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

Metaxas, Athena E.; Cort, John R.

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

Spin-echo based diagonal peak suppression in solid-state MAS NMR homonuclear chemical shift correlation spectra

NASA Astrophysics Data System (ADS)

Wang, Kaiyu; Zhang, Zhiyong; Ding, Xiaoyan; Tian, Fang; Huang, Yuqing; Chen, Zhong; Fu, Riqiang

2018-02-01

The feasibility of using the spin-echo based diagonal peak suppression method in solid-state MAS NMR homonuclear chemical shift correlation experiments is demonstrated. A complete phase cycling is designed in such a way that in the indirect dimension only the spin diffused signals are evolved, while all signals not involved in polarization transfer are refocused for cancellation. A data processing procedure is further introduced to reconstruct this acquired spectrum into a conventional two-dimensional homonuclear chemical shift correlation spectrum. A uniformly 13C, 15N labeled Fmoc-valine sample and the transmembrane domain of a human protein, LR11 (sorLA), in native Escherichia coli membranes have been used to illustrate the capability of the proposed method in comparison with standard 13C-13C chemical shift correlation experiments.

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

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

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

1990-04-10

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

Theoretical and experimental NMR study of protopine hydrochloride isomers.

PubMed

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

2005-07-01

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

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

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

Basse, Kristoffer; Shankar, Ravi; Bjerring, Morten

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

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-08-21

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

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

PubMed

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

2017-11-30

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

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

PubMed

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

2007-12-01

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

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

PubMed Central

Hong, Mei

2016-01-01

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

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

PubMed Central

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

2009-01-01

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

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.

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

NASA Astrophysics Data System (ADS)

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

2015-10-01

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), 1H MAS NMR spectra of rigid solids still suffer from poor resolution and severe peak overlap caused by the strong 1H-1H homonuclear dipolar couplings and narrow 1H 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) 1H 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 1H-1H 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 information for a variety of solid systems that possess high proton density.

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

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

Zhang, Rongchun; Mroue, Kamal H.; Ramamoorthy, Ayyalusamy, E-mail: ramamoor@umich.edu

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 rendermore » 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-level structural and dynamical information for a variety of solid systems that possess high proton density.« less

A Critical Assessment of the Performance of Protein-ligand Scoring Functions Based on NMR Chemical Shift Perturbations

PubMed Central

Wang, Bing; Westerhoff, Lance M.; Merz, Kenneth M.

2008-01-01

We have generated docking poses for the FKBP-GPI complex using eight docking programs, and compared their scoring functions with scoring based on NMR chemical shift perturbations (NMRScore). Because the chemical shift perturbation (CSP) is exquisitely sensitive on the orientation of ligand inside the binding pocket, NMRScore offers an accurate and straightforward approach to score different poses. All scoring functions were inspected by their abilities to highly rank the native-like structures and separate them from decoy poses generated for a protein-ligand complex. The overall performance of NMRScore is much better than that of energy-based scoring functions associated with docking programs in both aspects. In summary, we find that the combination of docking programs with NMRScore results in an approach that can robustly determine the binding site structure for a protein-ligand complex, thereby, providing a new tool facilitating the structure-based drug discovery process. PMID:17867664

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

PubMed

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

2018-05-10

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

Structure and electronic properties of azadirachtin.

PubMed

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

2014-02-01

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

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

PubMed

Hartman, Joshua D; Beran, Gregory J O

2014-11-11

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

NMR spectroscopic studies of a TAT-derived model peptide in imidazolium-based ILs: influence on chemical shifts and the cis/trans equilibrium state.

PubMed

Wiedemann, Christoph; Ohlenschläger, Oliver; Mrestani-Klaus, Carmen; Bordusa, Frank

2017-09-13

NMR spectroscopy was used to study systematically the impact of imidazolium-based ionic liquid (IL) solutions on a TAT-derived model peptide containing Xaa-Pro peptide bonds. The selected IL anions cover a wide range of the Hofmeister series of ions. Based on highly resolved one- and two-dimensional NMR spectra individual 1 H and 13 C peptide chemical shift differences were analysed and a classification of IL anions according to the Hofmeister series was derived. The observed chemical shift changes indicate significant interactions between the peptide and the ILs. In addition, we examined the impact of different ILs towards the cis/trans equilibrium state of the Xaa-Pro peptide bonds. In this context, the IL cations appear to be of exceptional importance for inducing an alteration of the native cis/trans equilibrium state of Xaa-Pro bonds in favour of the trans-isomers.

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

PubMed

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

2014-09-14

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

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

PubMed Central

Shen, Yang; Bax, Ad

2015-01-01

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

Osmotically shrunken LIPOCEST agents: an innovative class of magnetic resonance imaging contrast media based on chemical exchange saturation transfer.

PubMed

Terreno, Enzo; Delli Castelli, Daniela; Violante, Elisabetta; Sanders, Honorius M H F; Sommerdijk, Nico A J M; Aime, Silvio

2009-01-01

The peculiar properties of osmotically shrunken liposomes acting as magnetic resonance imaging-chemical exchange saturation transfer (MRI-CEST) contrast agents have been investigated. Attention has been primarily devoted to assessing the contribution arising from encapsulated and incorporated paramagnetic lanthanide(III)-based shift reagents in determining the chemical shift of the intraliposomal water protons, which is a relevant factor for generating the CEST contrast. It is demonstrated that a highly shifted resonance for the encapsulated water can be attained by increasing the percentage of the amphiphilic shift reagent incorporated in the liposome bilayer. It is also demonstrated that the shift contribution arising from the bulk magnetic susceptibility can be optimized through the modulation of the osmotic shrinkage. In terms of sensitivity, it is shown that the saturation transfer efficiency can be significantly improved by increasing the size of the vesicle, thus allowing a high number of exchangeable protons to be saturated. In addition, the role played by the intensity of the saturating radiofrequency field has also been highlighted.

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

PubMed

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

2008-03-01

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

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

PubMed

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

2008-06-01

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

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

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

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

2013-10-08

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

Application of ChemDraw NMR Tool: Correlation of Program-Generated 13C Chemical Shifts and pKa Values of para-Substituted Benzoic Acids

NASA Astrophysics Data System (ADS)

Wang, Hongyi

2005-09-01

An application of ChemDraw NMR Tool was demonstrated by correlation of program-generated 13 C NMR chemical shifts and p K a values of para-substituted benzoic acids. Experimental 13 C NMR chemical shifts were analyzed in the same way for comparison. The project can be used as an assignment at the end of the first-year organic chemistry course to review topics or explore new techniques: Hammett equation, acid base equilibrium theory, electronic nature of functional groups, inductive and resonance effects, structure reactivity relationship, NMR spectroscopy, literature search, database search, and ChemDraw software.

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

PubMed

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

2013-01-01

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

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

PubMed

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

1981-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2014-03-01

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

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

PubMed Central

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

2016-01-01

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

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

PubMed

Stueber, Dirk; Grant, David M

2002-09-04

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

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

PubMed

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

2016-01-01

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

INCORPORATING NONCHEMICAL STRESSORS INTO CUMMULATIVE RISK ASSESSMENTS

EPA Science Inventory

The risk assessment paradigm has begun to shift from assessing single chemicals using "reasonable worst case" assumptions for individuals to considering multiple chemicals and community-based models. Inherent in community-based risk assessment is examination of all stressors a...

Molecular dynamics averaging of Xe chemical shifts in liquids.

PubMed

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

2004-11-15

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

Knowledge-based nonuniform sampling in multidimensional NMR.

PubMed

Schuyler, Adam D; Maciejewski, Mark W; Arthanari, Haribabu; Hoch, Jeffrey C

2011-07-01

The full resolution afforded by high-field magnets is rarely realized in the indirect dimensions of multidimensional NMR experiments because of the time cost of uniformly sampling to long evolution times. Emerging methods utilizing nonuniform sampling (NUS) enable high resolution along indirect dimensions by sampling long evolution times without sampling at every multiple of the Nyquist sampling interval. While the earliest NUS approaches matched the decay of sampling density to the decay of the signal envelope, recent approaches based on coupled evolution times attempt to optimize sampling by choosing projection angles that increase the likelihood of resolving closely-spaced resonances. These approaches employ knowledge about chemical shifts to predict optimal projection angles, whereas prior applications of tailored sampling employed only knowledge of the decay rate. In this work we adapt the matched filter approach as a general strategy for knowledge-based nonuniform sampling that can exploit prior knowledge about chemical shifts and is not restricted to sampling projections. Based on several measures of performance, we find that exponentially weighted random sampling (envelope matched sampling) performs better than shift-based sampling (beat matched sampling). While shift-based sampling can yield small advantages in sensitivity, the gains are generally outweighed by diminished robustness. Our observation that more robust sampling schemes are only slightly less sensitive than schemes highly optimized using prior knowledge about chemical shifts has broad implications for any multidimensional NMR study employing NUS. The results derived from simulated data are demonstrated with a sample application to PfPMT, the phosphoethanolamine methyltransferase of the human malaria parasite Plasmodium falciparum.

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

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

PubMed

Mondal, Arobendo; Kaupp, Martin

2018-04-05

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

GIAO-DFT calculation of 15 N NMR chemical shifts of Schiff bases: Accuracy factors and protonation effects.

PubMed

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

2018-02-09

15 N NMR chemical shifts in the representative series of Schiff bases together with their protonated forms have been calculated at the density functional theory level in comparison with available experiment. A number of functionals and basis sets have been tested in terms of a better agreement with experiment. Complimentary to gas phase results, 2 solvation models, namely, a classical Tomasi's polarizable continuum model (PCM) and that in combination with an explicit inclusion of one molecule of solvent into calculation space to form supermolecule 1:1 (SM + PCM), were examined. Best results are achieved with PCM and SM + PCM models resulting in mean absolute errors of calculated 15 N NMR chemical shifts in the whole series of neutral and protonated Schiff bases of accordingly 5.2 and 5.8 ppm as compared with 15.2 ppm in gas phase for the range of about 200 ppm. Noticeable protonation effects (exceeding 100 ppm) in protonated Schiff bases are rationalized in terms of a general natural bond orbital approach. Copyright © 2018 John Wiley & Sons, Ltd.

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

PubMed

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

2016-01-05

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

Physics-based method to validate and repair flaws in protein structures

PubMed Central

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

2013-01-01

A method that makes use of information provided by the combination of 13Cα and 13Cβ chemical shifts, computed at the density functional level of theory, enables one to (i) validate, at the residue level, conformations of proteins and detect backbone or side-chain flaws by taking into account an ensemble average of chemical shifts over all of the conformations used to represent a protein, with a sensitivity of ∼90%; and (ii) provide a set of (χ1/χ2) torsional angles that leads to optimal agreement between the observed and computed 13Cα and 13Cβ chemical shifts. The method has been incorporated into the CheShift-2 protein validation Web server. To test the reliability of the provided set of (χ1/χ2) torsional angles, the side chains of all reported conformations of five NMR-determined protein models were refined by a simple routine, without using NOE-based distance restraints. The refinement of each of these five proteins leads to optimal agreement between the observed and computed 13Cα and 13Cβ chemical shifts for ∼94% of the flaws, on average, without introducing a significantly large number of violations of the NOE-based distance restraints for a distance range ≤ 0.5 Ǻ, in which the largest number of distance violations occurs. The results of this work suggest that use of the provided set of (χ1/χ2) torsional angles together with other observables, such as NOEs, should lead to a fast and accurate refinement of the side-chain conformations of protein models. PMID:24082119

Physics-based method to validate and repair flaws in protein structures.

PubMed

Martin, Osvaldo A; Arnautova, Yelena A; Icazatti, Alejandro A; Scheraga, Harold A; Vila, Jorge A

2013-10-15

A method that makes use of information provided by the combination of (13)C(α) and (13)C(β) chemical shifts, computed at the density functional level of theory, enables one to (i) validate, at the residue level, conformations of proteins and detect backbone or side-chain flaws by taking into account an ensemble average of chemical shifts over all of the conformations used to represent a protein, with a sensitivity of ∼90%; and (ii) provide a set of (χ1/χ2) torsional angles that leads to optimal agreement between the observed and computed (13)C(α) and (13)C(β) chemical shifts. The method has been incorporated into the CheShift-2 protein validation Web server. To test the reliability of the provided set of (χ1/χ2) torsional angles, the side chains of all reported conformations of five NMR-determined protein models were refined by a simple routine, without using NOE-based distance restraints. The refinement of each of these five proteins leads to optimal agreement between the observed and computed (13)C(α) and (13)C(β) chemical shifts for ∼94% of the flaws, on average, without introducing a significantly large number of violations of the NOE-based distance restraints for a distance range ≤ 0.5 , in which the largest number of distance violations occurs. The results of this work suggest that use of the provided set of (χ1/χ2) torsional angles together with other observables, such as NOEs, should lead to a fast and accurate refinement of the side-chain conformations of protein models.

APPROACHES FOR INCORPORATING NON-CHEMICAL STRESSORS INTO CUMULATIVE RISK ASSESSMENTS

EPA Science Inventory

Over the past twenty years, the risk assessment paradigm has gradually shifted from an individual chemical approach to a community-based model. Inherent in community-based risk assessment is consideration of the totality of stressors affecting a defined population including both ...

Chemical Mass Shifts in a Digital Linear Ion Trap as Analytical Identity of o-, m-, and p-Xylene.

PubMed

Sun, Lulu; Xue, Bing; Huang, Zhengxu; Cheng, Ping; Ma, Li; Ding, Li; Zhou, Zhen

2018-07-01

Chemical mass shifts between isomeric ions of o-, m-, and p-xylene were measured using a digital linear ion trap, and the directions and values of the shifts were found to be correlated to the collision cross sections of the isomers. Both forward and reverse scans were used and the chemical shifts for each pair of isomers in scans of opposite directions were in opposite signs. Using different voltage settings (namely the voltage dividing ratio-VDR) of the ion trap allows adding high order field components in the quadrupole field and results in larger chemical mass shifts. The differential chemical mass shift which combined the shifts from forward and reverse scans doubled the amount of chemical shift, e.g., 0.077 Th between o- and p-xylene, enough for identification of the type of isomer without using an additional ion mobility spectrometer. The feature of equal and opposite chemical mass shifts also allowed to null out the chemical mass shift by calculating the mean m/z value between the two opposite scans and remove or reduce the mass error caused by chemical mass shift. Graphical Abstract ᅟ.

Chemical Mass Shifts in a Digital Linear Ion Trap as Analytical Identity of o-, m-, and p-Xylene

NASA Astrophysics Data System (ADS)

Sun, Lulu; Xue, Bing; Huang, Zhengxu; Cheng, Ping; Ma, Li; Ding, Li; Zhou, Zhen

2018-04-01

Chemical mass shifts between isomeric ions of o-, m-, and p-xylene were measured using a digital linear ion trap, and the directions and values of the shifts were found to be correlated to the collision cross sections of the isomers. Both forward and reverse scans were used and the chemical shifts for each pair of isomers in scans of opposite directions were in opposite signs. Using different voltage settings (namely the voltage dividing ratio-VDR) of the ion trap allows adding high order field components in the quadrupole field and results in larger chemical mass shifts. The differential chemical mass shift which combined the shifts from forward and reverse scans doubled the amount of chemical shift, e.g., 0.077 Th between o- and p-xylene, enough for identification of the type of isomer without using an additional ion mobility spectrometer. The feature of equal and opposite chemical mass shifts also allowed to null out the chemical mass shift by calculating the mean m/z value between the two opposite scans and remove or reduce the mass error caused by chemical mass shift. [Figure not available: see fulltext.

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

PubMed Central

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

2014-01-01

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

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

PubMed

Klukowski, Piotr; Schubert, Mario

2018-06-15

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

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

PubMed

Yang, Kin S; Hudson, Bruce

2010-11-25

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

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

PubMed

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

2008-07-16

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

Chemical shifts of diamagnetic azafullerenes: (C 59N) 2 and C 59HN

NASA Astrophysics Data System (ADS)

Bühl, Michael; Curioni, Alessandro; Andreoni, Wanda

1997-08-01

13C and 15N chemical shifts have been calculated for the azafullerenes (C 59N) 2 and C 59HN using the GIAO (gauge including atomic orbitals)-SCF method based on the geometry obtained with the density functional theory BLYP scheme Our results are in good agreement with experimental data, in particular, for the "anomalous" shift of the saturated carbon. Combined with previous calculations of the structural stability and electronic as well as vibrational properties, the present findings confirm the calculated structures for both molecules and establish the [6,6]-closed configuration for the dimer.

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

PubMed

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

2014-01-21

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

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

PubMed

Karp, Jerome M; Eryilmaz, Ertan; Erylimaz, Ertan; Cowburn, David

2015-01-01

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

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

NASA Astrophysics Data System (ADS)

Ganesan, Aravindhan; Wang, Feng

2009-07-01

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

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

PubMed Central

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

2012-01-01

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

Animal-Free Chemical Safety Assessment

PubMed Central

Loizou, George D.

2016-01-01

The exponential growth of the Internet of Things and the global popularity and remarkable decline in cost of the mobile phone is driving the digital transformation of medical practice. The rapidly maturing digital, non-medical world of mobile (wireless) devices, cloud computing and social networking is coalescing with the emerging digital medical world of omics data, biosensors and advanced imaging which offers the increasingly realistic prospect of personalized medicine. Described as a potential “seismic” shift from the current “healthcare” model to a “wellness” paradigm that is predictive, preventative, personalized and participatory, this change is based on the development of increasingly sophisticated biosensors which can track and measure key biochemical variables in people. Additional key drivers in this shift are metabolomic and proteomic signatures, which are increasingly being reported as pre-symptomatic, diagnostic and prognostic of toxicity and disease. These advancements also have profound implications for toxicological evaluation and safety assessment of pharmaceuticals and environmental chemicals. An approach based primarily on human in vivo and high-throughput in vitro human cell-line data is a distinct possibility. This would transform current chemical safety assessment practice which operates in a human “data poor” to a human “data rich” environment. This could also lead to a seismic shift from the current animal-based to an animal-free chemical safety assessment paradigm. PMID:27493630

Use of 13Cα Chemical-Shifts in Protein Structure Determination

PubMed Central

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

2008-01-01

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

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

PubMed

Nakamura, S; Yang, H; Hirata, C; Kersaudy, F; Fujimoto, K

2017-06-28

Various DNA conformational changes are in correlation with biological events. In particular, DNA B-Z equilibrium showed a high correlation with translation and transcription. In this study, we developed a DNA probe containing 5-trifluoromethylcytidine or 5-trifluoromethylthymidine to detect DNA B-Z equilibrium using 19 F-NMR. Its probe enabled the quantitative detection of B-, Z-, and ss-DNA based on 19 F-NMR chemical shift change.

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. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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. Copyright (c) 2006 John Wiley & Sons, Ltd.

Influence of levels of information as presented by different technologies on students' understanding of acid, base, and ph concepts

NASA Astrophysics Data System (ADS)

Nakhleh, Mary B.; Krajcik, Joseph S.

We investigated how different levels of information presented by various technologies affected secondary students' understanding of acid, base, and pH concepts. Secondary students who were selected for the study had just completed their study of acid-base chemistry. No attempt was made to provide further instruction. We analyzed changes in the understanding of individual students by constructing concept maps from the propositions that the students used in interviews conducted before and after a series of acid-base titrations. After the initial interview, students were divided into three groups. Within each group, students individually performed the same set of titrations using different technologies: chemical indicators, pH meters, and microcomputer-based laboratories (MBL). After the titrations were completed, all students were interviewed again. We found that students using MBL exhibited a larger positive shift in their concept map scores, which indicates a greater differentiation and integration of their knowledge of acids and bases. The chemical indicator students exhibited a more moderate positive shift in their concept map scores, and the pH meter students exhibited a smaller positive shift. We also found that the MBL students constructed more inappropriate links in their concept maps than the chemical indicator or pH meter students. However, we speculate that this increased number of inappropriate links indicates a high level of involvement with the technology. We therefore argue that the level of information offered by the technology affected students' understanding of the chemical concepts.Received: 24 February 1993; Revised: 21 February 1994;

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

PubMed

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

2016-11-14

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

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

NASA Astrophysics Data System (ADS)

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

2017-09-01

An improved implementation of single-crystal magic-angle-spinning (MAS) NMR is presented which gives access to chemical shift tensors both in orientation (relative to the crystal axis system) and principal axis values. For mounting arbitrary crystals inside ordinary MAS rotors, a mounting tool is described which allows to relate the crystal orientation determined by diffraction techniques to the rotor coordinate system. The crystal is finally mounted into a MAS rotor equipped with a special insert which allows a defined reorientation of the single-crystal by 90°. The approach is based on the idea that the dispersive spectra, which are obtained when applying read-pulses at specific rotor-phases, not only yield the size of the eigenvalues but also encode the orientation of the different chemical shift (rank-2) tensors. For this purpose two 2D-data sets with orthogonal crystal orientation are fitted simultaneously. The presented analysis for chemical shift tensors is supported by an analytical formula which allows fast calculation of phase and amplitude of individual spinning side-bands and by a protocol which solves the problem of finding the correct reference phase of the spectrum. Different rotor-synchronized pulse-sequences are introduced for the same reason. Experiments are performed on L-alanine and O-phosphorylethanolamine and the observed errors are analyzed in detail. The experimental data are opposed to DFT-computed chemical shift tensors which have been obtained by the extended embedded ion method.

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…

Coupled-cluster based approach for core-level states in condensed phase: Theory and application to different protonated forms of aqueous glycine

DOE PAGES

Sadybekov, Arman; Krylov, Anna I.

2017-07-07

A theoretical approach for calculating core-level states in condensed phase is presented. The approach is based on equation-of-motion coupled-cluster theory (EOMCC) and effective fragment potential (EFP) method. By introducing an approximate treatment of double excitations in the EOM-CCSD (EOM-CC with single and double substitutions) ansatz, we address poor convergence issues that are encountered for the core-level states and significantly reduce computational costs. While the approximations introduce relatively large errors in the absolute values of transition energies, the errors are systematic. Consequently, chemical shifts, changes in ionization energies relative to reference systems, are reproduced reasonably well. By using different protonation formsmore » of solvated glycine as a benchmark system, we show that our protocol is capable of reproducing the experimental chemical shifts with a quantitative accuracy. The results demonstrate that chemical shifts are very sensitive to the solvent interactions and that explicit treatment of solvent, such as EFP, is essential for achieving quantitative accuracy.« less

Coupled-cluster based approach for core-level states in condensed phase: Theory and application to different protonated forms of aqueous glycine

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

Sadybekov, Arman; Krylov, Anna I.

A theoretical approach for calculating core-level states in condensed phase is presented. The approach is based on equation-of-motion coupled-cluster theory (EOMCC) and effective fragment potential (EFP) method. By introducing an approximate treatment of double excitations in the EOM-CCSD (EOM-CC with single and double substitutions) ansatz, we address poor convergence issues that are encountered for the core-level states and significantly reduce computational costs. While the approximations introduce relatively large errors in the absolute values of transition energies, the errors are systematic. Consequently, chemical shifts, changes in ionization energies relative to reference systems, are reproduced reasonably well. By using different protonation formsmore » of solvated glycine as a benchmark system, we show that our protocol is capable of reproducing the experimental chemical shifts with a quantitative accuracy. The results demonstrate that chemical shifts are very sensitive to the solvent interactions and that explicit treatment of solvent, such as EFP, is essential for achieving quantitative accuracy.« less

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

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

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

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

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

DOE PAGES

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

2017-12-06

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

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

NASA Astrophysics Data System (ADS)

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

2012-11-01

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

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.

[Study of the stability of pyrimido-[5,4-e]-1,2,4-triazine antibiotics in acid-base media by NMR spectroscopy].

PubMed

Esipov, S E; Chernyshev, A I; Shorshnev, S V; Iakushkina, N I; Antonovskiĭ, V L

1985-02-01

A comparative study of the NMR 1H and 13C spectra of reumycin, fervenulin and xanthothricin in aqueous acid-base media showed that at pH or pD ranging from 8.0 to 1.0 the antibiotics were chemically stable. By the ratio of the 1H and 13C chemical shifts of reumycin at pH 4.0-10.0 the pKa values of this antibiotic were determined: 6.7 in aqueous (D2O) solution and 8.76 in dimethylsulfoxide media. Alkalization of the solutions of reumycin (pH 12.0), fervenulin (pH 9.0) and xanthothricin (pH 8.0) resulted in irreversible chemical transformation of the antibiotics. The analysis of the chemical shifts in the PMR spectra of the transformation products revealed transformation of the uracil ring in reumycin and uracil and triazine rings in fervenulin and xanthothricin. Alkalization of the xanthothricin solutions resulted also in demethylation with formation of reumycin.

31P NMR Chemical Shifts of Solvents and Products Impurities in Biomass Pretreatments

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

Li, Mi; Yoo, Chang Geun; Pu, Yunqiao

The identification of chemical impurities is crucial in elucidating the structures of biorefinery products using nuclear magnetic resonance (NMR) spectroscopic analysis. In the current biorefinery platform, contaminants derived from pretreatment solvents and decomposition byproducts may lead to misassignment of the NMR spectra of biorefinery products (e.g, lignin and bio-oils). Therefore, we investigated in this paper 54 commonly reported compounds including alcohols, carbohydrates, organic acids, aromatics, aldehydes, and ionic liquids associated with biomass pretreatment using 31P NMR. The chemical shifts of these chemicals after derivatizing with 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane (TMDP) were provided. Finally, the 31P NMR signals of these derivatives could serve asmore » valuable and informative spectral data in characterizing lignocellulose-based compounds.« less

31P NMR Chemical Shifts of Solvents and Products Impurities in Biomass Pretreatments

DOE PAGES

Li, Mi; Yoo, Chang Geun; Pu, Yunqiao; ...

2017-12-05

The identification of chemical impurities is crucial in elucidating the structures of biorefinery products using nuclear magnetic resonance (NMR) spectroscopic analysis. In the current biorefinery platform, contaminants derived from pretreatment solvents and decomposition byproducts may lead to misassignment of the NMR spectra of biorefinery products (e.g, lignin and bio-oils). Therefore, we investigated in this paper 54 commonly reported compounds including alcohols, carbohydrates, organic acids, aromatics, aldehydes, and ionic liquids associated with biomass pretreatment using 31P NMR. The chemical shifts of these chemicals after derivatizing with 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane (TMDP) were provided. Finally, the 31P NMR signals of these derivatives could serve asmore » valuable and informative spectral data in characterizing lignocellulose-based compounds.« less

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

NASA Astrophysics Data System (ADS)

Belyakov, Vladimir A.; Burdov, Vladimir A.

2007-07-01

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

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

PubMed

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

2012-03-07

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

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

PubMed

Stephane Mananga, Eugene

2013-01-01

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

Calcium hydroxide as a processing base in alkali-aided pH-shift protein recovery process.

PubMed

Paker, Ilgin; Jaczynski, Jacek; Matak, Kristen E

2017-02-01

Protein may be recovered by using pH shifts to solubilize and precipitate protein. Typically, sodium hydroxide is used as the processing base; however, this has been shown to significantly increase sodium in the final recovered protein. Protein was extracted from black bullhead catfish (Ameiurus melas) using a pH-shift method. Protein was solubilized using either sodium hydroxide (NaOH) or calcium hydroxide (Ca(OH) 2 ) and precipitated at pH 5.5 using hydrochloric acid (HCl). Protein solubility was greater when Ca(OH) 2 was used compared to NaOH during this process. Using Ca(OH) 2 as the processing base yielded the greatest lipid recovery (P < 0.05) at 77 g 100 g -1 , whereas the greatest (P < 0.05) protein recovery yield was recorded as 53 g 100 g -1 protein using NaOH. Protein solubilized with Ca(OH) 2 had more (P < 0.05) calcium in the protein fraction, whereas using NaOH increased (P < 0.05) sodium content. Results of our study showed that protein solubility was increased and the recovered protein had significantly more calcium when Ca(OH) 2 was used as the processing base. Results showed both NaOH and Ca(OH) 2 to be an effective processing base for pH-shift protein recovery processes. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

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

NASA Astrophysics Data System (ADS)

Olsson, Lars; Cremer, Dieter

1996-11-01

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

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

PubMed

Dumez, Jean-Nicolas; Pickard, Chris J

2009-03-14

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

A Vision of the Chemical Engineering Curriculum of the Future

ERIC Educational Resources Information Center

Armstrong, Robert C.

2006-01-01

A dramatic shift in chemical engineering undergraduate education is envisioned, based on discipline-wide workshop discussions that have taken place over the last two years. Faculty from more than 53 universities and industry representatives from 19 companies participated. Through this process broad consensus has been developed regarding basic…

Relative Configuration of Natural Products Using NMR Chemical Shifts

USDA-ARS?s Scientific Manuscript database

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

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories

PubMed Central

Maia, Paulo; Rocha, Miguel

2015-01-01

SUMMARY Shifting from chemical to biotechnological processes is one of the cornerstones of 21st century industry. The production of a great range of chemicals via biotechnological means is a key challenge on the way toward a bio-based economy. However, this shift is occurring at a pace slower than initially expected. The development of efficient cell factories that allow for competitive production yields is of paramount importance for this leap to happen. Constraint-based models of metabolism, together with in silico strain design algorithms, promise to reveal insights into the best genetic design strategies, a step further toward achieving that goal. In this work, a thorough analysis of the main in silico constraint-based strain design strategies and algorithms is presented, their application in real-world case studies is analyzed, and a path for the future is discussed. PMID:26609052

Arginine Interactions with Anatase TiO2 (100) Surface and the Perturbation of 49Ti NMR Chemical Shifts - A DFT Investigation: Relevance to Renu-Seeram Bio Solar Cell

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

Koch, Rainer; Lipton, Andrew S.; Filipek, S.

2011-06-01

Density functional theoretical calculations have been utilized to investigate the interaction of the amino acid arginine with the (100) surface of anatase and the reproduction of experimentally measured 49Ti NMR chemical shifts of anatase. Significant binding of arginine through electrostatic interaction and hydrogen bonds of the arginine guanidinium protons to the TiO2 surface oxygen atoms is observed, allowing attachment of proteins to titania surfaces in the construction of bio-sensitized solar cells. GIAO-B3LYP/6-31G(d) NMR calculation of a three-layer model based on the experimental structure of this TiO2 modification gives an excellent reproduction of the experimental value (-927 ppm) within +/- 7more » ppm, however, the change in relative chemical shifts, EFGs and CSA suggest that the effect of the electrostatic arginine binding might be too small for experimental detection.« less

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

PubMed

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

2018-03-22

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

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

PubMed

Koes, David R; Vries, John K

2017-01-01

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

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

PubMed Central

2017-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2014-06-01

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

Accurate MR thermometry by hyperpolarized 129 Xe.

PubMed

Zhang, Le; Burant, Alex; McCallister, Andrew; Zhao, Victor; Koshlap, Karl M; Degan, Simone; Antonacci, Michael; Branca, Rosa Tamara

2017-09-01

To investigate the temperature dependence of the resonance frequency of lipid-dissolved xenon (LDX) and to assess the accuracy of LDX-based MR thermometry. The chemical shift temperature dependence of water protons, methylene protons, and LDX was measured from samples containing tissues with varying fat contents using a high-resolution NMR spectrometer. LDX results were then used to acquire relative and absolute temperature maps in vivo and the results were compared with PRF-based MR thermometry. The temperature dependence of proton resonance frequency (PRF) is strongly affected by the specific distribution of water and fat. A redistribution of water and fat compartments can reduce the apparent temperature dependence of the water chemical shift from -0.01 ppm/°C to -0.006 ppm, whereas the LDX chemical shift shows a consistent temperature dependence of -0.21 ppm/°C. The use of the methylene protons resonance frequency as internal reference improves the accuracy of LDX-based MR thermometry, but degrades that of PRF-based MR thermometry, as microscopic susceptibility gradients affected lipid and water spins differently. The LDX resonance frequency, with its higher temperature dependence, provides more accurate and precise temperature measurements, both in vitro and in vivo. More importantly, the resonance frequency of nearby methylene protons can be used to extract absolute temperature information. Magn Reson Med 78:1070-1079, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

{sup 13}C chemical shift anisotropies for carbonate ions in cement minerals and the use of {sup 13}C, {sup 27}Al and {sup 29}Si MAS NMR in studies of Portland cement including limestone additions

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

Sevelsted, Tine F.; Herfort, Duncan; Skibsted, Jørgen, E-mail: jskib@chem.au.dk

2013-10-15

{sup 13}C isotropic chemical shifts and chemical shift anisotropy parameters have been determined for a number of inorganic carbonates relevant in cement chemistry from slow-speed {sup 13}C MAS or {sup 13}C({sup 1}H) CP/MAS NMR spectra (9.4 T or 14.1 T) for {sup 13}C in natural abundance. The variation in the {sup 13}C chemical shift parameters is relatively small, raising some doubts that different carbonate species in Portland cement-based materials may not be sufficiently resolved in {sup 13}C MAS NMR spectra. However, it is shown that by combining {sup 13}C MAS and {sup 13}C({sup 1}H) CP/MAS NMR carbonate anions in anhydrousmore » and hydrated phases can be distinguished, thereby providing valuable information about the reactivity of limestone in cement blends. This is illustrated for three cement pastes prepared from an ordinary Portland cement, including 0, 16, and 25 wt.% limestone, and following the hydration for up to one year. For these blends {sup 29}Si MAS NMR reveals that the limestone filler accelerates the hydration for alite and also results in a smaller fraction of tetrahedrally coordinated Al incorporated in the C-S-H phase. The latter result is more clearly observed in {sup 27}Al MAS NMR spectra of the cement–limestone blends and suggests that dissolved aluminate species in the cement–limestone blends readily react with carbonate ions from the limestone filler, forming calcium monocarboaluminate hydrate. -- Highlights: •{sup 13}C chemical shift anisotropies for inorganic carbonates from {sup 13}C MAS NMR. •Narrow {sup 13}C NMR chemical shift range (163–171 ppm) for inorganic carbonates. •Anhydrous and hydrated carbonate species by {sup 13}C MAS and {sup 13}C({sup 1}H) CP/MAS NMR. •Limestone accelerates the hydration for alite in Portland – limestone cements. •Limestone reduces the amount of aluminium incorporated in the C-S-H phase.« less

Conformational analysis of α-helical polypeptide included L-proline residue by high-resolution solid-state NMR measurement and quantum chemical calculation

NASA Astrophysics Data System (ADS)

Souma, Hiroyuki; Shoji, Akira; Kurosu, Hiromichi

2008-10-01

We challenged the problem about the stabilization mechanism of an α-helix formation for polypeptides containing L-proline (Pro) residue. We computed the optimized structure of α-helical poly( L-alanine) molecules including a Pro residue, H-(Ala) 8-Pro-(Ala) 9-OH, based on the molecular orbital calculation with density functional theory, B3LYP/6-31G(d) and the 13C and 15N chemical shift values based on the GIAO-CHF method with B3LYP/6-311G(d,p), respectively. It was found that two kinds of optimized structures, 'Bent structure' and 'Included α-helix structure', were preferred structures in H-(Ala) 8-Pro-(Ala) 9-OH. In addition, based on the precise 13C and 15N chemical shift data of the simple model, we successfully analyzed the secondary structure of well-defined synthetic polypeptide H-(Phe-Leu-Ala) 3-Phe C-Pro-Ala N-(Phe-Leu-Ala) 2-OH (FLA-11P), the secondary structure of which was proven to the 'Included α-helix structure'.

13C chemical-shift anisotropy of alkyl-substituted aromatic carbon in anthracene derivatives.

PubMed

Hoop, Cody L; Iuliucci, Robbie J

2013-06-01

The (13)C chemical-shift anisotropy in anthracene derivatives (9,10-dimethylanthracene, 9,10-dihydroanthracene, dianthracene, and triptycene) has been measured by the 2D FIREMAT timed pulse sequence and the corresponding set of principal values has been determined by the TIGER processing method. These molecules expand the data base of (13)C CSA measurements of fused aromatic rings some bridged by sp(3) carbon resulting in an unusual bonding configuration, which leads to distinctive aromatic (13)C CSA values. Crystal lattice distortions to the CSA were observed to change the isotropic shift by 2.5 to 3.3 ppm and changes as large as 8.3 ppm in principal components. Modeling of the CSA data by GIPAW DFT (GGA-PBE/ultrafine) shielding calculations resulted in an rms chemical-shift distance of 2.8 ppm after lattice including geometry optimization of the diffraction structures by the GIPAW method at GGA-PBE/ultrafine level. Attention is given to the substituted aromatic carbon in the phenyl groups (here forth referred to as the α-carbon) with respect to CSA modeling with electronic methods. The (13)C CSA of this position is accurately determined due to its spectral isolation of the isotropic shift that limits overlap in the FIREMAT spectrum. In cases where the bridging ring is sp(3) carbon, the current density is reduced from extending beyond the peripheral phenyl groups; this plays a significant role in the magnetic shielding of the α-position. Nuclear independent chemical-shift calculations based on GIAO DFT (B3LYP/6-31G(d)) shielding calculations were used to model the intramolecular π-interactions in dianthracene and triptycene. These NICS results estimate the isotropic shift of the α-position in dianthracene to be insignificantly affected by the presence of the neighboring aromatic rings. However, a notable change in isotropic shielding, Δσ(iso)=-2.1 ppm, is predicted for the α- position of triptycene. Experimentally, the δ22 principal component at the α-position for both dianthracene and triptycene increases by at least 12 ppm compared to 9,10-dihydroanthracene. To rationalize this change, shielding calculations in idealized structures are explored. The spatial position of the bicyclic scaffolding of the bridging ring plays a key role in the large increase in δ22 for the α-carbon. Copyright © 2013 Elsevier Inc. All rights reserved.

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

PubMed

Schreckenbach, Georg

2002-12-16

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

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

PubMed

Tamiola, Kamil; Mulder, Frans A A

2012-10-01

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

Theoretical NMR correlations based Structure Discussion.

PubMed

Junker, Jochen

2011-07-28

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

NMR crystallography of campho[2,3-c]pyrazole (Z' = 6): combining high-resolution 1H-13C solid-state MAS NMR spectroscopy and GIPAW chemical-shift calculations.

PubMed

Webber, Amy L; Emsley, Lyndon; Claramunt, Rosa M; Brown, Steven P

2010-09-30

(1)H-(13)C two-dimensional magic-angle spinning (MAS) solid-state NMR correlation spectra, recorded with the MAS-J-HMQC experiment, are presented for campho[2,3-c]pyrazole. For each (13)C moiety, there are six resonances associated with the six distinct molecules in the asymmetric unit cell (Z' = 6). The one-bond C-H correlations observed in the 2D (1)H-(13)C MAS-J-HMQC spectra allow the experimental determination of the (1)H and (13)C chemical shifts associated with the separate CH, CH(2), and CH(3) groups. (1)H and (13)C chemical shifts calculated by using the GIPAW (Gauge Including Projector Augmented Waves) plane-wave pseudopotential approach are presented. Calculations for the whole unit cell (12 × 29 = 348 atoms, with geometry optimization of all atoms) allow the assignment of the experimental (1)H and (13)C chemical shifts to the six distinct molecules. The calculated chemical shifts for the full crystal structure are compared with those for isolated molecules as extracted from the geometry-optimized crystal structure. In this way, the effect of intermolecular interactions on the observed chemical shifts is quantified. In particular, the calculations are sufficiently precise to differentiate the small (<1 ppm) differences between the (1)H chemical shifts of the six resonances associated with each distinct CH or CH(2) moiety.

NMR based solvent exchange experiments to understand the conformational preference of intrinsically disordered proteins using FG-nucleoporin peptide as a model

PubMed Central

Heisel, Kurt A.; Krishnan, V. V.

2014-01-01

The conformational preference of a peptide with three phenylalanine-glycine (FG) repeats from the intrinsically disordered domain of nucleoporin 159 (nup159) from the yeast nucleopore complex (NPC) is studied. Conformational states of this FG-peptide in dimethyl sulfoxide (DMSO), a non-native solvent are first studied. A solvent exchange scheme is designed and performed to understand how the conformational preferences of the peptide are altered as the solvent shifts from DMSO to water. An ensemble of structures of a 19-residue peptide is determined based on 13Cα, 1Hα, and 1HN chemical shifts and with inter-proton distances. An experimental model is then presented where chemical shifts and amide-proton temperature dependence is probed at changing DMSO to water ratios. These co-solvent experiments provide evidence of a conformational change as the fraction of water increases by the stark change in the behavior of amide protons under varied temperature. This investigation provides a NMR based experimental method in the field of intrinsically disordered proteins to realize conformational transitions from a non-native set of structures (in DMSO) to a native set of disordered conformers (in water). PMID:24037535

The effects of organosulfur compounds upon the storage stability of Jet A fuel. M.S. Thesis. Final Report

NASA Technical Reports Server (NTRS)

Heneman, F. C.

1981-01-01

This study examined the effect of sulfur-containing compounds on the storage stability of Jet A turbine fuel. It was found that alkyl sulfides and disulfides increased the fuel's stability while all thiols and thiophene derivatives tested decreased fuel stability (increased deposit formation) at temperatures and sulfur concentrations selected. Linear Arrhenius plots of sulfur-spiked fuel samples demonstrated that deposit formation decreased with increased slope for all alkyl sulfides, alkyl disulfides, thiols, and thiophene derivatives. A plot of insoluble deposit vs. concentration of added alkyl sulfide produces a negative slope. It appears that the inhibiting mechanism for alkyl sulfides is a result of the compound's reactivity with intermediate soluble precursors to deposit in the fuel. A method of approximating the relative basicity of weak organosulfur bases was developed via measurement of their resonance chemical shifts in proton NMR. Linear plots of log gm. deposit vs. change in chemical shift (shift differences between sulfur bases neat and complexed with I2) were found for alkyl sulfides and alkyl thiols. This suggests the possibility that increased deposit formation is due to base catalysis with these compound classes.

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

NASA Astrophysics Data System (ADS)

Ishii, Yoshitaka

2001-05-01

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

Solid-State 87Sr NMR Spectroscopy at Natural Abundance and High Magnetic Field Strength.

PubMed

Faucher, Alexandra; Terskikh, Victor V; Ye, Eric; Bernard, Guy M; Wasylishen, Roderick E

2015-12-10

Twenty-five strontium-containing solids were characterized via (87)Sr NMR spectroscopy at natural abundance and high magnetic field strength (B0 = 21.14 T). Strontium nuclear quadrupole coupling constants in these compounds are sensitive to the strontium site symmetry and range from 0 to 50.5 MHz. An experimental (87)Sr chemical shift scale is proposed, and available data indicate a chemical shift range of approximately 550 ppm, from -200 to +350 ppm relative to Sr(2+)(aq). In general, magnetic shielding increased with strontium coordination number. Experimentally measured chemical shift anisotropy is reported for stationary samples of solid powdered SrCl2·6H2O, SrBr2·6H2O, and SrCO3, with δaniso((87)Sr) values of +28, +26, and -65 ppm, respectively. NMR parameters were calculated using CASTEP, a gauge including projector augmented wave (GIPAW) DFT-based program, which addresses the periodic nature of solids using plane-wave basis sets. Calculated NMR parameters are in good agreement with those measured.

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

PubMed

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

2014-12-04

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

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

PubMed

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

2015-08-01

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

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

NASA Astrophysics Data System (ADS)

Pechkis, Daniel; Walter, Eric; Krakauer, Henry

2011-03-01

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

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

NASA Astrophysics Data System (ADS)

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

1998-11-01

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

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

PubMed

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

2014-01-14

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

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

NASA Astrophysics Data System (ADS)

Filatov, Michael; Cremer, Dieter

2003-07-01

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

Lanthanide ion (III) complexes of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate (DOTA-4AmP8−) for dual biosensing of pH with CEST (chemical exchange saturation transfer) and BIRDS (biosensor imaging of redundant deviation in shifts)

PubMed Central

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

2014-01-01

Relaxivity based magnetic resonance of phosphonated ligands chelated with gadolinium (Gd3+) shows promise for pH imaging. However instead of monitoring the paramagnetic effect of lanthanide complexes on the relaxivity of water protons, biosensor (or molecular) imaging with magnetic resonance is also possible by detecting either the non-exchangeable or the exchangeable protons on the lanthanide complexes themselves. The non-exchangeable protons (e.g., –CHx, where 3≥x≥1) are detected using a three-dimensional chemical shift imaging method called Biosensor Imaging of Redundant Deviation in Shifts (BIRDS), whereas the exchangeable protons (e.g., –OH or –NHy, where 2≥y≥1) are measured with Chemical Exchange Saturation Transfer (CEST) contrast. Here we tested the feasibility of BIRDS and CEST for pH imaging of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate (DOTA-4AmP8−) chelated with thulium (Tm3+) and ytterbium (Yb3+). BIRDS and CEST experiments show that both complexes are responsive to pH and temperature changes. Higher pH and temperature sensitivities are obtained with BIRDS for either complex when using the chemical shift difference between two proton resonances vs. using the chemical shift of a single proton resonance, thereby eliminating the need to use water resonance as reference. While CEST contrast for both agents is linearly dependent on pH within a relatively large range (i.e., 6.3-7.9), much stronger CEST contrast is obtained with YbDOTA-4AmP5− than with TmDOTA-4AmP5−. In addition, we demonstrate the prospect of using BIRDS to calibrate CEST as new platform for quantitative pH imaging. PMID:24801742

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

PubMed

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

2015-01-01

Relaxivity-based magnetic resonance of phosphonated ligands chelated with gadolinium (Gd(3+)) shows promise for pH imaging. However instead of monitoring the paramagnetic effect of lanthanide complexes on the relaxivity of water protons, biosensor (or molecular) imaging with magnetic resonance is also possible by detecting either the nonexchangeable or the exchangeable protons on the lanthanide complexes themselves. The nonexchangeable protons (e.g. -CHx, where 3 ≥ x ≥ 1) are detected using a three-dimensional chemical shift imaging method called biosensor imaging of redundant deviation in shifts (BIRDS), whereas the exchangeable protons (e.g. -OH or -NHy , where 2 ≥ y ≥ 1) are measured with chemical exchange saturation transfer (CEST) contrast. Here we tested the feasibility of BIRDS and CEST for pH imaging of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate (DOTA-4AmP(8-)) chelated with thulium (Tm(3+) ) and ytterbium (Yb(3+)). BIRDS and CEST experiments show that both complexes are responsive to pH and temperature changes. Higher pH and temperature sensitivities are obtained with BIRDS for either complex when using the chemical shift difference between two proton resonances vs using the chemical shift of a single proton resonance, thereby eliminating the need to use water resonance as reference. While CEST contrast for both agents is linearly dependent on pH within a relatively large range (i.e. 6.3-7.9), much stronger CEST contrast is obtained with YbDOTA-4AmP(5-) than with TmDOTA-4AmP(5-). In addition, we demonstrate the prospect of using BIRDS to calibrate CEST as new platform for quantitative pH imaging. Copyright © 2014 John Wiley & Sons, Ltd.

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

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

PubMed

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

2014-07-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

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

PubMed

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

2017-04-01

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

Solid-state NMR studies of form I of atorvastatin calcium.

PubMed

Wang, Wei David; Gao, Xudong; Strohmeier, Mark; Wang, Wei; Bai, Shi; Dybowski, Cecil

2012-03-22

Solid-state (13)C, (19)F, and (15)N magic angle spinning NMR studies of Form I of atorvastatin calcium are reported, including chemical shift tensors of all resolvable carbon sites and fluorine sites. The complete (13)C and (19)F chemical shift assignments are given based on an extensive analysis of (13)C-(1)H HETCOR and (13)C-(19)F HETCOR results. The solid-state NMR data indicate that the asymmetric unit of this material contains two atorvastatin molecules. A possible structure of Form I of atorvastatin calcium (ATC-I), derived from solid-state NMR data and density functional theory calculations of various structures, is proposed for this important active pharmaceutical ingredient (API).

Why is the antipodal effect in closo-1-SB9H9 so large? A possible explanation based on the geometry from the concerted use of gas electron diffraction and computational methods.

PubMed

Hnyk, Drahomír; Wann, Derek A; Holub, Josef; Samdal, Svein; Rankin, David W H

2011-06-07

The molecular structure of 1-thia-closo-decaborane(9), 1-SB(9)H(9), has been determined by the concerted use of gas electron diffraction and quantum-chemical calculations. Assuming C(4v) symmetry, the cage structure was distorted from a symmetrically bicapped square antiprism (D(4d) symmetry) mainly through substantial expansion of the tetragonal belt of boron atoms adjacent to sulfur. The S-B and (B-B)(mean) distances are well determined with r(h1) = 193.86(14) and 182.14(8) pm, respectively. Geometrical parameters calculated using the MP2(full)/6-311++G** method and at levels reported earlier [MP2(full)/6-311G**, B3LYP/6-311G** and B3LYP/cc-pVQZ], as well as calculated vibrational amplitudes and (11)B NMR chemical shifts, are in good agreement with the experimental findings. In particular, the so-called antipodal chemical shift of apical B(10) (71.8 ppm) is reproduced well by the GIAO-MP2 calculations and its large magnitude is schematically accounted for, as is the analogous antipodal chemical shift of B(12) in the twelve-vertex closo-1-SB(11)H(11).

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

Acid-base interactions and secondary structures of poly-L-lysine probed by 15N and 13C solid state NMR and Ab initio model calculations.

PubMed

Dos, Alexandra; Schimming, Volkmar; Tosoni, Sergio; Limbach, Hans-Heinrich

2008-12-11

The interactions of the 15N-labeled amino groups of dry solid poly-L-lysine (PLL) with various halogen and oxygen acids HX and the relation to the secondary structure have been studied using solid-state 15N and 13C CPMAS NMR spectroscopy (CP = cross polarization and MAS = magic angle spinning). For comparison, 15N NMR spectra of an aqueous solution of PLL were measured as a function of pH. In order to understand the effects of protonation and hydration on the 15N chemical shifts of the amino groups, DFT and chemical shielding calculations were performed on isolated methylamine-acid complexes and on periodic halide clusters of the type (CH3NH3(+)X(-))n. The combined experimental and computational results reveal low-field shifts of the amino nitrogens upon interaction with the oxygen acids HX = HF, H2SO4, CH3COOH, (CH3)2POOH, H3PO4, HNO3, and internal carbamic acid formed by reaction of the amino groups with gaseous CO2. Evidence is obtained that only hydrogen-bonded species of the type (Lys-NH2***H-X)n are formed in the absence of water. 15N chemical shifts are maximum when H is located in the hydrogen bond center and then decrease again upon full protonation, as found for aqueous solution at low pH. By contrast, halogen acids interact in a different way. They form internal salts of the type (Lys-NH3(+)X(-))n via the interaction of many acid-base pairs. This salt formation is possible only in the beta-sheet conformation. By contrast, the formation of hydrogen-bonded complexes can occur both in beta-sheet domains as well as in alpha-helical domains. The 15N chemical shifts of the protonated ammonium groups increase when the size of the interacting halogen anions is increased from chloride to iodide and when the number of the interacting anions is increased. Thus, the observed high-field 15N shift of ammonium groups upon hydration is the consequence of replacing interacting halogen atoms by oxygen atoms.

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

NASA Astrophysics Data System (ADS)

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

2009-03-01

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

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

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

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

2015-06-22

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

Molecular structure activity on pharmaceutical applications of Phenacetin using spectroscopic investigation

NASA Astrophysics Data System (ADS)

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

2017-01-01

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

Relationships Between Base-Catalyzed Hydrolysis Rates or Glutathione Reactivity for Acrylates and Methacrylates and Their NMR Spectra or Heat of Formation

PubMed Central

Fujisawa, Seiichiro; Kadoma, Yoshinori

2012-01-01

The NMR chemical shift, i.e., the π-electron density of the double bond, of acrylates and methacrylates is related to the reactivity of their monomers. We investigated quantitative structure-property relationships (QSPRs) between the base-catalyzed hydrolysis rate constants (k1) or the rate constant with glutathione (GSH) (log kGSH) for acrylates and methacrylates and the 13C NMR chemical shifts of their α,β-unsaturated carbonyl groups (δCα and δCβ) or heat of formation (Hf) calculated by the semi-empirical MO method. Reported data for the independent variables were employed. A significant linear relationship between k1 and δCβ, but not δCα, was obtained for methacrylates (r2 = 0.93), but not for acrylates. Also, a significant relationship between k1 and Hf was obtained for both acrylates and methacrylates (r2 = 0.89). By contrast, log kGSH for acrylates and methacrylates was linearly related to their δCβ (r2 = 0.99), but not to Hf. These findings indicate that the 13C NMR chemical shifts and calculated Hf values for acrylates and methacrylates could be valuable for estimating the hydrolysis rate constants and GSH reactivity of these compounds. Also, these data for monomers may be an important tool for examining mechanisms of reactivity. PMID:22754331

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

NASA Astrophysics Data System (ADS)

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

2011-11-01

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

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

NASA Astrophysics Data System (ADS)

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

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

Magic-angle spinning NMR of a class I filamentous bacteriophage virus.

PubMed

Abramov, Gili; Morag, Omry; Goldbourt, Amir

2011-08-11

The fd bacteriophage is a filamentous virus that is widely used for bio- and nanotechnology applications ranging from phage display to battery materials. The possibility of obtaining a detailed description of its structural properties regardless of its state is therefore essential not only for understanding its physical arrangement and its bacterial infection process but also for many other applications. Here we present a study of the fd phage by magic-angle spinning solid-state NMR. While current structures rely on a Y21M mutant, experiments performed on a strain bearing a wild-type capsid report on high symmetry of the phage and lack of explicit subunit polymorphism. Chemical shift analysis confirmed that the coat protein mostly consists of a rigid right-handed curved α-helix (residues 6-47 of 50), preceded by a flexible loop-structured N-terminus. We were able to qualitatively assign the resonances belonging to the DNA, including the deoxyribose sugars and the thymine bases. These chemical shifts are consistent with base stacking and a C2'-endo/C3'-exo sugar pucker. © 2011 American Chemical Society

Inner-shell chemical shift of DNA/RNA bases and inheritance from their parent purine and pyrimidine.

PubMed

Wang, Feng; Zhu, Quan; Ivanova, Elena

2008-11-01

Inner-shell electronic structures, properties and ionization spectra of DNA/RNA bases are studied with respect to their parent pyrimidine and purine species. Density functional theory B3LYP/aug-cc-pVTZ has been employed to produce the geometries of the bases, whereas LB94/et-pVQZ//B3LYP/aug-cc-pVTZ is used to calculate site-related Hirshfeld charges and core (vertical) ionization energies, as well as inner-shell spectra of C1s, N1s and O1s for DNA/RNA bases and their parent pyrimidine and purine species. The site-dependent variations of properties indicate the changes and inheritance of chemical environment when pyrimidine and purine become substituted. In general, although the changes are site-dependent, they are also ring-dependent. Pyrimidine bases change less significantly with respect to their parent pyrimidine than the purine bases with respect to their parent purine. Pyrimidine bases such as uracil, thymine and cytosine inherit certain properties from their parent pyrimidine, such as the Hirshfeld charge distributions and the order of core ionization energy level etc. No particular sites in the pyrimidine derivatives are engaged with a dramatic chemical shift nor with energy crossings to other sites. For the core shell spectra, the purine bases inherit very little from their parent purine, and guanine exhibits the least similarities to the parent among all the DNA/RNA bases.

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

PubMed

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

2006-02-23

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

Chemically cued suppression of coral reef resilience: Where is the tipping point?

NASA Astrophysics Data System (ADS)

Brooker, Rohan M.; Hay, Mark E.; Dixson, Danielle L.

2016-12-01

Coral reefs worldwide are shifting from high-diversity, coral-dominated communities to low-diversity systems dominated by seaweeds. This shift can impact essential recovery processes such as larval recruitment and ecosystem resilience. Recent evidence suggests that chemical cues from certain corals attract, and from certain seaweeds suppress, recruitment of juvenile fishes, with loss of coral cover and increases in seaweed cover creating negative feedbacks that prevent reef recovery and sustain seaweed dominance. Unfortunately, the level of seaweed increase and coral decline that creates this chemically cued tipping point remains unknown, depriving managers of data-based targets to prevent damaging feedbacks. We conducted flume and field assays that suggest juvenile fishes sense and respond to cues produced by low levels of seaweed cover. However, the herbivore species we tested was more tolerant of degraded reef cues than non-herbivores, possibly providing some degree of resilience if these fishes recruit, consume macroalgae, and diminish negative cues.

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

PubMed

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

2006-11-02

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

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2018-02-01

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

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.

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

PubMed Central

Vila, Jorge A.; Scheraga, Harold A.

2008-01-01

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

MetaboID: a graphical user interface package for assignment of 1H NMR spectra of bodyfluids and tissues.

PubMed

MacKinnon, Neil; Somashekar, Bagganahalli S; Tripathi, Pratima; Ge, Wencheng; Rajendiran, Thekkelnaycke M; Chinnaiyan, Arul M; Ramamoorthy, Ayyalusamy

2013-01-01

Nuclear magnetic resonance based measurements of small molecule mixtures continues to be confronted with the challenge of spectral assignment. While multi-dimensional experiments are capable of addressing this challenge, the imposed time constraint becomes prohibitive, particularly with the large sample sets commonly encountered in metabolomic studies. Thus, one-dimensional spectral assignment is routinely performed, guided by two-dimensional experiments on a selected sample subset; however, a publicly available graphical interface for aiding in this process is currently unavailable. We have collected spectral information for 360 unique compounds from publicly available databases including chemical shift lists and authentic full resolution spectra, supplemented with spectral information for 25 compounds collected in-house at a proton NMR frequency of 900 MHz. This library serves as the basis for MetaboID, a Matlab-based user interface designed to aid in the one-dimensional spectral assignment process. The tools of MetaboID were built to guide resonance assignment in order of increasing confidence, starting from cursory compound searches based on chemical shift positions to analysis of authentic spike experiments. Together, these tools streamline the often repetitive task of spectral assignment. The overarching goal of the integrated toolbox of MetaboID is to centralize the one dimensional spectral assignment process, from providing access to large chemical shift libraries to providing a straightforward, intuitive means of spectral comparison. Such a toolbox is expected to be attractive to both experienced and new metabolomic researchers as well as general complex mixture analysts. Copyright © 2012 Elsevier Inc. All rights reserved.

How do video-based demonstration assessment tasks affect problem-solving process, test anxiety, chemistry anxiety and achievement in general chemistry students?

NASA Astrophysics Data System (ADS)

Terrell, Rosalind Stephanie

2001-12-01

Because paper-and-pencil testing provides limited knowledge about what students know about chemical phenomena, we have developed video-based demonstrations to broaden measurement of student learning. For example, students might be shown a video demonstrating equilibrium shifts. Two methods for viewing equilibrium shifts are changing the concentration of the reactants and changing the temperature of the system. The students are required to combine the data collected from the video and their knowledge of chemistry to determine which way the equilibrium shifts. Video-based demonstrations are important techniques for measuring student learning because they require students to apply conceptual knowledge learned in class to a specific chemical problem. This study explores how video-based demonstration assessment tasks affect problem-solving processes, test anxiety, chemistry anxiety and achievement in general chemistry students. Several instruments were used to determine students' knowledge about chemistry, students' test and chemistry anxiety before and after treatment. Think-aloud interviews were conducted to determine students' problem-solving processes after treatment. The treatment group was compared to a control group and a group watching video demonstrations. After treatment students' anxiety increased and achievement decreased. There were also no significant differences found in students' problem-solving processes following treatment. These negative findings may be attributed to several factors that will be explored in this study.

Hyperpolarized 15N-pyridine Derivatives as pH-Sensitive MRI Agents

PubMed Central

Jiang, Weina; Lumata, Lloyd; Chen, Wei; Zhang, Shanrong; Kovacs, Zoltan; Sherry, A. Dean; Khemtong, Chalermchai

2015-01-01

Highly sensitive MR imaging agents that can accurately and rapidly monitor changes in pH would have diagnostic and prognostic value for many diseases. Here, we report an investigation of hyperpolarized 15N-pyridine derivatives as ultrasensitive pH-sensitive imaging probes. These molecules are easily polarized to high levels using standard dynamic nuclear polarization (DNP) techniques and their 15N chemical shifts were found to be highly sensitive to pH. These probes displayed sharp 15N resonances and large differences in chemical shifts (Δδ >90 ppm) between their free base and protonated forms. These favorable features make these agents highly suitable candidates for the detection of small changes in tissue pH near physiological values. PMID:25774436

Solution structure and stability of the DNA undecamer duplexes containing oxanine mismatch

PubMed Central

Pack, Seung Pil; Morimoto, Hirohisa; Makino, Keisuke; Tajima, Kunihiko; Kanaori, Kenji

2012-01-01

Solution structures of DNA duplexes containing oxanine (Oxa, O) opposite a cytosine (O:C duplex) and opposite a thymine (O:T duplex) have been solved by the combined use of 1H NMR and restrained molecular dynamics calculation. One mismatch pair was introduced into the center of the 11-mer duplex of [d(GTGACO6CACTG)/d(CAGTGX17GTCAC), X = C or T]. 1H NMR chemical shifts and nuclear Overhauser enhancement (NOE) intensities indicate that both the duplexes adopt an overall right-handed B-type conformation. Exchangeable resonances of C17 4-amino proton of the O:C duplex and of T17 imino proton of O:T duplex showed unusual chemical shifts, and disappeared with temperature increasing up to 30°C, although the melting temperatures were >50°C. The O:C mismatch takes a wobble geometry with positive shear parameter where the Oxa ring shifted toward the major groove and the paired C17 toward the minor groove, while, in the O:T mismatch pair with the negative shear, the Oxa ring slightly shifted toward the minor groove and the paired T17 toward the major groove. The Oxa mismatch pairs can be wobbled largely because of no hydrogen bond to the O1 position of the Oxa base, and may occupy positions in the strands that optimize the stacking with adjacent bases. PMID:22039100

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

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

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

2015-09-17

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

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

PubMed

Kanematsu, Yusuke; Tachikawa, Masanori

2014-04-28

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

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

PubMed

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

2017-06-29

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

Structure elucidation of the designer drug N-(1-amino-3,3-dimethyl-1-oxobutan-2-yl)-1-(5-fluoropentyl)-3-(4-fluorophenyl)-pyrazole-5-carboxamide and the relevance of predicted (13) C NMR shifts - a case study.

PubMed

Girreser, Ulrich; Rösner, Peter; Vasilev, Andrej

2016-07-01

The detailed structure elucidation process of the new cannabimimetic designer drug, N-(1-amino-3,3-dimethyl-1-oxobutan-2-yl)-1-(5-fluoropentyl)-3-(4-fluorophenyl)-pyrazole-5-carboxamide, with a highly substituted pyrazole skeleton, using nuclear magnetic resonance (NMR) spectroscopic and mass spectrometric (MS) techniques is described. After a first analysis of the NMR spectra and comparison with 48 possible pyrazole and imidazole structures, a subset of six positional isomeric pyrazoles and six imidazoles remained conceivable. Four substituents of the heterocyclic skeleton were identified: a proton bound to a pyrazole ring carbon atom; a 5-fluoropentyl group; a 4-fluorophenyl substituent; and a carbamoyl group, which is N-substituted with a methyl residue carrying a tert.-butyl and a carbamoyl substituent. The 5-fluoropentyl residue is situated at the nitrogen ring atom. Additional NMR experiments like the (1) H,(13) C HMBC were performed, but due to the small number of signals based on long-range couplings, the comparison of predicted and observed (13) C chemical shifts became necessary. The open access Internet shift prediction programs NMRDB, NMRSHIFTDB2, and CSEARCH were employed for the prediction of (13) C shift values which allowed an efficient and unambiguous structure determination. For the identified N-(1-amino-3,3-dimethyl-1-oxobutan-2-yl)-1-(5-fluoropentyl)-3-(4-fluorophenyl)-pyrazole-5-carboxamide, the best agreement between predicted (13) C shifts and the observed chemical shifts and long-range couplings for the pyrazole ring carbon atoms, with a standard error of about 2 ppm, was found with each of the predictions. For the comparison of measured and predicted chemical shifts model compounds with simple substituents proved helpful. The identified compound is a homologue of AZ-037 which is offered by Internet suppliers. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

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

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

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

2016-08-28

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

Role of 6-Mercaptopurine in the potential therapeutic targets DNA base pairs and G-quadruplex DNA: insights from quantum chemical and molecular dynamics simulations.

PubMed

Radhika, R; Shankar, R; Vijayakumar, S; Kolandaivel, P

2018-05-01

The theoretical studies on DNA with the anticancer drug 6-Mercaptopurine (6-MP) are investigated using theoretical methods to shed light on drug designing. Among the DNA base pairs considered, 6-MP is stacked with GC with the highest interaction energy of -46.19 kcal/mol. Structural parameters revealed that structure of the DNA base pairs is deviated from the planarity of the equilibrium position due to the formation of hydrogen bonds and stacking interactions with 6-MP. These deviations are verified through the systematic comparison between X-H bond contraction and elongation and the associated blue shift and red shift values by both NBO analysis and vibrational analysis. Bent's rule is verified for the C-H bond contraction in the 6-MP interacted base pairs. The AIM results disclose that the higher values of electron density (ρ) and Laplacian of electron density (∇ 2 ρ) indicate the increased overlap between the orbitals that represent the strong interaction and positive values of the total electron density show the closed-shell interaction. The relative sensitivity of the chemical shift values for the DNA base pairs with 6-MP is investigated to confirm the hydrogen bond strength. Molecular dynamics simulation studies of G-quadruplex DNA d(TGGGGT) 4 with 6-MP revealed that the incorporation of 6-MP appears to cause local distortions and destabilize the G-quadruplex DNA.

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

PubMed

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

2007-03-01

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

Water and lipid diffusion MRI using chemical shift displacement-based separation of lipid tissue (SPLIT).

PubMed

Ohno, Naoki; Kan, Hirohito; Miyati, Tosiaki; Aoki, Toshitaka; Ishida, Shota; Gabata, Toshifumi

2017-06-01

To obtain water and lipid diffusion-weighted images (DWIs) simultaneously, we devised a novel method utilizing chemical shift displacement-based separation of lipid tissue (SPLIT) imaging. Single-shot diffusion echo-planar imaging without fat suppression was used and the imaging parameters were optimized to separate water and lipid DWIs by chemical shift displacement of the lipid signals along the phase-encoding direction. Using the optimized conditions, transverse DWIs at the maximum diameter of the right calf were scanned with multiple b-values in five healthy subjects. Then, apparent diffusion coefficients (ADCs) were calculated in the tibialis anterior muscle (TA), tibialis bone marrow (TB), and subcutaneous fat (SF), as well as restricted and perfusion-related diffusion coefficients (D and D*, respectively) and the fraction of the perfusion-related diffusion component (F) for TA. Water and lipid DWIs were separated adequately. The mean ADCs of the TA, TB, and SF were 1.56±0.03mm 2 /s, 0.01±0.01mm 2 /s, and 0.06±0.02mm 2 /s, respectively. The mean D*, D, and F of the TA were 13.7±4.3mm 2 /s, 1.48±0.05mm 2 /s, and 4.3±1.6%, respectively. SPLIT imaging makes it possible to simply and simultaneously obtain water and lipid DWIs without special pulse sequence and increases the amount of diffusion information of water and lipid tissue. Copyright © 2017. Published by Elsevier Inc.

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

PubMed

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

2013-09-23

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

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

PubMed

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

2012-01-12

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

(3, 2)D 1H, 13C BIRDr,X-HSQC-TOCSY for NMR structure elucidation of mixtures: application to complex carbohydrates.

PubMed

Brodaczewska, Natalia; Košťálová, Zuzana; Uhrín, Dušan

2018-02-01

Overlap of NMR signals is the major cause of difficulties associated with NMR structure elucidation of molecules contained in complex mixtures. A 2D homonuclear correlation spectroscopy in particular suffers from low dispersion of 1 H chemical shifts; larger dispersion of 13 C chemical shifts is often used to reduce this overlap, while still providing the proton-proton correlation information e.g. in the form of a 2D 1 H, 13 C HSQC-TOCSY experiment. For this methodology to work, 13 C chemical shift must be resolved. In case of 13 C chemical shifts overlap, 1 H chemical shifts can be used to achieve the desired resolution. The proposed (3, 2)D 1 H, 13 C BIRD r,X -HSQC-TOCSY experiment achieves this while preserving singlet character of cross peaks in the F 1 dimension. The required high-resolution in the 13 C dimension is thus retained, while the cross peak overlap occurring in a regular HSQC-TOCSY experiment is eliminated. The method is illustrated on the analysis of a complex carbohydrate mixture obtained by depolymerisation of a fucosylated chondroitin sulfate isolated from the body wall of the sea cucumber Holothuria forskali.

NMR shifts for polycyclic aromatic hydrocarbons from first-principles

NASA Astrophysics Data System (ADS)

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

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

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

NASA Astrophysics Data System (ADS)

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

2016-11-01

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

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

PubMed

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

2018-01-19

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

Toxicity Testing in the 21st Century Beyond Environmental Chemicals

PubMed Central

Rovida, Costanza; Asakura, Shoji; Daneshian, Mardas; Hofman-Huether, Hana; Leist, Marcel; Meunier, Leo; Reif, David; Rossi, Anna; Schmutz, Markus; Valentin, Jean-Pierre; Zurlo, Joanne; Hartung, Thomas

2018-01-01

Summary After the publication of the report titled Toxicity Testing in the 21st Century – A Vision and a Strategy, many initiatives started to foster a major paradigm shift for toxicity testing – from apical endpoints in animal-based tests to mechanistic endpoints through delineation of pathways of toxicity (PoT) in human cell based systems. The US EPA has funded an important project to develop new high throughput technologies based on human cell based in vitro technologies. These methods are currently being incorporated into the chemical risk assessment process. In the pharmaceutical industry, the efficacy and toxicity of new drugs are evaluated during preclinical investigations that include drug metabolism, pharmacokinetics, pharmacodynamics and safety toxicology studies. The results of these studies are analyzed and extrapolated to predict efficacy and potential adverse effects in humans. However, due to the high failure rate of drugs during the clinical phases, a new approach for a more predictive assessment of drugs both in terms of efficacy and adverse effects is getting urgent. The food industry faces the challenge of assessing novel foods and food ingredients for the general population, while using animal safety testing for extrapolation purposes is often of limited relevance. The question is whether the latest paradigm shift proposed by the Tox21c report for chemicals may provide a useful tool to improve the risk assessment approach also for drugs and food ingredients. PMID:26168280

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

PubMed

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

2011-07-28

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

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

PubMed

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

2010-07-14

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

Crystal structure and X-ray photoemission spectroscopic study of A{sub 2}LaMO{sub 6} [A=Ba, Ca; M=Nb, Ta

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

Dutta, Alo, E-mail: alo_dutta@yahoo.com; Saha, Sujoy; Kumari, Premlata

2015-09-15

The X-ray photoemission spectroscopic (XPS) study of the double perovskite oxides A{sub 2}LaMO{sub 6} [A=Ba, Ca; M=Nb, Ta] synthesized by the solid-state reaction technique has been carried out to investigate the nature of the chemical state of the constituent ions and the bonding between them. The Rietveld refinement of the X-ray diffraction patterns suggests the monoclinic crystal structure of all the materials at room temperature. The negative and positive chemical shifts of the core level XPS spectrum of O-1s and Nb-3d{sub 3/2}/Ta-4f{sub 5/2} respectively suggest the covalent bonding between Nb/Ta cations and O ion. The change of the bonding strengthmore » between the anion and the cations from one material to another has been analyzed. The vibrational property of the materials is investigated using the room temperature Raman spectra. A large covalency of Ta-based compound than Nb compound is confirmed from the relative shifting of the Raman modes of the materials. - Graphical abstract: Crystal structure of two perovskite oxides CLN and CLT is investigated. XPS study confirms the two different co-ordination environments of Ca and covalent bonding between B-site cations and O-ion. - Highlights: • Ordered perovskite structure obtained by Rietveld refinement of XRD patterns. • Study of nature of chemical bonding by X-ray photoemission spectroscopy. • Opposite chemical shift of d-states of Nb/Ta with respect to O. • Covalent bonding between d-states of Nb/Ta and O. • Relative Raman shifts of CLN and CLT substantiate the more covalent character of Ta than Nb.« less

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…

Hydrogen bonds in betaine-acid (1:1) crystals revealed by Raman and 13C chemical shift tensors

NASA Astrophysics Data System (ADS)

Ilczyszyn, Marek; Ilczyszyn, Maria M.

2017-06-01

H-bonds of five betaine-acid (1:1) crystals are considered by analysis of tensors based on the Raman scissoring mode and 13C chemical shift of the betaine -CO1O2- carboxylate group. The leading structural factor in these systems is the strongest H-bond linking the betaine and the acidic moieties, (O1⋯H-O)com. The Raman and NMR tensors are strongly related to its character and to the R(O1⋯O)com distance. Very high molecular polarizability variation due to the scissoring vibration was found for the betaine-selenious acid crystal. The probable reason is modest network of H-bonds in this case and relatively high proton polarizability of these bonds.

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. Copyright © 2012 Elsevier Inc. All rights reserved.

The relativistic theory of the chemical shift

NASA Astrophysics Data System (ADS)

Pyper, N. C.

1983-04-01

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

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 solids. PMID:26801026

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

PubMed

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

2018-06-12

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

Chemical characterization of a prominent phosphomonoester resonance from mammalian brain. 31P and 1H NMR analysis at 4.7 and 14.1 tesla

NASA Astrophysics Data System (ADS)

Pettegrew, J. W.; Kopp, S. J.; Dadok, J.; Minshew, N. J.; Feliksik, J. M.; Glonek, T.; Cohen, M. M.

A prominent 31P NMR resonance at 3.84 ppm in mammalian brain has been identified as ethanolamine phosphate. The identification was based on 1H and 31P NMR findings (including pH titrations) at 4.7 and 14.1 T, as well as thin-layer chromatography studies. We previously incorrectly assigned the 3.84 ppm resonance to ribose-5-phosphate. The incorrect assignment occurred because the two compounds have very similar 31P chemical shifts, and because we did not carefully consider the effects of counter ions and ionic strengths when interpreting the 31P chemical shifts. In separate preliminary studies we have demonstrated ethanolamine phosphate to be high in immature developing brain and in the degenerating brain of Alzheimer's and Huntington's disease patients. Ethanolamine phosphate may therefore serve as a sensitive marker of membrane phospholipid turnover for both in vitro and in vivo31P NMR studies.

Molecular Docking and NMR Binding Studies to Identify Novel Inhibitors of Human Phosphomevalonate Kinase

PubMed Central

Boonsri, Pornthip; Neumann, Terrence S.; Olson, Andrew L.; Cai, Sheng; Herdendorf, Timothy J.; Miziorko, Henry M.; Hannongbua, Supa; Sem, Daniel S.

2012-01-01

Phosphomevalonate kinase (PMK) phosphorylates mevalonate-5-phosphate (M5P) in the mevalonate pathway, which is the sole source of isoprenoids and steroids in humans. We have identified new PMK inhibitors with virtual screening, using Autodock. Promising hits were verified and their affinity measured using NMR-based 1H-15N Heteronuclear Single Quantum Coherence (HSQC) chemical shift perturbation and fluorescence titrations. Chemical shift changes were monitored, plotted, and fitted to obtain dissociation constants (Kd). Tight binding compounds with Kd’s ranging from 6–60 µM were identified. These compounds tended to have significant polarity and negative charge, similar to the natural substrates (M5P and ATP). HSQC crosspeak changes suggest that binding induces a global conformational change, such as domain closure. Compounds identified in this study serve as chemical genetic probes of human PMK, to explore pharmacology of the mevalonate pathway, as well as starting points for further drug development. PMID:23146631

The application of tailor-made force fields and molecular dynamics for NMR crystallography: a case study of free base cocaine

PubMed Central

Neumann, Marcus A.

2017-01-01

Motional averaging has been proven to be significant in predicting the chemical shifts in ab initio solid-state NMR calculations, and the applicability of motional averaging with molecular dynamics has been shown to depend on the accuracy of the molecular mechanical force field. The performance of a fully automatically generated tailor-made force field (TMFF) for the dynamic aspects of NMR crystallography is evaluated and compared with existing benchmarks, including static dispersion-corrected density functional theory calculations and the COMPASS force field. The crystal structure of free base cocaine is used as an example. The results reveal that, even though the TMFF outperforms the COMPASS force field for representing the energies and conformations of predicted structures, it does not give significant improvement in the accuracy of NMR calculations. Further studies should direct more attention to anisotropic chemical shifts and development of the method of solid-state NMR calculations. PMID:28250956

Fluorescence-based thermal shift data on multidrug regulator AcrR from Salmonella enterica subsp. entrica serovar Typhimurium str. LT2.

PubMed

Manjasetty, Babu A; Halavaty, Andrei S; Luan, Chi-Hao; Osipiuk, Jerzy; Mulligan, Rory; Kwon, Keehwan; Anderson, Wayne F; Joachimiak, Andrzej

2016-06-01

The fluorescence-based thermal shift (FTS) data presented here include Table S1 and Fig. S1, and are supplemental to our original research article describing detailed structural, FTS, and fluorescence polarization analyses of the Salmonella enterica subsp. entrica serovar Typhimurium str. LT2 multidrug transcriptional regulator AcrR (StAcrR) (doi:10.1016/j.jsb.2016.01.008) (Manjasetty et al., 2015 [1]). Table S1 contains chemical formulas, a Chemical Abstracts Service (CAS) Registry Number (CAS no.), FTS rank (a ligand with the highest rank) has the largest difference in the melting temperature (ΔT m), and uses as drug molecules against various pathological conditions of sixteen small-molecule ligands that increase thermal stability of StAcrR. Thermal stability of human enolase 1, a negative control protein, was not affected in the presence of various concentrations of the top six StAcrR binders (Fig. S1).

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

PubMed

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

2018-08-01

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

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)

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

PubMed Central

Shen, Yang; Bax, Ad

2012-01-01

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

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

PubMed

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

2017-11-27

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

Energy barriers and rates of tautomeric transitions in DNA bases: ab initio quantum chemical study.

PubMed

Basu, Soumalee; Majumdar, Rabi; Das, Gourab K; Bhattacharyya, Dhananjay

2005-12-01

Tautomeric transitions of DNA bases are proton transfer reactions, which are important in biology. These reactions are involved in spontaneous point mutations of the genetic material. In the present study, intrinsic reaction coordinates (IRC) analyses through ab initio quantum chemical calculations have been carried out for the individual DNA bases A, T, G, C and also A:T and G:C base pairs to estimate the kinetic and thermodynamic barriers using MP2/6-31G** method for tautomeric transitions. Relatively higher values of kinetic barriers (about 50-60 kcal/mol) have been observed for the single bases, indicating that tautomeric alterations of isolated single bases are quite unlikely. On the other hand, relatively lower values of the kinetic barriers (about 20-25 kcal/mol) for the DNA base pairs A:T and G:C clearly suggest that the tautomeric shifts are much more favorable in DNA base pairs than in isolated single bases. The unusual base pairing A':C, T':G, C':A or G':T in the daughter DNA molecule, resulting from a parent DNA molecule with tautomeric shifts, is found to be stable enough to result in a mutation. The transition rate constants for the single DNA bases in addition to the base pairs are also calculated by computing the free energy differences between the transition states and the reactants.

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

PubMed

Fujisawa, Seiichiro; Kadoma, Yoshinori

2012-01-01

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

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

PubMed Central

Fujisawa, Seiichiro; Kadoma, Yoshinori

2012-01-01

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

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

PubMed Central

Viesser, Renan V.

2017-01-01

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

Quasichemical analysis of the cluster-pair approximation for the thermodynamics of proton hydration

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

Pollard, Travis; Beck, Thomas L.; Department of Physics, University of Cincinnati, Cincinnati, Ohio 45221

2014-06-14

A theoretical analysis of the cluster-pair approximation (CPA) is presented based on the quasichemical theory of solutions. The sought single-ion hydration free energy of the proton includes an interfacial potential contribution by definition. It is shown, however, that the CPA involves an extra-thermodynamic assumption that does not guarantee uniform convergence to a bulk free energy value with increasing cluster size. A numerical test of the CPA is performed using the classical polarizable AMOEBA force field and supporting quantum chemical calculations. The enthalpy and free energy differences are computed for the kosmotropic Na{sup +}/F{sup −} ion pair in water clusters ofmore » size n = 5, 25, 105. Additional calculations are performed for the chaotropic Rb{sup +}/I{sup −} ion pair. A small shift in the proton hydration free energy and a larger shift in the hydration enthalpy, relative to the CPA values, are predicted based on the n = 105 simulations. The shifts arise from a combination of sequential hydration and interfacial potential effects. The AMOEBA and quantum chemical results suggest an electrochemical surface potential of water in the range −0.4 to −0.5 V. The physical content of single-ion free energies and implications for ion-water force field development are also discussed.« less

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

PubMed

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

2017-02-28

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

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

PubMed

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

2018-05-01

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

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

PubMed

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

2003-03-03

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

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

NASA Astrophysics Data System (ADS)

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

2011-09-01

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

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

PubMed

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

2011-09-01

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

Chemical roots of biological evolution: the origins of life as a process of development of autonomous functional systems

PubMed Central

Ruiz-Mirazo, Kepa; Briones, Carlos

2017-01-01

In recent years, an extension of the Darwinian framework is being considered for the study of prebiotic chemical evolution, shifting the attention from homogeneous populations of naked molecular species to populations of heterogeneous, compartmentalized and functionally integrated assemblies of molecules. Several implications of this shift of perspective are analysed in this critical review, both in terms of the individual units, which require an adequate characterization as self-maintaining systems with an internal organization, and also in relation to their collective and long-term evolutionary dynamics, based on competition, collaboration and selection processes among those complex individuals. On these lines, a concrete proposal for the set of molecular control mechanisms that must be coupled to bring about autonomous functional systems, at the interface between chemistry and biology, is provided. PMID:28446711

Chemical roots of biological evolution: the origins of life as a process of development of autonomous functional systems.

PubMed

Ruiz-Mirazo, Kepa; Briones, Carlos; de la Escosura, Andrés

2017-04-01

In recent years, an extension of the Darwinian framework is being considered for the study of prebiotic chemical evolution, shifting the attention from homogeneous populations of naked molecular species to populations of heterogeneous, compartmentalized and functionally integrated assemblies of molecules. Several implications of this shift of perspective are analysed in this critical review, both in terms of the individual units, which require an adequate characterization as self-maintaining systems with an internal organization, and also in relation to their collective and long-term evolutionary dynamics, based on competition, collaboration and selection processes among those complex individuals. On these lines, a concrete proposal for the set of molecular control mechanisms that must be coupled to bring about autonomous functional systems, at the interface between chemistry and biology, is provided. © 2017 The Authors.

Non-Euclidean phasor analysis for quantification of oxidative stress in ex vivo human skin exposed to sun filters using fluorescence lifetime imaging microscopy

NASA Astrophysics Data System (ADS)

Osseiran, Sam; Roider, Elisabeth M.; Wang, Hequn; Suita, Yusuke; Murphy, Michael; Fisher, David E.; Evans, Conor L.

2017-12-01

Chemical sun filters are commonly used as active ingredients in sunscreens due to their efficient absorption of ultraviolet (UV) radiation. Yet, it is known that these compounds can photochemically react with UV light and generate reactive oxygen species and oxidative stress in vitro, though this has yet to be validated in vivo. One label-free approach to probe oxidative stress is to measure and compare the relative endogenous fluorescence generated by cellular coenzymes nicotinamide adenine dinucleotides and flavin adenine dinucleotides. However, chemical sun filters are fluorescent, with emissive properties that contaminate endogenous fluorescent signals. To accurately distinguish the source of fluorescence in ex vivo skin samples treated with chemical sun filters, fluorescence lifetime imaging microscopy data were processed on a pixel-by-pixel basis using a non-Euclidean separation algorithm based on Mahalanobis distance and validated on simulated data. Applying this method, ex vivo samples exhibited a small oxidative shift when exposed to sun filters alone, though this shift was much smaller than that imparted by UV irradiation. Given the need for investigative tools to further study the clinical impact of chemical sun filters in patients, the reported methodology may be applied to visualize chemical sun filters and measure oxidative stress in patients' skin.

Fiber-optic refractometer based on an etched high-Q π-phase-shifted fiber-Bragg-grating.

PubMed

Zhang, Qi; Ianno, Natale J; Han, Ming

2013-07-10

We present a compact and highly-sensitive fiber-optic refractometer based on a high-Q π-phase-shifted fiber-Bragg-grating (πFBG) that is chemically etched to the core of the fiber. Due to the p phase-shift, a strong πFBG forms a high-Q optical resonator and the reflection spectrum features an extremely narrow notch that can be used for highly sensitivity refractive index measurement. The etched πFBG demonstrated here has a diameter of ~9.3 μm and a length of only 7 mm, leading to a refractive index responsivity of 2.9 nm/RIU (RIU: refractive index unit) at an ambient refractive index of 1.318. The reflection spectrum of the etched πFBG features an extremely narrow notch with a linewidth of only 2.1 pm in water centered at ~1,550 nm, corresponding to a Q-factor of 7.4 × 10(5), which allows for potentially significantly improved sensitivity over refractometers based on regular fiber Bragg gratings.

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

PubMed Central

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

2009-01-01

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

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

PubMed

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

2016-11-01

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

Automation of the CAS Document Delivery Service.

ERIC Educational Resources Information Center

Steensland, M. C.; Soukup, K. M.

1986-01-01

The automation of online order retrieval for Chemical Abstracts Service Document Delivery Service was accomplished by shifting to an order retrieval/dispatch process linked to a Unix network. The Unix-based environment, its terminal emulation, page-break, and user-friendly interface software, and later enhancements are reviewed. Resultant increase…

Resonating periodic waveguides as ultraresolution sensors in biomedicine

NASA Astrophysics Data System (ADS)

Wawro, Debra D.; Priambodo, Purnomo; Magnusson, Robert

2004-10-01

Optical sensor technology based on subwavelength periodic waveguides is applied for tag-free, high-resolution biomedical and chemical detection. Measured resonance wavelength shifts of 6.4 nm for chemically attached Bovine Serum Albumin agree well with theory for a sensor tested in air. Reflection peak efficiencies of 90% are measured, and do not degrade upon biolayer attachment. Phase detection methods are investigated to enhance sensor sensitivity and resolution. Direct measurement of the resonant phase response is reported for the first time using ellipsometric measurement techniques.

Laser and biological methods of biomonitoring of surrounding waters

NASA Astrophysics Data System (ADS)

Posudin, Yuri I.

1994-02-01

Three main methods are proposed for the biomonitoring of chemicals in water medium: laser spectrofluorometry, which is based on the excitation and recording of the spectra of fluorescence; laser scattering, which is connected with measurement of the Doppler shifts of the scattered light from the motile cells; videomicrography, which provides the analysis of parameters of photomovement of motile cells via microscope and video system. Such chemicals as surface-active substances, heavy metals and pesticides were determined in water medium due to these methods.

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

PubMed

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

2014-03-18

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

Constant-time 2D and 3D through-bond correlation NMR spectroscopy of solids under 60 kHz MAS

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

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

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 themore » 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 3D {sup 1}H/{sup 13}C/{sup 1}H experiment would be useful to study the structure and dynamics of a variety of chemical and biological solids.« less

Protein Structure Determination from Pseudocontact Shifts Using ROSETTA

PubMed Central

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

2013-01-01

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

Pressure dependence of side chain 13C chemical shifts in model peptides Ac-Gly-Gly-Xxx-Ala-NH2.

PubMed

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

2017-10-01

For evaluating the pressure responses of folded as well as intrinsically unfolded proteins detectable by NMR spectroscopy the availability of data from well-defined model systems is indispensable. In this work we report the pressure dependence of 13 C chemical shifts of the side chain atoms in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH 2 (Xxx, one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of a number of nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The size of the polynomial pressure coefficients B 1 and B 2 is dependent on the type of atom and amino acid studied. For H N , N and C α the first order pressure coefficient B 1 is also correlated to the chemical shift at atmospheric pressure. The first and second order pressure coefficients of a given type of carbon atom 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 also are weakly correlated. The downfield shifts of the methyl resonances suggest that gauche conformers of the side chains are not preferred with pressure. The valine and leucine methyl groups in the model peptides were assigned using stereospecifically 13 C enriched amino acids with the pro-R carbons downfield shifted relative to the pro-S carbons.

Conceptual Change and Science Achievement Related to a Lesson Sequence on Acids and Bases Among African American Alternative High School Students: A Teacher's Practical Arguments and the Voice of the "Other"

NASA Astrophysics Data System (ADS)

Wood, Lynda Charese

The study of teaching and learning during the period of translating ideals of reform into classroom practice enables us to understand student-teacher-researcher symbiotic learning. In line with this assumption, the purpose of this study is threefold:(1) observe effects of the Common Knowledge Construction Model (CKCM), a conceptual change inquiry model of teaching and learning, on African American students' conceptual change and achievement; (2) observe the shift in teacher's practical arguments; and (3) narrate the voice of "the Other" about teacher professional learning. This study uses retrospective data from a mixed-method approach consisting of Phenomenography, practical arguments and story-telling. Data sources include audio-recordings of a chemistry teacher's individual interviews of her students' prior- and post-intervention conceptions of acids and bases; results of Acid-Base Achievement Test (ABA-T); video-recordings of a chemistry teacher's enactment of CKCM acid-base lesson sequence; audio-recordings of teacher-researcher reflective discourse using classroom video-clips; teacher interviews; and teacher and researcher personal reflective journals. Students' conceptual changes reflect change in the number of categories of description; shift in language use from everyday talk to chemical talk; and development of a hierarchy of chemical knowledge. ABA-T results indicated 17 students in the experimental group achieved significantly higher scores than 22 students in the control group taught by traditional teaching methods. The teacher-researcher reflective discourse about enactment of the CKCM acid-base lesson sequence reveals three major shifts in teacher practical arguments: teacher inadequate preparedness to adequate preparedness; lack of confidence to gain in confidence; and surface learning to deep learning. The developing story uncovers several aspects about teaching and learning of African American students: teacher caring for the uncared; cultivating student and teacher confidence; converting dependence on teacher and self to peer interdependence. The study outlines six implications: caring conceptual change inquiry model for the often unreached mind; developing simple chemical talk into coherent chemical explanation; using CKCM for alternative high school students' conceptual change and achievement; engaging teachers in elicitation and appraisal of practical arguments for reconstruction of beliefs; overcoming challenges in teacher practical argument research; and "storytelling" as a way of unpacking teacher transformation amidst complexities of classroom teaching and learning.

Resonance assignment of the NMR spectra of disordered proteins using a multi-objective non-dominated sorting genetic algorithm.

PubMed

Yang, Yu; Fritzsching, Keith J; Hong, Mei

2013-11-01

A multi-objective genetic algorithm is introduced to predict the assignment of protein solid-state NMR (SSNMR) spectra with partial resonance overlap and missing peaks due to broad linewidths, molecular motion, and low sensitivity. This non-dominated sorting genetic algorithm II (NSGA-II) aims to identify all possible assignments that are consistent with the spectra and to compare the relative merit of these assignments. Our approach is modeled after the recently introduced Monte-Carlo simulated-annealing (MC/SA) protocol, with the key difference that NSGA-II simultaneously optimizes multiple assignment objectives instead of searching for possible assignments based on a single composite score. The multiple objectives include maximizing the number of consistently assigned peaks between multiple spectra ("good connections"), maximizing the number of used peaks, minimizing the number of inconsistently assigned peaks between spectra ("bad connections"), and minimizing the number of assigned peaks that have no matching peaks in the other spectra ("edges"). Using six SSNMR protein chemical shift datasets with varying levels of imperfection that was introduced by peak deletion, random chemical shift changes, and manual peak picking of spectra with moderately broad linewidths, we show that the NSGA-II algorithm produces a large number of valid and good assignments rapidly. For high-quality chemical shift peak lists, NSGA-II and MC/SA perform similarly well. However, when the peak lists contain many missing peaks that are uncorrelated between different spectra and have chemical shift deviations between spectra, the modified NSGA-II produces a larger number of valid solutions than MC/SA, and is more effective at distinguishing good from mediocre assignments by avoiding the hazard of suboptimal weighting factors for the various objectives. These two advantages, namely diversity and better evaluation, lead to a higher probability of predicting the correct assignment for a larger number of residues. On the other hand, when there are multiple equally good assignments that are significantly different from each other, the modified NSGA-II is less efficient than MC/SA in finding all the solutions. This problem is solved by a combined NSGA-II/MC algorithm, which appears to have the advantages of both NSGA-II and MC/SA. This combination algorithm is robust for the three most difficult chemical shift datasets examined here and is expected to give the highest-quality de novo assignment of challenging protein NMR spectra.

On the use of the exact exchange optimized effective potential method for static response properties

NASA Astrophysics Data System (ADS)

Krykunov, Mykhaylo; Ziegler, Tom

In the present work, we question the notion that the modified Kohn-Sham orbital energies and smaller HOMO-LUMO gaps, produced from the exact exchange optimized effective potential (EXX-OEP) method, might significantly improve the paramagnetic contribution to the NMR chemical shifts compared with the regular Hartree-Fock (HF) scheme. First of all, it is shown analytically that if there is such a local potential that produces the HF energy, and the Kohn-Sham orbitals are obtained as a result of separate rotations of the occupied and virtual HF orbitals, any static magnetic property obtained from the coupled perturbed HF method will be identical to that obtained from the EXX-OEP approach. In fact the EXX-OEP method is equivalent to the improved virtual orbitals (IVO) scheme in which the energies of the virtual orbitals are modified by an effective potential. It is shown that the IVO procedure leaves static response properties unchanged. To test our analysis numerically we have employed several variants of the EXX-OEP method, based on the expansion of the local exchange potential into a linear combination of fit functions. The different EXX-OEP schemes have been used to calculate the NMR chemical shifts for a set of small molecules containing C, H, N, O, and F atoms. Comparison of the deviation between experimental and calculated chemical shifts from the HF, the EXX-OEP, and the common energy denominator approximation (CEDA) approximation to the EXX-OEP methods has shown that for carbon, hydrogen, and fluorine the EXX-OEP methods do not yield any improvement over the HF method. For nitrogen and oxygen we have found that the EXX-OEP performs better than the HF method. However, in the limit of infinite fit basis set and, as a consequence of it, a perfect fit of the HF potential the EXX-OEP and the HF methods would afford the same chemical shifts according to our theoretical analysis. Unfortunately, without a perfect fit the chemical shifts from the EXX-OEP method strongly depend on the fit convergence. In our opinion, the EXX-OEP method should not be used for response properties as it is numerically unstable. Thus, any apparent improvement of the EXX-OEP method over the HF scheme for a finite fit basis set must be considered spurious.

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

PubMed

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

2018-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

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

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

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

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

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

DOE PAGES

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

2018-03-23

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

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

PubMed

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

2017-03-01

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

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

PubMed

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

2015-01-01

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

Silicon K-edge XANES spectra of silicate minerals

NASA Astrophysics Data System (ADS)

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

1995-03-01

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

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

PubMed

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

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

Fast CT-PRESS-based spiral chemical shift imaging at 3 Tesla.

PubMed

Mayer, Dirk; Kim, Dong-Hyun; Adalsteinsson, Elfar; Spielman, Daniel M

2006-05-01

A new sequence is presented that combines constant-time point-resolved spectroscopy (CT-PRESS) with fast spiral chemical shift imaging. It allows the acquisition of multivoxel spectra without line splitting with a minimum total measurement time of less than 5 min for a field of view of 24 cm and a nominal 1.5x1.5-cm2 in-plane resolution. Measurements were performed with 17 CS encoding steps in t1 (Deltat1=12.8 ms) and an average echo time of 151 ms, which was determined by simulating the CT-PRESS experiment for the spin systems of glutamate (Glu) and myo-inositol (mI). Signals from N-acetyl-aspartate, total creatine, choline-containing compounds (Cho), Glu, and mI were detected in a healthy volunteer with no or only minor baseline distortions within 14 min on a 3 T MR scanner. Copyright (c) 2006 Wiley-Liss, Inc.

13Check_RNA: A tool to evaluate 13C chemical shifts assignments of RNA.

PubMed

Icazatti, A A; Martin, O A; Villegas, M; Szleifer, I; Vila, J A

2018-06-19

Chemical shifts (CS) are an important source of structural information of macromolecules such as RNA. In addition to the scarce availability of CS for RNA, the observed values are prone to errors due to a wrong re-calibration or miss assignments. Different groups have dedicated their efforts to correct CS systematic errors on RNA. Despite this, there are not automated and freely available algorithms for correct assignments of RNA 13C CS before their deposition to the BMRB or re-reference already deposited CS with systematic errors. Based on an existent method we have implemented an open source python module to correct 13C CS (from here on 13Cexp) systematic errors of RNAs and then return the results in 3 formats including the nmrstar one. This software is available on GitHub at https://github.com/BIOS-IMASL/13Check_RNA under a MIT license. Supplementary data are available at Bioinformatics online.

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

PubMed

Hanni, Matti; Lantto, Perttu; Vaara, Juha

2011-08-14

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

Magnetization transfer from laser-polarized xenon to protons located in the hydrophobic cavity of the wheat nonspecific lipid transfer protein

PubMed Central

Landon, Céline; Berthault, Patrick; Vovelle, Françoise; Desvaux, Hervé

2001-01-01

Nonspecific lipid transfer protein from wheat is studied by liquid-state NMR in the presence of xenon. The gas–protein interaction is indicated by the dependence of the protein proton chemical shifts on the xenon pressure and formally confirmed by the first observation of magnetization transfer from laser-polarized xenon to the protein protons. Twenty-six heteronuclear nOes have allowed the characterization of four interaction sites inside the wheat ns-LTP cavity. Their locations are in agreement with the variations of the chemical shifts under xenon pressure and with solvation simulations. The richness of the information obtained by the noble gas with a nuclear polarization multiplied by ∼12,000 makes this approach based on dipolar cross-relaxation with laser-polarized xenon promising for probing protein hydrophobic pockets at ambient pressure. PMID:11274467

Specific 13C labeling of leucine, valine and isoleucine methyl groups for unambiguous detection of long-range restraints in protein solid-state NMR studies

NASA Astrophysics Data System (ADS)

Fasshuber, Hannes Klaus; Demers, Jean-Philippe; Chevelkov, Veniamin; Giller, Karin; Becker, Stefan; Lange, Adam

2015-03-01

Here we present an isotopic labeling strategy to easily obtain unambiguous long-range distance restraints in protein solid-state NMR studies. The method is based on the inclusion of two biosynthetic precursors in the bacterial growth medium, α-ketoisovalerate and α-ketobutyrate, leading to the production of leucine, valine and isoleucine residues that are exclusively 13C labeled on methyl groups. The resulting spectral simplification facilitates the collection of distance restraints, the verification of carbon chemical shift assignments and the measurement of methyl group dynamics. This approach is demonstrated on the type-three secretion system needle of Shigella flexneri, where 49 methyl-methyl and methyl-nitrogen distance restraints including 10 unambiguous long-range distance restraints could be collected. By combining this labeling scheme with ultra-fast MAS and proton detection, the assignment of methyl proton chemical shifts was achieved.

1H NMR spectra. Part 30(+): 1H chemical shifts in amides and the magnetic anisotropy, electric field and steric effects of the amide group.

PubMed

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

2013-03-01

The (1)H spectra of 37 amides in CDCl(3) solvent were analysed and the chemical shifts obtained. The molecular geometries and conformational analysis of these amides were considered in detail. The NMR spectral assignments are of interest, e.g. the assignments of the formamide NH(2) protons reverse in going from CDCl(3) to more polar solvents. The substituent chemical shifts of the amide group in both aliphatic and aromatic amides were analysed using an approach based on neural network data for near (≤3 bonds removed) protons and the electric field, magnetic anisotropy, steric and for aromatic systems π effects of the amide group for more distant protons. The electric field is calculated from the partial atomic charges on the N.C═O atoms of the amide group. The magnetic anisotropy of the carbonyl group was reproduced with the asymmetric magnetic anisotropy acting at the midpoint of the carbonyl bond. The values of the anisotropies Δχ(parl) and Δχ(perp) were for the aliphatic amides 10.53 and -23.67 (×10(-6) Å(3)/molecule) and for the aromatic amides 2.12 and -10.43 (×10(-6) Å(3)/molecule). The nitrogen anisotropy was 7.62 (×10(-6) Å(3)/molecule). These values are compared with previous literature values. The (1)H chemical shifts were calculated from the semi-empirical approach and also by gauge-independent atomic orbital calculations with the density functional theory method and B3LYP/6-31G(++) (d,p) basis set. The semi-empirical approach gave good agreement with root mean square error of 0.081 ppm for the data set of 280 entries. The gauge-independent atomic orbital approach was generally acceptable, but significant errors (ca. 1 ppm) were found for the NH and CHO protons and also for some other protons. Copyright © 2013 John Wiley & Sons, Ltd.

Molecular and Silica-Supported Molybdenum Alkyne Metathesis Catalysts: Influence of Electronics and Dynamics on Activity Revealed by Kinetics, Solid-State NMR, and Chemical Shift Analysis.

PubMed

Estes, Deven P; Gordon, Christopher P; Fedorov, Alexey; Liao, Wei-Chih; Ehrhorn, Henrike; Bittner, Celine; Zier, Manuel Luca; Bockfeld, Dirk; Chan, Ka Wing; Eisenstein, Odile; Raynaud, Christophe; Tamm, Matthias; Copéret, Christophe

2017-12-06

Molybdenum-based molecular alkylidyne complexes of the type [MesC≡Mo{OC(CH 3 ) 3-x (CF 3 ) x } 3 ] (MoF 0 , x = 0; MoF 3 , x = 1; MoF 6 , x = 2; MoF 9 , x = 3; Mes = 2,4,6-trimethylphenyl) and their silica-supported analogues are prepared and characterized at the molecular level, in particular by solid-state NMR, and their alkyne metathesis catalytic activity is evaluated. The 13 C NMR chemical shift of the alkylidyne carbon increases with increasing number of fluorine atoms on the alkoxide ligands for both molecular and supported catalysts but with more shielded values for the supported complexes. The activity of these catalysts increases in the order MoF 0 < MoF 3 < MoF 6 before sharply decreasing for MoF 9 , with a similar effect for the supported systems (MoF 0 ≈ MoF 9 < MoF 6 < MoF 3 ). This is consistent with the different kinetic behavior (zeroth order in alkyne for MoF 9 derivatives instead of first order for the others) and the isolation of stable metallacyclobutadiene intermediates of MoF 9 for both molecular and supported species. Detailed solid-state NMR analysis of molecular and silica-supported metal alkylidyne catalysts coupled with DFT/ZORA calculations rationalize the NMR spectroscopic signatures and discernible activity trends at the frontier orbital level: (1) increasing the number of fluorine atoms lowers the energy of the π*(M≡C) orbital, explaining the more deshielded chemical shift values; it also leads to an increased electrophilicity and higher reactivity for catalysts up to MoF 6 , prior to a sharp decrease in reactivity for MoF 9 due to the formation of stable metallacyclobutadiene intermediates; (2) the silica-supported catalysts are less active than their molecular analogues because they are less electrophilic and dynamic, as revealed by their 13 C NMR chemical shift tensors.

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

ERIC Educational Resources Information Center

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

2014-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2009-07-01

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

17O NMR studies on 4- and 4'-substituted chalcones and p-substituted β-nitrostyrenes

NASA Astrophysics Data System (ADS)

Boykin, D. W.; Baumstark, A. L.; Balakrishnan, P.; Perjéssy, A.; Hrnc˜iar, P.

The 17O NMR chemical shift data for 17O-enriched 4- and 4'-chalcones in toluene at 90°C and for p-substituted β-nitrostyrenes (natural abundance) in acetonitrile at 70°C are reported. The SCS (substituent chemical shift) range for the 4-chalcones p-CH 3O to p-NO 2 is 16.3 ppm; the range for the 4'-chalcones p-CH 3O to p-NO 2 is 32.4 ppm. The SCS range for the p-substituted-β-nitrostyrenes p-CH 3O to p-NO 2 is 13.2 ppm. The data for the three series gave good correlations with σ + constants, while the Dual Substitutent Parameter treatment only slightly improved the correlations using σ R+ constants. Plots of the 17O chemical shifts for both 4- and 4'-chalcones with 17O data for acetophenones and correlation of 17O chemical shift data for the β-nitrostyrenes with that of nitrobenzenes gave good correlations. Plots of the 17O data for all the three series with their respective functional group stretching frequencies gave fair correlations.

Protein dielectric constants determined from NMR chemical shift perturbations.

PubMed

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

2013-11-13

Understanding the connection between protein structure and function requires a quantitative understanding of electrostatic effects. Structure-based electrostatic calculations are essential for this purpose, but their use has been limited by a long-standing discussion on which value to use for the dielectric constants (ε(eff) and ε(p)) required in Coulombic and Poisson-Boltzmann models. The currently used values for ε(eff) and ε(p) are essentially empirical parameters calibrated against thermodynamic properties that are indirect measurements of protein electric fields. We determine optimal values for ε(eff) and ε(p) by measuring protein electric fields in solution using direct detection of NMR chemical shift perturbations (CSPs). We measured CSPs in 14 proteins to get a broad and general characterization of electric fields. Coulomb's law reproduces the measured CSPs optimally with a protein dielectric constant (ε(eff)) from 3 to 13, with an optimal value across all proteins of 6.5. However, when the water-protein interface is treated with finite difference Poisson-Boltzmann calculations, the optimal protein dielectric constant (ε(p)) ranged from 2 to 5 with an optimum of 3. It is striking how similar this value is to the dielectric constant of 2-4 measured for protein powders and how different it is from the ε(p) of 6-20 used in models based on the Poisson-Boltzmann equation when calculating thermodynamic parameters. Because the value of ε(p) = 3 is obtained by analysis of NMR chemical shift perturbations instead of thermodynamic parameters such as pK(a) values, it is likely to describe only the electric field and thus represent a more general, intrinsic, and transferable ε(p) common to most folded proteins.

Backbone-only restraints for fast determination of the protein fold: The role of paramagnetism-based restraints. Cytochrome b562 as an example

NASA Astrophysics Data System (ADS)

Banci, Lucia; Bertini, Ivano; Felli, Isabella C.; Sarrou, Josephine

2005-02-01

CH α residual dipolar couplings (Δ rdc's) were measured for the oxidized cytochrome b562 from Escherichia coli as a result of its partial self-orientation in high magnetic fields due to the anisotropy of the overall magnetic susceptibility tensor. Both the low spin iron (III) heme and the four-helix bundle fold contribute to the magnetic anisotropy tensor. CH α Δ rdc's, which span a larger range than the analogous NH values (already available in the literature) sample large space variations at variance with NH Δ rdc's, which are largely isooriented within α helices. The whole structure is now significantly refined with the chemical shift index and CH α Δ rdc's. The latter are particularly useful also in defining the molecular magnetic anisotropy parameters. It is shown here that the backbone folding can be conveniently and accurately determined using backbone restraints only, which include NOEs, hydrogen bonds, residual dipolar couplings, pseudocontact shifts, and chemical shift index. All these restraints are easily and quickly determined from the backbone assignment. The calculated backbone structure is comparable to that obtained by using also side chain restraint. Furthermore, the structure obtained with backbone only restraints is, in its whole, very similar to that obtained with the complete set of restraints. The paramagnetism based restraints are shown to be absolutely relevant, especially for Δ rdc's.

Theoretical study of NMR, infrared and Raman spectra on triple-decker phthalocyanines

NASA Astrophysics Data System (ADS)

Suzuki, Atsushi; Oku, Takeo

2016-02-01

Electronic structures and magnetic properties of multi-decker phthalocyanines were studied by theoretical calculation. Electronic structures, excited processes at multi-states, isotropic chemical shifts of 13C, 14N and 1H-nuclear magnetic resonance (NMR), principle V-tensor in electronic field gradient (EFG) tensor and asymmetry parameters (η), vibration mode in infrared (IR) and Raman spectra of triple-decker phthalocyanines were calculated by density functional theory (DFT) and time-dependent DFT using B3LYP as basis function. Electron density distribution was delocalized on the phthalocyanine rings with electron static potential. Considerable separation of chemical shifts in 13C, 14N and 1H-NMR was originated from nuclear spin interaction between nitrogen and carbon atoms, nuclear quadrupole interaction based on EFG and η of central metal under crystal field. Calculated optical absorption at multi-excited process was derived from overlapping π-orbital on the phthalocyanine rings. The vibration modes in IR and Raman spectra were based on in-plane deformation and stretching vibrations of metal-ligand coordination bond on the deformed structure.

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

NASA Astrophysics Data System (ADS)

Perera, Ajith

2007-12-01

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

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

PubMed

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

2007-11-01

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

Theoretical study of the NMR chemical shift of Xe in supercritical condition.

PubMed

Lacerda, Evanildo G; Sauer, Stephan P A; Mikkelsen, Kurt V; Coutinho, Kaline; Canuto, Sylvio

2018-02-20

In this work we investigate the level of theory necessary for reproducing the non-linear variation of the 129 Xe nuclear magnetic resonance (NMR) chemical shift with the density of Xe in supercritical conditions. In detail we study how the 129 Xe chemical shift depends under supercritical conditions on electron correlation, relativistic and many-body effects. The latter are included using a sequential-QM/MM methodology, in which a classical MD simulation is performed first and the chemical shift is then obtained as an average of quantum calculations of 250 MD snapshots conformations carried out for Xe n clusters (n = 2 - 8 depending on the density). The analysis of the relativistic effects is made at the level of 4-component Hartree-Fock calculations (4c-HF) and electron correlation effects are considered using second order Møller-Plesset perturbation theory (MP2). To simplify the calculations of the relativistic and electron correlation effects we adopted an additive scheme, where the calculations on the Xe n clusters are carried out at the non-relativistic Hartree-Fock (HF) level, while electron correlation and relativistic corrections are added for all the pairs of Xe atoms in the clusters. Using this approach we obtain very good agreement with the experimental data, showing that the chemical shift of 129 Xe in supercritical conditions is very well described by cluster calculations at the HF level, with small contributions from relativistic and electron correlation effects.

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

PubMed

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

2015-04-01

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

Improved olefinic fat suppression in skeletal muscle DTI using a magnitude-based dixon method.

PubMed

Burakiewicz, Jedrzej; Hooijmans, Melissa T; Webb, Andrew G; Verschuuren, Jan J G M; Niks, Erik H; Kan, Hermien E

2018-01-01

To develop a method of suppressing the multi-resonance fat signal in diffusion-weighted imaging of skeletal muscle. This is particularly important when imaging patients with muscular dystrophies, a group of diseases which cause gradual replacement of muscle tissue by fat. The signal from the olefinic fat peak at 5.3 ppm can significantly confound diffusion-tensor imaging measurements. Dixon olefinic fat suppression (DOFS), a magnitude-based chemical-shift-based method of suppressing the olefinic peak, is proposed. It is verified in vivo by performing diffusion tensor imaging (DTI)-based quantification in the lower leg of seven healthy volunteers, and compared to two previously described fat-suppression techniques in regions with and without fat contamination. In the region without fat contamination, DOFS produces similar results to existing techniques, whereas in muscle contaminated by subcutaneous fat signal moved due to the chemical shift artefact, it consistently showed significantly higher (P = 0.018) mean diffusivity (MD). Because fat presence lowers MD, this suggests improved fat suppression. DOFS offers superior fat suppression and enhances quantitative measurements in the muscle in the presence of fat. DOFS is an alternative to spectral olefinic fat suppression. Magn Reson Med 79:152-159, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Amplitude and phase modulation in microwave ring resonators by doped CVD graphene.

PubMed

Grande, M; Bianco, G V; Capezzuto, P; Petruzzelli, V; Prudenzano, F; Scalora, M; Bruno, G; D'Orazio, A

2018-08-10

In this paper, we numerically and experimentally demonstrate how to modulate the amplitude and phase of a microwave ring resonator by means of few-layers chemical vapour deposition graphene. In particular, both numerical and experimental results show a modulation of about 10 dB and a 90 degrees-shift (quadrature phase shift) when the graphene sheet-resistance is varied. These findings prove once again that graphene could be efficiently exploited for the dynamically tuning and modulation of microwave devices fostering the realization of (i) innovative beam-steering and beam-forming systems and (ii) graphene-based sensors.

Non-Euclidean phasor analysis for quantification of oxidative stress in ex vivo human skin exposed to sun filters using fluorescence lifetime imaging microscopy.

PubMed

Osseiran, Sam; Roider, Elisabeth M; Wang, Hequn; Suita, Yusuke; Murphy, Michael; Fisher, David E; Evans, Conor L

2017-12-01

Chemical sun filters are commonly used as active ingredients in sunscreens due to their efficient absorption of ultraviolet (UV) radiation. Yet, it is known that these compounds can photochemically react with UV light and generate reactive oxygen species and oxidative stress in vitro, though this has yet to be validated in vivo. One label-free approach to probe oxidative stress is to measure and compare the relative endogenous fluorescence generated by cellular coenzymes nicotinamide adenine dinucleotides and flavin adenine dinucleotides. However, chemical sun filters are fluorescent, with emissive properties that contaminate endogenous fluorescent signals. To accurately distinguish the source of fluorescence in ex vivo skin samples treated with chemical sun filters, fluorescence lifetime imaging microscopy data were processed on a pixel-by-pixel basis using a non-Euclidean separation algorithm based on Mahalanobis distance and validated on simulated data. Applying this method, ex vivo samples exhibited a small oxidative shift when exposed to sun filters alone, though this shift was much smaller than that imparted by UV irradiation. Given the need for investigative tools to further study the clinical impact of chemical sun filters in patients, the reported methodology may be applied to visualize chemical sun filters and measure oxidative stress in patients' skin. (2017) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Metal alkyls programmed to generate metal alkylidenes by α-H abstraction: prognosis from NMR chemical shift† †Electronic supplementary information (ESI) available: Experimental and computational details, NMR spectra, results of NMR calculations and NCS analysis, graphical representation of shielding tensors, molecular orbital diagrams of selected compounds, optimized structures for all calculated species. See DOI: 10.1039/c7sc05039a

PubMed Central

Gordon, Christopher P.; Yamamoto, Keishi; Searles, Keith; Shirase, Satoru

2018-01-01

Metal alkylidenes, which are key organometallic intermediates in reactions such as olefination or alkene and alkane metathesis, are typically generated from metal dialkyl compounds [M](CH2R)2 that show distinctively deshielded chemical shifts for their α-carbons. Experimental solid-state NMR measurements combined with DFT/ZORA calculations and a chemical shift tensor analysis reveal that this remarkable deshielding originates from an empty metal d-orbital oriented in the M–Cα–Cα′ plane, interacting with the Cα p-orbital lying in the same plane. This π-type interaction inscribes some alkylidene character into Cα that favors alkylidene generation via α-H abstraction. The extent of the deshielding and the anisotropy of the alkyl chemical shift tensors distinguishes [M](CH2R)2 compounds that form alkylidenes from those that do not, relating the reactivity to molecular orbitals of the respective molecules. The α-carbon chemical shifts and tensor orientations thus predict the reactivity of metal alkyl compounds towards alkylidene generation. PMID:29675237

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.

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

PubMed

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

2011-12-14

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

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

PubMed

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

2018-01-01

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

Hydrogen Atomic Positions of O-H···O Hydrogen Bonds in Solution and in the Solid State: The Synergy of Quantum Chemical Calculations with ¹H-NMR Chemical Shifts and X-ray Diffraction Methods.

PubMed

Siskos, Michael G; Choudhary, M Iqbal; Gerothanassis, Ioannis P

2017-03-07

The exact knowledge of hydrogen atomic positions of O-H···O hydrogen bonds in solution and in the solid state has been a major challenge in structural and physical organic chemistry. The objective of this review article is to summarize recent developments in the refinement of labile hydrogen positions with the use of: (i) density functional theory (DFT) calculations after a structure has been determined by X-ray from single crystals or from powders; (ii) ¹H-NMR chemical shifts as constraints in DFT calculations, and (iii) use of root-mean-square deviation between experimentally determined and DFT calculated ¹H-NMR chemical shifts considering the great sensitivity of ¹H-NMR shielding to hydrogen bonding properties.

Effect of a Perturbation on the Chemical Equilibrium: Comparison with Le Chatelier's Principle

ERIC Educational Resources Information Center

Torres, Emilio Martinez

2007-01-01

This article develops a general thermodynamic treatment to predict the direction of shift in a chemical equilibrium when it is subjected to a stress. This treatment gives an inequality that relates the change in the perturbed variable and the change that the equilibrium shift produces in the conjugated variable. To illustrate the generality of…

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

NASA Astrophysics Data System (ADS)

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

2015-05-01

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

Reliable Resonance Assignments of Selected Residues of Proteins with Known Structure Based on Empirical NMR Chemical Shift Prediction

PubMed Central

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

2015-01-01

A robust NMR resonance assignment method is introduced for proteins whose 3D structure has previously been determined by X-ray crystallography. The goal of the method is to obtain a subset of correct assignments from a parsimonious set of 3D NMR experiments of 15N, 13C labeled proteins. Chemical shifts of sequential residue pairs are predicted from static protein structures using PPM_One, which are then compared with the corresponding experimental shifts. Globally optimized weighted matching identifies the assignments that are robust with respect to small changes in NMR cross-peak positions. The method, termed PASSPORT, is demonstrated for 4 proteins with 100 – 250 amino acids using 3D NHCA and a 3D CBCA(CO)NH experiments as input producing correct assignments with high reliability for 22% of the residues. The method, which works best for Gly, Ala, Ser, and Thr residues, provides assignments that serve as anchor points for additional assignments by both manual and semi-automated methods or they can be directly used for further studies, e.g. on ligand binding, protein dynamics, or post-translational modification, such as phosphorylation. PMID:25863893

A Selective-Echo Method for Chemical-Shift Imaging of Two-Component Systems

NASA Astrophysics Data System (ADS)

Gerald, Rex E., II; Krasavin, Anatoly O.; Botto, Robert E.

A simple and effective method for selectively imaging either one of two chemical species in a two-component system is presented and demonstrated experimentally. The pulse sequence employed, selective- echo chemical- shift imaging (SECSI), is a hybrid (frequency-selective/ T1-contrast) technique that is executed in a short period of time, utilizes the full Boltzmann magnetization of each chemical species to form the corresponding image, and requires only hard pulses of quadrature phase. This approach provides a direct and unambiguous representation of the spatial distribution of the two chemical species. In addition, the performance characteristics and the advantages of the SECSI sequence are compared on a common basis to those of other pulse sequences.

A High-Resolution 3D Separated-Local-Field Experiment by Means of Magic-Angle Turning

PubMed

Hu; Alderman; Pugmire; Grant

1997-05-01

A 3D separated-local-field (SLF) experiment based on the 2D PHORMAT technique is described. In the 3D experiment, the conventional 2D SLF powder pattern for each chemically inequivalent carbon is separated according to their different isotropic chemical shifts. The dipolar coupling constant of a C-H pair, hence the bond distance, and the relative orientation of the chemical-shift tensor to the C-H vector can all be determined for the protonated carbons with a single measurement. As the sample turns at only about 30 Hz in a MAT experiment, the SLF patterns obtained approach those of a stationary sample, and an accuracy in the measurement similar to that obtained on a stationary sample is expected. The technique is demonstrated on 2,6-dimethoxynaphthalene, where the 13 C-1 H separated-local-field powder patterns for the six chemically inequivalent carbons are clearly identified and measured. The observed dipolar coupling for the methoxy carbon is effectively reduced by the fast rotation of the group about its C3 symmetry axis. The average angle between the C-H bond direction and the C3 rotation axis in the OCH3 group is found to be about 66°.

Fiber-Optic Refractometer Based on an Etched High-Q π-Phase-Shifted Fiber-Bragg-Grating

PubMed Central

Zhang, Qi; Ianno, Natale J.; Han, Ming

2013-01-01

We present a compact and highly-sensitive fiber-optic refractometer based on a high-Q π-phase-shifted fiber-Bragg-grating (πFBG) that is chemically etched to the core of the fiber. Due to the π phase-shift, a strong πFBG forms a high-Q optical resonator and the reflection spectrum features an extremely narrow notch that can be used for highly sensitivity refractive index measurement. The etched πFBG demonstrated here has a diameter of ∼9.3 μm and a length of only 7 mm, leading to a refractive index responsivity of 2.9 nm/RIU (RIU: refractive index unit) at an ambient refractive index of 1.318. The reflection spectrum of the etched πFBG features an extremely narrow notch with a linewidth of only 2.1 pm in water centered at ∼1,550 nm, corresponding to a Q-factor of 7.4 × 105, which allows for potentially significantly improved sensitivity over refractometers based on regular fiber Bragg gratings. PMID:23845932

Corrosion in low dielectric constant Si-O based thin films: Buffer concentration effects

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

Zeng, F. W.; Lane, M. W., E-mail: mlane@ehc.edu; Gates, S. M.

2014-05-15

Organosilicate glass (OSG) is often used as an interlayer dielectric (ILD) in high performance integrated circuits. OSG is a brittle material and prone to stress-corrosion cracking reminiscent of that observed in bulk glasses. Of particular concern are chemical-mechanical planarization techniques and wet cleans involving solvents commonly encountered in microelectronics fabrication where the organosilicate film is exposed to aqueous environments. Previous work has focused on the effect of pH, surfactant, and peroxide concentration on the subcritical crack growth of these films. However, little or no attention has focused on the effect of the conjugate acid/base concentration in a buffer. Accordingly, thismore » work examines the “strength” of the buffer solution in both acidic and basic environments. The concentration of the buffer components is varied keeping the ratio of acid/base and therefore pH constant. In addition, the pH was varied by altering the acid/base ratio to ascertain any additional effect of pH. Corrosion tests were conducted with double-cantilever beam fracture mechanics specimens and fracture paths were verified with ATR-FTIR. Shifts in the threshold fracture energy, the lowest energy required for bond rupture in the given environment, G{sub TH}, were found to shift to lower values as the concentration of the base in the buffer increased. This effect was found to be much larger than the effect of the hydroxide ion concentration in unbuffered solutions. The results are rationalized in terms of the salient chemical bond breaking process occurring at the crack tip and modeled in terms of the chemical potential of the reactive species.« less

A heteronuclear zero quantum coherence Nz-exchange experiment that resolves resonance overlap and its application to measure the rates of heme binding to the IsdC protein.

PubMed

Robson, Scott A; Peterson, Robert; Bouchard, Louis-S; Villareal, Valerie A; Clubb, Robert T

2010-07-21

Chemical exchange phenomena in NMR spectra can be quantitatively interpreted to measure the rates of ligand binding, as well as conformational and chemical rearrangements. In macromolecules, processes that occur slowly on the chemical shift time scale are frequently studied using 2D heteronuclear ZZ or N(z)-exchange spectroscopy. However, to successfully apply this method, peaks arising from each exchanging species must have unique chemical shifts in both dimensions, a condition that is often not satisfied in protein-ligand binding equilibria for (15)N nuclei. To overcome the problem of (15)N chemical shift degeneracy we developed a heteronuclear zero-quantum (and double-quantum) coherence N(z)-exchange experiment that resolves (15)N chemical shift degeneracy in the indirect dimension. We demonstrate the utility of this new experiment by measuring the heme binding kinetics of the IsdC protein from Staphylococcus aureus. Because of peak overlap, we could not reliably analyze binding kinetics using conventional methods. However, our new experiment resulted in six well-resolved systems that yielded interpretable data. We measured a relatively slow k(off) rate of heme from IsdC (<10 s(-1)), which we interpret as necessary so heme loaded IsdC has time to encounter downstream binding partners to which it passes the heme. The utility of using this new exchange experiment can be easily expanded to (13)C nuclei. We expect our heteronuclear zero-quantum coherence N(z)-exchange experiment will expand the usefulness of exchange spectroscopy to slow chemical exchange events that involve ligand binding.

Characterization of Graphene-based FET Fabricated using a Shadow Mask

PubMed Central

Tien, Dung Hoang; Park, Jun-Young; Kim, Ki Buem; Lee, Naesung; Seo, Yongho

2016-01-01

To pattern electrical metal contacts, electron beam lithography or photolithography are commonly utilized, and these processes require polymer resists with solvents. During the patterning process the graphene surface is exposed to chemicals, and the residue on the graphene surface was unable to be completely removed by any method, causing the graphene layer to be contaminated. A lithography free method can overcome these residue problems. In this study, we use a micro-grid as a shadow mask to fabricate a graphene based field-effect-transistor (FET). Electrical measurements of the graphene based FET samples are carried out in air and vacuum. It is found that the Dirac peaks of the graphene devices on SiO2 or on hexagonal boron nitride (hBN) shift from a positive gate voltage region to a negative region as air pressure decreases. In particular, the Dirac peaks shift very rapidly when the pressure decreases from ~2 × 10−3 Torr to ~5 × 10−5 Torr within 5 minutes. These Dirac peak shifts are known as adsorption and desorption of environmental gases, but the shift amounts are considerably different depending on the fabrication process. The high gas sensitivity of the device fabricated by shadow mask is attributed to adsorption on the clean graphene surface. PMID:27169620

Conformational analysis of the chemical shifts for molecules containing diastereotopic methylene protons

NASA Astrophysics Data System (ADS)

Borowski, Piotr

2012-01-01

Quantum chemistry SCF/GIAO calculations were carried out on a set of compounds containing diastereotopic protons. Five molecules, including recently synthesized 1,3-di(2,3-epoxypropoxy)benzene, containing the chiral or pro-chiral center and the neighboring methylene group, were chosen. The rotational averages (i.e. normalized averages with respect to the rotation about the torsional angle τ with the exponential energy weight at temperature T) calculated individually for each of the methylene protons in 1,3-di(2,3-epoxypropoxy)benzene differ by ca. 0.6 ppm, which is significantly less than the value calculated for the lowest energy conformer. This value turned out to be low enough to guarantee the proper ordering of theoretical chemical shifts, supporting the interpretation of the 1H NMR spectrum of this important compound. The rotational averages of chemical shifts for methylene protons for a given type of conformer are shown to be essentially equal to the Boltzmann averages (here, the population-weighted averages for the individual conformers representing minima on the E( τ) cross-section). The calculated Boltzmann averages in the representative conformational space may exhibit completely different ordering as compared to the chemical shifts calculated for the lowest-energy conformer. This is especially true in the case of molecules, for which no significant steric effects are present. In this case, only Boltzmann averages account for the experimental pattern of proton signals. In addition, better overall agreement with experiment (lower value of the root-mean-square deviation between calculated and measured chemical shifts) is typically obtained when Boltzmann averages are used.

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.

Direct measurement for organic solvents diffusion using ultra-sensitive optical resonator

NASA Astrophysics Data System (ADS)

Ali, Amir R.; Elias, Catherine M.

2017-06-01

In this paper, novel techniques using ultra-sensitive chemical optical sensor based on whispering gallery modes (WGM) are proposed through two different configurations. The first one will use a composite micro-sphere, when the solvent interacts with the polymeric optical sensors through diffusion the sphere start to swallow that solvent. In turn, that leads to change the morphology and mechanical properties of the polymeric spheres. Also, these changes could be measured by tracking the WGM shifts. Several experiments were carried out to study the solvent induced WGM shift using microsphere immersed in a solvent atmosphere. It can be potentially used for sensing the trace organic solvents like ethanol and methanol. The second configuration will use a composite beam nitrocellulose composite (NC) structure that acts as a sensing element. In this configuration, a beam is anchored to a substrate in one end, and the other end is compressing the polymeric sphere causing a shift in its WGM. When a chemical molecule is attached to the beam, the resonant frequency of the cantilever will be changed for a certain amount. By sensing this certain resonant frequency change, the existence of a single chemical molecule can be detected. A preliminary experimental model is developed to describe the vibration of the beam structure. The resonant frequency change of the cantilever due to attached mass is examined imperially using acetone as an example. Breath diagnosis can use this configuration in diabetic's diagnosis. Since, solvent like acetone concentration in human breath leads to a quick, convenient, accurate and painless breath diagnosis of diabetics. These micro-optical sensors have been examined using preliminary experiments to fully investigate its response. The proposed chemical sensor can achieve extremely high sensitivity in molecular level.

Effects of protein-pheromone complexation on correlated chemical shift modulations.

PubMed

Perazzolo, Chiara; Wist, Julien; Loth, Karine; Poggi, Luisa; Homans, Steve; Bodenhausen, Geoffrey

2005-12-01

Major urinary protein (MUP) is a pheromone-carrying protein of the lipocalin family. Previous studies by isothermal titration calorimetry (ITC) show that the affinity of MUP for the pheromone 2-methoxy-3-isobutylpyrazine (IBMP) is mainly driven by enthalpy, with a small unfavourable entropic contribution. Entropic terms can be attributed in part to changes in internal motions of the protein upon binding. Slow internal motions can lead to correlated or anti-correlated modulations of the isotropic chemical shifts of carbonyl C' and amide N nuclei. Correlated chemical shift modulations (CSM/CSM) in MUP have been determined by measuring differences of the transverse relaxation rates of zero- and double-quantum coherences ZQC{C'N} and DQC{C'N}, and by accounting for the effects of correlated fluctuations of dipole-dipole couplings (DD/DD) and chemical shift anisotropies (CSA/CSA). The latter can be predicted from tensor parameters of C' and N nuclei that have been determined in earlier work. The effects of complexation on slow time-scale protein dynamics can be determined by comparing the temperature dependence of the relaxation rates of APO-MUP (i.e., without ligand) and HOLO-MUP (i.e., with IBMP as a ligand).

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

Illman, D.L.

Green chemistry is an effort to change the very concept of efficiency as it is applied to industrial chemical processes, shifting the balance from an exclusive focus on yield to one that places economic value on minimizing or eliminating wasteful by-products. Judging from a week-long symposium on Design for the Environment: A New Paradigm for the 21st Century co-sponsored by the Division of Environmental Chemistry and the Committee on Environmental Improvement of the Chemical Society of Washington, the green movement is one that is gaining momentum and acceptance. Presentations ranged from futuristic visions of nanotechnology-based chemical manufacturing to prescriptions formore » reducing waste in today's chemical processes. Some schemes are still the stuff of dreams, while others have already been implemented. This paper summarizes the contents of this symposium.« less

Cryptophane Nanoscale Assemblies Expand 129Xe NMR Biosensing.

PubMed

Zemerov, Serge D; Roose, Benjamin W; Greenberg, Mara L; Wang, Yanfei; Dmochowski, Ivan J

2018-06-19

Cryptophane-based biosensors are promising agents for the ultrasensitive detection of biomedically relevant targets via 129 Xe NMR. Dynamic light scattering revealed that cryptophanes form water-soluble aggregates tens to hundreds of nanometers in size. Acridine orange fluorescence quenching assays allowed quantitation of the aggregation state, with critical concentrations ranging from 200 nM to 600 nM, depending on the cryptophane species in solution. The addition of excess carbonic anhydrase (CA) protein target to a benzenesulfonamide-functionalized cryptophane biosensor (C8B) led to C8B disaggregation and produced the expected 1:1 C8B-CA complex. C8B showed higher affinity at 298 K for the cytoplasmic isozyme CAII than the extracellular CAXII isozyme, which is a biomarker of cancer. Using hyper-CEST NMR, we explored the role of stoichiometry in detecting these two isozymes. Under CA-saturating conditions, we observed that isozyme CAII produces a larger 129 Xe NMR chemical shift change (δ = 5.9 ppm, relative to free biosensor) than CAXII (δ = 2.7 ppm), which indicates the strong potential for isozyme-specific detection. However, stoichiometry-dependent chemical shift data indicated that biosensor disaggregation contributes to the observed 129 Xe NMR chemical shift change that is normally assigned to biosensor-target binding. Finally, we determined that monomeric cryptophane solutions improve hyper-CEST saturation contrast, which enables ultrasensitive detection of biosensor-protein complexes. These insights into cryptophane-solution behavior support further development of xenon biosensors, but will require reinterpretation of the data previously obtained for many water-soluble cryptophanes.

Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy

PubMed Central

Vallurupalli, Pramodh; Hansen, D. Flemming; Kay, Lewis E.

2008-01-01

Molecular function is often predicated on excursions between ground states and higher energy conformers that can play important roles in ligand binding, molecular recognition, enzyme catalysis, and protein folding. The tools of structural biology enable a detailed characterization of ground state structure and dynamics; however, studies of excited state conformations are more difficult because they are of low population and may exist only transiently. Here we describe an approach based on relaxation dispersion NMR spectroscopy in which structures of invisible, excited states are obtained from chemical shifts and residual anisotropic magnetic interactions. To establish the utility of the approach, we studied an exchanging protein (Abp1p SH3 domain)–ligand (Ark1p peptide) system, in which the peptide is added in only small amounts so that the ligand-bound form is invisible. From a collection of 15N, 1HN, 13Cα, and 13CO chemical shifts, along with 1HN-15N, 1Hα-13Cα, and 1HN-13CO residual dipolar couplings and 13CO residual chemical shift anisotropies, all pertaining to the invisible, bound conformer, the structure of the bound state is determined. The structure so obtained is cross-validated by comparison with 1HN-15N residual dipolar couplings recorded in a second alignment medium. The methodology described opens up the possibility for detailed structural studies of invisible protein conformers at a level of detail that has heretofore been restricted to applications involving visible ground states of proteins. PMID:18701719

Effect of a Perturbation on the Chemical Equilibrium: Comparison with Le Châtelier's Principle

NASA Astrophysics Data System (ADS)

Martínez Torres, Emilio

2007-03-01

This article develops a general thermodynamic treatment to predict the direction of shift in a chemical equilibrium when it is subjected to a stress. This treatment gives an inequality that relates the change in the perturbed variable and the change that the equilibrium shift produces in the conjugated variable. To illustrate the generality of this approach, it has been applied to predict the direction of shift caused by changes of pressure, volume, and amount of substance. In this last case, the well-known unexpected shift in the ammonia synthesis equilibrium upon addition of nitrogen is easily explained. From the above referred inequality and the stability criteria of thermodynamics some conclusions have been obtained about the direction of shift in terms of extensive and extensive variables. This article is suitable for physical chemistry courses.

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

PubMed

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

2016-07-18

High-pressure (HP) NMR spectroscopy is an important method for detecting rare functional states of proteins by analyzing the pressure response of chemical shifts. However, for the analysis of the shifts it is mandatory to understand the origin of the observed pressure dependence. Here we present experimental HP NMR data on the (15) N-enriched peptide bond model, N-methylacetamide (NMA), in water, combined with quantum-chemical computations of the magnetic parameters using a pressure-sensitive solvation model. Theoretical analysis of NMA and the experimentally used internal reference standard 4,4-dimethyl-4-silapentane-1-sulfonic (DSS) reveal that a substantial part of observed shifts can be attributed to purely solvent-induced electronic polarization of the backbone. DSS is only marginally responsive to pressure changes and is therefore a reliable sensor for variations in the local magnetic field caused by pressure-induced changes of the magnetic susceptibility of the solvent. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Identifying Chemical Groups for Biomonitoring

PubMed Central

Krowech, Gail; Hoover, Sara; Plummer, Laurel; Sandy, Martha; Zeise, Lauren; Solomon, Gina

2016-01-01

Summary: Regulatory agencies face daunting challenges identifying emerging chemical hazards because of the large number of chemicals in commerce and limited data on exposure and toxicology. Evaluating one chemical at a time is inefficient and can lead to replacement with uncharacterized chemicals or chemicals with structural features already linked to toxicity. The Office of Environmental Health Hazard Assessment (OEHHA) has developed a process for constructing and assessing chemical groups for potential biomonitoring in California. We screen for chemicals with significant exposure potential and propose possible chemical groups, based on structure and function. To support formal consideration of these groups by Biomonitoring California’s Scientific Guidance Panel, we conduct a detailed review of exposure and toxicity data and examine the likelihood of detection in biological samples. To date, 12 chemical groups have been constructed and added to the pool of chemicals that can be selected for Biomonitoring California studies, including p,p´-bisphenols, brominated and chlorinated organic compounds used as flame retardants, non-halogenated aromatic phosphates, and synthetic polycyclic musks. Evaluating chemical groups, rather than individual chemicals, is an efficient way to respond to shifts in chemical use and the emergence of new chemicals. This strategy can enable earlier identification of important chemicals for monitoring and intervention. PMID:27905275

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

PubMed

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

2017-04-01

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

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

PubMed

Markin, Craig J; Spyracopoulos, Leo

2012-12-01

NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K ( D )) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K ( D ) value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of (1)H-(15)N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k ( off )). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k ( off ) ~ 3,000 s(-1) in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k ( off ) from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k ( off ) values over a wide range, from 100 to 15,000 s(-1). The validity of line shape analysis for k ( off ) values approaching intermediate exchange (~100 s(-1)), may be facilitated by more accurate K ( D ) measurements from NMR-monitored chemical shift titrations, for which the dependence of K ( D ) on the chemical shift difference (Δω) between free and bound states is extrapolated to Δω = 0. The demonstrated accuracy and precision for k ( off ) will be valuable for the interpretation of biological kinetics in weakly interacting protein-protein networks, where a small change in the magnitude of the underlying kinetics of a given pathway may lead to large changes in the associated downstream signaling cascade.

¹H-MAS-NMR chemical shifts in hydrogen-bonded complexes of chlorophenols (pentachlorophenol, 2,4,6-trichlorophenol, 2,6-dichlorophenol, 3,5-dichlorophenol, and p-chlorophenol) and amine, and H/D isotope effects on ¹H-MAS-NMR spectra.

PubMed

Honda, Hisashi

2013-04-22

Chemical shifts (CS) of the ¹H nucleus in N···H···O type hydrogen bonds (H-bond) were observed in some complexes between chlorophenols [pentachlorophenol (PCP), 2,4,6-tricholorophenol (TCP), 2,6-dichlorophenol (26DCP), 3,5-dichlorophenol (35DCP), and p-chlorophenol (pCP)] and nitrogen-base (N-Base) by solid-state high-resolution ¹H-NMR with the magic-angle-spinning (MAS) method. Employing N-Bases with a wide range of pKa values (0.65-10.75), ¹H-MAS-NMR CS values of bridging H atoms in H-bonds were obtained as a function of the N-Base's pKa. The result showed that the CS values were increased with increasing pKa values in a range of DpKa < 0 [DpKa = pKa(N-Base)-pKa(chlorophenols)] and decreased when DpKa > 2: The maximum CS values was recorded in the PCP (pKa = 5.26)-4-methylpyridine (6.03), TCP (6.59)-imidazole (6.99), 26DCP (7.02)-2-amino-4-methylpyridine (7.38), 35DCP (8.04)-4-dimethylaminopyridine (9.61), and pCP (9.47)-4-dimethylaminopyridine (9.61) complexes. The largest CS value of 18.6 ppm was recorded in TCP-imidazole crystals. In addition, H/D isotope effects on ¹H-MAS-NMR spectra were observed in PCP-2-amino-3-methylpyridine. Based on the results of CS simulation using a B3LYP/6-311+G** function, it can be explained that a little changes of the N-H length in H-bond contribute to the H/D isotope shift of the ¹H-MAS-NMR peaks.

Interfacial chemical and electronic structure of cobalt deposition on 2,7-dioctyl[1]benzothieno[3,2-b]benzothiophene (C8-BTBT)

NASA Astrophysics Data System (ADS)

Zhu, Menglong; Lyu, Lu; Niu, Dongmei; Zhang, Hong; Zhang, Yuhe; Liu, Peng; Gao, Yongli

2017-04-01

Interfacial chemical and electronic structure of Co deposition on 2,7-dioctyl[1]benzothieno[3,2-b]benzothiophene(C8-BTBT) was investigated by ultraviolet photoemission spectroscopy (UPS) and X-ray photoemission spectroscopy (XPS). Chemical reaction of cobalt with C8-BTBT at the interface is confirmed by a new component of S 2s peak which is electron-rich compared to the original one of C8-BTBT molecules. Intensity evolution of the core level in XPS indicates that the adsorption of Co atoms is mainly at the surface without deeper diffusion into C8-BTBT layer. Initial deposition of Co atoms downward shifts the core levels of C8-BTBT by electron transfer from isolated Co atoms or clusters to the C8-BTBT. Further deposition of Co upward shifts the core levels of C8-BTBT because of the neutralization of the thicker metal Co film. Our investigation suggests an inert buffer layer inserted to protect organic layer from reaction or decomposition and to lower the carrier barriers for both the electron and hole to improve the performance of Co/C8-BTBT-based OFETs.

Determination of accurate 1H positions of an alanine tripeptide with anti-parallel and parallel β-sheet structures by high resolution 1H solid state NMR and GIPAW chemical shift calculation.

PubMed

Yazawa, Koji; Suzuki, Furitsu; Nishiyama, Yusuke; Ohata, Takuya; Aoki, Akihiro; Nishimura, Katsuyuki; Kaji, Hironori; Shimizu, Tadashi; Asakura, Tetsuo

2012-11-25

The accurate (1)H positions of alanine tripeptide, A(3), with anti-parallel and parallel β-sheet structures could be determined by highly resolved (1)H DQMAS solid-state NMR spectra and (1)H chemical shift calculation with gauge-including projector augmented wave calculations.

A Three-Dimensional DOSY HMQC Experiment for the High-Resolution Analysis of Complex Mixtures

NASA Astrophysics Data System (ADS)

Barjat, Hervé; Morris, Gareth A.; Swanson, Alistair G.

1998-03-01

A three-dimensional experiment is described in which NMR signals are separated according to their proton chemical shift,13C chemical shift, and diffusion coefficient. The sequence is built up from a stimulated echo sequence with bipolar field gradient pulses and a conventional decoupled HMQC sequence. Results are presented for a model mixture of quinine, camphene, and geraniol in deuteriomethanol.

Food for Thought …

PubMed Central

Smirnova, Lena; Hogberg, Helena T.; Leist, Marcel; Hartung, Thomas

2016-01-01

Summary In recent years neurodevelopmental problems in children have increased at a rate that suggests lifestyle factors and chemical exposures as likely contributors. When environmental chemicals contribute to neurodevelopmental disorders developmental neurotoxicity (DNT) becomes an enormous concern. But how can it be tackled? Current animal test-based guidelines are prohibitively expensive, at $1.4 million per substance, while their predictivity for human health effects may be limited, and mechanistic data that would help species extrapolation are not available. A broader screening for substances of concern requires a reliable testing strategy, applicable to larger numbers of substances, and sufficiently predictive to warrant further testing. This review discusses the evidence for possible contributions of environmental chemicals to DNT, limitations of the current test paradigm, emerging concepts and technologies pertinent to in vitro DNT testing and assay evaluation, as well as the prospect of a paradigm shift based on 21st century technologies. PMID:24687333

Chemical Sensors Based on Optical Ring Resonators

NASA Technical Reports Server (NTRS)

Homer, Margie; Manfreda, Allison; Mansour, Kamjou; Lin, Ying; Ksendzov, Alexander

2005-01-01

Chemical sensors based on optical ring resonators are undergoing development. A ring resonator according to this concept is a closed-circuit dielectric optical waveguide. The outermost layer of this waveguide, analogous to the optical cladding layer on an optical fiber, is a made of a polymer that (1) has an index of refraction lower than that of the waveguide core and (2) absorbs chemicals from the surrounding air. The index of refraction of the polymer changes with the concentration of absorbed chemical( s). The resonator is designed to operate with relatively strong evanescent-wave coupling between the outer polymer layer and the electromagnetic field propagating along the waveguide core. By virtue of this coupling, the chemically induced change in index of refraction of the polymer causes a measurable shift in the resonance peaks of the ring. In a prototype that has been used to demonstrate the feasibility of this sensor concept, the ring resonator is a dielectric optical waveguide laid out along a closed path resembling a racetrack (see Figure 1). The prototype was fabricated on a silicon substrate by use of standard techniques of thermal oxidation, chemical vapor deposition, photolithography, etching, and spin coating. The prototype resonator waveguide features an inner cladding of SiO2, a core of SixNy, and a chemical-sensing outer cladding of ethyl cellulose. In addition to the ring Chemical sensors based on optical ring resonators are undergoing development. A ring resonator according to this concept is a closed-circuit dielectric optical waveguide. The outermost layer of this waveguide, analogous to the optical cladding layer on an optical fiber, is a made of a polymer that (1) has an index of refraction lower than that of the waveguide core and (2) absorbs chemicals from the surrounding air. The index of refraction of the polymer changes with the concentration of absorbed chemical( s). The resonator is designed to operate with relatively strong evanescent-wave coupling between the outer polymer layer and the electromagnetic field propagating along the waveguide core. By virtue of this coupling, the chemically induced change in index of refraction of the polymer causes a measurable shift in the resonance peaks of the ring. In a prototype that has been used to demonstrate the feasibility of this sensor concept, the ring resonator is a dielectric optical waveguide laid out along a closed path resembling a racetrack (see Figure 1). The prototype was fabricated on a silicon substrate by use of standard techniques of thermal oxidation, chemical vapor deposition, photolithography, etching, and spin coating. The prototype resonator waveguide features an inner cladding of SiO2, a core of SixNy, and a chemical-sensing outer cladding of ethyl cellulose. In addition to the ring res

Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental 129Xe NMR Spectroscopy

PubMed Central

Selent, Marcin; Nyman, Jonas; Roukala, Juho; Ilczyszyn, Marek; Oilunkaniemi, Raija; Bygrave, Peter J.; Laitinen, Risto; Jokisaari, Jukka

2017-01-01

Abstract An approach is presented for the structure determination of clathrates using NMR spectroscopy of enclathrated xenon to select from a set of predicted crystal structures. Crystal structure prediction methods have been used to generate an ensemble of putative structures of o‐ and m‐fluorophenol, whose previously unknown clathrate structures have been studied by 129Xe NMR spectroscopy. The high sensitivity of the 129Xe chemical shift tensor to the chemical environment and shape of the crystalline cavity makes it ideal as a probe for porous materials. The experimental powder NMR spectra can be used to directly confirm or reject hypothetical crystal structures generated by computational prediction, whose chemical shift tensors have been simulated using density functional theory. For each fluorophenol isomer one predicted crystal structure was found, whose measured and computed chemical shift tensors agree within experimental and computational error margins and these are thus proposed as the true fluorophenol xenon clathrate structures. PMID:28111848

Experimental Determination of pK[subscript a] Values by Use of NMR Chemical Shifts, Revisited

ERIC Educational Resources Information Center

Gift, Alan D.; Stewart, Sarah M.; Bokashanga, Patrick Kwete

2012-01-01

This laboratory experiment, using proton NMR spectroscopy to determine the dissociation constant for heterocyclic bases, has been modified from a previously described experiment. A solution of a substituted pyridine is prepared using deuterium oxide (D[subscript 2]O) as the solvent. The pH of the solution is adjusted and proton NMR spectra are…

Union Carbide's PECOP cops $500,000 fuel cut

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

Crawford, E.

1979-10-29

Union Carbide's Plant Energy Cost Optimization Program (POCOP) is saving $500,000 a year at a Taft, Louisiana chemical complex. Day-to-day decisions affecting fuel costs and plant operations are based on a system of computerized data-gathering and processing. Although Carbide's system is not unique, it is more extensive and more comprehensive than the systems used by other chemical companies. The plant has decreased its energy consumption 12% below the 1972 level while increasing production by 30%. The system was initiated in response to the shift from raw materials to energy as the major production cost.

Synthesis of first row transition metal selenomaltol complexes.

PubMed

Spiegel, Michael T; Hoogerbrugge, Amanda; Truksa, Shamus; Smith, Andrew G; Shuford, Kevin L; Klausmeyer, Kevin K; Farmer, Patrick J

2018-06-21

We report an efficient, one-step synthesis of the chelator 3-hydroxy-2-methyl-4-selenopyrone (selenomaltol). Complexes of selenomaltol with Fe(iii), Ni(ii), Cu(ii) and Zn(ii) have been prepared and studied by NMR, X-ray crystallography, cyclic voltammetry, EPR and electronic absorption. The Ni(ii) and Cu(ii) complexes show chemically reversible oxidations which are suggested to be ligand-based. Nuclear independent chemical shifts (NICS) analysis is used to compare aromaticity of the heterocyclic rings of selenomaltol and its chelates. The compounds described here should significantly expand the scope and utility of unusual O,Se-donor chelates.

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

PubMed Central

Choi, In-Young; Lee, Phil

2012-01-01

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

A QSPR study on the solvent-induced frequency shifts of acetone and dimethyl sulfoxide in organic solvents.

PubMed

Ou, Yu Heng; Chang, Chia Ming; Chen, Ying Shao

2016-06-05

In this study, solvent-induced frequency shifts (SIFS) in the infrared spectrum of acetone and dimethyl sulfoxide in organic solvents were investigated by using four types of quantum-chemical reactivity descriptors. The results showed that the SIFS of acetone is mainly affected by the electron-acceptance chemical potential and the maximum nucleophilic condensed local softness of organic solvents, which represent the electron flow and the polarization between acetone and solvent molecules. On the other hand, the SIFS of dimethyl sulfoxide changes with the maximum positive charge of hydrogen atom and the inverse of apolar surface area of solvent molecules, showing that the electrostatic and hydrophilic interactions are main mechanisms between dimethyl sulfoxide and solvent molecules. The introduction of the four-element theory model-based quantitative structure-property relationship approach improved the assessing quality and provided a basis for interpreting the solute-solvent interactions. Copyright © 2016 Elsevier B.V. All rights reserved.

Assigning the stereochemistry of syn and anti β-trimethylsiloxy-α-trimethylsilyl alkanoic acid silyl esters using GIAO 1H NMR chemical shift calculations

NASA Astrophysics Data System (ADS)

Hadj Mohamed, Slim; Trabelsi, Mahmoud; Champagne, Benoît

2017-08-01

The stereostructure of β-trimethylsiloxy-α-trimethylsilyl alkanoic acid silyl esters synthesized by Bellassoued et al. [J. Org. Chem. 2001, 66, 5054-5057] using Mukaiyama aldol reaction has been reassigned using density functional theory NMR 1H chemical shifts calculations. It is now concluded that the major diastereoisomer is syn and the minor is anti. Within this assignment, for all silyl esters, δHa(anti) > δHa(syn), δHb(anti) < δHb(syn), and 3JHa-Hb (anti) > 3JHa-Hb (syn). Since the experimental assignment was based on the stereostructure (E/Z) of the cinnamic acid obtained by elimination of trimethylsilyl 3-phenyl-3-(trimethylsiloxy)-2-(trimethylsilyl)propanoate in the presence of TiCl4 and on the assumption that this elimination is anti stereospecific in acidic medium, one arrives at the conclusion that the elimination of syn and anti β-trimethylsiloxy-α-trimethylsilyl alkanoic acid silyl esters is not anti stereospecific.

Specific 13C labeling of leucine, valine and isoleucine methyl groups for unambiguous detection of long-range restraints in protein solid-state NMR studies.

PubMed

Fasshuber, Hannes Klaus; Demers, Jean-Philippe; Chevelkov, Veniamin; Giller, Karin; Becker, Stefan; Lange, Adam

2015-03-01

Here we present an isotopic labeling strategy to easily obtain unambiguous long-range distance restraints in protein solid-state NMR studies. The method is based on the inclusion of two biosynthetic precursors in the bacterial growth medium, α-ketoisovalerate and α-ketobutyrate, leading to the production of leucine, valine and isoleucine residues that are exclusively (13)C labeled on methyl groups. The resulting spectral simplification facilitates the collection of distance restraints, the verification of carbon chemical shift assignments and the measurement of methyl group dynamics. This approach is demonstrated on the type-three secretion system needle of Shigella flexneri, where 49 methyl-methyl and methyl-nitrogen distance restraints including 10 unambiguous long-range distance restraints could be collected. By combining this labeling scheme with ultra-fast MAS and proton detection, the assignment of methyl proton chemical shifts was achieved. Copyright © 2015 Elsevier Inc. All rights reserved.

New perspectives in the PAW/GIPAW approach: J(P-O-Si) coupling constants, antisymmetric parts of shift tensors and NQR predictions.

PubMed

Bonhomme, Christian; Gervais, Christel; Coelho, Cristina; Pourpoint, Frédérique; Azaïs, Thierry; Bonhomme-Coury, Laure; Babonneau, Florence; Jacob, Guy; Ferrari, Maude; Canet, Daniel; Yates, Jonathan R; Pickard, Chris J; Joyce, Siân A; Mauri, Francesco; Massiot, Dominique

2010-12-01

In 2001, Pickard and Mauri implemented the gauge including projected augmented wave (GIPAW) protocol for first-principles calculations of NMR parameters using periodic boundary conditions (chemical shift anisotropy and electric field gradient tensors). In this paper, three potentially interesting perspectives in connection with PAW/GIPAW in solid-state NMR and pure nuclear quadrupole resonance (NQR) are presented: (i) the calculation of J coupling tensors in inorganic solids; (ii) the calculation of the antisymmetric part of chemical shift tensors and (iii) the prediction of (14)N and (35)Cl pure NQR resonances including dynamics. We believe that these topics should open new insights in the combination of GIPAW, NMR/NQR crystallography, temperature effects and dynamics. Points (i), (ii) and (iii) will be illustrated by selected examples: (i) chemical shift tensors and heteronuclear (2)J(P-O-Si) coupling constants in the case of silicophosphates and calcium phosphates [Si(5)O(PO(4))(6), SiP(2)O(7) polymorphs and α-Ca(PO(3))(2)]; (ii) antisymmetric chemical shift tensors in cyclopropene derivatives, C(3)X(4) (X = H, Cl, F) and (iii) (14)N and (35)Cl NQR predictions in the case of RDX (C(3)H(6)N(6)O(6)), β-HMX (C(4)H(8)N(8)O(8)), α-NTO (C(2)H(2)N(4)O(3)) and AlOPCl(6). RDX, β-HMX and α-NTO are explosive compounds. Copyright © 2010 John Wiley & Sons, Ltd.

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

PubMed

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

1994-08-01

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

PACSY, a relational database management system for protein structure and chemical shift analysis.

PubMed

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L

2012-10-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.

Randic and Schultz molecular topological indices and their correlation with some X-ray absorption parameters

NASA Astrophysics Data System (ADS)

Khatri, Sunil; Kekre, Pravin A.; Mishra, Ashutosh

2016-10-01

The properties of a molecular system are affected by the topology of molecule. Therefore many studies have been made where the various physic-chemical properties are correlated with the topological indices. These studies have shown a very good correlation demonstrating the utility of the graph theoretical approach. It is, therefore, very natural to expect that the various physical properties obtained by the X-ray absorption spectra may also show correlation with the topological indices. Some complexes were used to establish correlation between topological indices and some X-ray absorption parameters like chemical shift. The chemical shift is on the higher energy side of the metal edge in these complexes. The result obtained in these studies shows that the topological indices of organic molecule acting as a legands can be used for estimating edge shift theoretically.

Hydroxy protons as structural probes to reveal hydrogen bonding properties of polyols in aqueous solution by NMR spectroscopy

NASA Astrophysics Data System (ADS)

Oruc, Gizem; Varnali, Tereza; Bekiroglu, Somer

2018-05-01

The solution properties of ethylene glycol (ethane-1,2-diol), glycerol (propane-1,2,3-triol), erythritol ((2R,3S)-butane-1,2,3,4-tetraol), D-xylitol ((2R,3r,4S)-pentane-1,2,3,4,5-pentaol), D-mannitol ((2R,3R,4R,5R)-hexane-1,2,3,4,5,6-hexaol), and D-sorbitol ((2S,3R,4R,5R)-hexane-1,2,3,4,5,6-hexaol), constituting a subgroup of polyalcohols/polyols of maximum six carbon atoms have been investigated using 1H NMR chemical shifts, coupling constants, temperature coefficients, and chemical exchange rates of hydroxy protons in aqueous medium. Relative within a molecule, minimum two-fold difference in rate of exchange values and higher temperature dependence of chemical shifts of the hydroxy protons on terminal carbon atoms confirm that sustainable hydrogen bonding interactions is accentuated for the hydroxyl groups on secondary carbons. Compared to the primary carbons i.e. terminal ones, the hydroxy protons on second and third carbon atoms exhibit much lower rate of exchange and smaller temperature coefficients, indicating that they are further involved in transient hydrogen bonding interactions. Scalar 3JOH,CH-couplings ranging between 3.9 and 7.2 Hz imply that the hydroxyl groups are practically in free rotation regime. Examination of the chemical shift differences with respect to the shift of glycol hydroxy proton reveals that the disparity between terminal and inner hydroxyl groups disclosed by the exchange rates and temperature coefficients is sustained with the exception of 0.003 and 0.053 ppm for O(3)H of mannitol and O(5)H of sorbitol respectively. The experimental findings have been augmented by quantum chemical calculations targeting theoretical NMR chemical shifts, as well as the conformational analysis of the structures.

Chemical Behavior of Sulfur in Minerals and Silicate Glasses Studied Using Inner Shell Spectroscopy

NASA Astrophysics Data System (ADS)

Alonso Mori, R.; Paris, E.; Glatzel, P.; Giuli, G.; Scaillet, B.

2008-12-01

Understanding the chemical behaviour of sulfur is of fundamental importance in explaining different geological mechanisms ranging from volcano-climatic interactions to the genesis of ore deposits. Understanding how sulphur behaves is also of great economic importance in industrial activities including glass-forming processes and the treatment of vitreous waste material from refuse incineration. The chemical behaviour of sulfur in minerals and glasses has been widely studied via X-ray absorption near edge structure (XANES) spectroscopy, which probes the unoccupied density of states and thus provides information on the oxidation state and local structure of the species under study. However, the XANES spectral shape is influenced by various effects, namely the local symmetry, the ligand type, even up to high coordination spheres, and the valence electron occupation, making it difficult to systematically analyze the different spectral contributions. We use X-ray emission spectroscopy (XES) as a complementary technique to avoid some of the inherent difficulties of XANES analysis, and to extract additional information on the electronic structure. The Kb lines, close to the K-edge, directly yield the p-density of occupied valence states, giving valuable information on the local coordination. We have compared XANES and Kb XES experimental data on sulfur- bearing minerals with ab initio quantum-chemical calculations based on density functional theory (DFT), in order to visualize the molecular orbitals and to extract information about the chemical bonding in these compounds. The S Ka emission lines, which arise from 2p to 1s transitions, are expected to be mostly free from chemical bond effects except for small energy shifts that reflect the valence orbital electron population via screening effects. S Ka shifts can be readily used to determine the speciation of sulfur in silicate glasses. The electronic configuration of the sulfur atoms is obtained by calculating the effective charge around the sulfur atom based on the Mulliken population analysis generated by DFT calculations, and then successfully correlated with the observed experimental shifts. In order to check these results using a theoretical framework other than DFT, we also performed calculations using a multiple scattering approach (FEFF8.4). X-ray absorption and emission spectroscopy has been applied to three series of peralkaline rhyolitic obsidians each with different alkali/alumina ratios ((Na2O + K2O)/Al2O3). The occurrence of sulfur was accurately determined by using the energy shift of the S Ka emission lines to make a quantitative analysis. We observe that we can follow the evolution of sulfur as a function of controlled formation conditions with respect to pressure, temperature or oxygen fugacity, and determine whether it is present as sulfate or sulfide. XANES and Kb emission lines also yield detailed information on the local chemistry and structure, and thus help us to understand the geochemical role of S in these systems.

Monitoring the refinement of crystal structures with {sup 15}N solid-state NMR shift tensor data

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

Kalakewich, Keyton; Eloranta, Harriet; Harper, James K.

The {sup 15}N chemical shift tensor is shown to be extremely sensitive to lattice structure and a powerful metric for monitoring density functional theory refinements of crystal structures. These refinements include lattice effects and are applied here to five crystal structures. All structures improve based on a better agreement between experimental and calculated {sup 15}N tensors, with an average improvement of 47.0 ppm. Structural improvement is further indicated by a decrease in forces on the atoms by 2–3 orders of magnitude and a greater similarity in atom positions to neutron diffraction structures. These refinements change bond lengths by more thanmore » the diffraction errors including adjustments to X–Y and X–H bonds (X, Y = C, N, and O) of 0.028 ± 0.002 Å and 0.144 ± 0.036 Å, respectively. The acquisition of {sup 15}N tensors at natural abundance is challenging and this limitation is overcome by improved {sup 1}H decoupling in the FIREMAT method. This decoupling dramatically narrows linewidths, improves signal-to-noise by up to 317%, and significantly improves the accuracy of measured tensors. A total of 39 tensors are measured with shifts distributed over a range of more than 400 ppm. Overall, experimental {sup 15}N tensors are at least 5 times more sensitive to crystal structure than {sup 13}C tensors due to nitrogen’s greater polarizability and larger range of chemical shifts.« less

Protein NMR Studies of Substrate Binding to Human Blood Group A and B Glycosyltransferases.

PubMed

Grimm, Lena Lisbeth; Weissbach, Sophie; Flügge, Friedemann; Begemann, Nora; Palcic, Monica M; Peters, Thomas

2017-07-04

Donor and acceptor substrate binding to human blood group A and B glycosyltransferases (GTA, GTB) has been studied by a variety of protein NMR experiments. Prior crystallographic studies had shown these enzymes to adopt an open conformation in the absence of substrates. Binding either of the donor substrate UDP-Gal or of UDP induces a semiclosed conformation. In the presence of both donor and acceptor substrates, the enzymes shift towards a closed conformation with ordering of an internal loop and the C-terminal residues, which then completely cover the donor-binding pocket. Chemical-shift titrations of uniformly 2 H, 15 N-labeled GTA or GTB with UDP affected about 20 % of all crosspeaks in 1 H, 15 N TROSY-HSQC spectra, reflecting substantial plasticity of the enzymes. On the other hand, it is this conformational flexibility that impedes NH backbone assignments. Chemical-shift-perturbation experiments with δ1-[ 13 C]methyl-Ile-labeled samples revealed two Ile residues-Ile123 at the bottom of the UDP binding pocket, and Ile192 as part of the internal loop-that were significantly disturbed upon stepwise addition of UDP and H-disaccharide, also revealing long-range perturbations. Finally, methyl TROSY-based relaxation dispersion experiments do not reveal micro- to millisecond timescale motions. Although this study reveals substantial conformational plasticity of GTA and GTB, the matter of how binding of substrates shifts the enzymes into catalytically competent states remains enigmatic. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

PubMed

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

2016-02-05

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

Self-reported Occupational Exposures Relevant for Cancer among 28,000 Offshore Oil Industry Workers Employed between 1965 and 1999

PubMed Central

Stenehjem, Jo S; Friesen, Melissa C; Eggen, Tone; Kjærheim, Kristina; Bråtveit, Magne; Grimsrud, Tom K

2016-01-01

The objective of this study was to examine self-reported frequency of occupational exposure reported by 28,000 Norwegian offshore oil workers in a 1998 survey. Predictors of self-reported exposure frequency were identified to aid future refinements of an expert-based job-exposure-time matrix (JEM). We focus here on reported frequencies for skin contact with oil and diesel, exposure to oil vapor from shaker, to exhaust fumes, vapor from mixing chemicals used for drilling, natural gas, chemicals used for water injection and processing, and to solvent vapor. Exposure frequency was reported by participants as the exposed proportion of the work shift, defined by six categories, in their current or last position offshore (between 1965 and 1999). Binary Poisson regression models with robust variance were used to examine the probabilities of reporting frequent exposure (≥¼ vs. <¼ of work shift) according to main activity, time period, supervisory position, type of company, type of installation, work schedule, and education. Holding a non-supervisory position, working shifts, being employed in the early period of the offshore industry, and having only compulsory education increased the probability of reporting frequent exposure. The identified predictors and group-level patterns may aid future refinement of the JEM previously developed for the present cohort. PMID:25671393

Self-reported Occupational Exposures Relevant for Cancer among 28,000 Offshore Oil Industry Workers Employed between 1965 and 1999.

PubMed

Stenehjem, Jo S; Friesen, Melissa C; Eggen, Tone; Kjærheim, Kristina; Bråtveit, Magne; Grimsrud, Tom K

2015-01-01

The objective of this study was to examine self-reported frequency of occupational exposure reported by 28,000 Norwegian offshore oil workers in a 1998 survey. Predictors of self-reported exposure frequency were identified to aid future refinements of an expert-based job-exposure-time matrix (JEM). We focus here on reported frequencies for skin contact with oil and diesel; exposure to oil vapor from shaker, to exhaust fumes, vapor from mixing chemicals used for drilling, natural gas, chemicals used for water injection and processing, and to solvent vapor. Exposure frequency was reported by participants as the exposed proportion of the work shift, defined by six categories, in their current or last position offshore (between 1965 and 1999). Binary Poisson regression models with robust variance were used to examine the probabilities of reporting frequent exposure (≥¼ vs. <¼ of work shift) according to main activity, time period, supervisory position, type of company, type of installation, work schedule, and education. Holding a non-supervisory position, working shifts, being employed in the early period of the offshore industry, and having only compulsory education increased the probability of reporting frequent exposure. The identified predictors and group-level patterns may aid future refinement of the JEM previously developed for the present cohort.

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

PubMed

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

2008-08-11

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

Method Of Signal Amplification In Multi-Chromophore Luminescence Sensors

DOEpatents

Levitsky, Igor A.; Krivoshlykov, Sergei G.

2004-02-03

A fluorescence-based method for highly sensitive and selective detection of analyte molecules is proposed. The method employs the energy transfer between two or more fluorescent chromophores in a carefully selected polymer matrix. In one preferred embodiment, signal amplification has been achieved in the fluorescent sensing of dimethyl methylphosphonate (DMMP) using two dyes, 3-aminofluoranthene (AM) and Nile Red (NR), in a hydrogen bond acidic polymer matrix. The selected polymer matrix quenches the fluorescence of both dyes and shifts dye emission and absorption spectra relative to more inert matrices. Upon DMMP sorption, the AM fluorescence shifts to the red at the same time the NR absorption shifts to the blue, resulting in better band overlap and increased energy transfer between chromophores. In another preferred embodiment, the sensitive material is incorporated into an optical fiber system enabling efficient excitation of the dye and collecting the fluorescent signal form the sensitive material on the remote end of the system. The proposed method can be applied to multichromophore luminescence sensor systems incorporating N-chromophores leading to N-fold signal amplification and improved selectivity. The method can be used in all applications where highly sensitive detection of basic gases, such as dimethyl methylphosphonate (DMMP), Sarin, Soman and other chemical warfare agents having basic properties, is required, including environmental monitoring, chemical industry and medicine.

Predicting the future: opportunities and challenges for the chemical industry to apply 21st-century toxicity testing.

PubMed

Settivari, Raja S; Ball, Nicholas; Murphy, Lynea; Rasoulpour, Reza; Boverhof, Darrell R; Carney, Edward W

2015-03-01

Interest in applying 21st-century toxicity testing tools for safety assessment of industrial chemicals is growing. Whereas conventional toxicology uses mainly animal-based, descriptive methods, a paradigm shift is emerging in which computational approaches, systems biology, high-throughput in vitro toxicity assays, and high-throughput exposure assessments are beginning to be applied to mechanism-based risk assessments in a time- and resource-efficient fashion. Here we describe recent advances in predictive safety assessment, with a focus on their strategic application to meet the changing demands of the chemical industry and its stakeholders. The opportunities to apply these new approaches is extensive and include screening of new chemicals, informing the design of safer and more sustainable chemical alternatives, filling information gaps on data-poor chemicals already in commerce, strengthening read-across methodology for categories of chemicals sharing similar modes of action, and optimizing the design of reduced-risk product formulations. Finally, we discuss how these predictive approaches dovetail with in vivo integrated testing strategies within repeated-dose regulatory toxicity studies, which are in line with 3Rs principles to refine, reduce, and replace animal testing. Strategic application of these tools is the foundation for informed and efficient safety assessment testing strategies that can be applied at all stages of the product-development process.

Self-association and base pairing of guanosine, cytidine, adenosine, and uridine in dimethyl sulfoxide solution measured by 15N nuclear magnetic resonance spectroscopy.

PubMed Central

Dyllick-Brenzinger, C; Sullivan, G R; Pang, P P; Roberts, J D

1980-01-01

The self-association of guanosine, cytidine, and adenosine and base pairing between guanosine, cytidine, adenosine, and uridine in dimethyl sulfoxide have been investigated by the variation of their 15N NMR chemical shifts with concentration and temperature. Guanosine, cytidine, and adenosine all showed evidence of self-association by hydrogen bonding. In guanosine/cytidine mixtures, a hydrogen-bonded dimer is formed; however, no base pairing could be detected with adenosine/cytidine or adenosine/uridine mixtures. PMID:6932658

pH Dependent Spin State Population and 19F NMR Chemical Shift via Remote Ligand Protonation in an Iron(II) Complex (Postprint)

DTIC Science & Technology

2017-12-11

AFRL-RX-WP-JA-2017-0501 pH- DEPENDENT SPIN STATE POPULATION AND 19F NMR CHEMICAL SHIFT VIA REMOTE LIGAND PROTONATION IN AN IRON(II...From - To) 16 November 2017 Interim 24 January 2014 – 16 October 2017 4. TITLE AND SUBTITLE PH- DEPENDENT SPIN STATE POPULATION AND 19F NMR CHEMICAL...dx.doi.org/10.1039/C7CC08099A 14. ABSTRACT (Maximum 200 words) An FeII complex that features a pH- dependent spin state population, by virtue of a

An extrapolation scheme for solid-state NMR chemical shift calculations

NASA Astrophysics Data System (ADS)

Nakajima, Takahito

2017-06-01

Conventional quantum chemical and solid-state physical approaches include several problems to accurately calculate solid-state nuclear magnetic resonance (NMR) properties. We propose a reliable computational scheme for solid-state NMR chemical shifts using an extrapolation scheme that retains the advantages of these approaches but reduces their disadvantages. Our scheme can satisfactorily yield solid-state NMR magnetic shielding constants. The estimated values have only a small dependence on the low-level density functional theory calculation with the extrapolation scheme. Thus, our approach is efficient because the rough calculation can be performed in the extrapolation scheme.

Comparing REACH Chemical Safety Assessment information with practice-a case-study of polymethylmethacrylate (PMMA) in floor coating in The Netherlands.

PubMed

Spee, Ton; Huizer, Daan

2017-10-01

On June 1st, 2007 the European regulation on Registration, Evaluation and Restriction of Chemical substances (REACH) came into force. Aim of the regulation is safe use of chemicals for humans and for the environment. The core element of REACH is chemical safety assessment of chemicals and communication of health and safety hazards and risk management measures throughout the supply chain. Extended Safety Data Sheets (Ext-SDS) are the primary carriers of health and safety information. The aim of our project was to find out whether the actual exposure to methyl methacrylate (MMA) during the application of polymethylmethacrylate (PMMA) in floor coatings as assessed in the chemical safety assessment, reflect the exposure situations as observed in the Dutch building practice. Use of PMMA flooring and typical exposure situations during application were discussed with twelve representatives of floor laying companies. Representative situations for exposure measurements were designated on the basis of this inventory. Exposure to MMA was measured in the breathing zone of the workers at four construction sites, 14 full shift samples and 14 task based samples were taken by personal air sampling. The task-based samples were compared with estimates from the Targeted Risk Assessment Tool (v3.1) of the European Centre for Ecotoxicology and Toxicology of Chemicals (ECETOC-TRA) as supplied in the safety assessment from the manufacturer. For task-based measurements, in 12 out of 14 (86%) air samples measured exposure was higher than estimated exposure. Recalculation with a lower ventilation rate (50% instead of 80%) together with a higher temperature during mixing (40°C instead of 20°C) in comparison with the CSR, reduced the number of underestimated exposures to 10 (71%) samples. Estimation with the EMKG-EXPO-Tool resulted in unsafe exposure situations for all scenarios, which is in accordance with the measurement outcomes. In indoor situations, 5 out of 8 full shift exposures (62%) to MMA were higher than the Dutch occupational exposure limit of 205mg/m 3 (8h TWA), which equals the DNEL. For semi-enclosed situations this was 1 out of 6 (17%). Exposures varied from 31 to 367mg/m 3 . The results emphasize that ECETOC-TRA exposure estimates in poorly controlled situations need better underpinning. Copyright © 2017 Elsevier GmbH. All rights reserved.

Direct Simulation of Magnetic Resonance Relaxation Rates and Line Shapes from Molecular Trajectories

PubMed Central

Rangel, David P.; Baveye, Philippe C.; Robinson, Bruce H.

2012-01-01

We simulate spin relaxation processes, which may be measured by either continuous wave or pulsed magnetic resonance techniques, using trajectory-based simulation methodologies. The spin–lattice relaxation rates are extracted numerically from the relaxation simulations. The rates obtained from the numerical fitting of the relaxation curves are compared to those obtained by direct simulation from the relaxation Bloch–Wangsness–Abragam– Redfield theory (BWART). We have restricted our study to anisotropic rigid-body rotational processes, and to the chemical shift anisotropy (CSA) and a single spin–spin dipolar (END) coupling mechanisms. Examples using electron paramagnetic resonance (EPR) nitroxide and nuclear magnetic resonance (NMR) deuterium quadrupolar systems are provided. The objective is to compare those rates obtained by numerical simulations with the rates obtained by BWART. There is excellent agreement between the simulated and BWART rates for a Hamiltonian describing a single spin (an electron) interacting with the bath through the chemical shift anisotropy (CSA) mechanism undergoing anisotropic rotational diffusion. In contrast, when the Hamiltonian contains both the chemical shift anisotropy (CSA) and the spin–spin dipolar (END) mechanisms, the decay rate of a single exponential fit of the simulated spin–lattice relaxation rate is up to a factor of 0.2 smaller than that predicted by BWART. When the relaxation curves are fit to a double exponential, the slow and fast rates extracted from the decay curves bound the BWART prediction. An extended BWART theory, in the literature, includes the need for multiple relaxation rates and indicates that the multiexponential decay is due to the combined effects of direct and cross-relaxation mechanisms. PMID:22540276

Hybrid quantitative MRI using chemical shift displacement and recovery-based simultaneous water and lipid imaging: A preliminary study.

PubMed

Ohno, Naoki; Miyati, Tosiaki; Suzuki, Shuto; Kan, Hirohito; Aoki, Toshitaka; Nakamura, Yoshitaka; Hiramatsu, Yuki; Kobayashi, Satoshi; Gabata, Toshifumi

2018-07-01

To suppress olefinic signals and enable simultaneous and quantitative estimation of multiple functional parameters associated with water and lipid, we investigated a modified method using chemical shift displacement and recovery-based separation of lipid tissue (SPLIT) involving acquisitions with different inversion times (TIs), echo times (TEs), and b-values. Single-shot diffusion echo-planar imaging (SSD-EPI) with multiple b-values (0-3000 s/mm 2 ) was performed without fat suppression to separate water and lipid images using the chemical shift displacement of lipid signals in the phase-encoding direction. An inversion pulse (TI = 292 ms) was applied to SSD-EPI to remove olefinic signals. Consecutively, SSD-EPI (b = 0 s/mm 2 ) was performed with TI = 0 ms and TE = 31.8 ms for T 1 and T 2 measurements, respectively. Under these conditions, transverse water and lipid images at the maximum diameter of the right calf were obtained in six healthy subjects. T 1 , T 2 , and the apparent diffusion coefficients (ADC) were then calculated for the tibialis anterior (TA), gastrocnemius (GM), and soleus (SL) muscles, tibialis bone marrow (TB), and subcutaneous fat (SF). Perfusion-related (D*) and restricted diffusion coefficients (D) were calculated for the muscles. Lastly, the lipid fractions (LF) of the muscles were determined after T 1 and T 2 corrections. The modified SPLIT method facilitated sufficient separation of water and lipid images of the calf, and the inversion pulse with TI of 292 ms effectively suppressed olefinic signals. All quantitative parameters obtained with the modified SPLIT method were found to be in general agreement with those previously reported in the literature. The modified SPLIT technique enabled sufficient suppression of olefinic signals and simultaneous acquisition of quantitative parameters including diffusion, perfusion, T 1 and T 2 relaxation times, and LF. Copyright © 2018. Published by Elsevier Inc.

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

NASA Astrophysics Data System (ADS)

Zhang, Rongchun; Ramamoorthy, Ayyalusamy

2015-05-01

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

Dynamical measurement of refractive index distribution using digital holographic interferometry based on total internal reflection.

PubMed

Zhang, Jiwei; Di, Jianglei; Li, Ying; Xi, Teli; Zhao, Jianlin

2015-10-19

We present a method for dynamically measuring the refractive index distribution in a large range based on the combination of digital holographic interferometry and total internal reflection. A series of holograms, carrying the index information of mixed liquids adhered on a total reflection prism surface, are recorded with CCD during the diffusion process. Phase shift differences of the reflected light are reconstructed exploiting the principle of double-exposure holographic interferometry. According to the relationship between the reflection phase shift difference and the liquid index, two dimensional index distributions can be directly figured out, assuming that the index of air near the prism surface is constant. The proposed method can also be applied to measure the index of solid media and monitor the index variation during some chemical reaction processes.

Ligand Binding Analysis and Screening by Chemical Denaturation Shift

PubMed Central

Sch n, Arne; Brown, Richard K.; Hutchins, Burleigh M.; Freire, Ernesto

2013-01-01

The identification of small molecule ligands is an important first step in drug development, especially drugs that target proteins with no intrinsic activity. Towards this goal, it is important to have access to technologies that are able to measure binding affinities for a large number of potential ligands in a fast and accurate way. Since ligand binding stabilizes the protein structure in a manner dependent on concentration and binding affinity, the magnitude of the protein stabilization effect elicited by binding can be used to identify and characterize ligands. For example, the shift in protein denaturation temperature (Tm shift) has become a popular approach to identify potential ligands. However, Tm shifts cannot be readily transformed into binding affinities and the ligand rank order obtained at denaturation temperatures (60°C or higher) does not necessarily coincide with the rank order at physiological temperature. An alternative approach is the use of chemical denaturation, which can be implemented at any temperature. Chemical denaturation shifts allow accurate determination of binding affinities with a surprisingly wide dynamic range (high micromolar to sub nanomolar) and in situations in which binding changes the cooperativity of the unfolding transition. In this paper we develop the basic analytical equations and provide several experimental examples. PMID:23994566

Ligand binding analysis and screening by chemical denaturation shift.

PubMed

Schön, Arne; Brown, Richard K; Hutchins, Burleigh M; Freire, Ernesto

2013-12-01

The identification of small molecule ligands is an important first step in drug development, especially drugs that target proteins with no intrinsic activity. Toward this goal, it is important to have access to technologies that are able to measure binding affinities for a large number of potential ligands in a fast and accurate way. Because ligand binding stabilizes the protein structure in a manner dependent on concentration and binding affinity, the magnitude of the protein stabilization effect elicited by binding can be used to identify and characterize ligands. For example, the shift in protein denaturation temperature (Tm shift) has become a popular approach to identify potential ligands. However, Tm shifts cannot be readily transformed into binding affinities, and the ligand rank order obtained at denaturation temperatures (≥60°C) does not necessarily coincide with the rank order at physiological temperature. An alternative approach is the use of chemical denaturation, which can be implemented at any temperature. Chemical denaturation shifts allow accurate determination of binding affinities with a surprisingly wide dynamic range (high micromolar to sub nanomolar) and in situations where binding changes the cooperativity of the unfolding transition. In this article, we develop the basic analytical equations and provide several experimental examples. Copyright © 2013 Elsevier Inc. All rights reserved.

Evidence of chemical-potential shift with hole doping in Bi2Sr2CaCu2O8+δ

NASA Astrophysics Data System (ADS)

Shen, Z.-X.; Dessau, D. S.; Wells, B. O.; Olson, C. G.; Mitzi, D. B.; Lombado, Lou; List, R. S.; Arko, A. J.

1991-12-01

We have performed photoemission studies on high-quality Bi2Sr2CaCu2O8+δ samples with various δ. Our results show a clear chemical-potential shift (0.15-0.2 eV) as a function of doping. This result and the existing angle-resolved-photoemission data give a rather standard doping behavior of this compound in its highly doped regime.

13C nuclear magnetic resonance data of lanosterol derivatives—Profiling the steric topology of the steroid skeleton via substituent effects on its 13C NMR

NASA Astrophysics Data System (ADS)

Dias, Jerry Ray; Gao, Hongwu

2009-12-01

The 13C NMR spectra of over 24 tetracyclic triterpenoid derivatives have been structurally analyzed. The 13C NMR chemical shifts allow one to probe the steric topology of the rigid steroid skeleton and inductive effects of its substituents. Use of deuterium labeling in chemical shift assignment and B-ring aromatic terpenoids are also featured.

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

PubMed Central

Shen, Yang; Bax, Ad

2013-01-01

A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, ≥ 90% fraction of the residues, with an error rate smaller than ca 3.5%, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed (φ,ψ) torsion angles of ca 12°. TALOS-N also reports sidechain χ1 rotameric states for about 50% of the residues, and a consistency with reference structures of 89%. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts. PMID:23728592

PACSY, a relational database management system for protein structure and chemical shift analysis

PubMed Central

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo

2012-01-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu. PMID:22903636

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

PubMed

Kara, Yesim S

2015-12-05

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

Nuclear magnetic resonance spectral analysis and molecular properties of berberine

NASA Astrophysics Data System (ADS)

Huang, Ming-Ju; Lee, Ken S.; Hurley, Sharon J.

An extensive theoretical study of berberine has been performed at the ab initio HF/6-31G**, HF/6-311G**, and B3LYP/6-311G** levels with and without solvent effects. The optimized structures are compared with X-ray data. We found that the optimized structures with solvent effects are in slightly better agreement with X-ray data than those without solvent effects. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of berberine were calculated by using the gauge-independent atomic orbital (GIAO) (with and without solvent effects), CSGT, and IGAIM methods. The calculated chemical shifts were compared with the two-dimensional NMR experimental data. Overall, the calculated chemical shifts show very good agreement with the experimental results. The harmonic vibrational frequencies for berberine were calculated at the B3LYP/6-311G** level.

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

PubMed

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

2014-01-01

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

Triple Resonance Solid State NMR Experiments with Reduced Dimensionality Evolution Periods

NASA Astrophysics Data System (ADS)

Astrof, Nathan S.; Lyon, Charles E.; Griffin, Robert G.

2001-10-01

Two solid state NMR triple resonance experiments which utilize the simultaneous incrementation of two chemical shift evolution periods to obtain a spectrum with reduced dimensionality are described. The CON CA experiment establishes the correlation of 13Ci-1 to 13Cαi and 15Ni by simultaneously encoding the 13COi-1 and 15Ni chemical shifts. The CAN COCA experiment establishes the correlation 13Cai and 15COi to 13Cαi-1 and 15Ni-1 within a single experiment by simultaneous encoding of the 13Cαi and 15Ni chemical shifts. This experiment establishes sequential amino acid correlations in close analogy to the solution state HNCA experiment. Reduced dimensionality 2D experiments are a practical alternative to recording multiple 3D data sets for the purpose of obtaining sequence-specific resonance assignments of peptides and proteins in the solid state.

Hydride ions in oxide hosts hidden by hydroxide ions

PubMed Central

Hayashi, Katsuro; Sushko, Peter V.; Hashimoto, Yasuhiro; Shluger, Alexander L.; Hosono, Hideo

2014-01-01

The true oxidation state of formally ‘H−’ ions incorporated in an oxide host is frequently discussed in connection with chemical shifts of 1H nuclear magnetic resonance spectroscopy, as they can exhibit values typically attributed to H+. Here we systematically investigate the link between geometrical structure and chemical shift of H− ions in an oxide host, mayenite, with a combination of experimental and ab initio approaches, in an attempt to resolve this issue. We demonstrate that the electron density near the hydrogen nucleus in an OH− ion (formally H+ state) exceeds that in an H− ion. This behaviour is the opposite to that expected from formal valences. We deduce a relationship between the chemical shift of H− and the distance from the H− ion to the coordinating electropositive cation. This relationship is pivotal for resolving H− species that are masked by various states of H+ ions. PMID:24662678

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

PubMed Central

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

2012-01-01

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

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

PubMed

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

2014-08-28

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

Sub-millisecond 125Te NMR spin-lattice relaxation times and large Knight shifts in complex tellurides: Validation of a quadratic relation across the spectrum

DOE PAGES

Levin, E. M.; Iowa State Univ., Ames, IA; Cui, J. -F.; ...

2016-07-16

125Te NMR spectra and spin-lattice relaxation times, T 1, have been measured for several GeTe-based materials with Te excess. In this paper, the spectra show inhomogeneous broadening by several thousand ppm and a systematic variation in T 1 relaxation time with resonance frequency. The quadratic dependence of the spin-lattice relaxation rate, 1/T 1, on the Knight shift in the Korringa relation is found to be valid over a wide range of Knight shifts. This result confirms that T 1 relaxation in GeTe-based materials is mostly dominated by hyperfine interaction between nuclei and free charge carriers. In GeTe with 2.5% excessmore » of Te, about 15% of the material exhibits a Knight shift of ≥4500 ppm and a T 1 of only 0.3 ms, indicating a high hole concentration that could correspond to close to 50% vacancies on the Ge sublattice in this component. Lastly, our findings provide a basis for determining the charge carrier concentration and its distribution in complex thermoelectric and phase-change tellurides, which should lead to a better understanding of electronic and thermal transport properties as well as chemical bonding in these materials.« less

Nuclear magnetic resonance, vibrational spectroscopic studies, physico-chemical properties and computational calculations on (nitrophenyl) octahydroquinolindiones by DFT method.

PubMed

Pasha, M A; Siddekha, Aisha; Mishra, Soni; Azzam, Sadeq Hamood Saleh; Umapathy, S

2015-02-05

In the present study, 2'-nitrophenyloctahydroquinolinedione and its 3'-nitrophenyl isomer were synthesized and characterized by FT-IR, FT-Raman, (1)H NMR and (13)C NMR spectroscopy. The molecular geometry, vibrational frequencies, (1)H and (13)C NMR chemical shift values of the synthesized compounds in the ground state have been calculated by using the density functional theory (DFT) method with the 6-311++G (d,p) basis set and compared with the experimental data. The complete vibrational assignments of wave numbers were made on the basis of potential energy distribution using GAR2PED programme. Isotropic chemical shifts for (1)H and (13)C NMR were calculated using gauge-invariant atomic orbital (GIAO) method. The experimental vibrational frequencies, (1)H and (13)C NMR chemical shift values were found to be in good agreement with the theoretical values. On the basis of vibrational analysis, molecular electrostatic potential and the standard thermodynamic functions have been investigated. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

Novel Hybrid Virtual Screening Protocol Based on Molecular Docking and Structure-Based Pharmacophore for Discovery of Methionyl-tRNA Synthetase Inhibitors as Antibacterial Agents

PubMed Central

Liu, Chi; He, Gu; Jiang, Qinglin; Han, Bo; Peng, Cheng

2013-01-01

Methione tRNA synthetase (MetRS) is an essential enzyme involved in protein biosynthesis in all living organisms and is a potential antibacterial target. In the current study, the structure-based pharmacophore (SBP)-guided method has been suggested to generate a comprehensive pharmacophore of MetRS based on fourteen crystal structures of MetRS-inhibitor complexes. In this investigation, a hybrid protocol of a virtual screening method, comprised of pharmacophore model-based virtual screening (PBVS), rigid and flexible docking-based virtual screenings (DBVS), is used for retrieving new MetRS inhibitors from commercially available chemical databases. This hybrid virtual screening approach was then applied to screen the Specs (202,408 compounds) database, a structurally diverse chemical database. Fifteen hit compounds were selected from the final hits and shifted to experimental studies. These results may provide important information for further research of novel MetRS inhibitors as antibacterial agents. PMID:23839093

Metamaterial Absorber Based Multifunctional Sensor Application

NASA Astrophysics Data System (ADS)

Ozer, Z.; Mamedov, A. M.; Ozbay, E.

2017-02-01

In this study metamaterial based (MA) absorber sensor, integrated with an X-band waveguide, is numerically and experimentally suggested for important application including pressure, density sensing and marble type detecting applications based on rectangular split ring resonator, sensor layer and absorber layer that measures of changing in the dielectric constant and/or the thickness of a sensor layer. Changing of physical, chemical or biological parameters in the sensor layer can be detected by measuring the resonant frequency shifting of metamaterial absorber based sensor. Suggested MA based absorber sensor can be used for medical, biological, agricultural and chemical detecting applications in microwave frequency band. We compare the simulation and experimentally obtained results from the fabricated sample which are good agreement. Simulation results show that the proposed structure can detect the changing of the refractive indexes of different materials via special resonance frequencies, thus it could be said that the MA-based sensors have high sensitivity. Additionally due to the simple and tiny structures it could be adapted to other electronic devices in different sizes.

Improving chemical shift encoding‐based water–fat separation based on a detailed consideration of magnetic field contributions

PubMed Central

Ruschke, Stefan; Eggers, Holger; Meineke, Jakob; Rummeny, Ernst J.; Karampinos, Dimitrios C.

2018-01-01

Purpose To improve the robustness of existing chemical shift encoding‐based water–fat separation methods by incorporating a priori information of the magnetic field distortions in complex‐based water–fat separation. Methods Four major field contributions are considered: inhomogeneities of the scanner magnet, the shim field, an object‐based field map estimate, and a residual field. The former two are completely determined by spherical harmonic expansion coefficients directly available from the magnetic resonance (MR) scanner. The object‐based field map is forward simulated from air–tissue interfaces inside the field of view (FOV). The missing residual field originates from the object outside the FOV and is investigated by magnetic field simulations on a numerical whole body phantom. In vivo the spatially linear first‐order component of the residual field is estimated by measuring echo misalignments after demodulation of other field contributions resulting in a linear residual field. Gradient echo datasets of the cervical and the ankle region without and with shimming were acquired, where all four contributions were incorporated in the water–fat separation with two algorithms from the ISMRM water–fat toolbox and compared to water–fat separation with less incorporated field contributions. Results Incorporating all four field contributions as demodulation steps resulted in reduced temporal and spatial phase wraps leading to almost swap‐free water–fat separation results in all datasets. Conclusion Demodulating estimates of major field contributions reduces the phase evolution to be driven by only small differences in local tissue susceptibility, which supports the field smoothness assumption of existing water–fat separation techniques. PMID:29424458

Continuum in the X-Z---Y weak bonds: Z= main group elements.

PubMed

Joy, Jyothish; Jose, Anex; Jemmis, Eluvathingal D

2016-01-15

The Continuum in the variation of the X-Z bond length change from blue-shifting to red-shifting through zero- shifting in the X-Z---Y complex is inevitable. This has been analyzed by ab-initio molecular orbital calculations using Z= Hydrogen, Halogens, Chalcogens, and Pnicogens as prototypical examples. Our analysis revealed that, the competition between negative hyperconjugation within the donor (X-Z) molecule and Charge Transfer (CT) from the acceptor (Y) molecule is the primary reason for the X-Z bond length change. Here, we report that, the proper tuning of X- and Y-group for a particular Z- can change the blue-shifting nature of X-Z bond to zero-shifting and further to red-shifting. This observation led to the proposal of a continuum in the variation of the X-Z bond length during the formation of X-Z---Y complex. The varying number of orbitals and electrons available around the Z-atom differentiates various classes of weak interactions and leads to interactions dramatically different from the H-Bond. Our explanations based on the model of anti-bonding orbitals can be transferred from one class of weak interactions to another. We further take the idea of continuum to the nature of chemical bonding in general. © 2015 Wiley Periodicals, Inc.

FACILITATED CHEMICAL SYNTHESIS UNDER ALTERNATE REACTION CONDITIONS

EPA Science Inventory

The chemical research in the late 1990's witnessed a paradigm shift towards "environmentally-friendly chemistry" more popularly known as "green chemistry" due to the increasing environmental concerns and legislative requirements to curb the release of chemical waste into the atmo...

CHEMICAL SYNTHESIS USING 'GREENER' ALTERNATIVE REACTION CONDITIONS AND MEDIA

EPA Science Inventory

The chemical research during the last decade has witnessed a paradigm shift towards "environmentally-friendly chemistry" more popularly known as "green chemistry" due to the increasing environmental concerns and legislative requirements to curb the release of chemical waste into ...

Ab Initio Theory of Nuclear Magnetic Resonance Shifts in Metals

NASA Astrophysics Data System (ADS)

D'Avezac, Mayeul; Marzari, Nicola; Mauri, Francesco

2005-03-01

A comprehensive approach for the first-principles determination of all-electron NMR shifts in metallic systems is presented. Our formulation is based on a combination of density-functional perturbation theory and all-electron wavefunction reconstruction, starting from periodic-boundary calculations in the pseudopotential approximation. The orbital contribution to the NMR shift (the chemical shift) is obtained by combining the gauge-including projector augmented-wave approach (GIPAW), originally developed for the case of insulatorsootnotetextC. J. Pickard, Francesco Mauri, Phys. Rev. B, 63, 245101(2001), with the extension of linear-response theory to the case of metallic systemsootnotetextS. de Gironcoli, Phys. Rev. B, 51, 6773(1995). The spin contribution (the Knight shift) is obtained as a response to a finite uniform magnetic field, and through reconstructing the hyperfine interaction between the electron-spin density and the nuclear spins with the projector augmented-wave method (PAWootnotetextC. G. Van de Walle, P. E. Blöchl, Phys. Rev. B, 47, 4244(1993)). Our method is validated with applications to the case of the homogeneous electron gas and of simple metals. (Work supported by MURI grant DAAD 19-03-1-0169 and MIT-France)

Chemical exchange rotation transfer imaging of intermediate-exchanging amines at 2 ppm.

PubMed

Zu, Zhongliang; Louie, Elizabeth A; Lin, Eugene C; Jiang, Xiaoyu; Does, Mark D; Gore, John C; Gochberg, Daniel F

2017-10-01

Chemical exchange saturation transfer (CEST) imaging of amine protons exchanging at intermediate rates and whose chemical shift is around 2 ppm may provide a means of mapping creatine. However, the quantification of this effect may be compromised by the influence of overlapping CEST signals from fast-exchanging amines and hydroxyls. We aimed to investigate the exchange rate filtering effect of a variation of CEST, named chemical exchange rotation transfer (CERT), as a means of isolating creatine contributions at around 2 ppm from other overlapping signals. Simulations were performed to study the filtering effects of CERT for the selection of transfer effects from protons of specific exchange rates. Control samples containing the main metabolites in brain, bovine serum albumin (BSA) and egg white albumen (EWA) at their physiological concentrations and pH were used to study the ability of CERT to isolate molecules with amines at 2 ppm that exchange at intermediate rates, and corresponding methods were used for in vivo rat brain imaging. Simulations showed that exchange rate filtering can be combined with conventional filtering based on chemical shift. Studies on samples showed that signal contributions from creatine can be separated from those of other metabolites using this combined filter, but contributions from protein amines may still be significant. This exchange filtering can also be used for in vivo imaging. CERT provides more specific quantification of amines at 2 ppm that exchange at intermediate rates compared with conventional CEST imaging. Copyright © 2017 John Wiley & Sons, Ltd.

A method for probing the mutational landscape of amyloid structure.

PubMed

O'Donnell, Charles W; Waldispühl, Jérôme; Lis, Mieszko; Halfmann, Randal; Devadas, Srinivas; Lindquist, Susan; Berger, Bonnie

2011-07-01

Proteins of all kinds can self-assemble into highly ordered β-sheet aggregates known as amyloid fibrils, important both biologically and clinically. However, the specific molecular structure of a fibril can vary dramatically depending on sequence and environmental conditions, and mutations can drastically alter amyloid function and pathogenicity. Experimental structure determination has proven extremely difficult with only a handful of NMR-based models proposed, suggesting a need for computational methods. We present AmyloidMutants, a statistical mechanics approach for de novo prediction and analysis of wild-type and mutant amyloid structures. Based on the premise of protein mutational landscapes, AmyloidMutants energetically quantifies the effects of sequence mutation on fibril conformation and stability. Tested on non-mutant, full-length amyloid structures with known chemical shift data, AmyloidMutants offers roughly 2-fold improvement in prediction accuracy over existing tools. Moreover, AmyloidMutants is the only method to predict complete super-secondary structures, enabling accurate discrimination of topologically dissimilar amyloid conformations that correspond to the same sequence locations. Applied to mutant prediction, AmyloidMutants identifies a global conformational switch between Aβ and its highly-toxic 'Iowa' mutant in agreement with a recent experimental model based on partial chemical shift data. Predictions on mutant, yeast-toxic strains of HET-s suggest similar alternate folds. When applied to HET-s and a HET-s mutant with core asparagines replaced by glutamines (both highly amyloidogenic chemically similar residues abundant in many amyloids), AmyloidMutants surprisingly predicts a greatly reduced capacity of the glutamine mutant to form amyloid. We confirm this finding by conducting mutagenesis experiments. Our tool is publically available on the web at http://amyloid.csail.mit.edu/. lindquist_admin@wi.mit.edu; bab@csail.mit.edu.

Performance of a compact, hybrid optical evanescent-wave sensor for chemical and biological applications

NASA Astrophysics Data System (ADS)

Helmers, H.; Greco, Pierre; Benech, Pierre; Rustad, Rolf; Kherrat, Rochdi; Bouvier, Gérard

1996-02-01

We describe a hybrid evanescent-wave sensor component that we fabricated by using an integrated optical interferometer with a specially adapted photodetector array. The design of the interferometer is based on the use of tapered waveguides to obtain two intersecting collimated beams. Phase shifts can be measured with an angular precision of better than 10-3 rad, which corresponds to a superstrate index change inferior of 10-6 with our structure. The interest in the device as a chemical sensor is experimentally demonstrated. The same optical component could be used in a variety of other sensor applications, e.g., biological and immunological sensors.

¹H, ¹³C, ¹⁵N and ³¹P chemical shift assignments of a human Xist RNA A-repeat tetraloop hairpin essential for X-chromosome inactivation.

PubMed

Duszczyk, Malgorzata M; Sattler, Michael

2012-04-01

Initiation of X-chromosome inactivation in female mammals depends on the non-coding RNA Xist. We have solved the NMR structure of a 14-nucleotide hairpin with a novel AUCG tetraloop fold from a Xist A-repeat that is essential for silencing. The (1)H, (13)C, (15)N and (31)P chemical shift assignments are reported.

Dynamic metabolic imaging of hyperpolarized [2-(13) C]pyruvate using spiral chemical shift imaging with alternating spectral band excitation.

PubMed

Josan, Sonal; Hurd, Ralph; Park, Jae Mo; Yen, Yi-Fen; Watkins, Ron; Pfefferbaum, Adolf; Spielman, Daniel; Mayer, Dirk

2014-06-01

In contrast to [1-(13) C]pyruvate, hyperpolarized [2-(13) C]pyruvate permits the ability to follow the (13) C label beyond flux through pyruvate dehydrogenase complex and investigate the incorporation of acetyl-coenzyme A into different metabolic pathways. However, chemical shift imaging (CSI) with [2-(13) C]pyruvate is challenging owing to the large spectral dispersion of the resonances, which also leads to severe chemical shift displacement artifacts for slice-selective acquisitions. This study introduces a sequence for three-dimensional CSI of [2-(13) C]pyruvate using spectrally selective excitation of limited frequency bands containing a subset of metabolites. Dynamic CSI data were acquired alternately from multiple frequency bands in phantoms for sequence testing and in vivo in rat heart. Phantom experiments verified the radiofrequency pulse design and demonstrated that the signal behavior of each group of resonances was unaffected by excitation of the other frequency bands. Dynamic three-dimensional (13) C CSI data demonstrated the sequence capability to image pyruvate, lactate, acetylcarnitine, glutamate, and acetoacetate, enabling the analysis of organ-specific spectra and metabolite time courses. The presented method allows CSI of widely separated resonances without chemical shift displacement artifact, acquiring multiple frequency bands alternately to obtain dynamic time-course information. This approach enables robust imaging of downstream metabolic products of acetyl-coenzyme A with hyperpolarized [2-(13) C]pyruvate. Copyright © 2013 Wiley Periodicals, Inc.

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

NASA Astrophysics Data System (ADS)

Tycko, Robert

2015-04-01

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

Inclusion compound of vitamin B6 in β-CD. Physico-chemical and structural investigations

NASA Astrophysics Data System (ADS)

Borodi, Gheorghe; Kacso, Irina; Farcaş, Sorin I.; Bratu, Ioan

2009-08-01

Structural and physico-chemical characterization of supramolecular assembly of vitamin B6 with β-cyclodextrin (β-CD) prepared by different methods (kneading, co-precipitation and freeze-drying) has been performed by using several spectroscopic techniques (FTIR, 1H NMR, UV-Vis), powder X-ray diffraction and DSC in order to evidence the inclusion compound formation. An analysis of the chemical shifts observed in the 1H-NMR spectra and of the vibrational frequency shifts led to the tentative conclusion that the vitamin B6 probably enters the cyclodextrin torus when forming the β-CD-vitamin B6 inclusion complex.

NMR Chemical Exchange as a Probe for Ligand-Binding Kinetics in a Theophylline-Binding RNA Aptamer

PubMed Central

Latham, Michael P.; Zimmermann, Grant R.; Pardi, Arthur

2009-01-01

The apparent on- and off-rate constants for theophylline binding to its RNA aptamer in the absence of Mg2+ were determined here by 2D 1H-1H NMR ZZ-exchange spectroscopy. Analysis of the build-up rate of the exchange cross peaks for several base-paired imino protons in the RNA yielded an apparent kon of 600 M-1 s-1. This small apparent kon results from the free RNA existing as a dynamic equilibrium of inactive states rapidly interconverting with a low population of active species. The data here indicate that the RNA aptamer employs a conformational selection mechanism for binding theophylline in the absence of Mg2+. The kinetic data here also explain a very unusual property of this RNA-theophylline system, slow exchange on the NMR chemical shift timescale for a weak-binding complex. To our knowledge, it is unprecedented to have such a weak binding complex (Kd ≈ 3.0 mM at 15 °C) show slow exchange on the NMR chemical shift timescale, but the results clearly demonstrate that slow exchange and weak binding are readily rationalized by a small kon. Comparisons with other ligand-receptor interactions are presented. PMID:19317486

Molecular docking and NMR binding studies to identify novel inhibitors of human phosphomevalonate kinase

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

Boonsri, Pornthip; Department of Chemistry, NANOTEC Center of Nanotechnology, National Nanotechnology Center, Faculty of Science, Kasetsart University, Bangkok 10900; Neumann, Terrence S.

2013-01-04

Highlights: Black-Right-Pointing-Pointer Natural and synthetic inhibitors of human phosphomevalonate kinase identified. Black-Right-Pointing-Pointer Virtual screening yielded a hit rate of 15%, with inhibitor K{sub d}'s of 10-60 {mu}M. Black-Right-Pointing-Pointer NMR studies indicate significant protein conformational changes upon binding. -- Abstract: Phosphomevalonate kinase (PMK) phosphorylates mevalonate-5-phosphate (M5P) in the mevalonate pathway, which is the sole source of isoprenoids and steroids in humans. We have identified new PMK inhibitors with virtual screening, using autodock. Promising hits were verified and their affinity measured using NMR-based {sup 1}H-{sup 15}N heteronuclear single quantum coherence (HSQC) chemical shift perturbation and fluorescence titrations. Chemical shift changes were monitored,more » plotted, and fitted to obtain dissociation constants (K{sub d}). Tight binding compounds with K{sub d}'s ranging from 6-60 {mu}M were identified. These compounds tended to have significant polarity and negative charge, similar to the natural substrates (M5P and ATP). HSQC cross peak changes suggest that binding induces a global conformational change, such as domain closure. Compounds identified in this study serve as chemical genetic probes of human PMK, to explore pharmacology of the mevalonate pathway, as well as starting points for further drug development.« less

Resilience in ecotoxicology: Toward a multiple equilibrium concept

USGS Publications Warehouse

Bundschuh, Mirco; Schulz, Ralf; Allen, Craig R.; Angeler, David G.

2017-01-01

The term resilience describes stress–response patterns across scientific disciplines. In ecology, advances have been made to clearly define resilience based on underlying mechanistic assumptions. Engineering resilience (rebound) is used to describe the ability of organisms to recover from adverse conditions (disturbances), which is termed the rate of recovery. By contrast, the ecological resilience definition considers a systemic change, that is, when ecosystems reorganize into a new regime following disturbance. Under this new regime, structural and functional aspects change considerably relative to the previous regime, without recovery. In this context, resilience is an emergent property of complex systems. In the present study, we argue that both definitions and uses are appropriate in ecotoxicology, and although the differences are subtle, the implications and uses are profoundly different. We discuss resilience concepts in ecotoxicology, where the prevailing view of resilience is engineering resilience from chemical stress. Ecological resilience may also be useful for describing systemic ecological changes because of chemical stress. We present quantitative methods that allow ecotoxicologists and risk managers to assess whether an ecosystem faces an impending regime shift or whether it has already undergone such a shift. We contend that engineering and ecological resilience help to distinguish ecotoxicological responses to chemical stressors mechanistically and thus have implications for theory, policy, and application.

Rationalising pKa shifts in Bacillus circulans xylanase with computational studies.

PubMed

Xiao, Kela; Yu, Haibo

2016-11-09

Bacillus circulans xylanase (BcX), a family 11 glycoside hydrolase, catalyses the hydrolysis of xylose polymers with a net retention of stereochemistry. Glu172 in BcX is believed to act as a general acid by protonating the aglycone during glycosylation, and then as a general base to facilitate the deglycosylation step. The key to the dual role of this general acid/base lies in its protonation states, which depend on its intrinsic pK a value and the specific environment which it resides within. To fully understand the detailed molecular features in BcX to establish the dual role of Glu172, we present a combined study based on both atomistic simulations and empirical models to calculate pK a shifts for the general acid/base Glu172 in BcX at different functional states. Its pK a values and those of nearby residues, obtained based on QM/MM free energy calculations, MCCE and PROPKA, show a good agreement with available experimental data. Additionally, our study provides additional insights into the effects of structural and electrostatic perturbations caused by mutations and chemical modifications, suggesting that the local solvation environment and mutagenesis of the residues adjacent to Glu172 establish its dual role during hydrolysis. The strengths and limitations of various methods for calculating pK a s and pK a shifts have also been discussed.

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

PubMed

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

2017-06-22

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

Chemical Speciation and Bond Lengths of Organic Solutes by Core-Level Spectroscopy: pH and Solvent Influence on p-Aminobenzoic Acid.

PubMed

Stevens, Joanna S; Gainar, Adrian; Suljoti, Edlira; Xiao, Jie; Golnak, Ronny; Aziz, Emad F; Schroeder, Sven L M

2015-05-04

Through X-ray absorption and emission spectroscopies, the chemical, electronic and structural properties of organic species in solution can be observed. Near-edge X-ray absorption fine structure (NEXAFS) and resonant inelastic X-ray scattering (RIXS) measurements at the nitrogen K-edge of para-aminobenzoic acid reveal both pH- and solvent-dependent variations in the ionisation potential (IP), 1s→π* resonances and HOMO-LUMO gap. These changes unequivocally identify the chemical species (neutral, cationic or anionic) present in solution. It is shown how this incisive chemical state sensitivity is further enhanced by the possibility of quantitative bond length determination, based on the analysis of chemical shifts in IPs and σ* shape resonances in the NEXAFS spectra. This provides experimental access to detecting even minor variations in the molecular structure of solutes in solution, thereby providing an avenue to examining computational predictions of solute properties and solute-solvent interactions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chemical Speciation and Bond Lengths of Organic Solutes by Core-Level Spectroscopy: pH and Solvent Influence on p -Aminobenzoic Acid

DOE PAGES

Stevens, Joanna S.; Gainar, Adrian; Suljoti, Edlira; ...

2015-03-18

Through X-ray absorption and emission spectroscopies, the chemical, electronic and structural properties of organic species in solution can be observed. Near-edge X-ray absorption fine structure (NEXAFS) and resonant inelastic X-ray scattering (RIXS) measurements at the nitrogen K-edge of para-aminobenzoic acid reveal both pH- and solvent-dependent variations in the ionisation potential (IP), 1s→π* resonances and HOMO–LUMO gap. These changes unequivocally identify the chemical species (neutral, cationic or anionic) present in solution. It is shown how this incisive chemical state sensitivity is further enhanced by the possibility of quantitative bond length determination, based on the analysis of chemical shifts in IPs andmore » σ* shape resonances in the NEXAFS spectra. Finally, this provides experimental access to detecting even minor variations in the molecular structure of solutes in solution, thereby providing an avenue to examining computational predictions of solute properties and solute–solvent interactions.« less

Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK.

PubMed

Würz, Julia M; Güntert, Peter

2017-01-01

The automated identification of signals in multidimensional NMR spectra is a challenging task, complicated by signal overlap, noise, and spectral artifacts, for which no universally accepted method is available. Here, we present a new peak picking algorithm, CYPICK, that follows, as far as possible, the manual approach taken by a spectroscopist who analyzes peak patterns in contour plots of the spectrum, but is fully automated. Human visual inspection is replaced by the evaluation of geometric criteria applied to contour lines, such as local extremality, approximate circularity (after appropriate scaling of the spectrum axes), and convexity. The performance of CYPICK was evaluated for a variety of spectra from different proteins by systematic comparison with peak lists obtained by other, manual or automated, peak picking methods, as well as by analyzing the results of automated chemical shift assignment and structure calculation based on input peak lists from CYPICK. The results show that CYPICK yielded peak lists that compare in most cases favorably to those obtained by other automated peak pickers with respect to the criteria of finding a maximal number of real signals, a minimal number of artifact peaks, and maximal correctness of the chemical shift assignments and the three-dimensional structure obtained by fully automated assignment and structure calculation.

An NMR study of microvoids in polymers

NASA Technical Reports Server (NTRS)

Toy, James; Mattix, Larry

1995-01-01

An understanding of polymer defect structures, like microvoids in polymeric matrices, is crucial to their fabrication and application potential. In this project guest atoms are introduced into the microvoids in PMR-15 and NMR is used to determine microvoid sizes and locations. Xenon is a relatively inert probe that would normally be found naturally in polymer or in NMR probe materials. There are two NMR active xenon isotopes, Xe-129 and Xe-131. The Xe atom has a very high polarizability, which makes it sensitive to the intracrystalline environment of polymers. Interactions between the Xe atoms and the host matrix perturb the Xe electron cloud, deshielding the nuclei, and thereby expanding the range of the observed NMR chemical shifts. This chemical shift range which may be as large as 5000 ppm, permits subtle structural and chemical effects to be studied with high sensitivity. The Xe(129)-NMR line shape has been found to vary in response to changes in the pore symmetry of the framework hosts line Zeolites and Clathrasil compounds. Before exposure to Xe gas, the PMR-15 samples were dried in a vacuum oven at 150 C for 48 hours. The samples were then exposed to Xe gas at 30 psi for 72 hours and sealed in glass tubes with 1 atmosphere of xenon gas. Xenon gas at 1 atmosphere was used to tune up the spectrometer and to set up the appropriate NMR parameters. A single Xe-129 line at 83.003498 Mhz (with protons at 300 Mhz) was observed for the gas. With the xenon charged PMR-15 samples, a second broader line is observed 190 ppm downfield from the gas line (also observed). The width of the NMR line from the Xe-129 absorbed in the polymer is at least partially due to the distribution of microvoid sizes. From the chemical shift (relative to the gas line) and the line width, we estimate the average void sizes to be 2.74 +/- 0.20 angstroms. Since Xe-129 has such a large chemical shift range (approximately 5000 ppm), we expect the chemical shift anisotropy to contribute to the line width (delta upsilon = 2.5 kHz).

White light phase shifting interferometry and color fringe analysis for the detection of contaminants in water

NASA Astrophysics Data System (ADS)

Dubey, Vishesh; Singh, Veena; Ahmad, Azeem; Singh, Gyanendra; Mehta, Dalip Singh

2016-03-01

We report white light phase shifting interferometry in conjunction with color fringe analysis for the detection of contaminants in water such as Escherichia coli (E.coli), Campylobacter coli and Bacillus cereus. The experimental setup is based on a common path interferometer using Mirau interferometric objective lens. White light interferograms are recorded using a 3-chip color CCD camera based on prism technology. The 3-chip color camera have lesser color cross talk and better spatial resolution in comparison to single chip CCD camera. A piezo-electric transducer (PZT) phase shifter is fixed with the Mirau objective and they are attached with a conventional microscope. Five phase shifted white light interferograms are recorded by the 3-chip color CCD camera and each phase shifted interferogram is decomposed into the red, green and blue constituent colors, thus making three sets of five phase shifted intererograms for three different colors from a single set of white light interferogram. This makes the system less time consuming and have lesser effect due to surrounding environment. Initially 3D phase maps of the bacteria are reconstructed for red, green and blue wavelengths from these interferograms using MATLAB, from these phase maps we determines the refractive index (RI) of the bacteria. Experimental results of 3D shape measurement and RI at multiple wavelengths will be presented. These results might find applications for detection of contaminants in water without using any chemical processing and fluorescent dyes.

pH-sensitive pHluorins as a molecular sensor for in situ monitoring of enzyme-catalyzed prodrug activation.

PubMed

Liu, Hui; Cao, Xiaodan; Wang, Ping; Ma, Xingyuan

2017-07-01

This work examines the feasibility of using a pH-sensitive fluorescent protein as a molecular reporter for enzyme-catalyzed prodrug activation reaction. Specifically, a ratiometric pHluorins was examined for detection of the activity of horseradish peroxidase (HRP) for the activation of indole-3-acetic acid. The pHluorins and HRP were conjugated chemically, forming a biocatalyst with a self-reporting function. Results showed that the characteristic fluorescence intensity ratio of the conjugate shifted from 1.47 to 1.40 corresponding to the progress of the prodrug activation reaction. The effectiveness of applying the conjugate for inhibition of the growth of Bcap-37 cells was also demonstrated simultaneously with reaction monitoring. The results reveal a very promising approach to realizing in situ monitoring of enzyme activities based on pH shifting for enzyme-based prodrug therapy applications. © 2016 International Union of Biochemistry and Molecular Biology, Inc.

Computing the Absorption and Emission Spectra of 5-Methylcytidine in Different Solvents: A Test-Case for Different Solvation Models.

PubMed

Martínez-Fernández, L; Pepino, A J; Segarra-Martí, J; Banyasz, A; Garavelli, M; Improta, R

2016-09-13

The optical spectra of 5-methylcytidine in three different solvents (tetrahydrofuran, acetonitrile, and water) is measured, showing that both the absorption and the emission maximum in water are significantly blue-shifted (0.08 eV). The absorption spectra are simulated based on CAM-B3LYP/TD-DFT calculations but including solvent effects with three different approaches: (i) a hybrid implicit/explicit full quantum mechanical approach, (ii) a mixed QM/MM static approach, and (iii) a QM/MM method exploiting the structures issuing from molecular dynamics classical simulations. Ab-initio Molecular dynamics simulations based on CAM-B3LYP functionals have also been performed. The adopted approaches all reproduce the main features of the experimental spectra, giving insights on the chemical-physical effects responsible for the solvent shifts in the spectra of 5-methylcytidine and providing the basis for discussing advantages and limitations of the adopted solvation models.

Dynamical patterns and regime shifts in the nonlinear model of soil microorganisms growth

NASA Astrophysics Data System (ADS)

Zaitseva, Maria; Vladimirov, Artem; Winter, Anna-Marie; Vasilyeva, Nadezda

2017-04-01

Dynamical model of soil microorganisms growth and turnover is formulated as a system of nonlinear partial differential equations of reaction-diffusion type. We consider spatial distributions of concentrations of several substrates and microorganisms. Biochemical reactions are modelled by chemical kinetic equations. Transport is modelled by simple linear diffusion for all chemical substances, while for microorganisms we use different transport functions, e.g. some of them can actively move along gradient of substrate concentration, while others cannot move. We solve our model in two dimensions, starting from uniform state with small initial perturbations for various parameters and find parameter range, where small initial perturbations grow and evolve. We search for bifurcation points and critical regime shifts in our model and analyze time-space profile and phase portraits of these solutions approaching critical regime shifts in the system, exploring possibility to detect such shifts in advance. This work is supported by NordForsk, project #81513.

The application of chemical leasing business models in Mexico.

PubMed

Schwager, Petra; Moser, Frank

2006-03-01

To better address the requirements of the changing multilateral order, the United Nations Industrial Development Organization (UNIDO) Cleaner Production Programme, in 2004, developed the new Sustainable Industrial Resource Management (SIRM) approach. This approach is in accordance with the principles decided at the United Nations Conference on Environment and Development (UNCED) in Rio de Janeiro, Brazil in 1992. Unlike the traditional approaches to environmental management, the SIRM concept captures the idea of achieving sustainable industrial development through the implementation of circular material and energy flows in the entire production chain and reduction of the amount of material and energy used with greater efficiency solutions. The SIRM approach seeks to develop new models to encourage a shift from selling products to supplying services, modifying, in this manner, the supplier/user relationship and resulting in a win-win situation for the economy and the environment. Chemical Leasing represents such a new service-oriented business model and is currently being promoted by UNIDO's Cleaner Production Programme. MAIN FEATURES. One of the potential approaches to address the problems related to ineffective use and over-consumption of chemicals is the development and implementation of Chemical Leasing business models. These provide concrete solutions to the effective management of chemicals and on the ways negative releases to the environment can be reduced. The Chemical Leasing approach is a strategy that addresses the obligations of the changing international chemicals policy by focusing on a more service-oriented strategy. Mexico is one of the countries that were selected for the implementation of UNIDO's demonstration project to promote Chemical Leasing models in the country. The target sector of this project is the chemical industry, which is expected to shift their traditional business concept towards a more service and value-added approach. This is being achieved through the development of company specific business models that implement the above-indicated Chemical Leasing concept with the support from the Mexican National Cleaner Production Centre (NCPC). The implementation of Chemical Leasing in Mexico has proven to be an efficient instrument in enhancing sustainable chemical management and significantly reducing emissions in Mexico. Several companies from the chemical industrial sector implement or agreed to implement chemical leasing business models. Based on the positive findings of the project, several Mexican companies started to negotiate contents of possible Chemical Leasing contracts with suitable business partners. The project further aimed at disseminating information on Chemical Leasing. It successfully attracted globally operating companies in the chemicals sector to explore possibilities to implement Chemical Leasing business models in Mexico. At the international level, the results of the UNIDO project were presented on 20th September 2005 during a side event of the Strategic Approach to International Chemicals Management (SAICM) Preparation Conference in Vienna. To facilitate the promotion and application of Chemical Leasing project at international level, UNIDO is currently developing a number of tools to standardize Chemical Leasing projects. These include, among others, Chemical leasing contract models; Chemical Leasing data base to find partners for chemical leasing; and guidelines to implement Chemical Leasing projects and work programmes.

Predicting the Future: Opportunities and Challenges for the Chemical Industry to Apply 21st-Century Toxicity Testing

PubMed Central

Settivari, Raja S; Ball, Nicholas; Murphy, Lynea; Rasoulpour, Reza; Boverhof, Darrell R; Carney, Edward W

2015-01-01

Interest in applying 21st-century toxicity testing tools for safety assessment of industrial chemicals is growing. Whereas conventional toxicology uses mainly animal-based, descriptive methods, a paradigm shift is emerging in which computational approaches, systems biology, high-throughput in vitro toxicity assays, and high-throughput exposure assessments are beginning to be applied to mechanism-based risk assessments in a time- and resource-efficient fashion. Here we describe recent advances in predictive safety assessment, with a focus on their strategic application to meet the changing demands of the chemical industry and its stakeholders. The opportunities to apply these new approaches is extensive and include screening of new chemicals, informing the design of safer and more sustainable chemical alternatives, filling information gaps on data-poor chemicals already in commerce, strengthening read-across methodology for categories of chemicals sharing similar modes of action, and optimizing the design of reduced-risk product formulations. Finally, we discuss how these predictive approaches dovetail with in vivo integrated testing strategies within repeated-dose regulatory toxicity studies, which are in line with 3Rs principles to refine, reduce, and replace animal testing. Strategic application of these tools is the foundation for informed and efficient safety assessment testing strategies that can be applied at all stages of the product-development process. PMID:25836969

Phosphorus Imaging as a Tool for Studying the pH Metabolism in Living Insects

NASA Astrophysics Data System (ADS)

Skibbe, U.; Christeller, J. T.; Eccles, C. D.; Laing, W. A.; Callaghan, P. T.

1995-09-01

Comparative 31P NMR and 1H NMR imaging experiments at submillimeter pixel resolution were carried out, using a specially constructed solenoidal RF coil. Chemical-shift imaging is used to provide pH maps from the midgut of a Lepidopteran larvae and to demonstrate physiological dependence in the resulting images, The titration curve of pH versus chemical shift for inorganic phosphate is extended beyond the "normal" biological range to the strong alkaline limit.

Progress in Spin Dynamics Solid-State Nuclear Magnetic Resonance with the Application of Floquet-Magnus Expansion to Chemical Shift Anisotropy

PubMed Central

Mananga, Eugene Stephane

2013-01-01

The purpose of this article is to present an historical overview of theoretical approaches used for describing spin dynamics under static or rotating experiments in solid state nuclear magnetic resonance. The article gives a brief historical overview for major theories in nuclear magnetic resonance and the promising theories. We present the first application of Floquet-Magnus expansion to chemical shift anisotropy when irradiated by BABA pulse sequence. PMID:23711337

Job Relocation is High in Chemical Industry.

ERIC Educational Resources Information Center

Chemical and Engineering News, 1979

1979-01-01

The chances of an employee being relocated are higher in the chemical and plastics industries than in U.S. business as a whole. But the benefits provided by chemical and plastics companies to employees shifted to other locations are generally better than average. (Author/BB)

Velocity encoding with the slice select refocusing gradient for faster imaging and reduced chemical shift-induced phase errors.

PubMed

Middione, Matthew J; Thompson, Richard B; Ennis, Daniel B

2014-06-01

To investigate a novel phase-contrast MRI velocity-encoding technique for faster imaging and reduced chemical shift-induced phase errors. Velocity encoding with the slice select refocusing gradient achieves the target gradient moment by time shifting the refocusing gradient, which enables the use of the minimum in-phase echo time (TE) for faster imaging and reduced chemical shift-induced phase errors. Net forward flow was compared in 10 healthy subjects (N = 10) within the ascending aorta (aAo), main pulmonary artery (PA), and right/left pulmonary arteries (RPA/LPA) using conventional flow compensated and flow encoded (401 Hz/px and TE = 3.08 ms) and slice select refocused gradient velocity encoding (814 Hz/px and TE = 2.46 ms) at 3 T. Improved net forward flow agreement was measured across all vessels for slice select refocused gradient compared to flow compensated and flow encoded: aAo vs. PA (1.7% ± 1.9% vs. 5.8% ± 2.8%, P = 0.002), aAo vs. RPA + LPA (2.1% ± 1.7% vs. 6.0% ± 4.3%, P = 0.03), and PA vs. RPA + LPA (2.9% ± 2.1% vs. 6.1% ± 6.3%, P = 0.04), while increasing temporal resolution (35%) and signal-to-noise ratio (33%). Slice select refocused gradient phase-contrast MRI with a high receiver bandwidth and minimum in-phase TE provides more accurate and less variable flow measurements through the reduction of chemical shift-induced phase errors and a reduced TE/repetition time, which can be used to increase the temporal/spatial resolution and/or reduce breath hold durations. Copyright © 2013 Wiley Periodicals, Inc.

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

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

PubMed

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

2013-10-01

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. 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. 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) and fat (0.763 ± 0.006, 0.980 ± 0.004, and 0.941 ± 0.002 for DSC, sensitivity, and specificity, respectively). Temperature uncertainties, based on PRF uncertainties from a 5 × 5-voxel ROI, were 0.342 and 0.351°C for pure and mixed fat/water regions, respectively. Algorithm speed was tested using 25 × 25-voxel and whole image ROIs containing both fat and water, resulting in average processing times per acquisition of 2.00 ± 0.07 s and 146 ± 1 s, respectively, using uncompiled MATLAB scripts running on a shared CPU server with eight Intel Xeon(TM) E5640 quad-core processors (2.66 GHz, 12 MB cache) and 12 GB RAM. Results from both the mathematical and physical phantom suggest the k-means-based classification algorithm could be useful for rapid, dynamic imaging in an ROI for thermal interventions. Successful separation of fat/water information would aid in reducing errors from the nontemperature sensitive fat PRF, as well as potentially facilitate using fat as an internal reference for PRF shift thermometry when appropriate. Additionally, the T1-W or R2* signals may be used for monitoring temperature in surrounding adipose tissue.

Principal component analysis of chemical shift perturbation data of a multiple-ligand-binding system for elucidation of respective binding mechanism.

PubMed

Konuma, Tsuyoshi; Lee, Young-Ho; Goto, Yuji; Sakurai, Kazumasa

2013-01-01

Chemical shift perturbations (CSPs) in NMR spectra provide useful information about the interaction of a protein with its ligands. However, in a multiple-ligand-binding system, determining quantitative parameters such as a dissociation constant (K(d) ) is difficult. Here, we used a method we named CS-PCA, a principal component analysis (PCA) of chemical shift (CS) data, to analyze the interaction between bovine β-lactoglobulin (βLG) and 1-anilinonaphthalene-8-sulfonate (ANS), which is a multiple-ligand-binding system. The CSP on the binding of ANS involved contributions from two distinct binding sites. PCA of the titration data successfully separated the CSP pattern into contributions from each site. Docking simulations based on the separated CSP patterns provided the structures of βLG-ANS complexes for each binding site. In addition, we determined the K(d) values as 3.42 × 10⁻⁴ M² and 2.51 × 10⁻³ M for Sites 1 and 2, respectively. In contrast, it was difficult to obtain reliable K(d) values for respective sites from the isothermal titration calorimetry experiments. Two ANS molecules were found to bind at Site 1 simultaneously, suggesting that the binding occurs cooperatively with a partial unfolding of the βLG structure. On the other hand, the binding of ANS to Site 2 was a simple attachment without a significant conformational change. From the present results, CS-PCA was confirmed to provide not only the positions and the K(d) values of binding sites but also information about the binding mechanism. Thus, it is anticipated to be a general method to investigate protein-ligand interactions. Copyright © 2012 Wiley Periodicals, Inc.

On the crystal structure of the vaterite polymorph of CaCO3: a calcium-43 solid-state NMR and computational assessment.

PubMed

Burgess, Kevin M N; Bryce, David L

2015-02-01

The vaterite polymorph of CaCO3 has puzzled crystallographers for decades in part due to difficulties in obtaining single crystals. The multiple proposed structures for the vaterite polymorph of CaCO3 are assessed using a combined (43)Ca solid-state nuclear magnetic resonance (SSNMR) spectroscopic and computational approach. A combination of improved experimental and computational methods, along with a calibrated chemical shift scale and (43)Ca nuclear quadrupole moment, allow for improved insights relative to our earlier work (Bryce et al., J. Am. Chem. Soc. 2008, 130, 9282). Here, we synthesize a (43)Ca isotopically-enriched sample of vaterite and perform high-resolution quadrupolar SSNMR experiments including magic-angle spinning (MAS), double-rotation (DOR), and multiple-quantum (MQ) MAS experiments at magnetic field strengths of 9.4 and 21.1T. We identify one crystallographically unique Ca(2+) site in vaterite with a slight distribution in both chemical shifts and quadrupolar parameters. Both the experimental (43)Ca electric field gradient tensor and the isotropic chemical shift for vaterite are compared to those calculated with the gauge-including projector-augmented-wave (GIPAW) DFT method in an attempt to identify the model that best represents the crystal structure of vaterite. Simulations of (43)Ca DOR and MAS NMR spectra based on the NMR parameters computed for a total of 18 structural models for vaterite allow us to distinguish between these models. Among these 18, the P3221 and C2 structures provide simulated spectra and diffractograms in best agreement with all experimental data. Copyright © 2014 Elsevier Inc. All rights reserved.

High-Pressure Gaseous Burner (HPGB) Facility Completed for Quantitative Laser Diagnostics Calibration

NASA Technical Reports Server (NTRS)

Nguyen, Quang-Viet

2002-01-01

A gas-fueled high-pressure combustion facility with optical access, which was developed over the last 2 years, has just been completed. The High Pressure Gaseous Burner (HPGB) rig at the NASA Glenn Research Center can operate at sustained pressures up to 60 atm with a variety of gaseous fuels and liquid jet fuel. The facility is unique as it is the only continuous-flow, hydrogen-capable, 60-atm rig in the world with optical access. It will provide researchers with new insights into flame conditions that simulate the environment inside the ultra-high-pressure-ratio combustion chambers of tomorrow's advanced aircraft engines. The facility provides optical access to the flame zone, enabling the calibration of nonintrusive optical diagnostics to measure chemical species and temperature. The data from the HPGB rig enables the validation of numerical codes that simulate gas turbine combustors, such as the National Combustor Code (NCC). The validation of such numerical codes is often best achieved with nonintrusive optical diagnostic techniques that meet these goals: information-rich (multispecies) and quantitative while providing good spatial and time resolution. Achieving these goals is a challenge for most nonintrusive optical diagnostic techniques. Raman scattering is a technique that meets these challenges. Raman scattering occurs when intense laser light interacts with molecules to radiate light at a shifted wavelength (known as the Raman shift). This shift in wavelength is unique to each chemical species and provides a "fingerprint" of the different species present. The facility will first be used to gather a comprehensive data base of laser Raman spectra at high pressures. These calibration data will then be used to quantify future laser Raman measurements of chemical species concentration and temperature in this facility and other facilities that use Raman scattering.

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

NASA Astrophysics Data System (ADS)

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

2016-09-01

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

The structural study of acetohydroxamic and oxalodihydroxamic acids in DMSO solution based on the DFT calculations of NMR spectra

NASA Astrophysics Data System (ADS)

Kaczor, Agnieszka; Proniewicz, Leonard M.

2004-10-01

The 1H and 13C NMR spectra of acetohydroxamic (aha) and oxalodihydroxamic (oxha) acids were measured in DMSO- d6 solution. The atoms chemical shifts of chosen stable entgegen and zusammen conformers of monomeric acids were computed along with some clusters of the compounds with the solvent molecules [B3LYP/6-311++G(d,p), GIAO]. The latter were proposed to explain the differences between the theoretical and experimental resonances of the protons of the N-H and O-H groups. The computed chemical shifts of aha-(DMSO) 2 and oxha-(DMSO) 2 models are in good agreement with experimental data proving that the compounds existing in solution form aggregates with DMSO. The acids are H-bonded via all the labile protons to the oxygen atoms of the solvent molecules. aha exists in the zusammen and entgegen (relative to C-N bond) forms with the relative intensities of 8:1 while the sole z, E, z-conformers (notation refers to C-N, C-C and C-N bonds, respectively) were found for oxha.

Spectroscopic and DFT studies of bis-3-hydroxypyridinium and bis-3-hydroxymethylpyridinium dibromides with tetramethylene linker

NASA Astrophysics Data System (ADS)

Komasa, Anna

2018-01-01

Experimental and theoretical IR, Raman, UV-Vis, 1H and 13C NMR spectra of 1,4-di(3-hydroxypyridinium)butane dibromide and 1,4-di(3-hydroxymethylpyridinium)butane dibromide were obtained and analyzed. Optimized geometrical structures of the studied compounds were calculated by B3LYP method using 6-311++G(d,p) basis set and employed to determine the theoretical wavenumbers and intensities of IR and Raman spectra. The frequency assignments were supported by the potential energy distribution (PED) analysis. The significant role of the intermolecular interactions and the hydrogen bond was revealed on the basis of IR spectra. The calculated GIAO/B3LYP/6-311++G(d,p) isotropic magnetic shielding constants were used to predict the 1H and 13C chemical shifts for the optimized structures. Accuracy of the prediction of 1H and 13C chemical shifts was significantly improved by a simulation of the solvent in calculations. On the basis of UV-Vis spectra the acid-base equilibrium in the water solution of 1,4-di(3-hydroxypyridinium)butane dibromide was found.

Detailed solvent, structural, quantum chemical study and antimicrobial activity of isatin Schiff base

NASA Astrophysics Data System (ADS)

Brkić, Dominik R.; Božić, Aleksandra R.; Marinković, Aleksandar D.; Milčić, Miloš K.; Prlainović, Nevena Ž.; Assaleh, Fathi H.; Cvijetić, Ilija N.; Nikolić, Jasmina B.; Drmanić, Saša Ž.

2018-05-01

The ratios of E/Z isomers of sixteen synthesized 1,3-dihydro-3-(substituted phenylimino)-2H-indol-2-one were studied using experimental and theoretical methodology. Linear solvation energy relationships (LSER) rationalized solvent influence of the solvent-solute interactions on the UV-Vis absorption maxima shifts (νmax) of both geometrical isomers using the Kamlet-Taft equation. Linear free energy relationships (LFER) in the form of single substituent parameter equation (SSP) was used to analyze substituent effect on pKa, NMR chemical shifts and νmax values. Electron charge density was obtained by the use of Quantum Theory of Atoms in Molecules, i.e. Bader's analysis. The substituent and solvent effect on intramolecular charge transfer (ICT) were interpreted with the aid of time-dependent density functional (TD-DFT) method. Additionally, the results of TD-DFT calculations quantified the efficiency of ICT from the calculated charge-transfer distance (DCT) and amount of transferred charge (QCT). The antimicrobial activity was evaluated using broth microdilution method. 3D QSAR modeling was used to demonstrate the influence of substituents effect as well as molecule geometry on antimicrobial activity.

Synthesis, molecular structure and spectroscopic investigations of novel fluorinated spiro heterocycles.

PubMed

Islam, Mohammad Shahidul; Al-Majid, Abdullah Mohammed; Barakat, Assem; Soliman, Saied M; Ghabbour, Hazem A; Quah, Ching Kheng; Fun, Hoong-Kun

2015-05-07

This paper describes an efficient and regioselective method for the synthesis of novel fluorinated spiro-heterocycles in excellent yield by cascade [5+1] double Michael addition reactions. The compounds 7,11-bis(4-fluorophenyl)-2,4-dimethyl- 2,4-diazaspiro[5.5] undecane-1,3,5,9-tetraone (3a) and 2,4-dimethyl-7,11-bis (4-(trifluoromethyl)phenyl)-2,4-diazaspiro[5.5]undecane-1,3,5,9-tetraone (3b) were characterized by single-crystal X-ray diffraction, FT-IR and NMR techniques. The optimized geometrical parameters, infrared vibrational frequencies and NMR chemical shifts of the studied compounds have also been calculated using the density functional theory (DFT) method, using Becke-3-Lee-Yang-Parr functional and the 6-311G(d,p) basis set. There is good agreement between the experimentally determined structural parameters, vibrational frequencies and NMR chemical shifts of the studied compounds and those predicted theoretically. The calculated natural atomic charges using NBO method showed higher polarity of 3a compared to 3b.The calculated electronic spectra are also discussed based on the TD-DFT calculations.

Study on structural and spectral properties of isobavachalcone and 4-hydroxyderricin by computational method

NASA Astrophysics Data System (ADS)

Rong, Yuzhi; Wu, Jinhong; Liu, Xing; Zhao, Bo; Wang, Zhengwu

Isobavachalcone and 4-hydroxyderricin, two major chalcone constituents isolated from the roots of Angelica keiskei KOIDZUMI, exhibit numerous biological activities. Quantum chemical methods have been employed to investigate their structural and spectral properties. The ground state structures were optimized using density functional B3LYP method with 6-311G (d, p) basis set in both gas and solvent phases. Based on the optimized geometries, the harmonic vibrational frequency, the 1H and 13C nuclear magnetic resonance (NMR) chemical shift using the GIAO method were calculated at the same level of theory, with the aim of verifying the experimental values. Results reveal that B3LYP has been a good method to study their vibrational spectroscopic and NMR spectral properties of the two chalcones. The electronic absorption spectra were calculated using the time-dependent density functional theory (TDDFT) method. The solvent polarity effects were considered and calculated using the polarizable continuum model (PCM). Results also show that substitutions of different electron donating groups can alter the absorption properties and shift the spectra to a higher wavelength region.

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.

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

NASA Technical Reports Server (NTRS)

Shiner, C. S.

1986-01-01

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

The molecular structure and vibrational, 1H and 13C NMR spectra of lidocaine hydrochloride monohydrate

NASA Astrophysics Data System (ADS)

Badawi, Hassan M.; Förner, Wolfgang; Ali, Shaikh A.

2016-01-01

The structure, vibrational and NMR spectra of the local anesthetic drug lidocaine hydrochloride monohydrate salt were investigated by B3LYP/6-311G∗∗ calculations. The lidocaine·HCl·H2O salt is predicted to have the gauche structure as the predominant form at ambient temperature with NCCN and CNCC torsional angles of 110° and -123° as compared to 10° and -64°, respectively in the base lidocaine. The repulsive interaction between the two N-H bonds destabilized the gauche structure of lidocaine·HCl·H2O salt. The analysis of the observed vibrational spectra is consistent with the presence of the lidocaine salt in only one gauche conformation at room temperature. The 1H and 13C NMR spectra of lidocaine·HCl·H2O were interpreted by experimental and DFT calculated chemical shifts of the lidocaine salt. The RMSD between experimental and theoretical 1H and 13C chemical shifts for lidocaine·HCl·H2O is 2.32 and 8.21 ppm, respectively.

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

PubMed

Jurd, Andrew P S; Titman, Jeremy J

2009-08-28

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

1H, 13C, 15N NMR analysis of sildenafil base and citrate (Viagra) in solution, solid state and pharmaceutical dosage forms.

PubMed

Wawer, Iwona; Pisklak, Maciej; Chilmonczyk, Zdzisław

2005-08-10

Sildenafil citrate (SC) (Viagra) and sildenafil base in pure form are easily and unequivocally characterized by multinuclear NMR spectroscopy. Analysis of chemical shifts indicates that: (i) N6-H forms intramolecular hydrogen bonds, (ii) N25 is protonated in the salt and (iii) intermolecular OH...N hydrogen bonds involving N2 and N4 are present in the solid sildenafil citrate. 13C CPMAS NMR method has been proposed for the identification and quantitation of Viagra in its pharmaceutical formulations.

Red-Shifting versus Blue-Shifting Hydrogen Bonds: Perspective from Ab Initio Valence Bond Theory.

PubMed

Chang, Xin; Zhang, Yang; Weng, Xinzhen; Su, Peifeng; Wu, Wei; Mo, Yirong

2016-05-05

Both proper, red-shifting and improper, blue-shifting hydrogen bonds have been well-recognized with enormous experimental and computational studies. The current consensus is that there is no difference in nature between these two kinds of hydrogen bonds, where the electrostatic interaction dominates. Since most if not all the computational studies are based on molecular orbital theory, it would be interesting to gain insight into the hydrogen bonds with modern valence bond (VB) theory. In this work, we performed ab initio VBSCF computations on a series of hydrogen-bonding systems, where the sole hydrogen bond donor CF3H interacts with ten hydrogen bond acceptors Y (═NH2CH3, NH3, NH2Cl, OH(-), H2O, CH3OH, (CH3)2O, F(-), HF, or CH3F). This series includes four red-shifting and six blue-shifting hydrogen bonds. Consistent with existing findings in literature, VB-based energy decomposition analyses show that electrostatic interaction plays the dominating role and polarization plays the secondary role in all these hydrogen-bonding systems, and the charge transfer interaction, which denotes the hyperconjugation effect, contributes only slightly to the total interaction energy. As VB theory describes any real chemical bond in terms of pure covalent and ionic structures, our fragment interaction analysis reveals that with the approaching of a hydrogen bond acceptor Y, the covalent state of the F3C-H bond tends to blue-shift, due to the strong repulsion between the hydrogen atom and Y. In contrast, the ionic state F3C(-) H(+) leads to the red-shifting of the C-H vibrational frequency, owing to the attraction between the proton and Y. Thus, the relative weights of the covalent and ionic structures essentially determine the direction of frequency change. Indeed, we find the correlation between the structural weights and vibrational frequency changes.

Mutual orientation of three magnetic tensors in a polycrystalline dipeptide by dipole-modulated 15N chemical shift spectroscopy

NASA Astrophysics Data System (ADS)

Hartzell, C. J.; Pratum, T. K.; Drobny, G.

1987-10-01

This study demonstrates the mutual orientation of three tensor interactions in a single NMR experiment. The orientation of the 15N chemical shift tensor relative to the molecular frame has thus been determined in polycrystalline L-[1-13C] alanyl-L-[15N] alanine. The 13C-15N and 15N-1H dipole interactions are determined using the 1H dipole-modulated, 13C dipole-coupled 15N spectrum obtained as a transform of the data in t2. From simulations of the experimental spectra, two sets of polar angles have been determined relating the 13C-15N and 15N-1H dipoles to the 15N chemical shift tensor. The values determined are βCN =106°, αCN =5° and βNH =-19°, αNH =12°. The experiment verifies, without reference to single crystal data, that σ33 lies in the peptide plane and σ22 is nearly perpendicular to the plane.

Identifying stereoisomers by ab-initio calculation of secondary isotope shifts on NMR chemical shieldings.

PubMed

Böhm, Karl-Heinz; Banert, Klaus; Auer, Alexander A

2014-04-23

We present ab-initio calculations of secondary isotope effects on NMR chemical shieldings. The change of the NMR chemical shift of a certain nucleus that is observed if another nucleus is replaced by a different isotope can be calculated by computing vibrational corrections on the NMR parameters using electronic structure methods. We demonstrate that the accuracy of the computational results is sufficient to even distinguish different conformers. For this purpose, benchmark calculations for fluoro(2-2H)ethane in gauche and antiperiplanar conformation are carried out at the HF, MP2 and CCSD(T) level of theory using basis sets ranging from double- to quadruple-zeta quality. The methodology is applied to the secondary isotope shifts for 2-fluoronorbornane in order to resolve an ambiguity in the literature on the assignment of endo- and exo-2-fluoronorbornanes with deuterium substituents in endo-3 and exo-3 positions, also yielding insight into mechanistic details of the corresponding synthesis.

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

NASA Astrophysics Data System (ADS)

Durbeej, Bo; Eriksson, Leif A.

2003-06-01

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

125Te NMR shielding and optoelectronic spectra in XTe3O8 (X = Ti, Zr, Sn and Hf) compounds: Ab initio calculations

NASA Astrophysics Data System (ADS)

Bashi, M.; Rahnamaye Aliabad, H. A.; Mowlavi, A. A.; Ahmad, Iftikhar

2017-11-01

We have calculated the NMR shielding, structural properties and optoelectronic spectra of XTe3O8 (X = Ti, Zr, Sn and Hf) compounds. The full potential linearized augmented plane wave (FP-LAPW) method and the modified Becke-Johnson (mBJ) are used by density functional theory schemes. The calculated shielding and measured shifts are arranged in a straight line and the tensors of magnetic shielding have a low symmetry and the shielding along the x direction is greater than the y and z directions. Obtained results show that the X ions have the most important influence on the 125Te chemical shift. Calculated chemical shielding components (σii) decrease from Ti to Sn then increases from Sn to Hf so that these behaviors are vice versa for 125Te isotropic chemical shift (δiso). Density of states spectra show that the X-p and d states play key role in the optical and NMR calculations. Optical results illustrate that there is a direct relation between the chemical shielding components for Te atom and the static dielectric function, refractive index and Plasmon energies.

Updates in MRI characterization of the thymus in myasthenic patients.

PubMed

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

2012-06-12

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

Characterization of human brown adipose tissue by chemical-shift water-fat MRI.

PubMed

Hu, Houchun H; Perkins, Thomas G; Chia, Jonathan M; Gilsanz, Vicente

2013-01-01

The purpose of this study was to characterize human brown adipose tissue (BAT) with chemical-shift water-fat MRI and to determine whether trends and differences in fat-signal fractions and T2(*) relaxation times between BAT and white adipose tissue (WAT) are consistently observed postmortem and in vivo in infants, adolescents, and adults. A postmortem body and eight patients were studied. A six-echo spoiled gradient-echo chemical-shift water-fat MRI sequence was performed at 3 T to jointly quantify fat-signal fraction and T2(*) in interscapular-supraclavicular BAT and subcutaneous WAT. To confirm BAT identity, biopsy and histology served as the reference in the postmortem study and PET/CT was used in five of the eight patients who required examination for medical care. Fat-signal fractions and T2(*) times were lower in BAT than in WAT in the postmortem example and in seven of eight patients. With the exception of one case, nominal comparisons between brown and white adipose tissues were statistically significant (p < 0.05). Between subjects, a large range of fat-signal fraction values was observed in BAT but not in WAT. We have shown that fat-signal fractions and T2(*) values jointly derived from chemical-shift water-fat MRI are lower in BAT than in WAT likely because of differences in cellular structures, triglyceride content, and vascularization. The two metrics can serve as complementary biomarkers in the detection of BAT.

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

PubMed Central

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

2015-01-01

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

Adducts of nitrogenous ligands with rhodium(II) tetracarboxylates and tetraformamidinate: NMR spectroscopy and density functional theory calculations.

PubMed

Cmoch, Piotr; Głaszczka, Rafał; Jaźwiński, Jarosław; Kamieński, Bohdan; Senkara, Elżbieta

2014-03-01

Complexation of tetrakis(μ2-N,N'-diphenylformamidinato-N,N')-di-rhodium(II) with ligands containing nitrile, isonitrile, amine, hydroxyl, sulfhydryl, isocyanate, and isothiocyanate functional groups has been studied in liquid and solid phases using (1)H, (13)C and (15)N NMR, (13)C and (15)N cross polarisation-magic angle spinning NMR, and absorption spectroscopy in the visible range. The complexation was monitored using various NMR physicochemical parameters, such as chemical shifts, longitudinal relaxation times T1 , and NOE enhancements. Rhodium(II) tetraformamidinate selectively bonded only unbranched amine (propan-1-amine), pentanenitrile, and (1-isocyanoethyl)benzene. No complexation occurred in the case of ligands having hydroxyl, sulfhydryl, isocyanate, and isothiocyanate functional groups, and more expanded amine molecules such as butan-2-amine and 1-azabicyclo[2.2.2]octane. Such features were opposite to those observed in rhodium(II) tetracarboxylates, forming adducts with all kind of ligands. Special attention was focused on the analysis of Δδ parameters, defined as a chemical shift difference between signal in adduct and corresponding signal in free ligand. In the case of (1)H NMR, Δδ values were either negative in adducts of rhodium(II) tetraformamidinate or positive in adducts of rhodium(II) tetracarboxylates. Experimental findings were supported by density functional theory molecular modelling and gauge independent atomic orbitals chemical shift calculations. The calculation of chemical shifts combined with scaling procedure allowed to reproduce qualitatively Δδ parameters. Copyright © 2013 John Wiley & Sons, Ltd.

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

PubMed Central

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

2012-01-01

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

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

PubMed

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

2017-03-01

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

Coronary artery atherosclerosis associated with shift work in chemical plant workers by using coronary CT angiography.

PubMed

Kang, WonYang; Park, Won-Ju; Jang, Keun-Ho; Kim, Soo-Hyeon; Gwon, Do-Hyeong; Lim, Hyeong-Min; Ahn, Ji-Sung; Moon, Jai-Dong

2016-08-01

The aim of this study was to investigate whether shift work is related to elevated risk of coronary artery disease (CAD) by determining the coronary artery calcium (CAC) score and the presence of coronary artery stenosis by using coronary artery CT angiography (CCTA). In this study, 110 male workers participated and underwent a CCTA examination for CAC scoring, which represents coronary artery plaque, and were evaluated for luminal stenosis. All of the participants were working in the same chemical plant, of whom 70 worked day shifts and 40 worked rotating shifts. In a multivariate logistic regression analysis, including age, smoking status, alcohol consumption, regular exercise and waist circumference, shift work was associated with a 2.89-fold increase in the odds of developing coronary plaque compared with day work (OR, 2.89; 95% CI 1.07 to 7.82). The association between shift work and coronary plaque was strong after adjustment for age, low-density lipoprotein cholesterol, hypertension and diabetes mellitus (OR, 2.92; 95% CI 1.02 to 8.33). In addition, the number of years of shift work employment was associated with coronary plaque. However, no association was found between shift work and coronary artery stenosis. Shift work could induce CAD onset via the atherosclerotic process, and shift work employment duration was associated with an increased risk of atherosclerosis in male workers. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Sensitivity of Fischer-Tropsch Synthesis and Water-Gas Shift Catalystes to Poisons form High-Temperature High-Pressure Entrained-Flow (EF) Oxygen-Blown Gasifier Gasification of Coal/Biomass Mixtures

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

Burton Davis; Gary Jacobs; Wenping Ma

2009-09-30

There has been a recent shift in interest in converting not only natural gas and coal derived syngas to Fischer-Tropsch synthesis products, but also converting biomass-derived syngas, as well as syngas derived from coal and biomass mixtures. As such, conventional catalysts based on iron and cobalt may not be suitable without proper development. This is because, while ash, sulfur compounds, traces of metals, halide compounds, and nitrogen-containing chemicals will likely be lower in concentration in syngas derived from mixtures of coal and biomass (i.e., using entrained-flow oxygen-blown gasifier gasification gasification) than solely from coal, other compounds may actually be increased.more » Of particular concern are compounds containing alkali chemicals like the chlorides of sodium and potassium. In the first year, University of Kentucky Center for Applied Energy Research (UK-CAER) researchers completed a number of tasks aimed at evaluating the sensitivity of cobalt and iron-based Fischer-Tropsch synthesis (FT) catalysts and a commercial iron-chromia high temperature water-gas shift catalyst (WGS) to alkali halides. This included the preparation of large batches of 0.5%Pt-25%Co/Al{sub 2}O{sub 3} and 100Fe: 5.1Si: 3.0K: 2.0Cu (high alpha) catalysts that were split up among the four different entities participating in the overall project; the testing of the catalysts under clean FT and WGS conditions; the testing of the Fe-Cr WGS catalyst under conditions of co-feeding NaCl and KCl; and the construction and start-up of the continuously stirred tank reactors (CSTRs) for poisoning investigations.« less

Simultaneous Chemical and Optical Patterning of Polyacrylonitrile Film by Vapor-Based Reaction.

PubMed

Shin, Jae-Won; Lee, Choonghyeon; Cha, Sang-Ho; Jang, Jyongsik; Lee, Kyung Jin

2015-06-01

The surface of polyacrylonitrile (PAN) film is treated with ethyleneamines (EDA) in a simple chemical vapor phase reaction. Successful introduction of amine functional groups on the cyano group of PAN backbone is verified by FT-IR and NMR measurements. Further UV-vis and photoluminescence analyses show a red shift of the emission peak after repeated EDA treatment, which might be attributed to the formation of imine conjugation from newly formed carbon-nitrogen bonds on the PAN backbone. Further confocal laser scanning microscopy reveals that selective patterning of EDA on PAN films is possible via local polydimethylsiloxane masking. The results indicate that both chemical and optical patterning on PAN film can be realized via a single reaction and show the potential of this novel methodology in selective patterning. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Benchmarking Hydrogen and Carbon NMR Chemical Shifts at HF, DFT, and MP2 Levels.

PubMed

Flaig, Denis; Maurer, Marina; Hanni, Matti; Braunger, Katharina; Kick, Leonhard; Thubauville, Matthias; Ochsenfeld, Christian

2014-02-11

An extensive study of error distributions for calculating hydrogen and carbon NMR chemical shifts at Hartree-Fock (HF), density functional theory (DFT), and Møller-Plesset second-order perturbation theory (MP2) levels is presented. Our investigation employs accurate CCSD(T)/cc-pVQZ calculations for providing reference data for 48 hydrogen and 40 carbon nuclei within an extended set of chemical compounds covering a broad range of the NMR scale with high relevance to chemical applications, especially in organic chemistry. Besides the approximations of HF, a variety of DFT functionals, and conventional MP2, we also present results with respect to a spin component-scaled MP2 (GIAO-SCS-MP2) approach. For each method, the accuracy is analyzed in detail for various basis sets, allowing identification of efficient combinations of method and basis set approximations.

Condensed tannins: The formation of a diarylpropanol-catechinic acid dimer from base-catalyzed reactions of (+)-catechin

Treesearch

Seiji Ohara; Richard W. Hemingway

1991-01-01

Reaction of (+ )-catechin at pH 12 and 40 DC results in the stereoselective (if not stereospecific) formation of an enolic form of 1-[6-(3',4'-dihydroxyphenyl)-7-hydroxybicyclo[3.3.1]nonane-2,4,9-trione-3-yl]-1-(3,4-dihyroxyphenyl)-3-(2,-4,6-trihydroxyphenyl)-propan-2-ol. The n.m.r. chemical shift assignments determined by a variety of two-dimensional...

7-epi-griffonilide, a new lactone from Bauhinia pentandra: complete 1H and 13C chemical shift assignments.

PubMed

Almeida, Macia C S DE; Souza, Luciana G S; Ferreira, Daniele A; Pinto, Francisco C L; Oliveira, Débora R DE; Santiago, Gilvandete M P; Monte, Francisco J Q; Braz-Filho, Raimundo; Lemos, Telma L G DE

2017-01-01

A new lactone, 7-epi-griffonilide (1), and six known compounds, 2, 3a - 3c, 4a and 4b, were isolated from the leaves of Bauhinia pentandra (Fabaceae). The structures elucidation of 1 and 2 were based on detailed 2D NMR techniques and spectral comparison with related compounds, leading to complete assignment of the 1H and 13C NMR spectra.

High SNR Acquisitions Improve the Repeatability of Liver Fat Quantification Using Confounder-corrected Chemical Shift-encoded MR Imaging

PubMed Central

Motosugi, Utaroh; Hernando, Diego; Wiens, Curtis; Bannas, Peter; Reeder, Scott. B

2017-01-01

Purpose: To determine whether high signal-to-noise ratio (SNR) acquisitions improve the repeatability of liver proton density fat fraction (PDFF) measurements using confounder-corrected chemical shift-encoded magnetic resonance (MR) imaging (CSE-MRI). Materials and Methods: Eleven fat-water phantoms were scanned with 8 different protocols with varying SNR. After repositioning the phantoms, the same scans were repeated to evaluate the test-retest repeatability. Next, an in vivo study was performed with 20 volunteers and 28 patients scheduled for liver magnetic resonance imaging (MRI). Two CSE-MRI protocols with standard- and high-SNR were repeated to assess test-retest repeatability. MR spectroscopy (MRS)-based PDFF was acquired as a standard of reference. The standard deviation (SD) of the difference (Δ) of PDFF measured in the two repeated scans was defined to ascertain repeatability. The correlation between PDFF of CSE-MRI and MRS was calculated to assess accuracy. The SD of Δ and correlation coefficients of the two protocols (standard- and high-SNR) were compared using F-test and t-test, respectively. Two reconstruction algorithms (complex-based and magnitude-based) were used for both the phantom and in vivo experiments. Results: The phantom study demonstrated that higher SNR improved the repeatability for both complex- and magnitude-based reconstruction. Similarly, the in vivo study demonstrated that the repeatability of the high-SNR protocol (SD of Δ = 0.53 for complex- and = 0.85 for magnitude-based fit) was significantly higher than using the standard-SNR protocol (0.77 for complex, P < 0.001; and 0.94 for magnitude-based fit, P = 0.003). No significant difference was observed in the accuracy between standard- and high-SNR protocols. Conclusion: Higher SNR improves the repeatability of fat quantification using confounder-corrected CSE-MRI. PMID:28190853

Enhancing Thai Students' Learning of Chemical Kinetics

ERIC Educational Resources Information Center

Chairam, Sanoe; Somsook, Ekasith; Coll, Richard K.

2009-01-01

Chemical kinetics is an extremely important concept for introductory chemistry courses. The literature suggests that instruction in chemical kinetics is often teacher-dominated at both the secondary school and tertiary levels, and this is the case in Thailand--the educational context for this inquiry. The work reported here seeks to shift students…

Hydrodynamic fluctuations, nonequilibrium equations of state, and the shift of the spinodal line in polymer solutions under flow

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

Criado-Sancho, M.; Casas-Vazquez, J.; Jou, D.

1997-08-01

In the literature, the shift of the spinodal line of polymer solutions under flow is attributed either to an actual shift of the spinodal due to a nonequilibrium modification of the equation of state for the chemical potential, or to an apparent shift due to an increase of hydrodynamic fluctuations owing to the flow. Here we see that both approaches are compatible and that both effects add up. {copyright} {ital 1997} {ital The American Physical Society}

Efficiency enhancement of ZnO nanostructure assisted Si solar cell based on fill factor enlargement and UV-blue spectral down-shifting

NASA Astrophysics Data System (ADS)

Gholizadeh, A.; Reyhani, A.; Parvin, P.; Mortazavi, S. Z.

2017-05-01

ZnO nanostructures (including nano-plates and nano-rods (NRs)) are grown in various temperatures and Ar/O2 flow rates using thermal chemical vapor deposition, which affect the structure, nano-plate/NR population, and the quality of ZnO nanostructures. X-ray diffraction (XRD) attests that the peak intensity of the crystallographic plane (1 0 0) is correlated to nano-plate abundance. Moreover, optical properties elucidate that the population of nano-plates in samples strongly affect the band gap, binding energy of the exciton, and UV-visible (UV-vis) absorption and spectral luminescence emissions. In fact, the exciton binding energy reduces from ~100 to 80 meV when the population of nano-plates increases in samples. Photovoltaic characteristics based on the drop-casting on Si solar cells reveals three dominant factors, namely, the equivalent series resistance, decreasing reflectance, and down-shifting, in order to scale up the absolute efficiency by 3%. As a consequence, the oxygen vacancies in ZnO nanostructures give rise to the down-shifting and increase of free-carriers, leading to a reduction in the equivalent series resistance and an enlargement of fill factor. To obtain a larger I sc, reduction of spectral reflectance is essential; however, the down-shifting process is shown to be dominant by lessening the surface electron-hole recombination rate over the UV-blue spectral range.

Evaluation of COSHH essentials: methylene chloride, isopropanol, and acetone exposures in a small printing plant.

PubMed

Lee, Eun Gyung; Harper, Martin; Bowen, Russell B; Slaven, James

2009-07-01

The current study evaluated the Control of Substances Hazardous to Health (COSHH) Essentials model for short-term task-based exposures and full-shift exposures using measured concentrations of three volatile organic chemicals at a small printing plant. A total of 188 exposure measurements of isopropanol and 187 measurements of acetone were collected and each measurement took approximately 60 min. Historically, collected time-weighted average concentrations (seven results) were evaluated for methylene chloride. The COSHH Essentials model recommended general ventilation control for both isopropanol and acetone. There was good agreement between the task-based exposure measurements and the COSHH Essentials predicted exposure range (PER) for cleaning and print preparation with isopropanol and for cleaning with acetone. For the other tasks and for full-shift exposures, agreement between the exposure measurements and the PER was either moderate or poor. However, for both isopropanol and acetone, our findings suggested that the COSHH Essentials model worked reasonably well because the probabilities of short-term exposure measurements exceeding short-term occupational exposure limits (OELs) or full-shift exposures exceeding the corresponding full-shift OELs were <0.05 under the recommended control strategy. For methylene chloride, the COSHH Essentials recommended containment control but a follow-up study was not able to be performed because it had already been replaced with a less hazardous substance (acetone). This was considered a more acceptable alternative to increasing the level of control.

Portable IR dye laser optofluidic microresonator as a temperature and chemical sensor.

PubMed

Lahoz, F; Martín, I R; Gil-Rostra, J; Oliva-Ramirez, M; Yubero, F; Gonzalez-Elipe, A R

2016-06-27

A compact and portable optofluidic microresonator has been fabricated and characterized. It is based on a Fabry-Perot microcavity consisting essentially of two tailored dichroic Bragg mirrors prepared by reactive magnetron sputtering deposition. The microresonator has been filled with an ethanol solution of Nile-Blue dye. Infrared laser emission has been measured with a pump threshold as low as 0.12 MW/cm² and an external energy conversion efficiency of 41%. The application of the device as a temperature and a chemical sensor is demonstrated. Small temperature variations as well as small amount of water concentrations in the liquid laser medium are detected as a shift of the resonant laser modes.

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

Levin, E. M.; Iowa State Univ., Ames, IA; Cui, J. -F.

125Te NMR spectra and spin-lattice relaxation times, T 1, have been measured for several GeTe-based materials with Te excess. In this paper, the spectra show inhomogeneous broadening by several thousand ppm and a systematic variation in T 1 relaxation time with resonance frequency. The quadratic dependence of the spin-lattice relaxation rate, 1/T 1, on the Knight shift in the Korringa relation is found to be valid over a wide range of Knight shifts. This result confirms that T 1 relaxation in GeTe-based materials is mostly dominated by hyperfine interaction between nuclei and free charge carriers. In GeTe with 2.5% excessmore » of Te, about 15% of the material exhibits a Knight shift of ≥4500 ppm and a T 1 of only 0.3 ms, indicating a high hole concentration that could correspond to close to 50% vacancies on the Ge sublattice in this component. Lastly, our findings provide a basis for determining the charge carrier concentration and its distribution in complex thermoelectric and phase-change tellurides, which should lead to a better understanding of electronic and thermal transport properties as well as chemical bonding in these materials.« less

Iron isotope fractionation during pyrite formation in a sulfidic Precambrian ocean analogue

NASA Astrophysics Data System (ADS)

Rolison, John M.; Stirling, Claudine H.; Middag, Rob; Gault-Ringold, Melanie; George, Ejin; Rijkenberg, Micha J. A.

2018-04-01

The chemical response of the Precambrian oceans to rising atmospheric O2 levels remains controversial. The iron isotope signature of sedimentary pyrite is widely used to trace the microbial and redox states of the ocean, yet the iron isotope fractionation accompanying pyrite formation in nature is difficult to constrain due to the complexity of the pyrite formation process, difficulties in translating the iron isotope systematics of experimental studies to natural settings, and insufficient iron isotope datasets for natural euxinic (i.e. anoxic and sulfidic) marine basins where pyrite formation occurs. Herein we demonstrate, that a large, permil-level shift in the isotope composition of dissolved iron occurs in the Black Sea euxinic water column during syngenetic pyrite formation. Specifically, iron removal to syngenetic pyrite gives rise to an iron isotope fractionation factor between Fe(II) and FeS2 of 2.75 permil (‰), the largest yet reported for reactions under natural conditions that do not involve iron redox chemistry. These iron isotope systematics offer the potential to generate permil-level shifts in the sedimentary pyrite iron isotope record due to partial drawdown of the oceanic iron inventory. The implication is that the iron stable isotope signatures of sedimentary pyrites may record fundamental regime shifts between pyrite formation under sulfur-limited conditions and pyrite formation under iron-limited conditions. To this end, the iron isotope signatures of sedimentary pyrite may best represent the extent of euxinia in the past global ocean, rather than its oxygenation state. On this basis, the reinterpreted sedimentary pyrite Fe isotope record suggests a fundamental shift towards more sulfidic oceanic conditions coincident with the 'Great Oxidation Event' around 2.3 billion years ago. Importantly, this does not require the chemical state of the ocean to shift from mainly de-oxygenated to predominantly oxygenated in parallel with the permanent rise in atmospheric oxygen, contrary to other interpretations based on iron isotope systematics.

Biochemical stabilization of glucagon at alkaline pH.

PubMed

Caputo, Nicholas; Jackson, Melanie A; Castle, Jessica R; El Youssef, Joseph; Bakhtiani, Parkash A; Bergstrom, Colin P; Carroll, Julie M; Breen, Matthew E; Leonard, Gerald L; David, Larry L; Roberts, Charles T; Ward, W Kenneth

2014-11-01

For patients with type 1 diabetes mellitus, a bihormonal artificial endocrine pancreas system utilizing glucagon and insulin has been found to stabilize glycemic control. However, commercially available formulations of glucagon cannot currently be used in such systems because of physical instability characterized by aggregation and chemical degradation. Storing glucagon at pH 10 blocks protein aggregation but results in chemical degradation. Reductions in pH minimize chemical degradation, but even small reductions increase protein aggregation. We hypothesized that common pharmaceutical excipients accompanied by a new excipient would inhibit glucagon aggregation at an alkaline pH. As measured by tryptophan intrinsic fluorescence shift and optical density at 630 nm, protein aggregation was indeed minimized when glucagon was formulated with curcumin and albumin. This formulation also reduced chemical degradation, measured by liquid chromatography with mass spectrometry. Biological activity was retained after aging for 7 days in an in vitro cell-based bioassay and also in Yorkshire swine. Based on these findings, a formulation of glucagon stabilized with curcumin, polysorbate-80, l-methionine, and albumin at alkaline pH in glycine buffer may be suitable for extended use in a portable pump in the setting of a bihormonal artificial endocrine pancreas.

Biochemical Stabilization of Glucagon at Alkaline pH

PubMed Central

Jackson, Melanie A.; Castle, Jessica R.; El Youssef, Joseph; Bakhtiani, Parkash A.; Bergstrom, Colin P.; Carroll, Julie M.; Breen, Matthew E.; Leonard, Gerald L.; David, Larry L.; Roberts, Charles T.; Ward, W. Kenneth

2014-01-01

Abstract Background: For patients with type 1 diabetes mellitus, a bihormonal artificial endocrine pancreas system utilizing glucagon and insulin has been found to stabilize glycemic control. However, commercially available formulations of glucagon cannot currently be used in such systems because of physical instability characterized by aggregation and chemical degradation. Storing glucagon at pH 10 blocks protein aggregation but results in chemical degradation. Reductions in pH minimize chemical degradation, but even small reductions increase protein aggregation. We hypothesized that common pharmaceutical excipients accompanied by a new excipient would inhibit glucagon aggregation at an alkaline pH. Methods and Results: As measured by tryptophan intrinsic fluorescence shift and optical density at 630 nm, protein aggregation was indeed minimized when glucagon was formulated with curcumin and albumin. This formulation also reduced chemical degradation, measured by liquid chromatography with mass spectrometry. Biological activity was retained after aging for 7 days in an in vitro cell-based bioassay and also in Yorkshire swine. Conclusions: Based on these findings, a formulation of glucagon stabilized with curcumin, polysorbate-80, l-methionine, and albumin at alkaline pH in glycine buffer may be suitable for extended use in a portable pump in the setting of a bihormonal artificial endocrine pancreas. PMID:24968220

Backbone and sidechain methyl Ile (δ1), Leu and Val chemical shift assignments of RDE-4 (1-243), an RNA interference initiation protein in C. elegans.

PubMed

Chiliveri, Sai Chaitanya; Kumar, Sonu; Marelli, Udaya Kiran; Deshmukh, Mandar V

2012-10-01

The RNAi pathway of several organisms requires presence of double stranded RNA binding proteins for functioning of Dicer in gene regulation. In C. elegans, a double stranded RNA binding protein, RDE-4 (385 aa, 44 kDa) recognizes long exogenous dsRNA and initiates the RNAi pathway. We have achieved complete backbone and stereospecific methyl sidechain Ile (δ1), Leu and Val chemical shifts of first 243 amino acids of RDE-4, namely RDE-4ΔC.

Three model space experiments on chemical reactions. [Gibbs adsorption, equilibrium shift and electrodeposition

NASA Technical Reports Server (NTRS)

Grodzka, P.; Facemire, B.

1977-01-01

Three investigations conducted aboard Skylab IV and Apollo-Soyuz involved phenomena that are of interest to the biochemistry community. The formaldehyde clock reaction and the equilibrium shift reaction experiments conducted aboard Apollo Soyuz demonstrate the effect of low-g foams or air/liquid dispersions on reaction rate and chemical equilibrium. The electrodeposition reaction experiment conducted aboard Skylab IV demonstrate the effect of a low-g environment on an electrochemical displacement reaction. The implications of the three space experiments for various applications are considered.

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

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

Zhang, S.B.; Cohen, M.L.; Louie, S.G.

1991-04-15

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

Cortico-pontine theta carrier frequency phase shift across sleep/wake states following monoaminergic lesion in rat.

PubMed

Kalauzi, Aleksandar; Spasic, Sladjana; Petrovic, Jelena; Ciric, Jelena; Saponjic, Jelena

2012-06-01

This study was aimed to explore the sleep/wake states related cortico-pontine theta carrier frequency phase shift following a systemically induced chemical axotomy of the monoaminergic afferents within a brain of the freely moving rats. Our experiments were performed in 14 adult, male Sprague Dawley rats, chronically implanted for sleep recording. We recorded sleep during baseline condition, following sham injection (saline i.p. 1 ml/kg), and every week for 5 weeks following injection of the systemic neurotoxins (DSP-4 or PCA; 1 ml/kg, i.p.) for chemical axotomy of the locus coeruleus (LC) and dorsal raphe (DR) axon terminals. After sleep/wake states identification, FFT analysis was performed on 5 s epochs. Theta carrier frequency phase shift (∆Φ) was calculated for each epoch by averaging theta Fourier component phase shifts, and the ∆Φ values were plotted for each rat in control condition and 28 days following the monoaminergic lesions, as a time for permanently established DR or LC chemical axotomy. Calculated group averages have shown that ∆Φ increased between pons and cortex significantly in all sleep/wake states (Wake, NREM and REM) following the monoaminergic lesions, with respect to controls. Monoaminergic lesions established the pontine leading role in the brain theta oscillations during all sleep/wake states.

Resilience in ecotoxicology: Toward a multiple equilibrium concept.

PubMed

Bundschuh, Mirco; Schulz, Ralf; Schäfer, Ralf B; Allen, Craig R; Angeler, David G

2017-10-01

The term resilience describes stress-response patterns across scientific disciplines. In ecology, advances have been made to clearly define resilience based on underlying mechanistic assumptions. Engineering resilience (rebound) is used to describe the ability of organisms to recover from adverse conditions (disturbances), which is termed the rate of recovery. By contrast, the ecological resilience definition considers a systemic change, that is, when ecosystems reorganize into a new regime following disturbance. Under this new regime, structural and functional aspects change considerably relative to the previous regime, without recovery. In this context, resilience is an emergent property of complex systems. In the present study, we argue that both definitions and uses are appropriate in ecotoxicology, and although the differences are subtle, the implications and uses are profoundly different. We discuss resilience concepts in ecotoxicology, where the prevailing view of resilience is engineering resilience from chemical stress. Ecological resilience may also be useful for describing systemic ecological changes because of chemical stress. We present quantitative methods that allow ecotoxicologists and risk managers to assess whether an ecosystem faces an impending regime shift or whether it has already undergone such a shift. We contend that engineering and ecological resilience help to distinguish ecotoxicological responses to chemical stressors mechanistically and thus have implications for theory, policy, and application. Environ Toxicol Chem 2017;36:2574-2580. © 2017 SETAC. © 2017 SETAC.

Preparation and structural characterization of corn starch-aroma compound inclusion complexes.

PubMed

Zhang, Shu; Zhou, Yibin; Jin, Shanshan; Meng, Xin; Yang, Liping; Wang, Haisong

2017-01-01

Six corn starch inclusion complexes were synthesized using small nonpolar or weak polar aroma compounds (heptanolide, carvone and menthone) and small polar aroma compounds (linalool, heptanol and menthol). The objectives of this study were to (a) investigate the ability of corn starch to form inclusion complexes with these aroma compounds and (b) characterize the structure of the corn starch inclusion complexes. The resulting inclusion ratios were 75.6, 36.9, 43.8, 91.9, 67.2 and 54.7% for heptanolide, carvone, menthone, linalool, heptanol and menthol respectively. The inclusion complexes had laminated structures with a certain amount of holes or blocky constructions. Compared with gelatinized corn starch, the transition temperatures, peak temperatures and enthalpies of the inclusion complexes were significantly different. The major peak of CO at 1771 cm -1 and significant peak shifts revealed the formation of inclusion complexes. X-ray diffractometry (XRD) analyses revealed that the crystallinity of corn starch-polar aroma compound inclusion complexes increased. Based on cross-polarization magic angle spinning 13 C nuclear magnetic resonance (CP-MAS 13 C NMR) results, novel peaks and chemical shifts were attributed to the presence of small aroma compounds, thereby confirming the formation of corn starch inclusion complexes. Small nonpolar and polar aroma compounds can be complexed to corn starch. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

A multi-standard approach for GIAO (13)C NMR calculations.

PubMed

Sarotti, Ariel M; Pellegrinet, Silvina C

2009-10-02

The influence of the reference standard employed in the calculation of (13)C NMR chemical shifts was investigated over a large variety of known organic compounds, using different quantum chemistry methods and basis sets. After detailed analysis of the collected data, we found that methanol and benzene are excellent reference standards for computing NMR shifts of sp(3)- and sp-sp(2)-hybridized carbon atoms, respectively. This multi-standard approach (MSTD) performs better than TMS in terms of accuracy and precision and also displays much lower dependence on the level of theory employed. The use of mPW1PW91/6-31G(d)//mPW1PW91/6-31G(d) level is recommended for accurate (13)C NMR chemical shift prediction at low computational cost.

Potentiation of Chemical Ototoxicity by Noise

PubMed Central

Steyger, Peter S.

2010-01-01

High-intensity and/or prolonged exposure to noise causes temporary or permanent threshold shifts in auditory perception. Occupational exposure to solvents or administration of clinically important drugs, such as aminoglycoside antibiotics and cisplatin, also can induce permanent hearing loss. The mechanisms by which these ototoxic insults cause auditory dysfunction are still being unraveled, yet they share common sequelae, particularly generation of reactive oxygen species, that ultimately lead to hearing loss and deafness. Individuals are frequently exposed to ototoxic chemical contaminants (e.g., fuel) and noise simultaneously in a variety of work and recreational environments. Does simultaneous exposure to chemical ototoxins and noise potentiate auditory dysfunction? Exposure to solvent vapor in noisy environments potentiates the permanent threshold shifts induced by noise alone. Moderate noise levels potentiate both aminoglycoside- and cisplatin-induced ototoxicity in both rate of onset and in severity of auditory dysfunction. Thus, simultaneous exposure to chemical ototoxins and moderate levels of noise can potentiate auditory dysfunction. Preventing the ototoxic synergy of noise and chemical ototoxins requires removing exposure to ototoxins and/or attenuating noise exposure levels when chemical ototoxins are present. PMID:20523755

Characterization of Cleaning and Disinfecting Tasks and Product Use Among Hospital Occupations

PubMed Central

Saito, Rena; Virji, M. Abbas; Henneberger, Paul K.; Humann, Michael J.; LeBouf, Ryan F.; Stanton, Marcia L.; Liang, Xiaoming; Stefaniak, Aleksandr B.

2016-01-01

Background Healthcare workers have an elevated prevalence of asthma and related symptoms associated with the use of cleaning/disinfecting products. The objective of this study was to identify and characterize cleaning/disinfecting tasks and products used among hospital occupations. Methods Workers from 14 occupations at five hospitals were monitored for 216 shifts, and work tasks and products used were recorded at five-minute intervals. The major chemical constituents of each product were identified from safety data sheets. Results Cleaning and disinfecting tasks were performed with a high frequency at least once per shift in many occupations. Medical equipment preparers, housekeepers, floor strippers/waxers, and endoscopy technicians spent on average 108–177 min/shift performing cleaning/disinfecting tasks. Many occupations used products containing amines and quaternary ammonium compounds for > 100 min/shift. Conclusions This analysis demonstrates that many occupations besides housekeeping incur exposures to cleaning/disinfecting products, albeit for different durations and using products containing different chemicals. PMID:25351791

Nanostructured Photocatalysts and Their Applications in the Photocatalytic Transformation of Lignocellulosic Biomass: An Overview

PubMed Central

Colmenares, Juan Carlos; Luque, Rafael; Campelo, Juan Manuel; Colmenares, Fernando; Karpiński, Zbigniew; Romero, Antonio Angel

2009-01-01

Heterogeneous photocatalysis offer many possibilities for finding appropiate environmentally friendly solutions for many of the the problems affecting our society (i.e., energy issues). Researchers are still looking for novel routes to prepare solid photocatalysts able to transform solar into chemical energy more efficiently. In many developing countries, biomass is a major energy source, but currently such countries lack of the technology to sustainably obtain chemicals and/or fuels from it. The Roadmap for Biomass Technologies, authored by 26 leading experts from academia, industry, and government agencies, has predicted a gradual shift back to a carbohydrate-based economy. Biomass and biofuels appear to hold the key to satisfy the basic needs of our societies for the sustainable production of liquid fuels and high value-added chemicals without compromising the scenario of future generations. In this review, we aim to discuss various design routes for nanostructured photocatalytic solid materials in view of their applications in the selective transformation of lignocellulosic biomass to high value-added chemicals.

Intersection of toxicogenomics and high throughput screening in the Tox21 program: an NIEHS perspective.

PubMed

Merrick, B Alex; Paules, Richard S; Tice, Raymond R

Humans are exposed to thousands of chemicals with inadequate toxicological data. Advances in computational toxicology, robotic high throughput screening (HTS), and genome-wide expression have been integrated into the Tox21 program to better predict the toxicological effects of chemicals. Tox21 is a collaboration among US government agencies initiated in 2008 that aims to shift chemical hazard assessment from traditional animal toxicology to target-specific, mechanism-based, biological observations using in vitro assays and lower organism models. HTS uses biocomputational methods for probing thousands of chemicals in in vitro assays for gene-pathway response patterns predictive of adverse human health outcomes. In 1999, NIEHS began exploring the application of toxicogenomics to toxicology and recent advances in NextGen sequencing should greatly enhance the biological content obtained from HTS platforms. We foresee an intersection of new technologies in toxicogenomics and HTS as an innovative development in Tox21. Tox21 goals, priorities, progress, and challenges will be reviewed.

Advantages of paramagnetic chemical exchange saturation transfer (CEST) complexes having slow to intermediate water exchange properties as responsive MRI agents.

PubMed

Soesbe, Todd C; Wu, Yunkou; Dean Sherry, A

2013-07-01

Paramagnetic chemical exchange saturation transfer (PARACEST) complexes are exogenous contrast agents that have great potential to further extend the functional and molecular imaging capabilities of magnetic resonance. As a result of the presence of a central paramagnetic lanthanide ion (Ln(3+) ≠ La(3+) , Gd(3+) , Lu(3+) ) within the chelate, the resonance frequencies of exchangeable protons bound to the PARACEST agent are shifted far away from the bulk water frequency. This large chemical shift, combined with an extreme sensitivity to the chemical exchange rate, make PARACEST agents ideally suited for the reporting of significant biological metrics, such as temperature, pH and the presence of metabolites. In addition, the ability to turn PARACEST agents 'off' and 'on' using a frequency-selective saturation pulse gives them a distinct advantage over Gd(3+) -based contrast agents. A current challenge for PARACEST research is the translation of the promising in vitro results into in vivo systems. This short review article first describes the basic theory behind PARACEST contrast agents, their benefits over other contrast agents and their applications to MRI. It then describes some of the recent PARACEST research results: specifically, pH measurements using water molecule exchange rate modulation, T2 exchange contrast caused by water molecule exchange, the use of ultrashort TEs (TE < 10 µs) to overcome T2 exchange line broadening and the potential application of T2 exchange as a new contrast mechanism for MRI. Copyright © 2012 John Wiley & Sons, Ltd.

30 CFR 47.54 - Availability of an MSDS.

Code of Federal Regulations, 2010 CFR

2010-07-01

... make MSDSs accessible to miners during each work shift for each hazardous chemical to which they may be exposed either— (a) At each work area where the hazardous chemical is produced or used, or (b) At an...

Interspecies chemical communication in bacterial development.

PubMed

Straight, Paul D; Kolter, Roberto

2009-01-01

Our view of bacteria, from the earliest observations through the heyday of antibiotic discovery, has shifted dramatically. We recognize communities of bacteria as integral and functionally important components of diverse habitats, ranging from soil collectives to the human microbiome. To function as productive communities, bacteria coordinate metabolic functions, often requiring shifts in growth and development. The hallmark of cellular development, which we characterize as physiological change in response to environmental stimuli, is a defining feature of many bacterial interspecies interactions. Bacterial communities rely on chemical exchanges to provide the cues for developmental change. Traditional methods in microbiology focus on isolation and characterization of bacteria in monoculture, separating the organisms from the surroundings in which interspecies chemical communication has relevance. Developing multispecies experimental systems that incorporate knowledge of bacterial physiology and metabolism with insights from biodiversity and metagenomics shows great promise for understanding interspecies chemical communication in the microbial world.

Identification of anti-HIV active dicaffeoylquinic- and tricaffeoylquinic acids in Helichrysum populifolium by NMR-based metabolomic guided fractionation.

PubMed

Heyman, Heino Martin; Senejoux, François; Seibert, Isabell; Klimkait, Thomas; Maharaj, Vinesh Jaichand; Meyer, Jacobus Johannes Marion

2015-06-01

South Africa being home to more than 35% of the world's Helichrysum species (c.a. 244) of which many are used in traditional medicine, is seen potentially as a significant resource in the search of new anti-HIV chemical entities. It was established that five of the 30 Helichrysum species selected for this study had significant anti-HIV activity ranging between 12 and 21 μg/mL (IC50) by using an in-house developed DeCIPhR method on a full virus model. Subsequent toxicity tests also revealed little or no toxicity for these active extracts. With the use of NMR-based metabolomics, the search for common chemical characteristics within the plant extract was conducted, which resulted in specific chemical shift areas identified that could be linked to the anti-HIV activity of the extracts. The NMR chemical shifts associated with the activity were identified to be 2.56-3.08 ppm, 5.24-6.28 ppm, 6.44-7.04 ppm and 7.24-8.04 ppm. This activity profile was then used to guide the fractionation process by narrowing down and focusing the fractionation and purification processes to speed up the putative identification of five compounds with anti-HIV activity in the most active species, Helichrysum populifolium. The anti-HIV compounds identified for the first time from H. populifolium were three dicaffeoylquinic acid derivatives, i.e. 3,4-dicaffeoylquinic acid, 3,5-dicaffeoylquinic acid and 4,5-dicaffeoylquinic acid as well as two tricaffeoylquinic acid derivatives i.e. 1,3,5-tricaffeoylquinic acid and either 5-malonyl-1,3,4-tricaffeoylquinic or 3-malonyl-1,4,5-tricaffeoylquinic acid, with the latter being identified for the first time in the genus. Copyright © 2015 Elsevier B.V. All rights reserved.

[Shiftwork and health--experience from a chemical company].

PubMed

Oberlinner, C; Lang, S; Nasterlack, M; Yong, M

2013-03-01

Shiftwork is an essential part of our society. At the same time scientific evaluations demonstrate possible negative effects of shiftwork on the health status of the employees. Against this background we performed different studies to evaluate these effects within the specific shift system in a large chemical site in Germany. METHODS AND STUDY GROUP: To evaluate the impact of the different working times on job-related stress perception and work-life-balance we performed a cross-sectional study with 1494 blue collar workers (825 shift- and 669 day workers). Employees working in the rotating shift system reported lower frequencies of perceived time pressure (p = 0.008), and lower stress levels (p = 0.01), compared to the day workers. No significant difference was found with regard to work-life-balance and other aspects of job-related stress perception within both groups. Against the general opinion and study-results in the past we did not find a negative effect of our shift-system on self-reported stress. These results are in accordance with results of other cohort-studies on the specific shift system within the company demonstrating no difference in the health status of our shift workers compared to day workers. © Georg Thieme Verlag KG Stuttgart · New York.

NMR crystallography of 2-acylamino-6-[1 H]-pyridones: Solid-state NMR, GIPAW computational, and single crystal X-ray diffraction studies

NASA Astrophysics Data System (ADS)

Ośmiałowski, Borys; Kolehmainen, Erkki; Ikonen, Satu; Ahonen, Kari; Löfman, Miika

2011-12-01

2-Acylamino-6-[1 H]-pyridones [acyl = RCO, where R = methyl ( 1), ethyl ( 2), iso-propyl ( 3), tert-butyl ( 4), and 1-adamantyl ( 5)] have been synthesized and characterized by NMR spectroscopy. From three congeners, 2, 3 and 5, also single crystal X-ray structures have been solved. For these derivatives GIPAW calculations acts as a "bridge" between solid-state NMR data and calculated chemical shifts based on X-ray determined geometry. In crystals all three compounds exist as pyridone tautomers possessing similar six-membered ring structure stabilized by intramolecular C dbnd O⋯HN hydrogen bond. Theoretical GIPAW calculated and experimental 13C and 15N CPMAS NMR shifts are in excellent agreement with each other.

Relating the Chemical Composition of Dissolved Organic Matter Draining Permafrost Soils to its Photochemical Degradation in Arctic Surface Waters.

NASA Astrophysics Data System (ADS)

Ward, C.; Cory, R. M.

2015-12-01

Thawing permafrost soils are expected to shift the chemical composition of DOM exported to and degraded in arctic surface waters. While DOM photo-degradation is an important component of the freshwater C cycle in the Arctic, the molecular controls on DOM photo-degradation remain poorly understood, making it difficult to predict how shifting chemical composition may alter DOM photo-degradation in arctic surface waters. To address this knowledge gap, we quantified the susceptibility of DOM draining the shallow organic mat and the deeper permafrost layer to complete photo-oxidation to CO₂ and partial photo-oxidation to compounds that remain in the DOM pool, and investigated changes in DOM chemical composition following sunlight exposure. DOM leached from the organic mat contained higher molecular weight, more oxidized and unsaturated aromatic species compared to permafrost DOM. Despite significant differences in initial chemical composition, permafrost and organic mat DOM had similar susceptibilities to complete photo-oxidation to CO₂. Concurrent losses of carboxyl moieties and shifts in chemical composition during photo-degradation indicated that carboxyl-rich tannin-like compounds in both DOM sources were likely photo-decarboxylated to CO₂. Permafrost DOM had a higher susceptibility to partial photo-oxidation compared to organic mat DOM, potentially due to a lower abundance of phenolic compounds that act as "antioxidants" and slow the oxidation of DOM. These results demonstrated how chemical composition controls the photo-degradation of DOM in arctic surface waters, and that DOM photo-degradation will likely remain an important component of the freshwater C budget in the Arctic with increased export of permafrost DOM to surface waters.

Fat Quantification in the Abdomen.

PubMed

Hong, Cheng William; Fazeli Dehkordy, Soudabeh; Hooker, Jonathan C; Hamilton, Gavin; Sirlin, Claude B

2017-12-01

Fatty liver disease is characterized histologically by hepatic steatosis, the abnormal accumulation of lipid in hepatocytes. It is classified into alcoholic fatty liver disease and nonalcoholic fatty liver disease, and is an increasingly important cause of chronic liver disease and cirrhosis. Assessing the severity of hepatic steatosis in these conditions is important for diagnostic and prognostic purposes, as hepatic steatosis is potentially reversible if diagnosed early. The criterion standard for assessing hepatic steatosis is liver biopsy, which is limited by sampling error, its invasive nature, and associated morbidity. As such, noninvasive imaging-based methods of assessing hepatic steatosis are needed. Ultrasound and computed tomography are able to suggest the presence of hepatic steatosis based on imaging features, but are unable to accurately quantify hepatic fat content. Since Dixon's seminal work in 1984, magnetic resonance imaging has been used to compute the signal fat fraction from chemical shift-encoded imaging, commonly implemented as out-of-phase and in-phase imaging. However, signal fat fraction is confounded by several factors that limit its accuracy and reproducibility. Recently, advanced chemical shift-encoded magnetic resonance imaging methods have been developed that address these confounders and are able to measure the proton density fat fraction, a standardized, accurate, and reproducible biomarker of fat content. The use of these methods in the liver, as well as in other abdominal organs such as the pancreas, adrenal glands, and adipose tissue will be discussed in this review.

First Steps in Eukaryogenesis: Physical Phenomena in the Origin and Evolution of Chromosome Structure

NASA Astrophysics Data System (ADS)

Chela-Flores, Julian

1998-04-01

Our present understanding of the origin and evolution of chromosomes differs considerably from current understanding of the origin and evolution of the cell itself. Chromosome origins have been less prominent in research, as the emphasis has not shifted so far appreciably from the phenomenon of primeval nucleic acid encapsulation to that of the origin of gene organization, expression, and regulation. In this work we discuss some reasons why preliminary steps in this direction are being taken. We have been led to examine properties that have contributed to raise the ancestral prokaryotic programmes to a level where we can appreciate in eukaryotes a clear departure from earlier themes in the evolution of the cell from the last common ancestor. We shift our point of view from evolution of cell morphology to the point of view of the genes. In particular, we focus attention on possible physical bases for the way transmission of information has evolved in eukaryotes, namely, the inactivation of whole chromosomes. The special case of the inactivation of the X chromosome in mammals is discussed, paying particular attention to the physical process of the spread of X inactivation in monotremes (platypus and echidna). When experimental data is unavailable some theoretical analysis is possible based on the idea that in certain cases collective phenomena in genetics, rather than chemical detail, are better correlates of complex chemical processes.

Longitudinal relaxation optimized amide 1H-CEST experiments for studying slow chemical exchange processes in fully protonated proteins.

PubMed

Yuwen, Tairan; Kay, Lewis E

2017-04-01

Chemical Exchange Saturation Transfer (CEST) experiments are increasingly used to study slow timescale exchange processes in biomolecules. Although 15 N- and 13 C-CEST have been the approaches of choice, the development of spin state selective 1 H-CEST pulse sequences that separate the effects of chemical and dipolar exchange [T. Yuwen, A. Sekhar and L. E. Kay, Angew Chem Int Ed Engl 2016 doi: 10.1002/anie.201610759 (Yuwen et al. 2017)] significantly increases the utility of 1 H-based experiments. Pulse schemes have been described previously for studies of highly deuterated proteins. We present here longitudinal-relaxation optimized amide 1 H-CEST experiments for probing chemical exchange in protonated proteins. Applications involving a pair of proteins are presented establishing that accurate 1 H chemical shifts of sparsely populated conformers can be obtained from simple analyses of 1 H-CEST profiles. A discussion of the inherent differences between 15 N-/ 13 C- and 1 H-CEST experiments is presented, leading to an optimal strategy for recording 1 H-CEST experiments.

Alternate binding modes for a ubiquitin-SH3 domain interaction studied by NMR spectroscopy.

PubMed

Korzhnev, Dmitry M; Bezsonova, Irina; Lee, Soyoung; Chalikian, Tigran V; Kay, Lewis E

2009-02-20

Surfaces of many binding domains are plastic, enabling them to interact with multiple targets. An understanding of how they bind and recognize their partners is therefore predicated on characterizing such dynamic interfaces. Yet, these interfaces are difficult to study by standard biophysical techniques that often 'freeze' out conformations or that produce data averaged over an ensemble of conformers. In this study, we used NMR spectroscopy to study the interaction between the C-terminal SH3 domain of CIN85 and ubiquitin that involves the 'classical' binding sites of these proteins. Notably, chemical shift titration data of one target with another and relaxation dispersion data that report on millisecond time scale exchange processes are both well fit to a simple binding model in which free protein is in equilibrium with a single bound conformation. However, dissociation constants and chemical shift differences between free and bound states measured from both classes of experiment are in disagreement. It is shown that the data can be reconciled by considering three-state binding models involving two distinct bound conformations. By combining titration and dispersion data, kinetic and thermodynamic parameters of the three-state binding reaction are obtained along with chemical shifts for each state. A picture emerges in which one bound conformer has increased entropy and enthalpy relative to the second and chemical shifts similar to that of the free state, suggesting a less packed interface. This study provides an example of the interplay between entropy and enthalpy to fine-tune molecular interactions involving the same binding surfaces.

"Ask Ernö": a self-learning tool for assignment and prediction of nuclear magnetic resonance spectra.

PubMed

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

2016-01-01

We present "Ask Ernö", a self-learning system for the automatic analysis of NMR spectra, consisting of integrated chemical shift assignment and prediction tools. The output of the automatic assignment component initializes and improves a database of assigned protons that is used by the chemical shift predictor. In turn, the predictions provided by the latter facilitate improvement of the assignment process. Iteration on these steps allows Ask Ernö to improve its ability to assign and predict spectra without any prior knowledge or assistance from human experts. This concept was tested by training such a system with a dataset of 2341 molecules and their (1)H-NMR spectra, and evaluating the accuracy of chemical shift predictions on a test set of 298 partially assigned molecules (2007 assigned protons). After 10 iterations, Ask Ernö was able to decrease its prediction error by 17 %, reaching an average error of 0.265 ppm. Over 60 % of the test chemical shifts were predicted within 0.2 ppm, while only 5 % still presented a prediction error of more than 1 ppm. Ask Ernö introduces an innovative approach to automatic NMR analysis that constantly learns and improves when provided with new data. Furthermore, it completely avoids the need for manually assigned spectra. This system has the potential to be turned into a fully autonomous tool able to compete with the best alternatives currently available.Graphical abstractSelf-learning loop. Any progress in the prediction (forward problem) will improve the assignment ability (reverse problem) and vice versa.

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

PubMed

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

2015-07-01

The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Gold nanoparticles generated through "green route" bind Hg2+ with a concomitant blue shift in plasmon absorption peak.

PubMed

Radhakumary, C; Sreenivasan, K

2011-07-21

We discuss here a quick, simple, economic and ecofriendly method through a completely green route for the selective detection of Hg(2+) in aqueous samples. Here we exploited the ability of chitosan to generate gold nanoparticles and subsequently to act as a stabilizer for the formed nanoparticles. When chitosan stabilized gold nanoparticles (CH-Au NPs) are interacted with Hg(2+) a blue shift for its localized surface plasmon resonance absorbance (LSPR) band is observed. The blue shift is reasoned to be due to the formation of a thin layer of mercury over gold. A concentration as low as 0.01 ppm to a maximum of 100 ppm Hg(2+) can be detected based on this blue shift of the CH-Au NPs. While all other reported methods demand complex reaction steps and costly chemicals, the method we reported here is a simple, rapid and selective approach for the detection of Hg(2+). Our results also show that the CH-Au NPs have excellent selectivity to Hg(2+) over common cations namely, Pb(2+), Cd(2+), Mn(2+), Fe(2+), Ag(1+), Ce(4+), Ni(2+), and Cu(2+).

Advances of zeolite based membrane for hydrogen production via water gas shift reaction

NASA Astrophysics Data System (ADS)

Makertihartha, I. G. B. N.; Zunita, M.; Rizki, Z.; Dharmawijaya, P. T.

2017-07-01

Hydrogen is considered as a promising energy vector which can be obtained from various renewable sources. However, an efficient hydrogen production technology is still challenging. One technology to produce hydrogen with very high capacity with low cost is through water gas shift (WGS) reaction. Water gas shift reaction is an equilibrium reaction that produces hydrogen from syngas mixture by the introduction of steam. Conventional WGS reaction employs two or more reactors in series with inter-cooling to maximize conversion for a given volume of catalyst. Membrane reactor as new technology can cope several drawbacks of conventional reactor by removing reaction product and the reaction will favour towards product formation. Zeolite has properties namely high temperature, chemical resistant, and low price makes it suitable for membrane reactor applications. Moreover, it has been employed for years as hydrogen selective layer. This review paper is focusing on the development of membrane reactor for efficient water gas shift reaction to produce high purity hydrogen and carbon dioxide. Development of membrane reactor is discussed further related to its modification towards efficient reaction and separation from WGS reaction mixture. Moreover, zeolite framework suitable for WGS membrane reactor will be discussed more deeply.

NMR and transport measurements of copper chalcogenide and clathrate compounds

NASA Astrophysics Data System (ADS)

Sirusi Arvij, Ali

Due to limited sources of fossil fuels worldwide and a large percentage wasted as heat energy, searching for efficient thermoelectric materials to convert heat to electricity has gained a great deal of attention. Most of the attempts are focused on materials with substantially lower lattice thermal conductivity and narrow band gaps. Among them, inorganic clathrates and copper-based chalcogenides possess intrinsic low thermal conductivity which makes them promising thermoelectrics. In this work, nuclear magnetic resonance (NMR), transport, and magnetic measurements were performed on clathrates and copper-based chalcogenides to investigate their vibrational and electronic charge carrier properties, as well as the unknown structures of Cu2Se and Cu 2Te at low temperatures, and the effect of rattling of guest atoms in the clathrates. The NMR results in Ba8Ga16Ge30 indicate a pseudogap in the Ga electronic density of states, superposed upon a surprisingly large Ba contribution to the conduction band. Meanwhile, the phonon contributions to the Ga relaxation rates are large and increase more rapidly with temperature than typical semiconductors due to enhanced anharmonicity of the propagative phonon modes over a wide range. Moreover, the observed NMR shifts in the Ba8Cu5Si xGe41-x clathrates change in a nonlinear way with increasing Si substitution: from x = 0 to about 20 the shifts are essentially constant, while approaching x = 41 they increase rapidly, demonstrating a significant change in hybridizations vs Si substitution. NMR studies of Cu2Se show an initial appearance of ionic hopping in a narrow temperature range above 100 K, coinciding with the recently observed low-temperature phase transition. At room temperature and above, this goes over to rapid Cu-ion hopping and a single motionally narrowed line both above and below the alpha-beta structural transition. Furthermore, the NMR results on Cu2Te and Cu 1.98Ag0.2Te demonstrate unusually large negative chemical shifts, as well as large Cu and Te s-state contributions in the valence band. The large diamagnetic chemical shifts coincide with behavior previously identified for materials with topologically nontrivial band inversion, and in addition, the large metallic shifts point to analogous features in the valence band density of states, suggesting that Cu2Te may have similar inverted features.

MRS of pilocytic astrocytoma: The peak at 2 ppm may not be NAA.

PubMed

Tamrazi, Benita; Nelson, Marvin D; Blüml, Stefan

2017-08-01

To determine whether the chemical shift of residual N-acetylaspartate (NAA) signal in pilocytic astrocytomas (PA) is consistent with the position of the NAA peak in controls. MR spectra from 27 pediatric World Health Organization (WHO) grade I pilocytic astrocytoma patients, fifteen patients with WHO grade II and high-grade (III-IV) astrocytomas, and 36 controls were analyzed. All spectra were acquired with a short echo time (35 ms), single voxel point-resolved spectroscopy sequence on clinical 3 tesla scanners. Fully automated LCModel software was used for processing, which included the fitting of peak positions for NAA and creatine (Cr). The chemical shift difference between the NAA and Cr peaks was significantly smaller (by 0.016 ± 0.005 parts per million, P < 1e-10) in PAs than in controls and was also smaller than what was observed in infiltrative astrocytomas. The chemical shift position of the residual NAA peak in PAs is not consistent with NAA. The signal likely originates from an N-acetyl group of one or more other chemicals such as N-acetylated sugars. Magn Reson Med 78:452-456, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

FTIR, FT-Raman, FT-NMR, UV-visible and quantum chemical investigations of 2-amino-4-methylbenzothiazole.

PubMed

Arjunan, V; Sakiladevi, S; Rani, T; Mythili, C V; Mohan, S

2012-03-01

The FT-IR (4000-400 cm(-1)) and FT-Raman (4000-100 cm(-1)) spectral measurements and complete assignments of the observed spectra of 2-amino-4-methylbenzothiazole (2A4MBT) have been proposed. Ab initio and DFT calculations have been performed and the structural parameters of the compound were determined from the optimised geometry with 6-31G(d,p), 6-311++G(d,p) and cc-pVDZ basis sets and giving energies, harmonic vibrational frequencies, depolarisation ratios, IR intensities and Raman activities. (1)H and (13)C NMR spectra were recorded and (1)H and (13)C nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO, LUMO and band gap energies were measured by time-dependent DFT (TD-DFT) approach. The geometric parameters, energies, harmonic vibrational frequencies, IR intensities, Raman activities chemical shifts and absorption wavelengths were compared with the available experimental data of the molecule. The influences of methyl and amino groups on the skeletal modes and on the proton chemical shifts have been investigated. Copyright © 2011 Elsevier B.V. All rights reserved.

Multidimensional High-Resolution Magic Angle Spinning and Solution-State NMR Characterization of 13C-labeled Plant Metabolites and Lignocellulose

PubMed Central

Mori, Tetsuya; Tsuboi, Yuuri; Ishida, Nobuhiro; Nishikubo, Nobuyuki; Demura, Taku; Kikuchi, Jun

2015-01-01

Lignocellulose, which includes mainly cellulose, hemicellulose, and lignin, is a potential resource for the production of chemicals and for other applications. For effective production of materials derived from biomass, it is important to characterize the metabolites and polymeric components of the biomass. Nuclear magnetic resonance (NMR) spectroscopy has been used to identify biomass components; however, the NMR spectra of metabolites and lignocellulose components are ambiguously assigned in many cases due to overlapping chemical shift peaks. Using our 13C-labeling technique in higher plants such as poplar samples, we demonstrated that overlapping peaks could be resolved by three-dimensional NMR experiments to more accurately assign chemical shifts compared with two-dimensional NMR measurements. Metabolites of the 13C-poplar were measured by high-resolution magic angle spinning NMR spectroscopy, which allows sample analysis without solvent extraction, while lignocellulose components of the 13C-poplar dissolved in dimethylsulfoxide/pyridine solvent were analyzed by solution-state NMR techniques. Using these methods, we were able to unambiguously assign chemical shifts of small and macromolecular components in 13C-poplar samples. Furthermore, using samples of less than 5 mg, we could differentiate between two kinds of genes that were overexpressed in poplar samples, which produced clearly modified plant cell wall components. PMID:26143886

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

PubMed

Levine, Daniel S; Head-Gordon, Martin

2017-11-28

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

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

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

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

PubMed

Kara, Yesim Saniye

2015-01-01

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

Solution Structures of Mycobacterium tuberculosis Thioredoxin C and Models of the Intact Thioredoxin System Suggest New Approaches to Inhibitor and Drug Design

PubMed Central

Olson, Andrew L.; Neumann, Terrence S.; Cai, Sheng; Sem, Daniel S.

2012-01-01

Here we report the NMR solution structures of Mycobacterium tuberculosis (M. tuberculosis) thioredoxin C in both oxidized and reduced states, with discussion of structural changes that occur in going between redox states. The NMR solution structure of the oxidized TrxC corresponds closely to that of the crystal structure, except in the C-terminal region. It appears that crystal packing effects have caused an artifactual shift in the α4 helix in the previously reported crystal structure, compared to the solution structure. Based on these TrxC structures, chemical shift mapping, a previously reported crystal structure of the M. tuberculosis thioredoxin reductase (not bound to a Trx) and structures for intermediates in the E. coli thioredoxin catalytic cycle, we have modeled the complete M. tuberculosis thioredoxin system for the various steps in the catalytic cycle. These structures and models reveal pockets at the TrxR/TrxC interface in various steps in the catalytic cycle, which can be targeted in the design of uncompetitive inhibitors as potential anti-mycobacterial agents, or as chemical genetic probes of function. PMID:23229911

Optical micro-bubble resonators as promising biosensors

NASA Astrophysics Data System (ADS)

Giannetti, A.; Barucci, A.; Berneschi, S.; Cosci, A.; Cosi, F.; Farnesi, D.; Nunzi Conti, G.; Pelli, S.; Soria, S.; Tombelli, S.; Trono, C.; Righini, G. C.; Baldini, F.

2015-05-01

Recently, optical micro-bubble resonators (OMBRs) have gained an increasing interest in many fields of photonics thanks to their particular properties. These hollow microstructures can be suitable for the realization of label - free optical biosensors by combining the whispering gallery mode (WGM) resonator properties with the intrinsic capability of integrated microfluidics. In fact, the WGMs are morphology-dependent modes: any change on the OMBR inner surface (due to chemical and/or biochemical binding) causes a shift of the resonance position and reduces the Q factor value of the cavity. By measuring this shift, it is possible to obtain information on the concentration of the analyte to be detected. A crucial step for the development of an OMBR-based biosensor is constituted by the functionalization of its inner surface. In this work we report on the development of a physical and chemical process able to guarantee a good homogeneity of the deposed bio-layer and, contemporary, to preserve a high quality factor Q of the cavity. The OMBR capability of working as bioassay was proved by different optical techniques, such as the real time measurement of the resonance broadening after each functionalization step and fluorescence microscopy.

Association of 2-acylaminopyridines and benzoic acids. Steric and electronic substituent effect studied by XRD, solution and solid-state NMR and calculations

NASA Astrophysics Data System (ADS)

Ośmiałowski, Borys; Kolehmainen, Erkki; Ejsmont, Krzysztof; Ikonen, Satu; Valkonen, Arto; Rissanen, Kari; Nonappa

2013-12-01

Eight single crystal X-ray structures, solid-state NMR spectroscopic, and theoretical studies utilizing QTAIM methodology were used to characterize the 2-acyl (alkyl in acyl = methyl, ethyl, t-butyl, and 1-adamantyl) amino-6-R-pyridine/4-R‧-benzoic acid (R,R‧ = H or Me) cocrystals. As expected among alkyl groups 1-adamantyl due to its bulkiness has the most significant effect on the relative positions of molecules in cocrystals. In addition, the subtle electronic and steric effects by the methyl substituents were observed. The theoretical calculations with full geometry optimizations are in agreement with the experimental findings (geometry, energy of hydrogen bonds). Based on the crystal structures and calculations it is concluded that p-methyl substituent in benzoic acid increase the hydrogen bond accepting ability of the CO oxygen and decreases the hydrogen bond donating ability of OH proton. The 15N solid-state (CP MAS) NMR chemical shifts prove that molecules in cocrystal are held together by hydrogen bonding. The biggest variation in the 15N chemical shift of acylamino nitrogen can be related with the size of the alkyl group in acyl moiety.

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

PubMed Central

2013-01-01

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

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

PubMed

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

2013-06-13

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

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

NASA Astrophysics Data System (ADS)

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

2005-06-01

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

Terminal base pairs of oligodeoxynucleotides: imino proton exchange and fraying.

PubMed

Nonin, S; Leroy, J L; Guéron, M

1995-08-22

We have estimated the dissociation constant of the terminal base pairs of the B-DNA duplexes formed by 5'-d(CGCGATCGCG) and 5'-d(TAGCGCTA) by two methods, one based on the change in imino proton chemical shift with temperature and the other on the apparent pK shift of the imino proton, as monitored by the change in chemical shift of aromatic protons. These methods do not rely on imino proton exchange, whose rate was also measured. (1) The effect of ammonia on the imino proton exchange rate of the terminal pair of the 5'-d(CGCGATCGCG) duplex is 67 times less than on the isolated nucleoside. This provides an upper limit on the exchange rate from the closed pair. In fact, the effect is just as predicted from the dissociation constant, assuming that there is no exchange at all from the closed pair and that, as has been argued previously, external catalysts act on the open state as they do on the isolated nucleoside. The inhibition of catalyzed proton exchange in the closed pair, despite exposure of one face of the pair to solvent, is a new feature of the exchange process. It will allow determination of the dissociation constant of terminal pairs from the exchange rate. (2) Intrinsic catalysis of proton exchange is less efficient for the terminal pair than for an internal one. A possible explanation is that proton transfer across the water bridge responsible for intrinsic catalysis is slower, as expected if the open-state separation of the bases is larger in a terminal pair. This observation may lead to a direct method for the study of fraying. (3) At 0 degrees C, the dissociation constant of the second pair of the 5'-d(CGCGATCGCG) duplex is close to the square of the constant for the terminal pair, as predicted from a simple model of fraying. The enthalpy and entropy of opening of the terminal pairs may be compared with those of nearest neighbor interactions derived from calorimetry [Breslauer, K. J., et al. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 3746-3750].

Sensitivity of Fischer-Tropsch Synthesis and Water-Gas Shift Catalysts to Poisons from High-Temperature High-Pressure Entrained-Flow (EF) Oxygen-Blown Gasifier Gasification of Coal/Biomass Mixtures

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

Burton Davis; Gary Jacobs; Wenping Ma

2011-09-30

There has been a recent shift in interest in converting not only natural gas and coal derived syngas to Fischer-Tropsch synthesis products, but also converting biomass-derived syngas, as well as syngas derived from coal and biomass mixtures. As such, conventional catalysts based on iron and cobalt may not be suitable without proper development. This is because, while ash, sulfur compounds, traces of metals, halide compounds, and nitrogen-containing chemicals will likely be lower in concentration in syngas derived from mixtures of coal and biomass (i.e., using entrained-flow oxygen-blown gasifier gasification gasification) than solely from coal, other compounds may actually be increased.more » Of particular concern are compounds containing alkali chemicals like the chlorides of sodium and potassium. In the first year, University of Kentucky Center for Applied Energy Research (UK-CAER) researchers completed a number of tasks aimed at evaluating the sensitivity of cobalt and iron-based Fischer-Tropsch synthesis (FT) catalysts and a commercial iron-chromia high temperature water-gas shift catalyst (WGS) to alkali halides. This included the preparation of large batches of 0.5%Pt-25%Co/Al{sub 2}O{sub 3} and 100Fe: 5.1Si: 3.0K: 2.0Cu (high alpha) catalysts that were split up among the four different entities participating in the overall project; the testing of the catalysts under clean FT and WGS conditions; the testing of the Fe-Cr WGS catalyst under conditions of co-feeding NaCl and KCl; and the construction and start-up of the continuously stirred tank reactors (CSTRs) for poisoning investigations. In the second and third years, researchers from the University of Kentucky Center for Applied Energy Research (UK-CAER) continued the project by evaluating the sensitivity of a commercial iron-chromia high temperature water-gas shift catalyst (WGS) to a number of different compounds, including KHCO{sub 3}, NaHCO{sub 3}, HCl, HBr, HF, H{sub 2}S, NH{sub 3}, and a combination of H{sub 2}S and NH{sub 3}. Cobalt and iron-based Fischer-Tropsch synthesis (FT) catalysts were also subjected to a number of the same compounds in order to evaluate their sensitivities at different concentration levels of added contaminant.« less

Cantilevered probe detector with piezoelectric element

DOEpatents

Adams, Jesse D; Sulchek, Todd A; Feigin, Stuart C

2014-04-29

A disclosed chemical detection system for detecting a target material, such as an explosive material, can include a cantilevered probe, a probe heater coupled to the cantilevered probe, and a piezoelectric element disposed on the cantilevered probe. The piezoelectric element can be configured as a detector and/or an actuator. Detection can include, for example, detecting a movement of the cantilevered probe or a property of the cantilevered probe. The movement or a change in the property of the cantilevered probe can occur, for example, by adsorption of the target material, desorption of the target material, reaction of the target material and/or phase change of the target material. Examples of detectable movements and properties include temperature shifts, impedance shifts, and resonant frequency shifts of the cantilevered probe. The overall chemical detection system can be incorporated, for example, into a handheld explosive material detection system.

Cantilevered probe detector with piezoelectric element

DOEpatents

Adams, Jesse D; Sulchek, Todd A; Feigin, Stuart C

2013-04-30

A disclosed chemical detection system for detecting a target material, such as an explosive material, can include a cantilevered probe, a probe heater coupled to the cantilevered probe, and a piezoelectric element disposed on the cantilevered probe. The piezoelectric element can be configured as a detector and/or an actuator. Detection can include, for example, detecting a movement of the cantilevered probe or a property of the cantilevered probe. The movement or a change in the property of the cantilevered probe can occur, for example, by adsorption of the target material, desorption of the target material, reaction of the target material and/or phase change of the target material. Examples of detectable movements and properties include temperature shifts, impedance shifts, and resonant frequency shifts of the cantilevered probe. The overall chemical detection system can be incorporated, for example, into a handheld explosive material detection system.

Cantilevered probe detector with piezoelectric element

DOEpatents

Adams, Jesse D [Reno, NV; Sulchek, Todd A [Oakland, CA; Feigin, Stuart C [Reno, NV

2012-07-10

A disclosed chemical detection system for detecting a target material, such as an explosive material, can include a cantilevered probe, a probe heater coupled to the cantilevered probe, and a piezoelectric element disposed on the cantilevered probe. The piezoelectric element can be configured as a detector and/or an actuator. Detection can include, for example, detecting a movement of the cantilevered probe or a property of the cantilevered probe. The movement or a change in the property of the cantilevered probe can occur, for example, by adsorption of the target material, desorption of the target material, reaction of the target material and/or phase change of the target material. Examples of detectable movements and properties include temperature shifts, impedance shifts, and resonant frequency shifts of the cantilevered probe. The overall chemical detection system can be incorporated, for example, into a handheld explosive material detection system.

Cantilevered probe detector with piezoelectric element

DOEpatents

Adams, Jesse D.; Sulchek, Todd A.; Feigin, Stuart C.

2010-04-06

A disclosed chemical detection system for detecting a target material, such as an explosive material, can include a cantilevered probe, a probe heater coupled to the cantilevered probe, and a piezoelectric element disposed on the cantilevered probe. The piezoelectric element can be configured as a detector and/or an actuator. Detection can include, for example, detecting a movement of the cantilevered probe or a property of the cantilevered probe. The movement or a change in the property of the cantilevered probe can occur, for example, by adsorption of the target material, desorption of the target material, reaction of the target material and/or phase change of the target material. Examples of detectable movements and properties include temperature shifts, impedance shifts, and resonant frequency shifts of the cantilevered probe. The overall chemical detection system can be incorporated, for example, into a handheld explosive material detection system.

Combining Fourier phase encoding and broadband inversion toward J-edited spectra

NASA Astrophysics Data System (ADS)

Lin, Yulan; Guan, Quanshuai; Su, Jianwei; Chen, Zhong

2018-06-01

Nuclear magnetic resonance (NMR) spectra are often utilized for gathering accurate information relevant to molecular structures and composition assignments. In this study, we develop a homonuclear encoding approach based on imparting a discrete phase modulation of the targeted cross peaks, and combine it with a pure shift experiments (PSYCHE) based J-modulated scheme, providing simple 2D J-edited spectra for accurate measurement of scalar coupling networks. Chemical shifts and J coupling constants of protons coupled to the specific protons are demonstrated along the F2 and F1 dimensions, respectively. Polychromatic pulses by Fourier phase encoding were performed to simultaneously detect several coupling networks. Proton-proton scalar couplings are chosen by a polychromatic pulse and a PSYCHE element. Axis peaks and unwanted couplings are complete eradicated by incorporating a selective COSY block as a preparation period. The theoretical principles and the signal processing procedure are laid out, and experimental observations are rationalized on the basis of theoretical analyses.

New class of 19F pH indicators: fluoroanilines.

PubMed Central

Deutsch, C J; Taylor, J S

1989-01-01

The pH dependence of the 19F chemical shift has been characterized for a number of fluorine-substituted aniline derivatives. These compounds constitute a new class of 19F nuclear magnetic resonance (NMR) pH indicators, characterized by single 19F resonance lines with sensitivities ranging from 2 to 7 ppm/pH unit near the aniline pKa; total shifts between conjugate acid and base of 5-15 ppm; and pKas ranging from 1 to 7. One compound, N,N-(methyl-2-carboxyisopropyl)-4-fluoroaniline, has a pKa of 6.8 and a sensitivity of 5 ppm/pH unit. This compound displays significant broadening of its 19F resonance near the aniline pKa (6.8), due to a decreased rate of exchange between conjugate acid and base species. Our results are consistent with slow dissociation of an intramolecular hydrogen bond in the zwitterionic species that limits the exchange rate between protonated and unprotonated forms for N,N-(methyl-2-carboxyisopropyl)-4-fluoroaniline. PMID:2720073

Divided-evolution-based pulse scheme for quantifying exchange processes in proteins: powerful complement to relaxation dispersion experiments.

PubMed

Bouvignies, Guillaume; Hansen, D Flemming; Vallurupalli, Pramodh; Kay, Lewis E

2011-02-16

A method for quantifying millisecond time scale exchange in proteins is presented based on scaling the rate of chemical exchange using a 2D (15)N, (1)H(N) experiment in which (15)N dwell times are separated by short spin-echo pulse trains. Unlike the popular Carr-Purcell-Meiboom-Gill (CPMG) experiment where the effects of a radio frequency field on measured transverse relaxation rates are quantified, the new approach measures peak positions in spectra that shift as the effective exchange time regime is varied. The utility of the method is established through an analysis of data recorded on an exchanging protein-ligand system for which the exchange parameters have been accurately determined using alternative approaches. Computations establish that a combined analysis of CPMG and peak shift profiles extends the time scale that can be studied to include exchanging systems with highly skewed populations and exchange rates as slow as 20 s(-1).

MODELING THE INTERACTION THRESHOLD: THE BREAK-POINT BETWEEN ADDITIVITY AND NON-ADDITIVITY

EPA Science Inventory

Dose-dependent changes in toxicity mechanisms of single chemicals may take place along the full dose-response spectrum. At high doses, the possibility exists for some steps in the principle mechanism of toxicity to shift to other mechanisms. The possibility of mechanism shifts fo...

Characterizing Chemical Similarity with Vibrational Spectroscopy: New Insights into the Substituent Effects in Monosubstituted Benzenes.

PubMed

Tao, Yunwen; Zou, Wenli; Cremer, Dieter; Kraka, Elfi

2017-10-26

A novel approach is presented to assess chemical similarity based the local vibrational mode analysis developed by Konkoli and Cremer. The local mode frequency shifts are introduced as similarity descriptors that are sensitive to any electronic structure change. In this work, 59 different monosubstituted benzenes are compared. For a subset of 43 compounds, for which experimental data was available, the ortho-/para- and meta-directing effect in electrophilic aromatic substitution reactions could be correctly reproduced, proving the robustness of the new similarity index. For the remaining 16 compounds, the directing effect was predicted. The new approach is broadly applicable to all compounds for which either experimental or calculated vibrational frequency information is available.

Fabrication of a Graphene/ZnO based p-n junction device and its ultraviolet photoresponse properties

NASA Astrophysics Data System (ADS)

Kwon, Young-Tae; Kang, Sung-Oong; Cheon, Ji-Ae; Song, Yoseb; Lee, Jong-Jin; Choa, Yong-Ho

2017-09-01

Graphene with a zero-bandgap energy is easily doped using a chemical dopant, and a shift upwards or downwards in the Fermi level is generated. Moreover, the integration of inorganic material into the doped graphene changes the physical and chemical properties of the material. For this purpose, we successfully fabricated a p-n junction device by depositing an n-typed ZnO layer on p-doped graphene and studied the ultraviolet (UV) photoresponse properties under a photocurrent (UV light on) and a dark current (UV light off). Two devices, lateral and vertical, were developed by alternating the thickness of the ZnO layer, and the photoresponse mechanisms were described on the basis of the contact potential difference.

Robustness of Fat Quantification using Chemical Shift Imaging

PubMed Central

Hansen, Katie H; Schroeder, Michael E; Hamilton, Gavin; Sirlin, Claude B; Bydder, Mark

2011-01-01

This purpose of this study was to investigate the effect of parameter changes that can potentially lead to unreliable measurements in fat quantification. Chemical shift imaging was performed using spoiled gradient echo sequences with systematic variations in the following: 2D/3D sequence, number of echoes, delta echo time, fractional echo factor, slice thickness, repetition time, flip angle, bandwidth, matrix size, flow compensation and field strength. Results indicated no significant (or significant but small) changes in fat fraction with parameter. The significant changes can be attributed to known effects of T1 bias and the two forms of noise bias. PMID:22055856

Sesterterpenes from a common marine sponge, Hyrtios erecta.

PubMed

Crews, P; Bescansa, P

1986-01-01

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

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

PubMed

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

2015-10-01

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

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

PubMed

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

2016-06-13

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

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

PubMed Central

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

2017-01-01

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

Miniaturised wireless smart tag for optical chemical analysis applications.

PubMed

Steinberg, Matthew D; Kassal, Petar; Tkalčec, Biserka; Murković Steinberg, Ivana

2014-01-01

A novel miniaturised photometer has been developed as an ultra-portable and mobile analytical chemical instrument. The low-cost photometer presents a paradigm shift in mobile chemical sensor instrumentation because it is built around a contactless smart card format. The photometer tag is based on the radio-frequency identification (RFID) smart card system, which provides short-range wireless data and power transfer between the photometer and a proximal reader, and which allows the reader to also energise the photometer by near field electromagnetic induction. RFID is set to become a key enabling technology of the Internet-of-Things (IoT), hence devices such as the photometer described here will enable numerous mobile, wearable and vanguard chemical sensing applications in the emerging connected world. In the work presented here, we demonstrate the characterisation of a low-power RFID wireless sensor tag with an LED/photodiode-based photometric input. The performance of the wireless photometer has been tested through two different model analytical applications. The first is photometry in solution, where colour intensity as a function of dye concentration was measured. The second is an ion-selective optode system in which potassium ion concentrations were determined by using previously well characterised bulk optode membranes. The analytical performance of the wireless photometer smart tag is clearly demonstrated by these optical absorption-based analytical experiments, with excellent data agreement to a reference laboratory instrument. © 2013 Elsevier B.V. All rights reserved.

Soil biota and agriculture production in conventional and organic farming

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

New methods to monitor emerging chemicals in the drinking water production chain.

PubMed

van Wezel, Annemarie; Mons, Margreet; van Delft, Wouter

2010-01-01

New techniques enable a shift in monitoring chemicals that affect water quality from mainly at the end product, tap water, towards monitoring during the whole process along the production chain. This is congruent with the 'HACCP' system (hazard analysis of critical control points) that is fairly well integrated into food production but less well in drinking water production. This shift brings about more information about source quality, the efficiency of treatment and distribution, and understanding of processes within the production chain, and therefore can lead to a more pro-active management of drinking water production. At present, monitoring is focused neither on emerging chemicals, nor on detection of compounds with chronic toxicity. We discuss techniques to be used, detection limits compared to quality criteria, data interpretation and possible interventions in production.

Aggregate exposure pathways in support of risk assessment

EPA Science Inventory

Over time, risk assessment has shifted from establishing relationships between exposure to a single chemical and a resulting adverse health outcome, to evaluating multiple chemicals and disease outcomes simultaneously. As a result, there is an increasing need to better understand...

A multinuclear solid-state NMR study of the dimethyltin chalcogenides ((CH 3) 2SnE) 3, E  S,Se,Te

NASA Astrophysics Data System (ADS)

Gay, Ian D.; Jones, C. H. W.; Sharma, R. D.

The solid-state NMR spectra, measured using MAS, are reported for 13C, 119Sn, 77Se, and 125Te in the compounds (Me 2SnE) 3, E  S, Se, or Te. For ((CH 3) 2SnS) 3, tetragonal, three inequivalent carbons and two inequivalent tins are observed consistent with a reinterpretation of the crystal structure data of this compound which shows a twofold axis through opposing tin and sulfur atoms, the molecule being in a twisted-boat conformation. For the monoclinic form six inequivalent carbons and three inequivalent tins were observed. Chemical shifts for 13C and 119Sn and the magnitudes of the 2JSn Sn coupling constants are reported. The tetragonal forms of ((CH 3) 2SnSe) 3 and ((CH 3) 2SnTe) 3 show the presence of two inequivalent tin and chalcogen atoms and three inequivalent carbons, again consistent with a twofold axis. In these compounds it is possible to identify the three different observed single-bond coupling constants with the distinct crystallographically determined tin-chalcogen bonds. The 13C, 119Sn, 77Se, and 125Te chemical shifts are reported, together with the magnitude of 1JSn E (E  Se or Te). In addition to isotropic shifts and couplings, chemical-shift anisotropies are reported for Sn, Se, and Te.

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

PubMed Central

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

2013-01-01

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

Crystal structures, spectroscopic and theoretical study of novel Schiff bases of 2-(methylthiomethyl)anilines.

PubMed

Olalekan, Temitope E; Adejoro, Isaiah A; VanBrecht, Bernardus; Watkins, Gareth M

2015-03-15

New Schiff bases derived from p-methoxysalicylaldehyde and 2-(methylthiomethyl)anilines (substituted with methyl, methoxy, nitro) were synthesized and characterized by elemental analyses, FT-IR, NMR, electronic spectra and quantum chemical calculations. X-ray crystallography of two compounds showed the solid structures are stabilized by intramolecular and intermolecular H-bonds. The effect of OH⋯N interaction between the phenolic hydrogen and imine nitrogen on the proton and carbon NMR shifts, and the role of CH⋯O and CH⋯S contacts are discussed. The bond lengths and angles, (1)H and (13)C NMR data, E(LUMO-HOMO), dipole moments and polarizability of the compounds were predicted by density functional theory, DFT (B3LYP/6-31G∗∗) method. The experimental geometric parameters and the NMR shifts were compared with the calculated values, which gave good correlations. The electronic effects of aryl ring substituents (methyl, methoxy and nitro) on the properties of the resulting compounds, such as the color, NMR shifts, electronic spectra and the calculated energy band gaps, dipole moments and polarizability are discussed. Increase in electron density shifted the phenolic proton resonance to lower fields. The methoxy-substituted compound has a small dipole moment and subsequent large polarizability value. Highest polarity was indicated by the nitro compound which also showed high polarizability due to its larger size. The energy gaps obtained from E(LUMO-HOMO) calculations suggest these compounds may have applications as organic semiconducting materials. Copyright © 2014 Elsevier B.V. All rights reserved.

Advanced MRI Methods for Assessment of Chronic Liver Disease

PubMed Central

Taouli, Bachir; Ehman, Richard L.; Reeder, Scott B.

2010-01-01

MRI plays an increasingly important role for assessment of patients with chronic liver disease. MRI has numerous advantages, including lack of ionizing radiation and the possibility of performing multiparametric imaging. With recent advances in technology, advanced MRI methods such as diffusion-, perfusion-weighted MRI, MR elastography, chemical shift based fat-water separation and MR spectroscopy can now be applied to liver imaging. We will review the respective roles of these techniques for assessment of chronic liver disease. PMID:19542391

Design of Geopolymeric Materials Based on Nanostructural Characterization and Modeling

DTIC Science & Technology

2006-04-01

composition M2O.mAl2O3.nSiO2, usually with m 1 and 2 ≤ n ≤ 6, and where M represents one or more alkali metals. Some geopolymers also contain alkaline...shown to have interesting and potentially very useful properties. Geopolymer -calcium phosphate composites are also being investigated for potential...110-100-90-80-70 Chemical shift (ppm from TMS) Figure 5. Deconvoluted 29Si MAS NMR spectra of Na- geopolymers with compositions (a) x = 0.535, (b

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

PubMed Central

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

2017-01-01

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

Sonochemical synthesis and DFT studies of nano novel Schiff base cadmium complexes: Green, efficient, recyclable catalysts and precursors of Cd NPs

NASA Astrophysics Data System (ADS)

Parsaee, Zohreh

2017-10-01

Novel asymmetric (N4) Schiff bases (Ln, n = 1-3) and their nanosized cadmium complexes derived of 4,4'-(pentylazanediyl) dibenzaldehyde and aminobenzaldehyde are synthesized by sonochemical method and characterized based on physicochemical analysis including 1H NMR, 13C NMR, SEM, TGA, Mass, FT-IR, UV-Vis spectroscopy, elemental analysis, magnetic moment and molar conductance measurements. According to the analytic results of the NMR, UV-Vis and magnetic moment studies, it is found that the geometrical structures of these complexes [CdII2LnCl4], (L = C45H40N5X, X = CH3, Cl, OH) are square planer. The synthesized complexes were so effective as nanocatalyst on the oxidation of primary and secondary alcohols. The oxidation reactions were carried out in ethyl-methyl-imidazolium ionic liquid in presence of NaOCl. In addition Cd NPs were synthesized through the thermal decomposition of mentioned complexes and characterized by using FT-IR, SEM, TEM, EDX and XRD methods, which indicated close accordance to the standard pattern of CdO nanoparticles and an acceptable size at the nanorange (22-27 nm). Furthermore geometrical optimization of the Cd2LnCl4 calculated using DFT/B3LYP with LanL2DZ/6-311+G (d,p) level. The electronic parameter including HOMO-LUMO orbitals, bond gap, chemical hardness-softness, electronegativity, electrophilicity, NMR chemical shifts and IR frequencies were calculated. The calculated NMR shifts and vibrational frequencies showed excellent agreement with experimental data.

[Changes in functional state during occupational activities in workers at objects for chemical weapons destruction].

PubMed

2010-01-01

The authors studied functional state before and after the working shift in workers at objects for chemical weapons destruction, analyzed changes in central and peripheral hemodynamics parameters, vegetative regulation of heart rhythm, stabilographic and psychophysiologic values.

Peptides containing internal residues of pyroglutamic acid: proton NMR characteristics

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

Khan, S.A.

1986-05-01

The proton NMR characteristics of internal pyroglutamic acid (Glp; 5-oxoproline) residues in seven tripeptides of the general structure Boc-Xxx-Glp-Yyy-NH/sub 2/ were studied. In general, the chemical shifts of several diagnostic protons moved downfield on going from the Glu-containing peptides (Boc-Xxx-Glu-Yyy-NH/sub 2/) to the corresponding Glp-containing peptides. The C-2 proton of the Xxx residue was shifted by about 1.1 ppm. The N-2 proton of the Yyy residue was shifted by about 0.5 ppm. The C-2 proton of the Glx residue itself was shifted by about 0.5 ppm. One of the Glx C-3 protons was also shifted by about 0.5 ppm, butmore » the other remained essentially unchanged. Finally, the Glx C-4 protons were shifted by about 0.3 ppm. Internal Glu residues are readily converted chemically into internal Glp residues. This conversion also occurs as a side reaction during HP cleavage of the protecting group from Glu(OBzl) residues. The spontaneous fragmentation of serum proteins C3, C4 and lambda/sub 2/-macroglobulin under denaturing conditions is probably due to regioselective hydrolysis of an internal Glp residue formed in each of these proteins upon denaturation. These proton NMR characteristics may be useful in establishing the presence of internal Glp residues in synthetic and natural peptides.« less

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2009-01-01

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

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

PubMed

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

2014-06-01

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

NMR Spectroscopy Using a Chiral Lanthanide Shift Reagent to Assess the Optical Purity of 1-Phenylethylamine

NASA Astrophysics Data System (ADS)

Viswanathan, Tito; Toland, Alan

1995-10-01

Enantiomeric forms of 1-phenylethylamine cannot be distinguished by 1H or 13C-NMR because the groups attached to the stereocenter are in an enantiopic environment. However, the chemical shifts of the protons in the groups attached to the stereocenter can be differentially altered to appear as distinct peaks in the NMR spectrum. This is accomplished by the use of a commercially available chiral lanthanide shift reagent, Yb(tfC)3. The NMR spectrum after the addition of a chiral shift reagent allows one to assess the optical purity of the sample.

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

PubMed

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

2012-06-28

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

pH-dependent electron-transport properties of carbon nanotubes.

PubMed

Back, Ju Hee; Shim, Moonsub

2006-11-30

Carbon nanotube electrochemical transistors integrated with microfluidic channels are utilized to examine the effects of aqueous electrolyte solutions on the electron-transport properties of single isolated carbon nanotubes. In particular, pH and concentration of supporting inert electrolytes are examined. A systematic threshold voltage shift with pH is observed while the transconductance and subthreshold swing remain independent of pH and concentration. Decreasing pH leads to a negative shift of the threshold voltage, indicating that protonation does not lead to hole doping. Changing the type of contact metal does not alter the observed pH response. The pH-dependent charging of SiO2 substrate is ruled out as the origin based on measurements with suspended nanotube transistors. Increasing the ionic strength leads to reduced pH response. Contributions from possible surface chargeable chemical groups are considered.

Knowledge management in a waste based biorefinery in the QbD paradigm.

PubMed

Rathore, Anurag S; Chopda, Viki R; Gomes, James

2016-09-01

Shifting resource base from fossil feedstock to renewable raw materials for production of chemical products has opened up an area of novel applications of industrial biotechnology-based process tools. This review aims to provide a concise and focused discussion on recent advances in knowledge management to facilitate efficient and optimal operation of a biorefinery. Application of quality by design (QbD) and process analytical technology (PAT) as tools for knowledge creation and management at different levels has been highlighted. Role of process integration, government policies, knowledge exchange through collaboration, and use of databases and computational tools have also been touched upon. Copyright © 2016 Elsevier Ltd. All rights reserved.

Electrochemical and spectroscopic characteristics of p-acryloyloxybenzoyl chloride and p-acryloyloxybenzoic acid and antimicrobial activity of organic compounds

NASA Astrophysics Data System (ADS)

Cakir, I.; Soykan, U.; Cetin, S.; Karaboga, F.; Zalaoglu, Y.; Dogruer, M.; Terzioglu, C.; Yildirim, G.

2014-11-01

The purpose of this multidisciplinary work is to characterize title compounds, p-acryloyloxybenzoyl chloride (ABC) and p-acryloyloxybenzoic acid (ABA) by means of experimental and theoretical evidences. As experimental research, Fourier transformation-infrared spectra (in the region 400-4000 cm-1) and nuclear magnetic resonance (NMR) chemical shifts (with a frequency of 400 MHz) are examined for spectroscopic properties belonging to the new synthesized compounds. Moreover, the compounds are investigated for antimicrobial activity against various microorganisms (Gram-positive and Gram-negative) by means of the visual inhibition zone technique on the agar media. The experimental results observed indicate that ABA exhibits more powerful inhibitors of microorganisms due to the presence of the hydroxyl group leading to higher reactive system, one of the most striking features of the paper. As for the theoretical studies, the optimized molecular structures, vibrational frequencies, corresponding vibrational spectra interpreted with the aid of normal coordinate analysis based on scaled density functional force field, atomic charges, thermodynamic properties at different temperature, 1H NMR chemical shifts by way of density functional theory (DFT) with the standard (B3LYP) methods at 6-311G++(d,p) basis set combination for the first time. According to findings, the 1H NMR chemical shifts and vibrational frequencies are obtained to be in good agreement with the suitable experimental results. Thus, it would be more precise to say that the calculation level chosen is powerful approach for understanding in the identification of the molecules investigated. At the same time, we determine the electrochemical characteristics belonging to the samples via the simulation of translation energy (HOMO-LUMO), molecular electrostatic potential (MEP) and electrostatic potential (ESP) investigations. It is observed that the strong intra-molecular charge transfer (ICT) appears between the donor and acceptor in the both compounds (especially ABA) due to the existence of the strong electronic donating groups and effective π-π* conjugated segments with high electronic donor ability for the electrophilic attack (intermolecular interactions).

Reduced dimensionality tailored HN(C)N experiments for facile backbone resonance assignment of proteins through unambiguous identification of sequential HSQC peaks

NASA Astrophysics Data System (ADS)

Kumar, Dinesh

2013-12-01

Two novel reduced dimensionality (RD) tailored HN(C)N [S.C. Panchal, N.S. Bhavesh, R.V. Hosur, Improved 3D triple resonance experiments, HNN and HN(C)N, for HN and 15N sequential correlations in (13C, 15N) labeled proteins: application to unfolded proteins, J. Biomol. NMR 20 (2001) 135-147] experiments are proposed to facilitate the backbone resonance assignment of proteins both in terms of its accuracy and speed. These experiments - referred here as (4,3)D-hNCOcaNH and (4,3)D-hNcoCANH - exploit the linear combination of backbone 15N and 13C‧/13Cα chemical shifts simultaneously to achieve higher peak dispersion and randomness along their respective F1 dimensions. Simply, this has been achieved by modulating the backbone 15N(i) chemical shifts with that of 13C‧ (i - 1)/13Cα (i - 1) spins following the established reduced dimensionality NMR approach [T. Szyperski, D.C. Yeh, D.K. Sukumaran, H.N. Moseley, G.T. Montelione, Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment, Proc. Natl. Acad. Sci. USA 99 (2002) 8009-8014]. Though the modification is simple it has resulted an ingenious improvement of HN(C)N both in terms of peak dispersion and easiness of establishing the sequential connectivities. The increased dispersion along F1 dimension solves two purposes here: (i) resolves the ambiguities arising because of degenerate 15N chemical shifts and (ii) reduces the signal overlap in F2(15N)-F3(1H) planes (an important requisite in HN(C)N based assignment protocol for facile and unambiguous identification of sequentially connected HSQC peaks). The performance of both these experiments and the assignment protocol has been demonstrated using bovine apo Calbindin-d9k (75 aa) and urea denatured UNC60B (a 152 amino acid ADF/cofilin family protein of Caenorhabditis elegans), as representatives of folded and unfolded protein systems, respectively.

Whole-heart chemical shift encoded water-fat MRI.

PubMed

Taviani, Valentina; Hernando, Diego; Francois, Christopher J; Shimakawa, Ann; Vigen, Karl K; Nagle, Scott K; Schiebler, Mark L; Grist, Thomas M; Reeder, Scott B

2014-09-01

To develop and evaluate a free-breathing chemical-shift-encoded (CSE) spoiled gradient-recalled echo (SPGR) technique for whole-heart water-fat imaging at 3 Tesla (T). We developed a three-dimensional (3D) multi-echo SPGR pulse sequence with electrocardiographic gating and navigator echoes and evaluated its performance at 3T in healthy volunteers (N = 6) and patients (N = 20). CSE-SPGR, 3D SPGR, and 3D balanced-SSFP with chemical fat saturation were compared in six healthy subjects with images evaluated for overall image quality, level of residual artifacts, and quality of fat suppression. A similar scoring system was used for the patient datasets. Images of diagnostic quality were acquired in all but one subject. CSE-SPGR performed similarly to SPGR with fat saturation, although it provided a more uniform fat suppression over the whole field of view. Balanced-SSFP performed worse than SPGR-based methods. In patients, CSE-SPGR produced excellent fat suppression near metal. Overall image quality was either good (7/20) or excellent (12/20) in all but one patient. There were significant artifacts in 5/20 clinical cases. CSE-SPGR is a promising technique for whole-heart water-fat imaging during free-breathing. The robust fat suppression in the water-only image could improve assessment of complex morphology at 3T and in the presence of off-resonance, with additional information contained in the fat-only image. Copyright © 2013 Wiley Periodicals, Inc.

Advantages of paramagnetic CEST complexes having slow-to-intermediate water exchange properties as responsive MRI agents

PubMed Central

Soesbe, Todd C.; Wu, Yunkou; Sherry, A. Dean

2012-01-01

Paramagnetic saturation transfer chemical exchange (PARACEST) complexes are exogenous contrast agents that have great potential to further extend the functional and molecular imaging capabilities of magnetic resonance. Due to the presence of a central paramagnetic lanthanide ion (Ln3+ ≠ La3+, Gd3+, Lu3+) within the chelate, the resonance frequencies of protons and water molecules bound to the PARACEST agent are shifted far away from the bulk water frequency. This large chemical shift combined with an extreme sensitivity to the chemical exchange rate make PARACEST agents ideally suited for reporting significant biological metrics such as temperature, pH, and the presence of metabolites. Also, the ability to turn PARACEST agents “off” and “on” using a frequency selective saturation pulse gives them a distinct advantage over Gd3+-based contrast agents. A current challenge for PARACEST research is translating the promising in vitro results into in vivo systems. This short review article first describes the basic theory behind PARACEST contrast agents, their benefits over other contrast agents, and their applications to magnetic resonance imaging. It then describes some of the recent PARACEST research results. Specifically, pH measurements using water molecule exchange rate modulation, T2-exchange contrast due to water molecule exchange, the use of ultra-short echo times (TE<10 μs) to overcome T2-exchange line-broadening, and the potential application of T2-exchange as a new contrast mechanism for magnetic resonance imaging. PMID:23055299

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

PubMed

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

2011-01-01

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

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

Gao, X.; Patel, D.J.

The authors report on two-dimensional proton NMR studies of echinomycin complexes with the self-complementary d(A1-C2-G3-Tr) and d(T1-C2-G3-A4) duplexes in aqueous solution. The exchangeable and nonexchangeable antibiotic and nucleic acid protons in the 1 echinomycin per tetranucleotide duplex complexes have been assigned from analyses of scalar coupling and distance connectivities in two-dimensional data sets records in H/sub 2/O and D/sub 2/O solution. An analysis of the intermolecular NOE patterns for both complexes combined with large upfield imino proton and large downfield phosphorus complexation chemical shift changes demonstrates that the two quinoxaline chromophores of echinomycin bisintercalate into the minor groove surrounding themore » dC-dG step of each tetranucleotide duplex. Further, the quinoxaline rings selectively stack between A1 and C2 bases in the d(ACGT) complex and between T1 and C2 bases in the d(TCGA) complex. The intermolecular NOE patterns and the base and sugar proton chemical shifts for residues C2 and G3 are virtually identical for the d(ACGT) and d(TCGA) complexes. A large set of intermolecular contacts established from nuclear Overhauser effects (NOEs) between antibiotic and nucleic acid protons in the echinomycin-tetranucleotide complexes in solution are consistent with corresponding contacts reported for echinomycin-oligonucleotide complexes in the crystalline state. The authors demonstrate that the G x G base pairs adopt Watson-Crick pairing in both d(ACGT) and d(TCGA) complexes in solution. By contrast, the A1 x T4 base pairs adopt Hoogsteen pairing for the echinomycin-d(A1-C2-G3-Tr) complex while the T1 x A4 base pairs adopt Watson-Crick pairing for the echinomycin-d(T1-C2-G3-A4) complex in aqueous solution. These results emphasize the role of sequence in discriminating between Watson-Crick and Hoogsteen pairs at base pairs flanking the echinomycin bisintercalation site in solution.« less

Board of Regents of the Nevada System of Higher Education, on behalf of the University of Nevada, Reno

DOEpatents

Adams, Jesse D.; Sulchek, Todd A.; Feigin, Stuart C.

2017-07-11

A disclosed chemical detection system for detecting a target material, such as an explosive material, can include a cantilevered probe, a probe heater coupled to the cantilevered probe, and a piezoelectric element disposed on the cantilevered probe. The piezoelectric element can be configured as a detector and/or an actuator. Detection can include, for example, detecting a movement of the cantilevered probe or a property of the cantilevered probe. The movement or a change in the property of the cantilevered probe can occur, for example, by adsorption of the target material, desorption of the target material, reaction of the target material and/or phase change of the target material. Examples of detectable movements and properties include temperature shifts, impedance shifts, and resonant frequency shifts of the cantilevered probe. The overall chemical detection system can be incorporated, for example, into a handheld explosive material detection system.

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

Probing Structural Changes among Analogous Inhibitor-Bound Forms of HIV-1 Protease and a Drug-Resistant Mutant in Solution by Nuclear Magnetic Resonance.

PubMed

Khan, Shahid N; Persons, John D; Paulsen, Janet L; Guerrero, Michel; Schiffer, Celia A; Kurt-Yilmaz, Nese; Ishima, Rieko

2018-03-13

In the era of state-of-the-art inhibitor design and high-resolution structural studies, detection of significant but small protein structural differences in the inhibitor-bound forms is critical to further developing the inhibitor. Here, we probed differences in HIV-1 protease (PR) conformation among darunavir and four analogous inhibitor-bound forms and compared them with a drug-resistant mutant using nuclear magnetic resonance chemical shifts. Changes in amide chemical shifts of wild-type (WT) PR among these inhibitor-bound forms, ΔCSP, were subtle but detectable and extended >10 Å from the inhibitor-binding site, asymmetrically between the two subunits of PR. Molecular dynamics simulations revealed differential local hydrogen bonding as the molecular basis of this remote asymmetric change. Inhibitor-bound forms of the drug-resistant mutant also showed a similar long-range ΔCSP pattern. Differences in ΔCSP values of the WT and the mutant (ΔΔCSPs) were observed at the inhibitor-binding site and in the surrounding region. Comparing chemical shift changes among highly analogous inhibitors and ΔΔCSPs effectively eliminated local environmental effects stemming from different chemical groups and enabled exploitation of these sensitive parameters to detect subtle protein conformational changes and to elucidate asymmetric and remote conformational effects upon inhibitor interaction.

Has Chemical Education Reached Equilibrium?

NASA Astrophysics Data System (ADS)

Moore, John W.

1997-06-01

The other day I got to thinking about whether something akin to Le Chatelier's principle operates in chemical education. That is, whenever someone alters the conditions under which we interact with students, there is a shift in the system that attempts to minimize or counteract the change.

Dynamic rheological, microstructural and physicochemical properties of blend fish protein recovered from kilka (Clupeonella cultriventris) and silver carp (Hypophthalmichthys molitrix) by the pH-shift process or washing-based technology.

PubMed

Abdollahi, Mehdi; Rezaei, Masoud; Jafarpour, Ali; Undeland, Ingrid

2017-08-15

This study aimed to evaluate how blending pH-shift produced protein isolates from gutted kilka (Clupeonella cultriventris) and silver carp (Hypophthalmichthys molitrix) affected dynamic rheological and chemical properties of the proteins as well as microstructural and physico-mechanical properties of produced gels. Studied variables were protein solubilization pH (acid vs. alkaline) and blending step (before or after protein precipitation). Comparisons were made with conventionally washed minces from kilka and silver carp fillets; either alone or after blending. Rheological studies revealed that blending alkali-produced protein isolates before precipitation resulted in rapid increase of G' reflecting the formation of intermolecular protein-protein interactions with higher rate. Furthermore, blending of alkali-produced protein isolates and washed minces, respectively, of kilka and silver carp improved physico-mechanical properties of the resultant gels compared to pure kilka proteins. However, the pH-shift method showed higher efficacy in development of blend surimi at the same blending ratio compared to the conventional washing. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

PubMed

Straka, Michal; Lantto, Perttu; Vaara, Juha

2008-03-27

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

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

PubMed

Peng, Dungeng; Ogura, Hiroshi; Ma, Li-Hua; Evans, John P; de Montellano, Paul R Ortiz; La Mar, Gerd N

2013-04-01

Solution 2D (1)H NMR was carried out on the azide-ligated substrate complex of human heme oxygenase, hHO, to provide information on the active site molecular structure, chromophore electronic/magnetic properties, and the distal H-bond network linked to the exogenous ligand by catalytically relevant oriented water molecules. While 2D NMR exhibited very similar patterns of two-dimensional nuclear Overhauser spectroscopy cross peaks of residues with substrate and among residues as the previously characterized cyanide complex, significant, broadly distributed chemical shift differences were observed for both labile and non-labile protons. The anisotropy and orientation of the paramagnetic susceptibility tensor, χ, were determined for both the azide and cyanide complexes. The most significant difference observed is the tilt of the major magnetic axes from the heme normal, which is only half as large for the azide than cyanide ligand, with each ligand tilted toward the catalytically cleaved α-meso position. The difference in chemical shifts is quantitatively correlated with differences in dipolar shifts in the respective complexes for all but the distal helix. The necessity of considering dipolar shifts, and hence determination of the orientation/anisotropy of χ, in comparing chemical shifts involving paramagnetic complexes, is emphasized. The analysis shows that the H-bond network cannot detect significant differences in H-bond acceptor properties of cyanide versus azide ligands. Lastly, significant retardation of distal helix labile proton exchange upon replacing cyanide with azide indicates that the dynamic stability of the distal helix is increased upon decreasing the steric interaction of the ligand with the distal helix. Copyright © 2013. Published by Elsevier Inc.

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.

6-Aminopenicillanic acid revisited: A combined solid state NMR and in silico refinement

NASA Astrophysics Data System (ADS)

Aguiar, Daniel Lima Marques de; San Gil, Rosane Aguiar da Silva; Alencastro, Ricardo Bicca de; Souza, Eugenio Furtado de; Borré, Leandro Bandeira; Vaiss, Viviane da Silva; Leitão, Alexandre Amaral

2016-09-01

13C/15N (experimental and ab initio) solid-state NMR was used to achieve an affordable way to improve hydrogen refinement of 6-aminopenicillanic acid (6-APA) structure. The lattice effect on the isotropic chemical shifts was probed by using two different magnetic shielding calculations: isolated molecules and periodic crystal structure. The electron density difference maps of optimized and non-optimized structures were calculated in order to investigate the interactions inside the 6-APA unit cell. The 13C and 15N chemical shifts assignments were unambiguously stablished. In addition, some of the literature 13C resonances ambiguities could be properly solved.

Combining Nuclear Magnetic Resonance Spectroscopy and Density Functional Theory Calculations to Characterize Carvedilol Polymorphs.

PubMed

Rezende, Carlos A; San Gil, Rosane A S; Borré, Leandro B; Pires, José Ricardo; Vaiss, Viviane S; Resende, Jackson A L C; Leitão, Alexandre A; De Alencastro, Ricardo B; Leal, Katia Z

2016-09-01

The experiments of carvedilol form II, form III, and hydrate by (13)C and (15)N cross-polarization magic-angle spinning (CP MAS) are reported. The GIPAW (gauge-including projector-augmented wave) method from DFT (density functional theory) calculations was used to simulate (13)C and (15)N chemical shifts. A very good agreement was found for the comparison between the global results of experimental and calculated nuclear magnetic resonance (NMR) chemical shifts for carvedilol polymorphs. This work aims a comprehensive understanding of carvedilol crystalline forms employing solution and solid-state NMR as well as DFT calculations. Copyright © 2016. Published by Elsevier Inc.

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

NASA Astrophysics Data System (ADS)

Wachter-Jurcsak, Nanette; Zamani, Hossein

1999-05-01

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

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

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

Cort, John R.; Cho, Herman M.

2009-10-01

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

Bonding in Some Zintl Phases: A Study by Tin-119 Mössbauer Spectroscopy

NASA Astrophysics Data System (ADS)

Asbrand, M.; Berry, F. J.; Eisenmann, B.; Kniep, R.; Smart, L. E.; Thied, R. C.

1995-09-01

The 119Sn Mössbauer parameters for a range of Zintl phase compounds are reported. The compounds containing tetrahedrally coordinated tin of composition M5SnX3 (M = Na, K; X = P, As, Sb) have chemical isomer shifts close to that of grey-tin and can be considered to be covalently bonded species. The layer structures of composition KSnX (X = As, Sb) and double-layer compounds M Sn2X2 (M = Na, Sr; X = As, Sb) have tin in a distorted octahedral environment. The chemical isomer shifts are closer to that of white-tin and can be interpreted in terms of metallic bonding.

Improving the analysis of NMR spectra tracking pH-induced conformational changes: removing artefacts of the electric field on the NMR chemical shift.

PubMed

Kukić, Predrag; Farrell, Damien; Søndergaard, Chresten R; Bjarnadottir, Una; Bradley, John; Pollastri, Gianluca; Nielsen, Jens Erik

2010-03-01

pH-induced chemical shift perturbations (CSPs) can be used to study pH-dependent conformational transitions in proteins. Recently, an elegant principal component analysis (PCA) algorithm was developed and used to study the pH-dependent structural transitions in bovine beta-lactoglobulin (betaLG) by analyzing its NMR pH-titration spectra. Here, we augment this analysis method by filtering out changes in the NMR chemical shift that stem from effects that are electrostatic in nature. Specifically, we examine how many CSPs can be explained by purely electrostatic effects arising from titrational events in betaLG. The results show that around 20% of the amide nuclei CSPs in betaLG originate exclusively from "through-space" electric field effects. A PCA of NMR data where electric field artefacts have been removed gives a different picture of the pH-dependent structural transitions in betaLG. The method implemented here is well suited to be applied on a whole range of proteins, which experience at least one pH-dependent conformational change. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

Obtaining molecular and structural information from 13C-14N systems with 13C FIREMAT experiments.

PubMed

Strohmeier, Mark; Alderman, D W; Grant, David M

2002-04-01

The effect of dipolar coupling to 14N on 13C FIREMAT (five pi replicated magic angle turning) experiments is investigated. A method is developed for fitting the 13C FIREMAT FID employing the full theory to extract the 13C-14N dipolar and 13C chemical shift tensor information. The analysis requires prior knowledge of the electric field gradient (EFG) tensor at the 14N nucleus. In order to validate the method the analysis is done for the amino acids alpha-glycine, gamma-glycine, l-alanine, l-asparagine, and l-histidine on FIREMAT FIDs recorded at 13C frequencies of 50 and 100 MHz. The dipolar and chemical shift data obtained with this analysis are in very good agreement with the previous single-crystal 13C NMR results and neutron diffraction data on alpha-glycine, l-alanine, and l-asparagine. The values for gamma-glycine and l-histidine obtained with this new method are reported for the first time. The uncertainties in the EFG tensor on the resultant 13C chemical shift and dipolar tensor values are assessed. (c) 2002 Elsevier Science (USA).

The Impact of a Science Education Game on Students' Learning and Perception of Inhalants as Body Pollutants.

PubMed

Klisch, Yvonne; Miller, Leslie M; Wang, Shu; Epstein, Joel

2012-04-01

This study investigated the knowledge gains and attitude shifts attributable to a unique online science education game, Uncommon Scents. The game was developed to teach middle school students about the biological consequences of exposure to toxic chemicals in an environmental science context, as well as the risks associated with abusing these chemicals as inhalants. Middle school students ( n = 444) grades six through eight participated in the study consisting of a pre-test, three game-play sessions, and a delayed post-test. After playing the game, students demonstrated significant gains in science content knowledge, with game usability ratings emerging as the strongest predictor of post-test content knowledge scores. The intervention also resulted in a shift to more negative attitudes toward inhalants, with the most negative shift occurring among eighth grade students and post-test knowledge gains as the strongest predictor of attitude change across all grade levels. These findings suggest that the environmental science approach used in Uncommon Scents is an efficacious strategy for delivering both basic science content and influencing perceived harm relating to the inhalation of toxic chemicals from common household products.

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

NASA Astrophysics Data System (ADS)

Goudarzi, Nasser

2016-04-01

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

Probing hydrogen bonding in cocrystals and amorphous dispersions using (14)N-(1)H HMQC solid-state NMR.

PubMed

Tatton, Andrew S; Pham, Tran N; Vogt, Frederick G; Iuga, Dinu; Edwards, Andrew J; Brown, Steven P

2013-03-04

Cocrystals and amorphous solid dispersions have generated interest in the pharmaceutical industry as an alternative to more established solid delivery forms. The identification of intermolecular hydrogen bonding interactions in a nicotinamide palmitic acid cocrystal and a 50% w/w acetaminophen-polyvinylpyrrolidone solid dispersion are reported using advanced solid-state magic-angle spinning (MAS) NMR methods. The application of a novel (14)N-(1)H HMQC experiment, where coherence transfer is achieved via through-space couplings, is shown to identify specific hydrogen bonding motifs. Additionally, (1)H isotropic chemical shifts and (14)N electric field gradient (EFG) parameters, both accessible from (14)N-(1)H HMQC experiments, are shown to be sensitive to changes in hydrogen bonding geometry. Numerous indicators of molecular association are accessible from this experiment, including NH cross-peaks occurring from intermolecular hydrogen bonds and changes in proton chemical shifts or electric field gradient parameters. First-principles calculations using the GIPAW approach that yield accurate estimates of isotropic chemical shifts, and EFG parameters were used to assist in assignment. It is envisaged that (14)N-(1)H HMQC solid state NMR experiments could become a valuable screening technique of solid delivery forms in the pharmaceutical industry.

The Impact of a Science Education Game on Students' Learning and Perception of Inhalants as Body Pollutants

NASA Astrophysics Data System (ADS)

Klisch, Yvonne; Miller, Leslie M.; Wang, Shu; Epstein, Joel

2012-04-01

This study investigated the knowledge gains and attitude shifts attributable to a unique online science education game, Uncommon Scents. The game was developed to teach middle school students about the biological consequences of exposure to toxic chemicals in an environmental science context, as well as the risks associated with abusing these chemicals as inhalants. Middle school students (n = 444) grades six through eight participated in the study consisting of a pre-test, three game-play sessions, and a delayed post-test. After playing the game, students demonstrated significant gains in science content knowledge, with game usability ratings emerging as the strongest predictor of post-test content knowledge scores. The intervention also resulted in a shift to more negative attitudes toward inhalants, with the most negative shift occurring among eighth grade students and post-test knowledge gains as the strongest predictor of attitude change across all grade levels. These findings suggest that the environmental science approach used in Uncommon Scents is an efficacious strategy for delivering both basic science content and influencing perceived harm relating to the inhalation of toxic chemicals from common household products.

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

NASA Astrophysics Data System (ADS)

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

2009-02-01

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

Combined Approach for the Structural Characterization of Alkali Fluoroscandates: Solid-State NMR, Powder X-ray Diffraction, and Density Functional Theory Calculations.

PubMed

Rakhmatullin, Aydar; Polovov, Ilya B; Maltsev, Dmitry; Allix, Mathieu; Volkovich, Vladimir; Chukin, Andrey V; Boča, Miroslav; Bessada, Catherine

2018-02-05

The structures of several fluoroscandate compounds are presented here using a characterization approach combining powder X-ray diffraction and solid-state NMR. The structure of K 5 Sc 3 F 14 was fully determined from Rietveld refinement performed on powder X-ray diffraction data. Moreover, the local structures of NaScF 4 , Li 3 ScF 6 , KSc 2 F 7 , and Na 3 ScF 6 compounds were studied in detail from solid-state 19 F and 45 Sc NMR experiments. The 45 Sc chemical shift ranges for six- and seven-coordinated scandium environments were defined. The 19 F chemical shift ranges for bridging and terminal fluorine atoms were also determined. First-principles calculations of the 19 F and 45 Sc NMR parameters were carried out using plane-wave basis sets and periodic boundary conditions (CASTEP), and the results were compared with the experimental data. A good agreement between the calculated shielding constants and experimental chemical shifts was obtained. This demonstrates the good potential of computational methods in spectroscopic assignments of solid-state 45 Sc NMR spectroscopy.

There is Diversity in Disorder-"In all Chaos there is a Cosmos, in all Disorder a Secret Order".

PubMed

Nielsen, Jakob T; Mulder, Frans A A

2016-01-01

The protein universe consists of a continuum of structures ranging from full order to complete disorder. As the structured part of the proteome has been intensively studied, stably folded proteins are increasingly well documented and understood. However, proteins that are fully, or in large part, disordered are much less well characterized. Here we collected NMR chemical shifts in a small database for 117 protein sequences that are known to contain disorder. We demonstrate that NMR chemical shift data can be brought to bear as an exquisite judge of protein disorder at the residue level, and help in validation. With the help of secondary chemical shift analysis we demonstrate that the proteins in the database span the full spectrum of disorder, but still, largely segregate into two classes; disordered with small segments of order scattered along the sequence, and structured with small segments of disorder inserted between the different structured regions. A detailed analysis reveals that the distribution of order/disorder along the sequence shows a complex and asymmetric distribution, that is highly protein-dependent. Access to ratified training data further suggests an avenue to improving prediction of disorder from sequence.

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

PubMed Central

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

2009-01-01

The authors investigated the performance of the iterative Steiglitz–McBride (SM) algorithm on an autoregressive moving average (ARMA) model of signals from a fast, sparsely sampled, multiecho, chemical shift imaging (CSI) acquisition using simulation, phantom, ex vivo, and in vivo experiments with a focus on its potential usage in magnetic resonance (MR)-guided interventions. The ARMA signal model facilitated a rapid calculation of the chemical shift, apparent spin-spin relaxation time (T2*), and complex amplitudes of a multipeak system from a limited number of echoes (≤16). Numerical simulations of one- and two-peak systems were used to assess the accuracy and uncertainty in the calculated spectral parameters as a function of acquisition and tissue parameters. The measured uncertainties from simulation were compared to the theoretical Cramer–Rao lower bound (CRLB) for the acquisition. Measurements made in phantoms were used to validate the T2* estimates and to validate uncertainty estimates made from the CRLB. We demonstrated application to real-time MR-guided interventions ex vivo by using the technique to monitor a percutaneous ethanol injection into a bovine liver and in vivo to monitor a laser-induced thermal therapy treatment in a canine brain. Simulation results showed that the chemical shift and amplitude uncertainties reached their respective CRLB at a signal-to-noise ratio (SNR)≥5 for echo train lengths (ETLs)≥4 using a fixed echo spacing of 3.3 ms. T2* estimates from the signal model possessed higher uncertainties but reached the CRLB at larger SNRs and∕or ETLs. Highly accurate estimates for the chemical shift (<0.01 ppm) and amplitude (<1.0%) were obtained with ≥4 echoes and for T2* (<1.0%) with ≥7 echoes. We conclude that, over a reasonable range of SNR, the SM algorithm is a robust estimator of spectral parameters from fast CSI acquisitions that acquire ≤16 echoes for one- and two-peak systems. Preliminary ex vivo and in vivo experiments corroborated the results from simulation experiments and further indicate the potential of this technique for MR-guided interventional procedures with high spatiotemporal resolution ∼1.6×1.6×4 mm3 in ≤5 s. PMID:19378736

Elucidating Adverse Nutritional Implications of Exposure to Endocrine-Disrupting Chemicals and Mycotoxins through Stable Isotope Techniques.

PubMed

Owino, Victor O; Cornelius, Carolin; Loechl, Cornelia U

2018-03-23

Multiple drivers of the double burden of malnutrition (DBM) include a rapid shift from predominantly plant-based diets to energy-dense foods based on meats, milk, animal fats and vegetable oils. The shift to overweight and obesity is driven by increased exposure to mass media, urbanization, technological advances in food processing, rising income and increased population density associated with increased access to cheap foods. At the same time, undernutrition persists mainly due to food insecurity and lack of access to safe water, sanitation and adequate health care. All known nutrition interventions result in only one third reduction in stunting. Little consideration has been given to hazardous exposure to endocrine disrupting chemicals (EDCs) and microbial toxins as major components of the malnutrition-causal framework. These hazards include microbial toxins, for example, mycotoxins, and environmental pollutants such as persistent organic pollutants (POPs), some of which are known to disrupt the endocrine system. These hazards sit at the cross road of undernutrition and overweight and obesity since the exposure cuts across the critical window of opportunity (the first 1000 days). In this review, we update on the role of food and environmental contaminants, especially EDCs and aflatoxins, in child growth and on the implications for metabolic dysfunction and disease risk in later life, and discuss potential applications of nuclear and isotopic techniques to elucidate the underlying biological mechanisms, outcome indicators, as well as occurrence levels.

Silicon nano-membrane based photonic crystal microcavities for high sensitivity bio-sensing.

PubMed

Lai, Wei-Cheng; Chakravarty, Swapnajit; Zou, Yi; Chen, Ray T

2012-04-01

We experimentally demonstrated photonic crystal microcavity based resonant sensors coupled to photonic crystal waveguides in silicon nano-membrane on insulator for chemical and bio-sensing. Linear L-type microcavities are considered. In contrast to cavities with small mode volumes, but low quality factors for bio-sensing, we showed increasing the length of the microcavity enhances the quality factor of the resonance by an order of magnitude and increases the resonance wavelength shift while retaining compact device characteristics. Q~26760 and sensitivity down to 15 ng/ml and ~110 pg/mm2 in bio-sensing was experimentally demonstrated on silicon-on-insulator devices.