Counterion influence on chemical shifts in strychnine salts

Energy Technology Data Exchange (ETDEWEB)

Metaxas, Athena E.; Cort, John R.

2013-05-01

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

A probabilistic approach for validating protein NMR chemical shift assignments

International Nuclear Information System (INIS)

Wang Bowei; Wang, Yunjun; Wishart, David S.

2010-01-01

It has been estimated that more than 20% of the proteins in the BMRB are improperly referenced and that about 1% of all chemical shift assignments are mis-assigned. These statistics also reflect the likelihood that any newly assigned protein will have shift assignment or shift referencing errors. The relatively high frequency of these errors continues to be a concern for the biomolecular NMR community. While several programs do exist to detect and/or correct chemical shift mis-referencing or chemical shift mis-assignments, most can only do one, or the other. The one program (SHIFTCOR) that is capable of handling both chemical shift mis-referencing and mis-assignments, requires the 3D structure coordinates of the target protein. Given that chemical shift mis-assignments and chemical shift re-referencing issues should ideally be addressed prior to 3D structure determination, there is a clear need to develop a structure-independent approach. Here, we present a new structure-independent protocol, which is based on using residue-specific and secondary structure-specific chemical shift distributions calculated over small (3-6 residue) fragments to identify mis-assigned resonances. The method is also able to identify and re-reference mis-referenced chemical shift assignments. Comparisons against existing re-referencing or mis-assignment detection programs show that the method is as good or superior to existing approaches. The protocol described here has been implemented into a freely available Java program called 'Probabilistic Approach for protein Nmr Assignment Validation (PANAV)' and as a web server (http://redpoll.pharmacy.ualberta.ca/PANAVhttp://redpoll.pharmacy.ualberta.ca/PANAV) which can be used to validate and/or correct as well as re-reference assigned protein chemical shifts.

Rapid and reliable protein structure determination via chemical shift threading.

Science.gov (United States)

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

2018-01-01

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

What can we learn by computing 13Cα chemical shifts for X-ray protein models?

International Nuclear Information System (INIS)

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

2009-01-01

The room-temperature X-ray structures of two proteins, solved at 1.8 and 1.9 Å resolution, are used to investigate whether a set of conformations, rather than a single X-ray structure, provides better agreement with both the X-ray data and the observed 13 C α chemical shifts in solution. The room-temperature X-ray structures of ubiquitin and of the RNA-binding domain of nonstructural protein 1 of influenza A virus solved at 1.8 and 1.9 Å resolution, respectively, were used to investigate whether a set of conformations rather than a single X-ray structure provides better agreement with both the X-ray data and the observed 13 C α chemical shifts in solution. For this purpose, a set of new conformations for each of these proteins was generated by fitting them to the experimental X-ray data deposited in the PDB. For each of the generated structures, which show R and R free factors similar to those of the deposited X-ray structure, the 13 C α chemical shifts of all residues in the sequence were computed at the DFT level of theory. The sets of conformations were then evaluated by their ability to reproduce the observed 13 C α chemical shifts by using the conformational average root-mean-square-deviation (ca-r.m.s.d.). For ubiquitin, the computed set of conformations is a better representation of the observed 13 C α chemical shifts in terms of the ca-r.m.s.d. than a single X-ray-derived structure. However, for the RNA-binding domain of nonstructural protein 1 of influenza A virus, consideration of an ensemble of conformations does not improve the agreement with the observed 13 C α chemical shifts. Whether an ensemble of conformations rather than any single structure is a more accurate representation of a protein structure in the crystal as well as of the observed 13 C α chemical shifts is determined by the dispersion of coordinates, in terms of the all-atom r.m.s.d. among the generated models; these generated models satisfy the experimental X-ray data with

Chemical dispersibility testing of fresh and weathered oils

International Nuclear Information System (INIS)

Brandvik, P.J.; Daling, P.S.; Aareskjold, K.

1991-05-01

This activity in the DIspersants on Weathered Oils-project (DIWO) is a continuation and an extended study of the dispersibility study described in DIWO report No. 3. The main objective has been to study the chemical dispersibility of fresh and weathered oils produced or transported in Norwegian waters. Other important aims of this study have been: To correlate the effectiveness results obtained by three different laboratory methods; to determine the relationship between the dispersant effectiveness and the change in the oils' physico-chemical properties due to weathering (topping, photo-oxidation and w/o-emulsification). This study has been performed with 8 different oil types and 12 different weathering degrees of each oil type. The work performed clearly demonstrates that the oil type and especially the weathering properties are essential for the performance of dispersants at sea. 41 figs., 5 tabs., 16 refs

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

International Nuclear Information System (INIS)

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

2013-01-01

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

The Theory of Thermodynamics for Chemical Reactions in Dispersed Heterogeneous Systems

Science.gov (United States)

Yongqiang; Baojiao; Jianfeng

1997-07-01

In this paper, the expressions of Gibbs energy change, enthalpy change, entropy change, and equilibrium constant for chemical reactions in dispersed heterogeneous systems are derived using classical thermodynamics theory. The thermodynamical relations for the same reaction system between the dispersed and the block state are also derived. The effects of degree of dispersion on thermodynamical properties, reaction directions, and chemical equilibria are discussed. The results show that the present equation of thermodynamics for chemical reactions is only a special case of the above-mentioned formulas and that the effect of the dispersity of a heterogeneous system on the chemical reaction obeys the Le Chatelier principle of movement of equilibria.

Chemical countermeasures: Dispersants overview of dispersant use (including application) and research issues

International Nuclear Information System (INIS)

Butler, J.N.

1992-01-01

I will attempt in twenty minutes to summarize the state of research on oil spill dispersants as I perceive it. The expertise I bring to this task includes 20 years of experience with the fate and effects of petroleum in the marine environment, including participation in the 1973 and 1981 NRC studies and three years as chairman of the NRC committee on oil spill dispersants. I More recently I served on a committee of the International Maritime Organization which reviewed the open-quotes Impact of oil and related chemicals and wastes on the marine environment.close quotes That report will be published this year. However, my statements in this paper are not made as a representative of either NRC or IMO. They are my own interpretation of scientific literature cited in the above reviews. Dispersants are chemical formulations, which include surface active agents, designed to decrease the interfacial tension between oil and water. Because the first attempts to disperse oil on a large scale, at the Torrey Canyon spill of 1967, used highly toxic degreasing agents, dispersants have an undeserved reputation for toxicity. In fact, for twenty years dispersant formulations have been developed with an emphasis on reducing their toxicity to marine life. The dispersal of oil in water has been documented in the laboratory by dozens of papers (see references in NRC 1989, pp 70-79), and in the field by dozens of studies (NRC 1989, pp 165- 193). The toxicity of commercial dispersant formulations (NRC 1989, pp 81-123) and dispersed oil (NRC 1989, pp 123-147) has been tested on a wide variety of marine organisms ranging from algae to salmonid fishes. The NRC review has been updated by the IMO/GESAMP (1992) study, but the conclusions remain unchanged

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

Energy Technology Data Exchange (ETDEWEB)

Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.; Hong Mei, E-mail: mhong@iastate.edu [Iowa State University, Department of Chemistry (United States)

2013-06-15

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

Empirical correlation between protein backbone {sup 15}N and {sup 13}C secondary chemical shifts and its application to nitrogen chemical shift re-referencing

Energy Technology Data Exchange (ETDEWEB)

Wang Liya [Cold Spring Harbor Laboratory (United States); Markley, John L. [University of Wisconsin, Biochemistry Department (United States)], E-mail: markley@nmrfam.wisc.edu

2009-06-15

The linear analysis of chemical shifts (LACS) has provided a robust method for identifying and correcting {sup 13}C chemical shift referencing problems in data from protein NMR spectroscopy. Unlike other approaches, LACS does not require prior knowledge of the three-dimensional structure or inference of the secondary structure of the protein. It also does not require extensive assignment of the NMR data. We report here a way of extending the LACS approach to {sup 15}N NMR data from proteins, so as to enable the detection and correction of inconsistencies in chemical shift referencing for this nucleus. The approach is based on our finding that the secondary {sup 15}N chemical shift of the backbone nitrogen atom of residue i is strongly correlated with the secondary chemical shift difference (experimental minus random coil) between the alpha and beta carbons of residue i - 1. Thus once alpha and beta {sup 13}C chemical shifts are available (their difference is referencing error-free), the {sup 15}N referencing can be validated, and an appropriate offset correction can be derived. This approach can be implemented prior to a structure determination and can be used to analyze potential referencing problems in database data not associated with three-dimensional structure. Application of the LACS algorithm to the current BMRB protein chemical shift database, revealed that nearly 35% of the BMRB entries have {delta}{sup 15}N values mis-referenced by over 0.7 ppm and over 25% of them have {delta}{sup 1}H{sup N} values mis-referenced by over 0.12 ppm. One implication of the findings reported here is that a backbone {sup 15}N chemical shift provides a better indicator of the conformation of the preceding residue than of the residue itself.

Unraveling the meaning of chemical shifts in protein NMR.

Science.gov (United States)

Berjanskii, Mark V; Wishart, David S

2017-11-01

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

Evaluating amber force fields using computed NMR chemical shifts.

Science.gov (United States)

Koes, David R; Vries, John K

2017-10-01

NMR chemical shifts can be computed from molecular dynamics (MD) simulations using a template matching approach and a library of conformers containing chemical shifts generated from ab initio quantum calculations. This approach has potential utility for evaluating the force fields that underlie these simulations. Imperfections in force fields generate flawed atomic coordinates. Chemical shifts obtained from flawed coordinates have errors that can be traced back to these imperfections. We use this approach to evaluate a series of AMBER force fields that have been refined over the course of two decades (ff94, ff96, ff99SB, ff14SB, ff14ipq, and ff15ipq). For each force field a series of MD simulations are carried out for eight model proteins. The calculated chemical shifts for the 1 H, 15 N, and 13 C a atoms are compared with experimental values. Initial evaluations are based on root mean squared (RMS) errors at the protein level. These results are further refined based on secondary structure and the types of atoms involved in nonbonded interactions. The best chemical shift for identifying force field differences is the shift associated with peptide protons. Examination of the model proteins on a residue by residue basis reveals that force field performance is highly dependent on residue position. Examination of the time course of nonbonded interactions at these sites provides explanations for chemical shift differences at the atomic coordinate level. Results show that the newer ff14ipq and ff15ipq force fields developed with the implicitly polarized charge method perform better than the older force fields. © 2017 Wiley Periodicals, Inc.

Effects of chemical dispersants on oil-brine interfacial tension and droplet formation

International Nuclear Information System (INIS)

Khelifa, A.; So, L.L.C.

2009-01-01

The dispersion of oil spilled in water is influenced by chemical dispersants via the modification of the interfacial properties of the oil, such as oil-brine interfacial tension (IFT). In this study, the physical properties and dispersion of oil were measured in order to determine the effects of chemical dispersants on IFT and oil viscosity and the effects on oil droplet formation. In theory, the maximum size of oil droplet that forms under turbulent mixing increases with IFT. Therefore, a reduction in IFT reduces the size distribution of oil droplets. This paper presented the results of an ongoing project aimed at providing quantitative understanding the influence that chemical dispersants have on the size distribution of oil droplets and oil dispersion. Findings showed that a valid approach is to separate the direct effects of chemical dispersants on oil properties, specifically oil-brine IFT and the effects of mixing on dispersion of chemically treated oil. Under constant mixing conditions, the reduction of the maximum oil droplet size that overcomes the breakage process is determined by the effects of chemical dispersant on oil properties. This correlates well with the dispersant-to-oil ratio (DOR) up to the critical micelle concentration (CMC). This good agreement can be attributed to the reduction of IFT with DOR. It was concluded that the reduction of IFT with dispersant concentration is an additional signature of oil composition on droplet formation, while mixing energy is an external parameter that is independent of oil properties. 17 refs., 3 tabs., 9 figs

Relative Configuration of Natural Products Using NMR Chemical Shifts

Science.gov (United States)

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...

PETROLEUM-COLLECTING AND DISPERSING CHEMICALS FOR ...

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Films of petroleum origin reflecting sunlight rays hinder absorption of energy by water necessary for life ... Dispersing chemicals like mechanical clean-up methods have their own place in fighting oil spills. They are ... yellow color, and filtered.

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

Energy Technology Data Exchange (ETDEWEB)

Ginzinger, Simon W. [Center of Applied Molecular Engineering, University of Salzburg, Department of Molecular Biology, Division of Bioinformatics (Austria)], E-mail: simon@came.sbg.ac.at; Coles, Murray [Max-Planck-Institute for Developmental Biology, Department of Protein Evolution (Germany)], E-mail: Murray.Coles@tuebingen.mpg.de

2009-03-15

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

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

International Nuclear Information System (INIS)

Ginzinger, Simon W.; Coles, Murray

2009-01-01

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

Role of quantitative chemical shift magnetic resonance imaging and chemical shift subtraction technique in discriminating adenomatous from non adenomatous adrenal solid lesions

Directory of Open Access Journals (Sweden)

Ahmed H. Afifi

2017-03-01

Conclusion: The signal intensity index and adrenal to spleen ratio are the most reliable quantitative chemical shift MRI methods in differentiation of adrenal adenomas from other non-adenomatous adrenal solid lesions. Chemical shift subtraction MRI is a recent technique that gives highly confident discrimination between two categories of pathology without using of any reference organ.

PPM-One: a static protein structure based chemical shift predictor

International Nuclear Information System (INIS)

Li, Dawei; Brüschweiler, Rafael

2015-01-01

We mined the most recent editions of the BioMagResDataBank and the protein data bank to parametrize a new empirical knowledge-based chemical shift predictor of protein backbone atoms using either a linear or an artificial neural network model. The resulting chemical shift predictor PPM-One accepts a single static 3D structure as input and emulates the effect of local protein dynamics via interatomic steric contacts. Furthermore, the chemical shift prediction was extended to most side-chain protons and it is found that the prediction accuracy is at a level allowing an independent assessment of stereospecific assignments. For a previously established set of test proteins some overall improvement was achieved over current top-performing chemical shift prediction programs

A robust algorithm for optimizing protein structures with NMR chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Berjanskii, Mark; Arndt, David; Liang, Yongjie; Wishart, David S., E-mail: david.wishart@ualberta.ca [University of Alberta, Department of Computing Science (Canada)

2015-11-15

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

The PROSECCO server for chemical shift predictions in ordered and disordered proteins.

Science.gov (United States)

Sanz-Hernández, Máximo; De Simone, Alfonso

2017-11-01

The chemical shifts measured in solution-state and solid-state nuclear magnetic resonance (NMR) are powerful probes of the structure and dynamics of protein molecules. The exploitation of chemical shifts requires methods to correlate these data with the protein structures and sequences. We present here an approach to calculate accurate chemical shifts in both ordered and disordered proteins using exclusively the information contained in their sequences. Our sequence-based approach, protein sequences and chemical shift correlations (PROSECCO), achieves the accuracy of the most advanced structure-based methods in the characterization of chemical shifts of folded proteins and improves the state of the art in the study of disordered proteins. Our analyses revealed fundamental insights on the structural information carried by NMR chemical shifts of structured and unstructured protein states.

Chemical shift of U L3 edges in different uranium compounds obtained by X-ray absorption spectroscopy with synchrotron radiation

International Nuclear Information System (INIS)

Joseph, D.; Jha, S.N.; Nayak, C.; Bhattacharyya, D.; Babu, P. Venu

2014-01-01

Uranium L 3 X-ray absorption edge was measured in various compounds containing uranium in U 4+ , U 5+ and U 5+ oxidation states. The measurements have been carried out at the Energy Dispersive EXAFS beamline (BL-08) at INDUS-2 synchrotron radiation source at RRCAT, Indore. Energy shifts of ∼ 2-3 eV were observed for U L 3 edge in the U-compounds compared to their value in elemental U. The different chemical shifts observed for the compounds having the same oxidation state of the cation but different anions or ligands show the effect of different chemical environments surrounding the cations in determining their X-ray absorption edges in the above compounds. The above chemical effect has been quantitatively described by determining the effective charges on U cation in the above compounds. (author)

Evaluating Chemical Dispersant Efficacy In An Experimental Wave Tank: 1, Dispersant Effectiveness As A Function Of Energy Dissipation Rate

Science.gov (United States)

Numerous laboratory test systems have been developed for the comparison of efficacy between various chemical oil dispersant formulations. However, for the assessment of chemical dispersant effectiveness under realistic sea state, test protocols are required to produce hydrodynam...

Chemical Shift Imaging (CSI) by precise object displacement

OpenAIRE

Leclerc, Sebastien; Trausch, Gregory; Cordier, Benoit; Grandclaude, Denis; Retournard, Alain; Fraissard, Jacques; Canet, Daniel

2006-01-01

International audience; A mechanical device (NMR lift) has been built for displacing vertically an object (typically a NMR sample tube) inside the NMR probe with an accuracy of 1 Μm. A series of single pulse experiments are performed for incremented vertical positions of the sample. With a sufficiently spatially selective rf field, one obtains chemical shift information along the displacement direction (one dimensional Chemical Shift Imaging – CSI). Knowing the vertical radio-frequency (rf) f...

Chemical shifts of oxygen-17 NMR in polyoxotungstates

International Nuclear Information System (INIS)

Kazanskij, L.P.; Fedotov, M.A.; Spitsyn, V.I.

1977-01-01

17 O NMR spectra of aqueous solutions containing paratungstate BH 2 W 12 O 42 10- and metatungstate H 2 W 12 O 40 6- anions have been measured. On the basis of the obtained data a scale of chemical shifts for oxygen atoms connected by various bonds with tungsten atoms is suggested. The obtained data are compared with the Raman spectra of crystalline salts and their aqueous solutions. Chemical shifts of 17 O NMR spectra have been also measured in other heteropolyanions

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

Energy Technology Data Exchange (ETDEWEB)

Karp, Jerome M.; Erylimaz, Ertan; Cowburn, David, E-mail: cowburn@cowburnlab.org, E-mail: David.cowburn@einstein.yu.edu [Albert Einstein College of Medicine of Yeshiva University, Department of Biochemistry (United States)

2015-01-15

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.

Widely tunable dispersive wave generation and soliton self-frequency shift in a tellurite microstructured optical fiber pumped near the zero dispersion wavelength

International Nuclear Information System (INIS)

Zhang, Lei; Tuan, Tong-Hoang; Liu, Lai; Gao, Wei-Qing; Kawamura, Harutaka; Suzuki, Takenobu; Ohishi, Yasutake

2015-01-01

Widely tunable dispersive waves (DW) and Raman solitons are generated in a tellurite microstructured optical fiber (TMOF) by pumping in the anomalous dispersion regime, close to the zero dispersion wavelength (ZDW). The DW can be generated from 1518.3 nm to 1315.5 nm, and the soliton can be shifted from the pump wavelength of 1570 nm to 1828.7 nm, by tuning the average pump power from 3 dBm to 17.5 dBm. After the average pump power is increased to 18.8 dBm, two DW peaks (centered at 1323 nm and 1260 nm) and three soliton peaks (centered at 1762 nm, 1825 nm, and 1896 nm) can be observed simultaneously. When the average pump power is greater than 23.4 dBm, a flat and broadband supercontinuum (SC) can be formed by the combined nonlinear effects of soliton self-frequency shift (SSFS), DW generation, and cross phase modulation (XPM). (paper)

Nucleic acid helix structure determination from NMR proton chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Werf, Ramon M. van der; Tessari, Marco; Wijmenga, Sybren S., E-mail: S.Wijmenga@science.ru.nl [Radboud University Nijmegen, Department of Biophysical Chemistry, Institute of Molecules and Materials (Netherlands)

2013-06-15

We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called chemical shift de novo structure derivation protocol employing singular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids.

Accessible surface area from NMR chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Hafsa, Noor E.; Arndt, David; Wishart, David S., E-mail: david.wishart@ualberta.ca [University of Alberta, Department of Computing Science (Canada)

2015-07-15

Accessible surface area (ASA) is the surface area of an atom, amino acid or biomolecule that is exposed to solvent. The calculation of a molecule’s ASA requires three-dimensional coordinate data and the use of a “rolling ball” algorithm to both define and calculate the ASA. For polymers such as proteins, the ASA for individual amino acids is closely related to the hydrophobicity of the amino acid as well as its local secondary and tertiary structure. For proteins, ASA is a structural descriptor that can often be as informative as secondary structure. Consequently there has been considerable effort over the past two decades to try to predict ASA from protein sequence data and to use ASA information (derived from chemical modification studies) as a structure constraint. Recently it has become evident that protein chemical shifts are also sensitive to ASA. Given the potential utility of ASA estimates as structural constraints for NMR we decided to explore this relationship further. Using machine learning techniques (specifically a boosted tree regression model) we developed an algorithm called “ShiftASA” that combines chemical-shift and sequence derived features to accurately estimate per-residue fractional ASA values of water-soluble proteins. This method showed a correlation coefficient between predicted and experimental values of 0.79 when evaluated on a set of 65 independent test proteins, which was an 8.2 % improvement over the next best performing (sequence-only) method. On a separate test set of 92 proteins, ShiftASA reported a mean correlation coefficient of 0.82, which was 12.3 % better than the next best performing method. ShiftASA is available as a web server ( http://shiftasa.wishartlab.com http://shiftasa.wishartlab.com ) for submitting input queries for fractional ASA calculation.

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

Science.gov (United States)

Kumari, Amrita; Dorai, Kavita

2013-06-01

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

Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Shen Yang; Bax, Ad, E-mail: bax@nih.go [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Laboratory of Chemical Physics (United States)

2010-03-15

We present a program, named Promega, to predict the Xaa-Pro peptide bond conformation on the basis of backbone chemical shifts and the amino acid sequence. Using a chemical shift database of proteins of known structure together with the PDB-extracted amino acid preference of cis Xaa-Pro peptide bonds, a cis/trans probability score is calculated from the backbone and {sup 13}C{sup {beta}} chemical shifts of the proline and its neighboring residues. For an arbitrary number of input chemical shifts, which may include Pro-{sup 13}C{sup {gamma}}, Promega calculates the statistical probability that a Xaa-Pro peptide bond is cis. Besides its potential as a validation tool, Promega is particularly useful for studies of larger proteins where Pro-{sup 13}C{sup {gamma}} assignments can be challenging, and for on-going efforts to determine protein structures exclusively on the basis of backbone and {sup 13}C{sup {beta}} chemical shifts.

Protein Structure Determination Using Chemical Shifts

DEFF Research Database (Denmark)

Christensen, Anders Steen

is determined using only chemical shifts recorded and assigned through automated processes. The CARMSD to the experimental X-ray for this structure is 1.1. Å. Additionally, the method is combined with very sparse NOE-restraints and evolutionary distance restraints and tested on several protein structures >100...

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

Energy Technology Data Exchange (ETDEWEB)

Harris, R.K. [University of Durham, Durham (United Kingdom). Dept. of Chemistry; Becker, E.D. [National Institutes of Health, Bethesda, MD (United States); Menezes, S.M. Cabral de [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas (CENPES); Granger, P. [University Louis Pasteur, Strasbourg (France). Inst. of Chemistry; Hoffman, R.E. [The Hebrew University of Jerusalem, Safra Campus, Jerusalem (Israel). Dept. of Organic Chemistry; Zilm, K.W., E-mail: r.k.harris@durham.ac.uk [Yale University, New Haven, CT (United States). Dept. of Chemistry

2008-07-01

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 {sup 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 {sup 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. (author)

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

International Nuclear Information System (INIS)

Harris, R.K.; Menezes, S.M. Cabral de; Granger, P.; Hoffman, R.E.; Zilm, K.W.

2008-01-01

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. (author)

Histidine side-chain dynamics and protonation monitored by C-13 CPMG NMR relaxation dispersion

DEFF Research Database (Denmark)

Hass, M. A. S.; Yilmaz, A.; Christensen, Hans Erik Mølager

2009-01-01

the chemical shift titration experiments, and the CPMG derived exchange rates agree with those obtained previously from N-15 backbone relaxation measurements. Compared to measurements of backbone nuclei, C-13(epsilon 1) dispersion provides a more direct method to monitor interchanging protonation states...... or other kinds of conformational changes of histidine side chains or their environment. Advantages and shortcomings of using the C-13(epsilon 1) dispersion experiments in combination with chemical shift titration experiments to obtain information on exchange dynamics of the histidine side chains...

The direct measurement of the heteronuclear chemical shifts relative to tetramethylsilane

International Nuclear Information System (INIS)

Moritz, A.G.

1988-12-01

The measurement of heteronuclear chemical shifts using absolute frequencies of the heteronucleus and the 1 H resonance of tetramethylsilane has been examined. This method avoids the problems associated with external standards and gives results which can be obtained quickly and with high precision. The method has a number of advantages in the accurate measurement of chemical shifts, as for example 31 P in chemical warfare agents and related chemicals and allows multinuclear data to be obtained without dynamic range or potential interference problems. 15 refs., 4 tabs

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

International Nuclear Information System (INIS)

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

2002-01-01

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

Chemical oil-spill dispersants: evaluation of three laboratory procedures for estimating performance

International Nuclear Information System (INIS)

Clayton, J.R.; Marsden, P.

1992-09-01

The report presents data from studies designed to evaluate characteristics of selected bench-scale test methods for estimating performance of chemical agents for dispersing oil from surface slicks into an underlying water column. In order to mitigate the effect of surface slicks with chemical dispersant agents, however, an on-scene coordinator must have information and an understanding of performance characteristics for available dispersant agents. Performance of candidate dispersant agents can be estimated on the basis of laboratory testing procedures that are designed to evaluate performance of different agents. Data presented in the report assist in the evaluation of candidate test methods for estimating performance of candidate dispersant agents. Three test methods were selected for evaluating performance: the currently accepted Revised Standard EPA test, Environmental Canada's Swirling Flask test, and the IFP-Dilution test

Temperature dependence of 1H NMR chemical shifts and its influence on estimated metabolite concentrations.

Science.gov (United States)

Wermter, Felizitas C; Mitschke, Nico; Bock, Christian; Dreher, Wolfgang

2017-12-01

Temperature dependent chemical shifts of important brain metabolites measured by localised 1 H MRS were investigated to test how the use of incorrect prior knowledge on chemical shifts impairs the quantification of metabolite concentrations. Phantom measurements on solutions containing 11 metabolites were performed on a 7 T scanner between 1 and 43 °C. The temperature dependence of the chemical shift differences was fitted by a linear model. Spectra were simulated for different temperatures and analysed by the AQSES program (jMRUI 5.2) using model functions with chemical shift values for 37 °C. Large differences in the temperature dependence of the chemical shift differences were determined with a maximum slope of about ±7.5 × 10 -4  ppm/K. For 32-40 °C, only minor quantification errors resulted from using incorrect chemical shifts, with the exception of Cr and PCr. For 1-10 °C considerable quantification errors occurred if the temperature dependence of the chemical shifts was neglected. If 1 H MRS measurements are not performed at 37 °C, for which the published chemical shift values have been determined, the temperature dependence of chemical shifts should be considered to avoid systematic quantification errors, particularly for measurements on animal models at lower temperatures.

Theoretical Study of the NMR Chemical Shift of Xe in Supercritical Condition

DEFF Research Database (Denmark)

Lacerda Junior, Evanildo Gomes; Sauer, Stephan P. A.; Mikkelsen, Kurt Valentin

2018-01-01

In this work we investigate the level of theory necessary for reproducing the non-linear variation of the 129Xe nuclear magnetic resonance (NMR) chemical shift with the density of Xe in supercritical conditions. In detail we study how the 129Xe chemical shift depends under these 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 Xen...... this approach we obtain very good agreement with the experimental data, showing that the chemical shift of 129Xe in supercritical conditions is very well described by cluster calculations at the HF level, with small contributions from relativistic and electron correlation effects....

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

Science.gov (United States)

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

2005-05-01

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

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

International Nuclear Information System (INIS)

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

2015-01-01

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), 1 H MAS NMR spectra of rigid solids still suffer from poor resolution and severe peak overlap caused by the strong 1 H– 1 H homonuclear dipolar couplings and narrow 1 H chemical shift (CS) ranges, which render it difficult to determine the CSA of specific proton sites in the standard CSA/single-quantum (SQ) chemical shift correlation experiment. Herein, we propose a three-dimensional (3D) 1 H double-quantum (DQ) chemical shift/CSA/SQ chemical shift correlation experiment to extract the CS tensors of proton sites whose signals are not well resolved along the single-quantum chemical shift dimension. As extracted from the 3D spectrum, the F1/F3 (DQ/SQ) projection provides valuable information about 1 H– 1 H proximities, which might also reveal the hydrogen-bonding connectivities. In addition, the F2/F3 (CSA/SQ) correlation spectrum, which is similar to the regular 2D CSA/SQ correlation experiment, yields chemical shift anisotropic line shapes at different isotropic chemical shifts. More importantly, since the F2/F1 (CSA/DQ) spectrum correlates the CSA with the DQ signal induced by two neighboring proton sites, the CSA spectrum sliced at a specific DQ chemical shift position contains the CSA information of two neighboring spins indicated by the DQ chemical shift. If these two spins have different CS tensors, both tensors can be extracted by numerical fitting. We believe that this robust and elegant single-channel proton-based 3D experiment provides useful atomistic-level structural and dynamical

Resolution of NMR chemical shift images into real and imaginary components

International Nuclear Information System (INIS)

Yamamoto, E.; Kohno, H.

1986-01-01

Fast chemical shift imaging of two-line materials is described using a modified spin-echo sequence. The method resolves the two chemical shift images into real and imaginary components representing the reconstructed image. The measuring time is reduced to half of that for the conventional method proposed by Dixon et al, and quantitative evaluation of the images becomes possible. Reference material with a single resonant line is used to eliminate the phase error caused by static field inhomogeneity and the inherent apparatus offset phase. Experiments are conducted using acetone and benzene with a medium-bore superconductive magnet operating at 0.5T. From these experiments, two chemical shift images are obtained. These images are then superimposed to produce a conventional density image. (author)

Random coil chemical shifts in acidic 8 M urea: Implementation of random coil shift data in NMRView

International Nuclear Information System (INIS)

Schwarzinger, Stephan; Kroon, Gerard J.A.; Foss, Ted R.; Wright, Peter E.; Dyson, H. Jane

2000-01-01

Studies of proteins unfolded in acid or chemical denaturant can help in unraveling events during the earliest phases of protein folding. In order for meaningful comparisons to be made of residual structure in unfolded states, it is necessary to use random coil chemical shifts that are valid for the experimental system under study. We present a set of random coil chemical shifts obtained for model peptides under experimental conditions used in studies of denatured proteins. This new set, together with previously published data sets, has been incorporated into a software interface for NMRView, allowing selection of the random coil data set that fits the experimental conditions best

Prediction of proton chemical shifts in RNA - Their use in structure refinement and validation

International Nuclear Information System (INIS)

Cromsigt, Jenny A.M.T.C.; Hilbers, Cees W.; Wijmenga, Sybren S.

2001-01-01

An analysis is presented of experimental versus calculated chemical shifts of the non-exchangeable protons for 28 RNA structures deposited in the Protein Data Bank, covering a wide range of structural building blocks. We have used existing models for ring-current and magnetic-anisotropy contributions to calculate the proton chemical shifts from the structures. Two different parameter sets were tried: (i) parameters derived by Ribas-Prado and Giessner-Prettre (GP set) [(1981) J. Mol. Struct.,76, 81-92.]; (ii) parameters derived by Case [(1995) J. Biomol. NMR, 6, 341-346]. Both sets lead to similar results. The detailed analysis was carried using the GP set. The root-mean-square-deviation between the predicted and observed chemical shifts of the complete database is 0.16 ppm with a Pearson correlation coefficient of 0.79. For protons in the usually well-defined A-helix environment these numbers are, 0.08 ppm and 0.96, respectively. As a result of this good correspondence, a reliable analysis could be made of the structural dependencies of the 1 H chemical shifts revealing their physical origin. For example, a down-field shift of either H2' or H3' or both indicates a high-syn/syn χ-angle. In an A-helix it is essentially the 5'-neighbor that affects the chemical shifts of H5, H6 and H8 protons. The H5, H6 and H8 resonances can therefore be assigned in an A-helix on the basis of their observed chemical shifts. In general, the chemical shifts were found to be quite sensitive to structural changes. We therefore propose that a comparison between calculated and observed 1 H chemical shifts is a good tool for validation and refinement of structures derived from NOEs and J-couplings

A procedure to validate and correct the {sup 13}C chemical shift calibration of RNA datasets

Energy Technology Data Exchange (ETDEWEB)

Aeschbacher, Thomas; Schubert, Mario, E-mail: schubert@mol.biol.ethz.ch; Allain, Frederic H.-T., E-mail: allain@mol.biol.ethz.ch [ETH Zuerich, Institute for Molecular Biology and Biophysics (Switzerland)

2012-02-15

Chemical shifts reflect the structural environment of a certain nucleus and can be used to extract structural and dynamic information. Proper calibration is indispensable to extract such information from chemical shifts. Whereas a variety of procedures exist to verify the chemical shift calibration for proteins, no such procedure is available for RNAs to date. We present here a procedure to analyze and correct the calibration of {sup 13}C NMR data of RNAs. Our procedure uses five {sup 13}C chemical shifts as a reference, each of them found in a narrow shift range in most datasets deposited in the Biological Magnetic Resonance Bank. In 49 datasets we could evaluate the {sup 13}C calibration and detect errors or inconsistencies in RNA {sup 13}C chemical shifts based on these chemical shift reference values. More than half of the datasets (27 out of those 49) were found to be improperly referenced or contained inconsistencies. This large inconsistency rate possibly explains that no clear structure-{sup 13}C chemical shift relationship has emerged for RNA so far. We were able to recalibrate or correct 17 datasets resulting in 39 usable {sup 13}C datasets. 6 new datasets from our lab were used to verify our method increasing the database to 45 usable datasets. We can now search for structure-chemical shift relationships with this improved list of {sup 13}C chemical shift data. This is demonstrated by a clear relationship between ribose {sup 13}C shifts and the sugar pucker, which can be used to predict a C2 Prime - or C3 Prime -endo conformation of the ribose with high accuracy. The improved quality of the chemical shift data allows statistical analysis with the potential to facilitate assignment procedures, and the extraction of restraints for structure calculations of RNA.

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

Energy Technology Data Exchange (ETDEWEB)

Cornilescu, Gabriel; Delaglio, Frank; Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

1999-03-15

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

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

Science.gov (United States)

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).

Include dispersion in quantum chemical modeling of enzymatic reactions: the case of isoaspartyl dipeptidase.

Science.gov (United States)

Zhang, Hai-Mei; Chen, Shi-Lu

2015-06-09

The lack of dispersion in the B3LYP functional has been proposed to be the main origin of big errors in quantum chemical modeling of a few enzymes and transition metal complexes. In this work, the essential dispersion effects that affect quantum chemical modeling are investigated. With binuclear zinc isoaspartyl dipeptidase (IAD) as an example, dispersion is included in the modeling of enzymatic reactions by two different procedures, i.e., (i) geometry optimizations followed by single-point calculations of dispersion (approach I) and (ii) the inclusion of dispersion throughout geometry optimization and energy evaluation (approach II). Based on a 169-atom chemical model, the calculations show a qualitative consistency between approaches I and II in energetics and most key geometries, demonstrating that both approaches are available with the latter preferential since both geometry and energy are dispersion-corrected in approach II. When a smaller model without Arg233 (147 atoms) was used, an inconsistency was observed, indicating that the missing dispersion interactions are essentially responsible for determining equilibrium geometries. Other technical issues and mechanistic characteristics of IAD are also discussed, in particular with respect to the effects of Arg233.

Relation between chemical shift artifact and infiltration on MR imaging of renal cell carcinoma

International Nuclear Information System (INIS)

Yoshigoe, Fukuo; Makino, Hideki; Yanada, Syuichi; Ohishi, Yukihiko; Mashima, Yasuoki; Yamada, Hideo.

1994-01-01

Retrospective study on the relation between existence of the interruption and disturbance of chemical shift artifact and tumor infiltration at the periphery of the kidney on MR imaging was evaluated in 28 cases with renal cell carcinoma. Judgement was possible in 9 out of the 11 cases with pathological stage below pT2 and 14 cases out of 17 pT3 cases. Judgement was impracticable in 5 cases because the peripheral fat tissue of the kidney was too less to observe chemical shift artifact and the tumor was spreading at the side opposite to the chemical shift artifact. Chemical shift artifact on MRI in this study correlated well with renal tumor infiltration. (author)

Contributions of chemical and diffusive exchange to T1ρ dispersion.

Science.gov (United States)

Cobb, Jared Guthrie; Xie, Jingping; Gore, John C

2013-05-01

Variations in local magnetic susceptibility may induce magnetic field gradients that affect the signals acquired for MR imaging. Under appropriate diffusion conditions, such fields produce effects similar to slow chemical exchange. These effects may also be found in combination with other chemical exchange processes at multiple time scales. We investigate these effects with simulations and measurements to determine their contributions to rotating frame (R1ρ ) relaxation in model systems. Simulations of diffusive and chemical exchange effects on R1ρ dispersion were performed using the Bloch equations. Additionally, R1ρ dispersion was measured in suspensions of Sephadex and latex beads with varying spin locking fields at 9.4 T. A novel analysis method was used to iteratively fit for apparent chemical and diffusive exchange rates with a model by Chopra et al. Single- and double-inflection points in R1ρ dispersion profiles were observed, respectively, in simulations of slow diffusive exchange alone and when combined with rapid chemical exchange. These simulations were consistent with measurements of R1ρ in latex bead suspensions and small-diameter Sephadex beads that showed single- and double-inflection points, respectively. These observations, along with measurements following changes in temperature and pH, are consistent with the combined effects of slow diffusion and rapid -OH exchange processes. Copyright © 2012 Wiley Periodicals, Inc.

Proposal of highly sensitive optofluidic sensors based on dispersive photonic crystal waveguides

DEFF Research Database (Denmark)

Xiao, Sanshui; Mortensen, Niels Asger

2007-01-01

Optofluidic sensors based on highly dispersive two-dimensional photonic crystal waveguides are studied theoretically. Results show that these structures are strongly sensitive to the refractive index of the infiltrated liquid (nl), which is used to tune dispersion of the photonic crystal waveguide....... The waveguide mode-gap edge shifts about 1.2 nm for δnl = 0.002. The shifts can be explained well by band structure theory combined with first-order perturbation theory. These devices are potentially interesting for chemical sensing applications....

Database proton NMR chemical shifts for RNA signal assignment and validation

Energy Technology Data Exchange (ETDEWEB)

Barton, Shawn; Heng Xiao [University of Maryland, Baltimore County, Howard Hughes Medical Institute (United States); Johnson, Bruce A., E-mail: bruce@onemoonscientific.com [University of Maryland, Baltimore County, Department of Chemistry and Biochemistry (United States); Summers, Michael F., E-mail: summers@hhmi.umbc.edu [University of Maryland, Baltimore County, Howard Hughes Medical Institute (United States)

2013-01-15

The Biological Magnetic Resonance Data Bank contains NMR chemical shift depositions for 132 RNAs and RNA-containing complexes. We have analyzed the {sup 1}H NMR chemical shifts reported for non-exchangeable protons of residues that reside within A-form helical regions of these RNAs. The analysis focused on the central base pair within a stretch of three adjacent base pairs (BP triplets), and included both Watson-Crick (WC; G:C, A:U) and G:U wobble pairs. Chemical shift values were included for all 4{sup 3} possible WC-BP triplets, as well as 137 additional triplets that contain one or more G:U wobbles. Sequence-dependent chemical shift correlations were identified, including correlations involving terminating base pairs within the triplets and canonical and non-canonical structures adjacent to the BP triplets (i.e. bulges, loops, WC and non-WC BPs), despite the fact that the NMR data were obtained under different conditions of pH, buffer, ionic strength, and temperature. A computer program (RNAShifts) was developed that enables convenient comparison of RNA {sup 1}H NMR assignments with database predictions, which should facilitate future signal assignment/validation efforts and enable rapid identification of non-canonical RNA structures and RNA-ligand/protein interaction sites.

/sup 1/H-NMR chemical shift imaging suitable for low field systems

Energy Technology Data Exchange (ETDEWEB)

Yamamoto, Etsuji; Onodera, Takashi; Shiono, Hidemi; Kohno, Hideki

1986-12-01

An echo-time encoding proton NMR chemical shift imaging proposed by Dixon is extended to be applicable to low filed systems. The method utilizes the small phase angle between magnetic vectors of water and lipid protons to decrease the signal decays with spin-spin relaxation. The inevitable phase error caused by the static field inhomogeneity is corrected by using phase images of phantom measured under the same conditions as the actual measurements. The experiments were carried out using CuSO/sub 4/ doped water and vegetable oil at 0.5 T. Two chemical shift images could be clearly resolved with only one scan when the field inhomogeneity was larger than the chemical shift difference.

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

Science.gov (United States)

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.

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

DEFF Research Database (Denmark)

Bratholm, Lars Andersen

to within 3 A. Furthermore, a fast quantum mechanics based chemical shift predictor was developed together with methodology for using chemical shifts in structure simulations. The developed predictor was used for renement of several protein structures and for reducing the computational cost of quantum...... mechanics / molecular mechanics (QM/MM) computations of chemical shieldings. Several improvements to the predictor is ongoing, where among other things, kernel based machine learning techniques have successfully been used to improve the quantum mechanical level of theory used in the predictions....

Improving 3D structure prediction from chemical shift data

Energy Technology Data Exchange (ETDEWEB)

Schot, Gijs van der [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Zhang, Zaiyong [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany); Vernon, Robert [University of Washington, Department of Biochemistry (United States); Shen, Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Vranken, Wim F. [VIB, Department of Structural Biology (Belgium); Baker, David [University of Washington, Department of Biochemistry (United States); Bonvin, Alexandre M. J. J., E-mail: a.m.j.j.bonvin@uu.nl [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Lange, Oliver F., E-mail: oliver.lange@tum.de [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany)

2013-09-15

We report advances in the calculation of protein structures from chemical shift nuclear magnetic resonance data alone. Our previously developed method, CS-Rosetta, assembles structures from a library of short protein fragments picked from a large library of protein structures using chemical shifts and sequence information. Here we demonstrate that combination of a new and improved fragment picker and the iterative sampling algorithm RASREC yield significant improvements in convergence and accuracy. Moreover, we introduce improved criteria for assessing the accuracy of the models produced by the method. The method was tested on 39 proteins in the 50-100 residue size range and yields reliable structures in 70 % of the cases. All structures that passed the reliability filter were accurate (<2 A RMSD from the reference)

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Effects of Protein-pheromone Complexation on Correlated Chemical Shift Modulations

International Nuclear Information System (INIS)

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

2005-01-01

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)

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

Energy Technology Data Exchange (ETDEWEB)

Harsch, Tobias; Schneider, Philipp; Kieninger, Bärbel; Donaubauer, Harald; Kalbitzer, Hans Robert, E-mail: hans-robert.kalbitzer@biologie.uni-regensburg.de [University of Regensburg, Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (Germany)

2017-02-15

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

Deuterium isotope effects on 13C chemical shifts of 10-Hydroxybenzo[h]quinolines

DEFF Research Database (Denmark)

Hansen, Poul Erik; Kamounah, Fadhil S.; Gryko, Daniel T.

2013-01-01

Deuterium isotope effects on 13C-NMR chemical shifts are investigated in a series of 10-hydroxybenzo[h]quinolines (HBQ’s) The OH proton is deuteriated. The isotope effects on 13C chemical shifts in these hydrogen bonded systems are rather unusual. The formal four-bond effects are found to be nega...

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

Science.gov (United States)

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

1997-01-01

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

Identify Beta-Hairpin Motifs with Quadratic Discriminant Algorithm Based on the Chemical Shifts.

Directory of Open Access Journals (Sweden)

Feng YongE

Full Text Available Successful prediction of the beta-hairpin motif will be helpful for understanding the of the fold recognition. Some algorithms have been proposed for the prediction of beta-hairpin motifs. However, the parameters used by these methods were primarily based on the amino acid sequences. Here, we proposed a novel model for predicting beta-hairpin structure based on the chemical shift. Firstly, we analyzed the statistical distribution of chemical shifts of six nuclei in not beta-hairpin and beta-hairpin motifs. Secondly, we used these chemical shifts as features combined with three algorithms to predict beta-hairpin structure. Finally, we achieved the best prediction, namely sensitivity of 92%, the specificity of 94% with 0.85 of Mathew's correlation coefficient using quadratic discriminant analysis algorithm, which is clearly superior to the same method for the prediction of beta-hairpin structure from 20 amino acid compositions in the three-fold cross-validation. Our finding showed that the chemical shift is an effective parameter for beta-hairpin prediction, suggesting the quadratic discriminant analysis is a powerful algorithm for the prediction of beta-hairpin.

Identification of helix capping and {beta}-turn motifs from NMR chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Shen Yang; Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

2012-03-15

We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and {sup 13}C{sup {beta}} chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of {beta}-turns: I, II, I Prime , II Prime 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 {beta}-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 those 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.

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

International Nuclear Information System (INIS)

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 13 C β 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 those 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.

Chemical shift MRI can aid in the diagnosis of indeterminate skeletal lesions of the spine

Energy Technology Data Exchange (ETDEWEB)

Douis, H. [University Hospital Birmingham, Department of Radiology, Birmingham (United Kingdom); Royal Orthopaedic Hospital, Department of Radiology, Birmingham (United Kingdom); Davies, A.M. [Royal Orthopaedic Hospital, Department of Radiology, Birmingham (United Kingdom); Jeys, L. [Royal Orthopaedic Hospital, Department of Orthopaedic Oncology, Birmingham (United Kingdom); Sian, P. [Royal Orthopaedic Hospital, Department of Spinal Surgery and Spinal Oncology, Birmingham (United Kingdom)

2016-04-15

To evaluate the role of chemical shift MRI in the characterisation of indeterminate skeletal lesions of the spine as benign or malignant. Fifty-five patients (mean age 54.7 years) with 57 indeterminate skeletal lesions of the spine were included in this retrospective study. In addition to conventional MRI at 3 T which included at least sagittal T1WI and T2WI/STIR sequences, patients underwent chemical shift MRI. A cut-off value with a signal drop-out of 20 % was used to differentiate benign lesions from malignant lesions (signal drop-out <20 % being malignant). There were 45 benign lesions and 12 malignant lesions. Chemical shift imaging correctly diagnosed 33 of 45 lesions as benign and 11 of 12 lesions as malignant. In contrast, there were 12 false positive cases and 1 false negative case based on chemical shift MRI. This yielded a sensitivity of 91.7 %, a specificity of 73.3 %, a negative predictive value of 97.1 %, a positive predictive value of 47.8 % and a diagnostic accuracy of 82.5 %. Chemical shift MRI can aid in the characterisation of indeterminate skeletal lesions of the spine in view of its high sensitivity in diagnosing malignant lesions. Chemical shift MRI can potentially avoid biopsy in a considerable percentage of patients with benign skeletal lesions of the spine. (orig.)

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

DEFF Research Database (Denmark)

Kjærgaard, Magnus; Poulsen, Flemming Martin

2011-01-01

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

Effects of Protein-pheromone Complexation on Correlated Chemical Shift Modulations

Energy Technology Data Exchange (ETDEWEB)

Perazzolo, Chiara; Wist, Julien [Ecole Polytechnique Federale de Lausanne, Institut des Sciences et Ingenierie Chimiques (Switzerland); Loth, Karine; Poggi, Luisa [Ecole Normale Superieure, Departement de chimie, associe au CNRS (France); Homans, Steve [University of Leeds, School of Biochemistry and Microbiology (United Kingdom); Bodenhausen, Geoffrey [Ecole Polytechnique Federale de Lausanne, Institut des Sciences et Ingenierie Chimiques (Switzerland)], E-mail: Geoffrey.Bodenhausen@ens.fr

2005-12-15

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{l_brace}C'N{r_brace} and DQC{l_brace}C'N{r_brace}, 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)

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

International Nuclear Information System (INIS)

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

2016-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Fritzsching, Keith J., E-mail: kfritzsc@brandeis.edu [Brandeis University, Department of Chemistry (United States); Hong, Mei [Massachusetts Institute of Technology, Department of Chemistry (United States); Schmidt-Rohr, Klaus, E-mail: srohr@brandeis.edu [Brandeis University, Department of Chemistry (United States)

2016-02-15

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

DFT/GIAO calculations of the relative contributions of hyperconjugation to the chemical shifts of ethanol

International Nuclear Information System (INIS)

Carneiro, J. Walkimar de M.; Dias, Jacques F.; Seidl, Peter R.; Tostes, J. Glauco R.

2002-01-01

Our previous DFT/GIAO calculations on different types of alcohols reveal that the rotation of the hydroxyl group can affect the chemical shift of carbons and hydrogens close to the substituent in different ways. Besides the steric and electrostatic effects that have been widely studied, hyperconjugation with the lone pairs on oxygen of the hydroxyl group leads to changes in bond lengths and angles as well as to different charge distributions. As all three of these factors also affect chemical shifts, we undertook a systematic investigation of their relative contributions to the chemical shifts of ethanol, a molecule in which there is minimum interference among these factors. Calculations by the B3LYP method at the 6-31G(d) level for ethanol conformers corresponding to a rotation around the carbon-oxygen bond at 30 dec increments are used to show how relative contributions vary with the dihedral angle formed between the carbon-carbon and oxygen-hydrogen bonds (C-C-O-H). Largest contributions to carbon chemical shifts can be attributed to changes in bond lengths while for hydrogen chemical shifts also contribute significantly differences in charge distribution. (author)

Anisotropy of the fluorine chemical shift tensor in UF6

International Nuclear Information System (INIS)

Rigny, P.

1965-04-01

An 19 F magnetic resonance study of polycrystalline UF 6 is presented. The low temperature complex line can be analyzed as the superposition of two distinct lines, which is attributed to a distortion of the UF 6 octahedron in the solid. The shape of the two components is studied. Their width is much larger than the theoretical dipolar width, and must be explained by large anisotropies of the fluorine chemical shift tensors. The resulting shape functions of the powder spectra are determined. The values of the parameters of the chemical shift tensors yield estimates of the characters of the U-F bonds, and this gives some information on the ground state electronic wave function of the UF 6 molecule in the solid. (author) [fr

Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression

Energy Technology Data Exchange (ETDEWEB)

Brown, Joshua D.; Summers, Michael F. [University of Maryland Baltimore County, Howard Hughes Medical Institute (United States); Johnson, Bruce A., E-mail: bruce.johnson@asrc.cuny.edu [University of Maryland Baltimore County, Department of Chemistry and Biochemistry (United States)

2015-09-15

The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the {sup 1}H NMR and {sup 13}C chemical shifts reported for non-exchangeable protons of 187 of these RNAs. Software was developed that downloads BMRB datasets and corresponding PDB structure files, and then generates residue-specific attributes based on the calculated secondary structure. Attributes represent properties present in each sequential stretch of five adjacent residues and include variables such as nucleotide type, base-pair presence and type, and tetraloop types. Attributes and {sup 1}H and {sup 13}C NMR chemical shifts of the central nucleotide are then used as input to train a predictive model using support vector regression. These models can then be used to predict shifts for new sequences. The new software tools, available as stand-alone scripts or integrated into the NMR visualization and analysis program NMRViewJ, should facilitate NMR assignment and/or validation of RNA {sup 1}H and {sup 13}C chemical shifts. In addition, our findings enabled the re-calibration a ring-current shift model using published NMR chemical shifts and high-resolution X-ray structural data as guides.

A simple method for measuring signs of {sup 1}H{sup N} chemical shift differences between ground and excited protein states

Energy Technology Data Exchange (ETDEWEB)

Bouvignies, Guillaume; Korzhnev, Dmitry M.; Neudecker, Philipp; Hansen, D. Flemming [University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry (Canada); Cordes, Matthew H. J. [University of Arizona, Department of Chemistry and Biochemistry (United States); Kay, Lewis E., E-mail: kay@pound.med.utoronto.c [University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry (Canada)

2010-06-15

NMR relaxation dispersion spectroscopy is a powerful method for studying protein conformational dynamics whereby visible, ground and invisible, excited conformers interconvert on the millisecond time-scale. In addition to providing kinetics and thermodynamics parameters of the exchange process, the CPMG dispersion experiment also allows extraction of the absolute values of the chemical shift differences between interconverting states, |{Delta}{omega}-tilde|, opening the way for structure determination of excited state conformers. Central to the goal of structural analysis is the availability of the chemical shifts of the excited state that can only be obtained once the signs of {Delta}{omega}-tilde are known. Herein we describe a very simple method for determining the signs of {sup 1}H{sup N} {Delta}{omega}-tilde values based on a comparison of peak positions in the directly detected dimensions of a pair of {sup 1}H{sup N}-{sup 15}N correlation maps recorded at different static magnetic fields. The utility of the approach is demonstrated for three proteins that undergo millisecond time-scale conformational rearrangements. Although the method provides fewer signs than previously published techniques it does have a number of strengths: (1) Data sets needed for analysis are typically available from other experiments, such as those required for measuring signs of {sup 15}N {Delta}{omega}-tilde values, thus requiring no additional experimental time, (2) acquisition times in the critical detection dimension can be as long as necessary and (3) the signs obtained can be used to cross-validate those from other approaches.

Error estimation and global fitting in transverse-relaxation dispersion experiments to determine chemical-exchange parameters

International Nuclear Information System (INIS)

Ishima, Rieko; Torchia, Dennis A.

2005-01-01

Off-resonance effects can introduce significant systematic errors in R 2 measurements in constant-time Carr-Purcell-Meiboom-Gill (CPMG) transverse relaxation dispersion experiments. For an off-resonance chemical shift of 500 Hz, 15 N relaxation dispersion profiles obtained from experiment and computer simulation indicated a systematic error of ca. 3%. This error is three- to five-fold larger than the random error in R 2 caused by noise. Good estimates of total R 2 uncertainty are critical in order to obtain accurate estimates in optimized chemical exchange parameters and their uncertainties derived from χ 2 minimization of a target function. Here, we present a simple empirical approach that provides a good estimate of the total error (systematic + random) in 15 N R 2 values measured for the HIV protease. The advantage of this empirical error estimate is that it is applicable even when some of the factors that contribute to the off-resonance error are not known. These errors are incorporated into a χ 2 minimization protocol, in which the Carver-Richards equation is used fit the observed R 2 dispersion profiles, that yields optimized chemical exchange parameters and their confidence limits. Optimized parameters are also derived, using the same protein sample and data-fitting protocol, from 1 H R 2 measurements in which systematic errors are negligible. Although 1 H and 15 N relaxation profiles of individual residues were well fit, the optimized exchange parameters had large uncertainties (confidence limits). In contrast, when a single pair of exchange parameters (the exchange lifetime, τ ex , and the fractional population, p a ), were constrained to globally fit all R 2 profiles for residues in the dimer interface of the protein, confidence limits were less than 8% for all optimized exchange parameters. In addition, F-tests showed that quality of the fits obtained using τ ex , p a as global parameters were not improved when these parameters were free to fit the R

Chemically dispersed oil is cytotoxic and genotoxic to sperm whale skin cells.

Science.gov (United States)

Wise, Catherine F; Wise, James T F; Wise, Sandra S; Wise, John Pierce

2018-06-01

Two major oil crises in United States history, the 1989 Exxon-Valdez oil spill in Alaska and the 2010 Deepwater Horizon Oil Rig explosion in the Gulf of Mexico, drew attention to the need for toxicological experiments on oil and chemically dispersed oil. We are still learning the effects these spills had on wildlife. However, little data is known about the toxicity of these substances in marine mammals. The objective of this study is to determine the toxicity of Alaskan oil, as well as chemically dispersed oil. Oil experiments were performed using the water accommodated fraction of Alaskan oil (WAF) and the chemically enhanced water accommodated fraction of Alaskan oil (CEWAF). The Alaskan WAF is not cytotoxic to sperm whale skin cells though it did induce chromosome damage; S9-mediated metabolism did not affect the cytotoxicity of WAF but did increase the levels of chromosome damage. Alaskan CEWAF is more cytotoxic and genotoxic than the WAF; S9 mediated metabolism increased both cytotoxicity and genotoxicity of CEWAF. Analysis of the PAH content of Alaskan WAF and CEWAF revealed a forty-fold increase in the total levels of PAHs in CEWAF compared to WAF. These findings show that chemically dispersed oil leads to higher levels of PAH exposure which are more toxic and likely to lead to longer and more persistent health effects. Copyright © 2017 Elsevier Inc. All rights reserved.

Skeletal and chlorine effects on 13C-NMR chemical shifts of chlorinated polycyclic systems

Directory of Open Access Journals (Sweden)

Costa V.E.U.

1999-01-01

Full Text Available In order to establish a comparative analysis of chemical shifts caused by ring compression effects or by the presence of a chlorine atom on strained chlorinated carbons, a series of the chlorinated and dechlorinated polycyclic structures derived from "aldrin" (5 and "isodrin" (14 was studied. Compounds were classified in four different groups, according to their conformation and number of ring such as: endo-exo and endo-endo tetracyclics, pentacyclics and hexacyclics. The 13C chemical shift comparison between the chlorinated and dechlorinated compounds showed that when C-9 and C-10 are olefinic carbons, it occurs a shielding of 0.5-2.4 ppm for endo-endo tetracyclics and of 4.7-7.6 ppm for endo-exo tetracyclic. The chemical shift variation for C-11 reaches 49-53 ppm for endo-exo and endo-endo tetracyclics, 54 ppm for pentacyclic and 56-59 ppm for hexacyclic compounds. From these data, it was possible to observe the influence of ring compression on the chemical shifts.

SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

International Nuclear Information System (INIS)

Shen Yang; Bax, Ad

2010-01-01

NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and 13 C β chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures, including backbone and side-chain conformation, H-bonding, electric fields and ring-current effects. The trained neural network yields rapid chemical shift prediction for backbone and 13 C β atoms, with standard deviations of 2.45, 1.09, 0.94, 1.14, 0.25 and 0.49 ppm for δ 15 N, δ 13 C', δ 13 C α , δ 13 C β , δ 1 H α and δ 1 H N , respectively, between the SPARTA+ predicted and experimental shifts for a set of eleven validation proteins. These results represent a modest but consistent improvement (2-10%) over the best programs available to date, and appear to be approaching the limit at which empirical approaches can predict chemical shifts.

Cyclohexanecarbonitriles: Assigning Configurations at Quaternary Centers From 13C NMR CN Chemical Shifts.1

Science.gov (United States)

Wei, Guoqing

2009-01-01

13C NMR chemical shifts of the nitrile carbon in cyclohexanecarbonitriles directly correlate with the configuration of the quaternary, nitrile-bearing stereocenter. Comparing 13C NMR chemical shifts for over 200 cyclohexanecarbonitriles reveals that equatorially oriented nitriles resonate 3.3 ppm downfield, on average, from their axial counterparts. Pairs of axial/equatorial diastereomers varying only at the nitrile-bearing carbon consistently exhibit downfield shifts of δ 0.4–7.2 for the equatorial nitrile carbon, even in angularly substituted decalins and hydrindanes. PMID:19348434

Chemical composition dispersion in bi-metallic nanoparticles: semi-automated analysis using HAADF-STEM

International Nuclear Information System (INIS)

Epicier, T.; Sato, K.; Tournus, F.; Konno, T.

2012-01-01

We present a method using high-angle annular dark field scanning transmission electron microscopy (HAADF-STEM) to determine the chemical composition of bi-metallic nanoparticles. This method, which can be applied in a semi-automated way, allows large scale analysis with a statistical number of particles (several hundreds) in a short time. Once a calibration curve has been obtained, e.g., using energy-dispersive X-ray spectroscopy (EDX) measurements on a few particles, the HAADF integrated intensity of each particle can indeed be directly related to its chemical composition. After a theoretical description, this approach is applied to the case of iron–palladium nanoparticles (expected to be nearly stoichiometric) with a mean size of 8.3 nm. It will be shown that an accurate chemical composition histogram is obtained, i.e., the Fe content has been determined to be 49.0 at.% with a dispersion of 10.4 %. HAADF-STEM analysis represents a powerful alternative to fastidious single particle EDX measurements, for the compositional dispersion in alloy nanoparticles.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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

Treatment of oil spill fire hazards with chemical dispersants: a case history

Energy Technology Data Exchange (ETDEWEB)

Kaufmann, S.

1982-10-01

Federal contingency plans include the use of chemical dispersants to ameliorate hazardous situations caused by spills of flammable or explosive petroleum products. The closing of the Williamsburg Bridge in New York City, when a gasoline tanker exploded and sank under it, was nearly overshadowed by the leakage of 7 750 000 L (2 000 000 gal) of gasoline from a storage facility in Boston. The threat to a densely populated neighborhood of six-family tenement houses and a large racetrack that stabled hundreds of Thoroughbred horses led to the use of a chemical dispersant to neutralize the fire hazard. Favorable results by fire departments in recent years, as a result of training, have established dispersants as the method of choice to handle nonburning spill incidents. Even though the teams that responded to several such emergencies of course held the protection of life and property as paramount, no toxicological environmental effects were noted during subsequent observations.

Sequential nearest-neighbor effects on computed {sup 13}C{sup {alpha}} chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Vila, Jorge A. [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States); Serrano, Pedro; Wuethrich, Kurt [The Scripps Research Institute, Department of Molecular Biology (United States); Scheraga, Harold A., E-mail: has5@cornell.ed [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States)

2010-09-15

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

Isotope effects on chemical shifts in tautomeric systems with double proton transfer. Citronin

International Nuclear Information System (INIS)

Hansen, P.E.; Langgard, M.; Bolvig, S.

1998-01-01

Primary and secondary deuterium isotope effects on 1 H and 13 C chemical shifts are measured in citrinin, a tautomeric compound with an unusual doubly intramolecularly hydrogen bonded structure. The isotope effects are to a large extent dominated by equilibrium contributions and deuteration leads to more of the deuterated enol forms rather than the deuterated acid form. 1 H 13 C and 17 O nuclear shieldings are calculated using density functional ab initio methods. A very good correlation between calculated nuclear shieldings and experimental 1 H and 13 C chemical shifts is obtained. The tautomeric equilibrium can be analyzed based on the isotope effects on B-6 and C-8 carbons and shows an increase in the o-quinone form on lowering the temperature. Furthermore, upon deuteration the largest equilibrium shift is found for deuteration at OH-8 and the shift in the tautomeric equilibrium upon deuteration at OH-8 and the shift in the tautomeric equilibrium upon deuteration is increasing at lower temperature. (author)

SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

Energy Technology Data Exchange (ETDEWEB)

Shen Yang; Bax, Ad, E-mail: bax@nih.go [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

2010-09-15

NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and {sup 13}C{sup {beta}} chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures, including backbone and side-chain conformation, H-bonding, electric fields and ring-current effects. The trained neural network yields rapid chemical shift prediction for backbone and {sup 13}C{sup {beta}} atoms, with standard deviations of 2.45, 1.09, 0.94, 1.14, 0.25 and 0.49 ppm for {delta}{sup 15}N, {delta}{sup 13}C', {delta}{sup 13}C{sup {alpha}}, {delta}{sup 13}C{sup {beta}}, {delta}{sup 1}H{sup {alpha}} and {delta}{sup 1}H{sup N}, respectively, between the SPARTA+ predicted and experimental shifts for a set of eleven validation proteins. These results represent a modest but consistent improvement (2-10%) over the best programs available to date, and appear to be approaching the limit at which empirical approaches can predict chemical shifts.

The interplay between transient a-helix formation and side chain rotamer distributions in disordered proteins probed by methyl chemical shifts

DEFF Research Database (Denmark)

Kjærgaard, Magnus; Iesmantavicius, Vytautas; Poulsen, Flemming M

2011-01-01

and retinoid receptors (ACTR). We find that small differences in the methyl carbon chemical shifts due to the ¿-gauche effect may provide information about the side chain rotamer distributions. However, the effects of neighboring residues on the methyl group chemical shifts obscure the direct observation...... of ¿-gauche effect. To overcome this, we reference the chemical shifts to those in a more disordered state resulting in residue specific random coil chemical shifts. The (13)C secondary chemical shifts of the methyl groups of valine, leucine, and isoleucine show sequence specific effects, which allow...

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

Science.gov (United States)

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.

Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology

International Nuclear Information System (INIS)

Shen Yang; Bax, Ad

2007-01-01

Chemical shifts of nuclei in or attached to a protein backbone are exquisitely sensitive to their local environment. A computer program, SPARTA, is described that uses this correlation with local structure to predict protein backbone chemical shifts, given an input three-dimensional structure, by searching a newly generated database for triplets of adjacent residues that provide the best match in φ/ψ/χ 1 torsion angles and sequence similarity to the query triplet of interest. The database contains 15 N, 1 H N , 1 H α , 13 C α , 13 C β and 13 C' chemical shifts for 200 proteins for which a high resolution X-ray (≤2.4 A) structure is available. The relative importance of the weighting factors for the φ/ψ/χ 1 angles and sequence similarity was optimized empirically. The weighted, average secondary shifts of the central residues in the 20 best-matching triplets, after inclusion of nearest neighbor, ring current, and hydrogen bonding effects, are used to predict chemical shifts for the protein of known structure. Validation shows good agreement between the SPARTA-predicted and experimental shifts, with standard deviations of 2.52, 0.51, 0.27, 0.98, 1.07 and 1.08 ppm for 15 N, 1 H N , 1 H α , 13 C α , 13 C β and 13 C', respectively, including outliers

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

Science.gov (United States)

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.

Facile Synthesis of Mono-Dispersed Polystyrene (PS/Ag Composite Microspheres via Modified Chemical Reduction

Directory of Open Access Journals (Sweden)

Wen Zhu

2013-12-01

Full Text Available A modified method based on in situ chemical reduction was developed to prepare mono-dispersed polystyrene/silver (PS/Ag composite microspheres. In this approach; mono-dispersed PS microspheres were synthesized through dispersion polymerization using poly-vinylpyrrolidone (PVP as a dispersant at first. Then, poly-dopamine (PDA was fabricated to functionally modify the surfaces of PS microspheres. With the addition of [Ag(NH32]+ to the PS dispersion, [Ag(NH32]+ complex ions were absorbed and reduced to silver nanoparticles on the surfaces of PS-PDA microspheres to form PS/Ag composite microspheres. PVP acted both as a solvent of the metallic precursor and as a reducing agent. PDA also acted both as a chemical protocol to immobilize the silver nanoparticles at the PS surface and as a reducing agent. Therefore, no additional reducing agents were needed. The resulting composite microspheres were characterized by TEM, field emission scanning electron microscopy (FESEM, energy-dispersive X-ray spectroscopy (EDS, XRD, UV-Vis and surface-enhanced Raman spectroscopy (SERS. The results showed that Ag nanoparticles (NPs were homogeneously immobilized onto the PS microspheres’ surface in the presence of PDA and PVP. PS/Ag composite microspheres were well formed with a uniform and compact shell layer and were adjustable in terms of their optical property.

Chemical and phase composition of powders obtained by electroerosion dispersion from alloys WC-Co

International Nuclear Information System (INIS)

Putintseva, M.N.

2004-01-01

A consideration is given to the dependence of chemical and phase compositions of dispersed powders on the conditions, the medium of electroerosion dispersing and the content of cobalt in an initial alloy. It is shown that dissociation of carbon from tungsten carbide proceeds even on dispersing in liquid hydrocarbon-containing media (kerosene and machine oil). The phase composition is determined to a large extent by a medium of dispersing and a cobalt content in the initial alloy. In all powders complex tungsten-cobalt carbides and even Co 7 W 6 intermetallic compounds are found [ru

Chemical and Phase Composition of Powders Obtained by Electroerosion Dispersion from WC - Co Alloys

Science.gov (United States)

Putintseva, M. N.

2004-03-01

The dependence of the chemical and phase composition of dispersed powders on the mode and medium of electroerosion dispersion and the content of cobalt in the initial alloy is considered. It is shown that the dissociation of carbon from tungsten carbide occurs even in dispersion in liquid hydrocarbon-bearing media (kerosene and industrial oils). The phase composition is primarily determined by the dispersion medium and the content of cobalt in the initial alloy. Compound tungsten-cobalt carbides and even a Co7W6 intermetallic are determined in all the powders.

Proton chemical shift imaging after myocardial infarction

International Nuclear Information System (INIS)

Bouchard, A.; Doyle, M.; Pohost, G.M.

1989-01-01

The present study was undertaken to test whether chemical shift imaging could detect spatially the lipids known to accumulate in myocardium after an ischemic insult. Seven dogs underwent a 24-hour coronary artery occlusion. Hearts were removed and imaged ex vivo by the Dixon method (1.5 T), and myocardial samples were obtained for high-resolution H-1 spectroscopy. Lipid images revealed regions of increased signal intensity in the periphery f the myocardial infarction. The zones of high lipid signal corresponded to zones with elevated mobile lipids as detected by H-1 spectroscopy

Dispersion of carbon nanotubes in hydroxyapatite powder by in situ chemical vapor deposition

International Nuclear Information System (INIS)

Li Haipeng; Wang Lihui; Liang, Chunyong; Wang Zhifeng; Zhao Weimin

2010-01-01

In the present work, we use chemical vapor deposition of methane to disperse carbon nanotubes (CNTs) within hydroxyapatite (HA) powder. The effect of different catalytic metal particles (Fe, Ni or Co) on the morphological and structural development of the powder and dispersion of CNTs in HA powder was investigated. The results show that the technique is effective in dispersing the nanotubes within HA powder, which simultaneously protects the nanotubes from damage. The results can have important and promising speculations for the processing of CNT-reinforced HA-matrix composites in general.

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

International Nuclear Information System (INIS)

Markin, Craig J.; Spyracopoulos, Leo

2012-01-01

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

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

Science.gov (United States)

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

13C NMR Chemical Shifts of the Triclinic and Monoclinic Crystal forms of Valinomycin

International Nuclear Information System (INIS)

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

2004-01-01

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

Bright broadband coherent fiber sources emitting strongly blue-shifted resonant dispersive wave pulses

DEFF Research Database (Denmark)

Tu, Haohua; Lægsgaard, Jesper; Zhang, Rui

2013-01-01

We predict and realize the targeted wavelength conversion from the 1550-nm band of a fs Er:fiber laser to an isolated band inside 370-850 nm, corresponding to a blue-shift of 700-1180 nm. The conversion utilizes resonant dispersive wave generation in widely available optical fibers with good...... efficiency (~7%). The converted band has a large pulse energy (~1 nJ), high spectral brightness (~1 mW/nm), and broad Gaussian-like spectrum compressible to clean transform-limited ~17 fs pulses. The corresponding coherent fiber sources open up portable applications of optical parametric oscillators and dual......-output synchronized ultrafast lasers....

Fitness declines towards range limits and local adaptation to climate affect dispersal evolution during climate‐induced range shifts

DEFF Research Database (Denmark)

Hargreaves, Anna; Bailey, Susan; Laird, Robert

2015-01-01

Dispersal ability will largely determine whether species track their climatic niches during climate change, a process especially important for populations at contracting (low-latitude/low-elevation) range limits that otherwise risk extinction. We investigate whether dispersal evolution....... We simulate a species distributed continuously along a temperature gradient using a spatially explicit, individual-based model. We compare range-wide dispersal evolution during climate stability vs. directional climate change, with uniform fitness vs. fitness that declines towards range limits (RLs...... at contracting range limits is facilitated by two processes that potentially enable edge populations to experience and adjust to the effects of climate deterioration before they cause extinction: (i) climate-induced fitness declines towards range limits and (ii) local adaptation to a shifting climate gradient...

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

Science.gov (United States)

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.

Bioavailability of chemically-dispersed crude oil

International Nuclear Information System (INIS)

Harris, B.C.; Bonner, J.S.; McDonald, T.J.; Fuller, C.B.; Page, C.A.; Dimitriou-Christidis, P.; Sterling, M.C.; Autenrieth, R.L.

2002-01-01

Oil spills can be treated with surfactant compounds to disperse them. This method enables the hydrophobic compounds to overcome their repulsion for water, enter the water phase and be diluted. Once in the water, the biodegradation fraction of the oil biodegrades over time and the residual fraction is deposited over a large area. One major issue which is not fully understood is whether oil compounds pass through the water phase to free floating cells or directly enter oil-attached microbial cells from the oil particle. In this study, crude oil was placed in a swirling flask with Corpus Christi Bay water and was then chemically dispersed with Corexit 9500. The biodegradation was then monitored and assessed. First order rate coefficients were determined based on the disappearance of specific compounds. The rate coefficients for total target PAHs were consistent for all tests. Napthalene, phenanthrene, dibenzothiophene and their alkylated homologs were among the target compounds. The trend was also observed for total target analytes and for total target saturates. The results indicate that the biodegradation rate coefficient was not dependent on the bulk concentration of oil in the water column. It was concluded that biodegradation rates was controlled by partitioning of the compounds between the two phases, and other factors such as particle size distribution and the capability of the microbial culture, temperature and nutrients. 13 refs., 1 tab., 6 figs

Elucidation of the substitution pattern of 9,10-anthraquinones through the chemical shifts of peri-hydroxyl protons

DEFF Research Database (Denmark)

Schripsema, Jan; Danigno, Denise

1996-01-01

In 9,10-anthraquinones the chemical shift of a peri-hydroxyl proton is affected by the substituents in the other benzenoid ring. These effects are additive. They are useful for the determination of substitution patterns and have been used to revise the structures of six previously reported...... anthraquinones containing methoxyl, hydroxyl, methylenedioxy and beta-methyl substituents. Because the chemical shifts of the other protons are hardly affected by substitutions in the other ring, the characteristic chemical shifts for a wide variety of substitution patterns could be derived....

Vanadium NMR Chemical Shifts of (Imido)vanadium(V) Dichloride Complexes with Imidazolin-2-iminato and Imidazolidin-2-iminato Ligands: Cooperation with Quantum-Chemical Calculations and Multiple Linear Regression Analyses.

Science.gov (United States)

Yi, Jun; Yang, Wenhong; Sun, Wen-Hua; Nomura, Kotohiro; Hada, Masahiko

2017-11-30

The NMR chemical shifts of vanadium ( 51 V) in (imido)vanadium(V) dichloride complexes with imidazolin-2-iminato and imidazolidin-2-iminato ligands were calculated by the density functional theory (DFT) method with GIAO. The calculated 51 V NMR chemical shifts were analyzed by the multiple linear regression (MLR) analysis (MLRA) method with a series of calculated molecular properties. Some of calculated NMR chemical shifts were incorrect using the optimized molecular geometries of the X-ray structures. After the global minimum geometries of all of the molecules were determined, the trend of the observed chemical shifts was well reproduced by the present DFT method. The MLRA method was performed to investigate the correlation between the 51 V NMR chemical shift and the natural charge, band energy gap, and Wiberg bond index of the V═N bond. The 51 V NMR chemical shifts obtained with the present MLR model were well reproduced with a correlation coefficient of 0.97.

Evaluation of the application of chemical shift for the detection of lipid in brain lesion

Energy Technology Data Exchange (ETDEWEB)

Lim, C.J. [Department of Biomedical Imaging, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur (Malaysia); Ng, K.H., E-mail: ngkh@um.edu.m [Department of Biomedical Imaging, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur (Malaysia); Ramli, N.; Azman, R.R. [Department of Biomedical Imaging, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur (Malaysia)

2011-02-15

Non-invasive detection of the presence of lipids is particularly important in staging of intracranial tumours. Presence of lipid peak in aggressive intracranial tumours has been reported widely using MR spectroscopy. However this method has limitation due to long imaging time and artefacts formed by adjacent bones. Chemical shift MR imaging (with has shorter imaging time) is an alternative method that had been used to detect presence of lipid in vivo by means of signal intensity loss. The purpose of this study was to evaluate gradient echo in- and opposed-phase chemical shift pulse sequences for detection of lipid elements in brain lesion. Ten cylindered phantoms measuring 3 x 3 cm were filled with various mixtures of lipid and water: 0-90% lipid, in 10% step by weight. The gradient echo in- and opposed-phase chemical shift sequences were performed using a 1.5 T MRI (Magnetom Vision, Siemens) with a head coil. In addition, we performed MRI and chemical shift studies on 32 patients with brain lesion. We then analysed the association between out of phase intensity value and classification of the lesions. For phantom containing 50% lipid, maximum signal loss on opposed-phase images was observed. There were significant differences between in- and opposed-phase lipid-water phantom images (P = 0.0054). Most of the benign lesions fall into the positive out of phase intensity value, and malignant lesions fall into negative out of phase intensity value. We conclude that chemical shift artefact can be applied in detecting and characterising lipid elements in brain lesion.

Evaluation of the application of chemical shift for the detection of lipid in brain lesion

International Nuclear Information System (INIS)

Lim, C.J.; Ng, K.H.; Ramli, N.; Azman, R.R.

2011-01-01

Non-invasive detection of the presence of lipids is particularly important in staging of intracranial tumours. Presence of lipid peak in aggressive intracranial tumours has been reported widely using MR spectroscopy. However this method has limitation due to long imaging time and artefacts formed by adjacent bones. Chemical shift MR imaging (with has shorter imaging time) is an alternative method that had been used to detect presence of lipid in vivo by means of signal intensity loss. The purpose of this study was to evaluate gradient echo in- and opposed-phase chemical shift pulse sequences for detection of lipid elements in brain lesion. Ten cylindered phantoms measuring 3 x 3 cm were filled with various mixtures of lipid and water: 0-90% lipid, in 10% step by weight. The gradient echo in- and opposed-phase chemical shift sequences were performed using a 1.5 T MRI (Magnetom Vision, Siemens) with a head coil. In addition, we performed MRI and chemical shift studies on 32 patients with brain lesion. We then analysed the association between out of phase intensity value and classification of the lesions. For phantom containing 50% lipid, maximum signal loss on opposed-phase images was observed. There were significant differences between in- and opposed-phase lipid-water phantom images (P = 0.0054). Most of the benign lesions fall into the positive out of phase intensity value, and malignant lesions fall into negative out of phase intensity value. We conclude that chemical shift artefact can be applied in detecting and characterising lipid elements in brain lesion.

Influence of physical and chemical dispersion on the biodegradation of oil under simulated marine conditions

International Nuclear Information System (INIS)

Swannell, R. P. J.; Daniel, F.; Croft, B. C.; Engelhardt, M. A.; Wilson, S.; Mitchell, D. J.; Lunel, T.

1997-01-01

Dispersion and biodegradation of oil was studied in marine microcosms designed to simulate oil dispersion at sea. Dispersion was studied using both Phase Doppler Particle Analyser and a Chamber Slide technique. In both natural and artificial seawater, oil addition was observed to encourage the growth of hydrocarbon-degrading bacteria in the presence of sufficient nitrogen and phosphorus. Results showed that microorganisms enhanced oil dispersion by colonizing physically-dispersed oil droplets and preventing re-coalescence with the surface slick. The addition of dispersants increased the rate of colonization as well as the number of degraded droplets. These results suggest that stimulation of physical dispersion by chemical means increase the rate of oil biodegradation under natural conditions. 25 refs., 3 tabs., 14 figs

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

Energy Technology Data Exchange (ETDEWEB)

Markin, Craig J.; Spyracopoulos, Leo, E-mail: leo.spyracopoulos@ualberta.ca [University of Alberta, Department of Biochemistry (Canada)

2012-12-15

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{sub 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{sub 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 {sup 1}H-{sup 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{sub off}). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k{sub off} {approx} 3,000 s{sup -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{sub 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{sub off} values over a wide range, from 100 to 15,000 s{sup -1}. The validity of line shape analysis for k{sub off} values approaching intermediate exchange ({approx}100 s{sup -1}), may be facilitated by

An extrapolation scheme for solid-state NMR chemical shift calculations

Science.gov (United States)

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.

Both solubility and chemical stability of curcumin are enhanced by solid dispersion in cellulose derivative matrices.

Science.gov (United States)

Li, Bin; Konecke, Stephanie; Wegiel, Lindsay A; Taylor, Lynne S; Edgar, Kevin J

2013-10-15

Amorphous solid dispersions (ASD) of curcumin (Cur) in cellulose derivative matrices, hydroxypropylmethylcellulose acetate succinate (HPMCAS), carboxymethylcellulose acetate butyrate (CMCAB), and cellulose acetate adipate propionate (CAAdP) were prepared in order to investigate the structure-property relationship and identify polymer properties necessary to effectively increase Cur aqueous solution concentration. XRD results indicated that all investigated solid dispersions were amorphous, even at a 9:1 Cur:polymer ratio. Both stability against crystallization and Cur solution concentration from these ASDs were significantly higher than those from physical mixtures and crystalline Cur. Remarkably, curcumin was also stabilized against chemical degradation in solution. Chemical stabilization was polymer-dependent, with stabilization in CAAdP>CMCAB>HPMCAS>PVP, while matrices enhanced solution concentration as PVP>HPMCAS>CMCAB≈CAAdP. HPMCAS/Cur dispersions have useful combinations of pH-triggered release profile, chemical stabilization, and strong enhancement of Cur solution concentration. Copyright © 2013 Elsevier Ltd. All rights reserved.

CHEMICAL OIL SPILL DISPERSANTS: UPDATE STATE-OF-THE- ART ON MECHANISM OF ACTION AND LABORATORY TESTING FOR PERFORMANCE

Science.gov (United States)

Chemical dispersants are formulations designed to facilitate dispersion of an oil slick into small droplets that disperse to non-problematic concentrations in an underlying water column. This project had two primary objectives: (1) update information on mechanisms of action of ...

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

Science.gov (United States)

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.

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

Energy Technology Data Exchange (ETDEWEB)

Jeong, K; Slack, CC; Vassiliou, CC; Dao, P; Gomes, MD; Kennedy, DJ; Truxal, AE; Sperling, LJ; Francis, MB; Wemmer, DE; Pines, A

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 Ca²⁺, Cu²⁺, Ce³⁺, Zn²⁺, Cd²⁺, Ni²⁺, Co²⁺, Cr²⁺, Fe³⁺, and Hg²⁺ are distinct. In addition, the different responses of the diastereomers for the same metal ion indicate that shifts are affected by partial folding with 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.

Pressure-dependent {sup 13}C chemical shifts in proteins: origins and applications

Energy Technology Data Exchange (ETDEWEB)

Wilton, David J. [University of Sheffield, Department of Molecular Biology and Biotechnology (United Kingdom); Kitahara, Ryo [Ritsumeikan University, College of Pharmaceutical Sciences (Japan); Akasaka, Kazuyuki [Kinki University, Department of Biotechnological Science, School of Biology-Oriented Science and Technology (Japan); Williamson, Mike P. [University of Sheffield, Department of Molecular Biology and Biotechnology (United Kingdom)], E-mail: m.williamson@sheffield.ac.uk

2009-05-15

Pressure-dependent {sup 13}C chemical shifts have been measured for aliphatic carbons in barnase and Protein G. Up to 200 MPa (2 kbar), most shift changes are linear, demonstrating pressure-independent compressibilities. CH{sub 3}, CH{sub 2} and CH carbon shifts change on average by +0.23, -0.09 and -0.18 ppm, respectively, due to a combination of bond shortening and changes in bond angles, the latter matching one explanation for the {gamma}-gauche effect. In addition, there is a residue-specific component, arising from both local compression and conformational change. To assess the relative magnitudes of these effects, residue-specific shift changes for protein G were converted into structural restraints and used to calculate the change in structure with pressure, using a genetic algorithm to convert shift changes into dihedral angle restraints. The results demonstrate that residual {sup 13}C{alpha} shifts are dominated by dihedral angle changes and can be used to calculate structural change, whereas {sup 13}C{beta} shifts retain significant dependence on local compression, making them less useful as structural restraints.

Modeling Dispersion of Chemical-Biological Agents in Three Dimensional Living Space

International Nuclear Information System (INIS)

William S. Winters

2002-01-01

This report documents a series of calculations designed to demonstrate Sandia's capability in modeling the dispersal of chemical and biological agents in complex three-dimensional spaces. The transport of particles representing biological agents is modeled in a single room and in several connected rooms. The influence of particle size, particle weight and injection method are studied

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

Science.gov (United States)

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.

Physical basis of the effect of hemoglobin on the 31P NMR chemical shifts of various phosphoryl compounds

International Nuclear Information System (INIS)

Kirk, K.; Kuchel, P.W.

1988-01-01

The marked difference between the intra- and extracellular 31 P NMR chemical shifts of various phosphoryl compounds when added to a red cell suspension may be largely understood in terms of the effects of hemoglobin on the 31 P NMR chemical shifts. The presence of [oxy- or (carbonmonoxy)-] hemoglobin inside the red cell causes the bulk magnetic susceptibility of the cell cytoplasm to be significantly less than that of the external solution. This difference is sufficient to account for the difference in the intra- and extracellular chemical shifts of the two phosphate esters trimethyl phosphate and triethyl phosphate. However, in the case of the compounds dimethyl methylphosphonate, diethyl methylphosphonate, and trimethylphosphine oxide as well as the hypophosphite, phenylphosphinate, and diphenylphosphinate ions, hemoglobin exerts an additional, much larger, effect, causing the 31 P NMR resonances to shift to lower frequency in a manner that cannot be accounted for in terms of magnetic susceptibility. Lysozyme is a protein structurally unrelated to hemoglobin and was shown to cause similar shifts to lower frequency of the resonances of these six compounds; this suggests that the mechanism may involve a property of proteins in general and not a specific property of hemoglobin. The effect of different solvents on the chemical shifts of the eight phosphoryl compounds provided an insight into the possible physical basis of the effect. It is proposed that, in addition to magnetic susceptibility effects, hemoglobin exerts its influence on phosphoryl chemical shifts by disrupting the hydrogen bonding of the phosphoryl group to solvent water

Dispersive shock mediated resonant radiations in defocused nonlinear medium

Science.gov (United States)

Bose, Surajit; Chattopadhyay, Rik; Bhadra, Shyamal Kumar

2018-04-01

We report the evolution of resonant radiation (RR) in a self-defocused nonlinear medium with two zero dispersion wavelengths. RR is generated from dispersive shock wave (DSW) front when the pump pulse is in non-solitonic regime close to first zero dispersion wavelength (ZDW). DSW is responsible for pulse splitting resulting in the generation of blue solitons when leading edge of the pump pulse hits the first ZDW. DSW also generates a red shifted dispersive wave (DW) in the presence of higher order dispersion coefficients. Further, DSW through cross-phase modulation with red shifted dispersive wave (DW) excites a localized radiation. The presence of zero nonlinearity point in the system restricts red-shift of RR and enhances the red shifting of DW. It also helps in the formation of DSW at shorter distance and squeezes the solitonic region beyond second zero dispersion point. Predicted results indicate that the spectral evolution depends on the product of Kerr nonlinearity and group velocity dispersion.

Improvement of the chromatic dispersion tolerance in coherent optical OFDM systems using shifted DFT windows for ultra-long-haul optical transmission systems.

Science.gov (United States)

Sung, Minkyu; Kim, Hoon; Lee, Jaehoon; Jeong, Jichai

2014-09-22

In a high-capacity ultra-long-haul optical coherent orthogonal frequency-division multiplexing (CO-OFDM) system, the dispersion tolerance is determined by the length of cyclic extension (CE). In this paper, we propose a novel scheme to substantially improve the dispersion tolerance of CO-OFDM systems without increasing the CE length. Multiple time-shifted discrete Fourier transform (DFT) windows are exploited at the receiver, each demodulating only a part of the subcarriers. Effectively, the proposed scheme reduces the bandwidth of the OFDM signals under demodulation. Numerical simulations are performed to show the improved dispersion tolerance of the proposed scheme in comparison with the conventional CO-OFDM system. We show that the dispersion tolerance improves by a factor equal to the number of DFT windows. The tradeoff between the improved dispersion tolerance and increased receiver complexity is also presented.

Binding energies and chemical shifts of least bound core electron excitations in cubic Asub(N)Bsub(8-N) semiconductors

International Nuclear Information System (INIS)

Bechstedt, F.; Enderlein, R.; Wischnewski, R.

1981-01-01

Core electron binding energies Esup(B) with respect to the vacuum level and their chemical shifts are calculated for the least bound core levels of cations and anions of cubic Asub(N)Bsub(8-N) semiconductors. Starting from the HF-binding energy of the free atom absolute values of Esup(B) are obtained by adding core level shifts and relaxation energies. Core level shifts are calculated by means of an electrostatic model with ionic and bond charges according to Phillips' bond charge model. For the calculation of relaxation energies the linear dielectric theory of electronic polarization is applied. Valence and core electrons, and diagonal and non-diagonal screening are taken into account. The theoretical results for chemical shifts of binding energies are compared with experimental values from XPS-measurements corrected by work function data. Good agreement is obtained in all cases within the error limit of about one eV. Chemical and atomic trends of core level shifts, relaxation energies, and binding energies are discussed in terms of changes of atomic and solid state parameters. Chemical shifts and relaxation energies are predicted for various ternary Asub(N)Bsub(8-N) compounds. (author)

Effectiveness and environmental considerations for non-dispersant chemical countermeasures

International Nuclear Information System (INIS)

Walker, A.H.; Kucklick, J.H.; Michel, J.

1999-01-01

Mechanical countermeasures for oil spill response have various effectiveness and operational limitations under certain spill situations. This has led to an interest in and use of alternative treatment methods. This chapter reviews the potential utility of one such group, nondispersant chemical countermeasures, in controlling the adverse impacts from marine oil spills. The types of nondispersant chemical countermeasures presented here include: herding agents, emulsion treating agents, solidifiers, elasticity modifiers, and shoreline cleaning agents. Each countermeasure group is discussed separately to provide a definition, mechanism of action, and effectiveness and environmental considerations for the group. Where ever possible, examples are given of countermeasure use during an actual spill. In addition to the groups mentioned above, a few other treating agents are briefly described under the section 'Miscellaneous Agents' to illustrate other, less prominent types of chemical countermeasures. Non-dispersant chemical countermeasures appear to have discrete response niches, i.e. situations where the countermeasures are well-suited and offer potential benefits. The key is matching conditions for optimal effectiveness with the appropriate incident-specific characteristics and window of opportunity. The practical aspects of logistics are not addressed because, if their potential utility can be demonstrated, the resolution of these issues would follow. (author)

Dispersion-engineered and highly-nonlinear microstructured polymer optical fibres

DEFF Research Database (Denmark)

Frosz, Michael Henoch; Nielsen, Kristian; Hlubina, Petr

2009-01-01

We demonstrate dispersion-engineering of microstructured polymer optical fibres (mPOFs) made of poly(methyl methacrylate) (PMMA). A significant shift of the total dispersion from the material dispersion is confirmed through measurement of the mPOF dispersion using white-light spectral interferome......We demonstrate dispersion-engineering of microstructured polymer optical fibres (mPOFs) made of poly(methyl methacrylate) (PMMA). A significant shift of the total dispersion from the material dispersion is confirmed through measurement of the mPOF dispersion using white-light spectral...

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

Energy Technology Data Exchange (ETDEWEB)

Hartman, Joshua D.; Beran, Gregory J. O., E-mail: gregory.beran@ucr.edu [Department of Chemistry, University of California, Riverside, California 92521 (United States); Monaco, Stephen; Schatschneider, Bohdan [The Pennsylvania State University, The Eberly Campus, 2201 University Dr, Lemont Furnace, Pennsylvania 15456 (United States)

2015-09-14

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

Carbon 13 nuclear magnetic resonance chemical shifts empiric calculations of polymers by multi linear regression and molecular modeling

International Nuclear Information System (INIS)

Da Silva Pinto, P.S.; Eustache, R.P.; Audenaert, M.; Bernassau, J.M.

1996-01-01

This work deals with carbon 13 nuclear magnetic resonance chemical shifts empiric calculations by multi linear regression and molecular modeling. The multi linear regression is indeed one way to obtain an equation able to describe the behaviour of the chemical shift for some molecules which are in the data base (rigid molecules with carbons). The methodology consists of structures describer parameters definition which can be bound to carbon 13 chemical shift known for these molecules. Then, the linear regression is used to determine the equation significant parameters. This one can be extrapolated to molecules which presents some resemblances with those of the data base. (O.L.). 20 refs., 4 figs., 1 tab

Cα and Cβ Carbon-13 Chemical Shifts in Proteins From an Empirical Database

International Nuclear Information System (INIS)

Iwadate, Mitsuo; Asakura, Tetsuo; Williamson, Michael P.

1999-01-01

We have constructed an extensive database of 13C Cα and Cβ chemical shifts in proteins of solution, for proteins of which a high-resolution crystal structure exists, and for which the crystal structure has been shown to be essentially identical to the solution structure. There is no systematic effect of temperature, reference compound, or pH on reported shifts, but there appear to be differences in reported shifts arising from referencing differences of up to 4.2 ppm. The major factor affecting chemical shifts is the backbone geometry, which causes differences of ca. 4 ppm between typical α- helix and β-sheet geometries for Cα, and of ca. 2 ppm for Cβ. The side-chain dihedral angle χ1 has an effect of up to 0.5 ppm on the Cα shift, particularly for amino acids with branched side-chains at Cβ. Hydrogen bonding to main-chain atoms has an effect of up to 0.9 ppm, which depends on the main- chain conformation. The sequence of the protein and ring-current shifts from aromatic rings have an insignificant effect (except for residues following proline). There are significant differences between different amino acid types in the backbone geometry dependence; the amino acids can be grouped together into five different groups with different φ,ψ shielding surfaces. The overall fit of individual residues to a single non-residue-specific surface, incorporating the effects of hydrogen bonding and χ1 angle, is 0.96 ppm for both Cα and Cβ. The results from this study are broadly similar to those from ab initio studies, but there are some differences which could merit further attention

Dispersion-optimized optical fiber for high-speed long-haul dense wavelength division multiplexing transmission

Science.gov (United States)

Wu, Jindong; Chen, Liuhua; Li, Qingguo; Wu, Wenwen; Sun, Keyuan; Wu, Xingkun

2011-07-01

Four non-zero-dispersion-shifted fibers with almost the same large effective area (Aeff) and optimized dispersion properties are realized by novel index profile designing and modified vapor axial deposition and modified chemical vapor deposition processes. An Aeff of greater than 71 μm2 is obtained for the designed fibers. Three of the developed fibers with positive dispersion are improved by reducing the 1550nm dispersion slope from 0.072ps/nm2/km to 0.063ps/nm2/km or 0.05ps/nm2/km, increasing the 1550nm dispersion from 4.972ps/nm/km to 5.679ps/nm/km or 7.776ps/nm/km, and shifting the zero-dispersion wavelength from 1500nm to 1450nm. One of these fibers is in good agreement with G655D and G.656 fibers simultaneously, and another one with G655E and G.656 fibers; both fibers are beneficial to high-bit long-haul dense wavelength division multiplexing systems over S-, C-, and L-bands. The fourth developed fiber with negative dispersion is also improved by reducing the 1550nm dispersion slope from 0.12ps/nm2/km to 0.085ps/nm2/km, increasing the 1550nm dispersion from -4ps/nm/km to -6.016ps/nm/km, providing facilities for a submarine transmission system. Experimental measurements indicate that the developed fibers all have excellent optical transmission and good macrobending and splice performances.

The 40th anniversary of the discovery of NMR-chemical shift and nuclear spin-spin coupling

International Nuclear Information System (INIS)

Zhu Zhenghe; Gou Qingquan

1989-01-01

After the discovery of NMR Phenomenon in the physics laboratories of E.M.Purcell at Harvard and F.Bloch at Stanford in 1946, W.G.Proctor and F.C.Yu made the successful discovery of NMR-chemical shift and nuclear spin-spin coupling at Stanford in 1950, Which brought NMR spectroscopy from the physics laboratory to the laboratories of many different fields. This is worth memorizing. Retrospecting the past 40 years, it is sure that chemical shift theory will be much more prosperous prospects

Measurement of the signs of methyl {sup 13}C chemical shift differences between interconverting ground and excited protein states by R{sub 1{rho}}: an application to {alpha}B-crystallin

Energy Technology Data Exchange (ETDEWEB)

Baldwin, Andrew J.; Kay, Lewis E., E-mail: kay@pound.med.utoronto.ca [University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry (Canada)

2012-05-15

Carr-Purcell-Meiboom-Gill relaxation dispersion (CPMG RD) NMR spectroscopy has emerged as a powerful tool for quantifying the kinetics and thermodynamics of millisecond time-scale exchange processes involving the interconversion between a visible ground state and one or more minor, sparsely populated invisible 'excited' conformational states. Recently it has also become possible to determine atomic resolution structural models of excited states using a wide array of CPMG RD approaches. Analysis of CPMG RD datasets provides the magnitudes of the chemical shift differences between the ground and excited states, {Delta}{omega}, but not the sign. In order to obtain detailed structural insights from, for example, excited state chemical shifts and residual dipolar coupling measurements, these signs are required. Here we present an NMR experiment for obtaining signs of {sup 13}C chemical shift differences of {sup 13}CH{sub 3} methyl groups using weak field off-resonance R{sub 1{rho}} relaxation measurements. The accuracy of the method is established by using an exchanging system where the invisible, excited state can be converted to the visible, ground state by altering sample conditions so that the signs of {Delta}{omega} values obtained from the spin-lock approach can be validated against those measured directly. Further, the spin-lock experiments are compared with the established H(S/M)QC approach for measuring signs of chemical shift differences and the relative strengths of each method are discussed. In the case of the 650 kDa human {alpha}B-crystallin complex where there are large transverse relaxation differences between ground and excited state spins the R{sub 1{rho}} method is shown to be superior to more 'traditional' experiments for sign determination.

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

Science.gov (United States)

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.

Fractional enrichment of proteins using [2-{sup 13}C]-glycerol as the carbon source facilitates measurement of excited state {sup 13}Cα chemical shifts with improved sensitivity

Energy Technology Data Exchange (ETDEWEB)

Ahlner, Alexandra; Andresen, Cecilia; Khan, Shahid N. [Linköping University, Division of Chemistry, Department of Physics, Chemistry and Biology (Sweden); Kay, Lewis E. [The University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry, One King’s College Circle (Canada); Lundström, Patrik, E-mail: patlu@ifm.liu.se [Linköping University, Division of Chemistry, Department of Physics, Chemistry and Biology (Sweden)

2015-07-15

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

H-1 chemical shift imaging characterization of human brain tumor and edema

NARCIS (Netherlands)

Sijens, PE; Oudkerk, M

Longitudinal (T1) and transverse (T2) relaxation times of metabolites in human brain tumor, peritumoral edema, and unaffected brain tissue were assessed from point resolved spectroscopy (PRESS) H-1 chemical shift imaging results at different repetition times (TR = 1500 and 5000 ms; T1: n = 19) and

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

Science.gov (United States)

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.

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

Energy Technology Data Exchange (ETDEWEB)

Lee, Woonghee, E-mail: whlee@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison, and Biochemistry Department (United States); Yu, Wookyung [Center for Proteome Biophysics, Pusan National University, Department of Physics (Korea, Republic of); Kim, Suhkmann [Pusan National University, Department of Chemistry and Chemistry Institute for Functional Materials (Korea, Republic of); Chang, Iksoo [Center for Proteome Biophysics, Pusan National University, Department of Physics (Korea, Republic of); Lee, Weontae, E-mail: wlee@spin.yonsei.ac.kr [Yonsei University, Structural Biochemistry and Molecular Biophysics Laboratory, Department of Biochemistry (Korea, Republic of); Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison, and Biochemistry Department (United States)

2012-10-15

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.eduhttp://pacsy.nmrfam.wisc.edu.

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

Science.gov (United States)

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

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

International Nuclear Information System (INIS)

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

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.eduhttp://pacsy.nmrfam.wisc.edu.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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

2016-01-01

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

The role of poly(methacrylic acid) conformation on dispersion behavior of nano TiO2 powder

Science.gov (United States)

Singh, Bimal P.; Nayak, Sasmita; Samal, Samata; Bhattacharjee, Sarama; Besra, Laxmidhar

2012-02-01

To exploit the advantages of nanoparticles for various applications, controlling the dispersion and agglomeration is of paramount importance. Agglomeration and dispersion behavior of titanium dioxide (TiO2) nanoparticles was investigated using electrokinetic and surface chemical properties. Nanoparticles are generally stabilized by the adsorption of a dispersant (polyelectrolyte) layer around the particle surface and in this connection ammonium salt of polymethacrylic acid (Darvan C) was used as dispersant to stabilize the suspension. The dosages of polyelectrolyte were optimized to get best dispersion stability by techniques namely particle charge detector (13.75 mg/g) and adsorption (14.57 mg/g). The surface charge of TiO2 particles changed significantly in presence of dispersant Darvan C and isoelectric point (iep) shifted significantly towards lower pH from 5.99 to 3.37. The shift in iep has been quantified in terms of free energy of interaction between the surface sites of TiO2 and the adsorbing dispersant Darvan C. Free energies of adsorption were calculated by electrokinetic data (-9.8 RT unit) and adsorption isotherms (-10.56 RT unit), which corroborated well. The adsorption isotherms are of typical Langmuir type and employed for calculation of free energy. The results indicated that adsorption occurs mainly through electrostatic interactions between the dispersant molecule and the TiO2 surface apart from hydrophobic interactions.

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

Science.gov (United States)

Mondal, Arobendo; Kaupp, Martin

2018-04-05

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

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

Science.gov (United States)

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

2018-05-10

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

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

Energy Technology Data Exchange (ETDEWEB)

Shen Yang; Delaglio, Frank [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Cornilescu, Gabriel [National Magnetic Resonance Facility (United States); Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: bax@nih.gov

2009-08-15

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

Dynamics of Dispersive Wave Generation in Gas-Filled Photonic Crystal Fiber with the Normal Dispersion

Directory of Open Access Journals (Sweden)

Zhixiang Deng

2017-01-01

Full Text Available The absence of Raman and unique pressure-tunable dispersion is the characteristic feature of gas-filled photonic crystal fiber (PCF, and its zero dispersion points can be extended to the near-infrared by increasing gas pressure. The generation of dispersive wave (DW in the normal group velocity dispersion (GVD region of PCF is investigated. It is demonstrated that considering the self-steepening (SS and introducing the chirp of the initial input pulse are two suitable means to control the DW generation. The SS enhances the relative average intensity of blue-shift DW while weakening that of red-shift DW. The required propagation distance of DW emission is markedly varied by introducing the frequency chirp. Manipulating DW generation in gas-filled PCF by the combined effects of either SS or chirp and three-order dispersion (TOD provides a method for a concentrated transfer of energy into the targeted wavelengths.

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

Science.gov (United States)

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 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.

Chemical shift of Mn and Cr K-edges in X-ray absorption

Indian Academy of Sciences (India)

... Lecture Workshops · Refresher Courses · Symposia · Live Streaming. Home; Journals; Bulletin of Materials Science; Volume 36; Issue 6. Chemical shift of Mn and Cr K-edges in X-ray absorption spectroscopy with synchrotron radiation. D Joseph A K Yadav S N Jha D Bhattacharyya. Volume 36 Issue 6 November 2013 pp ...

Assignment of protein backbone resonances using connectivity, torsion angles and 13Cα chemical shifts

International Nuclear Information System (INIS)

Morris, Laura C.; Valafar, Homayoun; Prestegard, James H.

2004-01-01

A program is presented which will return the most probable sequence location for a short connected set of residues in a protein given just 13 C α chemical shifts (δ( 13 C α )) and data restricting the φ and ψ backbone angles. Data taken from both the BioMagResBank and the Protein Data Bank were used to create a probability density function (PDF) using a multivariate normal distribution in δ( 13 C α ), φ, and ψ space for each amino acid residue. Extracting and combining probabilities for particular amino acid residues in a short proposed sequence yields a score indicative of the correctness of the proposed assignment. The program is illustrated using several proteins for which structure and 13 C α chemical shift data are available

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

DEFF Research Database (Denmark)

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

2006-01-01

the Ar-OCH3 torsion out of the ring plane, resulting in large stereoelectronic effects on the chemical shift of Hpara. Conformational searches and geometry optimizations for 3-16 at the B3LYP/6-31G** level, followed by B3LYP/6-311++G(2d,2p) calculations for all low-energy conformers, gave excellent...

The shifting roles of dispersal and vicariance in biogeography.

OpenAIRE

Zink, R M; Blackwell-Rago, R C; Ronquist, F

2000-01-01

Dispersal and vicariance are often contrasted as competing processes primarily responsible for spatial and temporal patterns of biotic diversity. Recent methods of biogeographical reconstruction recognize the potential of both processes, and the emerging question is about discovering their relative frequencies. Relatively few empirical studies, especially those employing molecular phylogenies that allow a temporal perspective, have attempted to estimate the relative roles of dispersal and vic...

Chemical shift-selective snapshot FLASH MR imaging in combination with inversion-recovery T1 contrast at different field strengths

International Nuclear Information System (INIS)

Matthaei, D.; Haase, A.; Henrich, D.; Duhmke, E.

1991-01-01

With fast MR imaging, chemical shift contract becomes available to the clinician in seconds. The purpose of this paper is to evaluate the combination of chemical shift selective (CHESS) MR imaging using the snapshot FLASH MR method with the inversion-recovery technique and to obtain information concerning the signal-to-noise and chemical shift with the presaturation method at different field strengths. Investigations with volunteers and experimental animals were done at 2 and 3 T (whole body) and in a 4.7-T animal image. For the inversion-recovery experiments, saturation was done before every snapshot FLASH image. With increasing field strength due to signal-to-noise and chemical shift advantages, the method performs better. Increasing T1 values are also important at high field strengths. The combined technique is useful only for T1 water images with fat saturation. It also allows fast quantification of T1 in water-containing organs and pathologic processes. At high field strengths, fast CHESS and T1 imaging promise fast quantitative information. This is a possible argument for clinical high-field-strength MR imagining along with MR spectroscopy

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

Science.gov (United States)

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.

Determination of the bonding of alkyl monolayers to the Si(111) surface using chemical-shift, scanned-energy photoelectron diffraction

Energy Technology Data Exchange (ETDEWEB)

Terry, J.; Linford, M.R.; Wigren, C.; Cao, R.; Pianetta, P.; Chidsey, C.E. [Stanford University, Stanford, California 94309 (United States)

1997-08-01

The bonding of alkyl monolayers to Si(111) surfaces has been studied by conventional x-ray photoelectron spectroscopy (XPS) and chemical-shift, scanned-energy photoelectron diffraction (PED) using synchrotron radiation. Two very different wet-chemical methods have been used to prepare the alkyl monolayers: (i) olefin insertion into the H{endash}Si bond on the H{endash}Si(111) surface, and (ii) replacement of Cl on the Cl{endash}Si(111) surface by an alkyl group from an alkyllithium reagent. In both cases, XPS has revealed a C 1s signal chemically shifted to lower binding energy, which we have assigned to carbon bonded to silicon. PED has shown that both preparative methods result in carbon bonded in an atop site with the expected C{endash}Si bond length of 1.85{plus_minus}0.05{Angstrom}. Chemical-shift, scanned-energy photoelectron diffraction is a particularly valuable probe of local structure at surfaces that contain the same element in multiple, chemically distinct environments. {copyright} {ital 1997 American Institute of Physics.}

Determination of the bonding of alkyl monolayers to the Si(111) surface using chemical-shift, scanned-energy photoelectron diffraction

International Nuclear Information System (INIS)

Terry, J.; Linford, M.R.; Wigren, C.; Cao, R.; Pianetta, P.; Chidsey, C.E.

1997-01-01

The bonding of alkyl monolayers to Si(111) surfaces has been studied by conventional x-ray photoelectron spectroscopy (XPS) and chemical-shift, scanned-energy photoelectron diffraction (PED) using synchrotron radiation. Two very different wet-chemical methods have been used to prepare the alkyl monolayers: (i) olefin insertion into the H endash Si bond on the H endash Si(111) surface, and (ii) replacement of Cl on the Cl endash Si(111) surface by an alkyl group from an alkyllithium reagent. In both cases, XPS has revealed a C 1s signal chemically shifted to lower binding energy, which we have assigned to carbon bonded to silicon. PED has shown that both preparative methods result in carbon bonded in an atop site with the expected C endash Si bond length of 1.85±0.05 Angstrom. Chemical-shift, scanned-energy photoelectron diffraction is a particularly valuable probe of local structure at surfaces that contain the same element in multiple, chemically distinct environments. copyright 1997 American Institute of Physics

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

Science.gov (United States)

Frach, Roland; Kast, Stefan M

2014-12-11

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

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

Science.gov (United States)

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.

Science.gov (United States)

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.

Chemical exchange effects during refocusing pulses in constant-time CPMG relaxation dispersion experiments

International Nuclear Information System (INIS)

Myint, Wazo; Ishima, Rieko

2009-01-01

In the analysis of the constant-time Carr-Purcell-Meiboom-Gill (CT-CPMG) relaxation dispersion experiment, chemical exchange parameters, such as rate of exchange and population of the exchanging species, are typically optimized using equations that predict experimental relaxation rates recorded as a function of effective field strength. In this process, the effect of chemical exchange during the CPMG pulses is typically assumed to be the same as during the free-precession. This approximation may introduce systematic errors into the analysis of data because the number of CPMG pulses is incremented during the constant-time relaxation period, and the total pulse duration therefore varies as a function of the effective field strength. In order to estimate the size of such errors, we simulate the time-dependence of magnetization during the entire constant time period, explicitly taking into account the effect of the CPMG pulses on the spin relaxation rate. We show that in general the difference in the relaxation dispersion profile calculated using a practical pulse width from that calculated using an extremely short pulse width is small, but under certain circumstances can exceed 1 s -1 . The difference increases significantly when CPMG pulses are miscalibrated

Orientation-dependent surface core-level shifts and chemical shifts on clean and H 2S-covered GaAs

Science.gov (United States)

Ranke, W.; Finster, J.; Kuhr, H. J.

1987-08-01

Photoelectron spectra of the As 3d and Ga 3d core levels were studied in situ on a cylindrically shaped GaAs single crystal for the six inequivalent orientations (001), (113), (111), (110), (11¯1) and (11¯3). On the clean surface, prepared by molecular beam epitaxy (MBE), surface core levels are shifted by 0.25 to 0.55 eV towards smaller binding energy (BE) for As 3d and -0.25 to -0.35 eV towards higher BE for Ga, depending on orientation. Additional As causes As 3d contributions shifted between -0.45 and -0.7 eV towards higher BE. The position and intensity of them is influenced by H 2S adsorption. At 150 K, H 2S adsorbs preferentially on As sites. As chemical shifts appear at -0.6 to -0.9 eV towards higher BE. Simultaneously, As accumulation occurs on all orientations with the exception of (110). High temperature adsorption (550 K, 720 K) influences mainly the Ga 3d peaks. Two peaks shifted by about -0.45 and -0.8 eV towards higher Be were found which are attributed to Ga atoms with one or two sulfur ligands, respectively. At 720 K, also As depletion is observed. The compatibility of surface core-level positions and intensities with recent structural models for the (111) and (11¯1) surfaces is discussed.

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

Science.gov (United States)

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.

Simultaneous all-optical demultiplexing and regeneration based on self-phase and cross-phase modulation in a dispersion shifted fiber

DEFF Research Database (Denmark)

Yu, Jianjun; Jeppesen, Palle

2001-01-01

Simultaneous demultiplexing and regeneration of 40-Gb/s optical time division multiplexed (OTDM) signal based on self-phase and cross-phase modulation in a dispersion shifted fiber is numerically and experimentally investigated. The optimal walkoff time between the control pulse and OTDM signal...... is obtained by numerical simulation. Our experiment also shows that it is an effective method for realizing simultaneous demultiplexing and regeneration when used in the middle of a system or in the receiver with a proper walkoff time....

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

DEFF Research Database (Denmark)

Christensen, Anders Steen; Linnet, Troels Emtekær; Borg, Mikael

2013-01-01

We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level...

Differentiation of osteoporotic and neoplastic vertebral fractures by chemical shift {in-phase and out-of phase} MR imaging

International Nuclear Information System (INIS)

Ragab, Yasser; Emad, Yasser; Gheita, Tamer; Mansour, Maged; Abou-Zeid, A.; Ferrari, Serge; Rasker, Johannes J.

2009-01-01

Objective: The objective of this study was to establish the cut-off value of the signal intensity drop on chemical shift magnetic resonance imaging (MRI) with appropriate sensitivity and specificity to differentiate osteoporotic from neoplastic wedging of the spine. Patients and methods: All patients with wedging of vertebral bodies were included consecutively between February 2006 and January 2007. A chemical shift MRI was performed and signal intensity after (in-phase and out-phase) images were obtained. A DXA was performed in all. Results: A total of 40 patients were included, 20 with osteoporotic wedging (group 1) and 20 neoplastic (group 2). They were 21 males and 19 females. Acute vertebral collapse was observed in 15 patients in group 1 and subacute collapse in another 5 patients, while in group 2, 11 patients showed acute collapse and 9 patients (45%) showed subacute vertebral collapse. On the chemical shift MRI a substantial reduction in signal intensity was found in all lesions in both groups. The proportional changes observed in signal intensity of bone marrow lesions on in-phase compared with out-of-phase images showed significant differences in both groups (P < 0.05). At a cut-off value of 35%, the observed sensitivity of out-of-phase images was 95%, specificity was 100%, positive predictive value was 100% and negative predictive value was 95.2%. Conclusion: A chemical shift MRI is useful in order to differentiate patients with vertebral collapse due to underlying osteoporosis or neoplastic process.

Application of ultraviolet fluorometry and excitation-emission matrix spectroscopy (EEMS) to fingerprint oil and chemically dispersed oil in seawater.

Science.gov (United States)

Bugden, J B C; Yeung, C W; Kepkay, P E; Lee, K

2008-04-01

Excitation-emission matrix spectroscopy (EEMS) was used to characterize the ultra violet fluorescence fingerprints of eight crude oils (with a 14,470-fold range of dynamic viscosity) in seawater. When the chemical dispersant Corexit 9500 was mixed with the oils prior to their dispersion in seawater, the fingerprints of each oil changed primarily as an increase in fluorescence over an emission band centered on 445 nm. In order to simplify the wealth of information available in the excitation-emission matrix spectra (EEMs), two ratios were calculated. A 66-90% decrease in the slope ratio was observed with the addition of Corexit. When the slope ratios were reduced in complexity to intensity ratios, similar trends were apparent. As a result either of the ratios could be used as a simple and rapid means of identifying and monitoring chemically dispersed oil in the open ocean.

Empirical isotropic chemical shift surfaces

International Nuclear Information System (INIS)

Czinki, Eszter; Csaszar, Attila G.

2007-01-01

A list of proteins is given for which spatial structures, with a resolution better than 2.5 A, are known from entries in the Protein Data Bank (PDB) and isotropic chemical shift (ICS) values are known from the RefDB database related to the Biological Magnetic Resonance Bank (BMRB) database. The structures chosen provide, with unknown uncertainties, dihedral angles φ and ψ characterizing the backbone structure of the residues. The joint use of experimental ICSs of the same residues within the proteins, again with mostly unknown uncertainties, and ab initio ICS(φ,ψ) surfaces obtained for the model peptides For-(l-Ala) n -NH 2 , with n = 1, 3, and 5, resulted in so-called empirical ICS(φ,ψ) surfaces for all major nuclei of the 20 naturally occurring α-amino acids. Out of the many empirical surfaces determined, it is the 13C α ICS(φ,ψ) surface which seems to be most promising for identifying major secondary structure types, α-helix, β-strand, left-handed helix (α D ), and polyproline-II. Detailed tests suggest that Ala is a good model for many naturally occurring α-amino acids. Two-dimensional empirical 13C α - 1 H α ICS(φ,ψ) correlation plots, obtained so far only from computations on small peptide models, suggest the utility of the experimental information contained therein and thus they should provide useful constraints for structure determinations of proteins

Lanthanide shift reagents, binding, shift mechanisms and exchange

International Nuclear Information System (INIS)

Boer, J.W.M. de

1977-01-01

Paramagnetic lanthanide shift reagents, when added to a solution of a substrate, induce shifts in the nuclear magnetic resonance (NMR) spectrum of the substrate molecules. The induced shifts contain information about the structure of the shift reagent substrate complex. The structural information, however, may be difficult to extract because of the following effects: (1) different complexes between shift reagent and substrate may be present in solution, e.g. 1:1 and 1:2 complexes, and the shift observed is a weighed average of the shifts of the substrate nuclei in the different complexes; (2) the Fermi contact interaction, arising from the spin density at the nucleus, contributes to the induced shift; (3) chemical exchange effects may complicate the NMR spectrum. In this thesis, the results of an investigation into the influence of these effects on the NMR spectra of solutions containing a substrate and LSR are presented. The equations describing the pseudo contact and the Fermi contact shift are derived. In addition, it is shown how the modified Bloch equations describing the effect of the chemical exchange processes occurring in the systems studied can be reduced to the familiar equations for a two-site exchange case. The binding of mono- and bifunctional ethers to the shift reagent are reported. An analysis of the induced shifts is given. Finally, the results of the experiments performed to study the exchange behavior of dimethoxyethane and heptafluorodimethyloctanedionato ligands are presented

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

Science.gov (United States)

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.

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

Science.gov (United States)

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…

Identifying Stereoisomers by ab-initio Calculation of Secondary Isotope Shifts on NMR Chemical Shieldings

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Karl-Heinz Böhm

2014-04-01

Full Text Available 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(2-2Hethane 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.

Identifying stereoisomers by ab-initio calculation of secondary isotope shifts on NMR chemical shieldings.

Science.gov (United States)

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.

Calculation of the NMR chemical shift for a 4d1 system in a strong crystal field environment of trigonal symmetry with a threefold axis of quantization

International Nuclear Information System (INIS)

Ahn, Sang Woon; Oh, Se Woung; Ro, Seung Woo

1986-01-01

The NMR chemical shift arising from 4d electron angular momentum and 4d electron angular momentum and 4d electron spin dipolar-nuclear spin angular momentum interactions for a 4d 1 system in a strong crystal field environment of trigonal symmetry, where the threefold axis is chosen to be the axis of quantization axis, has been examined. A general expression using the nonmultipole expansion method (exact method) is derived for the NMR chemical shift. From this expression all the multipolar terms are determined. we observe that along the (100), (010), (110), and (111) axes the NMR chemical shifts are positive while along the (001) axis, it is negative. We observe that the dipolar term (1/R 3 ) is the dominant contribution to the NMR chemical shift except for along the (111) axis. A comparison of the multipolar terms with the exact values shows also that the multipolar results are exactly in agreement with the exact values around R≥0.2 nm. The temperature dependence analysis on the NMR chemical shifts may imply that along the (111) axis the contribution to the NMR chemical shift is dominantly pseudo contact interaction. Separation of the contributions of the Fermi and the pseudo contact interactions would correctly imply that the dipolar interaction is the dominant contribution to the NMR chemical shifts along the (100), (010), (001), and (110) axes, but along the (111) axis the Fermi contact interaction is incorrectly the dominant contribution to the NMR chemical shift. (Author)

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

Energy Technology Data Exchange (ETDEWEB)

Shen Yang; Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

2013-07-15

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 ({phi}, {psi}) torsion angles of ca 12 Masculine-Ordinal-Indicator . TALOS-N also reports sidechain {chi}{sup 1} rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts.

Deuterium isotope shifts for backbone {sup 1}H, {sup 15}N and {sup 13}C nuclei in intrinsically disordered protein {alpha}-synuclein

Energy Technology Data Exchange (ETDEWEB)

Maltsev, Alexander S.; Ying Jinfa; Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

2012-10-15

Intrinsically disordered proteins (IDPs) are abundant in nature and characterization of their potential structural propensities remains a widely pursued but challenging task. Analysis of NMR secondary chemical shifts plays an important role in such studies, but the output of such analyses depends on the accuracy of reference random coil chemical shifts. Although uniform perdeuteration of IDPs can dramatically increase spectral resolution, a feature particularly important for the poorly dispersed IDP spectra, the impact of deuterium isotope shifts on random coil values has not yet been fully characterized. Very precise {sup 2}H isotope shift measurements for {sup 13}C{sup {alpha}}, {sup 13}C{sup {beta}}, {sup 13}C Prime , {sup 15}N, and {sup 1}H{sup N} have been obtained by using a mixed sample of protonated and uniformly perdeuterated {alpha}-synuclein, a protein with chemical shifts exceptionally close to random coil values. Decomposition of these isotope shifts into one-bond, two-bond and three-bond effects as well as intra- and sequential residue contributions shows that such an analysis, which ignores conformational dependence, is meaningful but does not fully describe the total isotope shift to within the precision of the measurements. Random coil {sup 2}H isotope shifts provide an important starting point for analysis of such shifts in structural terms in folded proteins, where they are known to depend strongly on local geometry.

Chromatic dispersion effects in ultra-low coherence interferometry

Energy Technology Data Exchange (ETDEWEB)

Lychagov, V V; Ryabukho, V P [N.G.Chernyshevsky Saratov State University (Russian Federation)

2015-06-30

We consider the properties of an interference signal shift from zero-path-difference position in the presence of an uncompensated dispersive layer in one of the interferometer arms. It is experimentally shown that in using an ultra-low coherence light source, the formation of the interference signal is also determined by the group velocity dispersion, which results in a nonlinear dependence of the position of the interference signal on the geometrical thickness of the dispersive layer. The discrepancy in the dispersive layer and compensator refractive indices in the third decimal place is experimentally shown to lead to an interference signal shift that is an order of magnitude greater than the pulse width. (interferometry)

Bioaccumulation and subacute toxicity of mechanically and chemically dispersed heavy fuel oil in sea urchin (Glyptocidaris crenulari

Directory of Open Access Journals (Sweden)

Bailin Yang

2015-12-01

Full Text Available Oil spills have a disastrous ecological impact on ecosystems but few data are available for the effects of dispersed oil on benthic marine organisms. In order to provide information for assessment, we analysed the hydrocarbon compositions of the mechanically dispersed water accommodated fraction (MDWAF and the chemically dispersed water accommodated fraction (CDWAF of No. 120 fuel oil, their bioaccumulation, and DNA damage related to oil exposure, using the sea urchin as a sentinel organism. The results show that the concentration of polycyclic aromatic hydrocarbon in the tissues of sea urchin exposed to the CDWAF is higher than that of those exposed to the MDWAF. The single cell gel electrophoresis assay results also indicated higher DNA damage from exposure to the CDWAF of oil. Thus, dispersants should be applied with caution in oil spill accidents.

Dispersion self-energy of the electron

International Nuclear Information System (INIS)

Hawton, M.

1991-01-01

Electron mass renormalization and the Lamb shift have been investigated using the dispersion self-energy formalism. If shifts of both the electromagnetic field and quantum-mechanical transitions frequencies are considered, absorption from the electromagnetic field is canceled by emission due to atomic fluctuations. The frequencies of all modes are obtained from the self-consistency condition that the field seen by the electron is the same as the field produced by the expectation value of current. The radiation present can thus be viewed as arising from emission and subsequent reabsorption by matter. As developed here, the numerical predictions of dispersion theory are identical to those of quantum electrodynamics. The physical picture implied by dispersion theory is discussed in the context of semiclassical theories and quantum electrodynamics

Accuracy of chemical shift MR imaging in diagnosing indeterminate bone marrow lesions in the pelvis: review of a single institution's experience

International Nuclear Information System (INIS)

Kohl, Chad A.; Chivers, F.S.; Lorans, Roxanne; Roberts, Catherine C.; Kransdorf, Mark J.

2014-01-01

To re-assess the accuracy of chemical shift imaging in diagnosing indeterminate bone marrow lesions as benign or malignant. We retrospectively reviewed our experience with MR imaging of the pelvis to assess the accuracy of chemical shift imaging in distinguishing benign from malignant bone lesions. Two musculoskeletal radiologists retrospectively reviewed all osseous lesions biopsied since 2006, when chemical shift imaging was added to our routine pelvic imaging protocol. Study inclusion criteria required (1) MR imaging of an indeterminate bone marrow lesion about the pelvis and (2) subsequent histologic confirmation. The study group included 50 patients (29 male, 21 female) with an average age of 67 years (range, 41-89 years). MR imaging results were evaluated using biopsy results as the ''gold standard.'' There were 27 malignant and 23 benign lesions. Chemical shift imaging using an opposed-phase signal loss criteria of less than 20 % to indicate a malignant lesion, correctly diagnosed 27/27 malignant lesions and 14/23 benign lesions, yielding a 100 % sensitivity, 61 % specificity, 75 % PPV, 100 % NPV, and 82 % accuracy. The area under the receiver operator characteristic (ROC) curve was 0.88. The inter-rater and intra-rater agreement K values were both 1.0. Chemical shift imaging is a useful adjunct MR technique to characterize focal and diffuse marrow abnormalities on routine non-contrast pelvic imaging. It is highly sensitive in identifying malignant disease. Despite its lower specificity, the need for biopsy could be eliminated in more than 60 % of patients with benign disease. (orig.)

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

Science.gov (United States)

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

2016-04-01

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

Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements

Energy Technology Data Exchange (ETDEWEB)

Eghbalnia, Hamid R.; Wang Liya; Bahrami, Arash [National Magnetic Resonance Facility at Madison, Biochemistry Department (United States); Assadi, Amir [University of Wisconsin-Madison, Mathematics Department (United States); Markley, John L. [National Magnetic Resonance Facility at Madison, Biochemistry Department (United States)], E-mail: eghbalni@nmrfam.wisc.edu

2005-05-15

We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ('PECAN', Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states.

Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements

International Nuclear Information System (INIS)

Eghbalnia, Hamid R.; Wang Liya; Bahrami, Arash; Assadi, Amir; Markley, John L.

2005-01-01

We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ('PECAN', Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states

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

Science.gov (United States)

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.

The evolution of Cayaponia (Cucurbitaceae): Repeated shifts from bat to bee pollination and long-distance dispersal to Africa 2-5 million years ago.

Science.gov (United States)

Duchen, Pablo; Renner, Susanne S

2010-07-01

The Cucurbitaceae genus Cayaponia comprises ∼60 species that occur from Uruguay to the southern United States and the Caribbean; C. africana occurs in West Africa and on Madagascar. Pollination is by bees or bats, raising the question of the evolutionary direction and frequency of pollinator shifts. Studies that investigated such shifts in other clades have suggested that bat pollination might be an evolutionary end point. • Plastid and nuclear DNA sequences were obtained for 50 accessions representing 30 species of Cayaponia and close relatives, and analyses were carried out to test monophyly, infer divergence times, and reconstruct ancestral states for habitat preferences and pollination modes. • The phylogeny shows that Cayaponia is monophyletic as long as Selysia (a genus with four species from Central and South America) is included. The required nomenclatural transfers are made in this paper. African and Madagascan accessions of C. africana form a clade that is part of a polytomy with Caribbean and South American species, and the inferred divergence time of 2-5 Ma implies a transoceanic dispersal event from the New World to Africa. The ancestral state reconstructions suggest that Cayaponia originated in tropical forests from where open savannas were reached several times and that bee pollination arose from bat pollination, roughly concomitant with the shifts from forests to savanna habitats. • Cayaponia provides the first example of evolutionary transitions from bat to bee pollination as well as another instance of transoceanic dispersal from the New World to Africa.

A new methodology for studying nanoparticle interactions in biological systems: Dispersing titania in biocompatible media using chemical stabilisers

Science.gov (United States)

Ramirez-Garcia, Sonia; Chen, Lan; Morris, Michael A.; Dawson, Kenneth A.

2011-11-01

We report here a highly successful and original protocol for the dispersion of nanoparticles in biocompatible fluids for in vitro and in vivo studies of the nanoparticle-biology interaction. Titania is chosen as a suitable model as it is one of the priority materials listed by the OECD and small particles of the anatase structure are extensively used as e.g. photocatalysts in solar cells. Consequently, its delivery into the environment and its interaction with biological organisms is unavoidable. Therefore, its biological effect needs to be understood. In this work, we prepared stable nanoparticle dispersions of anatase aggregates using citrate stabilisations between 45 and 55 nm at concentrations of up to 10 mg mL-1. The optimum pH for this type of suspension was 7, resulting in ζ-potentials of approximately -50 mV. The stabilised aggregates were the subject of dialysis to produce stable dispersions without the chemical stabiliser, thus allowing studies in the absence of potentially toxic chemicals. Different sizing techniques such as Dynamic Light Scattering (DLS), Nanoparticle Tracking Analysis (NTA) and Differential Centrifuge Sedimentation (DCS) were used to characterise the different suspensions. The results obtained with each of these techniques are compared and a critical analysis of the suitability of each technique is given.We report here a highly successful and original protocol for the dispersion of nanoparticles in biocompatible fluids for in vitro and in vivo studies of the nanoparticle-biology interaction. Titania is chosen as a suitable model as it is one of the priority materials listed by the OECD and small particles of the anatase structure are extensively used as e.g. photocatalysts in solar cells. Consequently, its delivery into the environment and its interaction with biological organisms is unavoidable. Therefore, its biological effect needs to be understood. In this work, we prepared stable nanoparticle dispersions of anatase aggregates

Shifts in Plant Chemical Defenses of Chile Pepper (Capsicum annuum L. Due to Domestication in Mesoamerica

Directory of Open Access Journals (Sweden)

Jose de Jesus Luna-Ruiz

2018-04-01

Full Text Available We propose that comparisons of wild and domesticated Capsicum species can serve as a model system for elucidating how crop domestication influences biotic and abiotic interactions mediated by plant chemical defenses. Perhaps no set of secondary metabolites (SMs used for plant defenses and human health have been better studied in the wild and in milpa agro-habitats than those found in Capsicum species. However, very few scientific studies on SM variation have been conducted in both the domesticated landraces of chile peppers and in their wild relatives in the Neotropics. In particular, capsaicinoids in Capsicum fruits and on their seeds differ in the specificity of their ecological effects from broad-spectrum toxins in other members of the Solanaceae. They do so in a manner that mediates specific ecological interactions with a variety of sympatric Neotropical vertebrates, invertebrates, nurse plants and microbes. Specifically, capsaicin is a secondary metabolite (SM in the placental tissues of the chile fruit that mediates interactions with seed dispersers such as birds, and with seed predators, ranging from fungi to insects and rodents. As with other Solanaceae, a wide range of SMs in Capsicum spp. function to ecologically mediate the effects of a variety of biotic and abiotic stresses on wild chile peppers in certain tropical and subtropical habitats. However, species in the genus Capsicum are the only ones found within any solanaceous genus that utilize capsaicinoids as their primary means of chemical defense. We demonstrate how exploring in tandem the evolutionary ecology and the ethnobotany of human-chile interactions can generate and test novel hypotheses with regard to how the domestication process shifts plant chemical defense strategies in a variety of tropical crops. To do so, we draw upon recent advances regarding the chemical ecology of a number of wild Capsicum species found in the Neotropics. We articulate three hypotheses regarding

Quantized beam shifts in graphene

Energy Technology Data Exchange (ETDEWEB)

de Melo Kort-Kamp, Wilton Junior [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Sinitsyn, Nikolai [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Dalvit, Diego Alejandro Roberto [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2015-10-08

We predict the existence of quantized Imbert-Fedorov, Goos-Hanchen, and photonic spin Hall shifts for light beams impinging on a graphene-on-substrate system in an external magnetic field. In the quantum Hall regime the Imbert-Fedorov and photonic spin Hall shifts are quantized in integer multiples of the fine structure constant α, while the Goos-Hanchen ones in multiples of α². We investigate the influence on these shifts of magnetic field, temperature, and material dispersion and dissipation. An experimental demonstration of quantized beam shifts could be achieved at terahertz frequencies for moderate values of the magnetic field.

NMR chemical shift and J coupling parameterization and quantum mechanical reference spectrum simulation for selected nerve agent degradation products in aqueous conditions.

Science.gov (United States)

Koskela, Harri; Anđelković, Boban

2017-10-01

The spectral parameters of selected nerve agent degradation products relevant to the Chemical Weapons Convention, namely, ethyl methylphosphonate, isopropyl methylphosphonate, pinacolyl methylphosphonate and methylphosphonic acid, were studied in wide range of pH conditions and selected temperatures. The pH and temperature dependence of chemical shifts and J couplings was parameterized using Henderson-Hasselbalch-based functions. The obtained parameters allowed calculation of precise chemical shifts and J coupling constants in arbitrary pH conditions and typical measurement temperatures, thus facilitating quantum mechanical simulation of reference spectra in the chosen magnetic field strength for chemical verification. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Exposure to Crude Oil and Chemical Dispersant May Impact Marine Microbial Biofilm Composition and Steel Corrosion

Directory of Open Access Journals (Sweden)

Jennifer L. Salerno

2018-06-01

Full Text Available The release of hydrocarbons and chemical dispersant in marine environments may disrupt benthic ecosystems, including artificial reefs, formed by historic steel shipwrecks, and their associated organisms. Experiments were performed to determine the impacts of crude oil, dispersed crude oil, and dispersant on the community structure and function of microorganisms in seawater (SW and biofilms formed on carbon steel, a common ship hull construction material. Steel corrosion was also monitored to illustrate how oil spills may impact preservation of steel shipwrecks. Microcosms were filled with seawater (SW and incubated at 4°C. Carbon steel disks (CSDs were placed in each tank, and tanks were amended with crude oil and/or dispersant or no treatment. SW and CSD biofilms were sampled biweekly for genetic analysis using Illumina sequencing of 16S ribosomal RNA gene amplicons. Predicted and sequenced bacterial metagenomes were analyzed to examine impacts of oil and dispersant on metabolic function. Gammaproteobacteria, Alphaproteobacteria, and Flavobacteriia dominated SW and biofilms. Bacterial community structure differed significantly between treatments for SW and biofilms. OTUs affiliated with known (Pseudomonas and potential (Marinomonas hydrocarbon-degraders were roughly twice as abundant in biofilms treated with oil and dispersed oil, and steel corrosion of CSDs in these treatments was higher compared to control and dispersant treatments. OTUs affiliated with the Rhodobacteraceae family (biofilm formers and potential oil degraders were less abundant in the dispersant treatment compared to other treatments in biofilm and SW samples, but OTUs affiliated with the Pseudoalteromonas genus (biofilm formers and proposed hydrocarbon degraders were more abundant in dispersant-treated biofilms. Overall, functional gene analyses revealed a decrease in genes (predicted using PICRUSt and observed in sequenced metagenomes associated with hydrocarbon degradation

Dispersing powders in liquids

CERN Document Server

Nelson, RD

1988-01-01

This book provides powder technologists with laboratory procedures for selecting dispersing agents and preparing stable dispersions that can then be used in particle size characterization instruments. Its broader goal is to introduce industrial chemists and engineers to the phenomena, terminology, physical principles, and chemical considerations involved in preparing and handling dispersions on a commercial scale. The book introduces novices to: - industrial problems due to improper degree of dispersion; - the nomenclature used in describing particles; - the basic physica

More rapid climate change promotes evolutionary rescue through selection for increased dispersal distance.

Science.gov (United States)

Boeye, Jeroen; Travis, Justin M J; Stoks, Robby; Bonte, Dries

2013-02-01

Species can either adapt to new conditions induced by climate change or shift their range in an attempt to track optimal environmental conditions. During current range shifts, species are simultaneously confronted with a second major anthropogenic disturbance, landscape fragmentation. Using individual-based models with a shifting climate window, we examine the effect of different rates of climate change on the evolution of dispersal distances through changes in the genetically determined dispersal kernel. Our results demonstrate that the rate of climate change is positively correlated to the evolved dispersal distances although too fast climate change causes the population to crash. When faced with realistic rates of climate change, greater dispersal distances evolve than those required for the population to keep track of the climate, thereby maximizing population size. Importantly, the greater dispersal distances that evolve when climate change is more rapid, induce evolutionary rescue by facilitating the population in crossing large gaps in the landscape. This could ensure population persistence in case of range shifting in fragmented landscapes. Furthermore, we highlight problems in using invasion speed as a proxy for potential range shifting abilities under climate change.

Shift of large-scale atmospheric systems over Europe during late MIS 3 and implications for Modern Human dispersal.

Science.gov (United States)

Obreht, Igor; Hambach, Ulrich; Veres, Daniel; Zeeden, Christian; Bösken, Janina; Stevens, Thomas; Marković, Slobodan B; Klasen, Nicole; Brill, Dominik; Burow, Christoph; Lehmkuhl, Frank

2017-07-19

Understanding the past dynamics of large-scale atmospheric systems is crucial for our knowledge of the palaeoclimate conditions in Europe. Southeastern Europe currently lies at the border between Atlantic, Mediterranean, and continental climate zones. Past changes in the relative influence of associated atmospheric systems must have been recorded in the region's palaeoarchives. By comparing high-resolution grain-size, environmental magnetic and geochemical data from two loess-palaeosol sequences in the Lower Danube Basin with other Eurasian palaeorecords, we reconstructed past climatic patterns over Southeastern Europe and the related interaction of the prevailing large-scale circulation modes over Europe, especially during late Marine Isotope Stage 3 (40,000-27,000 years ago). We demonstrate that during this time interval, the intensification of the Siberian High had a crucial influence on European climate causing the more continental conditions over major parts of Europe, and a southwards shift of the Westerlies. Such a climatic and environmental change, combined with the Campanian Ignimbrite/Y-5 volcanic eruption, may have driven the Anatomically Modern Human dispersal towards Central and Western Europe, pointing to a corridor over the Eastern European Plain as an important pathway in their dispersal.

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

Science.gov (United States)

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.

Gain-assisted control of the Goos-Haenchen shift

Energy Technology Data Exchange (ETDEWEB)

Ziauddin,; Qamar, Sajid [Centre for Quantum Physics, COMSATS Institute of Information Technology, Islamabad (Pakistan); Department of Physics, COMSATS Institute of Information Technology, Islamabad (Pakistan)

2011-11-15

A gain-assisted model is considered to study the Goos-Haenchen (GH) shift behavior in the reflected and transmitted light. In this model, a probe light is incident on a cavity containing three-level dilute gaseous atomic medium. The atom-field interaction follows two-photon Raman transitions, and the dielectric susceptibility of the medium exhibits dispersion and gain properties [L. J. Wang, A. Kuzmich, and A. Dogariu, Nature (London) 406, 227 (2000)]. Under appropriate conditions, two gain peaks are observed with anomalous dispersion between the peaks, whereas normal dispersion can be observed at and around the gain maxima. The manipulation of the detuning associated with the probe light field which interacts with the intracavity medium during its propagation through the cavity can lead to a control over negative and positive GH shift in the reflected and transmitted light beam via the anomalous and normal dispersion of the medium.

Benchmarking Hydrogen and Carbon NMR Chemical Shifts at HF, DFT, and MP2 Levels.

Science.gov (United States)

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.

A laboratory dispersant effectiveness test which reflects dispersant efficiency in the field

International Nuclear Information System (INIS)

Lunel, T.; Wood, P.

1996-01-01

Oil dispersion efficiencies of surfactants, from laboratory dispersion tests and field data were compared and calibrated. Data from an oil spill, where dispersants were used as a major part of the response, was analysed. The data was accumulated through the monitoring of the dispersant operation of the Sea Empress spill incident, in which Forties Blend oil was spilled at sea. This detailed data set was used to calibrate existing laboratory dispersant tests, and to devise a new International Dispersant Effectiveness Test. The objective was to create a comprehensive guide to decision making on whether and when to start a dispersant spraying operation. The dispersion efficiencies obtained from the laboratory dispersant tests were compared with field data. Flume tests produced the highest percentage of dispersed oil for all the dispersal tests. However, it was emphasised that the total percentage of oil dispersed should not be the only measure of dispersant effectiveness, since it does not distinguish between the contribution of natural and chemically enhanced dispersion. 9 refs., 1 tab., 9 figs

Experimental studies of thermal and chemical interactions between molten aluminum and nuclear dispersion fuels with water

International Nuclear Information System (INIS)

Farahani, A.A.

1997-01-01

Because of the possibility of rapid physical and chemical molten fuel-water interactions during a core melt accident in noncommercial or experimental reactors, it is important to understand the interactions that might occur if these materials were to contact water. An existing vertical 1-D shock tube facility was improved and a gas sampling device to measure the gaseous hydrogen in the upper chamber of the shock tube was designed and built to study the impact of a water column driven downward by a pressurized gas onto both molten aluminum (6061 alloy) and oxide and silicide depleted nuclear dispersion fuels in aluminum matrices. The experiments were carried out with melt temperatures initially at 750 to 1,000 C and water at room temperature and driving pressures of 0.5 and 1 MPa. Very high transient pressures, in many cases even larger than the thermodynamic critical pressure of the water (∼ 20 MPa), were generated due to the interactions between the water and the crucible and its contents. The molten aluminum always reacted chemically with the water but the reaction did not increase consistently with increasing melt temperature. An aluminum ignition occurred when water at room temperature impacted 28.48 grams of molten aluminum at 980.3 C causing transient pressures greater than 69 MPa. No signs of aluminum ignition were observed in any of the experiments with the depleted nuclear dispersion fuels, U 3 O 8 -Al and U 3 Si 2 -Al. The greater was the molten aluminum-water chemical reaction, the finer was the debris recovered for a given set of initial conditions. Larger coolant velocities (larger driving pressures) resulted in more melt fragmentation but did not result in more molten aluminum-water chemical reaction. Decreasing the water temperature also resulted in more melt fragmentation and did not suppress the molten aluminum-water chemical reaction

Optimal voxel size for measuring global gray and white matter proton metabolite concentrations using chemical shift imaging

DEFF Research Database (Denmark)

Hanson, Lars Peter Grüner; Adalsteinsson, E; Pfefferbaum, A

2000-01-01

Quantification of gray and white matter levels of spectroscopically visible metabolites can provide important insights into brain development and pathological conditions. Chemical shift imaging offers a gain in efficiency for estimation of global gray and white matter metabolite concentrations co...

Study of chemical shifts of the chloroform complexes with cyclic donors of electrons

International Nuclear Information System (INIS)

Blaszkiewicz, B.; Pajak, Z.

1973-01-01

Chemical shifts of chloroform complexes with the heterocyclic electron donors: pyridine, piperidine, alpha-picoline and gamma-picoline have been studied using the high resolution (5.10 -9 ) spectrometer operating at 80 MHz. An attempt has also been made to study the three - component solutions of : chloroform, a heterocyclic donor of electrons and carbon tetrachloride. The results, which have been obtained, indicate that the complex-forming power of pyridine and other electron donors is greater in carbon tetrachloride than in other solvents. (S.B.)

Coronary artery atherosclerosis associated with shift work in chemical plant workers by using coronary CT angiography.

Science.gov (United States)

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/

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

Science.gov (United States)

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.

Is the Lamb shift chemically significant?

Science.gov (United States)

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

2001-01-01

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

Multiple soliton self-frequency shift cancellations in a temporally tailored photonic crystal fiber

Energy Technology Data Exchange (ETDEWEB)

Liu, Lai; Kang, Zhe; Li, Qing; Gao, Xuejian; Qin, Guanshi, E-mail: qings@jlu.edu.cn, E-mail: wpqin@jlu.edu.cn; Qin, Weiping, E-mail: qings@jlu.edu.cn, E-mail: wpqin@jlu.edu.cn [State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, 2699 Qianjin Street, Changchun 130012 (China); Liao, Meisong; Hu, Lili [Key Laboratory of Materials for High Power Laser, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai 201800 (China); Ohishi, Yasutake [Research Center for Advanced Photon Technology, Toyota Technological Institute, 2-12-1 Hisakata, Tempaku, Nagoya 468-8511 (Japan)

2014-11-03

We report the generation of multiple soliton self-frequency shift cancellations in a temporally tailored tellurite photonic crystal fiber (PCF). The temporally regulated group velocity dispersion (GVD) is generated in the fiber by soliton induced optical Kerr effect. Two red-shifted dispersive waves spring up when two Raman solitons meet their own second zero-dispersion-wavelengths in the PCF. These results show how, through temporally tailored GVD, nonlinearities can be harnessed to generate unexpected effects.

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

International Nuclear Information System (INIS)

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

2015-01-01

Aim: 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. Materials and methods: 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. Results: 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). Conclusion: 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. - Highlights: • Chemical shift artefact in liver DWI is markedly decreased by applying SSGR. • Liver lesion conspicuity is improved by applying SSGR to DWI. • In SNR of the liver, SSGR-DWI is better than conventional DWI

Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction

International Nuclear Information System (INIS)

Lehtivarjo, Juuso; Tuppurainen, Kari; Hassinen, Tommi; Laatikainen, Reino; Peräkylä, Mikael

2012-01-01

While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein 1 H chemical shifts in which molecular motions, the 4th dimension, were modeled using molecular dynamics (MD) simulations. Although the approach clearly improved the prediction, the X-ray structures and single NMR conformers used in the model cannot be considered fully realistic models of protein in solution. In this work, NMR ensembles (NMRE) were used to expand the conformational space of proteins (e.g. side chains, flexible loops, termini), followed by MD simulations for each conformer to map the local fluctuations. Compared with the non-dynamic model, the NMRE+MD model gave 6–17% lower root-mean-square (RMS) errors for different backbone nuclei. The improved prediction indicates that NMR ensembles with MD simulations can be used to obtain a more realistic picture of protein structures in solutions and moreover underlines the importance of short and long time-scale dynamics for the prediction. The RMS errors of the NMRE+MD model were 0.24, 0.43, 0.98, 1.03, 1.16 and 2.39 ppm for 1 Hα, 1 HN, 13 Cα, 13 Cβ, 13 CO and backbone 15 N chemical shifts, respectively. The model is implemented in the prediction program 4DSPOT, available at http://www.uef.fi/4dspothttp://www.uef.fi/4dspot.

Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction

Energy Technology Data Exchange (ETDEWEB)

Lehtivarjo, Juuso, E-mail: juuso.lehtivarjo@uef.fi; Tuppurainen, Kari; Hassinen, Tommi; Laatikainen, Reino [University of Eastern Finland, School of Pharmacy (Finland); Peraekylae, Mikael [University of Eastern Finland, Institute of Biomedicine (Finland)

2012-03-15

While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein {sup 1}H chemical shifts in which molecular motions, the 4th dimension, were modeled using molecular dynamics (MD) simulations. Although the approach clearly improved the prediction, the X-ray structures and single NMR conformers used in the model cannot be considered fully realistic models of protein in solution. In this work, NMR ensembles (NMRE) were used to expand the conformational space of proteins (e.g. side chains, flexible loops, termini), followed by MD simulations for each conformer to map the local fluctuations. Compared with the non-dynamic model, the NMRE+MD model gave 6-17% lower root-mean-square (RMS) errors for different backbone nuclei. The improved prediction indicates that NMR ensembles with MD simulations can be used to obtain a more realistic picture of protein structures in solutions and moreover underlines the importance of short and long time-scale dynamics for the prediction. The RMS errors of the NMRE+MD model were 0.24, 0.43, 0.98, 1.03, 1.16 and 2.39 ppm for {sup 1}H{alpha}, {sup 1}HN, {sup 13}C{alpha}, {sup 13}C{beta}, {sup 13}CO and backbone {sup 15}N chemical shifts, respectively. The model is implemented in the prediction program 4DSPOT, available at http://www.uef.fi/4dspothttp://www.uef.fi/4dspot.

Effect of mechanical and chemical clay removals by hydrocyclone and dispersants on coal flotation

Energy Technology Data Exchange (ETDEWEB)

Oats, W.J.; Ozdemir, O.; Nguyen, A.V. [University of Queensland, Brisbane, Qld. (Australia). School of Chemical Engineering

2010-04-15

Fine minerals, mostly clays, are known to have a detrimental effect on coal flotation. This paper focuses on the effect of mechanical and chemical removals of fine minerals by hydrocyclone and dispersants on coal flotation. The experimental results showed that the flotation recovery slightly increased from medium acidic to medium alkaline ranges. The flotation experiments carried out with dispersants at different dosages showed that the dispersants did not enhance the flotation recovery significantly. However, the removal of the fine fraction from the feed using a hydrocyclone significantly increased the flotation recovery. The bubble-particle attachment tests also indicated that the attachment time between an air bubble and the coal particles increased in the presence of clay particles. These attachment time results clearly showed that the clay particles adversely affected the flotation of coal particles by covering the coal surfaces which reduced the efficiency of bubble-coal attachment. An analysis based on the colloid stability theory showed that the clay coating was governed by the van der Waals attraction and that the double-layer interaction played a secondary role. It was also concluded that the best way to increase the flotation recovery in the presence of clays was to remove these fine minerals by mechanical means such as hydrocylones.

Toxicity of Chevron Escravos crude oil and chemical dispersant on guinea pig testicular function.

Science.gov (United States)

Afonne, Onyenmechi Johnson; Onyiaorah, Igwebuike Victor; Orisakwe, Orish Ebere

2013-01-01

Chemical contaminants have been found to affect reproductive functions in mammals. This study investigated the effect of Chevron Escravos crude oil and Emulsol L.W. dispersant on the testicular functions of guinea pig. Eight groups of seven sexually mature male guinea pigs each were given 1250, 2500, or 5000 mg/kg of crude oil and dispersant for 7 days. The fluid and food intake and body weight of the animals were measured daily throughout the study. After the exposure period, sperm quality analysis was carried out, and fructose and lactate dehydrogenase were analyzed in tissue homogenate, while testosterone and estradiol were assayed in blood. The right testis was also processed for histological analysis. The epididymal sperm number and fructose level of treated animals showed a significant dose-dependent decrease (pguinea pigs. The possible mechanism of toxicity is suggested to be by stimulation of hormone production from the adrenal cortex, causing a negative feedback on gonadotropin-releasing hormone in the pituitary gland to suppress spermatogenesis.

NUMERICAL SIMULATION OF TOXIC CHEMICAL DISPERSION AFTER ACCIDENT AT RAILWAY

Directory of Open Access Journals (Sweden)

M. M. Biliaiev

2016-04-01

Full Text Available Purpose. This research focuses on the development of an applied numerical model to calculate the dynamics of atmospheric pollution in the emission of dangerous chemical substances in the event of transportation by railway. Methodology. For the numerical simulation of transport process of the dangerous chemical substance in the atmosphere the equation of convection-diffusion pollutant transport is used. This equation takes into account the effect of wind, atmospheric diffusion, the power of emission source, as well as the movement of the source of emission (depressurized tank on the process of pollutant dispersion. When carrying out computing experiment one also takes into account the profile of the speed of the wind flow. For the numerical integration of pollutant transport in the atmosphere implicit finite-difference splitting scheme is used. The numerical calculation is divided into four steps of splitting and at each step of splitting the unknown value of the concentration of hazardous substance is determined by the explicit running account scheme. On the basis of the numerical model it was created the code using the algorithmic language FORTRAN. One conducted the computational experiments to assess the level of air pollution near the railway station «Illarionovo» in the event of a possible accident during transportation of ammonia. Findings. The proposed model allows you to quickly calculate the air pollution after the emission of chemically hazardous substance, taking into account the motion of the emission source. The model makes it possible to determine the size of the land surface pollution zones and the amount of pollutants deposited on a specific area. Using the developed numerical model it was estimated the environmental damage near the railway station «Illarionovo». Originality. One can use the numerical model to calculate the size and intensity of the chemical contamination zones after accidents on transport. Practical value

Effects of temperature and wave conditions on chemical dispersion efficacy of heavy fuel oil in an experimental flow-through wave tank.

Science.gov (United States)

Li, Zhengkai; Lee, Kenneth; King, Thomas; Boufadel, Michel C; Venosa, Albert D

2010-09-01

The effectiveness of chemical dispersants (Corexit 9500 and SPC 1000) on heavy fuel oil (IFO180 as test oil) has been evaluated under different wave conditions in a flow-through wave tank. The dispersant effectiveness was determined by measuring oil concentrations and droplet size distributions. An analysis of covariance (ANCOVA) model indicated that wave type and temperature significantly (p or = 400 microm). Copyright 2010 Elsevier Ltd. All rights reserved.

Pressure dependence of backbone chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH{sub 2}

Energy Technology Data Exchange (ETDEWEB)

Erlach, Markus Beck; Koehler, Joerg [University of Regensburg, Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (Germany); Crusca, Edson [University of São Paulo, Physics Institute of São Carlos (Brazil); Kremer, Werner [University of Regensburg, Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (Germany); Munte, Claudia E. [University of São Paulo, Physics Institute of São Carlos (Brazil); Kalbitzer, Hans Robert, E-mail: hans-robert.kalbitzer@biologie.uni-regensburg.de [University of Regensburg, Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (Germany)

2016-06-15

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 {sup 1}H{sup α}, {sup 13}C{sup α} and {sup 13}C′ in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH{sub 2} (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{sub 1} and B{sub 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.Graphical Abstract.

Application of the Fenske-Hall molecular orbital method to the calculation of 11B NMR chemical shifts. Antipodal substituent effects in deltahedral clusters

International Nuclear Information System (INIS)

Fehlner, T.P.; Czech, P.T.; Fenske, R.F.

1990-01-01

Utilizing Fenske-Hall wave functions and eigenvalues combined with the Ramsey sum over states (SOS) approximation, it is demonstrated that the sign and magnitude of the paramagnetic contribution to the shielding correlates well with the observed 11 B chemical shifts of a substantial variety of boron- and metal-containing compounds. Analysis of the molecular orbital (MO) contributions in the SOS approximation leads to an explanation of the large downfield shifts associated with metal-rich metallaboranes. A similar analysis demonstrates the importance of selected cluster occupied and unoccupied MO's in explaining both exo-cage substituent effects in which the antipodal boron resonance is shifted upfield and endo-cage substituent effects (interchange of isolobal fragments within the cage framework) in which the antipodal boron resonance is shifted downfield. Exo- and endo-cage substitution perturbs these MO's in an understandable fashion, leading to an internally consistent explanation of the observed chemical shift changes. 36 refs., 8 figs., 4 tabs

Dispersibility and chemical bonds between multi-walled carbon nanotubes and poly(ether ether ketone) in nanocomposite fibers

International Nuclear Information System (INIS)

Yanmei, Jin; Haihui, Liu; Ning, Wang; Lichen, Hou; Xing-Xiang, Zhang

2012-01-01

A series of multi-walled carbon nanotubes (MWNTs)/poly(ether ether ketone)(PEEK) nanocomposite fibers were fabricated by mixing, melt extruding PEEK with different loadings and species of MWNTs, and melt-spun the blended chips. Nanocomposite fibers were heat-stretched and heat-treated. The morphology and dispersibility of MWNTs in nanocomposite fibers were observed using a field emission environmental scanning electron microscope (FESEM) and a transmission electron microscope (TEM). The thermal and crystallization behavior of nanocomposite fibers were characterized using differential scanning calorimetry (DSC) and an X-ray diffractometer (XRD). Mechanical properties were tested using a tensile strength tester. MWNTs tend to aggregate when the loading exceeds 0.8 wt%. Functional groups on MWNTs improve the hydrophobicity and the dispersibility of MWNTs in PEEK matrix. The enhancement of mechanical properties depends on the loading and species of functional groups. The most effectively reinforced effect is in the sequence, carboxylic MWNTs (MWNT–COOH) > hydroxyl MWNTs (MWNT–OH) > MWNTs, which can be explained by the strong hydrogen bonding and the affinity between MWNT–COOH and PEEK, MWNT–OH and PEEK, and possible formation of a chemical bond between MWNT–COOH and PEEK. A nanocomposite fiber with excellent mechanical property was fabricated using 0.8 wt% MWNT–COOH as filler. The Young's modulus is 1.7 GPa; and the stress is 648 MPa. -- Highlights: ► Functional groups on MWNTs improve their hydrophobility and dispersability. ► Mechanical properties depend on the content and species of the functional groups. ► The reinforced effect is in the sequence, carboxylic MWNTs > hydroxyl MWNTs > MWNTs. ► The strength behavior was result of hydrogen bond, affinity and chemical bond. ► Dispersability of MWNTs in matrix was analyzed by calculating solubility parameter.

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

Science.gov (United States)

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.

Dispersion cancellation in a triple Laue interferometer

International Nuclear Information System (INIS)

Lemmel, Hartmut

2014-01-01

The concept of dispersion cancellation has been established in light optics to improve the resolution of interferometric measurements on dispersive media. Odd order dispersion cancellation allows to measure phase shifts without defocusing the interferometer due to wave packet displacements, while even order dispersion cancellation allows to measure time lags without losing resolution due to wave packet spreading. We report that either type of dispersion cancellation can be realized very easily in a triple Laue interferometer. Such interferometers are Mach–Zehnder interferometers based on Bragg diffraction, and are commonly used for neutrons and x-rays. Although the first x-ray interferometer was built nearly five decades ago, the feature of dispersion cancellation hasn't been recognized so far because the concept was hardly known in the neutron and x-ray community. However, it explains right away the surprising decoupling of phase shift and spatial displacement that we have discovered recently in neutron interferometry (Lemmel and Wagh 2010 Phys. Rev. A 82 033626). Furthermore, this article might inspire the light optics community to consider whether a triple Laue interferometer for laser light would be useful and feasible. We explain how dispersion cancellation works in neutron interferometry, and we describe the setup rigorously by solving the Schrödinger equation and by calculating the path integral. We point out, that the latter has to be evaluated with special care since in our setup the beam trajectory moves with respect to the crystal lattice of the interferometer. (paper)

Differentiation of osteoporotic and neoplastic vertebral fractures by chemical shift {l_brace}in-phase and out-of phase{r_brace} MR imaging

Energy Technology Data Exchange (ETDEWEB)

Ragab, Yasser [Radiology Department, Faculty of Medicine, Cairo University (Egypt); Radiology Department, Dr Erfan and Bagedo General Hospital (Saudi Arabia)], E-mail: yragab61@hotmail.com; Emad, Yasser [Rheumatology and Rehabilitation Department, Faculty of Medicine, Cairo University (Egypt); Rheumatology and Rehabilitation Department, Dr Erfan and Bagedo General Hospital (Saudi Arabia)], E-mail: yasseremad68@yahoo.com; Gheita, Tamer [Rheumatology and Rehabilitation Department, Faculty of Medicine, Cairo University (Egypt)], E-mail: gheitamer@yahoo.com; Mansour, Maged [Oncology Department, Faculty of Medicine, Cairo University (Egypt); Oncology Department, Dr Erfan and Bagedo General Hospital (Saudi Arabia)], E-mail: magedmansour@yahoo.com; Abou-Zeid, A. [Public Health Department, Faculty of Medicine, Cairo University, Cairo (Egypt)], E-mail: alaabouzeid@yahoo.com; Ferrari, Serge [Division of Bone Diseases, Department of Rehabilitation and Geriatrics, and WHO, Collaborating Center for Osteoporosis Prevention, Geneva University Hospital (Switzerland)], E-mail: serge.ferrari@medecine.unige.ch; Rasker, Johannes J. [Rheumatologist University of Twente, Enschede (Netherlands)], E-mail: j.j.rasker@utwente.nl

2009-10-15

Objective: The objective of this study was to establish the cut-off value of the signal intensity drop on chemical shift magnetic resonance imaging (MRI) with appropriate sensitivity and specificity to differentiate osteoporotic from neoplastic wedging of the spine. Patients and methods: All patients with wedging of vertebral bodies were included consecutively between February 2006 and January 2007. A chemical shift MRI was performed and signal intensity after (in-phase and out-phase) images were obtained. A DXA was performed in all. Results: A total of 40 patients were included, 20 with osteoporotic wedging (group 1) and 20 neoplastic (group 2). They were 21 males and 19 females. Acute vertebral collapse was observed in 15 patients in group 1 and subacute collapse in another 5 patients, while in group 2, 11 patients showed acute collapse and 9 patients (45%) showed subacute vertebral collapse. On the chemical shift MRI a substantial reduction in signal intensity was found in all lesions in both groups. The proportional changes observed in signal intensity of bone marrow lesions on in-phase compared with out-of-phase images showed significant differences in both groups (P < 0.05). At a cut-off value of 35%, the observed sensitivity of out-of-phase images was 95%, specificity was 100%, positive predictive value was 100% and negative predictive value was 95.2%. Conclusion: A chemical shift MRI is useful in order to differentiate patients with vertebral collapse due to underlying osteoporosis or neoplastic process.

Effects of species biological traits and environmental heterogeneity on simulated tree species distribution shifts under climate change.

Science.gov (United States)

Wang, Wen J; He, Hong S; Thompson, Frank R; Spetich, Martin A; Fraser, Jacob S

2018-09-01

Demographic processes (fecundity, dispersal, colonization, growth, and mortality) and their interactions with environmental changes are not well represented in current climate-distribution models (e.g., niche and biophysical process models) and constitute a large uncertainty in projections of future tree species distribution shifts. We investigate how species biological traits and environmental heterogeneity affect species distribution shifts. We used a species-specific, spatially explicit forest dynamic model LANDIS PRO, which incorporates site-scale tree species demography and competition, landscape-scale dispersal and disturbances, and regional-scale abiotic controls, to simulate the distribution shifts of four representative tree species with distinct biological traits in the central hardwood forest region of United States. Our results suggested that biological traits (e.g., dispersal capacity, maturation age) were important for determining tree species distribution shifts. Environmental heterogeneity, on average, reduced shift rates by 8% compared to perfect environmental conditions. The average distribution shift rates ranged from 24 to 200myear -1 under climate change scenarios, implying that many tree species may not able to keep up with climate change because of limited dispersal capacity, long generation time, and environmental heterogeneity. We suggest that climate-distribution models should include species demographic processes (e.g., fecundity, dispersal, colonization), biological traits (e.g., dispersal capacity, maturation age), and environmental heterogeneity (e.g., habitat fragmentation) to improve future predictions of species distribution shifts in response to changing climates. Copyright © 2018 Elsevier B.V. All rights reserved.

Correlations of the chemical shift on fasly rotating biological solids by means of NMR spectroscopy

International Nuclear Information System (INIS)

Herbst, Christian

2010-01-01

The basic aim of the thesis was the development and improvement of homo- and heteronuclear feedback sequences for the generation of correlation spectra of the chemical shift. In a first step the possibility of the acquisition of 13 C- 13 correlation spectra of the chemical shift by means of inversion pulses with low RF power factor was studied. Furthermore it was shown that broad-band phase-modulated inversion and universal rotational pulses can be constructed by means of global optimization procedures like the genetic algorithms under regardment of the available RF field strength. By inversion, universal rotational, and 360 pulses as starting values of the optimization efficient homonuclear CN n ν and RN n ν mixing sequences as well as heteronuclear RN n ν s ,ν k feedback sequences were generated. The satisfactory power of the numerically optimized sequences was shown by means of the simulation as well by means of correlation experiments of the chemical shift of L-histidine, L-arginine, and the (CUG) 97 -RNA. This thesis deals furthermore with the possibility to acquire simultaneously different signals with several receivers. By means of numerically optimized RN n ν s ,ν k pulse sequences both 15 N- 13 C and 13 C- 15 N correlation spectra were simultaneously generated. Furthermore it could be shown that the simultaneous acquisition of 3D- 15 N- 13 C- 13 C and 13 C- 15 N-( 1 H)- 1 H correlation spectra is possible. By this in only one measurement process resonance assignments can be met and studies of the global folding performed. A further application of several receivers is the simultaneous acquisition of CHHC, NHHN, NHHC, as well as CHHN spectra. By such experiments it is possible to characterize the hydrogen-bonding pattern and the glycosidic torsion angle χ in RNA. This was demonstrated by means of the (CUG) 97 -RNA. The simultaneous acquisition of all relevant crossing signals of the correlation spectra leads not only to an essential time saving, but

Determination of hydration numbers of electrolytes from temperature dependence of PMR chemical shifts

International Nuclear Information System (INIS)

Subramanian, N.

1979-01-01

The method proposed by Malinowski et al. for the determination of effective hydration numbers (h) of electrolytes leads to a consistent incrrease in the observed values of 'h' with increase in solution concentration. An attempt is made to rationalize the experimental results by cosidering the simultaneous effects of temperature and concentration on the proton chemical shift. It is suggested that Malinowski's technique might yeld 'h' values very close to the true value for those ions for which there is a fortuitous cancellation of structure-making and structure-breaking properties. (Author) [pt

THE STUDYING OF COLLOIDAL-CHEMICAL PROPERTIES OF CLAY MINERALS DISPERSIONS

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A. F. Tymchuk

2015-02-01

Full Text Available The element structure is studied, the microscopic analysis of fine-dispersed min­eral systems (ground sediments of a mouth of the river Danube is carried out. The sedimentation process of clay minerals dispersions in solutions of surfactants and macromolecular substances is studied. Concentration intervals of stabilization of investigating dispersions were defined.

Discobiol program : investigation of dispersant use in coastal and estuarine waters

Energy Technology Data Exchange (ETDEWEB)

Merlin, F.X.; Le Floch, S.; Dussauze, M. [Cedre, Brest Cedex (France); Theron, M. [Brest Univ., European University of Britanny, Rennes (France); Quentel, C. [AFSSA, French Food Safety Agency, Paris (France); Thomas, H. [LIENS, CNRS-Univ. of La Rochelle, La Rochelle Cedex (France)

2009-07-01

This paper reported on the Discobiol work program designed to acquire comparable information on the impact of mechanically and chemically dispersed oil on different habitats and resources, particularly in estuaries or close to bays. The study involved 3 phases for the analysis of lethal and sub-lethal effects in pelagic and benthic communities, notably organisms in the water column, mudflats and salt marshes. The ultimate objective was to use the information to make recommendations regarding the use of dispersants in these 3 areas. Dispersants are known to be effective for offshore oil spill response when dilution conditions are high and dispersed oil concentrations decrease rapidly below levels that could harm the environment. However, dilution can be restricted in coastal areas, thus limiting the use of dispersant. All the tests conducted in this study were conducted using brut Arabian light oil that was pre-evaporated to simulate realistic conditions. The study examined whether the presence of oil leads to different effects than the control and whether the chemically dispersed oil gave different effects than the mechanical dispersion. The comparison with chemical dispersion in clear sea water examined whether the presence of suspended materials change the effect of the chemical dispersion. Results for the different phases of the project were presented. The preliminary results tend to open the use of chemical dispersion of oil slicks in coastal areas. The mixture of dispersant plus oil seems to be less detrimental than oil alone, particularly for turbot. The final conclusion regarding chemical dispersion of oil slicks in coastal areas will have to be formulated at the end of the project because coastal ecosystems depend on biotic and abiotic factors. The final phase will take place in a realistic environment in a salt marsh ecosystem at La Rochelle, France. 6 refs., 6 tabs., 6 figs.

Discobiol program : investigation of dispersant use in coastal and estuarine waters

International Nuclear Information System (INIS)

Merlin, F.X.; Le Floch, S.; Dussauze, M.; Theron, M.; Quentel, C.; Thomas, H.

2009-01-01

This paper reported on the Discobiol work program designed to acquire comparable information on the impact of mechanically and chemically dispersed oil on different habitats and resources, particularly in estuaries or close to bays. The study involved 3 phases for the analysis of lethal and sub-lethal effects in pelagic and benthic communities, notably organisms in the water column, mudflats and salt marshes. The ultimate objective was to use the information to make recommendations regarding the use of dispersants in these 3 areas. Dispersants are known to be effective for offshore oil spill response when dilution conditions are high and dispersed oil concentrations decrease rapidly below levels that could harm the environment. However, dilution can be restricted in coastal areas, thus limiting the use of dispersant. All the tests conducted in this study were conducted using brut Arabian light oil that was pre-evaporated to simulate realistic conditions. The study examined whether the presence of oil leads to different effects than the control and whether the chemically dispersed oil gave different effects than the mechanical dispersion. The comparison with chemical dispersion in clear sea water examined whether the presence of suspended materials change the effect of the chemical dispersion. Results for the different phases of the project were presented. The preliminary results tend to open the use of chemical dispersion of oil slicks in coastal areas. The mixture of dispersant plus oil seems to be less detrimental than oil alone, particularly for turbot. The final conclusion regarding chemical dispersion of oil slicks in coastal areas will have to be formulated at the end of the project because coastal ecosystems depend on biotic and abiotic factors. The final phase will take place in a realistic environment in a salt marsh ecosystem at La Rochelle, France. 6 refs., 6 tabs., 6 figs.

Automated NMR relaxation dispersion data analysis using NESSY

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Gooley Paul R

2011-10-01

Full Text Available Abstract Background Proteins are dynamic molecules with motions ranging from picoseconds to longer than seconds. Many protein functions, however, appear to occur on the micro to millisecond timescale and therefore there has been intense research of the importance of these motions in catalysis and molecular interactions. Nuclear Magnetic Resonance (NMR relaxation dispersion experiments are used to measure motion of discrete nuclei within the micro to millisecond timescale. Information about conformational/chemical exchange, populations of exchanging states and chemical shift differences are extracted from these experiments. To ensure these parameters are correctly extracted, accurate and careful analysis of these experiments is necessary. Results The software introduced in this article is designed for the automatic analysis of relaxation dispersion data and the extraction of the parameters mentioned above. It is written in Python for multi platform use and highest performance. Experimental data can be fitted to different models using the Levenberg-Marquardt minimization algorithm and different statistical tests can be used to select the best model. To demonstrate the functionality of this program, synthetic data as well as NMR data were analyzed. Analysis of these data including the generation of plots and color coded structures can be performed with minimal user intervention and using standard procedures that are included in the program. Conclusions NESSY is easy to use open source software to analyze NMR relaxation data. The robustness and standard procedures are demonstrated in this article.

A Core-Offset Mach Zehnder Interferometer Based on A Non-Zero Dispersion-Shifted Fiber and Its Torsion Sensing Application

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Eduardo Huerta-Mascotte

2016-06-01

Full Text Available In this paper, an all-fiber Mach-Zehnder interferometer (MZI based on a non-zero dispersion-shifted fiber (NZ-DSF is presented. The MZI was implemented by core-offset fusion splicing one section of a NZ-DSF fiber between two pieces of single mode fibers (SMFs. Here, the NZ-DSF core and cladding were used as the arms of the MZI, while the core-offset sections acted as optical fiber couplers. Thus, a MZI interference spectrum with a fringe contrast (FC of about 20 dB was observed. Moreover, its response spectrum was experimentally characterized to the torsion parameter and a sensitivity of 0.070 nm/° was achieved. Finally, these MZIs can be implemented in a compact size and low cost.

Tracer dispersion in two-dimensional rough fractures.

Science.gov (United States)

Drazer, G; Koplik, J

2001-05-01

Tracer diffusion and hydrodynamic dispersion in two-dimensional fractures with self-affine roughness are studied by analytic and numerical methods. Numerical simulations were performed via the lattice-Boltzmann approach, using a boundary condition for tracer particles that improves the accuracy of the method. The reduction in the diffusive transport, due to the fractal geometry of the fracture surfaces, is analyzed for different fracture apertures. In the limit of small aperture fluctuations we derive the correction to the diffusive coefficient in terms of the tortuosity, which accounts for the irregular geometry of the fractures. Dispersion is studied when the two fracture surfaces are simply displaced normally to the mean fracture plane and when there is a lateral shift as well. Numerical results are analyzed using the Lambda parameter, related to convective transport within the fracture, and simple arguments based on lubrication approximation. At very low Péclet number, in the case where fracture surfaces are laterally shifted, we show using several different methods that convective transport reduces dispersion.

Chemical constituents of Ottonia corcovadensis Miq. from Amazon forest: 1H and 13C chemical shift assignments

International Nuclear Information System (INIS)

Facundo, Valdir A.; Morais, Selene M.; Braz Filho, Raimundo

2004-01-01

In an ethanolic extract of leaves of Ottonia corcovadensis (Piperaceae) were identified sixteen terpenoids of essential oil and the three flavonoids 3',4',5,5',7-penta methoxyflavone (1), 3',4',5,7-tetra methoxyflavone (2) and 5-hydroxy-3',4',5',7-tetra methoxyflavone (3) and cafeic acid (4). Two amides (5 and 6) were isolated from an ethanolic extract of the roots. The structures were established by spectral analysis, meanly NMR (1D and 2D) and mass spectra. Extensive NMR analysis was also used to complete 1 H and 13 C chemical shift assignments of the flavonoids and amides. The components of the essential oil were identified by computer library search, retention indices and visual interpretation of mass spectra. (author)

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

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Phoebe Dreux Chappell

2013-09-01

Full Text Available 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 three-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 three-month-old Haida eddy remained largely (>80% similar over a two-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.

Coping with power dispersion?

DEFF Research Database (Denmark)

2014-01-01

The last decades have witnessed a significant shift in policy competences away from central governments in Europe. The reallocation of competences spans over three dimensions: upwards; sideways; and downwards. This collection takes the dispersion of powers as a starting point and seeks to assess...... how the actors involved cope with the new configurations. In this introduction, we discuss the conceptualization of power dispersion and highlight the ways in which the contributions add to this research agenda. We then outline some general conclusions and end by indicating future avenues of research....... Taken together, the collection contributes some answers to the challenge of defining and measuring – in a comparative way – the control and co-ordination mechanisms which power dispersion generates. It also explores the tension between political actors' quest for autonomy and the acknowledgement...

Applications of Chemical Shift Imaging to Marine Sciences

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Haakil Lee

2010-08-01

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

Improved new generation dispersants

International Nuclear Information System (INIS)

Anon.

1993-01-01

The use of dispersants to combat oil spills has attracted controversy over the years, and there has been a number of accusations of the chemicals involved doing more harm than good. A new study by the International Petroleum Industry Environmental Conservation Association discusses the positive and the negatives of dispersant use to be considered when drawing up spill contingency plans. (author)

Production of Flocculants, Adsorbents, and Dispersants from Lignin.

Science.gov (United States)

Chen, Jiachuan; Eraghi Kazzaz, Armin; AlipoorMazandarani, Niloofar; Hosseinpour Feizi, Zahra; Fatehi, Pedram

2018-04-10

Currently, lignin is mainly produced in pulping processes, but it is considered as an under-utilized chemical since it is being mainly used as a fuel source. Lignin contains many hydroxyl groups that can participate in chemical reactions to produce value-added products. Flocculants, adsorbents, and dispersants have a wide range of applications in industry, but they are mainly oil-based chemicals and expensive. This paper reviews the pathways to produce water soluble lignin-based flocculants, adsorbents, and dispersants. It provides information on the recent progress in the possible use of these lignin-based flocculants, adsorbents, and dispersants. It also critically discusses the advantages and disadvantages of various approaches to produce such products. The challenges present in the production of lignin-based flocculants, adsorbents, and dispersants and possible scenarios to overcome these challenges for commercial use of these products in industry are discussed.

Variance as a Leading Indicator of Regime Shift in Ecosystem Services

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William A. Brock

2006-12-01

Full Text Available Many environmental conflicts involve pollutants such as greenhouse gas emissions that are dispersed through space and cause losses of ecosystem services. As pollutant emissions rise in one place, a spatial cascade of declining ecosystem services can spread across a larger landscape because of the dispersion of the pollutant. This paper considers the problem of anticipating such spatial regime shifts by monitoring time series of the pollutant or associated ecosystem services. Using such data, it is possible to construct indicators that rise sharply in advance of regime shifts. Specifically, the maximum eigenvalue of the variance-covariance matrix of the multivariate time series of pollutants and ecosystem services rises prior to the regime shift. No specific knowledge of the mechanisms underlying the regime shift is needed to construct the indicator. Such leading indicators of regime shifts could provide useful signals to management agencies or to investors in ecosystem service markets.

Improvement of chemical shift selective saturation (CHESS) pulse for MR angiography

International Nuclear Information System (INIS)

Ishimori, Yoshiyuki; Sashie, Hiroyuki; Hiraga, Akira; Matsuda, Tsuyoshi

2000-01-01

We improved the fat suppression technique based on chemical shift selective saturation (CHESS). To do this, we shortened the duration of the CHESS pulse to achieve a short repetition time (TR) for MR angiography (MRA). A short-duration CHESS pulse causes broad frequency band saturation, creating extensive offset from the resonance frequency of water. In our phantom experiment, the best parameters of the short-duration CHESS pulse were 3.84 ms in duration, -650 Hz in offset frequency from water resonance, and had a 130-degree flip angle. With this technique, MRA will be able to be carried out without a significant increase in TR. Thus, better vessel contrast will be maintained in time-of-flight (TOF) MRA or contrast-enhanced MRA when using the maximum intensity projection (MIP) method. (author)

Isomer shifts and chemical bonding in crystalline Sn(II) and Sn(IV) compounds

International Nuclear Information System (INIS)

Terra, J.; Guenzburger, D.

1991-01-01

First-principles self-consistent Local Density calculations of the electronic structure of clusters representing Sn(II) (SnO, SnF 2 , SnS, SnSe) and Sn(IV) (SnO 2 , SnF 4 ) crystalline compounds were performed. Values of the electron density at the Sn nucleus were obtained and related to measured values of the Moessbauer Isomer Shifts reported in the literature. The nuclear parameter of 119 Sn derived was ΔR/R=(1.58±0.14)x10 -4 . The chemical bonding in the solids was analysed and related to the electron densities obtained. (author)

Predicting Heats of Explosion of Nitroaromatic Compounds through NBO Charges and 15N NMR Chemical Shifts of Nitro Groups

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Ricardo Infante-Castillo

2012-01-01

Full Text Available This work presents a new quantitative model to predict the heat of explosion of nitroaromatic compounds using the natural bond orbital (NBO charge and 15N NMR chemical shifts of the nitro groups (15NNitro as structural parameters. The values of the heat of explosion predicted for 21 nitroaromatic compounds using the model described here were compared with experimental data. The prediction ability of the model was assessed by the leave-one-out cross-validation method. The cross-validation results show that the model is significant and stable and that the predicted accuracy is within 0.146 MJ kg−1, with an overall root mean squared error of prediction (RMSEP below 0.183 MJ kg−1. Strong correlations were observed between the heat of explosion and the charges (R2 = 0.9533 and 15N NMR chemical shifts (R2 = 0.9531 of the studied compounds. In addition, the dependence of the heat of explosion on the presence of activating or deactivating groups of nitroaromatic explosives was analyzed. All calculations, including optimizations, NBO charges, and 15NNitro NMR chemical shifts analyses, were performed using density functional theory (DFT and a 6-311+G(2d,p basis set. Based on these results, this practical quantitative model can be used as a tool in the design and development of highly energetic materials (HEM based on nitroaromatic compounds.

CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.

Science.gov (United States)

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.

Iron oxide functionalized graphene nano-composite for dispersive solid phase extraction of chemical warfare agents from aqueous samples.

Science.gov (United States)

Chinthakindi, Sridhar; Purohit, Ajay; Singh, Varoon; Tak, Vijay; Goud, D Raghavender; Dubey, D K; Pardasani, Deepak

2015-05-15

Present study deals with the preparation and evaluation of graphene based magnetic nano-composite for dispersive solid phase extraction of Chemical Weapons Convention (CWC) relevant chemicals from aqueous samples. Nano-composite, Fe3O4@SiO2-G was synthesized by covalently bonding silica coated Fe3O4 onto the graphene sheets. Nerve agents (NA), Sulfur mustard (SM) and their non-toxic environmental markers were the target analytes. Extraction parameters like amount of sorbent, extraction time and desorption conditions were optimized. Dispersion of 20 milligram of sorbent in 200mL of water sample for 20min. followed by methanol/chloroform extraction produced average to good recoveries (27-94%) of targeted analytes. Recoveries of real agents exhibited great dependency upon sample pH and ionic strength. Sarin produced maximum recovery under mild acidic conditions (56% at pH 5) while VX demanded alkaline media (83% at pH 9). Salts presence in the aqueous samples was found to be advantageous, raising the recoveries to as high as 94% for SM. Excellent limits of detection (LOD) for sulphur mustard and VX (0.11ngmL(-1) and 0.19ngmL(-1) respectively) proved the utility of the developed method for the off-site analysis of CWC relevant chemicals. Copyright © 2015 Elsevier B.V. All rights reserved.

Parameter-free calculation of K alpha chemical shifts for Al, Si, and Ge oxides

DEFF Research Database (Denmark)

Lægsgaard, Jesper

2001-01-01

The chemical shifts of the K alpha radiation line from Al, Si, and Ge ions between their elemental and oxide forms are calculated within the framework of density functional theory using ultrasoft pseudopotentials. It is demonstrated that this theoretical approach yields quantitatively accurate...... results fur the systems investigated, provided that relaxations of the valence electrons upon the core-hole transition are properly accounted for. Therefore, such calculations provide a powerful tool for identification of impurity states based on x-ray fluorescence data. Results for an Al impurity...

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

Energy Technology Data Exchange (ETDEWEB)

Wang Jun; Liu Haiyan [University of Science and Technology of China, Hefei National Laboratory for Physical Sciences at the Microscale, and Key Laboratory of Structural Biology, School of Life Sciences (China)], E-mail: hyliu@ustc.edu.cn

2007-01-15

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

UV curable aqueous dispersions for wood coatings

International Nuclear Information System (INIS)

Peeters, S.; Bleus, J.P.; Wang, Z.J.; Arceneaux, J. A.; Hall, J.

1999-01-01

In this paper the characterisation of aqueous dispersions of UV curable resins is described. Two types of dispersions were used: dispersions that are tacky after water evaporation and tack - free before cure dispersions. The physical and rheological properties of these products have been determined and the performance of these dispersions in various formulations, especially for wood applications has been studied. With these dispersions, it is possible to produce coatings having a good cure speed, good surface hardness and good solvent -, chemical - and water resistance

Characterization of Chemical Exchange Using Relaxation Dispersion of Hyperpolarized Nuclear Spins.

Science.gov (United States)

Liu, Mengxiao; Kim, Yaewon; Hilty, Christian

2017-09-05

Chemical exchange phenomena are ubiquitous in macromolecules, which undergo conformational change or ligand complexation. NMR relaxation dispersion (RD) spectroscopy based on a Carr-Purcell-Meiboom-Gill pulse sequence is widely applied to identify the exchange and measure the lifetime of intermediate states on the millisecond time scale. Advances in hyperpolarization methods improve the applicability of NMR spectroscopy when rapid acquisitions or low concentrations are required, through an increase in signal strength by several orders of magnitude. Here, we demonstrate the measurement of chemical exchange from a single aliquot of a ligand hyperpolarized by dissolution dynamic nuclear polarization (D-DNP). Transverse relaxation rates are measured simultaneously at different pulsing delays by dual-channel 19 F NMR spectroscopy. This two-point measurement is shown to allow the determination of the exchange term in the relaxation rate expression. For the ligand 4-(trifluoromethyl)benzene-1-carboximidamide binding to the protein trypsin, the exchange term is found to be equal within error limits in neutral and acidic environments from D-DNP NMR spectroscopy, corresponding to a pre-equilibrium of trypsin deprotonation. This finding illustrates the capability for determination of binding mechanisms using D-DNP RD. Taking advantage of hyperpolarization, the ligand concentration in the exchange measurements can reach on the order of tens of μM and protein concentration can be below 1 μM, i.e., conditions typically accessible in drug discovery.

Measurement and Characterization of Hydrogen-Deuterium Exchange Chemistry Using Relaxation Dispersion NMR Spectroscopy.

Science.gov (United States)

Khirich, Gennady; Holliday, Michael J; Lin, Jasper C; Nandy, Aditya

2018-03-01

One-dimensional heteronuclear relaxation dispersion NMR spectroscopy at 13 C natural abundance successfully characterized the dynamics of the hydrogen-deuterium exchange reaction occurring at the N ε position in l-arginine by monitoring C δ in varying amounts of D 2 O. A small equilibrium isotope effect was observed and quantified, corresponding to ΔG = -0.14 kcal mol -1 . A bimolecular rate constant of k D = 5.1 × 10 9 s -1 M -1 was determined from the pH*-dependence of k ex (where pH* is the direct electrode reading of pH in 10% D 2 O and k ex is the nuclear spin exchange rate constant), consistent with diffusion-controlled kinetics. The measurement of ΔG serves to bridge the millisecond time scale lifetimes of the detectable positively charged arginine species with the nanosecond time scale lifetime of the nonobservable low-populated neutral arginine intermediate species, thus allowing for characterization of the equilibrium lifetimes of the various arginine species in solution as a function of fractional solvent deuterium content. Despite the system being in fast exchange on the chemical shift time scale, the magnitude of the secondary isotope shift due to the exchange reaction at N ε was accurately measured to be 0.12 ppm directly from curve-fitting D 2 O-dependent dispersion data collected at a single static field strength. These results indicate that relaxation dispersion NMR spectroscopy is a robust and general method for studying base-catalyzed hydrogen-deuterium exchange chemistry at equilibrium.

Production of Flocculants, Adsorbents, and Dispersants from Lignin

Directory of Open Access Journals (Sweden)

Jiachuan Chen

2018-04-01

Full Text Available Currently, lignin is mainly produced in pulping processes, but it is considered as an under-utilized chemical since it is being mainly used as a fuel source. Lignin contains many hydroxyl groups that can participate in chemical reactions to produce value-added products. Flocculants, adsorbents, and dispersants have a wide range of applications in industry, but they are mainly oil-based chemicals and expensive. This paper reviews the pathways to produce water soluble lignin-based flocculants, adsorbents, and dispersants. It provides information on the recent progress in the possible use of these lignin-based flocculants, adsorbents, and dispersants. It also critically discusses the advantages and disadvantages of various approaches to produce such products. The challenges present in the production of lignin-based flocculants, adsorbents, and dispersants and possible scenarios to overcome these challenges for commercial use of these products in industry are discussed.

Dispersant affects the cellular influences of single-wall carbon nanotube: the role of CNT as carrier of dispersants.

Science.gov (United States)

Horie, Masanori; Stowe, Mayumi; Tabei, Miki; Kato, Haruhisa; Nakamura, Ayako; Endoh, Shigehisa; Morimoto, Yasuo; Fujita, Katsuhide

2013-06-01

The application of carbon nanotube (CNT) as a functional material to engineering and life sciences is advanced. In order to evaluate the cytotoxicity of CNT in vitro, some chemical and biological reagents are used for dispersants. In the present study, the cellular influences of six kinds of chemical or biological reagents used as dispersants were examined. Pluronic F-127, Pluronic F-68, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), pulmonary surfactant preparation Surfacten®, bovine serum albumin (BSA) and Tween 80 were used in the preparation of CNT-medium dispersants. The influences of each reagent on cell viability in human lung carcinoma A549 cells were small. However, Pluronic F-127, DPPC, Surfacten® and Tween 80 induced an increase of intracellular reactive oxygen species (ROS) level. Next, CNT-medium dispersions were prepared, using each reagent as a dispersant and applied to A549 cells. The cellular influences depended on the kind of dispersant. Cells exposed to CNT dispersion including Pluronic® F-127, Surfacten®, DPPC and Tween 80 showed LDH release to the culture supernatant. Induction of intracellular ROS level was observed in cells exposed to CNT dispersion including each reagent except BSA. These results suggest that the adsorbed dispersant reagents on the surface of the CNT affect its cellular influences, particularly the induction of oxidative stress.

Nonsuppressing normal thymus on chemical-shift MR imaging and anterior mediastinal lymphoma. Differentiation with diffusion-weighted MR imaging by using the apparent diffusion coefficient

International Nuclear Information System (INIS)

Priola, Adriano Massimiliano; Priola, Sandro Massimo; Gned, Dario; Veltri, Andrea; Giraudo, Maria Teresa

2018-01-01

To prospectively evaluate usefulness of the apparent diffusion coefficient (ADC) in differentiating anterior mediastinal lymphoma from nonsuppressing normal thymus on chemical-shift MR, and to look at the relationship between patient age and ADC. Seventy-three young subjects (25 men, 48 women; age range, 9-29 years), who underwent chemical-shift MR and diffusion-weighted MR were divided into a normal thymus group (group A, 40 subjects), and a lymphoma group (group B, 33 patients). For group A, all subjects had normal thymus with no suppression on opposed-phase chemical-shift MR. Two readers measured the signal intensity index (SII) and ADC. Differences in SII and ADC between groups were tested using t-test. ADC was correlated with age using Pearson correlation coefficient. Mean SII±standard deviation was 2.7±1.8% for group A and 2.2±2.4% for group B, with no significant difference between groups (P=.270). Mean ADC was 2.48±0.38 x 10 -3 mm 2 /s for group A and 1.24±0.23 x 10 -3 mm 2 /s for group B. A significant difference between groups was found (P<.001), with no overlap in range. Lastly, significant correlation was found between age and ADC (r=0.935, P<.001) in group A. ADC of diffusion-weighted MR is a noninvasive and accurate parameter for differentiating lymphoma from nonsuppressing thymus on chemical-shift MR in young subjects. (orig.)

Illusion optics via one-dimensional ultratransparent photonic crystals with shifted spatial dispersions.

Science.gov (United States)

Yao, Zhongqi; Luo, Jie; Lai, Yun

2017-12-11

In this work, we propose that one-dimensional ultratransparent dielectric photonic crystals with wide-angle impedance matching and shifted elliptical equal frequency contours are promising candidate materials for illusion optics. The shift of the equal frequency contour does not affect the refractive behaviors, but enables a new degree of freedom in phase modulation. With such ultratransparent photonic crystals, we demonstrate some applications in illusion optics, including creating illusions of a different-sized scatterer and a shifted source with opposite phase. Such ultratransparent dielectric photonic crystals may establish a feasible platform for illusion optics devices at optical frequencies.

MR chemical shift imaging and spectroscopy of atherosclerotic plaque

International Nuclear Information System (INIS)

Vinitski, S.; Consigny, P.M.; Shapiro, M.J.; Janes, N.; Smullens, S.N.; Rifkin, M.D.

1989-01-01

The purpose of this study was to develop a technique for in vivo imaging and characterization of atherosclerotic plaque. The authors used a spin-echo technique with a short echo time (TE) of 11 msec. Lipid/water suppression was achieved by means of hybrid chemical shift imaging. Lesions were induced in three rabbits by a combination of balloon denudation of the abdominal aorta and a high-cholesterol diet. Following in vivo imaging of these rabbit aortas and human carotid arteries (1.5 T), the animals were killed or carotid endarterectomy was performed so that the plaques could be excised. The plaques were then analyzed in vitro both histologically and with high-resolution spectroscopy (8.5 T). Use of the short TE improved lesion visualization. The fat/water suppression showed only a small amount of mobile lipids in plaque. Both MR spectroscopic and histologic analysis corroborated these images. The composition of atherosclerotic plaques in both humans and rabbits was demonstrated to be heterogeneous, with predominantly nonmobile lipids. These results suggest that the combination of short TE MR imaging and fat/water suppression can identify plaque and delineate areas containing mobile lipids

Analytic description of Raman-induced frequency shift in the case of non-soliton ultrashort pulses

Energy Technology Data Exchange (ETDEWEB)

Bugay, Aleksandr N., E-mail: bugay_aleksandr@mail.ru [Joint Institute for Nuclear Research, Joliot-Curie 6, 141980, Dubna, Moscow Region (Russian Federation); Khalyapin, Vyacheslav A., E-mail: slavasxi@gmail.com [Immanuel Kant Baltic Federal University, Kaliningrad, 236041 (Russian Federation); Kaliningrad State Technical University, Kaliningrad, 236000 (Russian Federation)

2017-01-30

Raman-induced frequency shift of ultrashort pulses have been studied extensively for the soliton propagation regime. Here we derive explicit analytic expressions for the evolution of Raman-induced frequency shift in much less studied case of non-soliton ultrashort pulses. Pulse spectra may belong to any region of group velocity dispersion including zero group dispersion point. The analysis is based on the moment method. Obtained expressions fit well to the numerical solution of the nonlinear wave equation. - Highlights: • Explicit analytic formulas for the evolution of Raman-induced frequency shift are derived in the case of non-soliton pulses. • Dynamics of non-soliton ultrashort pulses in the cases of positive and zero group dispersion is considered. • The deceleration and the saturation of Raman-induced frequency shift are analyzed. • The calculation relies on the moment method and fit well to the numerical solution of the nonlinear wave equation.

Analytic description of Raman-induced frequency shift in the case of non-soliton ultrashort pulses

International Nuclear Information System (INIS)

Bugay, Aleksandr N.; Khalyapin, Vyacheslav A.

2017-01-01

Raman-induced frequency shift of ultrashort pulses have been studied extensively for the soliton propagation regime. Here we derive explicit analytic expressions for the evolution of Raman-induced frequency shift in much less studied case of non-soliton ultrashort pulses. Pulse spectra may belong to any region of group velocity dispersion including zero group dispersion point. The analysis is based on the moment method. Obtained expressions fit well to the numerical solution of the nonlinear wave equation. - Highlights: • Explicit analytic formulas for the evolution of Raman-induced frequency shift are derived in the case of non-soliton pulses. • Dynamics of non-soliton ultrashort pulses in the cases of positive and zero group dispersion is considered. • The deceleration and the saturation of Raman-induced frequency shift are analyzed. • The calculation relies on the moment method and fit well to the numerical solution of the nonlinear wave equation.

Solid state NMR of proteins at high MAS frequencies: symmetry-based mixing and simultaneous acquisition of chemical shift correlation spectra

International Nuclear Information System (INIS)

Bellstedt, Peter; Herbst, Christian; Häfner, Sabine; Leppert, Jörg; Görlach, Matthias; Ramachandran, Ramadurai

2012-01-01

We have carried out chemical shift correlation experiments with symmetry-based mixing sequences at high MAS frequencies and examined different strategies to simultaneously acquire 3D correlation spectra that are commonly required in the structural studies of proteins. The potential of numerically optimised symmetry-based mixing sequences and the simultaneous recording of chemical shift correlation spectra such as: 3D NCAC and 3D NHH with dual receivers, 3D NC′C and 3D C′NCA with sequential 13 C acquisitions, 3D NHH and 3D NC′H with sequential 1 H acquisitions and 3D CANH and 3D C’NH with broadband 13 C– 15 N mixing are demonstrated using microcrystalline samples of the β1 immunoglobulin binding domain of protein G (GB1) and the chicken α-spectrin SH3 domain.

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.

Science.gov (United States)

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.

Relative toxicity of oil dispersants to Mytilus viridis and Macrobrachium idella

Digital Repository Service at National Institute of Oceanography (India)

DeSilva, C.; Row, A.

) was almost identical for both the species tested, although there was a significant shift in the range of LC sub(50) values, indicating that one species is less sensitive than the other. Oil dispersant mixtures were less toxic than the dispersants alone...

A New Paradigm for Chemical Engineering?

DEFF Research Database (Denmark)

Gani, Rafiqul

evidence of this change comes from the jobs taken by graduating chemical engineering professionals in North America, Europe, and some of the Asian countries. In terms of where the graduating chemical engineers are going to work, a clear shift from the commodity chemical industry to the product oriented...... businesses has been observed. There is an increasing trend within the chemical industry to focus on products and the sustainable processes that can make them. Do these changes point to a paradigm shift in chemical engineering as a discipline? Historically, two previous paradigm shifts in chemical engineering...... corresponded to major shifts in chemical engineering as a discipline, which affected not only the education of chemical engineers, but also the development of chemical engineering as a discipline. Has the time come for a new paradigm shift that will prepare the current and future chemical engineering graduates...

Conformational exchange of aromatic side chains characterized by L-optimized TROSY-selected ¹³C CPMG relaxation dispersion.

Science.gov (United States)

Weininger, Ulrich; Respondek, Michal; Akke, Mikael

2012-09-01

Protein dynamics on the millisecond time scale commonly reflect conformational transitions between distinct functional states. NMR relaxation dispersion experiments have provided important insights into biologically relevant dynamics with site-specific resolution, primarily targeting the protein backbone and methyl-bearing side chains. Aromatic side chains represent attractive probes of protein dynamics because they are over-represented in protein binding interfaces, play critical roles in enzyme catalysis, and form an important part of the core. Here we introduce a method to characterize millisecond conformational exchange of aromatic side chains in selectively (13)C labeled proteins by means of longitudinal- and transverse-relaxation optimized CPMG relaxation dispersion. By monitoring (13)C relaxation in a spin-state selective manner, significant sensitivity enhancement can be achieved in terms of both signal intensity and the relative exchange contribution to transverse relaxation. Further signal enhancement results from optimizing the longitudinal relaxation recovery of the covalently attached (1)H spins. We validated the L-TROSY-CPMG experiment by measuring fast folding-unfolding kinetics of the small protein CspB under native conditions. The determined unfolding rate matches perfectly with previous results from stopped-flow kinetics. The CPMG-derived chemical shift differences between the folded and unfolded states are in excellent agreement with those obtained by urea-dependent chemical shift analysis. The present method enables characterization of conformational exchange involving aromatic side chains and should serve as a valuable complement to methods developed for other types of protein side chains.

Quality in the chemical analysis of biological matrices by fluorescence X-ray by energy dispersive

International Nuclear Information System (INIS)

Sousa, Evely E. de; Paiva, Jose Daniel S. de; Franca, Elvis J. de; Almeida, Macio E.S.; Cantinha, Rebeca S.; Hazin, Clovis A.

2013-01-01

The aim of this study was to obtain multielement analytical curves of high analytical rigor to the analysis of biological matrices by the technique of fluorescence x-ray energy dispersive - EDXRF. Calibration curves were constructed from the reference materials IAEA 140, IAEA 155, IAEA V8, V10 to the International Atomic Energy Agency - IAEA, and SRM1515, SRM 1547, SRM 1570a, SRM 1573a, SEM 1567a, to the National Institute of Standards and Technology - NIST. After energy calibration, all samples were subjected to vacuum to the analyzes by 100 seconds for each group of chemical elements. The voltages used were respectively 15 keV for chemical elements with less than atomic number 22 and 50 keV for the others. After the construction of the curves, the analytical quality was assessed by the analysis of a portion-test of the reference material SRM 2976, also produced by NIST. Based on the number of certified reference materials used for construction of calibration curves in this work, quality analytical protocol was originated with considerable reliability for quantification of chemical elements in biological samples by EDXR

Hydrogen exchange rate of tyrosine hydroxyl groups in proteins as studied by the deuterium isotope effect on C(zeta) chemical shifts.

Science.gov (United States)

Takeda, Mitsuhiro; Jee, Jungoo; Ono, Akira Mei; Terauchi, Tsutomu; Kainosho, Masatsune

2009-12-30

We describe a new NMR method for monitoring the individual hydrogen exchange rates of the hydroxyl groups of tyrosine (Tyr) residues in proteins. The method utilizes (2S,3R)-[beta(2),epsilon(1,2)-(2)H(3);0,alpha,beta,zeta-(13)C(4);(15)N]-Tyr, zeta-SAIL Tyr, to detect and assign the (13)C(zeta) signals of Tyr rings efficiently, either by indirect (1)H-detection through 7-8 Hz (1)H(delta)-(13)C(zeta) spin couplings or by direct (13)C(zeta) observation. A comparison of the (13)C(zeta) chemical shifts of three Tyr residues of an 18.2 kDa protein, EPPIb, dissolved in H(2)O and D(2)O, revealed that all three (13)C(zeta) signals in D(2)O appeared at approximately 0.13 ppm ( approximately 20 Hz at 150.9 MHz) higher than those in H(2)O. In a H(2)O/D(2)O (1:1) mixture, however, one of the three signals for (13)C(zeta) appeared as a single peak at the averaged chemical shifts, and the other two appeared as double peaks at exactly the same chemical shifts in H(2)O and D(2)O, in 50 mM phosphate buffer (pH 6.6) at 40 degrees C. These three peaks were assigned to Tyr-36, Tyr-120, and Tyr-30, from the lower to higher chemical shifts, respectively. The results indicate that the hydroxyl proton of Tyr-120 exchanges faster than a few milliseconds, whereas those of Tyr-30 and Tyr-36 exchange more slowly. The exchange rate of the Tyr-30 hydroxyl proton, k(ex), under these conditions was determined by (13)C NMR exchange spectroscopy (EXSY) to be 9.2 +/- 1.1 s(-1). The Tyr-36 hydroxyl proton, however, exchanges too slowly to be determined by EXSY. These profound differences among the hydroxyl proton exchange rates are closely related to their relative solvent accessibility and the hydrogen bonds associated with the Tyr hydroxyl groups in proteins.

Performance test of multicomponent quantum mechanical calculation with polarizable continuum model for proton chemical shift.

Science.gov (United States)

Kanematsu, Yusuke; Tachikawa, Masanori

2015-05-21

Multicomponent quantum mechanical (MC_QM) calculations with polarizable continuum model (PCM) have been tested against liquid (1)H NMR chemical shifts for a test set of 80 molecules. Improvement from conventional quantum mechanical calculations was achieved for MC_QM calculations. The advantage of the multicomponent scheme could be attributed to the geometrical change from the equilibrium geometry by the incorporation of the hydrogen nuclear quantum effect, while that of PCM can be attributed to the change of the electronic structure according to the polarization by solvent effects.

Clinical application of 1H-chemical-shift imaging (CSI) to brain diseases

International Nuclear Information System (INIS)

Naruse, Shoji; Furuya, Seiichi; Ide, Mariko

1992-01-01

An H-1 chemical shift imaging (CSI) was developed as part of the clinical MRI system, by which magnetic resonance spectra (MRS) can be obtained from multiple small voxels and metabolite distribution in the brain can be visualized. The present study was to determine the feasibility and clinical potential of using an H-1 CSI. The device used was a Magnetom H 15 apparatus. The study population was comprised of 25 healthy subjects, 20 patients with brain tumor, 4 with ischemic disease, and 6 with miscellaneous degenerative disease. The H-1 CSI was obtained by the 3-dimensional Fourier transformation. After suppressing the lipid signal by the inversion-recovery method and the water signal by the chemical-shift selective pulse with a following dephasing gradient, 2-directional 16 x 16 phase encodings were applied to the 16 x 16∼18 x 18 cm field of view, in which a 8 x 8 x 2∼10 x 10 x 2 cm area was selected by the stimulated echo or spin-echo method. The metabolite mapping and its contour mapping were created by using the curve-fitted area, with interpolation to the 256 x 256 matrix. In the healthy group, high resolution spectra for N-acetyl aspartate (NAA), creatine, choline (Cho), and glutamine/glutamate were obtained from each voxel; and metabolite mapping and contour mapping also clearly showed metabolite distribution in the brain. In the group of brain tumor, an increased Cho and lactate and loss of NAA were observed, along with heterogeneity within the tumor and changes in the surrounding tissue; and there was a good correlation between lactate peak and tumor malignancy. The group of ischemic and degenerative disease had a decreased NAA and increased lactate on both spectra and metabolite mapping, depending on disease stage. These findings indicated that H-1 CSI is helpful for detecting spectra over the whole brain, as well as for determining metabolite distribution. (N.K.)

Sensitivity of the deep-sea amphipod Eurythenes gryllus to chemically dispersed oil.

Science.gov (United States)

Olsen, Gro Harlaug; Coquillé, Nathalie; Le Floch, Stephane; Geraudie, Perrine; Dussauze, Matthieu; Lemaire, Philippe; Camus, Lionel

2016-04-01

In the context of an oil spill accident and the following oil spill response, much attention is given to the use of dispersants. Dispersants are used to disperse an oil slick from the sea surface into the water column generating a cloud of dispersed oil droplets. The main consequence is an increasing of the sea water-oil interface which induces an increase of the oil biodegradation. Hence, the use of dispersants can be effective in preventing oiling of sensitive coastal environments. Also, in case of an oil blowout from the seabed, subsea injection of dispersants may offer some benefits compared to containment and recovery of the oil or in situ burning operation at the sea surface. However, biological effects of dispersed oil are poorly understood for deep-sea species. Most effects studies on dispersed oil and also other oil-related compounds have been focusing on more shallow water species. This is the first approach to assess the sensitivity of a macro-benthic deep-sea organism to dispersed oil. This paper describes a toxicity test which was performed on the macro-benthic deep-sea amphipod (Eurythenes gryllus) to determine the concentration causing lethality to 50% of test individuals (LC50) after an exposure to dispersed Brut Arabian Light (BAL) oil. The LC50 (24 h) was 101 and 24 mg L(-1) after 72 h and 12 mg L(-1) at 96 h. Based on EPA scale of toxicity categories to aquatic organisms, an LC50 (96 h) of 12 mg L(-1) indicates that the dispersed oil was slightly to moderately toxic to E. gryllus. As an attempt to compare our results to others, a literature study was performed. Due to limited amount of data available for dispersed oil and amphipods, information on other crustacean species and other oil-related compounds was also collected. Only one study on dispersed oil and amphipods was found, the LC50 value in this study was similar to the LC50 value of E. gryllus in our study. Since toxicity data are important input to risk assessment and net environmental

On the Confounding Effect of Temperature on Chemical Shift-Encoded Fat Quantification

Science.gov (United States)

Hernando, Diego; Sharma, Samir D.; Kramer, Harald; Reeder, Scott B.

2014-01-01

Purpose To characterize the confounding effect of temperature on chemical shift-encoded (CSE) fat quantification. Methods The proton resonance frequency of water, unlike triglycerides, depends on temperature. This leads to a temperature dependence of the spectral models of fat (relative to water) that are commonly used by CSE-MRI methods. Simulation analysis was performed for 1.5 Tesla CSE fat–water signals at various temperatures and echo time combinations. Oil–water phantoms were constructed and scanned at temperatures between 0 and 40°C using spectroscopy and CSE imaging at three echo time combinations. An explanted human liver, rejected for transplantation due to steatosis, was scanned using spectroscopy and CSE imaging. Fat–water reconstructions were performed using four different techniques: magnitude and complex fitting, with standard or temperature-corrected signal modeling. Results In all experiments, magnitude fitting with standard signal modeling resulted in large fat quantification errors. Errors were largest for echo time combinations near TEinit ≈ 1.3 ms, ΔTE ≈ 2.2 ms. Errors in fat quantification caused by temperature-related frequency shifts were smaller with complex fitting, and were avoided using a temperature-corrected signal model. Conclusion Temperature is a confounding factor for fat quantification. If not accounted for, it can result in large errors in fat quantifications in phantom and ex vivo acquisitions. PMID:24123362

Electrostatics determine vibrational frequency shifts in hydrogen bonded complexes.

Science.gov (United States)

Dey, Arghya; Mondal, Sohidul Islam; Sen, Saumik; Ghosh, Debashree; Patwari, G Naresh

2014-12-14

The red-shifts in the acetylenic C-H stretching vibration of C-H∙∙∙X (X = O, N) hydrogen-bonded complexes increase with an increase in the basicity of the Lewis base. Analysis of various components of stabilization energy suggests that the observed red-shifts are correlated with the electrostatic component of the stabilization energy, while the dispersion modulates the stabilization energy.

Solid state NMR of proteins at high MAS frequencies: symmetry-based mixing and simultaneous acquisition of chemical shift correlation spectra

Energy Technology Data Exchange (ETDEWEB)

Bellstedt, Peter [Fritz Lipmann Institute, Biomolecular NMR spectroscopy, Leibniz Institute for Age Research (Germany); Herbst, Christian [Ubon Ratchathani University, Department of Physics, Faculty of Science (Thailand); Haefner, Sabine; Leppert, Joerg; Goerlach, Matthias; Ramachandran, Ramadurai, E-mail: raman@fli-leibniz.de [Fritz Lipmann Institute, Biomolecular NMR spectroscopy, Leibniz Institute for Age Research (Germany)

2012-12-15

We have carried out chemical shift correlation experiments with symmetry-based mixing sequences at high MAS frequencies and examined different strategies to simultaneously acquire 3D correlation spectra that are commonly required in the structural studies of proteins. The potential of numerically optimised symmetry-based mixing sequences and the simultaneous recording of chemical shift correlation spectra such as: 3D NCAC and 3D NHH with dual receivers, 3D NC Prime C and 3D C Prime NCA with sequential {sup 13}C acquisitions, 3D NHH and 3D NC Prime H with sequential {sup 1}H acquisitions and 3D CANH and 3D C'NH with broadband {sup 13}C-{sup 15}N mixing are demonstrated using microcrystalline samples of the {beta}1 immunoglobulin binding domain of protein G (GB1) and the chicken {alpha}-spectrin SH3 domain.

Characterization of mu s-ms dynamics of proteins using a combined analysis of N-15 NMR relaxation and chemical shift: Conformational exchange in plastocyanin induced by histidine protonations

DEFF Research Database (Denmark)

Hass, M. A. S.; Thuesen, Marianne Hallberg; Christensen, Hans Erik Mølager

2004-01-01

of the exchanging species can be determined independently of the relaxation rates. The applicability of the approach is demonstrated by a detailed analysis of the conformational exchange processes previously observed in the reduced form of the blue copper protein, plastocyanin from the cyanobacteria Anabaena......An approach is presented that allows a detailed, quantitative characterization of conformational exchange processes in proteins on the mus-ms time scale. The approach relies on a combined analysis of NMR relaxation rates and chemical shift changes and requires that the chemical shift...... quantitatively by the correlation between the R-ex terms and the corresponding chemical shift differences of the exchanging species. By this approach, the R-ex terms of N-15 nuclei belonging to contiguous regions in the protein could be assigned to the same exchange process. Furthermore, the analysis...

CSSI-PRO: a method for secondary structure type editing, assignment and estimation in proteins using linear combination of backbone chemical shifts

International Nuclear Information System (INIS)

Swain, Monalisa; Atreya, Hanudatta S.

2009-01-01

Estimation of secondary structure in polypeptides is important for studying their structure, folding and dynamics. In NMR spectroscopy, such information is generally obtained after sequence specific resonance assignments are completed. We present here a new methodology for assignment of secondary structure type to spin systems in proteins directly from NMR spectra, without prior knowledge of resonance assignments. The methodology, named Combination of Shifts for Secondary Structure Identification in Proteins (CSSI-PRO), involves detection of specific linear combination of backbone 1 H α and 13 C' chemical shifts in a two-dimensional (2D) NMR experiment based on G-matrix Fourier transform (GFT) NMR spectroscopy. Such linear combinations of shifts facilitate editing of residues belonging to α-helical/β-strand regions into distinct spectral regions nearly independent of the amino acid type, thereby allowing the estimation of overall secondary structure content of the protein. Comparison of the predicted secondary structure content with those estimated based on their respective 3D structures and/or the method of Chemical Shift Index for 237 proteins gives a correlation of more than 90% and an overall rmsd of 7.0%, which is comparable to other biophysical techniques used for structural characterization of proteins. Taken together, this methodology has a wide range of applications in NMR spectroscopy such as rapid protein structure determination, monitoring conformational changes in protein-folding/ligand-binding studies and automated resonance assignment

The role of the second zero-dispersion wavelength in generation of supercontinua and brigth-bright soliton-pairs across the zero-dispersion wavelength

DEFF Research Database (Denmark)

Frosz, Michael Henoch; Falk, Peter Andreas; Bang, Ole

2005-01-01

Supercontinuum generation with femtosecond pulses in photonic crystal fibers with two zero-dispersion wavelengths (ZDWs) is investigated numerically. The role of the higher ZDW is examined for 5 fiber designs with a nearly constant lower ZDW. It is found that the resulting spectrum is mainly....... Further, the generation of a bright-bright soliton-pair from an initial single red-shifted soliton is found. The soliton-pair has one color in the anomalous dispersion region and the other color in the normal dispersion region, which has not previously been described for bright-bright soliton-pairs....

Toxicity of dispersant application: Biomarkers responses in gills of juvenile golden grey mullet (Liza aurata)

International Nuclear Information System (INIS)

Milinkovitch, Thomas; Godefroy, Joachim; Theron, Michael; Thomas-Guyon, Helene

2011-01-01

Dispersant use in nearshore areas is likely to increase the exposure of aquatic organisms to petroleum. To measure the toxicity of this controversial response technique, golden grey mullets (Liza aurata) were exposed to mechanically dispersed oil, chemically dispersed oil, dispersant alone in seawater, water-soluble fraction of oil and to seawater as a control treatment. Several biomarkers were assessed in the gills (enzymatic antioxidant activities, glutathione content, lipid peroxidation) and in the gallbladder (polycylic aromatic hydrocarbons metabolites). The significant differences between chemically dispersed oil and water soluble fraction of oil highlight the environmental risk to disperse an oil slick when containment and recovery can be conducted. The lack of significance between chemically and mechanically dispersed oil suggests that dispersant application is no more toxic than the natural dispersion of the oil slick. The results of this study are of interest in order to establish dispersant use policies in nearshore areas. - Highlights: → This study simulates and evaluates the toxicity of dispersant use in nearshore area. → Dispersant use toxicity is assessed through biomarkers measurement in a fish species. → Chemical dispersion of an oil slick increases the petroleum toxicity. → Dispersant use does not enhance the toxicity of a mechanically dispersed oil slick. → This work leads to conclusions concerning dispersant use policies in nearshore area. - When the meteorological conditions induce the dispersion of the oil slick (e.g. wave), the application of dispersant does not increase the toxicity of petroleum.

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

Science.gov (United States)

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

2017-06-28

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

Field-scale variation in colloid dispersibility and transport

DEFF Research Database (Denmark)

Nørgaard, Trine; Møldrup, Per; Ferré, T. P. A.

2014-01-01

comparison parameters including textural, chemical, and structural (e.g. air permeability) 8 soil properties. The soil dispersibility was determined (i) using a laser diffraction method on 1-2 mm aggregates equilibrated to an initial matric potential of -100 cm H2O, (ii) using an end-over-end shaking on 6......Colloids are potential carriers for strongly sorbing chemicals in macroporous soils, but predicting the amount of colloids readily available for facilitated chemical transport is an unsolved challenge. This study addresses potential key parameters and predictive indicators when assessing colloid....... Predictions of soil dispersibility and the risk of colloid-facilitated chemical transport will therefore need to be highly scale- and area-specific....

Re-dispersion of alumina particles in water: influence of the surface state

International Nuclear Information System (INIS)

Desset, Sabine

1999-01-01

The aim of this work was to determine the mechanisms by which suspensions of alpha alumina particles may be dried and then re-dispersed spontaneously in water. To get reproducible results, we designed appropriate protocols: (i) for preparing the surface state, and for generating controlled interparticle contacts (presence of water or complexing agents); (ii) for measuring the amount of re-dispersed material with a proper averaging over all interparticle bonds (turbidity). These results show that there are thresholds, determined by the conditions of drying and re-dispersion, where all the powder goes from the aggregated state to the dispersed state. With hydrated powders, it was found that mild changes in the chemical conditions (pH) and application of very weak mechanical forces (sedimentation) were enough to cause significant change in re-dispersion. According to these thresholds, a re-dispersion mechanism could be identified. Re-dispersion is ruled, indeed, by a balance of forces and the displacement of the re-dispersion thresholds indicates a shift in the balance of forces. These forces are the well known forces that control colloidal stability: van der Waals attraction, electrostatic repulsion and hydration forces. We found that hydration acts as a repulsive wall corresponding to one or two monolayers of water on each surface and depends on the Relative Humidity of drying. We also found that electrostatic repulsions at short separations are much weaker than the predictions based on the Poisson Boltzmann equation, but should be modelled according to the triple layer model. Repulsions to be considered are those calculated with the screened charges of the particles. Another aim of this work was to facilitate re-dispersion by using complexing agents that bind to the surfaces and add a steric repulsion We have found that molecules with carboxylic and hydroxyl groups can be efficient in this respect, if they are bound to surfaces before aggregation, if they are not

Re-dispersion of alumina particles in water: influence of the surface state

International Nuclear Information System (INIS)

Desset, Sabine

1999-01-01

The aim of this work was to determine the mechanisms by which suspensions of alpha alumina particles may be dried and then re-dispersed spontaneously in water. To get reproducible results, we designed appropriate protocols: (i) for preparing the surface state, and for generating controlled interparticle contacts (presence of water or complexing agents); (ii) for measuring the amount of re-dispersed material with a proper averaging over all interparticle bonds (turbidity). These results show that there are thresholds, determined by the conditions of drying and re-dispersion, where all the powder goes from the aggregated state to the dispersed state. With hydrated powders, it was found that mild changes in the chemical conditions (pH) and application of very weak mechanical forces (sedimentation) were enough to cause significant change in re-dispersion. According to these thresholds, a re-dispersion mechanism could be identified. Re-dispersion is ruled, indeed, by a balance of forces and the displacement of the re-dispersion thresholds indicates a shift in the balance of forces. These forces are the well-known forces that control colloidal stability: van der Waals attraction, electrostatic repulsion and hydration forces. We found that hydration acts as a repulsive wall corresponding to one or two monolayers of water on each surface and depends on the Relative Humidity of drying. We also found that electrostatic repulsions at short separations are much weaker than the predictions based on the Poisson Boltzmann equation, but should be modelled according to the triple layer model. Repulsions to be considered are those calculated with the screened charges of the particles. Another aim of this work was to facilitate re-dispersion by using complexing agents that bind to the surfaces and add a steric repulsion We have found that molecules with carboxylic and hydroxyl groups can be efficient in this respect, if they are bound to surfaces before aggregation, if they are not

A dispersion model of transport media in radiotracer investigations on selected chemical installations

International Nuclear Information System (INIS)

Iller, E.

1999-01-01

Tracer investigations of media transport through chemical reactors play a significant role in the chemical technology. They provide the basis for the determination of some important process parameters, such as flow character of the transported medium, degree of utilisation of the reactor volume during chemical transitions of substrates or even indicate possible mechanisms of chemical reactions. Determination of the medium flow characteristics is closely connected with the mathematical description of the process - a mathematical model of transport. The method of assessment of radiotracers suitability for the investigation of distillation processes presented in this paper allows to determine, in a simple manner, the parameters of distillation characteristics of the radionuclides, the average distillation temperature, the range of distillation temperatures, a suitable radiochemical purity. These parameters precisely determine the behavior of tracers to be expected in a wide range of variable conditions of the distillation process. Applications of tracer tested in such a manner to the investigations of dynamics of media in the industrial rectification columns has resulted in obtaining a dependable evaluation of the performance of these columns in a wide range of changes of their operational parameters. Particular attention has been paid to dynamics of the liquid [phase on the column plate. A dispersion model of liquid flow with hold-up zones has been proposed for the description of the liquid phase transport in the plate - overall assembly.The model consists of a number of flow and stagnant zones, with mass transfer between them. Another example of practical application of results from radiotracer investigation is an analysis of of phase dynamics in the installations designed for the process of liquefaction of Polish coals by means of their catalytic hydrogenation. For the analysis of phase transport in a reaction vessel various mathematical models were applied with

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

Science.gov (United States)

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.

High-frequency parameters of magnetic films showing magnetization dispersion

International Nuclear Information System (INIS)

Sidorenkov, V.V.; Zimin, A.B.; Kornev, Yu.V.

1988-01-01

Magnetization dispersion leads to skewed resonance curves shifted towards higher magnetizing fields, together with considerable reduction in the resonant absorption, while the FMR line width is considerably increased. These effects increase considerably with frequency, in contrast to films showing magnetic-anisotropy dispersion, where they decrease. It is concluded that there may be anomalies in the frequency dependence of the resonance parameters for polycrystalline magnetic films

Design of compact dispersion interferometer with a high efficiency nonlinear crystal and a low power CO2 laser

Science.gov (United States)

Akiyama, T.; Yoshimura, S.; Tomita, K.; Shirai, N.; Murakami, T.; Urabe, K.

2017-12-01

When the electron density of a plasma generated in high pressure environment is measured by a conventional interferometer, the phase shifts due to changes of the neutral gas density cause significant measurement errors. A dispersion interferometer, which measures the phase shift that arises from dispersion of medium between the fundamental and the second harmonic wavelengths of laser light, can suppress the measured phase shift due to the variations of neutral gas density. In recent years, the CO2 laser dispersion interferometer has been applied to the atmospheric pressure plasmas and its feasibility has been demonstrated. By combining a low power laser and a high efficiency nonlinear crystal for the second harmonic component generation, a compact dispersion interferometer can be designed. The optical design and preliminary experiments are conducted.

Latent effects of Iranian crude oil and a chemical oil dispersant on red sea molluscs

Energy Technology Data Exchange (ETDEWEB)

Eisler, R

1973-01-01

Predation rate of the gastropod drill, Drupa granulata, on the mussel, Mytilus variabilis, was measured over a period of 28 days after adults from both species had been immersed for 168 h in seawater solutions containing high sublethal concentrations (10 ml/liter) of Iranian crude oil. Predation rate was three times higher in controls than in the group where both predator and prey had been exposed initially; intermediate values were determined among groups where only one species had been treated initially. Fecundity of drills, as evidenced by number of egg cases deposited, was directly related to mussel consumption. In a similar study with a chemical oil dispersant, exposure to high (0.003 ml/liter) sublethal levels for 168 h did not affect markedly the rate at which mussels were destroyed and consumed during post-treatment. However, the fecundity of untreated drills feeding on untreated mussels (controls) was 3 to 10 times greater than among groups in which one or bothsc species had been exposed initially to dispersant. Except for mussels consumed by drills, there were no deaths during the post-treatment period in either study, and all organisms appeared normal.

Solid-state NMR chemical-shift perturbations indicate domain reorientation of the DnaG primase in the primosome of Helicobacter pylori

Energy Technology Data Exchange (ETDEWEB)

Gardiennet, Carole [Université de Lorraine, CNRS, CRM2, UMR 7036 (France); Wiegand, Thomas [ETH Zurich, Physical Chemistry (Switzerland); Bazin, Alexandre [Université de Lyon 1, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS (France); Cadalbert, Riccardo [ETH Zurich, Physical Chemistry (Switzerland); Kunert, Britta; Lacabanne, Denis [Université de Lyon 1, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS (France); Gutsche, Irina [Université Grenoble Alpes, Institut de Biologie Structurale (IBS), CNRS, IBS, CEA, IBS (France); Terradot, Laurent, E-mail: l.terradot@ibcp.fr [Université de Lyon 1, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS (France); Meier, Beat H., E-mail: beme@ethz.ch [ETH Zurich, Physical Chemistry (Switzerland); Böckmann, Anja, E-mail: a.bockmann@ibcp.fr [Université de Lyon 1, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS (France)

2016-03-15

We here investigate the interactions between the DnaB helicase and the C-terminal domain of the corresponding DnaG primase of Helicobacter pylori using solid-state NMR. The difficult crystallization of this 387 kDa complex, where the two proteins interact in a six to three ratio, is circumvented by simple co-sedimentation of the two proteins directly into the MAS-NMR rotor. While the amount of information that can be extracted from such a large protein is still limited, we can assign a number of amino-acid residues experiencing significant chemical-shift perturbations upon helicase-primase complex formation. The location of these residues is used as a guide to model the interaction interface between the two proteins in the complex. Chemical-shift perturbations also reveal changes at the interaction interfaces of the hexameric HpDnaB assembly on HpDnaG binding. A structural model of the complex that explains the experimental findings is obtained.

Chemical shift assignments of the partially deuterated Fyn SH2-SH3 domain.

Science.gov (United States)

Kieken, Fabien; Loth, Karine; van Nuland, Nico; Tompa, Peter; Lenaerts, Tom

2018-04-01

Src Homology 2 and 3 (SH2 and SH3) are two key protein interaction modules involved in regulating the activity of many proteins such as tyrosine kinases and phosphatases by respective recognition of phosphotyrosine and proline-rich regions. In the Src family kinases, the inactive state of the protein is the direct result of the interaction of the SH2 and the SH3 domain with intra-molecular regions, leading to a closed structure incompetent with substrate modification. Here, we report the 1 H, 15 N and 13 C backbone- and side-chain chemical shift assignments of the partially deuterated Fyn SH3-SH2 domain and structural differences between tandem and single domains. The BMRB accession number is 27165.

Rapid protein fold determination using secondary chemical shifts and cross-hydrogen bond 15N-13C’ scalar couplings (3hbJNC’)

NARCIS (Netherlands)

Bonvin, A.M.J.J.; Houben, K.; Guenneugues, M.N.L.; Kaptein, R.; Boelens, R.

2001-01-01

The possibility of generating protein folds at the stage of backbone assignment using structural restraints derived from experimentally measured cross-hydrogen bond scalar couplings and secondary chemical shift information is investigated using as a test case the small alpha/beta protein

SHIFTING WEED COMPOSITIONS AND BIOMASS PRODUCTION IN SWEET CORN FIELD TREATED WITH ORGANIC COMPOSTS AND CHEMICAL WEED CONTROLS

Directory of Open Access Journals (Sweden)

Marulak Simarmata

2015-10-01

Full Text Available The objectives of the research were to study the shift of weed compositions in sweet corn field treated with organic compost and chemical weed controls and to compare the effect of treatment combinations on weed growth, weed biomass and sweet corn biomass. The research was conducted in Bengkulu, Indonesia, from April to July 2014. Results showed that the number of weed species decreased after the trials from 14 to 13. There was a shift in weed compositions because 5 species of weeds did not emerge after the trials, but 4 new species were found. Chemical weed control used a herbiside mixture of atrazine and mesotrione applied during postemergence was the most effective method to control weeds, which was observed on decreased weed emergence and weed biomass down to 22.33 and 25.00 percent of control, respectively. Subsequently, biomass production of sweet corn increased up to 195.64 percent at the same trials. Biomass of weeds and sweet corn were also affected by the organic composts. Weed biomass was inhibited by treatment of composted empty fruith bunches of oil palm, whereas significantly increased of sweet corn biomass were observed in the plots of organic manure.

Oil spill dispersants. Risk assessment for Swedish waters

International Nuclear Information System (INIS)

Lindgren, C.; Lager, H.; Fejes, J.

2001-12-01

IVL has compiled a list of the international usage of oil spill dispersants and presents the technical limitations with the use of such agents as well as the biological effects of these chemical products. IVL, has also conducted an analysis of the pros and cons to using dispersants against oil spills in waters and has applied this with a risk assessment of chemical methods to combat oil spills in the Kattegat and Skagerrak and the Baltic Sea

Dispersion relations for η '→ η π π

Science.gov (United States)

Isken, Tobias; Kubis, Bastian; Schneider, Sebastian P.; Stoffer, Peter

2017-07-01

We present a dispersive analysis of the decay amplitude for η '→ η π π that is based on the fundamental principles of analyticity and unitarity. In this framework, final-state interactions are fully taken into account. Our dispersive representation relies only on input for the {π π } and {π }η scattering phase shifts. Isospin symmetry allows us to describe both the charged and neutral decay channel in terms of the same function. The dispersion relation contains subtraction constants that cannot be fixed by unitarity. We determine these parameters by a fit to Dalitz-plot data from the VES and BES-III experiments. We study the prediction of a low-energy theorem and compare the dispersive fit to variants of chiral perturbation theory.

Bidirectional shifts of TRPM8 channel gating by temperature and chemical agents modulate the cold sensitivity of mammalian thermoreceptors.

Science.gov (United States)

Mälkiä, Annika; Madrid, Rodolfo; Meseguer, Victor; de la Peña, Elvira; Valero, María; Belmonte, Carlos; Viana, Félix

2007-05-15

TRPM8, a member of the melastatin subfamily of transient receptor potential (TRP) cation channels, is activated by voltage, low temperatures and cooling compounds. These properties and its restricted expression to small sensory neurons have made it the ion channel with the most advocated role in cold transduction. Recent work suggests that activation of TRPM8 by cold and menthol takes place through shifts in its voltage-activation curve, which cause the channel to open at physiological membrane potentials. By contrast, little is known about the actions of inhibitors on the function of TRPM8. We investigated the chemical and thermal modulation of TRPM8 in transfected HEK293 cells and in cold-sensitive primary sensory neurons. We show that cold-evoked TRPM8 responses are effectively suppressed by inhibitor compounds SKF96365, 4-(3-chloro-pyridin-2-yl)-piperazine-1-carboxylic acid (4-tert-butyl-phenyl)-amide (BCTC) and 1,10-phenanthroline. These antagonists exert their effect by shifting the voltage dependence of TRPM8 activation towards more positive potentials. An opposite shift towards more negative potentials is achieved by the agonist menthol. Functionally, the bidirectional shift in channel gating translates into a change in the apparent temperature threshold of TRPM8-expressing cells. Accordingly, in the presence of the antagonist compounds, the apparent response-threshold temperature of TRPM8 is displaced towards colder temperatures, whereas menthol sensitizes the response, shifting the threshold in the opposite direction. Co-application of agonists and antagonists produces predictable cancellation of these effects, suggesting the convergence on a common molecular process. The potential for half maximal activation of TRPM8 activation by cold was approximately 140 mV more negative in native channels compared to recombinant channels, with a much higher open probability at negative membrane potentials in the former. In functional terms, this difference translates

(¹⁵N ± ¹³C') edited (4, 3)D-H(CC)CONH TOCSY and (4, 3)D-NOESY HNCO experiments for unambiguous side chain and NOE assignments of proteins with high shift degeneracy.

Science.gov (United States)

Kumar, Dinesh; Arora, Ashish

2011-11-01

Well-resolved and unambiguous through-bond correlations and NOE data are crucial for high-quality protein structure determination by NMR. In this context, we present here (4, 3)D reduced dimensionality (RD) experiments: H(CC)CONH TOCSY and NOESY HNCO--which instead of (15)N shifts exploit the linear combination of (15)N(i) and (13)C'(i-1) shifts (where i is a residue number) to resolve the through-bond (1)H-(1)H correlations and through-space (1)H-(1)H NOEs. The strategy makes use of the fact that (15)N and (13)C' chemical shifts when combined linearly provide a dispersion which is better compared to those of the individual chemical shifts. The extended dispersion thus available in these experiments will help to obtain the unambiguous side chain and accurate NOE assignments especially for medium-sized alpha-helical or partially unstructured proteins [molecular weight (MW) between 12-15 kDa] as well as higher MW (between 15-25 kDa) folded proteins where spectral overlap renders inaccurate and ambiguous NOEs. Further, these reduced dimensionality experiments in combination with routinely used (15)N and (13)C' edited TOCSY and NOESY experiments will provide an alternative way for high-quality NMR structure determination of large unstable proteins (with very high shift degeneracy), which are not at all amenable to 4D NMR. The utility of these experiments has been demonstrated here using (13)C/(15)N labeled ubiquitin (76 aa) protein. Copyright © 2011 John Wiley & Sons, Ltd.

The contribution of chemical shift imaging with digital subtracting images to the diagnosis of steatohepatitis

International Nuclear Information System (INIS)

Guo Xinghua; Wang Juanping; Zhang Chongjie; Zheng Guofang; Fan Ruiqiang; Zhu Sumei; Liu Qiwang

2006-01-01

Objective: To investigate the diagnosis value of chemical shift imaging with digital subtracting in steatohepatitis. Methods: The in-phase images were subtracted by the out-phase ones in 34 cases of steatohepatitis, and the CNR were measured on these subtracted images to estimate the steatosis of the liver. The relationship of CT grade of steatohepatitis and CNR from the subtracted images was analyzed to evaluate the relationship between CNR and the degree of hepatic steatosis. The sensitivity and specificity of the subtracting and eyeballing methods were compared with chi-square test. Results: On the subtracted images, the liver and spleen were seen nearly the same aspects as low signals, CNR=0.98±0.06, meanwhile the spongy vertebra and the subcutaneous or abdominal lipid were seen as obvious higher signals in 52 normal cases. On the 34 steatohepatitis, scattered high signals were seen in the liver, which made the signal of liver higher than that of spleen, CNR=3.25±0.91--14.35±6.10. There was positive correlation between CNR and CT grade in the 34 cases of steatohepatitis, r=0.893, P<0.01. The sensitivity and specificity of the subtracting method were 88.24% and 94. 23%, significantly higher than that of the eyeballing results, 32.35% and 80.77%, P<0.01 and P<0.05. Conclusion: Chemical shift imaging with digital subtracting is a sensitive, specific, objective method to diagnose steatohepatitis and it is of potential ability for quantitative diagnosis. (authors)

Toxicity of dispersant application: Biomarkers responses in gills of juvenile golden grey mullet (Liza aurata).

Science.gov (United States)

Milinkovitch, Thomas; Godefroy, Joachim; Théron, Michaël; Thomas-Guyon, Hélène

2011-10-01

Dispersant use in nearshore areas is likely to increase the exposure of aquatic organisms to petroleum. To measure the toxicity of this controversial response technique, golden grey mullets (Liza aurata) were exposed to mechanically dispersed oil, chemically dispersed oil, dispersant alone in seawater, water-soluble fraction of oil and to seawater as a control treatment. Several biomarkers were assessed in the gills (enzymatic antioxidant activities, glutathione content, lipid peroxidation) and in the gallbladder (polycylic aromatic hydrocarbons metabolites). The significant differences between chemically dispersed oil and water soluble fraction of oil highlight the environmental risk to disperse an oil slick when containment and recovery can be conducted. The lack of significance between chemically and mechanically dispersed oil suggests that dispersant application is no more toxic than the natural dispersion of the oil slick. The results of this study are of interest in order to establish dispersant use policies in nearshore areas. Copyright © 2011 Elsevier Ltd. All rights reserved.

Fuel oil and dispersant toxicity to the Antarctic sea urchin (Sterechinus neumayeri).

Science.gov (United States)

Alexander, Frances J; King, Catherine K; Reichelt-Brushett, Amanda J; Harrison, Peter L

2017-06-01

The risk of a major marine fuel spill in Antarctic waters is increasing, yet there are currently no standard or suitable response methods under extreme Antarctic conditions. Fuel dispersants may present a possible solution; however, little data exist on the toxicity of dispersants or fuels to Antarctic species, thereby preventing informed management decisions. Larval development toxicity tests using 3 life history stages of the Antarctic sea urchin (Sterechinus neumayeri) were completed to assess the toxicity of physically dispersed, chemically dispersed, and dispersant-only water-accommodated fractions (WAFs) of an intermediate fuel oil (IFO 180, BP) and the chemical dispersant Slickgone NS (Dasic International). Despite much lower total petroleum hydrocarbon concentrations, physically dispersed fuels contained higher proportions of low-to-intermediate weight carbon compounds and were generally at least an order of magnitude more toxic than chemically dispersed fuels. Based on concentrations that caused 50% abnormality (EC50) values, the embryonic unhatched blastula life stage was the least affected by fuels and dispersants, whereas the larval 4-armed pluteus stage was the most sensitive. The present study is the first to investigate the possible implications of the use of fuel dispersants for fuel spill response in Antarctica. The results indicate that the use of a fuel dispersant did not increase the hydrocarbon toxicity of IFO 180 to the early life stages of Antarctic sea urchins, relative to physical dispersal. Environ Toxicol Chem 2017;36:1563-1571. © 2016 SETAC. © 2016 SETAC.

Rapid Formation of Microbe-Oil Aggregates and Changes in Community Composition in Coastal Surface Water Following Exposure to Oil and the Dispersant Corexit

Directory of Open Access Journals (Sweden)

Shawn M. Doyle

2018-04-01

Full Text Available During the Deepwater Horizon (DWH oil spill, massive quantities of oil were deposited on the seafloor via a large-scale marine oil-snow sedimentation and flocculent accumulation (MOSSFA event. The role of chemical dispersants (e.g., Corexit applied during the DWH oil spill clean-up in helping or hindering the formation of this MOSSFA event are not well-understood. Here, we present the first experiment related to the DWH oil spill to specifically investigate the relationship between microbial community structure, oil and Corexit®, and marine oil-snow in coastal surface waters. We observed the formation of micron-scale aggregates of microbial cells around droplets of oil and dispersant and found that their rate of formation was directly related to the concentration of oil within the water column. These micro-aggregates are potentially important precursors to the formation of larger marine oil-snow particles. Therefore, our observation that Corexit® significantly enhanced their formation suggests dispersant application may play a role in the development of MOSSFA events. We also observed that microbial communities in marine surface waters respond to oil and oil plus Corexit® differently and much more rapidly than previously measured, with major shifts in community composition occurring within only a few hours of experiment initiation. In the oil-amended treatments without Corexit®, this manifested as an increase in community diversity due to the outgrowth of several putative aliphatic- and aromatic-hydrocarbon degrading genera, including phytoplankton-associated taxa. In contrast, microbial community diversity was reduced in mesocosms containing chemically dispersed oil. Importantly, different consortia of hydrocarbon degrading bacteria responded to oil and chemically dispersed oil, indicating that functional redundancy in the pre-spill community likely results in hydrocarbon consumption in both undispersed and dispersed oils, but by different

Rapid Formation of Microbe-Oil Aggregates and Changes in Community Composition in Coastal Surface Water Following Exposure to Oil and the Dispersant Corexit.

Science.gov (United States)

Doyle, Shawn M; Whitaker, Emily A; De Pascuale, Veronica; Wade, Terry L; Knap, Anthony H; Santschi, Peter H; Quigg, Antonietta; Sylvan, Jason B

2018-01-01

During the Deepwater Horizon (DWH) oil spill, massive quantities of oil were deposited on the seafloor via a large-scale marine oil-snow sedimentation and flocculent accumulation (MOSSFA) event. The role of chemical dispersants (e.g., Corexit) applied during the DWH oil spill clean-up in helping or hindering the formation of this MOSSFA event are not well-understood. Here, we present the first experiment related to the DWH oil spill to specifically investigate the relationship between microbial community structure, oil and Corexit®, and marine oil-snow in coastal surface waters. We observed the formation of micron-scale aggregates of microbial cells around droplets of oil and dispersant and found that their rate of formation was directly related to the concentration of oil within the water column. These micro-aggregates are potentially important precursors to the formation of larger marine oil-snow particles. Therefore, our observation that Corexit® significantly enhanced their formation suggests dispersant application may play a role in the development of MOSSFA events. We also observed that microbial communities in marine surface waters respond to oil and oil plus Corexit® differently and much more rapidly than previously measured, with major shifts in community composition occurring within only a few hours of experiment initiation. In the oil-amended treatments without Corexit®, this manifested as an increase in community diversity due to the outgrowth of several putative aliphatic- and aromatic-hydrocarbon degrading genera, including phytoplankton-associated taxa. In contrast, microbial community diversity was reduced in mesocosms containing chemically dispersed oil. Importantly, different consortia of hydrocarbon degrading bacteria responded to oil and chemically dispersed oil, indicating that functional redundancy in the pre-spill community likely results in hydrocarbon consumption in both undispersed and dispersed oils, but by different bacterial taxa

Combined echo offset (Dixon) and line volume chemical shift imaging as a clinical imaging protocol

International Nuclear Information System (INIS)

Listerud, J.; Chan, T.; Lenkinski, R.E.; Kressel, H.Y.; Chao, P.W.

1989-01-01

The authors have studied the sensitivity and specificity of the line-volume chemical-shift imaging (CSI) method as compared with the Dixon method they have recently implemented on a Signa, which supports a variety of options. Potential sources or error for the Dixon method include line broadening due to susceptibility, field inhomogeneity, and errors form olefinic resonances associated with fat, which behave like water in the Dixon regime. The authors investigate whether a combined Dixon/line-volume CSI method could be used to improve the placement of the line volume and to provide higher sensitivity and specificity than does the Dixon method alone

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

Energy Technology Data Exchange (ETDEWEB)

Markin, Craig J.; Spyracopoulos, Leo, E-mail: leo.spyracopoulos@ualberta.ca [University of Alberta, Department of Biochemistry (Canada)

2012-06-15

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

Micro energy-dispersive X-ray fluoresence mapping of enamel and dental materials after chemical erosion.

Science.gov (United States)

Soares, Luís Eduardo Silva; de Oliveira, Rodrigo; Nahórny, Sídnei; Santo, Ana Maria do Espírito; Martin, Airton Abrahão

2012-10-01

Energy-dispersive X-ray fluorescence was employed to test the hypothesis that beverage consumption or mouthwash utilization will change the chemical properties of dental materials and enamel mineral content. Bovine enamel samples (n = 45) each received two cavity preparations (n = 90), each pair filled with one of three dental materials (R: nanofilled composite resin; GIC: glass-ionomer cement; RMGIC: resin-modified GIC). Furthermore, they were treated with three different solutions (S: saliva; E: erosion/Pepsi Twist®; or EM: erosion+mouthwash/Colgate Plax®). It was found that mineral loss in enamel was greater in GICE samples than in RE > RMGICE > RMGICEM > REM > GICEM. An increased percentage of Zr was found in REM indicating organic matrix degradation. Dental materials tested (R, GIC, and RMGIC) were not able to protect adjacent enamel from acid erosion by the soft drink tested. The use of mouthwash promoted protection of enamel after erosion by the soft drink. To avoid chemical dissolution by mouthwashes, protection by resin composites with surface sealants is recommended.

MR imaging of osteonecrosis using frequency selective chemical shift sequences; Neue Aspekte in der MR-Diagnostik der Osteonekrose: Selektive Fett/Wasser-Bildgebung

Energy Technology Data Exchange (ETDEWEB)

Duda, S H [Abt. fuer Radiologische Diagnostik, Tuebingen Univ. (Germany); Laniado, M [Abt. fuer Radiologische Diagnostik, Tuebingen Univ. (Germany); Schick, F [Inst. fuer Physik, Tuebingen Univ. (Germany)

1994-12-31

The MR appearance of osteonecrosis was assessed on selective fat- and water images to further evaluate the nature of double-line sign. Conventional T1- and T2-weighted SE and frequency selective chemical shift images of eight patients with avascular necrosis of the femoral head and three patients with bone infarcts were retrospectively reviewed. Eight of 11 patients showed a double-line sign on T2-weighted SE images. In these cases, correlation with selective water images revealed that a chemical shift artifact contributed to appearance and location of the hyperintense line. The authors conclude that chemical shift imaging improves our understanding of the nature of the double-line sign. (orig.) [Deutsch] Das MR-tomographische Erscheinungsbild der Osteonekrose auf selektiven Fett- und Wasserbildern wurde analysiert, um das in der Literatur beschriebene Doppellinienzeichen naeher zu untersuchen. Hierfuer wurden sowohl die herkoemmlichen T1- und T2-gewichteten Spin-Echo-Sequenzen herangezogen, als auch frequenzselektive Bilder, die aufgrund chemischer Verschiebung gewonnen wurden (1,5 T). Es wurden die Untersuchungen von acht Patienten mit avaskulaerer Hueftkopfnekrose und von drei Patienten mit Knocheninfarkten retrospektiv ausgewertet. Acht von 11 Patienten zeigten ein Doppellinienzeichen auf den T2-gewichteten Bildern. Die Korrelation mit den selektiven Wasserbildern ergab, dass durch chemische Verschiebung bedingte Artefakte das Erscheinungsbild und den Ort der hyperintensen Linie beeinflussten. Die Bildgebung mit Hilfe der chemischen Verschiebung verbessert unser Verstaendnis der MRT-Charakteristika der Osteonekrose. (orig.)

Relaxation dispersion in MRI induced by fictitious magnetic fields.

Science.gov (United States)

Liimatainen, Timo; Mangia, Silvia; Ling, Wen; Ellermann, Jutta; Sorce, Dennis J; Garwood, Michael; Michaeli, Shalom

2011-04-01

A new method entitled Relaxation Along a Fictitious Field (RAFF) was recently introduced for investigating relaxations in rotating frames of rank ≥ 2. RAFF generates a fictitious field (E) by applying frequency-swept pulses with sine and cosine amplitude and frequency modulation operating in a sub-adiabatic regime. In the present work, MRI contrast is created by varying the orientation of E, i.e. the angle ε between E and the z″ axis of the second rotating frame. When ε > 45°, the amplitude of the fictitious field E generated during RAFF is significantly larger than the RF field amplitude used for transmitting the sine/cosine pulses. Relaxation during RAFF was investigated using an invariant-trajectory approach and the Bloch-McConnell formalism. Dipole-dipole interactions between identical (like) spins and anisochronous exchange (e.g., exchange between spins with different chemical shifts) in the fast exchange regime were considered. Experimental verifications were performed in vivo in human and mouse brain. Theoretical and experimental results demonstrated that changes in ε induced a dispersion of the relaxation rate constants. The fastest relaxation was achieved at ε ≈ 56°, where the averaged contributions from transverse components during the pulse are maximal and the contribution from longitudinal components are minimal. RAFF relaxation dispersion was compared with the relaxation dispersion achieved with off-resonance spin lock T(₁ρ) experiments. As compared with the off-resonance spin lock T(₁ρ) method, a slower rotating frame relaxation rate was observed with RAFF, which under certain experimental conditions is desirable. Copyright © 2011 Elsevier Inc. All rights reserved.

Implicit coupling of turbulent diffusion with chemical reaction mechanisms for prognostic atmospheric dispersion models

Energy Technology Data Exchange (ETDEWEB)

Berlowitz, D.R.

1996-11-01

In the last few decades the negative impact by humans on the thin atmospheric layer enveloping the earth, the basis for life on this planet, has increased steadily. In order to halt, or at least slow down this development, the knowledge and study of these anthropogenic influence has to be increased and possible remedies have to be suggested. An important tool for these studies are computer models. With their help the atmospheric system can be approximated and the various processes, which have led to the current situation can be quantified. They also serve as an instrument to assess short or medium term strategies to reduce this human impact. However, to assure efficiency as well as accuracy, a careful analysis of the numerous processes involved in the dispersion of pollutants in the atmosphere is called for. This should help to concentrate on the essentials and also prevent excessive usage of sometimes scarce computing resources. The basis of the presented work is the EUMAC Zooming Model (ETM), and particularly the component calculating the dispersion of pollutants in the atmosphere, the model MARS. The model has two main parts: an explicit solver, where the advection and the horizontal diffusion of pollutants are calculated, and an implicit solution mechanism, allowing the joint computation of the change of concentration due to chemical reactions, coupled with the respective influence of the vertical diffusion of the species. The aim of this thesis is to determine particularly the influence of the horizontal components of the turbulent diffusion on the existing implicit solver of the model. Suggestions for a more comprehensive inclusion of the full three dimensional diffusion operator in the implicit solver are made. This is achieved by an appropriate operator splitting. A selection of numerical approaches to tighten the coupling of the diffusion processes with the calculation of the applied chemical reaction mechanisms are examined. (author) figs., tabs., refs.

Application of Numerical Dispersion Compensation of the Yee-FDTD Algorithm on Elongated Domains

DEFF Research Database (Denmark)

Franek, Ondrej; Zhang, Shuai; Olesen, Kim

2017-01-01

A postprocessing method to compensate for the numerical dispersion of the Yee-FDTD scheme is presented. The method makes use of frequency domain deconvolution of the erroneous phase shift from the obtained results and can be applied on certain specific conditions, such as for simulations on elong......A postprocessing method to compensate for the numerical dispersion of the Yee-FDTD scheme is presented. The method makes use of frequency domain deconvolution of the erroneous phase shift from the obtained results and can be applied on certain specific conditions, such as for simulations...

Optimizing optical pre-dispersion using transmit DSP for mitigation of Kerr nonlinearities in dispersion managed cables

Science.gov (United States)

Hopkins, James; Gaudette, Jamie; Mehta, Priyanth

2013-10-01

With the advent of digital signal processing (DSP) in optical transmitters and receivers, the ability to finely tune the ratio of pre and post dispersion compensation can be exploited to best mitigate the nonlinear penalties caused by the Kerr effect. A portion of the nonlinear penalty in optical communication channels has been explained by an increase in peak to average power ratio (PAPR) inherent in highly dispersed signals. The standard approach for minimizing these impairments applies 50% pre dispersion compensation and 50% post dispersion compensation, thereby decreasing average PAPR along the length of the cable, as compared with either 100% pre or post dispersion compensation. In this paper we demonstrate that simply considering the net accumulated dispersion, and applying 50/50 pre/post dispersion is not necessarily the best way to minimize PAPR and subsequent Kerr nonlinearities. Instead, we consider the cumulative dispersion along the entire length of the cable, and, taking into account this additional information, derive an analytic formula for the minimization of PAPR. Alignment with simulation and experimental measurements is presented using a commercially available 100Gb/s dual-polarization binary phase-shift-keying (DP-BPSK) coherent modem, with transmitter and receiver DSP. Measurements are provided from two different 5000km dispersion managed Submarine test-beds, as well as a 3800km terrestrial test-bed with a mixture of SMF-28 and TWRS optical fiber. This method is shown to deviate significantly from the conventional 50/50 method described above, in dispersion managed communications systems, and more closely aligns with results obtained from simulation and data collected from laboratory test-beds.

Stabilized soliton self-frequency shift and 0.1- PHz sideband generation in a photonic-crystal fiber with an air-hole-modified core.

Science.gov (United States)

Liu, Bo-Wen; Hu, Ming-Lie; Fang, Xiao-Hui; Li, Yan-Feng; Chai, Lu; Wang, Ching-Yue; Tong, Weijun; Luo, Jie; Voronin, Aleksandr A; Zheltikov, Aleksei M

2008-09-15

Fiber dispersion and nonlinearity management strategy based on a modification of a photonic-crystal fiber (PCF) core with an air hole is shown to facilitate optimization of PCF components for a stable soliton frequency shift and subpetahertz sideband generation through four-wave mixing. Spectral recoil of an optical soliton by a red-shifted dispersive wave, generated through a soliton instability induced by high-order fiber dispersion, is shown to stabilize the soliton self-frequency shift in a highly nonlinear PCF with an air-hole-modified core relative to pump power variations. A fiber with a 2.3-microm-diameter core modified with a 0.9-microm-diameter air hole is used to demonstrate a robust soliton self-frequency shift of unamplified 50-fs Ti: sapphire laser pulses to a central wavelength of about 960 nm, which remains insensitive to variations in the pump pulse energy within the range from 60 to at least 100 pJ. In this regime of frequency shifting, intense high- and low-frequency branches of dispersive wave radiation are simultaneously observed in the spectrum of PCF output. An air-hole-modified-core PCF with appropriate dispersion and nonlinearity parameters is shown to provide efficient four-wave mixing, giving rise to Stokes and anti-Stokes sidebands whose frequency shift relative to the pump wavelength falls within the subpetahertz range, thus offering an attractive source for nonlinear Raman microspectroscopy.

Acute and chronic toxicity study of the water accommodated fraction (WAF), chemically enhanced WAF (CEWAF) of crude oil and dispersant in the rock pool copepod Tigriopus japonicus.

Science.gov (United States)

Lee, Kyun-Woo; Shim, Won Joon; Yim, Un Hyuk; Kang, Jung-Hoon

2013-08-01

We determined the toxicity of the water accommodated hydrocarbon fraction (WAF), two chemically enhanced WAFs (CEWAFs; CEWAF-C, Crude oil+Corexit 9500 and CEWAF-H, Crude oil+Hiclean) of crude oil and two dispersants (Corexit 9500 and Hiclean) to the rock pool copepod Tigriopus japonicus. In the acute toxicity test, Corexit 9500 was the most toxic of all the chemicals studied. The nauplius stage of T. japonicus was more susceptible to the toxic chemicals studied than the adult female. The toxicity data using the nauplius stage was then considered as baseline to determine the spiking concentration of chemicals for chronic toxicity tests on the copepod. As the endpoints in the chronic toxicity test, survival, sex ratio, developmental time and fecundity of the copepod were used. All chemicals used in this study resulted in increased toxicity in the F1 generation. The lowest-observed-adverse-effect (LOAE) concentrations of WAF, CEWAF-H, CEWAF-C, Hiclean and Corexit 9500 were observed to be 50%, 10%, 0.1%, 1% and 1%, respectively. The results in present study imply that copepods in marine may be negatively influenced by spilled oil and dispersant. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

Science.gov (United States)

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

Diagnostic value of chemical shift artifact in distinguishing benign lymphadenopathy

Energy Technology Data Exchange (ETDEWEB)

Farshchian, Nazanin, E-mail: farshchian.n@gmail.com [Department of Radiology, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Tamari, Saghar; Farshchian, Negin [Department of Radiology, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Madani, Hamid [Department of Pathology, Imam-Reza Hospital, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Rezaie, Mansour [Department of Biostatistics, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Mohammadi-Motlagh, Hamid-Reza, E-mail: mohammadimotlagh@gmail.com [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of)

2011-11-15

Purpose: Today, distinguishing metastatic lymph nodes from secondary benign inflammatory ones via using non-invasive methods is increasingly favorable. In this study, the diagnostic value of chemical shift artifact (CSA) in magnetic resonance imaging (MRI) was evaluated to distinguish benign lymphadenopathy. Subjects and methods: A prospective intraindividual internal review board-approved study was carried out on 15 men and 15 women having lymphadenopathic lesions in different locations of the body who underwent contrast-enhanced dynamic MR imaging at 1.5 T. Then, the imaging findings were compared with pathology reports, using the statistics analyses. Results: Due to the findings of the CSA existence in MRI, a total of 56.7% of the studied lesions (17 of 30) were identified as benign lesions and the rest were malignant, whereas the pathology reports distinguished twelve malignant and eighteen benign cases. Furthermore, the CSA findings comparing the pathology reports indicated that CSA, with confidence of 79.5%, has a significant diagnostic value to differentiate benign lesions from malignant ones. Conclusion: Our study demonstrated that CSA in MR imaging has a suitable diagnostic potential nearing readiness for clinical trials. Furthermore, CSA seems to be a feasible tool to differentiate benign lymph nodes from malignant ones; however, further studies including larger numbers of patients are required to confirm our results.

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

International Nuclear Information System (INIS)

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

1991-01-01

We have performed photoemission studies on high-quality Bi 2 Sr 2 CaCu 2 O 8+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

Aqueous solubility, dispersibility and toxicity of biodiesels

International Nuclear Information System (INIS)

Hollebone, B.P.; Fieldhouse, B.; Lumley, T.C.; Landriault, M.; Doe, K.; Jackman, P.

2007-01-01

The renewed interest in the use of biological fuels can be attributed to that fact that feedstocks for fatty-acid ester biodiesels are renewable and can be reclaimed from waste. Although there are significant benefits to using biodiesels, their increased use leaves potential for accidental release to the environment. Therefore, their environmental behaviours and impacts must be evaluated along with the risk associated with their use. Biodiesel fuels may be made from soy oil, canola oil, reclaimed restaurant grease, fish oil and animal fat. The toxicological fate of biofuel depends on the variability of its chemical composition. This study provided an initial assessment of the aqueous fate and effects of biodiesel from a broad range of commonly available feedstocks and their blends with petroleum diesels. The study focused primarily on the fate and impact of these fuels in fresh-water. The use of chemical dispersion as a countermeasure for saltwater was also investigated. The exposure of aquatic ecosystems to biodiesels and petroleum diesel occurs via the transfer of material from the non-aqueous phase liquid (NAPL) into the aqueous phase, as both soluble and dispersed components. The aqueous solubilities of the fuels were determined from the equilibrium water-accommodated fraction concentrations. The acute toxicities of many biodiesels were reported for 3 test species used by Environment Canada for toxicological evaluation, namely rainbow trout, the water flea and a luminescent bacterium. This study also evaluated the natural potential for dispersion of the fuels in the water column in both low and high-energy wave conditions. Chemical dispersion as a potential countermeasure for biodiesel spills was also evaluated using solubility testing, acute toxicity testing, and dispersibility testing. It was shown that biodiesels have much different fates and impacts from petroleum diesels. The compounds partitioning into the water column are also very different for each

Spectral fitting for signal assignment and structural analysis of uniformly {sup 13}C-labeled solid proteins by simulated annealing based on chemical shifts and spin dynamics

Energy Technology Data Exchange (ETDEWEB)

Matsuki, Yoh; Akutsu, Hideo; Fujiwara, Toshimichi [Osaka University, Institute for Protein Research (Japan)], E-mail: tfjwr@protein.osaka-u.ac.jp

2007-08-15

We describe an approach for the signal assignment and structural analysis with a suite of two-dimensional {sup 13}C-{sup 13}C magic-angle-spinning solid-state NMR spectra of uniformly {sup 13}C-labeled peptides and proteins. We directly fit the calculated spectra to experimental ones by simulated annealing in restrained molecular dynamics program CNS as a function of atomic coordinates. The spectra are calculated from the conformation dependent chemical shift obtained with SHIFTX and the cross-peak intensities computed for recoupled dipolar interactions. This method was applied to a membrane-bound 14-residue peptide, mastoparan-X. The obtained C', C{sup {alpha}} and C{sup {beta}} chemical shifts agreed with those reported previously at the precisions of 0.2, 0.7 and 0.4 ppm, respectively. This spectral fitting program also provides backbone dihedral angles with a precision of about 50 deg. from the spectra even with resonance overlaps. The restraints on the angles were improved by applying protein database program TALOS to the obtained chemical shifts. The peptide structure provided by these restraints was consistent with the reported structure at the backbone RMSD of about 1 A.

{sup 31}P-MR spectroscopy of all regions of the human heart at 1.5 T with acquisition-weighted chemical shift imaging; P-MR-Spektroskopie aller Wandabschnitte des menschlichen Herzens bei 1,5 T mit akquisitionsgewichteter Chemical-shift-Bildgebung

Energy Technology Data Exchange (ETDEWEB)

Koestler, H.; Beer, M.; Buchner, S.; Sandstede, J.; Pabst, T.; Kenn, W.; Hahn, D. [Wuerzburg Univ. (Germany). Abt. fuer Roentgendiagnostik; Landschuetz, W.; Kienlin, M. von [Wuerzburg Univ. (Germany). Physikalisches Inst.; Neubauer, S. [Dept. of Cardiovascular Medicine, John Radcliffe Hospital, Oxford (United Kingdom)

2001-12-01

Aim: Aim of this study was to show whether or not acquisition-weighted chemical shift imaging (AW-CSI) allows the determination of PCr and ATP in the lateral and posterior wall of the human heart at 1.5 T. Methods: 12 healthy volunteers were examined using a conventional chemical shift imaging (CSI) and an AW-CSI. The sequences differed only in the number of repetitions for each point in k space. A hanning function was used as filter function leading to 7 repetitions in the center of the k space and 0 in the corners. Thus, AW-CSI had the same resolution as the CSI sequence. The results for both sequences were analyzed using identically positioned voxels in the septal, anterior, lateral and posterior wall. Results: The determined averaged AW-CSI signal to noise ratios were higher for PCr by a factor of 1.3 and for ATP by 1.4 than those of CSI. The PCr/ATP ratios were higher by a factor of 1.2 - 1.3 and showed a smaller standard deviation in all locations for AW-CSI. The mean PCr/ATP ratios determined by AW-CSI of septal, lateral and posterior wall were almost identical (1.72 - 1.76), while it was higher in the anterior wall (1.9). Conclusions: The reduced contamination in AW-CSI improves the signal to noise ratio and the determination of the PCr/ATP ratio in cardiac {sup 31}P spectroscopy compared to CSI with the same resolution. The results in volunteers indicate that AW-CSI renders {sup 31}P spectroscopy of the lateral and posterior wall of the human heart feasible for patient studies at 1.5 T. (orig.) [German] Ziel: Ziel der Arbeit war es zu untersuchen, ob die akquisitionsgewichtete Chemical-shift-Bildgebung (AW-CSI) die Bestimmung von PCr und ATP in der Seiten- und Hinterwand des menschlichen Herzens an einem klinischen 1,5 T MR-Tomographen erlaubt. Methoden: 12 gesunde Probanden wurden jeweils mit einer chemical shift imaging (CSI) und einer AW-CSI-Sequenz untersucht. Die Sequenzen unterschieden sich lediglich in der Anzahl der Wiederholungen der einzelnen

Liquid agents for dispersion of hard alloys

International Nuclear Information System (INIS)

Putintseva, M.N.

2006-01-01

Effects of dispersant properties on granulometric, chemical, and phase composition of the products of WC hard alloy electroerosion are considered. It is established that an increase of liquid dispersant permittivity results in enhanced powder dispersity, and an increase of boiling temperature and kinematic viscosity of a hydrocarbon liquid promotes a carbon loss from WC and intensifies pyrolysis of the liquid.On electroerosion of WC base hard alloy in oil a powder particle consists of b-WC+W 2 C phases, in kerosine - of a-WC+b-WC, in distilled water - of W+W 2 C. The viscosity of liquid dispersants practically has no effect on powder particle size [ru

H-1 chemical shift imaging of the brain in guanidino methyltransferase deficiency, a creatine deficiency syndrome; guanidinoacetate accumulation in the gray matter

NARCIS (Netherlands)

Sijens, PE; Verbruggen, KT; Meiners, LC; Soorani-Lunsing, RJ; Rake, JP; Oudkerk, M

MR spectroscopy results in a mild case of guanidinoacetate methyltransferase (GAMT) deficiency are presented. The approach differs from previous MRS studies in the acquisition of a chemical shift imaging spectral map showing gray and white matter with the corresponding spectra in one overview. MR

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.

Science.gov (United States)

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.

Dispersion relation for pure dust Bernstein waves in a non-Maxwellian magnetized dusty plasma

International Nuclear Information System (INIS)

Deeba, F.; Ahmad, Zahoor; Murtaza, G.

2011-01-01

Pure dust Bernstein waves are investigated using non-Maxwellian kappa and (r,q) distribution functions in a collisionless, uniform magnetized dusty plasma. Dispersion relations for both the distributions are derived by considering waves whose frequency is of the order of dust cyclotron frequency, and dispersion curves are plotted. It is observed that the propagation band for dust Bernstein waves is rather narrow as compared with that of the electron Bernstein waves. However, the band width increases for higher harmonics, for both kappa and (r,q) distributions. Effect of dust charge on dispersion curves is also studied, and one observes that with increasing dust charge, the dispersion curves shift toward the lower frequencies. Increasing the dust to ion density ratio ((n d0 /n i0 )) causes the dispersion curve to shift toward the higher frequencies. It is also found that for large values of spectral index kappa (κ), the dispersion curves approach to the Maxwellian curves. The (r,q) distribution approaches the kappa distribution for r = 0, whereas for r > 0, the dispersion curves show deviation from the Maxwellian curves as expected. Relevance of this work can be found in astrophysical plasmas, where non-Maxwellian velocity distributions as well as dust particles are commonly observed.

Dispersion relation for pure dust Bernstein waves in a non-Maxwellian magnetized dusty plasma

Energy Technology Data Exchange (ETDEWEB)

Deeba, F. [National Tokamak Fusion Program, PAEC, P.O. Box 3329, Islamabad 44000 (Pakistan); Department of Physics, G.C. University, Lahore 54000 (Pakistan); Ahmad, Zahoor [National Tokamak Fusion Program, PAEC, P.O. Box 3329, Islamabad 44000 (Pakistan); Murtaza, G. [Salam Chair in Physics, G.C. University, Lahore 54000 (Pakistan)

2011-07-15

Pure dust Bernstein waves are investigated using non-Maxwellian kappa and (r,q) distribution functions in a collisionless, uniform magnetized dusty plasma. Dispersion relations for both the distributions are derived by considering waves whose frequency is of the order of dust cyclotron frequency, and dispersion curves are plotted. It is observed that the propagation band for dust Bernstein waves is rather narrow as compared with that of the electron Bernstein waves. However, the band width increases for higher harmonics, for both kappa and (r,q) distributions. Effect of dust charge on dispersion curves is also studied, and one observes that with increasing dust charge, the dispersion curves shift toward the lower frequencies. Increasing the dust to ion density ratio ((n{sub d0}/n{sub i0})) causes the dispersion curve to shift toward the higher frequencies. It is also found that for large values of spectral index kappa ({kappa}), the dispersion curves approach to the Maxwellian curves. The (r,q) distribution approaches the kappa distribution for r = 0, whereas for r > 0, the dispersion curves show deviation from the Maxwellian curves as expected. Relevance of this work can be found in astrophysical plasmas, where non-Maxwellian velocity distributions as well as dust particles are commonly observed.

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.

Science.gov (United States)

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.

Origins of Stokes shift in PbS nanocrystals

KAUST Repository

Voznyy, Oleksandr

2017-10-27

Stokes shift, an energy difference between the excitonic absorption and emission, is a property of colloidal quantum dots (CQDs) typically ascribed to splitting between dark and bright excitons. In some materials, e.g., PbS, CuInS2, CdHgTe, a Stokes shift of up to 200 meV is observed, substantially larger than the estimates of dark-bright state splitting or vibronic relaxations. The shift origin remains highly debated, as contradictory signatures of both surface and bulk character were reported for the Stokes-shifted electronic state. Here we show that the energy transfer among CQDs in a polydispersed ensemble in solution suffices to explain the excess Stokes shift. This energy transfer is primarily due to CQD aggregation, and can be substantially eliminated by extreme dilution, higher-viscosity solvent, or better-dispersed colloids. Our findings highlight that ensemble polydispersity remains the primary source of the Stokes shift in CQDs in solution, propagating into the Stokes shift in films and the open-circuit voltage deficit in CQD solar cells. Improved synthetic control can bring notable advancements in CQD photovoltaics, and the Stokes shift continues to provide a sensitive and significant metric to monitor ensemble size distribution.

FINDING EXTRATERRESTRIAL LIFE USING GROUND-BASED HIGH-DISPERSION SPECTROSCOPY

International Nuclear Information System (INIS)

Snellen, I. A. G.; Le Poole, R.; Brogi, M.; Birkby, J.; De Kok, R. J.

2013-01-01

Exoplanet observations promise one day to unveil the presence of extraterrestrial life. Atmospheric compounds in strong chemical disequilibrium would point to large-scale biological activity just as oxygen and methane do in the Earth's atmosphere. The cancellation of both the Terrestrial Planet Finder and Darwin missions means that it is unlikely that a dedicated space telescope to search for biomarker gases in exoplanet atmospheres will be launched within the next 25 years. Here we show that ground-based telescopes provide a strong alternative for finding biomarkers in exoplanet atmospheres through transit observations. Recent results on hot Jupiters show the enormous potential of high-dispersion spectroscopy to separate the extraterrestrial and telluric signals, making use of the Doppler shift of the planet. The transmission signal of oxygen from an Earth-twin orbiting a small red dwarf star is only a factor of three smaller than that of carbon monoxide recently detected in the hot Jupiter τ Boötis b, albeit such a star will be orders of magnitude fainter. We show that if Earth-like planets are common, the planned extremely large telescopes can detect oxygen within a few dozen transits. Ultimately, large arrays of dedicated flux-collector telescopes equipped with high-dispersion spectrographs can provide the large collecting area needed to perform a statistical study of life-bearing planets in the solar neighborhood.

Enhancing the functional and economical efficiency of a novel combined thermo chemical disperser disintegration of waste activated sludge for biogas production.

Science.gov (United States)

Kavitha, S; Jayashree, C; Adish Kumar, S; Kaliappan, S; Rajesh Banu, J

2014-12-01

In this investigation, an effort was made to pretreat surplus waste activated sludge (WAS) inexpensively by a novel combined process involving thermo chemical disperser pretreatment. This pretreatment was found to be efficient at a specific energy (SE) consumption of 3360.94 kJ/kg TS, with the chemical oxygen demand (COD) solubilization of 20%. This was comparatively higher than thermo chemically treated sludge where the solubilization was found to be 15.5% at a specific energy consumption of 10,330 kJ/kg TS respectively. Higher production of volatile fatty acids (VFA) (675 mg/L) in anaerobic fermentation of pretreated WAS indicates better hydrolysis performance. The biogas production potential of sludge pretreated through this combined technique was found to be 0.455 (L/gVS) and comparatively higher than thermo chemically pretreated sludge. Economic investigation provides 90% net energy savings in this combined pretreatment. Therefore, this combined process was considered to be potentially effective and economical in sludge disintegration. Copyright © 2014 Elsevier Ltd. All rights reserved.

How disturbance, competition and dispersal interact to prevent tree range boundaries from keeping pace with climate change

Science.gov (United States)

Liang, Y.; Duveneck, M.; Gustafson, E. J.; Serra-Diaz, J. M.; Thompson, J. R.

2017-12-01

Climate change is expected to cause geographic shifts in tree species' ranges, but such shifts may not keep pace with climate changes because seed dispersal distances are often limited and competition-induced changes in community composition can be relatively slow. Disturbances may speed changes in community composition, but the interactions among climate change, disturbance and competitive interactions to produce range shifts are poorly understood. We used a physiologically-based mechanistic landscape model to study these interactions in the northeastern United States. We designed a series of disturbance scenarios to represent varied disturbance regimes in terms of both disturbance extent and intensity. We simulated forest succession by incorporating climate change under a high emissions future, disturbances, seed dispersal, and competition using the landscape model parameterized with forest inventory data. Tree species range boundary shifts in the next century were quantified as the change in the location of the 5th (the trailing edge) and 95th (the leading edge) percentiles of the spatial distribution of simulated species. Simulated tree species range boundary shifts in New England over the next century were far below (usually Disturbances may expedite species` recruitment into new sites, but they had little effect on the velocity of simulated range boundary shifts. Range shifts at the trailing edge tended to be associated with photosynthetic capacity, competitive ability for light and seed dispersal ability, whereas shifts at the leading edge were associated only with photosynthetic capacity and competition for light. This study underscores the importance of understanding the role of interspecific competition and disturbance when studying tree range shifts.

Contact angle dependence on the fluid-wall dispersive energy

NARCIS (Netherlands)

Horsch, M.; Heitzig, M.; Dan, C.M.; Harting, J.D.R.; Hasse, H.; Vrabec, J.

2010-01-01

Menisci of the truncated and shifted Lennard-Jones fluid between parallel planar walls are investigated by molecular dynamics simulation. Thereby, the characteristic energy of the unlike dispersive interaction between fluid molecules and wall atoms is systematically varied to determine its influence

Round beams generated by vertical dispersion

International Nuclear Information System (INIS)

Bagley, P.

1990-01-01

Simulations suggest that in e + e - storage rings collisions of round beams (equal emittances and equal β*) can produce very large tune shifts and luminosities. We understand how to make equal β*s, but generating equal emittances is more difficult. We describe an equal emittance scheme that uses several skew quads to couple horizontal dispersion into vertical dispersion. These skew quads also produce a coupling bump. At the interaction point and at other points outside the coupling bump, the motion is not coupled, so that the 'A' normal mode corresponds to horizontal motion and the 'B' normal mode corresponds to vertical motion. We present a round beam lattice for CESR that incorporates this scheme

Unusually high dispersion of nitrogen-doped carbon nanotubes in DNA solution.

Science.gov (United States)

Kim, Jin Hee; Kataoka, Masakazu; Fujisawa, Kazunori; Tojo, Tomohiro; Muramatsu, Hiroyuki; Vega-Díaz, Sofía M; Tristán-López, F; Hayashi, Takuya; Kim, Yoong Ahm; Endo, Morinobu; Terrones, Mauricio; Dresselhaus, Mildred S

2011-12-08

The dispersibility in a DNA solution of bundled multiwalled carbon nanotubes (MWCNTs), having different chemical functional groups on the CNT sidewall, was investigated by optical spectroscopy. We observed that the dispersibility of nitrogen (N)-doped MWCNTs was significantly higher than that of pure MWCNTs and MWCNTs synthesized in the presence of ethanol. This result is supported by the larger amount of adsorbed DNA on N-doped MWCNTs, as well as by the higher binding energy established between nucleobases and the N-doped CNTs. Pure MWCNTs are dispersed in DNA solution via van der Waals and hydrophobic interactions; in contrast, the nitrogenated sites within N-doped MWCNTs provided additional sites for interactions that are important to disperse nanotubes in DNA solutions. © 2011 American Chemical Society

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

Energy Technology Data Exchange (ETDEWEB)

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

2010-01-01

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

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

Science.gov (United States)

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.

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

Science.gov (United States)

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

2010-03-17

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

Dispersion relations for η{sup '} → ηππ

Energy Technology Data Exchange (ETDEWEB)

Isken, Tobias; Kubis, Bastian; Schneider, Sebastian P. [Universitaet Bonn, Helmholtz-Institut fuer Strahlen- und Kernphysik and Bethe Center for Theoretical Physics, Bonn (Germany); Stoffer, Peter [Universitaet Bonn, Helmholtz-Institut fuer Strahlen- und Kernphysik and Bethe Center for Theoretical Physics, Bonn (Germany); University of California at San Diego, Department of Physics, La Jolla, CA (United States)

2017-07-15

We present a dispersive analysis of the decay amplitude for η{sup '} → ηππ that is based on the fundamental principles of analyticity and unitarity. In this framework, final-state interactions are fully taken into account. Our dispersive representation relies only on input for the ππ and πη scattering phase shifts. Isospin symmetry allows us to describe both the charged and neutral decay channel in terms of the same function. The dispersion relation contains subtraction constants that cannot be fixed by unitarity. We determine these parameters by a fit to Dalitz-plot data from the VES and BES-III experiments. We study the prediction of a low-energy theorem and compare the dispersive fit to variants of chiral perturbation theory. (orig.)

Ring current shifts in {sup 19}F-NMR of membrane proteins

Energy Technology Data Exchange (ETDEWEB)

Liu, Dongsheng, E-mail: liudsh@shanghaitech.edu.cn; Wüthrich, Kurt, E-mail: kwuthrich@shanghaitech.edu.cn [ShanghaiTech University, iHuman Institute (China)

2016-05-15

Fluorine-19 NMR markers are attractive reporter groups for use in studies of complex biomacromolecular systems, in particular also for studies of function-related conformational equilibria and rate processes in membrane proteins. Advantages of {sup 19}F-NMR probes include high sensitivity of the {sup 19}F chemical shifts to variations in the non-covalent environment. Nonetheless, in studies of G protein-coupled receptors (GPCR) we encountered situations where {sup 19}F chemical shifts were not responsive to conformational changes that had been implicated by other methods. This prompted us to examine possible effects of aromatic ring current fields on the chemical shifts of {sup 19}F-NMR probes used in GPCRs. Analysis of previously reported {sup 19}F-NMR data on the β{sub 2}-adrenergic receptor and mammalian rhodopsin showed that all {sup 19}F-labeling sites which manifested conformational changes are located near aromatic residues. Although ring current effects are small when compared to other known non-covalent effects on {sup 19}F chemical shifts, there is thus an indication that their contributions are significant when studying activation processes in GPCRs, since the observed activation-related {sup 19}F-NMR chemical shifts are comparable in size to the calculated ring current shifts. Considering the impact of ring current shifts may thus be helpful in identifying promising indigenous or engineered labeling sites for future {sup 19}F-NMR studies of GPCR activation, and novel information may be obtained on the nature of conformational rearrangements near the {sup 19}F-labels. It will then also be interesting to see if the presently indicated role of ring current shifts in membrane protein studies with {sup 19}F-NMR markers can be substantiated by a more extensive data base resulting from future studies.

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

Science.gov (United States)

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.

NMR spectroscopy of organic compounds of selenium and tellurium. Communication 9. Chemical shifts of /sup 13/C in isological series of unsaturated ethers, sulfides, selenides and tellurides

Energy Technology Data Exchange (ETDEWEB)

Kalabin, G.A.; Bzhezovskii, V.M.; Kushnarev, D.F.; Proidakov, A.G. (Irkutskii Gosudarstvennyj Univ. (USSR))

1981-06-01

The effects of heteroatoms Eh(Eh=O, S, Se, Te) on /sup 13/C chemical shifts in eleven isological series of R/sup 1/-Eh-R/sup 2/ unsaturated compounds are compared. A linear relation between /sup 13/C nuclei screening and tEh electronegativity is observed. An assumption is suggested that both likeness of the effects of 6A and 7A group elements on /sup 13/C chemical shifts of R/sup 1/ and R/sup 2/ substituents and their difference for elements of the 4A group are caused by unbonded interactions of the substituents with unshared electron pairs of heteroatoms.

Easy and unambiguous sequential assignments of intrinsically disordered proteins by correlating the backbone 15N or 13C′ chemical shifts of multiple contiguous residues in highly resolved 3D spectra

International Nuclear Information System (INIS)

Yoshimura, Yuichi; Kulminskaya, Natalia V.; Mulder, Frans A. A.

2015-01-01

Sequential resonance assignment strategies are typically based on matching one or two chemical shifts of adjacent residues. However, resonance overlap often leads to ambiguity in resonance assignments in particular for intrinsically disordered proteins. We investigated the potential of establishing connectivity through the three-bond couplings between sequentially adjoining backbone carbonyl carbon nuclei, combined with semi-constant time chemical shift evolution, for resonance assignments of small folded and larger unfolded proteins. Extended sequential connectivity strongly lifts chemical shift degeneracy of the backbone nuclei in disordered proteins. We show here that 3D (H)N(COCO)NH and (HN)CO(CO)NH experiments with relaxation-optimized multiple pulse mixing correlate up to seven adjacent backbone amide nitrogen or carbonyl carbon nuclei, respectively, and connections across proline residues are also obtained straightforwardly. Multiple, recurrent long-range correlations with ultra-high resolution allow backbone 1 H N , 15 N H , and 13 C′ resonance assignments to be completed from a single pair of 3D experiments

Measurement of temperature and concentration influence on the dispersion of fused silica glass photonic crystal fiber infiltrated with water-ethanol mixture

Science.gov (United States)

Van, Hieu Le; Buczynski, Ryszard; Long, Van Cao; Trippenbach, Marek; Borzycki, Krzysztof; Manh, An Nguyen; Kasztelanic, Rafal

2018-01-01

We present experimental and simulation results of the zero-dispersion shift in photonics crystal fibers infiltrated with water-ethanol mixture. The fiber based on the fused silica glass with a hexagonal lattice consists of seven rings of air-holes filled by liquid. We show that it is possible to shift the zero-dispersion wavelength by 35 ps/nm/km when changing the temperature by 60 °C, and by 42 ps/nm/km when changing the concentration of ethanol from 0 to 100%. The results also show that for the optical fiber filed with pure ethanol the flattened part of the dispersion shifts from anomalous to the normal regime at temperatures below -70 °C.

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

Czech Academy of Sciences Publication Activity Database

Vícha, J.; Novotný, J.; Straka, Michal; Repisky, M.; Ruud, K.; Komorovsky, S.; Marek, R.

2015-01-01

Roč. 17, č. 38 (2015), s. 24944-24955 ISSN 1463-9076 R&D Projects: GA ČR(CZ) GA14-03564S Institutional support: RVO:61388963 Keywords : NMR chemical shifts * transition metal complexes * relativistic effects * method calibration Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.449, year: 2015 http://pubs.rsc.org/en/content/articlepdf/2015/cp/c5cp04214c

Assessment of the use of dispersants on oil spills in California marine waters

International Nuclear Information System (INIS)

Trudel, K.; Ross, S.; Belore, R.; Buffington, S.; Ogawa, C.; Panzer, D.

2002-01-01

The technical issues regarding the use of dispersants to clean up oil spills from offshore production sources and transportation sources in California were assessed in this study which examined both operational and environmental issues. The operational issues included the dispersibility of produced and imported oils, along with the capabilities of California response resources to deal with typical spills and limiting environmental impacts to offshore environments. The environmental issues include the risks associated with typical spills and potential net environmental benefit of chemically dispersing oil spills. Most crude oils produced offshore California are heavy and border on the undispersable range, but the imported crudes are somewhat lighter. Modeling has shown that most produced oils and some imported oils emulsify quickly and weather more quickly to the point where they are no longer dispersible. There is a very narrow window of time for chemical dispersions to be used effectively. The net environmental benefit analysis demonstrates that the use of dispersants lessens the total environmental impact of spill scenarios. It was emphasized that it is necessary to act quickly if chemical dispersion is to be effective. Rapid response strategies are needed, including locally based vessel and helicopter spraying systems. 19 refs., 8 tabs., 1 fig

Increased diversification rates follow shifts to bisexuality in liverworts

DEFF Research Database (Denmark)

Laenen, Benjamin; Machac, Antonin; Gradstein, S. Robbert

2016-01-01

on diversification are presumably mediated by the interplay of high fertilization rates, massive spore production and long-distance dispersal, which may separately or together have facilitated liverwort speciation, suppressed their extinction, or both. Importantly, shifts in liverwort sexual systems have...... shifts in sexual systems influence diversification using hidden state speciation and extinction analysis (HiSSE). This new method compares the effects of the variable of interest to the best-fitting latent variable, yielding robust and conservative tests. We find that the transitions in sexual systems...

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

Czech Academy of Sciences Publication Activity Database

Vícha, J.; Marek, R.; Straka, Michal

2016-01-01

Roč. 55, č. 20 (2016), s. 10302-10309 ISSN 0020-1669 Institutional support: RVO:61388963 Keywords : hydrides of TlI and PbII * high-frequency 1H chemical shifts * relativistic effects Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.857, year: 2016

Physico-chemical and microstructural properties of food dispersions

OpenAIRE

Glicerina, Virginia Teresa

2014-01-01

The macroscopic properties of oily food dispersions, such as rheology, mechanical strength, sensory attributes (e.g. mouth feel, texture and even flavour release) and as well as engineering properties are strongly determined by their microstructure, that is considered a key parameter in the understanding of the foods behaviour . In particular the rheological properties of these matrices are largely influenced by their processing techniques, particle size distribution and composition of ingred...

The comparative effects of oil dispersants and oil/dispersant conjugates on germination of the marine macroalga Phyllospora comosa (Fucales: Phaeophyta)

International Nuclear Information System (INIS)

Burridge, T.R.; Shir, M.-A.

1995-01-01

Germination inhibition of the marine macrophyte Phyllospora comosa was utilized as a sub-lethal end-point to assess and compare the effects of four oil dispersants and dispersed diesel fuel and crude oil combinations. Inhibition of germination by the water-soluble fraction of diesel fuel increased following the addition of each of the dispersants; the nominal 48-h EC 50 concentration of diesel fuel declined from 6800 to approximately 400 μl 1 -1 nominal for each dispersed combination. This contrasted with crude oil, where the addition of two dispersants resulted in an enhanced germination rate and an increase in nominal EC 50 concentrations from 130 μl 1 -1 for the undispersed crude to 4000 and 2500 μl 1 -1 . The results indicate that, while germination inhibition of P. comosa may be enhanced by the chemical dispersal of oil response varies with type of both oil and oil dispersant. (author)

Development of a method for environmentally friendly chemical peptide synthesis in water using water-dispersible amino acid nanoparticles

Directory of Open Access Journals (Sweden)

Fukumori Yoshinobu

2011-08-01

Full Text Available Abstract Due to the vast importance of peptides in biological processes, there is an escalating need for synthetic peptides to be used in a wide variety of applications. However, the consumption of organic solvent is extremely large in chemical peptide syntheses because of the multiple condensation steps in organic solvents. That is, the current synthesis method is not environmentally friendly. From the viewpoint of green sustainable chemistry, we focused on developing an organic solvent-free synthetic method using water, an environmentally friendly solvent. Here we described in-water synthesis technology using water-dispersible protected amino acids.

Dispersive effects on multicomponent transport through porous media

Science.gov (United States)

Dutta, Sourav; Daripa, Prabir

2017-11-01

We use a hybrid numerical method to solve a global pressure based porous media flow model of chemical enhanced oil recovery. This is an extension of our recent work. The numerical method is based on the use of a discontinuous finite element method and the modified method of characteristics. The impact of molecular diffusion and mechanical dispersion on the evolution of scalar concentration distributions are studied through numerical simulations of various flooding schemes. The relative importance of the advective, capillary diffusive and dispersive fluxes are compared over different flow regimes defined in the parameter space of Capillary number, Peclet number, longitudinal and transverse dispersion coefficients. Such studies are relevant for the design of effective injection policies and determining optimal combinations of chemical components for improving recovery. This work has been possible due to financial support from the U.S. National Science Foundation Grant DMS-1522782.

In Situ Solid-State Reactions Monitored by X-ray Absorption Spectroscopy: Temperature-Induced Proton Transfer Leads to Chemical Shifts.

Science.gov (United States)

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.

Effects of Temperature and Axial Strain on Four-Wave Mixing Parametric Frequencies in Microstructured Optical Fibers Pumped in the Normal Dispersion Regime

Directory of Open Access Journals (Sweden)

Javier Abreu-Afonso

2014-10-01

Full Text Available A study of the effect of temperature and axial strain on the parametric wavelengths produced by four-wave mixing in microstructured optical fibers is presented. Degenerate four-wave mixing was generated in the fibers by pumping at normal dispersion, near the zero-dispersion wavelength, causing the appearance of two widely-spaced four-wave mixing spectral bands. Temperature changes, and/or axial strain applied to the fiber, affects the dispersion characteristics of the fiber, which can result in the shift of the parametric wavelengths. We show that the increase of temperature causes the signal and idler wavelengths to shift linearly towards shorter and longer wavelengths, respectively. For the specific fiber of the experiment, the band shift at rates ­–0.04 nm/ºC and 0.3 nm/ºC, respectively. Strain causes the parametric bands to shift in the opposite way. The signal band shifted 2.8 nm/me and the idler -5.4 nm/me. Experimental observations are backed by numerical simulations.

Saltmarsh boundary modulates dispersal of mangrove propagules: implications for mangrove migration with sea-level rise.

Science.gov (United States)

Peterson, Jennifer M; Bell, Susan S

2015-01-01

Few studies have empirically examined the suite of mechanisms that underlie the distributional shifts displayed by organisms in response to changing climatic condition. Mangrove forests are expected to move inland as sea-level rises, encroaching on saltmarsh plants inhabiting higher elevations. Mangrove propagules are transported by tidal waters and propagule dispersal is likely modified upon encountering the mangrove-saltmarsh ecotone, the implications of which are poorly known. Here, using an experimental approach, we record landward and seaward dispersal and subsequent establishment of mangrove propagules that encounter biotic boundaries composed of two types of saltmarsh taxa: succulents and grasses. Our findings revealed that propagules emplaced within saltmarsh vegetation immediately landward of the extant mangrove fringe boundary frequently dispersed in the seaward direction. However, propagules moved seaward less frequently and over shorter distances upon encountering boundaries composed of saltmarsh grasses versus succulents. We uniquely confirmed that the small subset of propagules dispersing landward displayed proportionately higher establishment success than those transported seaward. Although impacts of ecotones on plant dispersal have rarely been investigated in situ, our experimental results indicate that the interplay between tidal transport and physical attributes of saltmarsh vegetation influence boundary permeability to propagules, thereby directing the initial phase of shifting mangrove distributions. The incorporation of tidal inundation information and detailed data on landscape features, such as the structure of saltmarsh vegetation at mangrove boundaries, should improve the accuracy of models that are being developed to forecast mangrove distributional shifts in response to sea-level rise.

Dispersed oil decreases the ability of a model fish (Dicentrarchus labrax) to cope with hydrostatic pressure.

Science.gov (United States)

Dussauze, Matthieu; Pichavant-Rafini, Karine; Belhomme, Marc; Buzzacott, Peter; Privat, Killian; Le Floch, Stéphane; Lemaire, Philippe; Theron, Michaël

2017-01-01

Data on the biological impact of oil dispersion in deep-sea environment are scarce. Hence, the aim of this study was to evaluate the potential interest of a pressure challenge as a new experimental approach for the assessment of consequences of chemically dispersed oil, followed by a high hydrostatic pressure challenge. This work was conducted on a model fish: juvenile Dicentrarchus labrax. Seabass were exposed for 48 h to dispersant alone (nominal concentration (NC) = 4 mg L -1 ), mechanically dispersed oil (NC = 80 mg L -1 ), two chemically dispersed types of oil (NC = 50 and 80 mg L -1 with a dispersant/oil ratio of 1/20), or kept in clean seawater. Fish were then exposed for 30 min at a simulated depth of 1350 m, corresponding to pressure of 136 absolute atmospheres (ATA). The probability of fish exhibiting normal activity after the pressure challenge significantly increased from 0.40 to 0.55 when they were exposed to the dispersant but decreased to 0.26 and 0.11 in the case of chemical dispersion of oil (at 50 and 80 mg L -1 , respectively). The chemical dispersion at 80 mg L -1 also induced an increase in probability of death after the pressure challenge (from 0.08 to 0.26). This study clearly demonstrates the ability of a pressure challenge test to give evidence of the effects of a contaminant on the capacity of fish to face hydrostatic pressure. It opens new perspectives on the analysis of the biological impact of chemical dispersion of oil at depth, especially on marine species performing vertical migrations.

How disturbance, competition, and dispersal interact to prevent tree range boundaries from keeping pace with climate change.

Science.gov (United States)

Liang, Yu; Duveneck, Matthew J; Gustafson, Eric J; Serra-Diaz, Josep M; Thompson, Jonathan R

2018-01-01

Climate change is expected to cause geographic shifts in tree species' ranges, but such shifts may not keep pace with climate changes because seed dispersal distances are often limited and competition-induced changes in community composition can be relatively slow. Disturbances may speed changes in community composition, but the interactions among climate change, disturbance and competitive interactions to produce range shifts are poorly understood. We used a physiologically based mechanistic landscape model to study these interactions in the northeastern United States. We designed a series of disturbance scenarios to represent varied disturbance regimes in terms of both disturbance extent and intensity. We simulated forest succession by incorporating climate change under a high-emissions future, disturbances, seed dispersal, and competition using the landscape model parameterized with forest inventory data. Tree species range boundary shifts in the next century were quantified as the change in the location of the 5th (the trailing edge) and 95th (the leading edge) percentiles of the spatial distribution of simulated species. Simulated tree species range boundary shifts in New England over the next century were far below (usually change (usually more than 110 km over 100 years) under a high-emissions scenario. Simulated species` ranges shifted northward at both the leading edge (northern boundary) and trailing edge (southern boundary). Disturbances may expedite species' recruitment into new sites, but they had little effect on the velocity of simulated range boundary shifts. Range shifts at the trailing edge tended to be associated with photosynthetic capacity, competitive ability for light and seed dispersal ability, whereas shifts at the leading edge were associated only with photosynthetic capacity and competition for light. This study underscores the importance of understanding the role of interspecific competition and disturbance when studying tree range

Rapid protein fold determination using secondary chemical shifts and cross-hydrogen bond 15N-13C' scalar couplings (3hbJNC')

Energy Technology Data Exchange (ETDEWEB)

Bonvin, Alexandre M.J.J.; Houben, Klaartje; Guenneugues, Marc; Kaptein, Robert; Boelens, Rolf [Utrecht University, Bijvoet Center for Biomolecular Research, NMR Spectroscopy (Netherlands)

2001-11-15

The possibility of generating protein folds at the stage of backbone assignment using structural restraints derived from experimentally measured cross-hydrogen bond scalar couplings and secondary chemical shift information is investigated using as a test case the small {alpha}/{beta} protein chymotrypsin inhibitor 2. Dihedral angle restraints for the {phi} and {psi} angles of 32 out of 64 residues could be obtained from secondary chemical shift analysis with the TALOS program (Corneliscu et al., 1999a). This information was supplemented by 18 hydrogen-bond restraints derived from experimentally measured cross-hydrogen bond {sup 3hb}J{sub NC'} coupling constants. These experimental data were sufficient to generate structures that are as close as 1.0 A backbone rmsd from the crystal structure. The fold is, however, not uniquely defined and several solutions are generated that cannot be distinguished on the basis of violations or energetic considerations. Correct folds could be identified by combining clustering methods with knowledge-based potentials derived from structural databases.

Summary of breakout Session C1: C1, chemical countermeasures; dispersants

International Nuclear Information System (INIS)

Anon.

1992-01-01

The discussions in breakout session C1 are summarized. The topics discussed include the pros and cons of dispersant use. Many of the positions which have been heard for the last twenty years were restated. Neither group convinced the other of the advisability of easing the use of dispersants. There was better agreement on the need for research and development programs to get a better handle on some of the questions being raised. The R ampersand D needs on which the participants could agree are summarized

Resonant tunneling of UCN through the moving interference filter and experimental test of the UCN dispersion law

International Nuclear Information System (INIS)

Frank, A.I.; Bondarenko, I.V.; Balashov, S.N.; Geltenbort, P.; Hoghoj, P.; Kozlov, A.V.; Masalovich, S.V.; Toperverg, B.P.

2004-01-01

With the aim to test experimentally the dispersion law validity for very slow neutrons a spectrum of ultracold neutrons (UCN) under the condition of resonance tunneling through the moving Neutron Interference Filter was investigated. The neutron spectrum in this case has a narrow width resonance, whose parameters depend on the filter characteristics and dispersion law of neutron waves in matter. For a number of samples a noticeable shift of the resonance position when the filter moved parallel to its surface was detected. This shift is in strong contradiction with the commonly accepted dispersion law. Further investigations have shown that the spectrum of tunneling neutrons is not exactly defined by the solution of one-dimensional quantum problem, but substantially affected by neutron scattering from filter imperfections. The cross section of this scattering depends on the neutron wave number and increases dramatically in resonance conditions. Experimental results as well as comprehensive theoretical analysis have led us to the unambiguous conclusion that observed phenomena of the resonance shift in a moving sample are caused by scattering of neutron tunneling states rather than by a deviation from the commonly accepted dispersion law. (author)

Creatinine and creatininium cation in water solution. Tautomerism and quantitative interpretation of the solution acidity effect on 1H, 13C and 1:4N NMR chemical shifts

International Nuclear Information System (INIS)

Kotsyubynskyy, D.; Molchanov, S.; Gryff-Keller, A.

2004-01-01

1 H, 13 C and 1 :4N NMR chemical shifts for creatinine in water solution of various acidity have been measured. Analysis of these data enabled determination of the acidity constant of creatininium cation and the chemical shifts of the neutral and protonated forms of creatinine. Molecular energies and carbon and nitrogen magnetic shielding constants for various tautomeric structures of the investigated species have been calculated using the quantum chemistry method GIAO DFT B3LYP/6-311++G(2d,p). Compilation of the available experimental and theoretical results has provided additional information on the problem of tautomerism of this important biological molecule. (author)

Volumetric spiral chemical shift imaging of hyperpolarized [2-(13) c]pyruvate in a rat c6 glioma model.

Science.gov (United States)

Park, Jae Mo; Josan, Sonal; Jang, Taichang; Merchant, Milton; Watkins, Ron; Hurd, Ralph E; Recht, Lawrence D; Mayer, Dirk; Spielman, Daniel M

2016-03-01

MRS of hyperpolarized [2-(13)C]pyruvate can be used to assess multiple metabolic pathways within mitochondria as the (13)C label is not lost with the conversion of pyruvate to acetyl-CoA. This study presents the first MR spectroscopic imaging of hyperpolarized [2-(13)C]pyruvate in glioma-bearing brain. Spiral chemical shift imaging with spectrally undersampling scheme (1042 Hz) and a hard-pulse excitation was exploited to simultaneously image [2-(13)C]pyruvate, [2-(13)C]lactate, and [5-(13)C]glutamate, the metabolites known to be produced in brain after an injection of hyperpolarized [2-(13)C]pyruvate, without chemical shift displacement artifacts. A separate undersampling scheme (890 Hz) was also used to image [1-(13)C]acetyl-carnitine. Healthy and C6 glioma-implanted rat brains were imaged at baseline and after dichloroacetate administration, a drug that modulates pyruvate dehydrogenase kinase activity. The baseline metabolite maps showed higher lactate and lower glutamate in tumor as compared to normal-appearing brain. Dichloroacetate led to an increase in glutamate in both tumor and normal-appearing brain. Dichloroacetate-induced %-decrease of lactate/glutamate was comparable to the lactate/bicarbonate decrease from hyperpolarized [1-(13)C]pyruvate studies. Acetyl-carnitine was observed in the muscle/fat tissue surrounding the brain. Robust volumetric imaging with hyperpolarized [2-(13)C]pyruvate and downstream products was performed in glioma-bearing rat brains, demonstrating changes in mitochondrial metabolism with dichloroacetate. © 2015 Wiley Periodicals, Inc.

Evolution of Modulated Dispersive Electron Waves in a Plasma

DEFF Research Database (Denmark)

Sugai, H.; Lynov, Jens-Peter; Michelsen, Poul

1979-01-01

The linear propagation of amplitude-modulated electron waves was examined in a low-density Q-machine plasma. Three effects of the strong dispersion on the modulated wave have been demonstrated: (i) a wavepacket expands along its direction of propagation, followed by a shift of the frequency through...

Optimization of wind speed on dispersion of pollutants using ...

Indian Academy of Sciences (India)

Department of Chemical Engineering, National Institute of Technology Calicut, ... The classical approaches of dispersion model (Qian & Venkatram 2001; ..... of ambient fine organic carbon particles and source apportionment of PM2.5 in Indian ... matrix factorization and chemical mass balance applied to receptor modeling.

Comparison of the solution and crystal structures of staphylococcal nuclease with 13C and 15N chemical shifts used as structural fingerprints

International Nuclear Information System (INIS)

Cole, H.B.R.; Sparks, S.W.; Torchia, D.A.

1988-01-01

The authors report high-resolution 13 C and 15 N NMR spectra of crystalline staphylococcal nuclease (Nase) complexed to thymidine 3',5'-diphosphate and Ca 2+ . High sensitivity and resolution are obtained by applying solid-state NMR techniques-high power proton decoupling and cross-polarization magic angle sample spinning (CPMASS)-to protein samples that have been efficiently synthesized and labeled by an overproducing strain of Escherichia coli. A comparison of CPMASS and solution spectra of Nase labeled with either [methyl- 13 C]methionine or [ 15 ]valine shows that the chemical shifts in the crystalline and solution states are virtually identical. This result is strong evidence that the protein conformations in the solution and crystalline states are nearly the same. Because of the close correspondence of the crystal and solution chemical shifts, sequential assignments obtained in solution apply to the crystal spectra. It should therefore be possible to study the molecular structure and dynamics of many sequentially assigned atomic sites in Nase crystals. Similar experiments are applicable to the growing number of proteins that can be obtained from efficient expression systems

Tailoring of the free spectral range and geometrical cavity dispersion of a microsphere by a coating layer.

Science.gov (United States)

Ristić, Davor; Mazzola, Maurizio; Chiappini, Andrea; Rasoloniaina, Alphonse; Féron, Patrice; Ramponi, Roberta; Righini, Giancarlo C; Cibiel, Gilles; Ivanda, Mile; Ferrari, Maurizio

2014-09-01

The modal dispersion of a whispering gallery mode (WGM) resonator is a very important parameter for use in all nonlinear optics applications. In order to tailor the WGM modal dispersion of a microsphere, we have coated a silica microsphere with a high-refractive-index coating in order to study its effect on the WGM modal dispersion. We used Er(3+) ions as a probe for a modal dispersion assessment. We found that, by varying the coating thickness, the geometrical cavity dispersion can be used to shift overall modal dispersion in a very wide range in both the normal and anomalous dispersion regime.

mc1r Pathway regulation of zebrafish melanosome dispersion

DEFF Research Database (Denmark)

Richardson, Jennifer; Lundegaard, Pia Rengtved; Reynolds, Natalie L

2008-01-01

Zebrafish rapidly alter their pigmentation in response to environmental changes. For black melanocytes, this change is due to aggregation or dispersion of melanin in the cell. Dispersion and aggregation are controlled by intracellular cyclic adenosine monophosphate (cAMP) levels, which increase...... in mammals, and melanosome dispersal in cold-blood vertebrates, the pathway components are highly conserved. However, it has only been assumed that mc1r mediates melanosome dispersal in fish. Here, using morpholino oligonucleotides designed to knockdown mc1r expression, we find that mc1r morphants are unable...... to disperse melanosomes when grown in dark conditions. We also use chemical modifiers of the cAMP pathway, and find an unexpected response to the specific phosphodiesterase 4 (PDE4) inhibitor, rolipram, in melanosome dispersal. When treated with the drug, melanosomes fail to fully disperse in dark conditions...

Effectiveness of dispersants on thick oil slicks

International Nuclear Information System (INIS)

Ross, S.; Belore, R.

1993-01-01

Experiments were conducted to determine the relationship between dispersant effectiveness and oil slick thickness, and thereby determine the optimum time for applying dispersant onto spilled oil at sea. Tests were completed at a lab-scale level by varying the three parameters of oil type, dispersant application, and oil thickness. The tests were intended to be comparative only. The primary oils used were Alberta sweet mix blend and Hibernia B-27 crude. The dispersant, Corexit 9527, was applied either premixed with the oil, dropwise in one application, or dropwise in multiple applications to simulate a multi-hit aircraft operation. The apparatus used in the experiment was an oscillating hoop tank, with oil-containing rings used to obtain and maintain uniform slick thickness. The results indicate that the effectiveness potential of a chemical dispersant does not decrease as slick thickness increases. In fact, results of the tests involving Hibernia oil suggest that oils that tend to herd easily would be treated more effectively if dispersant were applied when the oil was relatively thick (1 mm or greater) to avoid herding problems. The oil slicks premixed with dispersant did not disperse well in the thick oil tests, not because of dispersant-oil interaction problems but because of reduced mixing energy. 6 refs., 4 figs., 1 tab

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.

Science.gov (United States)

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 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.

Atmospheric dispersion models help to improve air quality; Los modelos de dispersion atmosferica ayudan a mejorar la calidad del aire

Energy Technology Data Exchange (ETDEWEB)

Martin, F.

2013-07-01

One of the main challenges of the atmospheric sciences is to reproduce as well as possible the phenomena and processes of pollutants in the atmosphere. To do it, mathematical models based in this case on fluid dynamics and mass and energy conservation equations, equations that govern the atmospheric chemistry, etc., adapted to the spatial scales to be simulated, are developed. The dispersion models simulate the processes of transport, dispersion, chemical transformation and elimination by deposition that air pollutants undergo once they are emitted. Atmospheric dispersion models with their multiple applications have become essential tools for the air quality management. (Author)

Plasma influence on the dispersion properties of finite-length, corrugated waveguides

OpenAIRE

Shkvarunets, A.; Kobayashi, S.; Weaver, J.; Carmel, Y.; Rodgers, J.; Antonsen, T.; Granatstein, V.L.; Destler, W.W.; Ogura, K.; Minami, K.

1996-01-01

We present an experimental study of the electromagnetic properties of transverse magnetic modes in a corrugated-wall cavity filled with a radially inhomogeneous plasma. The shifts of the .resonant frequencies of a finite-length, corrugated cavity were measured as a function of the background plasma density and the dispersion diagram was reconstructed up to a peak plasma density of 1012 em - 3. Good agreement with a calculated dispersion diagram is obtained for plasma densities below 5 X 1011 ...

Detection of fat in focal liver lesions using chemical-shift MR imaging: its significance in patients with and without hepatic cirrhosis

International Nuclear Information System (INIS)

Martin, J.

1999-01-01

To determine the utility of the chemical shift technique in MRI for the detection of fact in focal hepatic lesions and to see its significance in patients with and without hepatic cirrhosis. 159 patients with 207 hepatic lesions were studied using MRI (IT). Two groups were established: a) patients with hepatic cirrhosis (n=63 with 69 lesions) and b) patients without cirrhosis (n=96 with 138 lesions). Images were obtained in phase (P) and in opposite phase (OP) with gradient echo sequences (RG). The parameter used to differentiate the lesions with fat from those without fat was the variation percentage of the intensity of the signal (VIS) between the images in P and in OP. The statistical valuation was carried out using Student's t tests and the area under the ROC curve. The chemical shift technique detected fat in 25 lesions (12%), 10 hepatocarcinomas in the patients with cirrhosis and two angiomyolipomas and 13 nodular fat infiltrations in the patients who did not have cirrhosis. The average VIS percentage in the 10 hepatocarcinomas was 174.77% (ranging from 88.64% to 369.33%) while in the remaining 59 hepatocarcinomas it was -4.03% (ranging from 12.79% to -19.10%) (p=0.003). In the patients who did not have cirrhosis the average VIS percentage of the lesions with fat was 161.23 (ranging from 19.82 to 605.78) while in the lesions without fat it was -0.41 (ranging from -18.96 to 19.52) (p=0.003). The area under the ROC curve was 1 for the VIS parameter. The chemical shift technique allowed for fat to be detected within hepatic lesions. Based on our study, a nodule with fat in a patient with hepatic cirrhosis is suspected to have hepatocarcinomas while in patients who do not suffer from cirrhosis the existence of fat in a nodule favours its bening nature. (Author) 39 refs

Fate of dispersed marine fuel oil in sediment under pre-spill application strategy

International Nuclear Information System (INIS)

Jian Hua

2004-01-01

A comparison of the movement of dispersed oil in marine sediment under two dispersant application scenarios, applied prior to and after oil being spilled overboard, was examined. The pre-spill application scenario caused much less oil to be retained in the top sediment than post-spill scenario. The difference in oil retention in the top sediment between pre- and post-spill application scenario increased with increase in fuel oil temperature. For fuel oil above 40 o C, the difference in the effect of pre-spill application strategy under various water temperatures was negligible. When soap water was used as replacement for chemical dispersant, almost one-half as much oil was retained in the top sediment as that when using chemical dispersant. The adsorption of dispersed oil to the top sediment was almost proportionally decreased with doubling of soap dosage. (Author)

Measuring proton shift tensors with ultrafast MAS NMR.

Science.gov (United States)

Miah, Habeeba K; Bennett, David A; Iuga, Dinu; Titman, Jeremy J

2013-10-01

A new proton anisotropic-isotropic shift correlation experiment is described which operates with ultrafast MAS, resulting in good resolution of isotropic proton shifts in the detection dimension. The new experiment makes use of a recoupling sequence designed using symmetry principles which reintroduces the proton chemical shift anisotropy in the indirect dimension. The experiment has been used to measure the proton shift tensor parameters for the OH hydrogen-bonded protons in tyrosine·HCl and citric acid at Larmor frequencies of up to 850 MHz. Copyright © 2013 Elsevier Inc. All rights reserved.

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

DEFF Research Database (Denmark)

Bratholm, Lars Andersen; Jensen, Jan Halborg

2017-01-01

The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor...... of a protein backbone and CB chemical shifts (ProCS15, PeerJ, 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic...

The case for using vessel-based systems to apply oil-spill dispersants

International Nuclear Information System (INIS)

Ross, S.

1998-01-01

Most emergency plans for dealing with marine oil spills include the use of chemical dispersants. This paper presents a comparison between the capabilities of aircraft-based dispersant application systems and vessel-based systems. The comparison was presented in terms of the logistics of treating offshore spills. Vessel-based systems have certain advantages in terms of their availability and cost. They have better spray control and accuracy and can dose thick slicks in one pass. However, this advantage is lost if the dispersant payload on the vessel is relatively small and the spill is located very far from the base of operations. Under certain conditions, vessel-based dispersant application systems can treat spills as quickly as aircraft-based systems. Most marine spills tend to occur in restricted waters near ports where dispersant stockpiles could be stored for ready use by vessels in the area. Development of a modern vessel-based, fire-monitor system for applying chemical dispersant onto marine oil spills was one of the recommendations emerging from the study. 32 refs., 6 tabs., 1 fig

Saltmarsh boundary modulates dispersal of mangrove propagules: implications for mangrove migration with sea-level rise.

Directory of Open Access Journals (Sweden)

Jennifer M Peterson

Full Text Available Few studies have empirically examined the suite of mechanisms that underlie the distributional shifts displayed by organisms in response to changing climatic condition. Mangrove forests are expected to move inland as sea-level rises, encroaching on saltmarsh plants inhabiting higher elevations. Mangrove propagules are transported by tidal waters and propagule dispersal is likely modified upon encountering the mangrove-saltmarsh ecotone, the implications of which are poorly known. Here, using an experimental approach, we record landward and seaward dispersal and subsequent establishment of mangrove propagules that encounter biotic boundaries composed of two types of saltmarsh taxa: succulents and grasses. Our findings revealed that propagules emplaced within saltmarsh vegetation immediately landward of the extant mangrove fringe boundary frequently dispersed in the seaward direction. However, propagules moved seaward less frequently and over shorter distances upon encountering boundaries composed of saltmarsh grasses versus succulents. We uniquely confirmed that the small subset of propagules dispersing landward displayed proportionately higher establishment success than those transported seaward. Although impacts of ecotones on plant dispersal have rarely been investigated in situ, our experimental results indicate that the interplay between tidal transport and physical attributes of saltmarsh vegetation influence boundary permeability to propagules, thereby directing the initial phase of shifting mangrove distributions. The incorporation of tidal inundation information and detailed data on landscape features, such as the structure of saltmarsh vegetation at mangrove boundaries, should improve the accuracy of models that are being developed to forecast mangrove distributional shifts in response to sea-level rise.

Modifying Silicates for Better Dispersion in Nanocomposites

Science.gov (United States)

Campbell, Sandi

2005-01-01

An improved chemical modification has been developed to enhance the dispersion of layered silicate particles in the formulation of a polymer/silicate nanocomposite material. The modification involves, among other things, the co-exchange of an alkyl ammonium ion and a monoprotonated diamine with interlayer cations of the silicate. The net overall effects of the improved chemical modification are to improve processability of the nanocomposite and maximize the benefits of dispersing the silicate particles into the polymer. Some background discussion is necessary to give meaning to a description of this development. Polymer/silicate nanocomposites are also denoted polymer/clay composites because the silicate particles in them are typically derived from clay particles. Particles of clay comprise layers of silicate platelets separated by gaps called "galleries." The platelet thickness is 1 nm. The length varies from 30 nm to 1 m, depending on the silicate. In order to fully realize the benefits of polymer/silicate nanocomposites, it is necessary to ensure that the platelets become dispersed in the polymer matrices. Proper dispersion can impart physical and chemical properties that make nanocomposites attractive for a variety of applications. In order to achieve nanometer-level dispersion of a layered silicate into a polymer matrix, it is typically necessary to modify the interlayer silicate surfaces by attaching organic functional groups. This modification can be achieved easily by ion exchange between the interlayer metal cations found naturally in the silicate and protonated organic cations - typically protonated amines. Long-chain alkyl ammonium ions are commonly chosen as the ion-exchange materials because they effectively lower the surface energies of the silicates and ease the incorporation of organic monomers or polymers into the silicate galleries. This completes the background discussion. In the present improved modification of the interlayer silicate surfaces

Dispersant effectiveness in the field on fresh oils and emulsions

International Nuclear Information System (INIS)

Lunel, T.; Davies, L.

1996-01-01

A detailed data set on the effectiveness of dispersants on fresh oils and emulsions, was presented. The data set could be used to calibrate laboratory dispersant tests and dispersion models so that oil spill response teams would have accurate information to make decisions regarding remediation processes. AEA Technology developed steady state continuous release experiments to provide a data set with quantitative measures of dispersant effectiveness in the field. The Sea Empress incident was closely monitored in order to compare the quantification obtained through field trials. It was noted that the prediction of the percentage of oil dispersed chemically is not the only indication of whether or not to use a dispersant. The important determinant to consider should be the extent to which the natural dispersion process would be enhanced by dispersant application. 17 refs., 5 tabs., 18 figs

Large-eddy simulation of pollutant dispersion from a ground-level area source over urban street canyons with irreversible chemical reactions

Science.gov (United States)

Du, T. Z.; Liu, C.-H.; Zhao, Y. B.

2014-10-01

In this study, the dispersion of chemically reactive pollutants is calculated by large-eddy simulation (LES) in a neutrally stratified urban canopy layer (UCL) over urban areas. As a pilot attempt, idealized street canyons of unity building-height-to-street-width (aspect) ratio are used. Nitric oxide (NO) is emitted from the ground surface of the first street canyon into the domain doped with ozone (O3). In the absence of ultraviolet radiation, this irreversible chemistry produces nitrogen dioxide (NO2), developing a reactive plume over the rough urban surface. A range of timescales of turbulence and chemistry are utilized to examine the mechanism of turbulent mixing and chemical reactions in the UCL. The Damköhler number (Da) and the reaction rate (r) are analyzed along the vertical direction on the plane normal to the prevailing flow at 10 m after the source. The maximum reaction rate peaks at an elevation where Damköhler number Da is equal or close to unity. Hence, comparable timescales of turbulence and reaction could enhance the chemical reactions in the plume.

In-town dispersion calculations with RIMPUFF and UDM

International Nuclear Information System (INIS)

Astrup, P.; Thykier-Nielsen, S.; Mikkelsen, Torben

2005-11-01

Input to ERMIN, deposition of radioactive matter inside inhabited areas from releases both within and outside such areas, shall in a decision support system be produced by dispersion codes, followed by data-assimilation. The present work focuses on the differences in near surface concentrations and in depositions obtained with a code designed for dispersion of a release from a nuclear power plant, typically situated at a distance from densely inhabited areas, and a code specifically designed for predicting dispersion from sources inside urban areas. The codes applied are the RIMPUFF code, RIsoe Mesoscale PUFF model from Risoe National Laboratory, Denmark, and the UDM code, Urban Dispersion Model, from 'dstl', Defence Science and Technology Laboratory, Porton Down, United Kingdom. For an above-town release only small differences are seen between the codes, but for a in-town ground release, e.g. a dirty bomb, the UDM code predicts much larger concentrations in an area close to the release point and, if wind shifts occur, gives a rather different plume all over. (au)

Prediction of microvascular invasion of hepatocellular carcinomas with gadoxetic acid-enhanced MR imaging: Impact of intra-tumoral fat detected on chemical-shift images

Energy Technology Data Exchange (ETDEWEB)

Min, Ji Hye [Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of); Kim, Young Kon, E-mail: jmyr@dreamwiz.com [Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of); Lim, Sanghyeok [Department of Radiology, Guri Hospital, Hanyang University College of Medicine, Guri (Korea, Republic of); Jeong, Woo Kyoung; Choi, Dongil; Lee, Won Jae [Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of)

2015-06-15

Highlights: • Intra-tumoral fat detected with MR imaging may suggest lower risk for MVI of HCC. • Alfa-fetoprotein, tumor size, and fat component were associated with MVI of HCC. • Chemical shift MRI should be considered for the evaluation of HCC. - Abstract: Purpose: To investigate the impact of intra-tumoral fat detected by chemical-shift MR imaging in predicting the MVI of HCC. Materials and methods: Gadoxetic acid-enhanced MR imaging of 365 surgically proven HCCs from 365 patients (306 men, 59 women; mean age, 55.6 years) were evaluated. HCCs were classified into two groups, fat-containing and non-fat-containing, based on the presence of fat on chemical-shift images. Fat-containing HCCs were subdivided into diffuse or focal fatty change groups. Logistic regression analyses were used to identify clinical and MR findings associated with MVI. Results: Based on MR imaging, 66 tumors were classified as fat-containing HCCs and 299 as non-fat-containing HCCs. Among the 66 fat-containing HCCs, 38 (57.6%) showed diffuse fatty changes and 28 (42.4%) showed focal fatty changes. MVI was present in 18 (27.3%) fat-containing HCCs and in 117 (39.1%) non-fat-containing HCCs (P = 0.07). Univariate analysis revealed that serum alpha-fetoprotein (AFP) and tumor size were significantly associated with MVI (P < 0.001). A multiple logistic regression analysis showed that log AFP (odds ratio 1.178, P = 0.0016), tumor size (odds ratio 1.809, P < 0.001), and intra-tumoral fat (odds ratio 0.515, P = 0.0387) were independent variables associated with MVI. Conclusion: Intra-tumoral fat detected with MR imaging may suggest lower risk for MVI of HCC and, therefore, a possibly more favorable prognosis, but the clinical value of this finding is uncertain.

Prediction of microvascular invasion of hepatocellular carcinomas with gadoxetic acid-enhanced MR imaging: Impact of intra-tumoral fat detected on chemical-shift images

International Nuclear Information System (INIS)

Min, Ji Hye; Kim, Young Kon; Lim, Sanghyeok; Jeong, Woo Kyoung; Choi, Dongil; Lee, Won Jae

2015-01-01

Highlights: • Intra-tumoral fat detected with MR imaging may suggest lower risk for MVI of HCC. • Alfa-fetoprotein, tumor size, and fat component were associated with MVI of HCC. • Chemical shift MRI should be considered for the evaluation of HCC. - Abstract: Purpose: To investigate the impact of intra-tumoral fat detected by chemical-shift MR imaging in predicting the MVI of HCC. Materials and methods: Gadoxetic acid-enhanced MR imaging of 365 surgically proven HCCs from 365 patients (306 men, 59 women; mean age, 55.6 years) were evaluated. HCCs were classified into two groups, fat-containing and non-fat-containing, based on the presence of fat on chemical-shift images. Fat-containing HCCs were subdivided into diffuse or focal fatty change groups. Logistic regression analyses were used to identify clinical and MR findings associated with MVI. Results: Based on MR imaging, 66 tumors were classified as fat-containing HCCs and 299 as non-fat-containing HCCs. Among the 66 fat-containing HCCs, 38 (57.6%) showed diffuse fatty changes and 28 (42.4%) showed focal fatty changes. MVI was present in 18 (27.3%) fat-containing HCCs and in 117 (39.1%) non-fat-containing HCCs (P = 0.07). Univariate analysis revealed that serum alpha-fetoprotein (AFP) and tumor size were significantly associated with MVI (P < 0.001). A multiple logistic regression analysis showed that log AFP (odds ratio 1.178, P = 0.0016), tumor size (odds ratio 1.809, P < 0.001), and intra-tumoral fat (odds ratio 0.515, P = 0.0387) were independent variables associated with MVI. Conclusion: Intra-tumoral fat detected with MR imaging may suggest lower risk for MVI of HCC and, therefore, a possibly more favorable prognosis, but the clinical value of this finding is uncertain

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

Science.gov (United States)

Bratholm, Lars A; Jensen, Jan H

2017-03-01

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

Adsorption of an anionic dispersant on lignite

Energy Technology Data Exchange (ETDEWEB)

Yavuz, R.; Kucukbayrak, S. [Istanbul Technical University, Istanbul (Turkey). Dept. of Chemical Engineering, Chemical & Metallurgical Engineering Faculty

2001-12-01

Since coal is not a homogeneous substance but a mixture of carbonaceous materials and mineral matter, it has a variety of surface properties. Therefore, it is not easy to control the properties of coal suspensions by simply adjusting variables, such as pH and/or electrolyte. A chemical agent needs to be added to control the properties of the coal suspensions. The adsorption behavior of an anionic dispersant in the presence of a wetting agent using some Turkish lignite samples was investigated. The effects of dispersant concentration, temperature and pH on the dispersant adsorption were studied systematically, and the experimental results are presented. Pellupur B69 as a dispersant, commercial mixture of formaldehyde condensate sodium salt of naphthalene sulphonic acid, and Texapon N{sub 2}5 as a wetting agent, a sodium lauryl ether sulfate, have been used.

Plasma influence on the dispersion properties of finite-length, corrugated waveguides

Science.gov (United States)

Shkvarunets, A.; Kobayashi, S.; Weaver, J.; Carmel, Y.; Rodgers, J.; Antonsen, T. M., Jr.; Granatstein, V. L.; Destler, W. W.; Ogura, K.; Minami, K.

1996-03-01

We present an experimental study of the electromagnetic properties of transverse magnetic modes in a corrugated-wall cavity filled with a radially inhomogeneous plasma. The shifts of the resonant frequencies of a finite-length, corrugated cavity were measured as a function of the background plasma density and the dispersion diagram was reconstructed up to a peak plasma density of 1012 cm-3. Good agreement with a calculated dispersion diagram is obtained for plasma densities below 5×1011 cm-3.

Humans as long-distance dispersers of rural plant communities.

Directory of Open Access Journals (Sweden)

Alistair G Auffret

Full Text Available Humans are known for their capacity to disperse organisms long distances. Long-distance dispersal can be important for species threatened by habitat destruction, but research into human-mediated dispersal is often focused upon few and/or invasive species. Here we use citizen science to identify the capacity for humans to disperse seeds on their clothes and footwear from a known species pool in a valuable habitat, allowing for an assessment of the fraction and types of species dispersed by humans in an alternative context. We collected material from volunteers cutting 48 species-rich meadows throughout Sweden. We counted 24,354 seeds of 197 species, representing 34% of the available species pool, including several rare and protected species. However, 71 species (36% are considered invasive elsewhere in the world. Trait analysis showed that seeds with hooks or other appendages were more likely to be dispersed by humans, as well as those with a persistent seed bank. More activity in a meadow resulted in more dispersal, both in terms of species and representation of the source communities. Average potential dispersal distances were measured at 13 km. We consider humans capable seed dispersers, transporting a significant proportion of the plant communities in which they are active, just like more traditional vectors such as livestock. When rural populations were larger, people might have been regular and effective seed dispersers, and the net rural-urban migration resulting in a reduction in humans in the landscape may have exacerbated the dispersal failure evident in declining plant populations today. With the fragmentation of habitat and changes in land use resulting from agricultural change, and the increased mobility of humans worldwide, the dispersal role of humans may have shifted from providers of regular local and landscape dispersal to providers of much rarer long-distance and regional dispersal, and international invasion.

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.

Science.gov (United States)

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 (+).

Effects of multi-walled carbon nanotube materials on Ruditapes philippinarum under climate change: The case of salinity shifts.

Science.gov (United States)

De Marchi, Lucia; Neto, Victor; Pretti, Carlo; Figueira, Etelvina; Chiellini, Federica; Morelli, Andrea; Soares, Amadeu M V M; Freitas, Rosa

2018-06-01

The toxicity of carbon nanotubes (CNTs) is closely related to their physico-chemical characteristics as well as the physico-chemical parameters of the media where CNTs are dispersed. In a climate change scenario, changes in seawater salinity are becoming a topic of concern particularly in estuarine and coastal areas. Nevertheless, to our knowledge no information is available on how salinity shifts may alter the sensitivity (in terms of biochemical responses) of bivalves when exposed to different CNTs. For this reason, a laboratory experiment was performed exposing the Manila clam Ruditapes philippinarum, one of the most dominant bivalves of the estuarine and coastal lagoon environments, for 28 days to unfunctionalized multi-walled carbon nanotube MWCNTs (Nf-MWCNTs) and carboxylated MWCNTs (f-MWCNTs), maintained at control salinity (28) and low salinity 21. Concentration-dependent toxicity was demonstrated in individuals exposed to both MWCNT materials and under both salinities, generating alterations of energy reserves and metabolism, oxidative status and neurotoxicity compared to non-contaminated clams. Moreover, our results showed greater toxic impacts induced in clams exposed to f-MWCNTs compared to Nf-MWCNTs. In the present study it was also demonstrated how salinity shifts altered the toxicity of both MWCNT materials as well as the sensitivity of R. philippinarum exposed to these contaminates in terms of clam metabolism, oxidative status and neurotoxicity. Copyright © 2018 Elsevier B.V. All rights reserved.

Chemical shifts as a novel measure of interactions between two binding sites of symmetric dialkyldimethylammonium bromides to α-cyclodextrin

International Nuclear Information System (INIS)

Funasaki, Noriaki; Ishikawa, Seiji; Hirota, Shun

2006-01-01

Complex formation of α-cyclodextrin (α-CD) with decyltrimethylammonium (DeTAB), N,N-dioctyldimethylammonium (DOAB), and N,N-didecyldimethylammonium bromides (DDeAB) was investigated by proton NMR spectroscopy. Analysis of chemical shifts yielded macroscopic 1:1 and 1:2 binding constants (K 1 and K 2 ) and chemical shift differences (Δδ SD and Δδ SD2 ) for the 1:1 and 1:2 complexes of DeTAB, DOAB, and DDeAB with α-CD. The K 1 and K 2 values of DDeAB were quantitatively explained on the basis of the assumption that the microscopic 1:1 binding constant of DDeAB is identical to the observed K 1 value of DeTAB. The K 2 value of DDeAB was also explained in terms of its observed K 1 value and the independent binding of two alkyl chains. Furthermore, the Δδ SD and Δδ SD2 values for protons of DDeAB and α-CD were quantitatively explained on the basis of the assumption that the geometry of the decyl group of DDeAB in an α-CD cavity is identical to that of DeTAB. The Δδ SD value was also explicable on the basis of the same geometric assumption and the observed Δδ SD2 value for this system. Similar results were obtained for the 1:1 and 1:2 DOAB-α-CD complexes

Reactive dispersive contaminant transport in coastal aquifers: Numerical simulation of a reactive Henry problem

KAUST Repository

Nick, H.M.

2013-02-01

The reactive mixing between seawater and terrestrial water in coastal aquifers influences the water quality of submarine groundwater discharge. While these waters come into contact at the seawater groundwater interface by density driven flow, their chemical components dilute and react through dispersion. A larger interface and wider mixing zone may provide favorable conditions for the natural attenuation of contaminant plumes. It has been claimed that the extent of this mixing is controlled by both, porous media properties and flow conditions. In this study, the interplay between dispersion and reactive processes in coastal aquifers is investigated by means of numerical experiments. Particularly, the impact of dispersion coefficients, the velocity field induced by density driven flow and chemical component reactivities on reactive transport in such aquifers is studied. To do this, a hybrid finite-element finite-volume method and a reactive simulator are coupled, and model accuracy and applicability are assessed. A simple redox reaction is considered to describe the degradation of a contaminant which requires mixing of the contaminated groundwater and the seawater containing the terminal electron acceptor. The resulting degradation is observed for different scenarios considering different magnitudes of dispersion and chemical reactivity. Three reactive transport regimes are found: reaction controlled, reaction-dispersion controlled and dispersion controlled. Computational results suggest that the chemical components\\' reactivity as well as dispersion coefficients play a significant role on controlling reactive mixing zones and extent of contaminant removal in coastal aquifers. Further, our results confirm that the dilution index is a better alternative to the second central spatial moment of a plume to describe the mixing of reactive solutes in coastal aquifers. © 2012 Elsevier B.V.

An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database

International Nuclear Information System (INIS)

Kobayashi, Naohiro; Harano, Yoko; Tochio, Naoya; Nakatani, Eiichi; Kigawa, Takanori; Yokoyama, Shigeyuki; Mading, Steve; Ulrich, Eldon L.; Markley, John L.; Akutsu, Hideo; Fujiwara, Toshimichi

2012-01-01

Biomolecular NMR chemical shift data are key information for the functional analysis of biomolecules and the development of new techniques for NMR studies utilizing chemical shift statistical information. Structural genomics projects are major contributors to the accumulation of protein chemical shift information. The management of the large quantities of NMR data generated by each project in a local database and the transfer of the data to the public databases are still formidable tasks because of the complicated nature of NMR data. Here we report an automated and efficient system developed for the deposition and annotation of a large number of data sets including 1 H, 13 C and 15 N resonance assignments used for the structure determination of proteins. We have demonstrated the feasibility of our system by applying it to over 600 entries from the internal database generated by the RIKEN Structural Genomics/Proteomics Initiative (RSGI) to the public database, BioMagResBank (BMRB). We have assessed the quality of the deposited chemical shifts by comparing them with those predicted from the PDB coordinate entry for the corresponding protein. The same comparison for other matched BMRB/PDB entries deposited from 2001–2011 has been carried out and the results suggest that the RSGI entries greatly improved the quality of the BMRB database. Since the entries include chemical shifts acquired under strikingly similar experimental conditions, these NMR data can be expected to be a promising resource to improve current technologies as well as to develop new NMR methods for protein studies.

Tunable dispersion compensator based on uniform fiber Bragg grating and its application to tunable pulse repetition-rate multiplication.

Science.gov (United States)

Han, Young-Geun; Lee, Sang

2005-11-14

A new technique to control the chromatic dispersion of a uniform fiber Bragg grating based on the symmetrical bending is proposed and experimentally demonstrated. The specially designed two translation stages with gears and a sawtooth wheel can simultaneously induce the tension and compression strain corresponding to the bending direction. The tension and compression strain can effectively control the chirp ratio along the fiber grating attached on a flexible cantilever beam and consequently the dispersion value without the center wavelength shift. We successfully achieve the wide tuning range of chromatic dispersion without the center wavelength shift, which is less than 0.02 nm. We also reduce the group delay ripple as low as ~+/-5 ps. And we also demonstrate the application of the proposed tunable dispersion compensation technique to the tunable pulse repetition-rate multiplication and obtain high-quality pulses at repetition rates of 20 ~ 40 GHz.

NMR Chemical Shift of a Helium Atom as a Probe for Electronic Structure of FH, F-, (FHF)-, and FH2.

Science.gov (United States)

Tupikina, E Yu; Efimova, A A; Denisov, G S; Tolstoy, P M

2017-12-21

In this work, we present the first results of outer electronic shell visualization by using a 3 He atom as a probe particle. As model objects we have chosen F - , FH, and FH 2 + species, as well as the hydrogen-bonded complex FH···F - at various H···F - distances (3.0, 2.5, 2.0, and 1.5 Å and equilibrium at ca. 1.14 Å). The interaction energy of investigated objects with helium atom (CCSD/aug-cc-pVTZ) and helium atom chemical shift (B3LYP/pcS-2) surfaces were calculated, and their topological analysis was performed. For comparison, the results of standard quantum mechanical approaches to electronic shell visualization were presented (ESP, ELF, ED, ∇ 2 ED). We show that the Laplacian of helium chemical shift, ∇ 2 δ He , is sensitive to fluorine atom lone pair localization regions, and it can be used for the visualization of the outer electronic shell, which could be used to evaluate the proton accepting ability. The sensitivity of ∇ 2 δ He to lone pairs is preserved at distances as large as 2.0-2.5 Å from the fluorine nucleus (in comparison with the distance to ESP minima, located at 1.0-1.5 Å or maxima of ELF, which are as close as 0.6 Å to the fluorine nucleus).

Influence of two-photon absorption on soliton self-frequency shift

DEFF Research Database (Denmark)

Steffensen, Henrik; Agger, Christian; Bang, Ole

2012-01-01

In this paper we develop an analytical model for the soliton self-frequency shift, which includes second- and thirdorder dispersion, self-steepening, the full Raman term, and, for the first time to our best knowledge, the effect of two-photon absorption (TPA). We show that TPA can have a signific...

Seed dispersal anachronisms: rethinking the fruits extinct megafauna ate.

Directory of Open Access Journals (Sweden)

Paulo R Guimarães

Full Text Available BACKGROUND: Some neotropical, fleshy-fruited plants have fruits structurally similar to paleotropical fruits dispersed by megafauna (mammals > 10(3 kg, yet these dispersers were extinct in South America 10-15 Kyr BP. Anachronic dispersal systems are best explained by interactions with extinct animals and show impaired dispersal resulting in altered seed dispersal dynamics. METHODOLOGY/PRINCIPAL FINDINGS: We introduce an operational definition of megafaunal fruits and perform a comparative analysis of 103 Neotropical fruit species fitting this dispersal mode. We define two megafaunal fruit types based on previous analyses of elephant fruits: fruits 4-10 cm in diameter with up to five large seeds, and fruits > 10 cm diameter with numerous small seeds. Megafaunal fruits are well represented in unrelated families such as Sapotaceae, Fabaceae, Solanaceae, Apocynaceae, Malvaceae, Caryocaraceae, and Arecaceae and combine an overbuilt design (large fruit mass and size with either a single or few ( 100 seeds. Within-family and within-genus contrasts between megafaunal and non-megafaunal groups of species indicate a marked difference in fruit diameter and fruit mass but less so for individual seed mass, with a significant trend for megafaunal fruits to have larger seeds and seediness. CONCLUSIONS/SIGNIFICANCE: Megafaunal fruits allow plants to circumvent the trade-off between seed size and dispersal by relying on frugivores able to disperse enormous seed loads over long-distances. Present-day seed dispersal by scatter-hoarding rodents, introduced livestock, runoff, flooding, gravity, and human-mediated dispersal allowed survival of megafauna-dependent fruit species after extinction of the major seed dispersers. Megafauna extinction had several potential consequences, such as a scale shift reducing the seed dispersal distances, increasingly clumped spatial patterns, reduced geographic ranges and limited genetic variation and increased among

Polarization dependent dispersion and its impact on optical parametric process in high nonlinear microstructure fibre

International Nuclear Information System (INIS)

Xiao Li; Zhang Wei; Huang Yidong; Peng Jiangde

2008-01-01

High nonlinear microstructure fibre (HNMF) is preferred in nonlinear fibre optics, especially in the applications of optical parametric effects, due to its high optical nonlinear coefficient. However, polarization dependent dispersion will impact the nonlinear optical parametric process in HNMFs. In this paper, modulation instability (MI) method is used to measure the polarization dependent dispersion of a piece of commercial HNMF, including the group velocity dispersion, the dispersion slope, the fourth-order dispersion and group birefringence. It also experimentally demonstrates the impact of the polarization dependent dispersion on the continuous wave supercontinuum (SC) generation. On one axis MI sidebands with symmetric frequency detunings are generated, while on the other axis with larger MI frequency detuning, SC is generated by soliton self-frequency shift

Synthesis and characterization of M-type barium hexferrite by ultrasonic inter-dispersion of chemical precipitate

International Nuclear Information System (INIS)

Garcia Junior, E.S.; Gomes Junior, G.G.; Ogasawara, T.

2010-01-01

This work is concerned with the study the synthesis and characterization of M-type barium hexaferrite powder by chemical precipitation type and ultrasonic interdispersion of precursor materials Fe(OH) 3 and Ba(OH) 2 ,separately and ultrasonic inter-dispersion, followed by drying and calcining. In order to guide the experimental work was carried out a preliminary thermodynamic analysis of the system Ba-Fe-H 2 O at 25 deg C. The study shows that the phase formation of M-type barium hexaferrite is obtained at a calcination at 1000 deg C, characterized by X-ray diffraction, the grain growth of the final product of synthesis depending on the calcination temperature is visible by SEM. The synthesis method developed in this research is an option to achieve the results that would be obtained if the co-precipitation of ferric and barium hydroxide was thermodynamically possible, where you can get crystallization of barium hexaferrite in a calcination at 1000 deg C. (author)

Automated Fragmentation Polarizable Embedding Density Functional Theory (PE-DFT) Calculations of Nuclear Magnetic Resonance (NMR) Shielding Constants of Proteins with Application to Chemical Shift Predictions

DEFF Research Database (Denmark)

Svendsen, Casper Steinmann; Bratholm, L.A.; Olsen, Jógvan Magnus Haugaard

2017-01-01

that are comparable with experiment. The introduction of a probabilistic linear regression model allows us to substantially reduce the number of snapshots that are needed to make comparisons with experiment. This approach is further improved by augmenting snapshot selection with chemical shift predictions by which we...

Well-dispersed gold nanowire suspension for assembly application