision changes and other elements of the VIIP syndrome. We also seek to determine whether the magnitude of fluid shifts during spaceflight, as well as the VIIP-related effects of those shifts, is predicted by the crewmember's preflight conditions and responses to acute hemodynamic manipulations (such as head-down tilt). Lastly, we will evaluate the patterns of fluid distribution in ISS astronauts during acute reversal of fluid shifts through application of lower body negative pressure (LBNP) interventions to characterize and explain general and individual responses. METHODS: We will examine a variety of physiologic variables in 10 long-duration ISS crewmembers using the test conditions and timeline presented in the Figure below. Measures include: (1) fluid compartmentalization (total body water by D2O, extracellular fluid by NaBr, intracellular fluid by calculation, plasma volume by CO rebreathe, interstitial fluid by calculation); (2) forehead/eyelids, tibia, calcaneus tissue thickness (by

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

    PubMed

    Sieh, Daniel; Kubiak, Clifford P

    2016-07-18

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

  12. A positioning QA procedure for 2D/2D (kV/MV) and 3D/3D (CT/CBCT) image matching for radiotherapy patient setup.

    PubMed

    Guan, Huaiqun; Hammoud, Rabih; Yin, Fang-Fang

    2009-10-06

    A positioning QA procedure for Varian's 2D/2D (kV/MV) and 3D/3D (planCT/CBCT) matching was developed. The procedure was to check: (1) the coincidence of on-board imager (OBI), portal imager (PI), and cone beam CT (CBCT)'s isocenters (digital graticules) to a linac's isocenter (to a pre-specified accuracy); (2) that the positioning difference detected by 2D/2D (kV/MV) and 3D/3D(planCT/CBCT) matching can be reliably transferred to couch motion. A cube phantom with a 2 mm metal ball (bb) at the center was used. The bb was used to define the isocenter. Two additional bbs were placed on two phantom surfaces in order to define a spatial location of 1.5 cm anterior, 1.5 cm inferior, and 1.5 cm right from the isocenter. An axial scan of the phantom was acquired from a multislice CT simulator. The phantom was set at the linac's isocenter (lasers); either AP MV/R Lat kV images or CBCT images were taken for 2D/2D or 3D/3D matching, respectively. For 2D/2D, the accuracy of each device's isocenter was obtained by checking the distance between the central bb and the digital graticule. Then the central bb in orthogonal DRRs was manually moved to overlay to the off-axis bbs in kV/MV images. For 3D/3D, CBCT was first matched to planCT to check the isocenter difference between the two CTs. Manual shifts were then made by moving CBCT such that the point defined by the two off-axis bbs overlay to the central bb in planCT. (PlanCT can not be moved in the current version of OBI1.4.) The manual shifts were then applied to remotely move the couch. The room laser was used to check the accuracy of the couch movement. For Trilogy (or Ix-21) linacs, the coincidence of imager and linac's isocenter was better than 1 mm (or 1.5 mm). The couch shift accuracy was better than 2 mm.

  13. Periodically sheared 2D Yukawa systems

    SciTech Connect

    Kovács, Anikó Zsuzsa; Hartmann, Peter; Donkó, Zoltán

    2015-10-15

    We present non-equilibrium molecular dynamics simulation studies on the dynamic (complex) shear viscosity of a 2D Yukawa system. We have identified a non-monotonic frequency dependence of the viscosity at high frequencies and shear rates, an energy absorption maximum (local resonance) at the Einstein frequency of the system at medium shear rates, an enhanced collective wave activity, when the excitation is near the plateau frequency of the longitudinal wave dispersion, and the emergence of significant configurational anisotropy at small frequencies and high shear rates.

  14. ENERGY LANDSCAPE OF 2D FLUID FORMS

    SciTech Connect

    Y. JIANG; ET AL

    2000-04-01

    The equilibrium states of 2D non-coarsening fluid foams, which consist of bubbles with fixed areas, correspond to local minima of the total perimeter. (1) The authors find an approximate value of the global minimum, and determine directly from an image how far a foam is from its ground state. (2) For (small) area disorder, small bubbles tend to sort inwards and large bubbles outwards. (3) Topological charges of the same sign repel while charges of opposite sign attract. (4) They discuss boundary conditions and the uniqueness of the pattern for fixed topology.

  15. Codon Constraints on Closed 2D Shapes,

    DTIC Science & Technology

    2014-09-26

    19843$ CODON CONSTRAINTS ON CLOSED 2D SHAPES Go Whitman Richards "I Donald D. Hoffman’ D T 18 Abstract: Codons are simple primitives for describing plane...RSONAL AUT"ORtIS) Richards, Whitman & Hoffman, Donald D. 13&. TYPE OF REPORT 13b. TIME COVERED N/A P8 AT F RRrT t~r. Ago..D,) is, PlE COUNT Reprint...outlines, if figure and ground are ignored. Later, we will address the problem of indexing identical codon descriptors that have different figure

  16. Search for H2D(+) at 372 GHz in dense interstellar clouds

    NASA Technical Reports Server (NTRS)

    Pagani, L.; Wannier, P. G.; Frerking, M. A.; Kuiper, T. B. H.; Gulkis, S.; Zimmermann, P.; Encrenaz, P. J.; Whiteoak, J. B.; Destombes, J. L.; Pickett, H. M.

    1992-01-01

    The 1(10)-1(11) transition of ortho-H2D(+) at 372 GHz has been sought in several dark clouds. The transition was not detected; the best upper limits obtained are about 0.3 K (3 sigma). We derive upper limits for the ortho-H2D(+) column density and briefly discuss their meaning in comparison with a simple chemical model we have developed (Pagani et al., 1992).

  17. Large-area high-quality 2D ultrathin Mo2C superconducting crystals.

    PubMed

    Xu, Chuan; Wang, Libin; Liu, Zhibo; Chen, Long; Guo, Jingkun; Kang, Ning; Ma, Xiu-Liang; Cheng, Hui-Ming; Ren, Wencai

    2015-11-01

    Transition metal carbides (TMCs) are a large family of materials with many intriguing properties and applications, and high-quality 2D TMCs are essential for investigating new physics and properties in the 2D limit. However, the 2D TMCs obtained so far are chemically functionalized, defective nanosheets having maximum lateral dimensions of ∼10 μm. Here we report the fabrication of large-area high-quality 2D ultrathin α-Mo2C crystals by chemical vapour deposition (CVD). The crystals are a few nanometres thick, over 100 μm in size, and very stable under ambient conditions. They show 2D characteristics of superconducting transitions that are consistent with Berezinskii-Kosterlitz-Thouless behaviour and show strong anisotropy with magnetic field orientation; moreover, the superconductivity is also strongly dependent on the crystal thickness. Our versatile CVD process allows the fabrication of other high-quality 2D TMC crystals, such as ultrathin WC and TaC crystals, which further expand the large family of 2D materials.

  18. Large-area high-quality 2D ultrathin Mo2C superconducting crystals

    NASA Astrophysics Data System (ADS)

    Xu, Chuan; Wang, Libin; Liu, Zhibo; Chen, Long; Guo, Jingkun; Kang, Ning; Ma, Xiu-Liang; Cheng, Hui-Ming; Ren, Wencai

    2015-11-01

    Transition metal carbides (TMCs) are a large family of materials with many intriguing properties and applications, and high-quality 2D TMCs are essential for investigating new physics and properties in the 2D limit. However, the 2D TMCs obtained so far are chemically functionalized, defective nanosheets having maximum lateral dimensions of ~10 μm. Here we report the fabrication of large-area high-quality 2D ultrathin α-Mo2C crystals by chemical vapour deposition (CVD). The crystals are a few nanometres thick, over 100 μm in size, and very stable under ambient conditions. They show 2D characteristics of superconducting transitions that are consistent with Berezinskii-Kosterlitz-Thouless behaviour and show strong anisotropy with magnetic field orientation; moreover, the superconductivity is also strongly dependent on the crystal thickness. Our versatile CVD process allows the fabrication of other high-quality 2D TMC crystals, such as ultrathin WC and TaC crystals, which further expand the large family of 2D materials.

  19. Remarks on thermalization in 2D CFT

    NASA Astrophysics Data System (ADS)

    de Boer, Jan; Engelhardt, Dalit

    2016-12-01

    We revisit certain aspects of thermalization in 2D conformal field theory (CFT). In particular, we consider similarities and differences between the time dependence of correlation functions in various states in rational and non-rational CFTs. We also consider the distinction between global and local thermalization and explain how states obtained by acting with a diffeomorphism on the ground state can appear locally thermal, and we review why the time-dependent expectation value of the energy-momentum tensor is generally a poor diagnostic of global thermalization. Since all 2D CFTs have an infinite set of commuting conserved charges, generic initial states might be expected to give rise to a generalized Gibbs ensemble rather than a pure thermal ensemble at late times. We construct the holographic dual of the generalized Gibbs ensemble and show that, to leading order, it is still described by a Banados-Teitelboim-Zanelli black hole. The extra conserved charges, while rendering c <1 theories essentially integrable, therefore seem to have little effect on large-c conformal field theories.

  20. Microwave Assisted 2D Materials Exfoliation

    NASA Astrophysics Data System (ADS)

    Wang, Yanbin

    Two-dimensional materials have emerged as extremely important materials with applications ranging from energy and environmental science to electronics and biology. Here we report our discovery of a universal, ultrafast, green, solvo-thermal technology for producing excellent-quality, few-layered nanosheets in liquid phase from well-known 2D materials such as such hexagonal boron nitride (h-BN), graphite, and MoS2. We start by mixing the uniform bulk-layered material with a common organic solvent that matches its surface energy to reduce the van der Waals attractive interactions between the layers; next, the solutions are heated in a commercial microwave oven to overcome the energy barrier between bulk and few-layers states. We discovered the minutes-long rapid exfoliation process is highly temperature dependent, which requires precise thermal management to obtain high-quality inks. We hypothesize a possible mechanism of this proposed solvo-thermal process; our theory confirms the basis of this novel technique for exfoliation of high-quality, layered 2D materials by using an as yet unknown role of the solvent.

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

    NASA Astrophysics Data System (ADS)

    Umezono, Satoru; Okuno, Tsunehisa

    2013-10-01

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

  2. {sup 13}C chemical shift anisotropies for carbonate ions in cement minerals and the use of {sup 13}C, {sup 27}Al and {sup 29}Si MAS NMR in studies of Portland cement including limestone additions

    SciTech Connect

    Sevelsted, Tine F.; Herfort, Duncan

    2013-10-15

    {sup 13}C isotropic chemical shifts and chemical shift anisotropy parameters have been determined for a number of inorganic carbonates relevant in cement chemistry from slow-speed {sup 13}C MAS or {sup 13}C({sup 1}H) CP/MAS NMR spectra (9.4 T or 14.1 T) for {sup 13}C in natural abundance. The variation in the {sup 13}C chemical shift parameters is relatively small, raising some doubts that different carbonate species in Portland cement-based materials may not be sufficiently resolved in {sup 13}C MAS NMR spectra. However, it is shown that by combining {sup 13}C MAS and {sup 13}C({sup 1}H) CP/MAS NMR carbonate anions in anhydrous and hydrated phases can be distinguished, thereby providing valuable information about the reactivity of limestone in cement blends. This is illustrated for three cement pastes prepared from an ordinary Portland cement, including 0, 16, and 25 wt.% limestone, and following the hydration for up to one year. For these blends {sup 29}Si MAS NMR reveals that the limestone filler accelerates the hydration for alite and also results in a smaller fraction of tetrahedrally coordinated Al incorporated in the C-S-H phase. The latter result is more clearly observed in {sup 27}Al MAS NMR spectra of the cement–limestone blends and suggests that dissolved aluminate species in the cement–limestone blends readily react with carbonate ions from the limestone filler, forming calcium monocarboaluminate hydrate. -- Highlights: •{sup 13}C chemical shift anisotropies for inorganic carbonates from {sup 13}C MAS NMR. •Narrow {sup 13}C NMR chemical shift range (163–171 ppm) for inorganic carbonates. •Anhydrous and hydrated carbonate species by {sup 13}C MAS and {sup 13}C({sup 1}H) CP/MAS NMR. •Limestone accelerates the hydration for alite in Portland – limestone cements. •Limestone reduces the amount of aluminium incorporated in the C-S-H phase.

  3. Solvent effects on 15N NMR coordination shifts.

    PubMed

    Kleinmaier, Roland; Arenz, Sven; Karim, Alavi; Carlsson, Anna-Carin C; Erdélyi, Máté

    2013-01-01

    (15)N NMR chemical shift became a broadly utilized tool for characterization of complex structures and comparison of their properties. Despite the lack of systematic studies, the influence of solvent on the nitrogen coordination shift, Δ(15)N(coord), was hitherto claimed to be negligible. Herein, we report the dramatic impact of the local environment and in particular that of the interplay between solvent and substituents on Δ(15)N(coord). The comparative study of CDCl(3) and CD(3)CN solutions of silver(I)-bis(pyridine) and silver(I)-bis(pyridylethynyl)benzene complexes revealed the strong solvent dependence of their (15)N NMR chemical shift, with a solvent dependent variation of up to 40 ppm for one and the same complex. The primary influence of the effect of substituent and counter ion on the (15)N NMR chemical shifts is rationalized by corroborating Density-Functional Theory (nor discrete Fourier transform) calculations on the B3LYP/6-311 + G(2d,p)//B3LYP/6-31G(d) level. Cooperative effects have to be taken into account for a comprehensive description of the coordination shift and thus the structure of silver complexes in solution. Our results demonstrate that interpretation of Δ(15)N(coord) in terms of coordination strength must always consider the solvent and counter ion. The comparable magnitude of Δ(15)N(coord) for reported transition metal complexes makes the principal findings most likely general for a broad scale of complexes of nitrogen donor ligands, which are in frequent use in modern organometallic chemistry.

  4. 2-D or not 2-D, that is the question: A Northern California test

    SciTech Connect

    Mayeda, K; Malagnini, L; Phillips, W S; Walter, W R; Dreger, D

    2005-06-06

    Reliable estimates of the seismic source spectrum are necessary for accurate magnitude, yield, and energy estimation. In particular, how seismic radiated energy scales with increasing earthquake size has been the focus of recent debate within the community and has direct implications on earthquake source physics studies as well as hazard mitigation. The 1-D coda methodology of Mayeda et al. has provided the lowest variance estimate of the source spectrum when compared against traditional approaches that use direct S-waves, thus making it ideal for networks that have sparse station distribution. The 1-D coda methodology has been mostly confined to regions of approximately uniform complexity. For larger, more geophysically complicated regions, 2-D path corrections may be required. The complicated tectonics of the northern California region coupled with high quality broadband seismic data provides for an ideal ''apples-to-apples'' test of 1-D and 2-D path assumptions on direct waves and their coda. Using the same station and event distribution, we compared 1-D and 2-D path corrections and observed the following results: (1) 1-D coda results reduced the amplitude variance relative to direct S-waves by roughly a factor of 8 (800%); (2) Applying a 2-D correction to the coda resulted in up to 40% variance reduction from the 1-D coda results; (3) 2-D direct S-wave results, though better than 1-D direct waves, were significantly worse than the 1-D coda. We found that coda-based moment-rate source spectra derived from the 2-D approach were essentially identical to those from the 1-D approach for frequencies less than {approx}0.7-Hz, however for the high frequencies (0.7{le} f {le} 8.0-Hz), the 2-D approach resulted in inter-station scatter that was generally 10-30% smaller. For complex regions where data are plentiful, a 2-D approach can significantly improve upon the simple 1-D assumption. In regions where only 1-D coda correction is available it is still preferable over 2

  5. Prediction of (195) Pt NMR chemical shifts of dissolution products of H2 [Pt(OH)6 ] in nitric acid solutions by DFT methods: how important are the counter-ion effects?

    PubMed

    Tsipis, Athanassios C; Karapetsas, Ioannis N

    2016-08-01

    (195) Pt NMR chemical shifts of octahedral Pt(IV) complexes with general formula [Pt(NO3 )n (OH)6 - n ](2-) , [Pt(NO3 )n (OH2 )6 - n ](4 - n) (n = 1-6), and [Pt(NO3 )6 - n  - m (OH)m (OH2 )n ](-2 + n - m) formed by dissolution of platinic acid, H2 [Pt(OH)6 ], in aqueous nitric acid solutions are calculated employing density functional theory methods. Particularly, the gauge-including atomic orbitals (GIAO)-PBE0/segmented all-electron relativistically contracted-zeroth-order regular approximation (SARC-ZORA)(Pt) ∪ 6-31G(d,p)(E)/Polarizable Continuum Model computational protocol performs the best. Excellent second-order polynomial plots of δcalcd ((195) Pt) versus δexptl ((195) Pt) chemical shifts and δcalcd ((195) Pt) versus the natural atomic charge QPt are obtained. Despite of neglecting relativistic and spin orbit effects the good agreement of the calculated δ (195) Pt chemical shifts with experimental values is probably because of the fact that the contribution of relativistic and spin orbit effects to computed σ(iso) (195) Pt magnetic shielding of Pt(IV) coordination compounds is effectively cancelled in the computed δ (195) Pt chemical shifts, because the relativistic corrections are expected to be similar in the complexes and the proper reference standard used. To probe the counter-ion effects on the (195) Pt NMR chemical shifts of the anionic [Pt(NO3 )n (OH)6 - n ](2-) and cationic [Pt(NO3 )n (OH2 )6 - n ](4 - n) (n = 0-3) complexes we calculated the (195) Pt NMR chemical shifts of the neutral (PyH)2 [Pt(NO3 )n (OH)6 - n ] (n = 1-6; PyH = pyridinium cation, C5 H5 NH(+) ) and [Pt(NO3 )n (H2 O)6 - n ](NO3 )4 - n (n = 0-3) complexes. Counter-anion effects are very important for the accurate prediction of the (195) Pt NMR chemical shifts of the cationic [Pt(NO3 )n (OH2 )6 - n ](4 - n) complexes, while counter-cation effects are less important for the anionic [Pt(NO3 )n (OH)6

  6. Fluid Shifts

    NASA Technical Reports Server (NTRS)

    Stenger, Michael; Hargens, A.; Dulchavsky, S.; Ebert, D.; Lee, S.; Sargsyan, A.; Martin, D.; Lui, J.; Macias, B.; Arbeille, P.; Platts, S.

    2014-01-01

    NASA is focusing on long-duration missions on the International Space Station (ISS) and future exploration-class missions beyond low Earth orbit. Visual acuity changes observed after short-duration missions were largely transient, but more than 30% of ISS astronauts experience more profound, chronic changes with objective structural and functional findings such as papilledema and choroidal folds. Globe flattening, optic nerve sheath dilation, and optic nerve tortuosity also are apparent. This pattern is referred to as the visual impairment and intracranial pressure (VIIP) syndrome. VIIP signs and symptoms, as well as postflight lumbar puncture data, suggest that elevated intracranial pressure (ICP) may be associated with the space flight-induced cephalad fluid shifts, but this hypothesis has not been tested. The purpose of this study is to characterize fluid distribution and compartmentalization associated with long-duration space flight, and to correlate these findings with vision changes and other elements of the VIIP syndrome. We also seek to determine whether the magnitude of fluid shifts during space flight, as well as the VIIP-related effects of those shifts, is predicted by the crewmember's pre-flight condition and responses to acute hemodynamic manipulations (such as head-down tilt). Lastly, we will evaluate the patterns of fluid distribution in ISS astronauts during acute reversal of fluid shifts through application of lower body negative pressure (LBNP) interventions to characterize and explain general and individual responses. We will examine a variety of physiologic variables in 10 long-duration ISS crewmembers using the test conditions and timeline presented in the Figure below. Measures include: (1) fluid compartmentalization (total body water by D2O, extracellular fluid by NaBr, intracellular fluid by calculation, plasma volume by CO rebreathe, interstitial fluid by calculation); (2) forehead/eyelids, tibia, calcaneus tissue thickness (by ultrasound

  7. 2D to 3D transition of polymeric carbon nitride nanosheets

    SciTech Connect

    Chamorro-Posada, Pedro; Vázquez-Cabo, José; Martín-Ramos, Pablo; Martín-Gil, Jesús; Navas-Gracia, Luis M.; Dante, Roberto C.

    2014-11-15

    The transition from a prevalent turbostratic arrangement with low planar interactions (2D) to an array of polymeric carbon nitride nanosheets with stronger interplanar interactions (3D), occurring for samples treated above 650 °C, was detected by terahertz-time domain spectroscopy (THz-TDS). The simulated 3D material made of stacks of shifted quasi planar sheets composed of zigzagged polymer ribbons, delivered a XRD simulated pattern in relatively good agreement with the experimental one. The 2D to 3D transition was also supported by the simulation of THz-TDS spectra obtained from quantum chemistry calculations, in which the same broad bands around 2 THz and 1.5 THz were found for 2D and 3D arrays, respectively. This transition was also in accordance with the tightening of the interplanar distance probably due to an interplanar π bond contribution, as evidenced also by a broad absorption around 2.6 eV in the UV–vis spectrum, which appeared in the sample treated at 650 °C, and increased in the sample treated at 700 °C. The band gap was calculated for 1D and 2D cases. The value of 3.374 eV for the 2D case is, within the model accuracy and precision, in a relative good agreement with the value of 3.055 eV obtained from the experimental results. - Graphical abstract: 2D lattice mode vibrations and structural changes correlated with the so called “2D to 3D transition”. - Highlights: • A 2D to 3D transition has been detected for polymeric carbon nitride. • THz-TDS allowed us to discover and detect the 2D to 3D transition of polymeric carbon nitride. • We propose a structure for polymeric carbon nitride confirming it with THz-TDS.

  8. Transition to turbulence: 2D directed percolation

    NASA Astrophysics Data System (ADS)

    Chantry, Matthew; Tuckerman, Laurette; Barkley, Dwight

    2016-11-01

    The transition to turbulence in simple shear flows has been studied for well over a century, yet in the last few years has seen major leaps forward. In pipe flow, this transition shows the hallmarks of (1 + 1) D directed percolation, a universality class of continuous phase transitions. In spanwisely confined Taylor-Couette flow the same class is found, suggesting the phenomenon is generic to shear flows. However in plane Couette flow the largest simulations and experiments to-date find evidence for a discrete transition. Here we study a planar shear flow, called Waleffe flow, devoid of walls yet showing the fundamentals of planar transition to turbulence. Working with a quasi-2D yet Navier-Stokes derived model of this flow we are able to attack the (2 + 1) D transition problem. Going beyond the system sizes previously possible we find all of the required scalings of directed percolation and thus establish planar shears flow in this class.

  9. 2D quantum gravity from quantum entanglement.

    PubMed

    Gliozzi, F

    2011-01-21

    In quantum systems with many degrees of freedom the replica method is a useful tool to study the entanglement of arbitrary spatial regions. We apply it in a way that allows them to backreact. As a consequence, they become dynamical subsystems whose position, form, and extension are determined by their interaction with the whole system. We analyze, in particular, quantum spin chains described at criticality by a conformal field theory. Its coupling to the Gibbs' ensemble of all possible subsystems is relevant and drives the system into a new fixed point which is argued to be that of the 2D quantum gravity coupled to this system. Numerical experiments on the critical Ising model show that the new critical exponents agree with those predicted by the formula of Knizhnik, Polyakov, and Zamolodchikov.

  10. Simulation of Yeast Cooperation in 2D.

    PubMed

    Wang, M; Huang, Y; Wu, Z

    2016-03-01

    Evolution of cooperation has been an active research area in evolutionary biology in decades. An important type of cooperation is developed from group selection, when individuals form spatial groups to prevent them from foreign invasions. In this paper, we study the evolution of cooperation in a mixed population of cooperating and cheating yeast strains in 2D with the interactions among the yeast cells restricted to their small neighborhoods. We conduct a computer simulation based on a game theoretic model and show that cooperation is increased when the interactions are spatially restricted, whether the game is of a prisoner's dilemma, snow drifting, or mutual benefit type. We study the evolution of homogeneous groups of cooperators or cheaters and describe the conditions for them to sustain or expand in an opponent population. We show that under certain spatial restrictions, cooperator groups are able to sustain and expand as group sizes become large, while cheater groups fail to expand and keep them from collapse.

  11. 2D Electrostatic Actuation of Microshutter Arrays

    NASA Technical Reports Server (NTRS)

    Burns, Devin E.; Oh, Lance H.; Li, Mary J.; Jones, Justin S.; Kelly, Daniel P.; Zheng, Yun; Kutyrev, Alexander S.; Moseley, Samuel H.

    2015-01-01

    An electrostatically actuated microshutter array consisting of rotational microshutters (shutters that rotate about a torsion bar) were designed and fabricated through the use of models and experiments. Design iterations focused on minimizing the torsional stiffness of the microshutters, while maintaining their structural integrity. Mechanical and electromechanical test systems were constructed to measure the static and dynamic behavior of the microshutters. The torsional stiffness was reduced by a factor of four over initial designs without sacrificing durability. Analysis of the resonant behavior of the microshutter arrays demonstrates that the first resonant mode is a torsional mode occurring around 3000 Hz. At low vacuum pressures, this resonant mode can be used to significantly reduce the drive voltage necessary for actuation requiring as little as 25V. 2D electrostatic latching and addressing was demonstrated using both a resonant and pulsed addressing scheme.

  12. Graphene suspensions for 2D printing

    NASA Astrophysics Data System (ADS)

    Soots, R. A.; Yakimchuk, E. A.; Nebogatikova, N. A.; Kotin, I. A.; Antonova, I. V.

    2016-04-01

    It is shown that, by processing a graphite suspension in ethanol or water by ultrasound and centrifuging, it is possible to obtain particles with thicknesses within 1-6 nm and, in the most interesting cases, 1-1.5 nm. Analogous treatment of a graphite suspension in organic solvent yields eventually thicker particles (up to 6-10 nm thick) even upon long-term treatment. Using the proposed ink based on graphene and aqueous ethanol with ethylcellulose and terpineol additives for 2D printing, thin (~5 nm thick) films with sheet resistance upon annealing ~30 MΩ/□ were obtained. With the ink based on aqueous graphene suspension, the sheet resistance was ~5-12 kΩ/□ for 6- to 15-nm-thick layers with a carrier mobility of ~30-50 cm2/(V s).

  13. Canard configured aircraft with 2-D nozzle

    NASA Technical Reports Server (NTRS)

    Child, R. D.; Henderson, W. P.

    1978-01-01

    A closely-coupled canard fighter with vectorable two-dimensional nozzle was designed for enhanced transonic maneuvering. The HiMAT maneuver goal of a sustained 8g turn at a free-stream Mach number of 0.9 and 30,000 feet was the primary design consideration. The aerodynamic design process was initiated with a linear theory optimization minimizing the zero percent suction drag including jet effects and refined with three-dimensional nonlinear potential flow techniques. Allowances were made for mutual interference and viscous effects. The design process to arrive at the resultant configuration is described, and the design of a powered 2-D nozzle model to be tested in the LRC 16-foot Propulsion Wind Tunnel is shown.

  14. Numerical Evaluation of 2D Ground States

    NASA Astrophysics Data System (ADS)

    Kolkovska, Natalia

    2016-02-01

    A ground state is defined as the positive radial solution of the multidimensional nonlinear problem \\varepsilon propto k_ bot 1 - ξ with the function f being either f(u) =a|u|p-1u or f(u) =a|u|pu+b|u|2pu. The numerical evaluation of ground states is based on the shooting method applied to an equivalent dynamical system. A combination of fourth order Runge-Kutta method and Hermite extrapolation formula is applied to solving the resulting initial value problem. The efficiency of this procedure is demonstrated in the 1D case, where the maximal difference between the exact and numerical solution is ≈ 10-11 for a discretization step 0:00025. As a major application, we evaluate numerically the critical energy constant. This constant is defined as a functional of the ground state and is used in the study of the 2D Boussinesq equations.

  15. Full-Quantum chemical calculation of the absorption maximum of bacteriorhodopsin: a comprehensive analysis of the amino acid residues contributing to the opsin shift

    PubMed Central

    Hayashi, Tomohiko; Matsuura, Azuma; Sato, Hiroyuki; Sakurai, Minoru

    2012-01-01

    Herein, the absorption maximum of bacteriorhodopsin (bR) is calculated using our recently developed method in which the whole protein can be treated quantum mechanically at the level of INDO/S-CIS//ONIOM (B3LYP/6-31G(d,p): AMBER). The full quantum mechanical calculation is shown to reproduce the so-called opsin shift of bR with an error of less than 0.04 eV. We also apply the same calculation for 226 different bR mutants, each of which was constructed by replacing any one of the amino acid residues of the wild-type bR with Gly. This substitution makes it possible to elucidate the extent to which each amino acid contributes to the opsin shift and to estimate the inter-residue synergistic effect. It was found that one of the most important contributions to the opsin shift is the electron transfer from Tyr185 to the chromophore upon excitation. We also indicate that some aromatic (Trp86, Trp182) and polar (Ser141, Thr142) residues, located in the vicinity of the retinal polyene chain and the β-ionone ring, respectively, play an important role in compensating for the large blue-shift induced by both the counterion residues (Asp85, Asp212) and an internal water molecule (W402) located near the Schiff base linkage. In particular, the effect of Trp86 is comparable to that of Tyr185. In addition, Ser141 and Thr142 were found to contribute to an increase in the dipole moment of bR in the excited state. Finally, we provide a complete energy diagram for the opsin shift together with the contribution of the chromophore-protein steric interaction. PMID:27493528

  16. Unusual dimensionality effects and surface charge density in 2D Mg(OH)2.

    PubMed

    Suslu, Aslihan; Wu, Kedi; Sahin, Hasan; Chen, Bin; Yang, Sijie; Cai, Hui; Aoki, Toshihiro; Horzum, Seyda; Kang, Jun; Peeters, Francois M; Tongay, Sefaattin

    2016-02-05

    We present two-dimensional Mg(OH)2 sheets and their vertical heterojunctions with CVD-MoS2 for the first time as flexible 2D insulators with anomalous lattice vibration and chemical and physical properties. New hydrothermal crystal growth technique enabled isolation of environmentally stable monolayer Mg(OH)2 sheets. Raman spectroscopy and vibrational calculations reveal that the lattice vibrations of Mg(OH)2 have fundamentally different signature peaks and dimensionality effects compared to other 2D material systems known to date. Sub-wavelength electron energy-loss spectroscopy measurements and theoretical calculations show that Mg(OH)2 is a 6 eV direct-gap insulator in 2D, and its optical band gap displays strong band renormalization effects from monolayer to bulk, marking the first experimental confirmation of confinement effects in 2D insulators. Interestingly, 2D-Mg(OH)2 sheets possess rather strong surface polarization (charge) effects which is in contrast to electrically neutral h-BN materials. Using 2D-Mg(OH)2 sheets together with CVD-MoS2 in the vertical stacking shows that a strong change transfer occurs from n-doped CVD-MoS2 sheets to Mg(OH)2, naturally depleting the semiconductor, pushing towards intrinsic doping limit and enhancing overall optical performance of 2D semiconductors. Results not only establish unusual confinement effects in 2D-Mg(OH)2, but also offer novel 2D-insulating material with unique physical, vibrational, and chemical properties for potential applications in flexible optoelectronics.

  17. Unusual dimensionality effects and surface charge density in 2D Mg(OH)2

    PubMed Central

    Suslu, Aslihan; Wu, Kedi; Sahin, Hasan; Chen, Bin; Yang, Sijie; Cai, Hui; Aoki, Toshihiro; Horzum, Seyda; Kang, Jun; Peeters, Francois M.; Tongay, Sefaattin

    2016-01-01

    We present two-dimensional Mg(OH)2 sheets and their vertical heterojunctions with CVD-MoS2 for the first time as flexible 2D insulators with anomalous lattice vibration and chemical and physical properties. New hydrothermal crystal growth technique enabled isolation of environmentally stable monolayer Mg(OH)2 sheets. Raman spectroscopy and vibrational calculations reveal that the lattice vibrations of Mg(OH)2 have fundamentally different signature peaks and dimensionality effects compared to other 2D material systems known to date. Sub-wavelength electron energy-loss spectroscopy measurements and theoretical calculations show that Mg(OH)2 is a 6 eV direct-gap insulator in 2D, and its optical band gap displays strong band renormalization effects from monolayer to bulk, marking the first experimental confirmation of confinement effects in 2D insulators. Interestingly, 2D-Mg(OH)2 sheets possess rather strong surface polarization (charge) effects which is in contrast to electrically neutral h-BN materials. Using 2D-Mg(OH)2 sheets together with CVD-MoS2 in the vertical stacking shows that a strong change transfer occurs from n-doped CVD-MoS2 sheets to Mg(OH)2, naturally depleting the semiconductor, pushing towards intrinsic doping limit and enhancing overall optical performance of 2D semiconductors. Results not only establish unusual confinement effects in 2D-Mg(OH)2, but also offer novel 2D-insulating material with unique physical, vibrational, and chemical properties for potential applications in flexible optoelectronics. PMID:26846617

  18. 2D NMR-spectroscopic screening reveals polyketides in ladybugs.

    PubMed

    Deyrup, Stephen T; Eckman, Laura E; McCarthy, Patrick H; Smedley, Scott R; Meinwald, Jerrold; Schroeder, Frank C

    2011-06-14

    Small molecules of biological origin continue to yield the most promising leads for drug design, but systematic approaches for exploring nature's cache of structural diversity are lacking. Here, we demonstrate the use of 2D NMR spectroscopy to screen a library of biorationally selected insect metabolite samples for partial structures indicating the presence of new chemical entities. This NMR-spectroscopic survey enabled detection of novel compounds in complex metabolite mixtures without prior fractionation or isolation. Our screen led to discovery and subsequent isolation of two families of tricyclic pyrones in Delphastus catalinae, a tiny ladybird beetle that is employed commercially as a biological pest control agent. The D. catalinae pyrones are based on 23-carbon polyketide chains forming 1,11-dioxo-2,6,10-trioxaanthracene and 4,8-dioxo-1,9,13-trioxaanthracene derivatives, representing ring systems not previously found in nature. This study highlights the utility of 2D NMR-spectroscopic screening for exploring nature's structure space and suggests that insect metabolomes remain vastly underexplored.

  19. 2D NMR-spectroscopic screening reveals polyketides in ladybugs

    PubMed Central

    Deyrup, Stephen T.; Eckman, Laura E.; McCarthy, Patrick H.; Smedley, Scott R.; Meinwald, Jerrold; Schroeder, Frank C.

    2011-01-01

    Small molecules of biological origin continue to yield the most promising leads for drug design, but systematic approaches for exploring nature’s cache of structural diversity are lacking. Here, we demonstrate the use of 2D NMR spectroscopy to screen a library of biorationally selected insect metabolite samples for partial structures indicating the presence of new chemical entities. This NMR-spectroscopic survey enabled detection of novel compounds in complex metabolite mixtures without prior fractionation or isolation. Our screen led to discovery and subsequent isolation of two families of tricyclic pyrones in Delphastus catalinae, a tiny ladybird beetle that is employed commercially as a biological pest control agent. The D. catalinae pyrones are based on 23-carbon polyketide chains forming 1,11-dioxo-2,6,10-trioxaanthracene and 4,8-dioxo-1,9,13-trioxaanthracene derivatives, representing ring systems not previously found in nature. This study highlights the utility of 2D NMR-spectroscopic screening for exploring nature’s structure space and suggests that insect metabolomes remain vastly underexplored. PMID:21646540

  20. High-Frequency (13)C and (29)Si NMR Chemical Shifts in Diamagnetic Low-Valence Compounds of Tl(I) and Pb(II): Decisive Role of Relativistic Effects.

    PubMed

    Vícha, Jan; Marek, Radek; Straka, Michal

    2016-02-15

    The (13)C and (29)Si NMR signals of ligand atoms directly bonded to Tl(I) or Pb(II) heavy-element centers are predicted to resonate at very high frequencies, up to 400 ppm for (13)C and over 1000 ppm for (29)Si, outside the typical experimental NMR chemical-shift ranges for a given type of nuclei. The large (13)C and (29)Si NMR chemical shifts are ascribed to sizable relativistic spin-orbit effects, which can amount to more than 200 ppm for (13)C and more than 1000 ppm for (29)Si, values unexpected for diamagnetic compounds of the main group elements. The origin of the vast spin-orbit contributions to the (13)C and (29)Si NMR shifts is traced to the highly efficient 6p → 6p* metal-based orbital magnetic couplings and related to the 6p orbital-based bonding together with the low-energy gaps between the occupied and virtual orbital subspaces in the subvalent Tl(I) and Pb(II) compounds. New NMR spectral regions for these compounds are suggested based on the fully relativistic density functional theory calculations in the Dirac-Coulomb framework carefully calibrated on the experimentally known NMR data for Tl(I) and Pb(II) complexes.

  1. Fluid Shifts

    NASA Technical Reports Server (NTRS)

    Stenger, M. B.; Hargens, A. R.; Dulchavsky, S. A.; Arbeille, P.; Danielson, R. W.; Ebert, D. J.; Garcia, K. M.; Johnston, S. L.; Laurie, S. S.; Lee, S. M. C.; Liu, J.; Macias, B.; Martin, D. S.; Minkoff, L.; Ploutz-Snyder, R.; Ribeiro, L. C.; Sargsyan, A.; Smith, S. M.

    2017-01-01

    Introduction. NASA's Human Research Program is focused on addressing health risks associated with long-duration missions on the International Space Station (ISS) and future exploration-class missions beyond low Earth orbit. Visual acuity changes observed after short-duration missions were largely transient, but now more than 50 percent of ISS astronauts have experienced more profound, chronic changes with objective structural findings such as optic disc edema, globe flattening and choroidal folds. These structural and functional changes are referred to as the visual impairment and intracranial pressure (VIIP) syndrome. Development of VIIP symptoms may be related to elevated intracranial pressure (ICP) secondary to spaceflight-induced cephalad fluid shifts, but this hypothesis has not been tested. The purpose of this study is to characterize fluid distribution and compartmentalization associated with long-duration spaceflight and to determine if a relation exists with vision changes and other elements of the VIIP syndrome. We also seek to determine whether the magnitude of fluid shifts during spaceflight, as well as any VIIP-related effects of those shifts, are predicted by the crewmember's pre-flight status and responses to acute hemodynamic manipulations, specifically posture changes and lower body negative pressure. Methods. We will examine a variety of physiologic variables in 10 long-duration ISS crewmembers using the test conditions and timeline presented in the figure below. Measures include: (1) fluid compartmentalization (total body wa