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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2015-01-01

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

Theoretical gas to liquid shift of (15)N isotropic nuclear magnetic shielding in nitromethane using ab initio molecular dynamics and GIAO/GIPAW calculations.

PubMed

Gerber, Iann C; Jolibois, Franck

2015-05-14

Chemical shift requires the knowledge of both the sample and a reference magnetic shielding. In few cases as nitrogen (15N), the standard experimental reference corresponds to its liquid phase. Theoretical estimate of NMR magnetic shielding parameters of compounds in their liquid phase is then mandatory but usually replaced by an easily-get gas phase value, forbidding direct comparisons with experiments. We propose here to combine ab initio molecular dynamic simulations with the calculations of magnetic shielding using GIAO approach on extracted cluster's structures from MD. Using several computational strategies, we manage to accurately calculate 15N magnetic shielding of nitromethane in its liquid phase. Theoretical comparison between liquid and gas phase allows us to extrapolate an experimental value for the 15N magnetic shielding of nitromethane in gas phase between -121.8 and -120.8 ppm.

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

PubMed

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

2018-06-19

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

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

PubMed

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

2018-07-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2014-06-01

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

Theoretical Modeling of 99 Tc NMR Chemical Shifts

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

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

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

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

PubMed

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

2014-07-01

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

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

PubMed

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

2010-05-05

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

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

PubMed

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

2015-01-01

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

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

PubMed

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

2016-04-01

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

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

PubMed

Hoop, Cody L; Iuliucci, Robbie J

2013-06-01

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

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

PubMed

Bratholm, Lars A; Jensen, Jan H

2017-03-01

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

Measuring molecular parity nonconservation using nuclear-magnetic-resonance spectroscopy

DOE PAGES

Eills, J.; Blanchard, J. W.; Bougas, L.; ...

2017-10-30

Here, the weak interaction does not conserve parity and therefore induces energy shifts in chiral enantiomers that should in principle be detectable in molecular spectra. Unfortunately, the magnitude of the expected shifts are small and in spectra of a mixture of enantiomers, the energy shifts are not resolvable. We propose a nuclear-magnetic-resonance (NMR) experiment in which we titrate the chirality (enantiomeric excess) of a solvent and measure the diasteriomeric splitting in the spectra of a chiral solute in order to search for an anomalous offset due to parity nonconservation (PNC). We present a proof-of-principle experiment in which we search formore » PNC in the 13C resonances of small molecules, and use the 1H resonances, which are insensitive to PNC, as an internal reference. We set a constraint on molecular PNC in 13C chemical shifts at a level of 10 –5 ppm, and provide a discussion of important considerations in the search for molecular PNC using NMR spectroscopy.« less

Measuring molecular parity nonconservation using nuclear-magnetic-resonance spectroscopy

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

Eills, J.; Blanchard, J. W.; Bougas, L.

Here, the weak interaction does not conserve parity and therefore induces energy shifts in chiral enantiomers that should in principle be detectable in molecular spectra. Unfortunately, the magnitude of the expected shifts are small and in spectra of a mixture of enantiomers, the energy shifts are not resolvable. We propose a nuclear-magnetic-resonance (NMR) experiment in which we titrate the chirality (enantiomeric excess) of a solvent and measure the diasteriomeric splitting in the spectra of a chiral solute in order to search for an anomalous offset due to parity nonconservation (PNC). We present a proof-of-principle experiment in which we search formore » PNC in the 13C resonances of small molecules, and use the 1H resonances, which are insensitive to PNC, as an internal reference. We set a constraint on molecular PNC in 13C chemical shifts at a level of 10 –5 ppm, and provide a discussion of important considerations in the search for molecular PNC using NMR spectroscopy.« less

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

PubMed

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

2016-11-02

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

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

PubMed Central

2016-01-01

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

Rapid and reliable protein structure determination via chemical shift threading.

PubMed

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

2018-01-01

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

NUCLEAR-MAGNETIC-RESONANCE STUDIES OF HYDROGEN BONDING (thesis)

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

Davis, J.C. Jr.

1959-10-26

The nuclear-magnetic-resonance spectra of hydrogen bonding systems in noninteracting solvents were studied at several concentrations at 20 to 100 deg C. Chemical shifts mic, acetic, and benzoic acids in benzene. The shifts characteristic of the monomer and dimer species were calculated. Shieldings of the monomer species were calculated to be of the same order as those of alcohol monomers. The dimer shieldings were found to be in the range of 300 to 400 cps below the benzene reference. The dimer shieldings increase with the strength of the hydrogen bond. Chemical shifts were also measured for methanol, etanol, isopropanol, and tertiarymore » butanol in carbon tetrschloride and for ethanol in benzene. The enthalpies of dimerization were estimated from the change in the limiting slopes of shift vs. concentration curves with temperature and found to be --9.3 plus or minus 2.5, --7.4 plus or minus 2.0, --6.5 plus or minus 1.5, --5.4 plus or minus 1.8, and--5.6 plu11.6 kcal per mole of dimer, respectively. At 22 deg C, the dimerization constant for ethanol in carbon tetrachloride is 11.0 for a cyclic dimer and twice this for a linear dimer. Probable higher polymers were estimated for the ethanol system, and the experimental data were fitted by adjusting polymer shieldings and equilibrium constants. (auth)« less

A Short History of Three Chemical Shifts

ERIC Educational Resources Information Center

Nagaoka, Shin-ichi

2007-01-01

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

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

PubMed Central

Hong, Mei

2016-01-01

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

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

PubMed Central

2017-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

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

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

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

1990-04-10

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

Sensitivity of Chemical Shift-Encoded Fat Quantification to Calibration of Fat MR Spectrum

PubMed Central

Wang, Xiaoke; Hernando, Diego; Reeder, Scott B.

2015-01-01

Purpose To evaluate the impact of different fat spectral models on proton density fat-fraction (PDFF) quantification using chemical shift-encoded (CSE) MRI. Material and Methods Simulations and in vivo imaging were performed. In a simulation study, spectral models of fat were compared pairwise. Comparison of magnitude fitting and mixed fitting was performed over a range of echo times and fat fractions. In vivo acquisitions from 41 patients were reconstructed using 7 published spectral models of fat. T2-corrected STEAM-MRS was used as reference. Results Simulations demonstrate that imperfectly calibrated spectral models of fat result in biases that depend on echo times and fat fraction. Mixed fitting is more robust against this bias than magnitude fitting. Multi-peak spectral models showed much smaller differences among themselves than when compared to the single-peak spectral model. In vivo studies show all multi-peak models agree better (for mixed fitting, slope ranged from 0.967–1.045 using linear regression) with reference standard than the single-peak model (for mixed fitting, slope=0.76). Conclusion It is essential to use a multi-peak fat model for accurate quantification of fat with CSE-MRI. Further, fat quantification techniques using multi-peak fat models are comparable and no specific choice of spectral model is shown to be superior to the rest. PMID:25845713

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

PubMed

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

2017-02-01

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

Accurate MR thermometry by hyperpolarized 129 Xe.

PubMed

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

2017-09-01

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

A self-reference PRF-shift MR thermometry method utilizing the phase gradient

NASA Astrophysics Data System (ADS)

Langley, Jason; Potter, William; Phipps, Corey; Huang, Feng; Zhao, Qun

2011-12-01

In magnetic resonance (MR) imaging, the most widely used and accurate method for measuring temperature is based on the shift in proton resonance frequency (PRF). However, inter-scan motion and bulk magnetic field shifts can lead to inaccurate temperature measurements in the PRF-shift MR thermometry method. The self-reference PRF-shift MR thermometry method was introduced to overcome such problems by deriving a reference image from the heated or treated image, and approximates the reference phase map with low-order polynomial functions. In this note, a new approach is presented to calculate the baseline phase map in self-reference PRF-shift MR thermometry. The proposed method utilizes the phase gradient to remove the phase unwrapping step inherent to other self-reference PRF-shift MR thermometry methods. The performance of the proposed method was evaluated using numerical simulations with temperature distributions following a two-dimensional Gaussian function as well as phantom and in vivo experimental data sets. The results from both the numerical simulations and experimental data show that the proposed method is a promising technique for measuring temperature.

Simple and robust referencing system enables identification of dissolved-phase xenon spectral frequencies.

PubMed

Antonacci, Michael A; Zhang, Le; Burant, Alex; McCallister, Drew; Branca, Rosa T

2018-08-01

To assess the effect of macroscopic susceptibility gradients on the gas-phase referenced dissolved-phase 129 Xe (DPXe) chemical shift (CS) and to establish the robustness of a water-based referencing system for in vivo DPXe spectra. Frequency shifts induced by spatially varying magnetic susceptibility are calculated by finite-element analysis for the human head and chest. Their effect on traditional gas-phase referenced DPXe CS is then assessed theoretically and experimentally. A water-based referencing system for the DPXe resonances that uses the local water protons as reference is proposed and demonstrated in vivo in rats. Across the human brain, macroscopic susceptibility gradients can induce an apparent variation in the DPXe CS of up to 2.5 ppm. An additional frequency shift as large as 6.5 ppm can exist between DPXe and gas-phase resonances. By using nearby water protons as reference for the DPXe CS, the effect of macroscopic susceptibility gradients is eliminated and consistent CS values are obtained in vivo, regardless of shimming conditions, region of interest analyzed, animal orientation, or lung inflation. Combining in vitro and in vivo spectroscopic measurements finally enables confident assignment of some of the DPXe peaks observed in vivo. To use hyperpolarized xenon as a biological probe in tissues, the DPXe CS in specific organs/tissues must be reliably measured. When the gas-phase is used as reference, variable CS values are obtained for DPXe resonances. Reliable peak assignments in DPXe spectra can be obtained by using local water protons as reference. Magn Reson Med 80:431-441, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Investigating lipids as a source of chemical exchange-induced MRI frequency shifts.

PubMed

Shmueli, K; Dodd, S J; van Gelderen, P; Duyn, J H

2017-04-01

While magnetic susceptibility is a major contributor to NMR resonance frequency variations in the human brain, a substantial contribution may come from the chemical exchange of protons between water and other molecules. Exchange-induced frequency shifts f e have been measured in tissue and protein solutions, but relatively lipid-rich white matter (WM) has a larger f e than gray matter, suggesting that lipids could contribute. Galactocerebrosides (GC) are a prime candidate as they are abundant in WM and susceptible to exchange. To investigate this, f e was measured in a model of WM lipid membranes in the form of multilamellar vesicles (MLVs), consisting of a 1:2 molar ratio of GC and phospholipids (POPC), and in MLVs with POPC only. Chemical shift imaging with 15% volume fraction of dioxane, an internal reference whose protons are assumed not to undergo chemical exchange, was used to remove susceptibility-induced frequency shifts in an attempt to measure f e in MLVs at several lipid concentrations. Initial analysis of these measurements indicated a necessity to correct for small unexpected variations in dioxane concentration due to its effect on the water frequency shift. To achieve this, the actual dioxane concentration was inferred from spectral analysis and its additional contribution to f e was removed through separate experiments which showed that the water-dioxane frequency shift depended linearly on the dioxane concentration at low concentrations with a proportionality constant of -0.021 ± 0.002 ppb/mM in agreement with published experiments. Contrary to expectations and uncorrected results, for GC + POPC vesicles, the dependence of the corrected f e on GC concentration was insignificant (0.023 ± 0.037 ppb/mM; r 2  = 0.085, p > 0.57), whereas for the POPC-only vesicles a small but significant linear increase with POPC concentration was found: 0.044 ± 0.008 ppb/mM (r 2  = 0.877, p < 0.01). These findings suggest that the exchange-induced contribution of lipids to frequency contrast in WM may be small. Published 2016. This article is a U.S. Government work and is in the public domain in the USA. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

Change from an 8-hour shift to a 12-hour shift, attitudes, sleep, sleepiness and performance.

PubMed

Lowden, A; Kecklund, G; Axelsson, J; Akerstedt, T

1998-01-01

The present study sought to evaluate the effect of a change from a rotating 3-shift (8-hour) to a 2-shift shift (12 hour) schedule on sleep, sleepiness, performance, perceived health, and well-being. Thirty-two shift workers at a chemical plant (control room operators) responded to a questionnaire a few months before a change was made in their shift schedule and 10 months after the change. Fourteen workers also filled out a diary, carried activity loggers, and carried out reaction-time tests (beginning and end of shift). Fourteen day workers served as a reference group for the questionnaires and 9 were intensively studied during a week with workdays and a free weekend. The questionnaire data showed that the shift change increased satisfaction with workhours, sleep, and time for social activities. Health, perceived accident risk, and reaction-time performance were not negatively affected. Alertness improved and subjective recovery time after night work decreased. The quick changes in the 8-hour schedule greatly increased sleep problems and fatigue. Sleepiness integrated across the entire shift cycle showed that the shift workers were less alert than the day workers, across workdays and days off (although alertness increased with the 12-hour shift). The change from 8-hour to 12-hour shifts was positive in most respects, possibly due to the shorter sequences of the workdays, the longer sequences of consecutive days off, the fewer types of shifts (easier planning), and the elimination of quick changes. The results may differ in groups with a higher work load.

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

NASA Astrophysics Data System (ADS)

Belyakov, Vladimir A.; Burdov, Vladimir A.

2007-07-01

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

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

PubMed

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

2012-03-07

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

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

PubMed

Stephane Mananga, Eugene

2013-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-10-01

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

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

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

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

2015-10-14

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

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

NASA Astrophysics Data System (ADS)

Olsson, Lars; Cremer, Dieter

1996-11-01

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

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

PubMed

Dumez, Jean-Nicolas; Pickard, Chris J

2009-03-14

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

Relative Configuration of Natural Products Using NMR Chemical Shifts

USDA-ARS?s Scientific Manuscript database

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

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

PubMed Central

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

2009-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

The structural study of acetohydroxamic and oxalodihydroxamic acids in DMSO solution based on the DFT calculations of NMR spectra

NASA Astrophysics Data System (ADS)

Kaczor, Agnieszka; Proniewicz, Leonard M.

2004-10-01

The 1H and 13C NMR spectra of acetohydroxamic (aha) and oxalodihydroxamic (oxha) acids were measured in DMSO- d6 solution. The atoms chemical shifts of chosen stable entgegen and zusammen conformers of monomeric acids were computed along with some clusters of the compounds with the solvent molecules [B3LYP/6-311++G(d,p), GIAO]. The latter were proposed to explain the differences between the theoretical and experimental resonances of the protons of the N-H and O-H groups. The computed chemical shifts of aha-(DMSO) 2 and oxha-(DMSO) 2 models are in good agreement with experimental data proving that the compounds existing in solution form aggregates with DMSO. The acids are H-bonded via all the labile protons to the oxygen atoms of the solvent molecules. aha exists in the zusammen and entgegen (relative to C-N bond) forms with the relative intensities of 8:1 while the sole z, E, z-conformers (notation refers to C-N, C-C and C-N bonds, respectively) were found for oxha.

Automation of peak-tracking analysis of stepwise perturbed NMR spectra.

PubMed

Banelli, Tommaso; Vuano, Marco; Fogolari, Federico; Fusiello, Andrea; Esposito, Gennaro; Corazza, Alessandra

2017-02-01

We describe a new algorithmic approach able to automatically pick and track the NMR resonances of a large number of 2D NMR spectra acquired during a stepwise variation of a physical parameter. The method has been named Trace in Track (TINT), referring to the idea that a gaussian decomposition traces peaks within the tracks recognised through 3D mathematical morphology. It is capable of determining the evolution of the chemical shifts, intensity and linewidths of each tracked peak.The performances obtained in term of track reconstruction and correct assignment on realistic synthetic spectra were high above 90% when a noise level similar to that of experimental data were considered. TINT was applied successfully to several protein systems during a temperature ramp in isotope exchange experiments. A comparison with a state-of-the-art algorithm showed promising results for great numbers of spectra and low signal to noise ratios, when the graduality of the perturbation is appropriate. TINT can be applied to different kinds of high throughput chemical shift mapping experiments, with quasi-continuous variations, in which a quantitative automated recognition is crucial.

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

PubMed

Jurd, Andrew P S; Titman, Jeremy J

2009-08-28

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

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

PubMed

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

2007-12-01

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

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

PubMed

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

2018-03-22

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

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

PubMed

Koes, David R; Vries, John K

2017-01-01

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

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

PubMed Central

2017-01-01

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

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

PubMed Central

Wang, Xianlong; Wang, Chengfei; Zhao, Hui

2012-01-01

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

Unraveling the meaning of chemical shifts in protein NMR.

PubMed

Berjanskii, Mark V; Wishart, David S

2017-11-01

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

Automated and assisted RNA resonance assignment using NMR chemical shift statistics

PubMed Central

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

2013-01-01

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

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

PubMed

Schreckenbach, Georg

2002-12-16

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

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

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

Shift Colors

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

PubMed Central

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

2013-01-01

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

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

PubMed

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

2014-02-01

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

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

PubMed

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

2010-09-30

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

Direct measurement of the Goos-Hänchen shift using a scanning quadrant detector and a polarization maintaining fiber.

PubMed

Yallapragada, Venkata Jayasurya; Mulay, Gajendra L; Rao, Ch N; Ravishankar, Ajith P; Achanta, Venu Gopal

2016-10-01

High precision measurements of optical beam shifts are important in various fields including sensing, atomic force microscopy, and measuring beam shifts at interfaces. Sub-micron shifts are generally measured by indirect techniques such as weak measurements. We demonstrate a straightforward and robust measurement scheme for the shift, based on a scanning quadrant photodiode (QPD) that is biased using a low noise electronic circuit. The shift is measured with respect to a reference beam that is co-propagating with the signal beam. Thus, the shift of the signal beam is readout directly as the difference between the x-intercepts of the QPD scan plot of the signal and reference beams versus the position of the detector. To measure the beam shift, we use polarization multiplexing scheme where the p-polarized signal and s-polarized reference beams are modulated at two different frequencies and co-launched into a polarization-maintaining fiber. Both the signal and reference beam positions are readout by two lock-in amplifiers simultaneously. In order to demonstrate the utility of this method, we perform a direct measurement of Goos-Hänchen shift of a beam that is reflected from a plane gold surface. Accuracy of 150 nm is achieved using this technique.

Direct measurement of the Goos-Hänchen shift using a scanning quadrant detector and a polarization maintaining fiber

NASA Astrophysics Data System (ADS)

Yallapragada, Venkata Jayasurya; Mulay, Gajendra L.; Rao, Ch. N.; Ravishankar, Ajith P.; Achanta, Venu Gopal

2016-10-01

High precision measurements of optical beam shifts are important in various fields including sensing, atomic force microscopy, and measuring beam shifts at interfaces. Sub-micron shifts are generally measured by indirect techniques such as weak measurements. We demonstrate a straightforward and robust measurement scheme for the shift, based on a scanning quadrant photodiode (QPD) that is biased using a low noise electronic circuit. The shift is measured with respect to a reference beam that is co-propagating with the signal beam. Thus, the shift of the signal beam is readout directly as the difference between the x-intercepts of the QPD scan plot of the signal and reference beams versus the position of the detector. To measure the beam shift, we use polarization multiplexing scheme where the p-polarized signal and s-polarized reference beams are modulated at two different frequencies and co-launched into a polarization-maintaining fiber. Both the signal and reference beam positions are readout by two lock-in amplifiers simultaneously. In order to demonstrate the utility of this method, we perform a direct measurement of Goos-Hänchen shift of a beam that is reflected from a plane gold surface. Accuracy of 150 nm is achieved using this technique.

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

NASA Astrophysics Data System (ADS)

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

2015-09-01

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

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

PubMed

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

2015-09-14

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

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

NASA Astrophysics Data System (ADS)

Pechkis, Daniel; Walter, Eric; Krakauer, Henry

2011-03-01

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

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

NASA Astrophysics Data System (ADS)

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

1998-11-01

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

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

PubMed

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

2014-01-14

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

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

NASA Astrophysics Data System (ADS)

Filatov, Michael; Cremer, Dieter

2003-07-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

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

PubMed

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

2014-07-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

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

PubMed

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

2017-04-01

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

Theoretical and experimental NMR study of protopine hydrochloride isomers.

PubMed

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

2005-07-01

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

Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY

PubMed Central

2012-01-01

Background Chemical shift mapping is an important technique in NMR-based drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule's introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically, which is not efficient for high-throughput drug screening. Results We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C-labeling, to resolve the ambiguities for a one-to-one mapping. On the three proteins, it achieves an average accuracy of 94% or better. Conclusions Our mathematical programming approach for modeling chemical shift mapping as a graph problem, while modeling the errors directly, is potentially a time- and cost-effective first step for high-throughput drug screening based on limited NMR data and homologous 3D structures. PMID:22536902

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

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

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

2013-10-08

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

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

Metaxas, Athena E.; Cort, John R.

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

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

NASA Astrophysics Data System (ADS)

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

2009-03-01

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

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

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

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

2015-06-22

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

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

NASA Astrophysics Data System (ADS)

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

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

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

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

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

2015-09-14

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

Acidity in DMSO from the embedded cluster integral equation quantum solvation model.

PubMed

Heil, Jochen; Tomazic, Daniel; Egbers, Simon; Kast, Stefan M

2014-04-01

The embedded cluster reference interaction site model (EC-RISM) is applied to the prediction of acidity constants of organic molecules in dimethyl sulfoxide (DMSO) solution. EC-RISM is based on a self-consistent treatment of the solute's electronic structure and the solvent's structure by coupling quantum-chemical calculations with three-dimensional (3D) RISM integral equation theory. We compare available DMSO force fields with reference calculations obtained using the polarizable continuum model (PCM). The results are evaluated statistically using two different approaches to eliminating the proton contribution: a linear regression model and an analysis of pK(a) shifts for compound pairs. Suitable levels of theory for the integral equation methodology are benchmarked. The results are further analyzed and illustrated by visualizing solvent site distribution functions and comparing them with an aqueous environment.

Molecular dynamics averaging of Xe chemical shifts in liquids.

PubMed

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

2004-11-15

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

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

PubMed

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

2013-01-01

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

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

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

Basse, Kristoffer; Shankar, Ravi; Bjerring, Morten

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

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2014-09-14

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

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

NASA Astrophysics Data System (ADS)

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

2016-08-01

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

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

PubMed Central

Vila, Jorge A.; Scheraga, Harold A.

2008-01-01

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

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

PubMed

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

2017-11-30

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

A 2x2 W-Band Reference Time-Shifted Phase-Locked Transmitter Array in 65nm CMOS Technology

NASA Technical Reports Server (NTRS)

Tang, Adrian; Virbila, Gabriel; Hsiao, Frank; Wu, Hao; Murphy, David; Mehdi, Imran; Siegel, P. H.; Chang, M-C. Frank

2013-01-01

This paper presents a complete 2x2 phased array transmitter system operating at W-band (90-95 GHz) which employs a PLL reference time-shifting approach instead of using traditional mm-wave phase shifters. PLL reference shifting enables a phased array to be distributed over multiple chips without the need for coherent mm-wave signal distribution between chips. The proposed phased array transmitter system consumes 248 mW per array element when implemented in a 65 nm CMOS technology.

Multi-pulse frequency shifted (MPFS) multiple access modulation for ultra wideband

DOEpatents

Nekoogar, Faranak [San Ramon, CA; Dowla, Farid U [Castro Valley, CA

2012-01-24

The multi-pulse frequency shifted technique uses mutually orthogonal short duration pulses o transmit and receive information in a UWB multiuser communication system. The multiuser system uses the same pulse shape with different frequencies for the reference and data for each user. Different users have a different pulse shape (mutually orthogonal to each other) and different transmit and reference frequencies. At the receiver, the reference pulse is frequency shifted to match the data pulse and a correlation scheme followed by a hard decision block detects the data.

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

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

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

2015-09-17

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

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

PubMed

Kanematsu, Yusuke; Tachikawa, Masanori

2014-04-28

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

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

PubMed Central

Shen, Yang; Bax, Ad

2015-01-01

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

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

PubMed

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

2017-06-29

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

Interaction of surface hydroxyls with adsorbed molecules. A quantum-chemical study

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

Geerlings, P.; Tariel, N.; Botrel, A.

1984-11-08

A study has been conducted to explain the interaction mechanisms of (bridging and terminal) surface hydroxyl groups with molecules, using ab initio, EHT, and CNDO/2-FA quantum-chemical calculations. Bond strength variations and charge shifts were found to be in complete agreement with Gutmann's rules, and provide a basis for the understanding of the Bronsted acid properties of zeolites and amorphous silica-alumina. A quantitative measure of the interaction strength is possible by referring to the experimentally determined donor number (Gutmann) following many molecules, but care should be taken for those molecules for which the donor strength was determined by indirect methods. Onlymore » a few exceptions to Gutmann's rules should exist, e.g., in those cases where the atom interacting with the proton is not the most electronegative of the donor molecule (such as for CO). Individual bonds in a given complex are more susceptible to perturbations (changes in composition and interactions with adsorbing molecules) if the coordination number increases. These rules are in agreement with the observations and apply to all reactions (inter- or intramolecular) involving a change in coordination. 52 references, 6 figures, 4 tables.« less

Motion compensation and noise tolerance in phase-shifting digital in-line holography.

PubMed

Stenner, Michael D; Neifeld, Mark A

2006-05-15

We present a technique for phase-shifting digital in-line holography which compensates for lateral object motion. By collecting two frames of interference between object and reference fields with identical reference phase, one can estimate the lateral motion that occurred between frames using the cross-correlation. We also describe a very general linear framework for phase-shifting holographic reconstruction which minimizes additive white Gaussian noise (AWGN) for an arbitrary set of reference field amplitudes and phases. We analyze the technique's sensitivity to noise (AWGN, quantization, and shot), errors in the reference fields, errors in motion estimation, resolution, and depth of field. We also present experimental motion-compensated images achieving the expected resolution.

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

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

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

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

2016-08-28

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

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

PubMed

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

2014-09-23

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

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

PubMed

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

2016-01-05

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

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

PubMed

Klukowski, Piotr; Schubert, Mario

2018-06-15

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

Grimm's Law: Fact or Myth?

ERIC Educational Resources Information Center

Gessman, Albert M.

1990-01-01

Discusses phonic shifting or sound shifts through an examination of Grimm's Law, or the Germanic Consonant Shift. The discussion includes comments on why the phonic shift developed and its pattern. (10 references) (GLR)

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

PubMed

Stueber, Dirk; Grant, David M

2002-09-04

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

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

PubMed

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

2007-03-01

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

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

PubMed

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

2013-09-23

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

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

PubMed

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

2012-01-12

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

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

PubMed

Brodaczewska, Natalia; Košťálová, Zuzana; Uhrín, Dušan

2018-02-01

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

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

PubMed

Sahakyan, Aleksandr B; Vendruscolo, Michele

2013-02-21

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

NMR shifts for polycyclic aromatic hydrocarbons from first-principles

NASA Astrophysics Data System (ADS)

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

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

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

PubMed

Mondal, Arobendo; Kaupp, Martin

2018-04-05

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

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

PubMed

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

2018-01-19

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

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

PubMed

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

2011-07-28

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

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

ERIC Educational Resources Information Center

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

2015-01-01

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

The U.S. Dairy Forage Research Center (USDFRC) Condensed Tannin NMR Database.

PubMed

Zeller, Wayne E; Schatz, Paul F

2017-06-28

This Perspective describes a solution-state NMR database for flavan-3-ol monomers and condensed tannin dimers through tetramers obtained from the literature to 2015, containing data searchable by structure, molecular formula, degrees of polymerization, and 1 H and 13 C chemical shifts of the condensed tannins. Citations for all literature references are provided and should serve as valuable resource for scientists working in the field of condensed tannin research. The database will be periodically updated as additional information becomes available, typically on a yearly basis and is available for use, free of charge, from the U.S. Dairy Forage Research Center (USDFRC) Website.

Predictive factors of life quality among packaging workers in Taiwan.

PubMed

Yang, Shang-Yu; Hsu, Der-Jen; Yen, Chun-Ming; Chang, Jer-Hao

2018-05-16

The semiconductor plants on the top of high-tech industrial chain hire many packaging workers to carry out miscellaneous packing tasks for various product orders from different companies and countries. Under tremendous workload the quality of life (QoL) of such packaging workers need to be concerned. The aim of this study was to explore factors influencing their QoL. This study recruited 247 packing workers (162 male and 85 female; mean age: 35.6 years old) in 2015 and 2016 from a semiconductor plant in Taiwan by convenience sampling. The questionnaire comprised four parts: demographics, the World Health Organization Quality of Life (WHOQOL-BREF), an occupational burnout inventory and the Nordic Musculoskeletal Questionnaire. The four domains of the WHOQOL-BREF were defined as outcome variables. Predictive factors included gender (reference: male), age (reference: ≤ 35), BMI (reference: ≤ 25), educational level (reference: below university), marital/partner status (reference: married/cohabiting), years of work (reference: ≤ 5), work shift (reference: day shift), personal burnout, work-related burnout, over-commitment to work and the number of body parts with discomfort (0-9). The findings showed that physical QoL was negatively correlated with night -shift work, personal burnout, and number of body parts with discomfort. Psychological QoL was negatively correlated with night shift work and personal burnout. Environment QoL was negatively correlated with being male, night shift work and personal burnout. The results showed that the QoL among the packaging workers could be improved by reducing musculoskeletal discomfort, personal burnout and by improving work schedules.

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

PubMed

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

2008-07-16

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

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2017-12-12

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

NMR structural and dynamic characterization of the acid-unfolded state of apomyoglobin provides insights into the early events in protein folding.

PubMed

Yao, J; Chung, J; Eliezer, D; Wright, P E; Dyson, H J

2001-03-27

Apomyoglobin forms a denatured state under low-salt conditions at pH 2.3. The conformational propensities and polypeptide backbone dynamics of this state have been characterized by NMR. Nearly complete backbone and some side chain resonance assignments have been obtained, using a triple-resonance assignment strategy tailored to low protein concentration (0.2 mM) and poor chemical shift dispersion. An estimate of the population and location of residual secondary structure has been made by examining deviations of (13)C(alpha), (13)CO, and (1)H(alpha) chemical shifts from random coil values, scalar (3)J(HN,H)(alpha) coupling constants and (1)H-(1)H NOEs. Chemical shifts constitute a highly reliable indicator of secondary structural preferences, provided the appropriate random coil chemical shift references are used, but in the case of acid-unfolded apomyoglobin, (3)J(HN,H)(alpha) coupling constants are poor diagnostics of secondary structure formation. Substantial populations of helical structure, in dynamic equilibrium with unfolded states, are formed in regions corresponding to the A and H helices of the folded protein. In addition, the deviation of the chemical shifts from random coil values indicates the presence of helical structure encompassing the D helix and extending into the first turn of the E helix. The polypeptide backbone dynamics of acid-unfolded apomyoglobin have been investigated using reduced spectral density function analysis of (15)N relaxation data. The spectral density J(omega(N)) is particularly sensitive to variations in backbone fluctuations on the picosecond to nanosecond time scale. The central region of the polypeptide spanning the C-terminal half of the E helix, the EF turn, and the F helix behaves as a free-flight random coil chain, but there is evidence from J(omega(N)) of restricted motions on the picosecond to nanosecond time scale in the A and H helix regions where there is a propensity to populate helical secondary structure in the acid-unfolded state. Backbone fluctuations are also restricted in parts of the B and G helices due to formation of local hydrophobic clusters. Regions of restricted backbone flexibility are generally associated with large buried surface area. A significant increase in J(0) is observed for the NH resonances of some residues located in the A and G helices of the folded protein and is associated with fluctuations on a microsecond to millisecond time scale that probably arise from transient contacts between these distant regions of the polypeptide chain. Our results indicate that the equilibrium unfolded state of apomyoglobin formed at pH 2.3 is an excellent model for the events that are expected to occur in the earliest stages of protein folding, providing insights into the regions of the polypeptide that spontaneously undergo local hydrophobic collapse and sample nativelike secondary structure.

The relativistic theory of the chemical shift

NASA Astrophysics Data System (ADS)

Pyper, N. C.

1983-04-01

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

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

PubMed Central

Zhang, Rongchun; Ramamoorthy, Ayyalusamy

2016-01-01

Establishing connectivity and proximity of nuclei is an important step in elucidating the structure and dynamics of molecules in solids using magic angle spinning (MAS) NMR spectroscopy. Although recent studies have successfully demonstrated the feasibility of proton-detected multidimensional solid-state NMR experiments under ultrafast-MAS frequencies and obtaining high-resolution spectral lines of protons, assignment of proton resonances is a major challenge. In this study, we first re-visit and demonstrate the feasibility of 2D constant-time uniform-sign cross-peak correlation (CTUC-COSY) NMR experiment on rigid solids under ultrafast-MAS conditions, where the sensitivity of the experiment is enhanced by the reduced spin-spin relaxation rate and the use of low radio-frequency power for heteronuclear decoupling during the evolution intervals of the pulse sequence. In addition, we experimentally demonstrate the performance of a proton-detected pulse sequence to obtain a 3D 1H/13C/1H chemical shift correlation spectrum by incorporating an additional cross-polarization period in the CTUC-COSY pulse sequence to enable proton chemical shift evolution and proton detection in the incrementable t1 and t3 periods, respectively. In addition to through-space and through-bond 13C/1H and 13C/13C chemical shift correlations, the 3D 1H/13C/1H experiment also provides a COSY-type 1H/1H chemical shift correlation spectrum, where only the chemical shifts of those protons, which are bonded to two neighboring carbons, are correlated. By extracting 2D F1/F3 slices (1H/1H chemical shift correlation spectrum) at different 13C chemical shift frequencies from the 3D 1H/13C/1H spectrum, resonances of proton atoms located close to a specific carbon atom can be identified. Overall, the through-bond and through-space homonuclear/heteronuclear proximities determined from the 3D 1H/13C/1H experiment would be useful to study the structure and dynamics of a variety of chemical and biological solids. PMID:26801026

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

PubMed

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

2018-06-12

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

Reduced dimensionality tailored HN(C)N experiments for facile backbone resonance assignment of proteins through unambiguous identification of sequential HSQC peaks

NASA Astrophysics Data System (ADS)

Kumar, Dinesh

2013-12-01

Two novel reduced dimensionality (RD) tailored HN(C)N [S.C. Panchal, N.S. Bhavesh, R.V. Hosur, Improved 3D triple resonance experiments, HNN and HN(C)N, for HN and 15N sequential correlations in (13C, 15N) labeled proteins: application to unfolded proteins, J. Biomol. NMR 20 (2001) 135-147] experiments are proposed to facilitate the backbone resonance assignment of proteins both in terms of its accuracy and speed. These experiments - referred here as (4,3)D-hNCOcaNH and (4,3)D-hNcoCANH - exploit the linear combination of backbone 15N and 13C‧/13Cα chemical shifts simultaneously to achieve higher peak dispersion and randomness along their respective F1 dimensions. Simply, this has been achieved by modulating the backbone 15N(i) chemical shifts with that of 13C‧ (i - 1)/13Cα (i - 1) spins following the established reduced dimensionality NMR approach [T. Szyperski, D.C. Yeh, D.K. Sukumaran, H.N. Moseley, G.T. Montelione, Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment, Proc. Natl. Acad. Sci. USA 99 (2002) 8009-8014]. Though the modification is simple it has resulted an ingenious improvement of HN(C)N both in terms of peak dispersion and easiness of establishing the sequential connectivities. The increased dispersion along F1 dimension solves two purposes here: (i) resolves the ambiguities arising because of degenerate 15N chemical shifts and (ii) reduces the signal overlap in F2(15N)-F3(1H) planes (an important requisite in HN(C)N based assignment protocol for facile and unambiguous identification of sequentially connected HSQC peaks). The performance of both these experiments and the assignment protocol has been demonstrated using bovine apo Calbindin-d9k (75 aa) and urea denatured UNC60B (a 152 amino acid ADF/cofilin family protein of Caenorhabditis elegans), as representatives of folded and unfolded protein systems, respectively.

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

ERIC Educational Resources Information Center

Boggess, Robert K.

1988-01-01

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

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

PubMed Central

Shen, Yang; Bax, Ad

2012-01-01

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

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

PubMed

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

2017-11-27

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

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

PubMed Central

Viesser, Renan V.

2017-01-01

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

Hepatic fat quantification: a prospective comparison of magnetic resonance spectroscopy and analysis methods for chemical-shift gradient echo magnetic resonance imaging with histologic assessment as the reference standard.

PubMed

Kang, Bo-Kyeong; Yu, Eun Sil; Lee, Seung Soo; Lee, Youngjoo; Kim, Namkug; Sirlin, Claude B; Cho, Eun Yoon; Yeom, Suk Keu; Byun, Jae Ho; Park, Seong Ho; Lee, Moon-Gyu

2012-06-01

The aims of this study were to assess the confounding effects of hepatic iron deposition, inflammation, and fibrosis on hepatic steatosis (HS) evaluation by magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS) and to assess the accuracies of MRI and MRS for HS evaluation, using histology as the reference standard. In this institutional review board-approved prospective study, 56 patients gave informed consents and underwent chemical-shift MRI and MRS of the liver on a 1.5-T magnetic resonance scanner. To estimate MRI fat fraction (FF), 4 analysis methods were used (dual-echo, triple-echo, multiecho, and multi-interference), and MRS FF was calculated with T2 correction. Degrees of HS, iron deposition, inflammation, and fibrosis were analyzed in liver resection (n = 37) and biopsy (n = 19) specimens. The confounding effects of histology on fat quantification were assessed by multiple linear regression analysis. Using the histologic degree of HS as the reference standard, the accuracies of each method in estimating HS and diagnosing an HS of 5% or greater were determined by linear regression and receiver operating characteristic analyses. Iron deposition significantly confounded estimations of FF by the dual-echo (P < 0.001) and triple-echo (P = 0.033) methods, whereas no histologic feature confounded the multiecho and multi-interference methods or MRS. The MRS (r = 0.95) showed the strongest correlation with histologic degree of HS, followed by the multiecho (r = 0.92), multi-interference (r = 0.91), triple-echo (r = 0.90), and dual-echo (r = 0.85) methods. For diagnosing HS, the areas under the curve tended to be higher for MRS (0.96) and the multiecho (0.95), multi-interference (0.95), and triple-echo (0.95) methods than for the dual-echo method (0.88) (P ≥ 0.13). The multiecho and multi-interference MRI methods and MRS can accurately quantify hepatic fat, with coexisting histologic abnormalities having no confounding effects.

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

PubMed

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

2017-02-28

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

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

PubMed

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

2018-05-01

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

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

PubMed

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

2003-03-03

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

Perceptual Integration and Differentiation of Directions in Moving Patterns

DTIC Science & Technology

1981-08-01

ceBssay and identify by block numnbe,) o ~ b 20 ABSTRACT (Continue oil rel’erse side II necosary aid idonlty, by block number) F . A- 1981. (-7 ATTACHED...process, are discussed. REFERENCES Mather, G. and Moulden, B . A simultaneous shift in apparent direction: Further evidence for a "distribution- shift" model...summing process, are discussed. REFERENCES Mather, G. and Moulden, B . A simultaneous shift in apparent direction: Further evidence for a "distribution

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

NASA Astrophysics Data System (ADS)

Ganesan, Aravindhan; Wang, Feng

2009-07-01

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

Chemical mutagenesis in laboratory mammals. A bibliography on the effects of chemicals on germ cells

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

Von Halle, E.S.

1973-09-01

A list of references is presented on chemical mutagenesis in laboratory mammals. The references relate primarily to chemical effects on germ cells. Only references to the use of chemicals or chemicals and radiation are included. The publication includes a citation index, agent index, chemical abstracts registry number index, organism index, KWIC index, author index, and first author index. (ERB)

Neuroendocrine recovery after 2-week 12-h day and night shifts: an 11-day follow-up.

PubMed

Merkus, Suzanne L; Holte, Kari Anne; Huysmans, Maaike A; Hansen, Åse Marie; van de Ven, Peter M; van Mechelen, Willem; van der Beek, Allard J

2015-02-01

The study aimed to investigate the course and duration of neuroendocrine recovery after 2-week 12-h day and night shift working periods and to study whether there were differences in recovery between the shift groups. Twenty-nine male offshore employees working 2-week 12-h shift tours participated in the study; 15 participated after a day shift tour and 14 after a night shift tour. Salivary cortisol was assessed at awakening, 30 min after awakening, and before bedtime on the 1st, 4th, 7th, and 11th day of the free period, with a reference day prior to the offshore tour. Differences were tested using generalised estimating equations analysis. Compared to the reference day, night shift workers had a significantly flatter cortisol profile on the 1st day off, significantly lower cortisol concentrations at 30 min after awakening on day 4 and at awakening on day 7, and a significantly smaller decline to evening concentration on days 4 and 11. Compared to the reference day, day shift workers only showed a significantly lower cortisol concentration at awakening on the 1st day off. Compared to day workers, night shift workers had a flatter profile on the 1st day off and a lower cortisol concentration at awakening on the 4th day. Following 2-week 12-h night shift working periods, recovery was not fully complete up to day 11. Following 2-week 12-h day shift working periods, an indication of incomplete recovery was found on the 1st day off, with full recovery reached on day 4.

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

NASA Astrophysics Data System (ADS)

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

2011-09-01

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

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

PubMed

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

2011-09-01

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

Identification of candidate reference chemicals for in vitro steroidogenesis assays.

PubMed

Pinto, Caroline Lucia; Markey, Kristan; Dix, David; Browne, Patience

2018-03-01

The Endocrine Disruptor Screening Program (EDSP) is transitioning from traditional testing methods to integrating ToxCast/Tox21 in vitro high-throughput screening assays for identifying chemicals with endocrine bioactivity. The ToxCast high-throughput H295R steroidogenesis assay may potentially replace the low-throughput assays currently used in the EDSP Tier 1 battery to detect chemicals that alter the synthesis of androgens and estrogens. Herein, we describe an approach for identifying in vitro candidate reference chemicals that affect the production of androgens and estrogens in models of steroidogenesis. Candidate reference chemicals were identified from a review of H295R and gonad-derived in vitro assays used in methods validation and published in the scientific literature. A total of 29 chemicals affecting androgen and estrogen levels satisfied all criteria for positive reference chemicals, while an additional set of 21 and 15 chemicals partially fulfilled criteria for positive reference chemicals for androgens and estrogens, respectively. The identified chemicals included pesticides, pharmaceuticals, industrial and naturally-occurring chemicals with the capability to increase or decrease the levels of the sex hormones in vitro. Additionally, 14 and 15 compounds were identified as potential negative reference chemicals for effects on androgens and estrogens, respectively. These candidate reference chemicals will be informative for performance-based validation of in vitro steroidogenesis models. Copyright © 2017. Published by Elsevier Ltd.

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

PubMed Central

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

2009-01-01

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

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

PubMed

Yang, Kin S; Hudson, Bruce

2010-11-25

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

Structure and electronic properties of azadirachtin.

PubMed

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

2014-02-01

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

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

NASA Astrophysics Data System (ADS)

Wang, Hongyi

2005-09-01

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

Use of 13Cα Chemical-Shifts in Protein Structure Determination

PubMed Central

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

2008-01-01

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

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

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

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

2016-01-21

Establishing connectivity and proximity of nuclei is an important step in elucidating the structure and dynamics of molecules in solids using magic angle spinning (MAS) NMR spectroscopy. Although recent studies have successfully demonstrated the feasibility of proton-detected multidimensional solid-state NMR experiments under ultrafast-MAS frequencies and obtaining high-resolution spectral lines of protons, assignment of proton resonances is a major challenge. In this study, we first re-visit and demonstrate the feasibility of 2D constant-time uniform-sign cross-peak correlation (CTUC-COSY) NMR experiment on rigid solids under ultrafast-MAS conditions, where the sensitivity of the experiment is enhanced by the reduced spin-spin relaxation rate and themore » use of low radio-frequency power for heteronuclear decoupling during the evolution intervals of the pulse sequence. In addition, we experimentally demonstrate the performance of a proton-detected pulse sequence to obtain a 3D {sup 1}H/{sup 13}C/{sup 1}H chemical shift correlation spectrum by incorporating an additional cross-polarization period in the CTUC-COSY pulse sequence to enable proton chemical shift evolution and proton detection in the incrementable t{sub 1} and t{sub 3} periods, respectively. In addition to through-space and through-bond {sup 13}C/{sup 1}H and {sup 13}C/{sup 13}C chemical shift correlations, the 3D {sup 1}H/{sup 13}C/{sup 1}H experiment also provides a COSY-type {sup 1}H/{sup 1}H chemical shift correlation spectrum, where only the chemical shifts of those protons, which are bonded to two neighboring carbons, are correlated. By extracting 2D F1/F3 slices ({sup 1}H/{sup 1}H chemical shift correlation spectrum) at different {sup 13}C chemical shift frequencies from the 3D {sup 1}H/{sup 13}C/{sup 1}H spectrum, resonances of proton atoms located close to a specific carbon atom can be identified. Overall, the through-bond and through-space homonuclear/heteronuclear proximities determined from the 3D {sup 1}H/{sup 13}C/{sup 1}H experiment would be useful to study the structure and dynamics of a variety of chemical and biological solids.« less

Protein Structure Determination from Pseudocontact Shifts Using ROSETTA

PubMed Central

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

2013-01-01

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

Improvement in Rayleigh Scattering Measurement Accuracy

NASA Technical Reports Server (NTRS)

Fagan, Amy F.; Clem, Michelle M.; Elam, Kristie A.

2012-01-01

Spectroscopic Rayleigh scattering is an established flow diagnostic that has the ability to provide simultaneous velocity, density, and temperature measurements. The Fabry-Perot interferometer or etalon is a commonly employed instrument for resolving the spectrum of molecular Rayleigh scattered light for the purpose of evaluating these flow properties. This paper investigates the use of an acousto-optic frequency shifting device to improve measurement accuracy in Rayleigh scattering experiments at the NASA Glenn Research Center. The frequency shifting device is used as a means of shifting the incident or reference laser frequency by 1100 MHz to avoid overlap of the Rayleigh and reference signal peaks in the interference pattern used to obtain the velocity, density, and temperature measurements, and also to calibrate the free spectral range of the Fabry-Perot etalon. The measurement accuracy improvement is evaluated by comparison of Rayleigh scattering measurements acquired with and without shifting of the reference signal frequency in a 10 mm diameter subsonic nozzle flow.

Method and apparatus for analyzing the fill characteristics of a packaging container

DOEpatents

Rodriguez, J.G.

1998-10-13

A system is described for analyzing the fill characteristics of a container. A container having a filling material therein is positioned adjacent a sound generator. Sound waves from the generator are applied to the container, causing it to vibrate. A vibration detector is used to determine the amount of container vibration. A preferred vibration detector involves a laser vibrometer which applies a reference laser beam to the vibrating container. The reference beam is reflected off of the container to generate a reflected laser beam. The reflected beam experiences a Doppler frequency shift compared with the reference beam which is caused by container vibration. The Doppler shift of the reflected beam is then compared with standardized Doppler shift data from a control container. Repeated Doppler shift measurements may also be undertaken which are converted into a vibration profile that is compared with a standardized vibration profile from a control container. 4 figs.

Method and apparatus for analyzing the fill characteristics of a packaging container

DOEpatents

Rodriguez, Julio G.

1998-01-01

A system for analyzing the fill characteristics of a container. A container having a filling material therein is positioned adjacent a sound generator. Sound waves from the generator are applied to the container, causing it to vibrate. A vibration detector is used to determine the amount of container vibration. A preferred vibration detector involves a laser vibrometer which applies a reference laser beam to the vibrating container. The reference beam is reflected off of the container to generate a reflected laser beam. The reflected beam experiences a Doppler frequency shift compared with the reference beam which is caused by container vibration. The Doppler shift of the reflected beam is then compared with standardized Doppler shift data from a control container. Repeated Doppler shift measurements may also be undertaken which are converted into a vibration profile that is compared with a standardized vibration profile from a control container.

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

PubMed

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

2017-10-01

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

Luminescence of BaBrI and SrBrI single crystals doped with Eu2+

NASA Astrophysics Data System (ADS)

Shalaev, A. A.; Shendrik, R.; Myasnikova, A. S.; Bogdanov, A.; Rusakov, A.; Vasilkovskyi, A.

2018-05-01

The crystal growth procedure and luminescence properties of pure and Eu2+-doped BaBrI and SrBrI crystals are reported. Emission and excitation spectra were recorded under ultraviolet and vacuum ultraviolet excitations. The energy of the first Eu2+ 4f-5d transition and SrBrI band gap are obtained. The electronic structure calculations were performed within GW approximation as implemented in the Vienna Ab Initio Simulation Package. The energy between lowest Eu2+ 5d state and the bottom of conduction band are found based on luminescence quenching parameters. The vacuum referred binding energy diagram of lanthanide levels was constructed using the chemical shift model.

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-08-21

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

15 CFR 200.105 - Standard reference data.

Code of Federal Regulations, 2013 CFR

2013-01-01

..., PROCEDURES, AND FEES § 200.105 Standard reference data. Data on the physical and chemical properties of the... application in research, development, engineering design, and commerce. The Office of Standard Reference Data... Physical and Chemical Reference Data, published jointly with the American Chemical Society and the American...

15 CFR 200.105 - Standard reference data.

Code of Federal Regulations, 2014 CFR

2014-01-01

..., PROCEDURES, AND FEES § 200.105 Standard reference data. Data on the physical and chemical properties of the... application in research, development, engineering design, and commerce. The Office of Standard Reference Data... Physical and Chemical Reference Data, published jointly with the American Chemical Society and the American...

15 CFR 200.105 - Standard reference data.

Code of Federal Regulations, 2012 CFR

2012-01-01

..., PROCEDURES, AND FEES § 200.105 Standard reference data. Data on the physical and chemical properties of the... application in research, development, engineering design, and commerce. The Office of Standard Reference Data... Physical and Chemical Reference Data, published jointly with the American Chemical Society and the American...

15 CFR 200.105 - Standard reference data.

Code of Federal Regulations, 2011 CFR

2011-01-01

..., PROCEDURES, AND FEES § 200.105 Standard reference data. Data on the physical and chemical properties of the... application in research, development, engineering design, and commerce. The Office of Standard Reference Data... Physical and Chemical Reference Data, published jointly with the American Chemical Society and the American...

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

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

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

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

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

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

DOE PAGES

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

2018-03-23

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

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

PubMed

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

2017-03-01

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

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

ERIC Educational Resources Information Center

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

2014-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2009-07-01

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

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

NASA Astrophysics Data System (ADS)

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

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

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

NASA Astrophysics Data System (ADS)

Perera, Ajith

2007-12-01

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

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

PubMed

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

2007-11-01

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

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

PubMed

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

2018-05-10

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

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

NASA Astrophysics Data System (ADS)

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

2014-03-01

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

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

PubMed

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

2016-11-14

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

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

PubMed

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

2018-02-20

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

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2015-04-01

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

Generation and structural validation of a library of diverse xyloglucan-derived oligosaccharides, including an update on xyloglucan nomenclature.

PubMed

Tuomivaara, Sami T; Yaoi, Katsuro; O'Neill, Malcolm A; York, William S

2015-01-30

Xyloglucans are structurally complex plant cell wall polysaccharides that are involved in cell growth and expansion, energy metabolism, and signaling. Determining the structure-function relationships of xyloglucans would benefit from the availability of a comprehensive and structurally diverse collection of rigorously characterized xyloglucan oligosaccharides. Here, we present a workflow for the semi-preparative scale generation and purification of neutral and acidic xyloglucan oligosaccharides using a combination of enzymatic and chemical treatments and size-exclusion chromatography. Twenty-six of these oligosaccharides were purified to near homogeneity and their structures validated using a combination of matrix-assisted laser desorption/ionization mass spectrometry, high-performance anion exchange chromatography, and 1H nuclear magnetic resonance spectroscopy. Mass spectrometry and analytical chromatography were compared as methods for xyloglucan oligosaccharide quantification. 1H chemical shifts were assigned using two-dimensional correlation spectroscopy. A comprehensive update of the nomenclature describing xyloglucan side-chain structures is provided for reference. Copyright © 2014 Elsevier Ltd. All rights reserved.

Sea-dumped chemical weapons: environmental risk, occupational hazard.

PubMed

Greenberg, M I; Sexton, K J; Vearrier, D

2016-01-01

Chemical weapons dumped into the ocean for disposal in the twentieth century pose a continuing environmental and human health risk. In this review we discuss locations, quantity, and types of sea-dumped chemical weapons, related environmental concerns, and human encounters with sea-dumped chemical weapons. We utilized the Ovid (http://ovidsp.tx.ovid.com) and PubMed (http://www.pubmed.org) search engines to perform MEDLINE searches for the terms 'sea-dumped chemical weapons', 'chemical warfare agents', and 'chemical munitions'. The searches returned 5863 articles. Irrelevant and non-English articles were excluded. A review of the references for these articles yielded additional relevant sources, with a total of 64 peer-reviewed articles cited in this paper. History and geography of chemical weapons dumping at sea: Hundreds of thousands of tons of chemical munitions were disposed off at sea following World War II. European, Russian, Japanese, and United States coasts are the areas most affected worldwide. Several areas in the Baltic and North Seas suffered concentrated large levels of dumping, and these appear to be the world's most studied chemical warfare agent marine dumping areas. Chemical warfare agents: Sulfur mustard, Lewisite, and the nerve agents appear to be the chemical warfare agents most frequently disposed off at sea. Multiple other type of agents including organoarsenicals, blood agents, choking agents, and lacrimators were dumped at sea, although in lesser volumes. Environmental concerns: Numerous geohydrologic variables contribute to the rate of release of chemical agents from their original casings, leading to difficult and inexact modeling of risk of release into seawater. Sulfur mustard and the organoarsenicals are the most environmentally persistent dumped chemical agents. Sulfur mustard in particular has a propensity to form a solid or semi-solid lump with a polymer coating of breakdown products, and can persist in this state on the ocean floor for decades. Rates of solubility and hydrolysis and levels of innate toxicity of a chemical agent are used to predict the risk to the marine environments. The organoarsenicals eventually breakdown into arsenic, and thus present an indefinite timeline for contamination. Generally, studies assaying sediment and water levels of parent chemical agents and breakdown products at dumpsites have found minimal amounts of relevant chemicals, although arsenic levels are typically higher in dumpsites than reference areas. Studies of marine organisms have not shown concerning amounts of chemical agents or breakdown products in tissue, but have shown evidence of chronic toxicity. There is believed to be minimal risk posed by seafood consumption. Microbiota assays of dumpsites are significantly altered in species composition compared to reference sites, which may imply unseen but significant changes to ecosystems of dumpsites. Human health concerns: The major human health risk at this time appears to arise from acute exposure to an agent by either accidental recovery of a chemical weapon on a fishing vessel, or by munitions washed ashore onto beaches. Improving technology continues to make the deep sea more accessible, thus increasing the risk of disturbing munitions lying on or buried in the seabed. Pipe laying, cable burying, drilling, scuba diving, trawling, and undersea scientific research are the activities posing the most risk. The long-term threat to the benthic habitat via increased arsenic concentrations, shifts in microbiota speciation, and chronic toxicity to vertebrates and invertebrates is not currently understood. The risk to the environment of massive release via disturbance remains a distinct possibility. Terrorist recovery and re-weaponization of chemical agents is a remote possibility.

Phase-shifting point diffraction interferometer

DOEpatents

Medecki, H.

1998-11-10

Disclosed is a point diffraction interferometer for evaluating the quality of a test optic. In operation, the point diffraction interferometer includes a source of radiation, the test optic, a beam divider, a reference wave pinhole located at an image plane downstream from the test optic, and a detector for detecting an interference pattern produced between a reference wave emitted by the pinhole and a test wave emitted from the test optic. The beam divider produces separate reference and test beams which focus at different laterally separated positions on the image plane. The reference wave pinhole is placed at a region of high intensity (e.g., the focal point) for the reference beam. This allows reference wave to be produced at a relatively high intensity. Also, the beam divider may include elements for phase shifting one or both of the reference and test beams. 8 figs.

Phase-shifting point diffraction interferometer

DOEpatents

Medecki, Hector

1998-01-01

Disclosed is a point diffraction interferometer for evaluating the quality of a test optic. In operation, the point diffraction interferometer includes a source of radiation, the test optic, a beam divider, a reference wave pinhole located at an image plane downstream from the test optic, and a detector for detecting an interference pattern produced between a reference wave emitted by the pinhole and a test wave emitted from the test optic. The beam divider produces separate reference and test beams which focus at different laterally separated positions on the image plane. The reference wave pinhole is placed at a region of high intensity (e.g., the focal point) for the reference beam. This allows reference wave to be produced at a relatively high intensity. Also, the beam divider may include elements for phase shifting one or both of the reference and test beams.

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

PubMed

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

2009-01-01

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

Accounting for phase drifts in SSVEP-based BCIs by means of biphasic stimulation.

PubMed

Wu, Hung-Yi; Lee, Po-Lei; Chang, Hsiang-Chih; Hsieh, Jen-Chuen

2011-05-01

This study proposes a novel biphasic stimulation technique to solve the issue of phase drifts in steady-state visual evoked potential (SSVEPs) in phase-tagged systems. Phase calibration was embedded in stimulus sequences using a biphasic flicker, which is driven by a sequence with alternating reference and phase-shift states. Nine subjects were recruited to participate in off-line and online tests. Signals were bandpass filtered and segmented by trigger signals into reference and phase-shift epochs. Frequency components of SSVEP in the reference and phase-shift epochs were extracted using the Fourier method with a 50% overlapped sliding window. The real and imaginary parts of the SSVEP frequency components were organized into complex vectors in each epoch. Hotelling's t-square test was used to determine the significances of nonzero mean vectors. The rejection of noisy data segments and the validation of gaze detections were made based on p values. The phase difference between the valid mean vectors of reference and phase-shift epochs was used to identify user's gazed targets in this system. Data showed an average information transfer rate of 44.55 and 38.21 bits/min in off-line and online tests, respectively. © 2011 IEEE

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

PubMed Central

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

2018-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2013-10-01

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

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

PubMed

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

2011-12-14

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

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

PubMed

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

2018-01-01

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

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

PubMed

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

2017-03-07

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

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

PubMed Central

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

2011-01-01

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

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

ERIC Educational Resources Information Center

Torres, Emilio Martinez

2007-01-01

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

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

NASA Astrophysics Data System (ADS)

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

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

Influence of OPD in wavelength-shifting interferometry

NASA Astrophysics Data System (ADS)

Wang, Hongjun; Tian, Ailing; Liu, Bingcai; Dang, Juanjuan

2009-12-01

Phase-shifting interferometry is a powerful tool for high accuracy optical measurement. It operates by change the optical path length in the reference arm or test arm. This method practices by move optical device. So it has much problem when the optical device is very large and heavy. For solve this problem, the wavelength-shifting interferometry was put forwarded. In wavelength-shifting interferometry, the phase shifting angle was achieved by change the wavelength of optical source. The phase shifting angle was decided by wavelength and OPD (Optical Path Difference) between test and reference wavefront. So the OPD is an important factor to measure results. But in measurement, because the positional error and profile error of under testing optical element is exist, the phase shifting angle is different in different test point when wavelength scanning, it will introduce phase shifting angle error, so it will introduce optical surface measure error. For analysis influence of OPD on optical surface error, the relation between surface error and OPD was researched. By simulation, the relation between phase shifting error and OPD was established. By analysis, the error compensation method was put forward. After error compensation, the measure results can be improved to great extend.

Influence of OPD in wavelength-shifting interferometry

NASA Astrophysics Data System (ADS)

Wang, Hongjun; Tian, Ailing; Liu, Bingcai; Dang, Juanjuan

2010-03-01

Phase-shifting interferometry is a powerful tool for high accuracy optical measurement. It operates by change the optical path length in the reference arm or test arm. This method practices by move optical device. So it has much problem when the optical device is very large and heavy. For solve this problem, the wavelength-shifting interferometry was put forwarded. In wavelength-shifting interferometry, the phase shifting angle was achieved by change the wavelength of optical source. The phase shifting angle was decided by wavelength and OPD (Optical Path Difference) between test and reference wavefront. So the OPD is an important factor to measure results. But in measurement, because the positional error and profile error of under testing optical element is exist, the phase shifting angle is different in different test point when wavelength scanning, it will introduce phase shifting angle error, so it will introduce optical surface measure error. For analysis influence of OPD on optical surface error, the relation between surface error and OPD was researched. By simulation, the relation between phase shifting error and OPD was established. By analysis, the error compensation method was put forward. After error compensation, the measure results can be improved to great extend.

Synergistic Interactions between Chemokine Receptor Elements in Recognition of Interleukin-8 by Soluble Receptor Mimics†

PubMed Central

Barter, Emily F.; Stone, Martin J.

2012-01-01

Interleukin-8 (IL-8 or CXCL8), the archetypal member of the CXC chemokine subfamily, stimulates neutrophil chemotaxis by activation of the receptors CXCR1/IL8RA and CXCR2/IL8RB. Previous mutational studies have implicated both the N-terminal and third extracellular loop (E3) regions of these receptors in binding to IL-8. To investigate the interactions of these receptor elements with IL-8, we have constructed soluble proteins in which the N-terminal and E3 elements of either CXCR1 or CXCR2 are juxtaposed on a soluble scaffold protein; these are referred to as CROSS-NX1E3X1 and CROSS-NX2E3X2, respectively. Isothermal titration calorimetry (ITC) and NMR spectroscopy were used to compare the IL-8 binding properties of the receptor mimics to those of control proteins containing only the N-terminal or the E3 receptor element. CROSS-NX2E3X2 bound to monomeric IL-8 with the same affinity and induced the same chemical shift changes as the control protein containing only the N-terminal element of CXCR2, indicating that the E3 element of CXCR2 did not contribute to IL-8 binding. In contrast, CROSS-NX1E3X1 bound to IL-8 with ~10-fold increased affinity and induced different chemical shift changes compared to the control protein containing only the N-terminal element of CXCR1, suggesting that the E3 region of CXCR1 was interacting with IL-8. However, a chimeric protein containing the N-terminal region of CXCR1 and the E3 region of CXCR2 (CROSS-NX1E3X2) bound to IL-8 with thermodynamic properties and induced chemical shift changes indistinguishable from those of CROSS-NX1E3X1 and substantially different from those of CROSS-NX2E3X2. These results indicate that the N-terminal and E3 regions of CXCR1 interact synergistically to achieve optimal binding interactions with IL-8. PMID:22242662

1H, 13C, and 15N resonance assignments for the protein coded by gene locus BB0938 of Bordetella bronchiseptica

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

Rossi, Paolo; Ramelot, Theresa A.; Xiao, Rong

2005-11-01

The product of gene locus BB0938 from Bordetella bronchiseptica (Swiss-Prot ID: Q7WNU7-BORBR; NESG target ID: BoR11; Wunderlich et al., 2004; Pfam ID: PF03476) is a 128-residue protein of unknown function. This broadly conserved protein family is found in eubacteria and eukaryotes. Using triple resonance NMR techniques, we have determined 98% of backbone and 94% of side chain 1H, 13C, and 15N resonance assignments. The chemical shift and 3J(HN?Ha) scalar coupling data reveal a b topology with a seven-residue helical insert, ??????????. BMRB deposit with accession number 6693. Reference: Wunderlich et al. (2004) Proteins, 56, 181?187.

1H, 13C, and 15N resonance assignments for Escherichia coli ytfP, a member of the broadly conserved UPF0131 protein domain family

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

Aramini, James M.; Swapna, G.V.T.; Huang, Yuanpeng

2005-11-01

Protein ytfP from Escherichia coli (Swiss-Prot ID: YTFP-ECOLI; NESG target ID: ER111; Wunderlich et al., 2004) is a 113-residue member of the UPF0131 protein family (Pfam ID: PF03674) of unknown function. This domain family is found in organisms from all three kingdoms, archaea, eubacteria and eukaryotes. Using triple resonance NMR techniques, we have determined 97% of backbone and 91% of side chain 1H, 13C, and 15N resonance assignments. The chemical shift and 3J(HN?Ha) scalar coupling data reveal a mixed a/b topology,????????. BMRB deposit with Accession No. 6448. Reference: Wunderlich et al. (2004) Proteins, 56, 181?187.

A Novel Multiple-Access Correlation-Delay-Shift-Keying

NASA Astrophysics Data System (ADS)

Duan, J. Y.; Jiang, G. P.; Yang, H.

In Correlation-Delay-Shift-Keying (CDSK), the reference signal and the information-bearing signal are added together during a certain time delay. Because the reference signal is not strictly orthogonal to the information-bearing signal, the cross-correlation between the adjacent chaotic signal (Intra-signal Interference, ISI) will be introduced into the demodulation at the receiver. Therefore, the Bit-Error Ratio (BER) of CDSK is higher than that of Differential-Chaos-Shift-Keying (DCSK). To avoid the ISI component and enhance the BER performance of CDSK in multiuser scenario, Multiple-Access CDSK with No Intra-signal Interference (MA-CDSK-NII) is proposed. By constructing the repeated chaotic generator and applying the Walsh code sequence to modulate the reference signal, in MA-CDSK-NII, the ISI component will be eliminated during the demodulation. Gaussian approximation method is adopted here to obtain the exact performance analysis of MA-CDSK-NII over additive white Gaussian noise (AWGN) channel and Rayleigh multipath fading channels. Results show that, due to no ISI component and lower transmitting power, the BER performance of MA-CDSK-NII can be better than that of multiple-access CDSK and Code-Shifted Differential-Chaos-Shift-Keying (CS-DCSK).

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

PubMed

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

2010-07-21

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

Phase-shifting point diffraction interferometer grating designs

DOEpatents

Naulleau, Patrick; Goldberg, Kenneth Alan; Tejnil, Edita

2001-01-01

In a phase-shifting point diffraction interferometer, by sending the zeroth-order diffraction to the reference pinhole of the mask and the first-order diffraction to the test beam window of the mask, the test and reference beam intensities can be balanced and the fringe contrast improved. Additionally, using a duty cycle of the diffraction grating other than 50%, the fringe contrast can also be improved.

Environmental odor intolerance in pregnant women.

PubMed

Nordin, Steven; Broman, Daniel A; Wulff, Marianne

2005-02-15

Previous findings indicating that pregnant women experience a shift in odor sensitivity and hedonics raise the question of whether these changes evoke adverse reactions to odorous and pungent environmental substances in daily activities, to a larger extent in pregnant than in nonpregnant women. Forty-four women in pregnancy weeks 21-23 and 44 nonpregnant women were therefore compared with respect to affective reactions to and behavioral disruptions by odorous/pungent daily environments by means of the questionnaire-based, 21-item Chemical Sensitivity Scale (CSS). This scale refers to neurasthenic and sensory/somatic symptoms and includes the 11 items of the Chemical Sensitivity Scale for Sensory Hyperreactivity (CSS-SHR). This latter scale refers predominantly to sensory/somatic symptoms. To investigate whether there is a general environmental hypersensitivity during pregnancy, the Noise Sensitivity Scale (NSS) was used that is analogous to the CSS (including 11 NSS items corresponding to those of the CSS-SHR; "NSS-SHR"). Results show that the two groups were similar with respect to scores on both the CSS and NSS, whereas the pregnant women had higher scores than the nonpregnant women on the CSS-SHR, but not on the "NSS-SHR". These results suggest that pregnant women to a larger extent than nonpregnant women manifest an odor intolerance that affects their daily activities, with predominantly sensory/somatic symptoms, which appears not to be due to a general environmental hypersensitivity. This behavior may have embryo- and maternal-protective functions.

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

NASA Astrophysics Data System (ADS)

Borowski, Piotr

2012-01-01

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

Effective Algorithm for Detection and Correction of the Wave Reconstruction Errors Caused by the Tilt of Reference Wave in Phase-shifting Interferometry

NASA Astrophysics Data System (ADS)

Xu, Xianfeng; Cai, Luzhong; Li, Dailin; Mao, Jieying

2010-04-01

In phase-shifting interferometry (PSI) the reference wave is usually supposed to be an on-axis plane wave. But in practice a slight tilt of reference wave often occurs, and this tilt will introduce unexpected errors of the reconstructed object wave-front. Usually the least-square method with iterations, which is time consuming, is employed to analyze the phase errors caused by the tilt of reference wave. Here a simple effective algorithm is suggested to detect and then correct this kind of errors. In this method, only some simple mathematic operation is used, avoiding using least-square equations as needed in most methods reported before. It can be used for generalized phase-shifting interferometry with two or more frames for both smooth and diffusing objects, and the excellent performance has been verified by computer simulations. The numerical simulations show that the wave reconstruction errors can be reduced by 2 orders of magnitude.

Capillary Electrophoresis - Optical Detection Systems

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

Sepaniak, M. J.

2001-08-06

Molecular recognition systems are developed via molecular modeling and synthesis to enhance separation performance in capillary electrophoresis and optical detection methods for capillary electrophoresis. The underpinning theme of our work is the rational design and development of molecular recognition systems in chemical separations and analysis. There have been, however, some subtle and exciting shifts in our research paradigm during this period. Specifically, we have moved from mostly separations research to a good balance between separations and spectroscopic detection for separations. This shift is based on our perception that the pressing research challenges and needs in capillary electrophoresis and electrokinetic chromatographymore » relate to the persistent detection and flow rate reproducibility limitations of these techniques (see page 1 of the accompanying Renewal Application for further discussion). In most of our work molecular recognition reagents are employed to provide selectivity and enhance performance. Also, an emerging trend is the use of these reagents with specially-prepared nano-scale materials. Although not part of our DOE BES-supported work, the modeling and synthesis of new receptors has indirectly supported the development of novel microcantilevers-based MEMS for the sensing of vapor and liquid phase analytes. This fortuitous overlap is briefly covered in this report. Several of the more significant publications that have resulted from our work are appended. To facilitate brevity we refer to these publications liberally in this progress report. Reference is also made to very recent work in the Background and Preliminary Studies Section of the Renewal Application.« less

New developments in electronic reference controls for frequency domain optical sensing

NASA Astrophysics Data System (ADS)

Chatni, M. R.; Li, G.; Porterfield, D. M.

2009-05-01

The reference optical path is essential for optical systems which function on the basis of light interference. In the case of frequency domain (FD) fluorescence life-time optrodes, a reference LED is used as a standard for calculating the phase angle. The reference LED is configured so that radiation travels the same length to the detector as that of the fluorescence signal being analyzed. The phase shift, which provides details of fluorescence lifetime, is measured between these two signals - the fluorescence signal and reference LED signal, using a photodetector. We have designed, developed and implemented a FD optrode system without a reference LED. The key requirement of such a system is that phase shifts due to optics at wavelength of fluorescence and electronics have to be calibrated. In the reference-free system, the reference signal comes from the lock-in-amplifier which also drives the excitation LED. The lock-in-amplifier measures the phase shift between the excitation signal and the fluorescence emission signal from the photodetector and is locked at the frequency of modulation of the excitation signal. This insures higher signal to noise ratio and low-noise measurements. The reference-free optrode system removes some constraints on the coupling optics, which help improve the overall performance of the system. After development of electronics, and optimization of coupling optics, the system was calibrated in different oxygen concentration solutions to measure fluorescence intensity and lifetime of the oxygen sensitive dye platinum tetrakis (pentafluorophenyl) porphine (PtTFPP).

Frequency-Modulation Correlation Spectrometer

NASA Technical Reports Server (NTRS)

Margolis, J. S.; Martonchik, J. V.

1985-01-01

New type of correlation spectrometer eliminates need to shift between two cells, one empty and one containing reference gas. Electrooptical phase modulator sinusoidally shift frequencies of sample transmission spectrum.

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

PubMed

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

2005-12-01

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

Algorithms for image recovery calculation in extended single-shot phase-shifting digital holography

NASA Astrophysics Data System (ADS)

Hasegawa, Shin-ya; Hirata, Ryo

2018-04-01

The single-shot phase-shifting method of image recovery using an inclined reference wave has the advantages of reducing the effects of vibration, being capable of operating in real time, and affording low-cost sensing. In this method, relatively low reference angles compared with that in the conventional method using phase shift between three or four pixels has been required. We propose an extended single-shot phase-shifting technique which uses the multiple-step phase-shifting algorithm and the corresponding multiple pixels which are the same as that of the period of an interference fringe. We have verified the theory underlying this recovery method by means of Fourier spectral analysis and its effectiveness by evaluating the visibility of the image using a high-resolution pattern. Finally, we have demonstrated high-contrast image recovery experimentally using a resolution chart. This method can be used in a variety of applications such as color holographic interferometry.

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

PubMed

Hartman, Joshua D; Beran, Gregory J O

2014-11-11

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

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

PubMed

Markin, Craig J; Spyracopoulos, Leo

2012-12-01

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

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

NASA Astrophysics Data System (ADS)

Bühl, Michael; Curioni, Alessandro; Andreoni, Wanda

1997-08-01

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

Crosstalk Cancellation for a Simultaneous Phase Shifting Interferometer

NASA Technical Reports Server (NTRS)

Olczak, Eugene (Inventor)

2014-01-01

A method of minimizing fringe print-through in a phase-shifting interferometer, includes the steps of: (a) determining multiple transfer functions of pixels in the phase-shifting interferometer; (b) computing a crosstalk term for each transfer function; and (c) displaying, to a user, a phase-difference map using the crosstalk terms computed in step (b). Determining a transfer function in step (a) includes measuring intensities of a reference beam and a test beam at the pixels, and measuring an optical path difference between the reference beam and the test beam at the pixels. Computing crosstalk terms in step (b) includes computing an N-dimensional vector, where N corresponds to the number of transfer functions, and the N-dimensional vector is obtained by minimizing a variance of a modulation function in phase shifted images.

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

PubMed

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

2012-11-25

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

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

NASA Astrophysics Data System (ADS)

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

1998-03-01

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

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

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

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

2013-10-15

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

SU-F-J-47: Inherent Uncertainty in the Positional Shifts Determined by a Volumetric Cone Beam Imaging System

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

Giri, U; Ganesh, T; Saini, V

2016-06-15

Purpose: To quantify inherent uncertainty associated with a volumetric imaging system in its determination of positional shifts. Methods: The study was performed on an Elekta Axesse™ linac’s XVI cone beam computed tomography (CBCT) system. A CT image data set of a Penta- Guide phantom was used as reference image by placing isocenter at the center of the phantom.The phantom was placed arbitrarily on the couch close to isocenter and CBCT images were obtained. The CBCT dataset was matched with the reference image using XVI software and the shifts were determined in 6-dimensions. Without moving the phantom, this process was repeatedmore » 20 times consecutively within 30 minutes on a single day. Mean shifts and their standard deviations in all 6-dimensions were determined for all the 20 instances of imaging. For any given day, the first set of shifts obtained was kept as reference and the deviations of the subsequent 19 sets from the reference set were scored. Mean differences and their standard deviations were determined. In this way, data were obtained for 30 consecutive working days. Results: Tabulating the mean deviations and their standard deviations observed on each day for the 30 measurement days, systematic and random errors in the determination of shifts by XVI software were calculated. The systematic errors were found to be 0.03, 0.04 and 0.03 mm while random errors were 0.05, 0.06 and 0.06 mm in lateral, craniocaudal and anterio-posterior directions respectively. For rotational shifts, the systematic errors were 0.02°, 0.03° and 0.03° and random errors were 0.06°, 0.05° and 0.05° in pitch, roll and yaw directions respectively. Conclusion: The inherent uncertainties in every image guidance system should be assessed and baseline values established at the time of its commissioning. These shall be periodically tested as part of the QA protocol.« less

Null test fourier domain alignment technique for phase-shifting point diffraction interferometer

DOEpatents

Naulleau, Patrick; Goldberg, Kenneth Alan

2000-01-01

Alignment technique for calibrating a phase-shifting point diffraction interferometer involves three independent steps where the first two steps independently align the image points and pinholes in rotation and separation to a fixed reference coordinate system, e.g, CCD. Once the two sub-elements have been properly aligned to the reference in two parameters (separation and orientation), the third step is to align the two sub-element coordinate systems to each other in the two remaining parameters (x,y) using standard methods of locating the pinholes relative to some easy to find reference point.

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

PubMed Central

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

2017-01-01

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

Effects of Aging-Time Reference on the Long Term Behavior of the IM7/K3B Composite

NASA Technical Reports Server (NTRS)

Veazie, David R.; Gates, Thomas S.

1998-01-01

An analytical study was undertaken to investigate the effects of the time-based shift reference on the long term behavior of the graphite reinforced thermoplastic polyimide composite IM7/K3B at elevated temperature. Creep compliance and the effects of physical aging on the time dependent response was measured for uniaxial loading at several isothermal conditions below the glass transition temperature (T(sub g). Two matrix dominated loading modes, shear and transverse, were investigated in tension and compression. The momentary sequenced creep/aging curves were collapsed through a horizontal (time) shift using the shortest, middle and longest aging time curve as the reference curve. Linear viscoelasticity was used to characterize the creep/recovery behavior and superposition techniques were used to establish the physical aging related material constants. The use of effective time expressions in a laminated plate model allowed for the prediction of long term creep compliance. The effect of using different reference curves with time/aging-time superposition was most sensitive to the physical aging shift rate at lower test temperatures. Depending on the loading mode, the reference curve used can result in a more accurate long term prediction, especially at lower test temperatures.

Chroma Shift and Gamut Shape: Going Beyond Average Color Fidelity and Gamut Area

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

Royer, Michael P.; Houser, Kevin W.; David, Aurélien

Though sometimes referred to as a two-measure system for evaluating color rendition, IES TM-30-15 includes other key components that go beyond the high-level average values IES Rf and IES Rg. This article focuses on the Color Vector Graphic and Local Chroma Shift (IES Rcs,hj), discussing the calculation methods for these evaluation tools and providing context for the interpretation of the values. It also presents alternatives for quantifying the same characteristics, which can inform the development of future measures. The Color Vector Graphic (CVG) is a visual representation of hue and chroma shifts across different hues. It quickly communicates complex informationmore » about how object colors will be rendered by a light source, although it is difficult or impossible to use for writing a specification. CVGs demonstrate that increases in chroma for certain hues sometimes means a decrease in chroma for other hues, and illustrates hue shifts for intermediate colors. The combination of shifts over different hues can be referred to as gamut shape. Complementing this information are the IES Rcs,hj values, which quantify the average relative chroma shift for samples in each of the 16 hue-angle bins (j) specified in IES TM-30-15. Unlike measures of average color fidelity and gamut area, gamut shape and hue-specific chroma shift are new concepts with no directly-comparable historical references. It will be critical to incorporate the Color Vector Graphic and Local Chroma Shift values into practice because they capture information about color rendition that is impossible to describe with average measures (such as CIE Ra, IES Rf, or IES Rg), but that is critical to understanding human evaluations of color quality in architectural environments.« less

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

PubMed

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

2010-12-01

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

Coordinates of Human Visual and Inertial Heading Perception.

PubMed

Crane, Benjamin Thomas

2015-01-01

Heading estimation involves both inertial and visual cues. Inertial motion is sensed by the labyrinth, somatic sensation by the body, and optic flow by the retina. Because the eye and head are mobile these stimuli are sensed relative to different reference frames and it remains unclear if a perception occurs in a common reference frame. Recent neurophysiologic evidence has suggested the reference frames remain separate even at higher levels of processing but has not addressed the resulting perception. Seven human subjects experienced a 2s, 16 cm/s translation and/or a visual stimulus corresponding with this translation. For each condition 72 stimuli (360° in 5° increments) were delivered in random order. After each stimulus the subject identified the perceived heading using a mechanical dial. Some trial blocks included interleaved conditions in which the influence of ±28° of gaze and/or head position were examined. The observations were fit using a two degree-of-freedom population vector decoder (PVD) model which considered the relative sensitivity to lateral motion and coordinate system offset. For visual stimuli gaze shifts caused shifts in perceived head estimates in the direction opposite the gaze shift in all subjects. These perceptual shifts averaged 13 ± 2° for eye only gaze shifts and 17 ± 2° for eye-head gaze shifts. This finding indicates visual headings are biased towards retina coordinates. Similar gaze and head direction shifts prior to inertial headings had no significant influence on heading direction. Thus inertial headings are perceived in body-centered coordinates. Combined visual and inertial stimuli yielded intermediate results.

Coordinates of Human Visual and Inertial Heading Perception

PubMed Central

Crane, Benjamin Thomas

2015-01-01

Heading estimation involves both inertial and visual cues. Inertial motion is sensed by the labyrinth, somatic sensation by the body, and optic flow by the retina. Because the eye and head are mobile these stimuli are sensed relative to different reference frames and it remains unclear if a perception occurs in a common reference frame. Recent neurophysiologic evidence has suggested the reference frames remain separate even at higher levels of processing but has not addressed the resulting perception. Seven human subjects experienced a 2s, 16 cm/s translation and/or a visual stimulus corresponding with this translation. For each condition 72 stimuli (360° in 5° increments) were delivered in random order. After each stimulus the subject identified the perceived heading using a mechanical dial. Some trial blocks included interleaved conditions in which the influence of ±28° of gaze and/or head position were examined. The observations were fit using a two degree-of-freedom population vector decoder (PVD) model which considered the relative sensitivity to lateral motion and coordinate system offset. For visual stimuli gaze shifts caused shifts in perceived head estimates in the direction opposite the gaze shift in all subjects. These perceptual shifts averaged 13 ± 2° for eye only gaze shifts and 17 ± 2° for eye-head gaze shifts. This finding indicates visual headings are biased towards retina coordinates. Similar gaze and head direction shifts prior to inertial headings had no significant influence on heading direction. Thus inertial headings are perceived in body-centered coordinates. Combined visual and inertial stimuli yielded intermediate results. PMID:26267865

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

PubMed

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

1994-08-01

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

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

PubMed

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

2012-10-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-10-01

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

Miniaturised wireless smart tag for optical chemical analysis applications.

PubMed

Steinberg, Matthew D; Kassal, Petar; Tkalčec, Biserka; Murković Steinberg, Ivana

2014-01-01

A novel miniaturised photometer has been developed as an ultra-portable and mobile analytical chemical instrument. The low-cost photometer presents a paradigm shift in mobile chemical sensor instrumentation because it is built around a contactless smart card format. The photometer tag is based on the radio-frequency identification (RFID) smart card system, which provides short-range wireless data and power transfer between the photometer and a proximal reader, and which allows the reader to also energise the photometer by near field electromagnetic induction. RFID is set to become a key enabling technology of the Internet-of-Things (IoT), hence devices such as the photometer described here will enable numerous mobile, wearable and vanguard chemical sensing applications in the emerging connected world. In the work presented here, we demonstrate the characterisation of a low-power RFID wireless sensor tag with an LED/photodiode-based photometric input. The performance of the wireless photometer has been tested through two different model analytical applications. The first is photometry in solution, where colour intensity as a function of dye concentration was measured. The second is an ion-selective optode system in which potassium ion concentrations were determined by using previously well characterised bulk optode membranes. The analytical performance of the wireless photometer smart tag is clearly demonstrated by these optical absorption-based analytical experiments, with excellent data agreement to a reference laboratory instrument. © 2013 Elsevier B.V. All rights reserved.

Cross-Link Guided Molecular Modeling with ROSETTA

PubMed Central

Leitner, Alexander; Rosenberger, George; Aebersold, Ruedi; Malmström, Lars

2013-01-01

Chemical cross-links identified by mass spectrometry generate distance restraints that reveal low-resolution structural information on proteins and protein complexes. The technology to reliably generate such data has become mature and robust enough to shift the focus to the question of how these distance restraints can be best integrated into molecular modeling calculations. Here, we introduce three workflows for incorporating distance restraints generated by chemical cross-linking and mass spectrometry into ROSETTA protocols for comparative and de novo modeling and protein-protein docking. We demonstrate that the cross-link validation and visualization software Xwalk facilitates successful cross-link data integration. Besides the protocols we introduce XLdb, a database of chemical cross-links from 14 different publications with 506 intra-protein and 62 inter-protein cross-links, where each cross-link can be mapped on an experimental structure from the Protein Data Bank. Finally, we demonstrate on a protein-protein docking reference data set the impact of virtual cross-links on protein docking calculations and show that an inter-protein cross-link can reduce on average the RMSD of a docking prediction by 5.0 Å. The methods and results presented here provide guidelines for the effective integration of chemical cross-link data in molecular modeling calculations and should advance the structural analysis of particularly large and transient protein complexes via hybrid structural biology methods. PMID:24069194

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

NASA Astrophysics Data System (ADS)

Oruc, Gizem; Varnali, Tereza; Bekiroglu, Somer

2018-05-01

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

Phase-shifting point diffraction interferometer mask designs

DOEpatents

Goldberg, Kenneth Alan

2001-01-01

In a phase-shifting point diffraction interferometer, different image-plane mask designs can improve the operation of the interferometer. By keeping the test beam window of the mask small compared to the separation distance between the beams, the problem of energy from the reference beam leaking through the test beam window is reduced. By rotating the grating and mask 45.degree., only a single one-dimensional translation stage is required for phase-shifting. By keeping two reference pinholes in the same orientation about the test beam window, only a single grating orientation, and thus a single one-dimensional translation stage, is required. The use of a two-dimensional grating allows for a multiplicity of pinholes to be used about the pattern of diffracted orders of the grating at the mask. Orientation marks on the mask can be used to orient the device and indicate the position of the reference pinholes.

A Method for Evaluating Outcomes of Restoration When No Reference Sites Exist

Treesearch

J. Stephen Brewer; Timothy Menzel

2009-01-01

Ecological restoration typically seeks to shift species composition toward that of existing reference sites. Yet, comparing the assemblages in restored and reference habitats assumes that similarity to the reference habitat is the optimal outcome of restoration and does not provide a perspective on regionally rare off-site species. When no such reference assemblages of...

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

PubMed

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

2016-02-05

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

A method to enhance the measurement accuracy of Raman shift based on high precision calibration technique

NASA Astrophysics Data System (ADS)

Ding, Xiang; Li, Fei; Zhang, Jiyan; Liu, Wenli

2016-10-01

Raman spectrometers are usually calibrated periodically to ensure their measurement accuracy of Raman shift. A combination of a piece of monocrystalline silicon chip and a low pressure discharge lamp is proposed as a candidate for the reference standard of Raman shift. A high precision calibration technique is developed to accurately determine the standard value of the silicon's Raman shift around 520cm-1. The technique is described and illustrated by measuring a piece of silicon chip against three atomic spectral lines of a neon lamp. A commercial Raman spectrometer is employed and its error characteristics of Raman shift are investigated. Error sources are evaluated based on theoretical analysis and experiments, including the sample factor, the instrumental factor, the laser factor and random factors. Experimental results show that the expanded uncertainty of the silicon's Raman shift around 520cm-1 can acheive 0.3 cm-1 (k=2), which is more accurate than most of currently used reference materials. The results are validated by comparison measurement between three Raman spectrometers. It is proved that the technique can remarkably enhance the accuracy of Raman shift, making it possible to use the silicon and the lamp to calibrate Raman spectrometers.

Comprehensive time average digital holographic vibrometry

NASA Astrophysics Data System (ADS)

Psota, Pavel; Lédl, Vít; Doleček, Roman; Mokrý, Pavel; Vojtíšek, Petr; Václavík, Jan

2016-12-01

This paper presents a method that simultaneously deals with drawbacks of time-average digital holography: limited measurement range, limited spatial resolution, and quantitative analysis of the measured Bessel fringe patterns. When the frequency of the reference wave is shifted by an integer multiple of frequency at which the object oscillates, the measurement range of the method can be shifted either to smaller or to larger vibration amplitudes. In addition, phase modulation of the reference wave is used to obtain a sequence of phase-modulated fringe patterns. Such fringe patterns can be combined by means of phase-shifting algorithms, and amplitudes of vibrations can be straightforwardly computed. This approach independently calculates the amplitude values in every single pixel. The frequency shift and phase modulation are realized by proper control of Bragg cells and therefore no additional hardware is required.

Attenuation analysis of real GPR wavelets: The equivalent amplitude spectrum (EAS)

NASA Astrophysics Data System (ADS)

Economou, Nikos; Kritikakis, George

2016-03-01

Absorption of a Ground Penetrating Radar (GPR) pulse is a frequency dependent attenuation mechanism which causes a spectral shift on the dominant frequency of GPR data. Both energy variation of GPR amplitude spectrum and spectral shift were used for the estimation of Quality Factor (Q*) and subsequently the characterization of the subsurface material properties. The variation of the amplitude spectrum energy has been studied by Spectral Ratio (SR) method and the frequency shift by the estimation of the Frequency Centroid Shift (FCS) or the Frequency Peak Shift (FPS) methods. The FPS method is more automatic, less robust. This work aims to increase the robustness of the FPS method by fitting a part of the amplitude spectrum of GPR data with Ricker, Gaussian, Sigmoid-Gaussian or Ricker-Gaussian functions. These functions fit different parts of the spectrum of a GPR reference wavelet and the Equivalent Amplitude Spectrum (EAS) is selected, reproducing Q* values used in forward Q* modeling analysis. Then, only the peak frequencies and the time differences between the reference wavelet and the subsequent reflected wavelets are used to estimate Q*. As long as the EAS is estimated, it is used for Q* evaluation in all the GPR section, under the assumption that the selected reference wavelet is representative. De-phasing and constant phase shift, for obtaining symmetrical wavelets, proved useful in the sufficiency of the horizons picking. Synthetic, experimental and real GPR data were examined in order to demonstrate the effectiveness of the proposed methodology.

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

DTIC Science & Technology

2017-12-11

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

An extrapolation scheme for solid-state NMR chemical shift calculations

NASA Astrophysics Data System (ADS)

Nakajima, Takahito

2017-06-01

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

An internal reference model-based PRF temperature mapping method with Cramer-Rao lower bound noise performance analysis.

PubMed

Li, Cheng; Pan, Xinyi; Ying, Kui; Zhang, Qiang; An, Jing; Weng, Dehe; Qin, Wen; Li, Kuncheng

2009-11-01

The conventional phase difference method for MR thermometry suffers from disturbances caused by the presence of lipid protons, motion-induced error, and field drift. A signal model is presented with multi-echo gradient echo (GRE) sequence using a fat signal as an internal reference to overcome these problems. The internal reference signal model is fit to the water and fat signals by the extended Prony algorithm and the Levenberg-Marquardt algorithm to estimate the chemical shifts between water and fat which contain temperature information. A noise analysis of the signal model was conducted using the Cramer-Rao lower bound to evaluate the noise performance of various algorithms, the effects of imaging parameters, and the influence of the water:fat signal ratio in a sample on the temperature estimate. Comparison of the calculated temperature map and thermocouple temperature measurements shows that the maximum temperature estimation error is 0.614 degrees C, with a standard deviation of 0.06 degrees C, confirming the feasibility of this model-based temperature mapping method. The influence of sample water:fat signal ratio on the accuracy of the temperature estimate is evaluated in a water-fat mixed phantom experiment with an optimal ratio of approximately 0.66:1. (c) 2009 Wiley-Liss, Inc.

Development of a Flow Injection Based High Frequency Dual Channel Quartz Crystal Microbalance

PubMed Central

Liang, Jinxing; Zhang, Jing; Zhou, Wenxiang; Ueda, Toshitsugu

2017-01-01

When the quartz crystal microbalance (QCM) is used in liquid for adsorption or desorption monitoring based bio- or chemical sensing applications, the frequency shift is not only determined by the surface mass change, but also by the change of liquid characteristics, such as density and viscosity, which are greatly affected by the liquid environmental temperature. A monolithic dual-channel QCM is designed and fabricated by arranging two QCM resonators on one single chip for cancelling the fluctuation induced by environmental factors. In actual applications, one QCM works as a specific sensor by modifying with functional membranes and the other acts as a reference, only measuring the liquid property. The dual-channel QCM is designed with an inverted-mesa structure, aiming to realize a high frequency miniaturized chip and suppress the frequency interference between the neighbored QCM resonators. The key problem of dual-channel QCMs is the interference between two channels, which is influenced by the distance of adjacent resonators. The diameter of the reference electrode has been designed into several values in order to find the optimal parameter. Experimental results demonstrated that the two QCMs could vibrate individually and the output frequency stability and drift can be greatly improved with the aid of the reference QCM. PMID:28509851

The neural basis of deictic shifting in linguistic perspective-taking in high-functioning autism.

PubMed

Mizuno, Akiko; Liu, Yanni; Williams, Diane L; Keller, Timothy A; Minshew, Nancy J; Just, Marcel Adam

2011-08-01

Personal pronouns, such as 'I' and 'you', require a speaker/listener to continuously re-map their reciprocal relation to their referent, depending on who is saying the pronoun. This process, called 'deictic shifting', may underlie the incorrect production of these pronouns, or 'pronoun reversals', such as referring to oneself with the pronoun 'you', which has been reported in children with autism. The underlying neural basis of deictic shifting, however, is not understood, nor has the processing of pronouns been studied in adults with autism. The present study compared the brain activation pattern and functional connectivity (synchronization of activation across brain areas) of adults with high-functioning autism and control participants using functional magnetic resonance imaging in a linguistic perspective-taking task that required deictic shifting. The results revealed significantly diminished frontal (right anterior insula) to posterior (precuneus) functional connectivity during deictic shifting in the autism group, as well as reliably slower and less accurate behavioural responses. A comparison of two types of deictic shifting revealed that the functional connectivity between the right anterior insula and precuneus was lower in autism while answering a question that contained the pronoun 'you', querying something about the participant's view, but not when answering a query about someone else's view. In addition to the functional connectivity between the right anterior insula and precuneus being lower in autism, activation in each region was atypical, suggesting over reliance on individual regions as a potential compensation for the lower level of collaborative interregional processing. These findings indicate that deictic shifting constitutes a challenge for adults with high-functioning autism, particularly when reference to one's self is involved, and that the functional collaboration of two critical nodes, right anterior insula and precuneus, may play a critical role for deictic shifting by supporting an attention shift between oneself and others.

Phase shifting diffraction interferometer

DOEpatents

Sommargren, Gary E.

1996-01-01

An interferometer which has the capability of measuring optical elements and systems with an accuracy of .lambda./1000 where .lambda. is the wavelength of visible light. Whereas current interferometers employ a reference surface, which inherently limits the accuracy of the measurement to about .lambda./50, this interferometer uses an essentially perfect spherical reference wavefront generated by the fundamental process of diffraction. This interferometer is adjustable to give unity fringe visibility, which maximizes the signal-to-noise, and has the means to introduce a controlled prescribed relative phase shift between the reference wavefront and the wavefront from the optics under test, which permits analysis of the interference fringe pattern using standard phase extraction algorithms.

Phase shifting diffraction interferometer

DOEpatents

Sommargren, G.E.

1996-08-29

An interferometer which has the capability of measuring optical elements and systems with an accuracy of {lambda}/1000 where {lambda} is the wavelength of visible light. Whereas current interferometers employ a reference surface, which inherently limits the accuracy of the measurement to about {lambda}/50, this interferometer uses an essentially perfect spherical reference wavefront generated by the fundamental process of diffraction. This interferometer is adjustable to give unity fringe visibility, which maximizes the signal-to-noise, and has the means to introduce a controlled prescribed relative phase shift between the reference wavefront and the wavefront from the optics under test, which permits analysis of the interference fringe pattern using standard phase extraction algorithms. 8 figs.

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

PubMed

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

1981-01-01

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

Ligand Binding Analysis and Screening by Chemical Denaturation Shift

PubMed Central

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

2013-01-01

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

Ligand binding analysis and screening by chemical denaturation shift.

PubMed

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

2013-12-01

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

Dual-domain point diffraction interferometer

DOEpatents

Naulleau, Patrick P.; Goldberg, Kenneth Alan

2000-01-01

A hybrid spatial/temporal-domain point diffraction interferometer (referred to as the dual-domain PS/PDI) that is capable of suppressing the scattered-reference-light noise that hinders the conventional PS/PDI is provided. The dual-domain PS/PDI combines the separate noise-suppression capabilities of the widely-used phase-shifting and Fourier-transform fringe pattern analysis methods. The dual-domain PS/PDI relies on both a more restrictive implementation of the image plane PS/PDI mask and a new analysis method to be applied to the interferograms generated and recorded by the modified PS/PDI. The more restrictive PS/PDI mask guarantees the elimination of spatial-frequency crosstalk between the signal and the scattered-light noise arising from scattered-reference-light interfering with the test beam. The new dual-domain analysis method is then used to eliminate scattered-light noise arising from both the scattered-reference-light interfering with the test beam and the scattered-reference-light interfering with the "true" pinhole-diffracted reference light. The dual-domain analysis method has also been demonstrated to provide performance enhancement when using the non-optimized standard PS/PDI design. The dual-domain PS/PDI is essentially a three-tiered filtering system composed of lowpass spatial-filtering the test-beam electric field using the more restrictive PS/PDI mask, bandpass spatial-filtering the individual interferogram irradiance frames making up the phase-shifting series, and bandpass temporal-filtering the phase-shifting series as a whole.

Electronically excited and ionized states in condensed phase: Theory and applications

NASA Astrophysics Data System (ADS)

Sadybekov, Arman

Predictive modeling of chemical processes in silico is a goal of XXI century. While robust and accurate methods exist for ground-state properties, reliable methods for excited states are still lacking and require further development. Electronically exited states are formed by interactions of matter with light and are responsible for key processes in solar energy harvesting, vision, artificial sensors, and photovoltaic applications. The greatest challenge to overcome on our way to a quantitative description of light-induced processes is accurate inclusion of the effect of the environment on excited states. All above mentioned processes occur in solution or solid state. Yet, there are few methodologies to study excited states in condensed phase. Application of highly accurate and robust methods, such as equation-of-motion coupled-cluster theory EOM-CC, is limited by a high computational cost and scaling precluding full quantum mechanical treatment of the entire system. In this thesis we present successful application of the EOM-CC family of methods to studies of excited states in liquid phase and build hierarchy of models for inclusion of the solvent effects. In the first part of the thesis we show that a simple gasphase model is sufficient to quantitatively analyze excited states in liquid benzene, while the latter part emphasizes the importance of explicit treatment of the solvent molecules in the case of glycine in water solution. In chapter 2, we use a simple dimer model to describe exciton formation in liquid and solid benzene. We show that sampling of dimer structures extracted from the liquid benzene is sufficient to correctly predict exited-state properties of the liquid. Our calculations explain experimentally observed features, which helped to understand the mechanism of the excimer formation in liquid benzene. Furthermore, we shed light on the difference between dimer configurations in the first solvation shell of liquid benzene and in unit cell of solid benzene and discussed the impact of these differences on the formation of the excimer state. In chapter 3, we present a theoretical approach for calculating core-level states in condensed phase. The approach is based on EOM-CC and effective fragment potential (EFP) method. By introducing an approximate treatment of double excitations in the EOM-CCSD (EOM-CC with single and double substitutions) ansatz, we addressed poor convergence issues that are encountered for the core-level states and significantly reduced computational costs. While the approximations introduce relatively large errors in the absolute values of transition energies, the errors are systematic. Consequently, chemical shifts, changes in ionization energies relative to the reference systems, are reproduced reasonably well. By using different protonation forms of solvated glycine as a benchmark system, we showed that our protocol is capable of reproducing the experimental chemical shifts with a quantitative accuracy. The results demonstrate that chemical shifts are very sensitive to the solvent interactions and that explicit treatment of solvent, such as EFP, is essential for achieving quantitative accuracy. In chapter 4, we outline future directions and discuss possible applications of the developed computational protocol for prediction of core chemical shifts in larger systems.

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

NASA Astrophysics Data System (ADS)

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

1991-12-01

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

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

NASA Astrophysics Data System (ADS)

Dias, Jerry Ray; Gao, Hongwu

2009-12-01

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

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

PubMed Central

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

2017-01-01

The detection of minor species in the presence of large amounts of similar main components remains a key challenge in analytical chemistry, for instance, to obtain isotopic fingerprints. As an alternative to the classical NMR scheme based on coherent excitation and detection, here we introduce an approach based on spin-noise detection. Chemical shifts and transverse relaxation rates are determined using only the detection circuit. Thanks to a nonlinear effect in mixtures with small chemical shift dispersion, small signals on top of a larger one can be observed with increased sensitivity as bumps on a dip; the latter being the signature of the main magnetization. Experimental observations are underpinned by an analytical theory: the coupling between the magnetization and the coil provides an amplified detection capability of both small static magnetic field inhomogeneities and small NMR signals. This is illustrated by two-bond 12C/13C isotopic measurements. PMID:28067218

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

PubMed Central

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

2012-01-01

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

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

PubMed

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

2017-09-13

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

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

PubMed

Kara, Yesim S

2015-12-05

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

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

PubMed Central

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

2008-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2012-11-01

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

Nuclear magnetic resonance spectral analysis and molecular properties of berberine

NASA Astrophysics Data System (ADS)

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

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

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

PubMed

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

2014-01-01

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

Triple Resonance Solid State NMR Experiments with Reduced Dimensionality Evolution Periods

NASA Astrophysics Data System (ADS)

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

2001-10-01

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

Hydride ions in oxide hosts hidden by hydroxide ions

PubMed Central

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

2014-01-01

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

Determination of oxidation state of iron in normal and pathologically altered human aortic valves

NASA Astrophysics Data System (ADS)

Czapla-Masztafiak, J.; Lis, G. J.; Gajda, M.; Jasek, E.; Czubek, U.; Bolechała, F.; Borca, C.; Kwiatek, W. M.

2015-12-01

In order to investigate changes in chemical state of iron in normal and pathologically altered human aortic valves X-ray absorption spectroscopy was applied. Since Fe is suspected to play detrimental role in aortic valve stenosis pathogenesis the oxidation state of this element has been determined. The experimental material consisted of 10 μm sections of valves excised during routine surgery and from autopsies. The experiment was performed at the MicroXAS beamline of the SLS synchrotron facility in Villigen (Switzerland). The Fe K-edge XANES spectra obtained from tissue samples were carefully analyzed and compared with the spectra of reference compounds containing iron in various chemical structures. The analysis of absorption edge position and shape of the spectra revealed that both chemical forms of iron are presented in valve tissue but Fe3+ is the predominant form. Small shift of the absorption edge toward higher energy in the spectra from stenotic valve samples indicates higher content of the Fe3+ form in pathological tissue. Such a phenomenon suggests the role of Fenton reaction and reactive oxygen species in the etiology of aortic valve stenosis. The comparison of pre-edge regions of XANES spectra for control and stenotic valve tissue confirmed no differences in local symmetry or spin state of iron in analyzed samples.

Reversible formation of ammonium persulfate/sulfuric acid graphite intercalation compounds and their peculiar Raman spectra.

PubMed

Dimiev, Ayrat M; Bachilo, Sergei M; Saito, Riichiro; Tour, James M

2012-09-25

Graphite intercalation compounds (GICs) can be considered stacks of individual doped graphene layers. Here we demonstrate a reversible formation of sulfuric acid-based GICs using ammonium persulfate as the chemical oxidizing agent. No covalent chemical oxidation leading to the formation of graphite oxide occurs, which inevitably happens when other compounds such as potassium permanganate are used to charge carbon layers. The resulting acid/persulfate-induced stage-1 and stage-2 GICs are characterized by suppression of the 2D band in the Raman spectra and by unusually strong enhancement of the G band. The G band is selectively enhanced at different doping levels with different excitations. These observations are in line with recent reports for chemically doped and gate-modulated graphene and support newly proposed theories of Raman processes. At the same time GICs have some advantageous differences over graphene, which are demonstrated in this report. Our experimental observations, along with earlier reported data, suggest that at high doping levels the G band cannot be used as the reference peak for normalizing Raman spectra, which is a commonly used practice today. A Fermi energy shift of 1.20-1.25 eV and ∼1.0 eV was estimated for the stage-1 and stage-2 GICs, respectively, from the Raman and optical spectroscopy data.

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

PubMed Central

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

2012-01-01

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

Acute suppression of serum IgM and IgA in tank workers exposed to benzene.

PubMed

Kirkeleit, J; Ulvestad, E; Riise, T; Bråtveit, M; Moen, B E

2006-12-01

We investigated associations between benzene exposure and alterations of proteins and cells of the immune system among workers maintaining cargo tanks containing crude oil residues. Individual exposure to benzene, benzene in blood and urine, peripheral blood lymphocytes (total lymphocytes, lymphocytes in subpopulations CD3, CD4, CD8, CD19, CD56 and CD4/CD8 ratio), complement factors C3 and C4 and serum concentration of immunoglobulins (IgG, IgA, IgM and IgE) were analysed among 13 tank workers and nine unexposed referents (catering section). Benzene exposure was measured during three consecutive 12-h work days. Blood and urine samples were collected pre-shift on the first day (baseline), post-shift on the third day, and pre-next shift on the following morning. The time spent in the cargo tank was logged. The individual geometric mean benzene exposure in the breathing zone of tank workers over 3 days was 0.15 p.p.m. (range 0.01-0.62 p.p.m.) (n = 26). The geometric mean benzene concentration in blood post-shift was 12.3 nmol/l among tank workers versus 0.7 nmol/l among the referents. Tank workers showed a decline (versus referents) in IgM from baseline to post-shift (t-test, P = 0.04) and IgA from baseline to pre-next shift (t-test, P = 0.01). They also showed a decline in CD4 T cells from baseline to post-shift (t-test, P = 0.04). Suppression correlated with benzene exposure, benzene concentrations in blood and urine and time spent in the tank. The groups did not differ significantly in the change in other immune parameters. The clinical significance is unknown and warrants further studies.

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

PubMed Central

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

2013-01-01

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

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

PubMed

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

2013-10-15

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

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

PubMed

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

2007-01-24

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

Thigh muscle segmentation of chemical shift encoding-based water-fat magnetic resonance images: The reference database MyoSegmenTUM.

PubMed

Schlaeger, Sarah; Freitag, Friedemann; Klupp, Elisabeth; Dieckmeyer, Michael; Weidlich, Dominik; Inhuber, Stephanie; Deschauer, Marcus; Schoser, Benedikt; Bublitz, Sarah; Montagnese, Federica; Zimmer, Claus; Rummeny, Ernst J; Karampinos, Dimitrios C; Kirschke, Jan S; Baum, Thomas

2018-01-01

Magnetic resonance imaging (MRI) can non-invasively assess muscle anatomy, exercise effects and pathologies with different underlying causes such as neuromuscular diseases (NMD). Quantitative MRI including fat fraction mapping using chemical shift encoding-based water-fat MRI has emerged for reliable determination of muscle volume and fat composition. The data analysis of water-fat images requires segmentation of the different muscles which has been mainly performed manually in the past and is a very time consuming process, currently limiting the clinical applicability. An automatization of the segmentation process would lead to a more time-efficient analysis. In the present work, the manually segmented thigh magnetic resonance imaging database MyoSegmenTUM is presented. It hosts water-fat MR images of both thighs of 15 healthy subjects and 4 patients with NMD with a voxel size of 3.2x2x4 mm3 with the corresponding segmentation masks for four functional muscle groups: quadriceps femoris, sartorius, gracilis, hamstrings. The database is freely accessible online at https://osf.io/svwa7/?view_only=c2c980c17b3a40fca35d088a3cdd83e2. The database is mainly meant as ground truth which can be used as training and test dataset for automatic muscle segmentation algorithms. The segmentation allows extraction of muscle cross sectional area (CSA) and volume. Proton density fat fraction (PDFF) of the defined muscle groups from the corresponding images and quadriceps muscle strength measurements/neurological muscle strength rating can be used for benchmarking purposes.

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

PubMed

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

2015-02-05

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

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

PubMed

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

2016-06-01

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

A bibliography of shift work research : 1950-1982.

DOT National Transportation Integrated Search

1983-09-01

This bibliography was developed as part of a research task concerning the impact of shift work on employee job satisfaction, productivity, perceived job difficulty, and subjective health. Some selectivity was exercised in the choice of references for...

Multilayer Volume Holographic Optical Memory

NASA Technical Reports Server (NTRS)

Markov, Vladimir; Millerd, James; Trolinger, James; Norrie, Mark; Downie, John; Timucin, Dogan; Lau, Sonie (Technical Monitor)

1998-01-01

We demonstrate a scheme for volume holographic storage based on the features of shift selectivity of a speckle reference wave hologram. The proposed recording method allows more efficient use of the recording medium and increases the storage density in comparison with spherical or plane-wave reference beams. Experimental results of multiple hologram storage and replay in a photorefractive crystal of iron-doped lithium niobate are presented. The mechanism of lateral and longitudinal shift selectivity are described theoretically and shown to agree with experimental measurements.

On-chip tunable dispersion in a ring laser gyroscope for enhanced rotation sensing

NASA Astrophysics Data System (ADS)

Zhang, Hao; Liu, Jiaming; Lin, Jian; Li, Wenxiu; Xue, Xia; Huang, Anping; Xiao, Zhisong

2016-05-01

A gyroscope structure with tailored local dispersion profile to enhance sensitivity is proposed, which uses lithium niobate (LiNbO3) thin film as the on-chip material of gyroscope's resonator. A Mach-Zehnder interferometer (MZI) structure as a coupler, which induces a different reference phase shift in each arm, is inserted into the position between ring resonator and output bus waveguide. Through modulating reference phase shift in MZI, theoretical rotation sensitivity enhancement as large as one order of magnitude is presented.

Resonant nonlinear ultrasound spectroscopy

DOEpatents

Johnson, Paul A.; TenCate, James A.; Guyer, Robert A.; Van Den Abeele, Koen E. A.

2001-01-01

Components with defects are identified from the response to strains applied at acoustic and ultrasound frequencies. The relative resonance frequency shift .vertline..DELTA..function./.function..sub.0.vertline., is determined as a function of applied strain amplitude for an acceptable component, where .function..sub.0 is the frequency of the resonance peak at the lowest amplitude of applied strain and .DELTA..function. is the frequency shift of the resonance peak of a selected mode to determine a reference relationship. Then, the relative resonance frequency shift .vertline..DELTA..function./.function..sub.0 is determined as a function of applied strain for a component under test, where fo .function..sub.0 the frequency of the resonance peak at the lowest amplitude of applied strain and .DELTA..function. is the frequency shift of the resonance peak to determine a quality test relationship. The reference relationship is compared with the quality test relationship to determine the presence of defects in the component under test.

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

PubMed

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

2013-10-01

A k-means-based classification algorithm is investigated to assess suitability for rapidly separating and classifying fat/water spectral peaks from a fast chemical shift imaging technique for magnetic resonance temperature imaging. Algorithm testing is performed in simulated mathematical phantoms and agar gel phantoms containing mixed fat/water regions. Proton resonance frequencies (PRFs), apparent spin-spin relaxation (T2*) times, and T1-weighted (T1-W) amplitude values were calculated for each voxel using a single-peak autoregressive moving average (ARMA) signal model. These parameters were then used as criteria for k-means sorting, with the results used to determine PRF ranges of each chemical species cluster for further classification. To detect the presence of secondary chemical species, spectral parameters were recalculated when needed using a two-peak ARMA signal model during the subsequent classification steps. Mathematical phantom simulations involved the modulation of signal-to-noise ratios (SNR), maximum PRF shift (MPS) values, analysis window sizes, and frequency expansion factor sizes in order to characterize the algorithm performance across a variety of conditions. In agar, images were collected on a 1.5T clinical MR scanner using acquisition parameters close to simulation, and algorithm performance was assessed by comparing classification results to manually segmented maps of the fat/water regions. Performance was characterized quantitatively using the Dice Similarity Coefficient (DSC), sensitivity, and specificity. The simulated mathematical phantom experiments demonstrated good fat/water separation depending on conditions, specifically high SNR, moderate MPS value, small analysis window size, and low but nonzero frequency expansion factor size. Physical phantom results demonstrated good identification for both water (0.997 ± 0.001, 0.999 ± 0.001, and 0.986 ± 0.001 for DSC, sensitivity, and specificity, respectively) and fat (0.763 ± 0.006, 0.980 ± 0.004, and 0.941 ± 0.002 for DSC, sensitivity, and specificity, respectively). Temperature uncertainties, based on PRF uncertainties from a 5 × 5-voxel ROI, were 0.342 and 0.351°C for pure and mixed fat/water regions, respectively. Algorithm speed was tested using 25 × 25-voxel and whole image ROIs containing both fat and water, resulting in average processing times per acquisition of 2.00 ± 0.07 s and 146 ± 1 s, respectively, using uncompiled MATLAB scripts running on a shared CPU server with eight Intel Xeon(TM) E5640 quad-core processors (2.66 GHz, 12 MB cache) and 12 GB RAM. Results from both the mathematical and physical phantom suggest the k-means-based classification algorithm could be useful for rapid, dynamic imaging in an ROI for thermal interventions. Successful separation of fat/water information would aid in reducing errors from the nontemperature sensitive fat PRF, as well as potentially facilitate using fat as an internal reference for PRF shift thermometry when appropriate. Additionally, the T1-W or R2* signals may be used for monitoring temperature in surrounding adipose tissue.

FACILITATED CHEMICAL SYNTHESIS UNDER ALTERNATE REACTION CONDITIONS

EPA Science Inventory

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

CHEMICAL SYNTHESIS USING 'GREENER' ALTERNATIVE REACTION CONDITIONS AND MEDIA

EPA Science Inventory

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

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

PubMed

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

2017-06-28

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

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

PubMed

Duszczyk, Malgorzata M; Sattler, Michael

2012-04-01

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

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

PubMed

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

2014-06-01

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

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

NASA Astrophysics Data System (ADS)

Tycko, Robert

2015-04-01

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

Measurement of absolute concentrations of individual compounds in metabolite mixtures by gradient-selective time-zero 1H-13C HSQC with two concentration references and fast maximum likelihood reconstruction analysis.

PubMed

Hu, Kaifeng; Ellinger, James J; Chylla, Roger A; Markley, John L

2011-12-15

Time-zero 2D (13)C HSQC (HSQC(0)) spectroscopy offers advantages over traditional 2D NMR for quantitative analysis of solutions containing a mixture of compounds because the signal intensities are directly proportional to the concentrations of the constituents. The HSQC(0) spectrum is derived from a series of spectra collected with increasing repetition times within the basic HSQC block by extrapolating the repetition time to zero. Here we present an alternative approach to data collection, gradient-selective time-zero (1)H-(13)C HSQC(0) in combination with fast maximum likelihood reconstruction (FMLR) data analysis and the use of two concentration references for absolute concentration determination. Gradient-selective data acquisition results in cleaner spectra, and NMR data can be acquired in both constant-time and non-constant-time mode. Semiautomatic data analysis is supported by the FMLR approach, which is used to deconvolute the spectra and extract peak volumes. The peak volumes obtained from this analysis are converted to absolute concentrations by reference to the peak volumes of two internal reference compounds of known concentration: DSS (4,4-dimethyl-4-silapentane-1-sulfonic acid) at the low concentration limit (which also serves as chemical shift reference) and MES (2-(N-morpholino)ethanesulfonic acid) at the high concentration limit. The linear relationship between peak volumes and concentration is better defined with two references than with one, and the measured absolute concentrations of individual compounds in the mixture are more accurate. We compare results from semiautomated gsHSQC(0) with those obtained by the original manual phase-cycled HSQC(0) approach. The new approach is suitable for automatic metabolite profiling by simultaneous quantification of multiple metabolites in a complex mixture.

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

NASA Astrophysics Data System (ADS)

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

2009-08-01

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

The neural basis of deictic shifting in linguistic perspective-taking in high-functioning autism

PubMed Central

Liu, Yanni; Williams, Diane L.; Keller, Timothy A.; Minshew, Nancy J.; Just, Marcel Adam

2011-01-01

Personal pronouns, such as ‘I’ and ‘you’, require a speaker/listener to continuously re-map their reciprocal relation to their referent, depending on who is saying the pronoun. This process, called ‘deictic shifting’, may underlie the incorrect production of these pronouns, or ‘pronoun reversals’, such as referring to oneself with the pronoun ‘you’, which has been reported in children with autism. The underlying neural basis of deictic shifting, however, is not understood, nor has the processing of pronouns been studied in adults with autism. The present study compared the brain activation pattern and functional connectivity (synchronization of activation across brain areas) of adults with high-functioning autism and control participants using functional magnetic resonance imaging in a linguistic perspective-taking task that required deictic shifting. The results revealed significantly diminished frontal (right anterior insula) to posterior (precuneus) functional connectivity during deictic shifting in the autism group, as well as reliably slower and less accurate behavioural responses. A comparison of two types of deictic shifting revealed that the functional connectivity between the right anterior insula and precuneus was lower in autism while answering a question that contained the pronoun ‘you’, querying something about the participant’s view, but not when answering a query about someone else’s view. In addition to the functional connectivity between the right anterior insula and precuneus being lower in autism, activation in each region was atypical, suggesting over reliance on individual regions as a potential compensation for the lower level of collaborative interregional processing. These findings indicate that deictic shifting constitutes a challenge for adults with high-functioning autism, particularly when reference to one’s self is involved, and that the functional collaboration of two critical nodes, right anterior insula and precuneus, may play a critical role for deictic shifting by supporting an attention shift between oneself and others. PMID:21733887

Double-Shift Schooling and EFA Goals: Assessing Economic, Educational and Social Impacts

ERIC Educational Resources Information Center

Orkodashvili, Mariam

2009-01-01

The aim of the paper is to discuss the system of double-shift schooling and assess it from economic, social and educational angles referring to different cases from Sub-Saharan African countries. The paper makes an attempt to prove that despite certain challenges that it faces, the system of double-shift schooling is the best solution for poor…

Establishing physico-chemical reference conditions in Mediterranean streams according to the European Water Framework Directive.

PubMed

Sánchez-Montoya, María del Mar; Arce, Maria Isabel; Vidal-Abarca, María Rosario; Suárez, María Luisa; Prat, Narcís; Gómez, Rosa

2012-05-01

Type-specific physico-chemical reference conditions are required for the assessment of ecological status in the Water Framework Directive context, similarly to the biological and hydro-morphological elements. This directive emphasises that natural variability of quality elements in high status (reference condition) needs to be quantified. Mediterranean streams often present a marked seasonal pattern in hydrological, biological and geochemical processes which could affect physico-chemical reference conditions. This study establishes general physico-chemical reference conditions (oxygenation, nutrient, salinity and acidification conditions) for different Mediterranean stream types. 116 potential reference sites located in 23 Mediterranean catchments in Spain were sampled in spring, summer and autumn in 2003. All sites were subjected to a screening method for the selection of reference sites in Mediterranean streams (Mediterranean Reference Criteria) and classified using a pre-established stream typology that establishes five different stream types (temporary streams, evaporite-calcareous at medium altitude, siliceous headwaters, calcareous headwaters and large watercourses). Reference conditions (reference value and reference threshold equivalents to high-good class boundary) were calculated using two different methods according to the availability of reference sites: the reference site 75th percentile approach of all reference sites and the 25th percentile of the population approach. The majority of the studied potential reference sites (76 out of 116) were selected as reference sites. Regarding type-specific reference conditions, only siliceous headwaters could be considered different from the rest of stream types because lower conductivity and pH. All reference stream types presented seasonal differences as regards some parameters, except for temporary streams due to the high natural variation of this stream type. For those parameters which presented seasonal differences in a specific stream type, the least restrictive values were proposed as reference conditions. Copyright © 2012 Elsevier Ltd. All rights reserved.

Spatial-heterodyne interferometry for transmission (SHIFT) measurements

DOEpatents

Bingham, Philip R.; Hanson, Gregory R.; Tobin, Ken W.

2006-10-10

Systems and methods are described for spatial-heterodyne interferometry for transmission (SHIFT) measurements. A method includes digitally recording a spatially-heterodyned hologram including spatial heterodyne fringes for Fourier analysis using a reference beam, and an object beam that is transmitted through an object that is at least partially translucent; Fourier analyzing the digitally recorded spatially-heterodyned hologram, by shifting an original origin of the digitally recorded spatially-heterodyned hologram to sit on top of a spatial-heterodyne carrier frequency defined by an angle between the reference beam and the object beam, to define an analyzed image; digitally filtering the analyzed image to cut off signals around the original origin to define a result; and performing an inverse Fourier transform on the result.

High capacitance density MIS capacitor using Si nanowires by MACE and ALD alumina dielectric

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

Leontis, I.; Nassiopoulou, A. G., E-mail: A.Nassiopoulou@inn.demokritos.gr; Botzakaki, M. A.

2016-06-28

High capacitance density three-dimensional (3D) metal-insulator-semiconductor (MIS) capacitors using Si nanowires (SiNWs) by metal-assisted chemical etching and atomic-layer-deposited alumina dielectric film were fabricated and electrically characterized. A chemical treatment was used to remove structural defects from the nanowire surface, in order to reduce the density of interface traps at the Al{sub 2}O{sub 3}/SiNW interface. SiNWs with two different lengths, namely, 1.3 μm and 2.4 μm, were studied. A four-fold capacitance density increase compared to a planar reference capacitor was achieved with the 1.3 μm SiNWs. In the case of the 2.4 μm SiNWs this increase was ×7, reaching a value of 4.1 μF/cm{sup 2}. Capacitance-voltagemore » (C-V) measurements revealed that, following a two-cycle chemical treatment, frequency dispersion at accumulation regime and flat-band voltage shift disappeared in the case of the 1.3 μm SiNWs, which is indicative of effective removal of structural defects at the SiNW surface. In the case of the 2.4 μm SiNWs, frequency dispersion at accumulation persisted even after the two-step chemical treatment. This is attributed to a porous Si layer at the SiNW tops, which is not effectively removed by the chemical treatment. The electrical losses of MIS capacitors in both cases of SiNW lengths were studied and will be discussed.« less

Search and Discovery Strategies for Biotechnology: the Paradigm Shift

PubMed Central

Bull, Alan T.; Ward, Alan C.; Goodfellow, Michael

2000-01-01

Profound changes are occurring in the strategies that biotechnology-based industries are deploying in the search for exploitable biology and to discover new products and develop new or improved processes. The advances that have been made in the past decade in areas such as combinatorial chemistry, combinatorial biosynthesis, metabolic pathway engineering, gene shuffling, and directed evolution of proteins have caused some companies to consider withdrawing from natural product screening. In this review we examine the paradigm shift from traditional biology to bioinformatics that is revolutionizing exploitable biology. We conclude that the reinvigorated means of detecting novel organisms, novel chemical structures, and novel biocatalytic activities will ensure that natural products will continue to be a primary resource for biotechnology. The paradigm shift has been driven by a convergence of complementary technologies, exemplified by DNA sequencing and amplification, genome sequencing and annotation, proteome analysis, and phenotypic inventorying, resulting in the establishment of huge databases that can be mined in order to generate useful knowledge such as the identity and characterization of organisms and the identity of biotechnology targets. Concurrently there have been major advances in understanding the extent of microbial diversity, how uncultured organisms might be grown, and how expression of the metabolic potential of microorganisms can be maximized. The integration of information from complementary databases presents a significant challenge. Such integration should facilitate answers to complex questions involving sequence, biochemical, physiological, taxonomic, and ecological information of the sort posed in exploitable biology. The paradigm shift which we discuss is not absolute in the sense that it will replace established microbiology; rather, it reinforces our view that innovative microbiology is essential for releasing the potential of microbial diversity for biotechnology penetration throughout industry. Various of these issues are considered with reference to deep-sea microbiology and biotechnology. PMID:10974127

An NMR study of microvoids in polymers

NASA Technical Reports Server (NTRS)

Toy, James; Mattix, Larry

1995-01-01

An understanding of polymer defect structures, like microvoids in polymeric matrices, is crucial to their fabrication and application potential. In this project guest atoms are introduced into the microvoids in PMR-15 and NMR is used to determine microvoid sizes and locations. Xenon is a relatively inert probe that would normally be found naturally in polymer or in NMR probe materials. There are two NMR active xenon isotopes, Xe-129 and Xe-131. The Xe atom has a very high polarizability, which makes it sensitive to the intracrystalline environment of polymers. Interactions between the Xe atoms and the host matrix perturb the Xe electron cloud, deshielding the nuclei, and thereby expanding the range of the observed NMR chemical shifts. This chemical shift range which may be as large as 5000 ppm, permits subtle structural and chemical effects to be studied with high sensitivity. The Xe(129)-NMR line shape has been found to vary in response to changes in the pore symmetry of the framework hosts line Zeolites and Clathrasil compounds. Before exposure to Xe gas, the PMR-15 samples were dried in a vacuum oven at 150 C for 48 hours. The samples were then exposed to Xe gas at 30 psi for 72 hours and sealed in glass tubes with 1 atmosphere of xenon gas. Xenon gas at 1 atmosphere was used to tune up the spectrometer and to set up the appropriate NMR parameters. A single Xe-129 line at 83.003498 Mhz (with protons at 300 Mhz) was observed for the gas. With the xenon charged PMR-15 samples, a second broader line is observed 190 ppm downfield from the gas line (also observed). The width of the NMR line from the Xe-129 absorbed in the polymer is at least partially due to the distribution of microvoid sizes. From the chemical shift (relative to the gas line) and the line width, we estimate the average void sizes to be 2.74 +/- 0.20 angstroms. Since Xe-129 has such a large chemical shift range (approximately 5000 ppm), we expect the chemical shift anisotropy to contribute to the line width (delta upsilon = 2.5 kHz).

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

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

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

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

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

DOE PAGES

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

2017-12-05

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

Surface-water-quality assessment of the Yakima River Basin in Washington: Overview of major findings, 1987-91

USGS Publications Warehouse

Morace, Jennifer L.; Fuhrer, Gregory J.; Rinella, Joseph F.; McKenzie, Stuart W.; Gannett, Marshall W.; Bramblett, Karen L.; Pogue, Ted R.; Skach, Kenneth A.; Embrey, Sandra S.; Cuffney, Thomas F.; Meador, Michael R.; Porter, Stephen D.; Gurtz, Martin E.

1999-01-01

An ecological assessment of the Yakima River Basin ranked physical, chemical, and biological conditions at impaired (degraded) sites against reference sites in an effort to understand how land use changes physical and chemical site characteristics and how biota respond to these changes. For this assessment, the basin was divided into four natural ecological categories: (1) Cascades ecoregion, (2) Eastern Cascades Slopes and Foothills ecoregion, (3) Columbia Basin ecoregion, and (4) large rivers. Each of these categories has a unique combination of climate and landscape features that produces a distinctive terrestrial vegetation assemblage. In the combined Cascades and Eastern Cascades site group, which had the fewest impaired sites, the metals index was the only physical and chemical index that indicated any impairment. The moderate levels of impairment noted in the invertebrate and algal communities were not, however, associated with metals, and may have been related to the effects of logging, although the intensity of logging was not directly quantified in this study. Sites in the Columbia Basin site group were all moderately or severely impaired with the exception of the two reference sites (Umtanum Creek and Satus Creek below Dry Creek), which showed no physical, chemical, or biological impairment. Three sites were heavily affected by agriculture (Granger Drain, Moxee Drain, and Spring Creek) and were listed as severely impaired by most of the physical, chemical, and biological condition indices. Agriculture was the primary cause of the impairment of biological communities in this site group. The primary physical and chemical indicators of agricultural effects were nutrients, pesticides, dissolved solids, and substrate embeddedness, which all tended to increase with agricultural intensity. The biological effects of agriculture were manifested by a decrease in the abundance and number of native species of fish and invertebrates, a shift in algal communities to species indicative of eutrophic conditions, and higher abundances. There was also an increase in the abundance and number of nonnative fish species due to the prevalence of fish that are largely tolerant of nutrient-rich conditions. Main stem (large river) sites downstream from the city of Yakima exhibited severe impairment of fish communities associated with high levels of pesticides in fish tissues and the presence of external anomalies on fish.

Dynamical patterns and regime shifts in the nonlinear model of soil microorganisms growth

NASA Astrophysics Data System (ADS)

Zaitseva, Maria; Vladimirov, Artem; Winter, Anna-Marie; Vasilyeva, Nadezda

2017-04-01

Dynamical model of soil microorganisms growth and turnover is formulated as a system of nonlinear partial differential equations of reaction-diffusion type. We consider spatial distributions of concentrations of several substrates and microorganisms. Biochemical reactions are modelled by chemical kinetic equations. Transport is modelled by simple linear diffusion for all chemical substances, while for microorganisms we use different transport functions, e.g. some of them can actively move along gradient of substrate concentration, while others cannot move. We solve our model in two dimensions, starting from uniform state with small initial perturbations for various parameters and find parameter range, where small initial perturbations grow and evolve. We search for bifurcation points and critical regime shifts in our model and analyze time-space profile and phase portraits of these solutions approaching critical regime shifts in the system, exploring possibility to detect such shifts in advance. This work is supported by NordForsk, project #81513.

Phosphorus Imaging as a Tool for Studying the pH Metabolism in Living Insects

NASA Astrophysics Data System (ADS)

Skibbe, U.; Christeller, J. T.; Eccles, C. D.; Laing, W. A.; Callaghan, P. T.

1995-09-01

Comparative 31P NMR and 1H NMR imaging experiments at submillimeter pixel resolution were carried out, using a specially constructed solenoidal RF coil. Chemical-shift imaging is used to provide pH maps from the midgut of a Lepidopteran larvae and to demonstrate physiological dependence in the resulting images, The titration curve of pH versus chemical shift for inorganic phosphate is extended beyond the "normal" biological range to the strong alkaline limit.

Progress in Spin Dynamics Solid-State Nuclear Magnetic Resonance with the Application of Floquet-Magnus Expansion to Chemical Shift Anisotropy

PubMed Central

Mananga, Eugene Stephane

2013-01-01

The purpose of this article is to present an historical overview of theoretical approaches used for describing spin dynamics under static or rotating experiments in solid state nuclear magnetic resonance. The article gives a brief historical overview for major theories in nuclear magnetic resonance and the promising theories. We present the first application of Floquet-Magnus expansion to chemical shift anisotropy when irradiated by BABA pulse sequence. PMID:23711337

The influence of global climate change on the scientific foundations and applications of Environmental Toxicology and Chemistry: introduction to a SETAC international workshop.

PubMed

Stahl, Ralph G; Hooper, Michael J; Balbus, John M; Clements, William; Fritz, Alyce; Gouin, Todd; Helm, Roger; Hickey, Christopher; Landis, Wayne; Moe, S Jannicke

2013-01-01

This is the first of seven papers resulting from a Society of Environmental Toxicology and Chemistry (SETAC) international workshop titled "The Influence of Global Climate Change on the Scientific Foundations and Applications of Environmental Toxicology and Chemistry." The workshop involved 36 scientists from 11 countries and was designed to answer the following question: How will global climate change influence the environmental impacts of chemicals and other stressors and the way we assess and manage them in the environment? While more detail is found in the complete series of articles, some key consensus points are as follows: (1) human actions (including mitigation of and adaptation to impacts of global climate change [GCC]) may have as much influence on the fate and distribution of chemical contaminants as does GCC, and modeled predictions should be interpreted cautiously; (2) climate change can affect the toxicity of chemicals, but chemicals can also affect how organisms acclimate to climate change; (3) effects of GCC may be slow, variable, and difficult to detect, though some populations and communities of high vulnerability may exhibit responses sooner and more dramatically than others; (4) future approaches to human and ecological risk assessments will need to incorporate multiple stressors and cumulative risks considering the wide spectrum of potential impacts stemming from GCC; and (5) baseline/reference conditions for estimating resource injury and restoration/rehabilitation will continually shift due to GCC and represent significant challenges to practitioners. Copyright © 2013 SETAC.

The influence of global climate change on the scientific foundations and applications of Environmental Toxicology and Chemistry: Introduction to a SETAC international workshop

USGS Publications Warehouse

Stahl, Ralph G.; Hooper, Michael J.; Balbus, John M.; Clements, William; Fritz, Alyce; Gouin, Todd; Helm, Roger; Hickey, Christopher; Landis, Wayne; Moe, S. Jannicke

2013-01-01

This is the first of seven papers resulting from a Society of Environmental Toxicology and Chemistry (SETAC) international workshop titled “The Influence of Global Climate Change on the Scientific Foundations and Applications of Environmental Toxicology and Chemistry.” The workshop involved 36 scientists from 11 countries and was designed to answer the following question: How will global climate change influence the environmental impacts of chemicals and other stressors and the way we assess and manage them in the environment? While more detail is found in the complete series of articles, some key consensus points are as follows: (1) human actions (including mitigation of and adaptation to impacts of global climate change [GCC]) may have as much influence on the fate and distribution of chemical contaminants as does GCC, and modeled predictions should be interpreted cautiously; (2) climate change can affect the toxicity of chemicals, but chemicals can also affect how organisms acclimate to climate change; (3) effects of GCC may be slow, variable, and difficult to detect, though some populations and communities of high vulnerability may exhibit responses sooner and more dramatically than others; (4) future approaches to human and ecological risk assessments will need to incorporate multiple stressors and cumulative risks considering the wide spectrum of potential impacts stemming from GCC; and (5) baseline/reference conditions for estimating resource injury and restoration/rehabilitation will continually shift due to GCC and represent significant challenges to practitioners.

Validity of self-reported exposure to shift work.

PubMed

Härmä, Mikko; Koskinen, Aki; Ropponen, Annina; Puttonen, Sampsa; Karhula, Kati; Vahtera, Jussi; Kivimäki, Mika

2017-03-01

To evaluate the validity of widely used questionnaire items on work schedule using objective registry data as reference. A cohort study of hospital employees who responded to a self-administered questionnaire on work schedule in 2008, 2012 and 2014 and were linked to individual-level pay-roll-based records on work shifts. For predictive validity, leisure-time fatigue was assessed. According to the survey data in 2014 (n=8896), 55% of the day workers had at least 1 year of earlier shift work experience. 8% of the night shift workers changed to day work during the follow-up. Using pay-roll data as reference, questions on 'shift work with night shifts' and 'permanent night work' showed high sensitivity (96% and 90%) and specificity (92% and 97%). Self-reported 'regular day work' showed moderate sensitivity (73%), but high specificity (99%) and 'shift work without night shifts' showed low sensitivity (62%) and moderate specificity (87%). In multivariate logistic regression analysis, the age-adjusted, sex-adjusted and baseline fatigue-adjusted association between 'shift work without night shifts' and leisure-time fatigue was lower for self-reported compared with objective assessment (1.30, 95% CI 0.94 to 1.82, n=1707 vs 1.89, 95% CI 1.06 to 3.39, n=1627). In contrast, shift work with night shifts, compared with permanent day work, was similarly associated with fatigue in the two assessments (2.04, 95% CI 1.62 to 2.57, n=2311 vs 1.82, 95% CI 1.28 to 2.58, n=1804). The validity of self-reported assessment of shift work varies between work schedules. Exposure misclassification in self-reported data may contribute to bias towards the null in shift work without night shifts. 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/.

How do different definitions of night shift affect the exposure assessment of night work?

PubMed

Garde, Anne Helene; Hansen, Johnni; Kolstad, Henrik A; Larsen, Ann Dyreborg; Hansen, Åse Marie

The aim is to show how different definitions affect the proportion of shifts classified as night shifts. The Danish Working Hour Database was used to calculate number of night shifts according to eight definitions. More than 98% of the total night shifts were night shifts by use of both the reference definition (at least 3 h of work between 24:00 and 05:00) and definitions using a period during the night. The overlap with definitions based on starting and ending time was less pronounced (64-71 %). The proportion of classified night shifts differs little when night shifts are based on definitions including a period during the night. Studies based on other definitions may be less comparable.

Job Relocation is High in Chemical Industry.

ERIC Educational Resources Information Center

Chemical and Engineering News, 1979

1979-01-01

The chances of an employee being relocated are higher in the chemical and plastics industries than in U.S. business as a whole. But the benefits provided by chemical and plastics companies to employees shifted to other locations are generally better than average. (Author/BB)

Velocity encoding with the slice select refocusing gradient for faster imaging and reduced chemical shift-induced phase errors.

PubMed

Middione, Matthew J; Thompson, Richard B; Ennis, Daniel B

2014-06-01

To investigate a novel phase-contrast MRI velocity-encoding technique for faster imaging and reduced chemical shift-induced phase errors. Velocity encoding with the slice select refocusing gradient achieves the target gradient moment by time shifting the refocusing gradient, which enables the use of the minimum in-phase echo time (TE) for faster imaging and reduced chemical shift-induced phase errors. Net forward flow was compared in 10 healthy subjects (N = 10) within the ascending aorta (aAo), main pulmonary artery (PA), and right/left pulmonary arteries (RPA/LPA) using conventional flow compensated and flow encoded (401 Hz/px and TE = 3.08 ms) and slice select refocused gradient velocity encoding (814 Hz/px and TE = 2.46 ms) at 3 T. Improved net forward flow agreement was measured across all vessels for slice select refocused gradient compared to flow compensated and flow encoded: aAo vs. PA (1.7% ± 1.9% vs. 5.8% ± 2.8%, P = 0.002), aAo vs. RPA + LPA (2.1% ± 1.7% vs. 6.0% ± 4.3%, P = 0.03), and PA vs. RPA + LPA (2.9% ± 2.1% vs. 6.1% ± 6.3%, P = 0.04), while increasing temporal resolution (35%) and signal-to-noise ratio (33%). Slice select refocused gradient phase-contrast MRI with a high receiver bandwidth and minimum in-phase TE provides more accurate and less variable flow measurements through the reduction of chemical shift-induced phase errors and a reduced TE/repetition time, which can be used to increase the temporal/spatial resolution and/or reduce breath hold durations. Copyright © 2013 Wiley Periodicals, Inc.

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

SU‐C‐105‐05: Reference Dosimetry of High‐Energy Electron Beams with a Farmer‐Type Ionization Chamber

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

Muir, B; Rogers, D

2013-06-15

Purpose: To investigate gradient effects and provide Monte Carlo calculated beam quality conversion factors to characterize the Farmer‐type NE2571 ion chamber for high‐energy reference dosimetry of clinical electron beams. Methods: The EGSnrc code system is used to calculate the absorbed dose to water and to the gas in a fully modeled NE2571 chamber as a function of depth in a water phantom. Electron beams incident on the surface of the phantom are modeled using realistic BEAMnrc accelerator simulations and electron beam spectra. Beam quality conversion factors are determined using calculated doses to water and to air in the chamber inmore » high‐energy electron beams and in a cobalt‐60 reference field. Calculated water‐to‐air stopping power ratios are employed for investigation of the overall ion chamber perturbation factor. Results: An upstream shift of 0.3–0.4 multiplied by the chamber radius, r-cav, both minimizes the variation of the overall ion chamber perturbation factor with depth and reduces the difference between the beam quality specifier (R{sub 5} {sub 0}) calculated using ion chamber simulations and that obtained with simulations of dose‐to‐water in the phantom. Beam quality conversion factors are obtained at the reference depth and gradient effects are optimized using a shift of 0.2r-cav. The photon‐electron conversion factor, k-ecal, amounts to 0.906 when gradient effects are minimized using the shift established here and 0.903 if no shift of the data is used. Systematic uncertainties in beam quality conversion factors are investigated and amount to between 0.4 to 1.1% depending on assumptions used. Conclusion: The calculations obtained in this work characterize the use of an NE2571 ion chamber for reference dosimetry of high‐energy electron beams. These results will be useful as the AAPM continues to review their reference dosimetry protocols.« less

Referential Choices in a Collaborative Storytelling Task: Discourse Stages and Referential Complexity Matter.

PubMed

Fossard, Marion; Achim, Amélie M; Rousier-Vercruyssen, Lucie; Gonzalez, Sylvia; Bureau, Alexandre; Champagne-Lavau, Maud

2018-01-01

During a narrative discourse, accessibility of the referents is rarely fixed once and for all. Rather, each referent varies in accessibility as the discourse unfolds, depending on the presence and prominence of the other referents. This leads the speaker to use various referential expressions to refer to the main protagonists of the story at different moments in the narrative. This study relies on a new, collaborative storytelling in sequence task designed to assess how speakers adjust their referential choices when they refer to different characters at specific discourse stages corresponding to the introduction, maintaining, or shift of the character in focus, in increasingly complex referential contexts. Referential complexity of the stories was manipulated through variations in the number of characters (1 vs. 2) and, for stories in which there were two characters, in their ambiguity in gender (different vs. same gender). Data were coded for the type of reference markers as well as the type of reference content (i.e., the extent of the information provided in the referential expression). Results showed that, beyond the expected effects of discourse stages on reference markers (more indefinite markers at the introduction stage, more pronouns at the maintaining stage, and more definite markers at the shift stage), the number of characters and their ambiguity in gender also modulated speakers' referential choices at specific discourse stages, For the maintaining stage, an effect of the number of characters was observed for the use of pronouns and of definite markers, with more pronouns when there was a single character, sometimes replaced by definite expressions when two characters were present in the story. For the shift stage, an effect of gender ambiguity was specifically noted for the reference content with more specific information provided in the referential expression when there was referential ambiguity. Reference content is an aspect of referential marking that is rarely addressed in a narrative context, yet it revealed a quite flexible referential behavior by the speakers.

Referential Choices in a Collaborative Storytelling Task: Discourse Stages and Referential Complexity Matter

PubMed Central

Fossard, Marion; Achim, Amélie M.; Rousier-Vercruyssen, Lucie; Gonzalez, Sylvia; Bureau, Alexandre; Champagne-Lavau, Maud

2018-01-01

During a narrative discourse, accessibility of the referents is rarely fixed once and for all. Rather, each referent varies in accessibility as the discourse unfolds, depending on the presence and prominence of the other referents. This leads the speaker to use various referential expressions to refer to the main protagonists of the story at different moments in the narrative. This study relies on a new, collaborative storytelling in sequence task designed to assess how speakers adjust their referential choices when they refer to different characters at specific discourse stages corresponding to the introduction, maintaining, or shift of the character in focus, in increasingly complex referential contexts. Referential complexity of the stories was manipulated through variations in the number of characters (1 vs. 2) and, for stories in which there were two characters, in their ambiguity in gender (different vs. same gender). Data were coded for the type of reference markers as well as the type of reference content (i.e., the extent of the information provided in the referential expression). Results showed that, beyond the expected effects of discourse stages on reference markers (more indefinite markers at the introduction stage, more pronouns at the maintaining stage, and more definite markers at the shift stage), the number of characters and their ambiguity in gender also modulated speakers' referential choices at specific discourse stages, For the maintaining stage, an effect of the number of characters was observed for the use of pronouns and of definite markers, with more pronouns when there was a single character, sometimes replaced by definite expressions when two characters were present in the story. For the shift stage, an effect of gender ambiguity was specifically noted for the reference content with more specific information provided in the referential expression when there was referential ambiguity. Reference content is an aspect of referential marking that is rarely addressed in a narrative context, yet it revealed a quite flexible referential behavior by the speakers. PMID:29515493

Allelochemicals Produced by Brown Macroalgae of the Lobophora Genus Are Active against Coral Larvae and Associated Bacteria, Supporting Pathogenic Shifts to Vibrio Dominance

PubMed Central

Bromhall, Katrina; Motti, Cherie A.; Munn, Colin B.; Bourne, David G.

2016-01-01

ABSTRACT Pervasive environmental stressors on coral reefs are attributed with shifting the competitive balance in favor of alternative dominants, such as macroalgae. Previous studies have demonstrated that macroalgae compete with corals via a number of mechanisms, including the production of potent primary and secondary metabolites that can influence coral-associated microbial communities. The present study investigates the effects of the Pacific brown macroalga Lobophora sp. (due to the shifting nature of the Lobophora species complex, it will be referred to here as Lobophora sp.) on coral bacterial isolates, coral larvae, and the microbiome associated with the coral Porites cylindrica. Crude aqueous and organic macroalgal extracts were found to inhibit the growth of coral-associated bacteria. Extracts and fractions were also shown to inhibit coral larval settlement and cause mortality at concentrations lower (<0.3 mg · ml−1) than calculated natural concentrations (4.4 mg · ml−1). Microbial communities associated with coral tissues exposed to aqueous (e.g., hydrophilic) crude extracts demonstrated a significant shift to Vibrio dominance and a loss of sequences related to the putative coral bacterial symbiont, Endozoicomonas sp., based on 16S rRNA amplicon sequencing. This study contributes to growing evidence that macroalgal allelochemicals, dissolved organic material, and native macroalgal microbial assemblages all play a role in shifting the microbial equilibrium of the coral holobiont away from a beneficial state, contributing to a decline in coral fitness and a shift in ecosystem structure. IMPORTANCE Diverse microbial communities associate with coral tissues and mucus, providing important protective and nutritional services, but once disturbed, the microbial equilibrium may shift from a beneficial state to one that is detrimental or pathogenic. Macroalgae (e.g., seaweeds) can physically and chemically interact with corals, causing abrasion, bleaching, and overall stress. This study contributes to a growing body of evidence suggesting that macroalgae play a critical role in shifting the coral holobiont equilibrium, which may promote the invasion of opportunistic pathogens and cause coral mortality, facilitating additional macroalgal growth and invasion in the reef. Thus, macroalgae not only contribute to a decline in coral fitness but also influence coral reef ecosystem structure. PMID:27795310

Allelochemicals Produced by Brown Macroalgae of the Lobophora Genus Are Active against Coral Larvae and Associated Bacteria, Supporting Pathogenic Shifts to Vibrio Dominance.

PubMed

Morrow, Kathleen M; Bromhall, Katrina; Motti, Cherie A; Munn, Colin B; Bourne, David G

2017-01-01

Pervasive environmental stressors on coral reefs are attributed with shifting the competitive balance in favor of alternative dominants, such as macroalgae. Previous studies have demonstrated that macroalgae compete with corals via a number of mechanisms, including the production of potent primary and secondary metabolites that can influence coral-associated microbial communities. The present study investigates the effects of the Pacific brown macroalga Lobophora sp. (due to the shifting nature of the Lobophora species complex, it will be referred to here as Lobophora sp.) on coral bacterial isolates, coral larvae, and the microbiome associated with the coral Porites cylindrica. Crude aqueous and organic macroalgal extracts were found to inhibit the growth of coral-associated bacteria. Extracts and fractions were also shown to inhibit coral larval settlement and cause mortality at concentrations lower (<0.3 mg · ml -1 ) than calculated natural concentrations (4.4 mg · ml -1 ). Microbial communities associated with coral tissues exposed to aqueous (e.g., hydrophilic) crude extracts demonstrated a significant shift to Vibrio dominance and a loss of sequences related to the putative coral bacterial symbiont, Endozoicomonas sp., based on 16S rRNA amplicon sequencing. This study contributes to growing evidence that macroalgal allelochemicals, dissolved organic material, and native macroalgal microbial assemblages all play a role in shifting the microbial equilibrium of the coral holobiont away from a beneficial state, contributing to a decline in coral fitness and a shift in ecosystem structure. Diverse microbial communities associate with coral tissues and mucus, providing important protective and nutritional services, but once disturbed, the microbial equilibrium may shift from a beneficial state to one that is detrimental or pathogenic. Macroalgae (e.g., seaweeds) can physically and chemically interact with corals, causing abrasion, bleaching, and overall stress. This study contributes to a growing body of evidence suggesting that macroalgae play a critical role in shifting the coral holobiont equilibrium, which may promote the invasion of opportunistic pathogens and cause coral mortality, facilitating additional macroalgal growth and invasion in the reef. Thus, macroalgae not only contribute to a decline in coral fitness but also influence coral reef ecosystem structure. © Crown copyright 2016.

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

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

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

2011-06-01

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

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

PubMed

Böhm, Karl-Heinz; Banert, Klaus; Auer, Alexander A

2014-04-23

We present ab-initio calculations of secondary isotope effects on NMR chemical shieldings. The change of the NMR chemical shift of a certain nucleus that is observed if another nucleus is replaced by a different isotope can be calculated by computing vibrational corrections on the NMR parameters using electronic structure methods. We demonstrate that the accuracy of the computational results is sufficient to even distinguish different conformers. For this purpose, benchmark calculations for fluoro(2-2H)ethane in gauche and antiperiplanar conformation are carried out at the HF, MP2 and CCSD(T) level of theory using basis sets ranging from double- to quadruple-zeta quality. The methodology is applied to the secondary isotope shifts for 2-fluoronorbornane in order to resolve an ambiguity in the literature on the assignment of endo- and exo-2-fluoronorbornanes with deuterium substituents in endo-3 and exo-3 positions, also yielding insight into mechanistic details of the corresponding synthesis.

Apparatus for controlling the firing of rectifiers in polyphase rectifying circuits

DOEpatents

Yarema, R.J.

1979-09-18

A polyphase rectifier is controlled with precision by a circuit that filters and shifts a reference signal associated with each phase and that starts a ramp signal at a zero crossing of the shifted reference signal. The difference between the ramp signal and an external trigger signal is used to generate a pulse that switches power rectifiers into conduction. The circuit reduces effects of variations that introduce subharmonics into a rectified signal and it can be used for constant or time-varying external trigger signals.

On the bathochromic shift of the absorption by astaxanthin in crustacyanin: a quantum chemical study

NASA Astrophysics Data System (ADS)

Durbeej, Bo; Eriksson, Leif A.

2003-06-01

The structural origin of the bathochromic shift assumed by the electronic absorption spectrum of protein-bound astaxanthin, the carotenoid that upon binding to crustacyanin is responsible for the blue colouration of lobster shell, is investigated by means of quantum chemical methods. The calculations suggest that the bathochromic shift is largely due to one of the astaxanthin C4 keto groups being hydrogen-bonded to a histidine residue of the surrounding protein, and that the effect of this histidine is directly dependent on its protonation state. Out of the different methodologies (CIS, TD-DFT, and ZINDO/S) employed to calculate wavelengths of maximum absorption, the best agreement with experimental data is obtained using the semiempirical ZINDO/S method.

Community College Faculty: Making the Paradigm Shift.

ERIC Educational Resources Information Center

Van Ast, John

1999-01-01

Discusses the need for paradigm shifts during the next decade that address the following challenges: (1) the wider range of student ability and mastery; (2) high attrition rates; and (3) differing and often contradicting perceptions of students, faculty, and administration. Contains 180 references. (TGO)

Accuracy of the vertical tube shift method in identifying the relationship between the third molars and the mandibular canal.

PubMed

de-Azevedo-Vaz, Sergio Lins; Oenning, Anne Caroline Costa; Felizardo, Marcela Graciano; Haiter-Neto, Francisco; de Freitas, Deborah Queiroz

2015-04-01

The objective of this study is to assess the accuracy of the vertical tube shift method in identifying the relationship between the mandibular canal (MC) and third molars. Two examiners assessed image sets of 173 lower third molar roots (55 patients) using forced consensus. The image sets comprised two methods: PERI, two periapical radiographs (taken at 0° and -30°), and PAN, a panoramic radiograph (vertical angulation of -8°) and a periapical radiograph taken at a vertical angulation of -30°. Cone beam computed tomography (CBCT) was the reference standard in the study. The responses were recorded for position (buccal, in-line with apex and lingual) and contact (present or absent). The McNemar-Bowker and McNemar tests were used to determine if the PERI and PAN methods would disagree with the reference standard (α = 5 %). The PERI and PAN methods disagreed with the reference standard for both position and contact (p < 0.05). The vertical tube shift method was not accurate in determining the relationship between lower third molars and the MC. The vertical tube shift is not a reliable method for predicting the relationship between lower third molars and the MC.

125Te NMR shielding and optoelectronic spectra in XTe3O8 (X = Ti, Zr, Sn and Hf) compounds: Ab initio calculations

NASA Astrophysics Data System (ADS)

Bashi, M.; Rahnamaye Aliabad, H. A.; Mowlavi, A. A.; Ahmad, Iftikhar

2017-11-01

We have calculated the NMR shielding, structural properties and optoelectronic spectra of XTe3O8 (X = Ti, Zr, Sn and Hf) compounds. The full potential linearized augmented plane wave (FP-LAPW) method and the modified Becke-Johnson (mBJ) are used by density functional theory schemes. The calculated shielding and measured shifts are arranged in a straight line and the tensors of magnetic shielding have a low symmetry and the shielding along the x direction is greater than the y and z directions. Obtained results show that the X ions have the most important influence on the 125Te chemical shift. Calculated chemical shielding components (σii) decrease from Ti to Sn then increases from Sn to Hf so that these behaviors are vice versa for 125Te isotropic chemical shift (δiso). Density of states spectra show that the X-p and d states play key role in the optical and NMR calculations. Optical results illustrate that there is a direct relation between the chemical shielding components for Te atom and the static dielectric function, refractive index and Plasmon energies.

Updates in MRI characterization of the thymus in myasthenic patients.

PubMed

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

2012-06-12

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

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

PubMed Central

Hafsa, Noor E.; Arndt, David; Wishart, David S.

2015-01-01

The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I′, II′ and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. PMID:25979265

Adducts of nitrogenous ligands with rhodium(II) tetracarboxylates and tetraformamidinate: NMR spectroscopy and density functional theory calculations.

PubMed

Cmoch, Piotr; Głaszczka, Rafał; Jaźwiński, Jarosław; Kamieński, Bohdan; Senkara, Elżbieta

2014-03-01

Complexation of tetrakis(μ2-N,N'-diphenylformamidinato-N,N')-di-rhodium(II) with ligands containing nitrile, isonitrile, amine, hydroxyl, sulfhydryl, isocyanate, and isothiocyanate functional groups has been studied in liquid and solid phases using (1)H, (13)C and (15)N NMR, (13)C and (15)N cross polarisation-magic angle spinning NMR, and absorption spectroscopy in the visible range. The complexation was monitored using various NMR physicochemical parameters, such as chemical shifts, longitudinal relaxation times T1 , and NOE enhancements. Rhodium(II) tetraformamidinate selectively bonded only unbranched amine (propan-1-amine), pentanenitrile, and (1-isocyanoethyl)benzene. No complexation occurred in the case of ligands having hydroxyl, sulfhydryl, isocyanate, and isothiocyanate functional groups, and more expanded amine molecules such as butan-2-amine and 1-azabicyclo[2.2.2]octane. Such features were opposite to those observed in rhodium(II) tetracarboxylates, forming adducts with all kind of ligands. Special attention was focused on the analysis of Δδ parameters, defined as a chemical shift difference between signal in adduct and corresponding signal in free ligand. In the case of (1)H NMR, Δδ values were either negative in adducts of rhodium(II) tetraformamidinate or positive in adducts of rhodium(II) tetracarboxylates. Experimental findings were supported by density functional theory molecular modelling and gauge independent atomic orbitals chemical shift calculations. The calculation of chemical shifts combined with scaling procedure allowed to reproduce qualitatively Δδ parameters. Copyright © 2013 John Wiley & Sons, Ltd.

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

PubMed Central

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

2012-01-01

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

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

PubMed

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

2017-03-01

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

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

PubMed

Kang, WonYang; Park, Won-Ju; Jang, Keun-Ho; Kim, Soo-Hyeon; Gwon, Do-Hyeong; Lim, Hyeong-Min; Ahn, Ji-Sung; Moon, Jai-Dong

2016-08-01

The aim of this study was to investigate whether shift work is related to elevated risk of coronary artery disease (CAD) by determining the coronary artery calcium (CAC) score and the presence of coronary artery stenosis by using coronary artery CT angiography (CCTA). In this study, 110 male workers participated and underwent a CCTA examination for CAC scoring, which represents coronary artery plaque, and were evaluated for luminal stenosis. All of the participants were working in the same chemical plant, of whom 70 worked day shifts and 40 worked rotating shifts. In a multivariate logistic regression analysis, including age, smoking status, alcohol consumption, regular exercise and waist circumference, shift work was associated with a 2.89-fold increase in the odds of developing coronary plaque compared with day work (OR, 2.89; 95% CI 1.07 to 7.82). The association between shift work and coronary plaque was strong after adjustment for age, low-density lipoprotein cholesterol, hypertension and diabetes mellitus (OR, 2.92; 95% CI 1.02 to 8.33). In addition, the number of years of shift work employment was associated with coronary plaque. However, no association was found between shift work and coronary artery stenosis. Shift work could induce CAD onset via the atherosclerotic process, and shift work employment duration was associated with an increased risk of atherosclerosis in male workers. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Enhancing Thai Students' Learning of Chemical Kinetics

ERIC Educational Resources Information Center

Chairam, Sanoe; Somsook, Ekasith; Coll, Richard K.

2009-01-01

Chemical kinetics is an extremely important concept for introductory chemistry courses. The literature suggests that instruction in chemical kinetics is often teacher-dominated at both the secondary school and tertiary levels, and this is the case in Thailand--the educational context for this inquiry. The work reported here seeks to shift students…

Hydrodynamic fluctuations, nonequilibrium equations of state, and the shift of the spinodal line in polymer solutions under flow

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

Criado-Sancho, M.; Casas-Vazquez, J.; Jou, D.

1997-08-01

In the literature, the shift of the spinodal line of polymer solutions under flow is attributed either to an actual shift of the spinodal due to a nonequilibrium modification of the equation of state for the chemical potential, or to an apparent shift due to an increase of hydrodynamic fluctuations owing to the flow. Here we see that both approaches are compatible and that both effects add up. {copyright} {ital 1997} {ital The American Physical Society}

A summary of chemical and biological testing of proposed disposal of sediment from Richmond Harbor relative to the Deep Off-Shelf Reference Area, the Bay Farm Borrow Area, and the Alcatraz Environs Reference Area

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

Mayhew, H.L.; Karle, L.M.; Gruendell, B.D.

The US Army Corps of Engineers was authorized to dredge Richmond Harbor to accomodate large, deep-draft vessels. An ecological evaluation of the Harbor sediments was performed describing the physical characteristics, toxic substances, effects on aquatic organisms,and potential for bioaccumulation of chemical contaminants. The objective of this report is to compare the sediment chemistry, acute toxicity, and bioaccumulation results of the Richmond Harbor sediments to each of the reference areas; i.e., the Deep Off-Shelf Reference Area, the Bay Farm Borrow Area, and the Alcatraz Environs Reference Area. This report will enable the US Army Corps of Engineers to determine whether disposalmore » at a reference area is appropriate for all or part of the dredged material from Richmond Harbor. Chemical analyses were performed on 30 sediment samples; 28 of those samples were then combined to form 7 composites. The seven composites plus sediment from two additional stations received both chemical and biological evaluations.« less

Registration uncertainties between 3D cone beam computed tomography and different reference CT datasets in lung stereotactic body radiation therapy.

PubMed

Oechsner, Markus; Chizzali, Barbara; Devecka, Michal; Combs, Stephanie Elisabeth; Wilkens, Jan Jakob; Duma, Marciana Nona

2016-10-26

The aim of this study was to analyze differences in couch shifts (setup errors) resulting from image registration of different CT datasets with free breathing cone beam CTs (FB-CBCT). As well automatic as manual image registrations were performed and registration results were correlated to tumor characteristics. FB-CBCT image registration was performed for 49 patients with lung lesions using slow planning CT (PCT), average intensity projection (AIP), maximum intensity projection (MIP) and mid-ventilation CTs (MidV) as reference images. Both, automatic and manual image registrations were applied. Shift differences were evaluated between the registered CT datasets for automatic and manual registration, respectively. Furthermore, differences between automatic and manual registration were analyzed for the same CT datasets. The registration results were statistically analyzed and correlated to tumor characteristics (3D tumor motion, tumor volume, superior-inferior (SI) distance, tumor environment). Median 3D shift differences over all patients were between 0.5 mm (AIPvsMIP) and 1.9 mm (MIPvsPCT and MidVvsPCT) for the automatic registration and between 1.8 mm (AIPvsPCT) and 2.8 mm (MIPvsPCT and MidVvsPCT) for the manual registration. For some patients, large shift differences (>5.0 mm) were found (maximum 10.5 mm, automatic registration). Comparing automatic vs manual registrations for the same reference CTs, ∆AIP achieved the smallest (1.1 mm) and ∆MIP the largest (1.9 mm) median 3D shift differences. The standard deviation (variability) for the 3D shift differences was also the smallest for ∆AIP (1.1 mm). Significant correlations (p < 0.01) between 3D shift difference and 3D tumor motion (AIPvsMIP, MIPvsMidV) and SI distance (AIPvsMIP) (automatic) and also for 3D tumor motion (∆PCT, ∆MidV; automatic vs manual) were found. Using different CT datasets for image registration with FB-CBCTs can result in different 3D couch shifts. Manual registrations achieved partly different 3D shifts than automatic registrations. AIP CTs yielded the smallest shift differences and might be the most appropriate CT dataset for registration with 3D FB-CBCTs.

Validation of goose liver fat measurement by QCT and CSE-MRI with biochemical extraction and pathology as reference.

PubMed

Xu, Li; Duanmu, Yangyang; Blake, Glen M; Zhang, Chenxin; Zhang, Yong; Brown, Keenan; Wang, Xiaoqi; Wang, Peng; Zhou, Xingang; Zhang, Manling; Wang, Chao; Guo, Zhe; Guglielmi, Giuseppe; Cheng, Xiaoguang

2018-05-01

This study aimed to validate the accuracy and reliability of quantitative computed tomography (QCT) and chemical shift encoded magnetic resonance imaging (CSE-MRI) to assess hepatic steatosis. Twenty-two geese with a wide range of hepatic steatosis were collected. After QCT and CSE-MRI examinations, the liver of each goose was removed and samples were taken from the left lobe, upper and lower half of the right lobe for biochemical measurement and histology. Fat percentages by QCT and proton density fat fraction by MRI (MRI-PDFF) were measured within the sample regions of biochemical measurement and histology. The accuracy of QCT and MR measurements were assessed through Spearman correlation coefficients (r) and Passing and Bablok regression equations using biochemical measurement as the "gold standard". Both QCT and MRI correlated highly with chemical extraction [r = 0.922 (p < 0.001) and r = 0.949 (p < 0.001) respectively]. Chemically extracted triglyceride was accurately predicted by both QCT liver fat percentages (Y = 0.6 + 0.866 × X) and by MRI-PDFF (Y = -1.8 + 0.773 × X). QCT and CSE-MRI measurements of goose liver fat were accurate and reliable compared with biochemical measurement. • QCT and CSE-MRI can measure liver fat content accurately and reliably • Histological grading of hepatic steatosis has larger sampling variability • QCT and CSE-MRI have potential in the clinical setting.

High SNR Acquisitions Improve the Repeatability of Liver Fat Quantification Using Confounder-corrected Chemical Shift-encoded MR Imaging

PubMed Central

Motosugi, Utaroh; Hernando, Diego; Wiens, Curtis; Bannas, Peter; Reeder, Scott. B

2017-01-01

Purpose: To determine whether high signal-to-noise ratio (SNR) acquisitions improve the repeatability of liver proton density fat fraction (PDFF) measurements using confounder-corrected chemical shift-encoded magnetic resonance (MR) imaging (CSE-MRI). Materials and Methods: Eleven fat-water phantoms were scanned with 8 different protocols with varying SNR. After repositioning the phantoms, the same scans were repeated to evaluate the test-retest repeatability. Next, an in vivo study was performed with 20 volunteers and 28 patients scheduled for liver magnetic resonance imaging (MRI). Two CSE-MRI protocols with standard- and high-SNR were repeated to assess test-retest repeatability. MR spectroscopy (MRS)-based PDFF was acquired as a standard of reference. The standard deviation (SD) of the difference (Δ) of PDFF measured in the two repeated scans was defined to ascertain repeatability. The correlation between PDFF of CSE-MRI and MRS was calculated to assess accuracy. The SD of Δ and correlation coefficients of the two protocols (standard- and high-SNR) were compared using F-test and t-test, respectively. Two reconstruction algorithms (complex-based and magnitude-based) were used for both the phantom and in vivo experiments. Results: The phantom study demonstrated that higher SNR improved the repeatability for both complex- and magnitude-based reconstruction. Similarly, the in vivo study demonstrated that the repeatability of the high-SNR protocol (SD of Δ = 0.53 for complex- and = 0.85 for magnitude-based fit) was significantly higher than using the standard-SNR protocol (0.77 for complex, P < 0.001; and 0.94 for magnitude-based fit, P = 0.003). No significant difference was observed in the accuracy between standard- and high-SNR protocols. Conclusion: Higher SNR improves the repeatability of fat quantification using confounder-corrected CSE-MRI. PMID:28190853

Quantification of liver fat with respiratory-gated quantitative chemical shift encoded MRI.

PubMed

Motosugi, Utaroh; Hernando, Diego; Bannas, Peter; Holmes, James H; Wang, Kang; Shimakawa, Ann; Iwadate, Yuji; Taviani, Valentina; Rehm, Jennifer L; Reeder, Scott B

2015-11-01

To evaluate free-breathing chemical shift-encoded (CSE) magnetic resonance imaging (MRI) for quantification of hepatic proton density fat-fraction (PDFF). A secondary purpose was to evaluate hepatic R2* values measured using free-breathing quantitative CSE-MRI. Fifty patients (mean age, 56 years) were prospectively recruited and underwent the following four acquisitions to measure PDFF and R2*; 1) conventional breath-hold CSE-MRI (BH-CSE); 2) respiratory-gated CSE-MRI using respiratory bellows (BL-CSE); 3) respiratory-gated CSE-MRI using navigator echoes (NV-CSE); and 4) single voxel MR spectroscopy (MRS) as the reference standard for PDFF. Image quality was evaluated by two radiologists. MRI-PDFF measured from the three CSE-MRI methods were compared with MRS-PDFF using linear regression. The PDFF and R2* values were compared using two one-sided t-test to evaluate statistical equivalence. There was no significant difference in the image quality scores among the three CSE-MRI methods for either PDFF (P = 1.000) or R2* maps (P = 0.359-1.000). Correlation coefficients (95% confidence interval [CI]) for the PDFF comparisons were 0.98 (0.96-0.99) for BH-, 0.99 (0.97-0.99) for BL-, and 0.99 (0.98-0.99) for NV-CSE. The statistical equivalence test revealed that the mean difference in PDFF and R2* between any two of the three CSE-MRI methods was less than ±1 percentage point (pp) and ±5 s(-1) , respectively (P < 0.046). Respiratory-gated CSE-MRI with respiratory bellows or navigator echo are feasible methods to quantify liver PDFF and R2* and are as valid as the standard breath-hold technique. © 2015 Wiley Periodicals, Inc.

Quantitative susceptibility mapping (QSM): Decoding MRI data for a tissue magnetic biomarker

PubMed Central

Wang, Yi; Liu, Tian

2015-01-01

In MRI, the main magnetic field polarizes the electron cloud of a molecule, generating a chemical shift for observer protons within the molecule and a magnetic susceptibility inhomogeneity field for observer protons outside the molecule. The number of water protons surrounding a molecule for detecting its magnetic susceptibility is vastly greater than the number of protons within the molecule for detecting its chemical shift. However, the study of tissue magnetic susceptibility has been hindered by poor molecular specificities of hitherto used methods based on MRI signal phase and T2* contrast, which depend convolutedly on surrounding susceptibility sources. Deconvolution of the MRI signal phase can determine tissue susceptibility but is challenged by the lack of MRI signal in the background and by the zeroes in the dipole kernel. Recently, physically meaningful regularizations, including the Bayesian approach, have been developed to enable accurate quantitative susceptibility mapping (QSM) for studying iron distribution, metabolic oxygen consumption, blood degradation, calcification, demyelination, and other pathophysiological susceptibility changes, as well as contrast agent biodistribution in MRI. This paper attempts to summarize the basic physical concepts and essential algorithmic steps in QSM, to describe clinical and technical issues under active development, and to provide references, codes, and testing data for readers interested in QSM. Magn Reson Med 73:82–101, 2015. © 2014 The Authors. Magnetic Resonance in Medicine Published by Wiley Periodicals, Inc. on behalf of International Society of Medicine in Resonance. This is an open access article under the terms of the Creative commons Attribution License, which permits use, distribution, and reproduction in any medium, provided the original work is properly cited. PMID:25044035

Backbone and sidechain methyl Ile (δ1), Leu and Val chemical shift assignments of RDE-4 (1-243), an RNA interference initiation protein in C. elegans.

PubMed

Chiliveri, Sai Chaitanya; Kumar, Sonu; Marelli, Udaya Kiran; Deshmukh, Mandar V

2012-10-01

The RNAi pathway of several organisms requires presence of double stranded RNA binding proteins for functioning of Dicer in gene regulation. In C. elegans, a double stranded RNA binding protein, RDE-4 (385 aa, 44 kDa) recognizes long exogenous dsRNA and initiates the RNAi pathway. We have achieved complete backbone and stereospecific methyl sidechain Ile (δ1), Leu and Val chemical shifts of first 243 amino acids of RDE-4, namely RDE-4ΔC.

Three model space experiments on chemical reactions. [Gibbs adsorption, equilibrium shift and electrodeposition

NASA Technical Reports Server (NTRS)

Grodzka, P.; Facemire, B.

1977-01-01

Three investigations conducted aboard Skylab IV and Apollo-Soyuz involved phenomena that are of interest to the biochemistry community. The formaldehyde clock reaction and the equilibrium shift reaction experiments conducted aboard Apollo Soyuz demonstrate the effect of low-g foams or air/liquid dispersions on reaction rate and chemical equilibrium. The electrodeposition reaction experiment conducted aboard Skylab IV demonstrate the effect of a low-g environment on an electrochemical displacement reaction. The implications of the three space experiments for various applications are considered.

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

NASA Astrophysics Data System (ADS)

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

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

Chemical shift and zone-folding effects on the energy gaps of GaAs-AlAs (001) superlattices

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

Zhang, S.B.; Cohen, M.L.; Louie, S.G.

1991-04-15

The chemical shift and zone-folding effects obtained from quasiparticle calculations for ultrathin GaAs-AlAs superlattices are incorporated within a Kronig-Penny model for superlattices of the arbitrary lattice period. We determine that superlattices with lattice periods in the range of 3{times}3 to 9{times}9 have an {ital X}-derived pseudodirect gap. This result explains both the results from first-principles calculations for ultrathin superlattices and those from experiments for a broader lattice period.

Cortico-pontine theta carrier frequency phase shift across sleep/wake states following monoaminergic lesion in rat.

PubMed

Kalauzi, Aleksandar; Spasic, Sladjana; Petrovic, Jelena; Ciric, Jelena; Saponjic, Jelena

2012-06-01

This study was aimed to explore the sleep/wake states related cortico-pontine theta carrier frequency phase shift following a systemically induced chemical axotomy of the monoaminergic afferents within a brain of the freely moving rats. Our experiments were performed in 14 adult, male Sprague Dawley rats, chronically implanted for sleep recording. We recorded sleep during baseline condition, following sham injection (saline i.p. 1 ml/kg), and every week for 5 weeks following injection of the systemic neurotoxins (DSP-4 or PCA; 1 ml/kg, i.p.) for chemical axotomy of the locus coeruleus (LC) and dorsal raphe (DR) axon terminals. After sleep/wake states identification, FFT analysis was performed on 5 s epochs. Theta carrier frequency phase shift (∆Φ) was calculated for each epoch by averaging theta Fourier component phase shifts, and the ∆Φ values were plotted for each rat in control condition and 28 days following the monoaminergic lesions, as a time for permanently established DR or LC chemical axotomy. Calculated group averages have shown that ∆Φ increased between pons and cortex significantly in all sleep/wake states (Wake, NREM and REM) following the monoaminergic lesions, with respect to controls. Monoaminergic lesions established the pontine leading role in the brain theta oscillations during all sleep/wake states.

The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank

PubMed Central

Westbrook, John D.; Shao, Chenghua; Feng, Zukang; Zhuravleva, Marina; Velankar, Sameer; Young, Jasmine

2015-01-01

Summary: The Chemical Component Dictionary (CCD) is a chemical reference data resource that describes all residue and small molecule components found in Protein Data Bank (PDB) entries. The CCD contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, chemical descriptors, systematic chemical names and idealized coordinates. The content, preparation, validation and distribution of this CCD chemical reference dataset are described. Availability and implementation: The CCD is updated regularly in conjunction with the scheduled weekly release of new PDB structure data. The CCD and amino acid variant reference datasets are hosted in the public PDB ftp repository at ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz, ftp://ftp.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif.gz, and its mirror sites, and can be accessed from http://wwpdb.org. Contact: jwest@rcsb.rutgers.edu. Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25540181

The characteristics of vibrotactile perception threshold among shipyard workers in a tropical environment.

PubMed

Tamrin, Shamsul Bahri Mohd; Jamalohdin, Mohd Nazri; Ng, Yee Guan; Maeda, Setsuo; Ali, Nurul Asyiqin Mohd

2012-01-01

The objectives of this study are to determine the prevalence of hand-arm vibration syndrome (HAVS) and the characteristics of the vibrotactile perception threshold (VPT) among users of hand-held vibrating tools working in a tropical environment. A cross sectional study was done among 47 shipyard workers using instruments and a questionnaire to determine HAVS related symptoms. The vibration acceleration magnitude was determined using a Human Vibration Meter (Maestro). A P8 Pallesthesiometer (EMSON-MAT, Poland) was used to determine the VPT of index and little finger at frequencies of 31.5 Hz and 125 Hz. The mean reference threshold shift was determined from the reference threshold shift derived from the VPT value. The results show a moderate prevalence of HAVS (49%) among the shipyard workers. They were exposed to the same high intensity level of HAVS (mean = 4.19 ± 1.94 m/s(2)) from the use of vibrating hand-held tools. The VPT values were found to be higher for both fingers and both frequencies (index, 31.5 Hz = 110.91 ± 7.36 dB, 125 Hz = 117.0 ± 10.25 dB; little, 31.5 Hz = 110.70 ± 6.75 dB, 125 Hz = 117.71 ± 10.25 dB) compared to the normal healthy population with a mean threshold shift of between 9.20 to 10.61 decibels. The frequency of 31.5 Hz had a higher percentage of positive mean reference threshold shift (index finger=93.6%, little finger=100%) compared to 125 Hz (index finger=85.1%, little finger=78.7%). In conclusion, the prevalence of HAVS was lower than those working in a cold environment; however, all workers had a higher mean VPT value compared to the normal population with all those reported as having HAVS showing a positive mean reference threshold shift of VPT value.

Methodology for Generating Conflict Scenarios by Time Shifting Recorded Traffic Data

NASA Technical Reports Server (NTRS)

Paglione, Mike; Oaks, Robert; Bilimoria, Karl D.

2003-01-01

A methodology is presented for generating conflict scenarios that can be used as test cases to estimate the operational performance of a conflict probe. Recorded air traffic data is time shifted to create traffic scenarios featuring conflicts with characteristic properties similar to those encountered in typical air traffic operations. First, a reference set of conflicts is obtained from trajectories that are computed using birth points and nominal flight plans extracted from recorded traffic data. Distributions are obtained for several primary properties (e.g., encounter angle) that are most likely to affect the performance of a conflict probe. A genetic algorithm is then utilized to determine the values of time shifts for the recorded track data so that the primary properties of conflicts generated by the time shifted data match those of the reference set. This methodology is successfully demonstrated using recorded traffic data for the Memphis Air Route Traffic Control Center; a key result is that the required time shifts are less than 5 min for 99% of the tracks. It is also observed that close matching of the primary properties used in this study additionally provides a good match for some other secondary properties.

Modeling nuclear field shift isotope fractionation in crystals

NASA Astrophysics Data System (ADS)

Schauble, E. A.

2013-12-01

In this study nuclear field shift fractionations in solids (and chemically similar liquids) are estimated using calibrated density functional theory calculations. The nuclear field shift effect is a potential driver of mass independent isotope fractionation(1,2), especially for elements with high atomic number such as Hg, Tl and U. This effect is caused by the different shapes and volumes of isotopic nuclei, and their interactions with electronic structures and energies. Nuclear field shift isotope fractionations can be estimated with first principles methods, but the calculations are computationally difficult, limiting most theoretical studies so far to small gas-phase molecules and molecular clusters. Many natural materials of interest are more complex, and it is important to develop ways to estimate field shift effects that can be applied to minerals, solutions, in biomolecules, and at mineral-solution interfaces. Plane-wave density functional theory, in combination with the projector augmented wave method (DFT-PAW), is much more readily adapted to complex materials than the relativistic all-electron calculations that have been the focus of most previous studies. DFT-PAW is a particularly effective tool for studying crystals with periodic boundary conditions, and may also be incorporated into molecular dynamics simulations of solutions and other disordered phases. Initial calibrations of DFT-PAW calculations against high-level all-electron models of field shift fractionation suggest that there may be broad applicability of this method to a variety of elements and types of materials. In addition, the close relationship between the isomer shift of Mössbauer spectroscopy and the nuclear field shift isotope effect makes it possible, at least in principle, to estimate the volume component of field shift fractionations in some species that are too complex even for DFT-PAW models, so long as there is a Mössbauer isotope for the element of interest. Initial results will be presented for calculations of liquid-vapor fractionation of cadmium and mercury, which indicate an affinity for heavy isotopes in the liquid phase. In the case of mercury the results match well with recent experiments. Mössbauer-calibrated fractionation factors will also be presented for tin and platinum species. Platinum isotope behaviour in metals appears to particularly interesting, with very distinct isotope partitioning behaviour for iron-rich alloys, relative to pure platinum metal. References: 1) Bigeleisen, J. (1996) J. Am. Chem. Soc. 118, 3676-3680. 2) Nomura, M., Higuchi, N., Fujii, Y. (1996) J. Am. Chem. Soc. 118, 9127-9130.

Synthesis of reference compounds related to Chemical Weapons Convention for verification and drug development purposes – a Brazilian endeavour

NASA Astrophysics Data System (ADS)

Cavalcante, S. F. A.; de Paula, R. L.; Kitagawa, D. A. S.; Barcellos, M. C.; Simas, A. B. C.; Granjeiro, J. M.

2018-03-01

This paper deals with challenges that Brazilian Army Organic Synthesis Laboratory has been going through to access reference compounds related to the Chemical Weapons Convention in order to support verification analysis and for research of novel antidotes. Some synthetic procedures to produce the chemicals, as well as Quality Assurance issues and a brief introduction of international agreements banning chemical weapons are also presented.

Potentiation of Chemical Ototoxicity by Noise

PubMed Central

Steyger, Peter S.

2010-01-01

High-intensity and/or prolonged exposure to noise causes temporary or permanent threshold shifts in auditory perception. Occupational exposure to solvents or administration of clinically important drugs, such as aminoglycoside antibiotics and cisplatin, also can induce permanent hearing loss. The mechanisms by which these ototoxic insults cause auditory dysfunction are still being unraveled, yet they share common sequelae, particularly generation of reactive oxygen species, that ultimately lead to hearing loss and deafness. Individuals are frequently exposed to ototoxic chemical contaminants (e.g., fuel) and noise simultaneously in a variety of work and recreational environments. Does simultaneous exposure to chemical ototoxins and noise potentiate auditory dysfunction? Exposure to solvent vapor in noisy environments potentiates the permanent threshold shifts induced by noise alone. Moderate noise levels potentiate both aminoglycoside- and cisplatin-induced ototoxicity in both rate of onset and in severity of auditory dysfunction. Thus, simultaneous exposure to chemical ototoxins and moderate levels of noise can potentiate auditory dysfunction. Preventing the ototoxic synergy of noise and chemical ototoxins requires removing exposure to ototoxins and/or attenuating noise exposure levels when chemical ototoxins are present. PMID:20523755

Limitations of carbon footprint as indicator of environmental sustainability.

PubMed

Laurent, Alexis; Olsen, Stig I; Hauschild, Michael Z

2012-04-03

Greenhouse gas accountings, commonly referred to with the popular term carbon footprints (CFP), are a widely used metric of climate change impacts and the main focus of many sustainability policies among companies and authorities. However, environmental sustainability concerns not just climate change but also other environmental problems, like chemical pollution or depletion of natural resources, and the focus on CFP brings the risk of problem shifting when reductions in CFP are obtained at the expense of increase in other environmental impacts. But how real is this risk? Here, we model and analyze the life cycle impacts from about 4000 different products, technologies, and services taken from several sectors, including energy generation, transportation, material production, infrastructure, and waste management. By investigating the correlations between the CFP and 13 other impact scores, we show that some environmental impacts, notably those related to emissions of toxic substances, often do not covary with climate change impacts. In such situations, carbon footprint is a poor representative of the environmental burden of products, and environmental management focused exclusively on CFP runs the risk of inadvertently shifting the problem to other environmental impacts when products are optimized to become more "green". These findings call for the use of more broadly encompassing tools to assess and manage environmental sustainability.

Characterization of Cleaning and Disinfecting Tasks and Product Use Among Hospital Occupations

PubMed Central

Saito, Rena; Virji, M. Abbas; Henneberger, Paul K.; Humann, Michael J.; LeBouf, Ryan F.; Stanton, Marcia L.; Liang, Xiaoming; Stefaniak, Aleksandr B.

2016-01-01

Background Healthcare workers have an elevated prevalence of asthma and related symptoms associated with the use of cleaning/disinfecting products. The objective of this study was to identify and characterize cleaning/disinfecting tasks and products used among hospital occupations. Methods Workers from 14 occupations at five hospitals were monitored for 216 shifts, and work tasks and products used were recorded at five-minute intervals. The major chemical constituents of each product were identified from safety data sheets. Results Cleaning and disinfecting tasks were performed with a high frequency at least once per shift in many occupations. Medical equipment preparers, housekeepers, floor strippers/waxers, and endoscopy technicians spent on average 108–177 min/shift performing cleaning/disinfecting tasks. Many occupations used products containing amines and quaternary ammonium compounds for > 100 min/shift. Conclusions This analysis demonstrates that many occupations besides housekeeping incur exposures to cleaning/disinfecting products, albeit for different durations and using products containing different chemicals. PMID:25351791

30 CFR 47.54 - Availability of an MSDS.

Code of Federal Regulations, 2010 CFR

2010-07-01

... make MSDSs accessible to miners during each work shift for each hazardous chemical to which they may be exposed either— (a) At each work area where the hazardous chemical is produced or used, or (b) At an...

3D flexible alignment using 2D maximum common substructure: dependence of prediction accuracy on target-reference chemical similarity.

PubMed

Kawabata, Takeshi; Nakamura, Haruki

2014-07-28

A protein-bound conformation of a target molecule can be predicted by aligning the target molecule on the reference molecule obtained from the 3D structure of the compound-protein complex. This strategy is called "similarity-based docking". For this purpose, we develop the flexible alignment program fkcombu, which aligns the target molecule based on atomic correspondences with the reference molecule. The correspondences are obtained by the maximum common substructure (MCS) of 2D chemical structures, using our program kcombu. The prediction performance was evaluated using many target-reference pairs of superimposed ligand 3D structures on the same protein in the PDB, with different ranges of chemical similarity. The details of atomic correspondence largely affected the prediction success. We found that topologically constrained disconnected MCS (TD-MCS) with the simple element-based atomic classification provides the best prediction. The crashing potential energy with the receptor protein improved the performance. We also found that the RMSD between the predicted and correct target conformations significantly correlates with the chemical similarities between target-reference molecules. Generally speaking, if the reference and target compounds have more than 70% chemical similarity, then the average RMSD of 3D conformations is <2.0 Å. We compared the performance with a rigid-body molecular alignment program based on volume-overlap scores (ShaEP). Our MCS-based flexible alignment program performed better than the rigid-body alignment program, especially when the target and reference molecules were sufficiently similar.

Interspecies chemical communication in bacterial development.

PubMed

Straight, Paul D; Kolter, Roberto

2009-01-01

Our view of bacteria, from the earliest observations through the heyday of antibiotic discovery, has shifted dramatically. We recognize communities of bacteria as integral and functionally important components of diverse habitats, ranging from soil collectives to the human microbiome. To function as productive communities, bacteria coordinate metabolic functions, often requiring shifts in growth and development. The hallmark of cellular development, which we characterize as physiological change in response to environmental stimuli, is a defining feature of many bacterial interspecies interactions. Bacterial communities rely on chemical exchanges to provide the cues for developmental change. Traditional methods in microbiology focus on isolation and characterization of bacteria in monoculture, separating the organisms from the surroundings in which interspecies chemical communication has relevance. Developing multispecies experimental systems that incorporate knowledge of bacterial physiology and metabolism with insights from biodiversity and metagenomics shows great promise for understanding interspecies chemical communication in the microbial world.

Optimized multiple quantum MAS lineshape simulations in solid state NMR

NASA Astrophysics Data System (ADS)

Brouwer, William J.; Davis, Michael C.; Mueller, Karl T.

2009-10-01

The majority of nuclei available for study in solid state Nuclear Magnetic Resonance have half-integer spin I>1/2, with corresponding electric quadrupole moment. As such, they may couple with a surrounding electric field gradient. This effect introduces anisotropic line broadening to spectra, arising from distinct chemical species within polycrystalline solids. In Multiple Quantum Magic Angle Spinning (MQMAS) experiments, a second frequency dimension is created, devoid of quadrupolar anisotropy. As a result, the center of gravity of peaks in the high resolution dimension is a function of isotropic second order quadrupole and chemical shift alone. However, for complex materials, these parameters take on a stochastic nature due in turn to structural and chemical disorder. Lineshapes may still overlap in the isotropic dimension, complicating the task of assignment and interpretation. A distributed computational approach is presented here which permits simulation of the two-dimensional MQMAS spectrum, generated by random variates from model distributions of isotropic chemical and quadrupole shifts. Owing to the non-convex nature of the residual sum of squares (RSS) function between experimental and simulated spectra, simulated annealing is used to optimize the simulation parameters. In this manner, local chemical environments for disordered materials may be characterized, and via a re-sampling approach, error estimates for parameters produced. Program summaryProgram title: mqmasOPT Catalogue identifier: AEEC_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 3650 No. of bytes in distributed program, including test data, etc.: 73 853 Distribution format: tar.gz Programming language: C, OCTAVE Computer: UNIX/Linux Operating system: UNIX/Linux Has the code been vectorised or parallelized?: Yes RAM: Example: (1597 powder angles) × (200 Samples) × (81 F2 frequency pts) × (31 F1 frequency points) = 3.5M, SMP AMD opteron Classification: 2.3 External routines: OCTAVE ( http://www.gnu.org/software/octave/), GNU Scientific Library ( http://www.gnu.org/software/gsl/), OPENMP ( http://openmp.org/wp/) Nature of problem: The optimal simulation and modeling of multiple quantum magic angle spinning NMR spectra, for general systems, especially those with mild to significant disorder. The approach outlined and implemented in C and OCTAVE also produces model parameter error estimates. Solution method: A model for each distinct chemical site is first proposed, for the individual contribution of crystallite orientations to the spectrum. This model is averaged over all powder angles [1], as well as the (stochastic) parameters; isotropic chemical shift and quadrupole coupling constant. The latter is accomplished via sampling from a bi-variate Gaussian distribution, using the Box-Muller algorithm to transform Sobol (quasi) random numbers [2]. A simulated annealing optimization is performed, and finally the non-linear jackknife [3] is applied in developing model parameter error estimates. Additional comments: The distribution contains a script, mqmasOpt.m, which runs in the OCTAVE language workspace. Running time: Example: (1597 powder angles) × (200 Samples) × (81 F2 frequency pts) × (31 F1 frequency points) = 58.35 seconds, SMP AMD opteron. References:S.K. Zaremba, Annali di Matematica Pura ed Applicata 73 (1966) 293. H. Niederreiter, Random Number Generation and Quasi-Monte Carlo Methods, SIAM, 1992. T. Fox, D. Hinkley, K. Larntz, Technometrics 22 (1980) 29.

High numerical aperture multilayer Laue lenses

DOE PAGES

Morgan, Andrew J.; Prasciolu, Mauro; Andrejczuk, Andrzej; ...

2015-06-01

The ever-increasing brightness of synchrotron radiation sources demands improved X-ray optics to utilise their capability for imaging and probing biological cells, nanodevices, and functional matter on the nanometer scale with chemical sensitivity. Here we demonstrate focusing a hard X-ray beam to an 8 nm focus using a volume zone plate (also referred to as a wedged multilayer Laue lens). This lens was constructed using a new deposition technique that enabled the independent control of the angle and thickness of diffracting layers to microradian and nanometer precision, respectively. This ensured that the Bragg condition is satisfied at each point along themore » lens, leading to a high numerical aperture that is limited only by its extent. We developed a phase-shifting interferometric method based on ptychography to characterise the lens focus. The precision of the fabrication and characterisation demonstrated here provides the path to efficient X-ray optics for imaging at 1 nm resolution.« less

Computational NMR, IR/RAMAN calculations in sodium pravastatin: Investigation of the Self-Assembled Nanostructure of Pravastatin-LDH (Layered Double Hydroxides) Systems

NASA Astrophysics Data System (ADS)

Petersen, Philippe; Cunha, Vanessa; Gonçalves, Marcos; Petrilli, Helena; Constantino, Vera; Instituto de Física, Departamento de Física de Materiais e Mecânica Team; Instituto de Química, Departamento de Química Fundamental Team

2013-03-01

Layered double hydroxides (LDH) can be used as nanocontainers for immobilization of Pravastatin, in order to obtain suitable drug carriers. The material's structure and spectroscopic properties were analyzed by NMR, IR/RAMAN and supported by theoretical calculations. Density Functional Theory (DFT) calculations were performed using the Gaussian03 package. The geometry optimizations were performed considering the single crystal X-ray diffraction data of tert-octylamonium salt of Pravastatin. Tetramethylsilane (TMS), obtained with the same basis set, was used as reference for calculating the chemical shift of 13C. A scaling factor was used to compare theoretical and experimental harmonic vibrational frequencies. Through the NMR and IR/RAMAN spectra, we were able to make precise assignments of the NMR and IR/RAMAN of Sodium Pravastatin. We acknowledge support from CAPES, INEO and CNPQ.

[Shiftwork and health--experience from a chemical company].

PubMed

Oberlinner, C; Lang, S; Nasterlack, M; Yong, M

2013-03-01

Shiftwork is an essential part of our society. At the same time scientific evaluations demonstrate possible negative effects of shiftwork on the health status of the employees. Against this background we performed different studies to evaluate these effects within the specific shift system in a large chemical site in Germany. METHODS AND STUDY GROUP: To evaluate the impact of the different working times on job-related stress perception and work-life-balance we performed a cross-sectional study with 1494 blue collar workers (825 shift- and 669 day workers). Employees working in the rotating shift system reported lower frequencies of perceived time pressure (p = 0.008), and lower stress levels (p = 0.01), compared to the day workers. No significant difference was found with regard to work-life-balance and other aspects of job-related stress perception within both groups. Against the general opinion and study-results in the past we did not find a negative effect of our shift-system on self-reported stress. These results are in accordance with results of other cohort-studies on the specific shift system within the company demonstrating no difference in the health status of our shift workers compared to day workers. © Georg Thieme Verlag KG Stuttgart · New York.

Work Shifts and Disability: A National View.

ERIC Educational Resources Information Center

Presser, Harriet B.; Altman, Barbara

2002-01-01

More than one-fifth of employed persons with disabilities work late or rotating shifts, about the same as nondisabled workers. Day workers with disabilities receive lower hourly wages than nondisabled workers. Except for men, nonday workers with disabilities receive wages similar to their nondisabled counterparts. (Contains 27 references.)…

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

PubMed

Girreser, Ulrich; Rösner, Peter; Vasilev, Andrej

2016-07-01

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

Relating the Chemical Composition of Dissolved Organic Matter Draining Permafrost Soils to its Photochemical Degradation in Arctic Surface Waters.

NASA Astrophysics Data System (ADS)

Ward, C.; Cory, R. M.

2015-12-01

Thawing permafrost soils are expected to shift the chemical composition of DOM exported to and degraded in arctic surface waters. While DOM photo-degradation is an important component of the freshwater C cycle in the Arctic, the molecular controls on DOM photo-degradation remain poorly understood, making it difficult to predict how shifting chemical composition may alter DOM photo-degradation in arctic surface waters. To address this knowledge gap, we quantified the susceptibility of DOM draining the shallow organic mat and the deeper permafrost layer to complete photo-oxidation to CO₂ and partial photo-oxidation to compounds that remain in the DOM pool, and investigated changes in DOM chemical composition following sunlight exposure. DOM leached from the organic mat contained higher molecular weight, more oxidized and unsaturated aromatic species compared to permafrost DOM. Despite significant differences in initial chemical composition, permafrost and organic mat DOM had similar susceptibilities to complete photo-oxidation to CO₂. Concurrent losses of carboxyl moieties and shifts in chemical composition during photo-degradation indicated that carboxyl-rich tannin-like compounds in both DOM sources were likely photo-decarboxylated to CO₂. Permafrost DOM had a higher susceptibility to partial photo-oxidation compared to organic mat DOM, potentially due to a lower abundance of phenolic compounds that act as "antioxidants" and slow the oxidation of DOM. These results demonstrated how chemical composition controls the photo-degradation of DOM in arctic surface waters, and that DOM photo-degradation will likely remain an important component of the freshwater C budget in the Arctic with increased export of permafrost DOM to surface waters.

Alternate binding modes for a ubiquitin-SH3 domain interaction studied by NMR spectroscopy.

PubMed

Korzhnev, Dmitry M; Bezsonova, Irina; Lee, Soyoung; Chalikian, Tigran V; Kay, Lewis E

2009-02-20

Surfaces of many binding domains are plastic, enabling them to interact with multiple targets. An understanding of how they bind and recognize their partners is therefore predicated on characterizing such dynamic interfaces. Yet, these interfaces are difficult to study by standard biophysical techniques that often 'freeze' out conformations or that produce data averaged over an ensemble of conformers. In this study, we used NMR spectroscopy to study the interaction between the C-terminal SH3 domain of CIN85 and ubiquitin that involves the 'classical' binding sites of these proteins. Notably, chemical shift titration data of one target with another and relaxation dispersion data that report on millisecond time scale exchange processes are both well fit to a simple binding model in which free protein is in equilibrium with a single bound conformation. However, dissociation constants and chemical shift differences between free and bound states measured from both classes of experiment are in disagreement. It is shown that the data can be reconciled by considering three-state binding models involving two distinct bound conformations. By combining titration and dispersion data, kinetic and thermodynamic parameters of the three-state binding reaction are obtained along with chemical shifts for each state. A picture emerges in which one bound conformer has increased entropy and enthalpy relative to the second and chemical shifts similar to that of the free state, suggesting a less packed interface. This study provides an example of the interplay between entropy and enthalpy to fine-tune molecular interactions involving the same binding surfaces.

"Ask Ernö": a self-learning tool for assignment and prediction of nuclear magnetic resonance spectra.

PubMed

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

2016-01-01

We present "Ask Ernö", a self-learning system for the automatic analysis of NMR spectra, consisting of integrated chemical shift assignment and prediction tools. The output of the automatic assignment component initializes and improves a database of assigned protons that is used by the chemical shift predictor. In turn, the predictions provided by the latter facilitate improvement of the assignment process. Iteration on these steps allows Ask Ernö to improve its ability to assign and predict spectra without any prior knowledge or assistance from human experts. This concept was tested by training such a system with a dataset of 2341 molecules and their (1)H-NMR spectra, and evaluating the accuracy of chemical shift predictions on a test set of 298 partially assigned molecules (2007 assigned protons). After 10 iterations, Ask Ernö was able to decrease its prediction error by 17 %, reaching an average error of 0.265 ppm. Over 60 % of the test chemical shifts were predicted within 0.2 ppm, while only 5 % still presented a prediction error of more than 1 ppm. Ask Ernö introduces an innovative approach to automatic NMR analysis that constantly learns and improves when provided with new data. Furthermore, it completely avoids the need for manually assigned spectra. This system has the potential to be turned into a fully autonomous tool able to compete with the best alternatives currently available.Graphical abstractSelf-learning loop. Any progress in the prediction (forward problem) will improve the assignment ability (reverse problem) and vice versa.

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

PubMed

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

2018-02-01

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

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

PubMed

Hafsa, Noor E; Arndt, David; Wishart, David S

2015-07-01

The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Long-Term Experimental Acidification Drives Watershed Scale Shift in Dissolved Organic Matter Composition and Flux.

PubMed

SanClements, Michael D; Fernandez, Ivan J; Lee, Robert H; Roberti, Joshua A; Adams, Mary Beth; Rue, Garret A; McKnight, Diane M

2018-03-06

Over the last several decades dissolved organic carbon concentrations (DOC) in surface waters have increased throughout much of the northern hemisphere. Several hypotheses have been proposed regarding the drivers of this phenomenon including decreased sulfur (S) deposition working via an acidity- change mechanism. Using fluorescence spectroscopy and data from two long-term (24+ years at completion of this study) whole watershed acidification experiments, that is, the Bear Brook Watershed in Maine (BBWM) and Fernow Experimental Forest in West Virginia (FEF) allowed us to control for factors other than the acidity-change mechanism (e.g., differing vegetation, shifting climate), resulting in the first study we are aware of where the acidity change mechanism could be experimentally isolated at the whole ecosystem and decadal scales as the driver of shifts in DOM dynamics. The multidecadal record of stream chemistry at BBWM demonstrates a significantly lower DOC concentration in the treated compared to the reference watershed. Additionally, at both BBWM and FEF we found significant and sustained differences in stream fluorescence index (FI) between the treated and reference watersheds, with the reference watersheds demonstrating a stronger terrestrial DOM signature. These data, coupled with evidence of pH shifts in upper soil horizons support the hypotheses that declines in S deposition are driving changes in the solubility of soil organic matter and increased flux of terrestrial DOC to water bodies.

MRS of pilocytic astrocytoma: The peak at 2 ppm may not be NAA.

PubMed

Tamrazi, Benita; Nelson, Marvin D; Blüml, Stefan

2017-08-01

To determine whether the chemical shift of residual N-acetylaspartate (NAA) signal in pilocytic astrocytomas (PA) is consistent with the position of the NAA peak in controls. MR spectra from 27 pediatric World Health Organization (WHO) grade I pilocytic astrocytoma patients, fifteen patients with WHO grade II and high-grade (III-IV) astrocytomas, and 36 controls were analyzed. All spectra were acquired with a short echo time (35 ms), single voxel point-resolved spectroscopy sequence on clinical 3 tesla scanners. Fully automated LCModel software was used for processing, which included the fitting of peak positions for NAA and creatine (Cr). The chemical shift difference between the NAA and Cr peaks was significantly smaller (by 0.016 ± 0.005 parts per million, P < 1e-10) in PAs than in controls and was also smaller than what was observed in infiltrative astrocytomas. The chemical shift position of the residual NAA peak in PAs is not consistent with NAA. The signal likely originates from an N-acetyl group of one or more other chemicals such as N-acetylated sugars. Magn Reson Med 78:452-456, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

FTIR, FT-Raman, FT-NMR, UV-visible and quantum chemical investigations of 2-amino-4-methylbenzothiazole.

PubMed

Arjunan, V; Sakiladevi, S; Rani, T; Mythili, C V; Mohan, S

2012-03-01

The FT-IR (4000-400 cm(-1)) and FT-Raman (4000-100 cm(-1)) spectral measurements and complete assignments of the observed spectra of 2-amino-4-methylbenzothiazole (2A4MBT) have been proposed. Ab initio and DFT calculations have been performed and the structural parameters of the compound were determined from the optimised geometry with 6-31G(d,p), 6-311++G(d,p) and cc-pVDZ basis sets and giving energies, harmonic vibrational frequencies, depolarisation ratios, IR intensities and Raman activities. (1)H and (13)C NMR spectra were recorded and (1)H and (13)C nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO, LUMO and band gap energies were measured by time-dependent DFT (TD-DFT) approach. The geometric parameters, energies, harmonic vibrational frequencies, IR intensities, Raman activities chemical shifts and absorption wavelengths were compared with the available experimental data of the molecule. The influences of methyl and amino groups on the skeletal modes and on the proton chemical shifts have been investigated. Copyright © 2011 Elsevier B.V. All rights reserved.

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

PubMed

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

2011-06-07

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

Animal-Free Chemical Safety Assessment

PubMed Central

Loizou, George D.

2016-01-01

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

Multidimensional High-Resolution Magic Angle Spinning and Solution-State NMR Characterization of 13C-labeled Plant Metabolites and Lignocellulose

PubMed Central

Mori, Tetsuya; Tsuboi, Yuuri; Ishida, Nobuhiro; Nishikubo, Nobuyuki; Demura, Taku; Kikuchi, Jun

2015-01-01

Lignocellulose, which includes mainly cellulose, hemicellulose, and lignin, is a potential resource for the production of chemicals and for other applications. For effective production of materials derived from biomass, it is important to characterize the metabolites and polymeric components of the biomass. Nuclear magnetic resonance (NMR) spectroscopy has been used to identify biomass components; however, the NMR spectra of metabolites and lignocellulose components are ambiguously assigned in many cases due to overlapping chemical shift peaks. Using our 13C-labeling technique in higher plants such as poplar samples, we demonstrated that overlapping peaks could be resolved by three-dimensional NMR experiments to more accurately assign chemical shifts compared with two-dimensional NMR measurements. Metabolites of the 13C-poplar were measured by high-resolution magic angle spinning NMR spectroscopy, which allows sample analysis without solvent extraction, while lignocellulose components of the 13C-poplar dissolved in dimethylsulfoxide/pyridine solvent were analyzed by solution-state NMR techniques. Using these methods, we were able to unambiguously assign chemical shifts of small and macromolecular components in 13C-poplar samples. Furthermore, using samples of less than 5 mg, we could differentiate between two kinds of genes that were overexpressed in poplar samples, which produced clearly modified plant cell wall components. PMID:26143886

THE INFLUENCE OF GLOBAL CLIMATE CHANGE ON THE SCIENTIFIC FOUNDATIONS AND APPLICATIONS OF ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY: INTRODUCTION TO A SETAC INTERNATIONAL WORKSHOP

PubMed Central

Stahl, Ralph G; Hooper, Michael J; Balbus, John M; Clements, William; Fritz, Alyce; Gouin, Todd; Helm, Roger; Hickey, Christopher; Landis, Wayne; Moe, S Jannicke

2013-01-01

This is the first of seven papers resulting from a Society of Environmental Toxicology and Chemistry (SETAC) international workshop titled “The Influence of Global Climate Change on the Scientific Foundations and Applications of Environmental Toxicology and Chemistry.” The workshop involved 36 scientists from 11 countries and was designed to answer the following question: How will global climate change influence the environmental impacts of chemicals and other stressors and the way we assess and manage them in the environment? While more detail is found in the complete series of articles, some key consensus points are as follows: (1) human actions (including mitigation of and adaptation to impacts of global climate change [GCC]) may have as much influence on the fate and distribution of chemical contaminants as does GCC, and modeled predictions should be interpreted cautiously; (2) climate change can affect the toxicity of chemicals, but chemicals can also affect how organisms acclimate to climate change; (3) effects of GCC may be slow, variable, and difficult to detect, though some populations and communities of high vulnerability may exhibit responses sooner and more dramatically than others; (4) future approaches to human and ecological risk assessments will need to incorporate multiple stressors and cumulative risks considering the wide spectrum of potential impacts stemming from GCC; and (5) baseline/reference conditions for estimating resource injury and restoration/rehabilitation will continually shift due to GCC and represent significant challenges to practitioners. Environ. Toxicol. Chem. 2013;32:13–19. © 2012 SETAC PMID:23097130

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

PubMed

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

2015-12-10

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

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

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

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

PubMed

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

2018-02-09

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

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

PubMed

Kara, Yesim Saniye

2015-01-01

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

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

PubMed

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

2014-12-04

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

Stuttering Thoughts: Negative Self-Referent Thinking Is Less Sensitive to Aversive Outcomes in People with Higher Levels of Depressive Symptoms

PubMed Central

Iijima, Yudai; Takano, Keisuke; Boddez, Yannick; Raes, Filip; Tanno, Yoshihiko

2017-01-01

Learning theories of depression have proposed that depressive cognitions, such as negative thoughts with reference to oneself, can develop through a reinforcement learning mechanism. This negative self-reference is considered to be positively reinforced by rewarding experiences such as genuine support from others after negative self-disclosure, and negatively reinforced by avoidance of potential aversive situations. The learning account additionally predicts that negative self-reference would be maintained by an inability to adjust one’s behavior when negative self-reference no longer leads to such reward. To test this prediction, we designed an adapted version of the reversal-learning task. In this task, participants were reinforced to choose and engage in either negative or positive self-reference by probabilistic economic reward and punishment. Although participants were initially trained to choose negative self-reference, the stimulus-reward contingencies were reversed to prompt a shift toward positive self-reference (Study 1) and a further shift toward negative self-reference (Study 2). Model-based computational analyses showed that depressive symptoms were associated with a low learning rate of negative self-reference, indicating a high level of reward expectancy for negative self-reference even after the contingency reversal. Furthermore, the difficulty in updating outcome predictions of negative self-reference was significantly associated with the extent to which one possesses negative self-images. These results suggest that difficulty in adjusting action-outcome estimates for negative self-reference increases the chance to be faced with negative aspects of self, which may result in depressive symptoms. PMID:28824511

Stuttering Thoughts: Negative Self-Referent Thinking Is Less Sensitive to Aversive Outcomes in People with Higher Levels of Depressive Symptoms.

PubMed

Iijima, Yudai; Takano, Keisuke; Boddez, Yannick; Raes, Filip; Tanno, Yoshihiko

2017-01-01

Learning theories of depression have proposed that depressive cognitions, such as negative thoughts with reference to oneself, can develop through a reinforcement learning mechanism. This negative self-reference is considered to be positively reinforced by rewarding experiences such as genuine support from others after negative self-disclosure, and negatively reinforced by avoidance of potential aversive situations. The learning account additionally predicts that negative self-reference would be maintained by an inability to adjust one's behavior when negative self-reference no longer leads to such reward. To test this prediction, we designed an adapted version of the reversal-learning task. In this task, participants were reinforced to choose and engage in either negative or positive self-reference by probabilistic economic reward and punishment. Although participants were initially trained to choose negative self-reference, the stimulus-reward contingencies were reversed to prompt a shift toward positive self-reference (Study 1) and a further shift toward negative self-reference (Study 2). Model-based computational analyses showed that depressive symptoms were associated with a low learning rate of negative self-reference, indicating a high level of reward expectancy for negative self-reference even after the contingency reversal. Furthermore, the difficulty in updating outcome predictions of negative self-reference was significantly associated with the extent to which one possesses negative self-images. These results suggest that difficulty in adjusting action-outcome estimates for negative self-reference increases the chance to be faced with negative aspects of self, which may result in depressive symptoms.

Changes in the referent body location and configuration may underlie human gait, as confirmed by findings of multi-muscle activity minimizations and phase resetting.

PubMed

Feldman, Anatol G; Krasovsky, Tal; Baniña, Melanie C; Lamontagne, Anouk; Levin, Mindy F

2011-04-01

Locomotion is presumably guided by feed-forward shifts in the referent body location in the desired direction in the environment. We propose that the difference between the actual and the referent body locations is transmitted to neurons that virtually diminish this difference by appropriately changing the referent body configuration, i.e. the body posture at which muscles reach their recruitment thresholds. Muscles are activated depending on the gap between the actual and the referent body configurations resulting in a step being made to minimize this gap. This hypothesis implies that the actual and the referent leg configurations can match each other at certain phases of the gait cycle, resulting in minimization of leg muscle activity. We found several leg configurations at which EMG minima occurred, both during forward and backward gait. It was also found that the set of limb configurations associated with EMG minima can be changed by modifying the pattern of forward and backward gait. Our hypothesis predicts that, in response to perturbations of gait, the rate of shifts in the referent body location can temporarily be changed to avoid falling. The rate influences the phase of rhythmic limb movements during gait. Therefore, following the change in the rate of the referent body location, the whole gait pattern, for all four limbs, will irreversibly be shifted in time (long-lasting and global phase resetting) with only transient changes in the gait speed, swing and stance timing and cycle duration. Aside from transient changes in the duration of the swing and/or stance phase in response to perturbation, few previous studies have documented long-lasting and global phase resetting of human gait in response to perturbation. Such resetting was a robust finding in our study. By confirming the notion that feed-forward changes in the referent body location and configuration underlie human locomotion, this study solves the classical problem in the relationship between stability of posture and gait and advances the understanding of how human locomotion involves the whole body and is accomplished in a spatial frame of reference associated with the environment.

INCORPORATING NONCHEMICAL STRESSORS INTO CUMMULATIVE RISK ASSESSMENTS

EPA Science Inventory

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

Knowledge-based nonuniform sampling in multidimensional NMR.

PubMed

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

2011-07-01

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

Cantilevered probe detector with piezoelectric element

DOEpatents

Adams, Jesse D; Sulchek, Todd A; Feigin, Stuart C

2014-04-29

A disclosed chemical detection system for detecting a target material, such as an explosive material, can include a cantilevered probe, a probe heater coupled to the cantilevered probe, and a piezoelectric element disposed on the cantilevered probe. The piezoelectric element can be configured as a detector and/or an actuator. Detection can include, for example, detecting a movement of the cantilevered probe or a property of the cantilevered probe. The movement or a change in the property of the cantilevered probe can occur, for example, by adsorption of the target material, desorption of the target material, reaction of the target material and/or phase change of the target material. Examples of detectable movements and properties include temperature shifts, impedance shifts, and resonant frequency shifts of the cantilevered probe. The overall chemical detection system can be incorporated, for example, into a handheld explosive material detection system.

Cantilevered probe detector with piezoelectric element

DOEpatents

Adams, Jesse D; Sulchek, Todd A; Feigin, Stuart C

2013-04-30

A disclosed chemical detection system for detecting a target material, such as an explosive material, can include a cantilevered probe, a probe heater coupled to the cantilevered probe, and a piezoelectric element disposed on the cantilevered probe. The piezoelectric element can be configured as a detector and/or an actuator. Detection can include, for example, detecting a movement of the cantilevered probe or a property of the cantilevered probe. The movement or a change in the property of the cantilevered probe can occur, for example, by adsorption of the target material, desorption of the target material, reaction of the target material and/or phase change of the target material. Examples of detectable movements and properties include temperature shifts, impedance shifts, and resonant frequency shifts of the cantilevered probe. The overall chemical detection system can be incorporated, for example, into a handheld explosive material detection system.

Cantilevered probe detector with piezoelectric element

DOEpatents

Adams, Jesse D [Reno, NV; Sulchek, Todd A [Oakland, CA; Feigin, Stuart C [Reno, NV

2012-07-10

A disclosed chemical detection system for detecting a target material, such as an explosive material, can include a cantilevered probe, a probe heater coupled to the cantilevered probe, and a piezoelectric element disposed on the cantilevered probe. The piezoelectric element can be configured as a detector and/or an actuator. Detection can include, for example, detecting a movement of the cantilevered probe or a property of the cantilevered probe. The movement or a change in the property of the cantilevered probe can occur, for example, by adsorption of the target material, desorption of the target material, reaction of the target material and/or phase change of the target material. Examples of detectable movements and properties include temperature shifts, impedance shifts, and resonant frequency shifts of the cantilevered probe. The overall chemical detection system can be incorporated, for example, into a handheld explosive material detection system.

Cantilevered probe detector with piezoelectric element

DOEpatents

Adams, Jesse D.; Sulchek, Todd A.; Feigin, Stuart C.

2010-04-06

A disclosed chemical detection system for detecting a target material, such as an explosive material, can include a cantilevered probe, a probe heater coupled to the cantilevered probe, and a piezoelectric element disposed on the cantilevered probe. The piezoelectric element can be configured as a detector and/or an actuator. Detection can include, for example, detecting a movement of the cantilevered probe or a property of the cantilevered probe. The movement or a change in the property of the cantilevered probe can occur, for example, by adsorption of the target material, desorption of the target material, reaction of the target material and/or phase change of the target material. Examples of detectable movements and properties include temperature shifts, impedance shifts, and resonant frequency shifts of the cantilevered probe. The overall chemical detection system can be incorporated, for example, into a handheld explosive material detection system.

MODELING THE INTERACTION THRESHOLD: THE BREAK-POINT BETWEEN ADDITIVITY AND NON-ADDITIVITY

EPA Science Inventory

Dose-dependent changes in toxicity mechanisms of single chemicals may take place along the full dose-response spectrum. At high doses, the possibility exists for some steps in the principle mechanism of toxicity to shift to other mechanisms. The possibility of mechanism shifts fo...

Robustness of Fat Quantification using Chemical Shift Imaging

PubMed Central

Hansen, Katie H; Schroeder, Michael E; Hamilton, Gavin; Sirlin, Claude B; Bydder, Mark

2011-01-01

This purpose of this study was to investigate the effect of parameter changes that can potentially lead to unreliable measurements in fat quantification. Chemical shift imaging was performed using spoiled gradient echo sequences with systematic variations in the following: 2D/3D sequence, number of echoes, delta echo time, fractional echo factor, slice thickness, repetition time, flip angle, bandwidth, matrix size, flow compensation and field strength. Results indicated no significant (or significant but small) changes in fat fraction with parameter. The significant changes can be attributed to known effects of T1 bias and the two forms of noise bias. PMID:22055856

Sesterterpenes from a common marine sponge, Hyrtios erecta.

PubMed

Crews, P; Bescansa, P

1986-01-01

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

Backbone chemical shift assignments for the sensor domain of the Burkholderia pseudomallei histidine kinase RisS: "missing" resonances at the dimer interface.

PubMed

Buchko, Garry W; Edwards, Thomas E; Hewitt, Stephen N; Phan, Isabelle Q H; Van Voorhis, Wesley C; Miller, Samuel I; Myler, Peter J

2015-10-01

Using a deuterated sample, all the observable backbone (1)H(N), (15)N, (13)C(a), and (13)C' chemical shifts for the dimeric, periplasmic sensor domain of the Burkholderia pseudomallei histidine kinase RisS were assigned. Approximately one-fifth of the amide resonances are "missing" in the (1)H-(15)N HSQC spectrum and map primarily onto α-helices at the dimer interface observed in a crystal structure suggesting this region either undergoes intermediate timescale motion (μs-ms) and/or is heterogeneous.

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

PubMed

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

2016-06-13

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

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

PubMed Central

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

2017-01-01

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

Mercury Trapped Ion Frequency Standard for Ultra-Stable Reference Applications

NASA Technical Reports Server (NTRS)

Larsen, Kameron (Inventor); Burt, Eric A. (Inventor); Tjoelker, Robert L. (Inventor); Hamell, Robert L. (Inventor); Tucker, Blake C. (Inventor)

2017-01-01

An atomic clock including an ion trap assembly, a C-field coil positioned for generating a first magnetic field in the interrogation region of the ion trap assembly, a compensation coil positioned for generating a second magnetic field in the interrogation region, wherein the combination of the first and second magnetic fields produces an ion number-dependent second order Zeeman shift (Zeeman shift) in the resonance frequency that is opposite in sign to an ion number-dependent second order Doppler shift (Doppler shift) in the resonance frequency, the C-field coil has a radius selected using data indicating how changes in the radius affect an ion-number-dependent shift in the resonance frequency, such that a difference in magnitude between the Doppler shift and the Zeeman shift is controlled or reduced, and the resonance frequency, including the adjustment by the Zeeman shift, is used to obtain the frequency standard.

New methods to monitor emerging chemicals in the drinking water production chain.

PubMed

van Wezel, Annemarie; Mons, Margreet; van Delft, Wouter

2010-01-01

New techniques enable a shift in monitoring chemicals that affect water quality from mainly at the end product, tap water, towards monitoring during the whole process along the production chain. This is congruent with the 'HACCP' system (hazard analysis of critical control points) that is fairly well integrated into food production but less well in drinking water production. This shift brings about more information about source quality, the efficiency of treatment and distribution, and understanding of processes within the production chain, and therefore can lead to a more pro-active management of drinking water production. At present, monitoring is focused neither on emerging chemicals, nor on detection of compounds with chronic toxicity. We discuss techniques to be used, detection limits compared to quality criteria, data interpretation and possible interventions in production.

Aggregate exposure pathways in support of risk assessment

EPA Science Inventory

Over time, risk assessment has shifted from establishing relationships between exposure to a single chemical and a resulting adverse health outcome, to evaluating multiple chemicals and disease outcomes simultaneously. As a result, there is an increasing need to better understand...

Quality Certification, Regulation and Power in Fair Trade

ERIC Educational Resources Information Center

Renard, Marie-Christine

2005-01-01

This article examines governance changes and shifting power relations within the fair-labelling network. These shifts are framed analytically by reference to broader changes in the agrofoods sector tied to the increasingly key role played by quality relations and standards in the production and marketing of food. The author argues that evident…

The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank.

PubMed

Westbrook, John D; Shao, Chenghua; Feng, Zukang; Zhuravleva, Marina; Velankar, Sameer; Young, Jasmine

2015-04-15

The Chemical Component Dictionary (CCD) is a chemical reference data resource that describes all residue and small molecule components found in Protein Data Bank (PDB) entries. The CCD contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, chemical descriptors, systematic chemical names and idealized coordinates. The content, preparation, validation and distribution of this CCD chemical reference dataset are described. The CCD is updated regularly in conjunction with the scheduled weekly release of new PDB structure data. The CCD and amino acid variant reference datasets are hosted in the public PDB ftp repository at ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz, ftp://ftp.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif.gz, and its mirror sites, and can be accessed from http://wwpdb.org. jwest@rcsb.rutgers.edu. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Quantification of hepatic steatosis with T1-independent, T2-corrected MR imaging with spectral modeling of fat: blinded comparison with MR spectroscopy.

PubMed

Meisamy, Sina; Hines, Catherine D G; Hamilton, Gavin; Sirlin, Claude B; McKenzie, Charles A; Yu, Huanzhou; Brittain, Jean H; Reeder, Scott B

2011-03-01

To prospectively compare an investigational version of a complex-based chemical shift-based fat fraction magnetic resonance (MR) imaging method with MR spectroscopy for the quantification of hepatic steatosis. This study was approved by the institutional review board and was HIPAA compliant. Written informed consent was obtained before all studies. Fifty-five patients (31 women, 24 men; age range, 24-71 years) were prospectively imaged at 1.5 T with quantitative MR imaging and single-voxel MR spectroscopy, each within a single breath hold. The effects of T2 correction, spectral modeling of fat, and magnitude fitting for eddy current correction on fat quantification with MR imaging were investigated by reconstructing fat fraction images from the same source data with different combinations of error correction. Single-voxel T2-corrected MR spectroscopy was used to measure fat fraction and served as the reference standard. All MR spectroscopy data were postprocessed at a separate institution by an MR physicist who was blinded to MR imaging results. Fat fractions measured with MR imaging and MR spectroscopy were compared statistically to determine the correlation (r(2)), and the slope and intercept as measures of agreement between MR imaging and MR spectroscopy fat fraction measurements, to determine whether MR imaging can help quantify fat, and examine the importance of T2 correction, spectral modeling of fat, and eddy current correction. Two-sided t tests (significance level, P = .05) were used to determine whether estimated slopes and intercepts were significantly different from 1.0 and 0.0, respectively. Sensitivity and specificity for the classification of clinically significant steatosis were evaluated. Overall, there was excellent correlation between MR imaging and MR spectroscopy for all reconstruction combinations. However, agreement was only achieved when T2 correction, spectral modeling of fat, and magnitude fitting for eddy current correction were used (r(2) = 0.99; slope ± standard deviation = 1.00 ± 0.01, P = .77; intercept ± standard deviation = 0.2% ± 0.1, P = .19). T1-independent chemical shift-based water-fat separation MR imaging methods can accurately quantify fat over the entire liver, by using MR spectroscopy as the reference standard, when T2 correction, spectral modeling of fat, and eddy current correction methods are used. © RSNA, 2011.

Objects but not concepts modulate the size of the attended region.

PubMed

Goodhew, Stephanie C; Edwards, Mark

2017-07-01

Here we investigated the types of stimuli that modulate the size of the attentional spotlight. In particular, it has been previously shown that conceptual cues that either directly refer to or are semantically related to particular spatial locations can shift attention to that location (known as "conceptual cueing"). For example, reading the word sun or joy can shift attention upward whereas the word boot or hostile can shift attention downward. Here, therefore, we tested whether words could modulate the size of the attended area. Across five experiments, we found that words that either directly referred to, or were abstractly associated with, particular sizes (small versus large) did not change the size of the attentional spotlight, whereas the presence of differently sized stimuli did, as evidenced by faster responses to targets when the spotlight is small than when it is large. This suggests that physical but not conceptual inducers can modulate the size of the attentional spotlight. This highlights an important difference between the regulation of spotlight size and shifts of attention, supporting the notion that they are subserved by distinct mechanisms.

Response to “Accurate Risk-Based Chemical Screening Relies on Robust Exposure Estimates”

EPA Science Inventory

This is a correspondence (letter to the editor) with reference to comments by Rudel and Perovich on the article "Integration of Dosimetry, Exposure, and High-Throughput Screening Data in Chemical Toxicity Assessment". Article Reference: SI # 238882

A multinuclear solid-state NMR study of the dimethyltin chalcogenides ((CH 3) 2SnE) 3, E  S,Se,Te

NASA Astrophysics Data System (ADS)

Gay, Ian D.; Jones, C. H. W.; Sharma, R. D.

The solid-state NMR spectra, measured using MAS, are reported for 13C, 119Sn, 77Se, and 125Te in the compounds (Me 2SnE) 3, E  S, Se, or Te. For ((CH 3) 2SnS) 3, tetragonal, three inequivalent carbons and two inequivalent tins are observed consistent with a reinterpretation of the crystal structure data of this compound which shows a twofold axis through opposing tin and sulfur atoms, the molecule being in a twisted-boat conformation. For the monoclinic form six inequivalent carbons and three inequivalent tins were observed. Chemical shifts for 13C and 119Sn and the magnitudes of the 2JSn Sn coupling constants are reported. The tetragonal forms of ((CH 3) 2SnSe) 3 and ((CH 3) 2SnTe) 3 show the presence of two inequivalent tin and chalcogen atoms and three inequivalent carbons, again consistent with a twofold axis. In these compounds it is possible to identify the three different observed single-bond coupling constants with the distinct crystallographically determined tin-chalcogen bonds. The 13C, 119Sn, 77Se, and 125Te chemical shifts are reported, together with the magnitude of 1JSn E (E  Se or Te). In addition to isotropic shifts and couplings, chemical-shift anisotropies are reported for Sn, Se, and Te.

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

PubMed Central

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

2013-01-01

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

Measurement of Absolute Concentrations of Individual Compounds in Metabolite Mixtures by Gradient-Selective Time-Zero 1H-13C HSQC (gsHSQC0) with Two Concentration References and Fast Maximum Likelihood Reconstruction Analysis

PubMed Central

Hu, Kaifeng; Ellinger, James J.; Chylla, Roger A.; Markley, John L.

2011-01-01

Time-zero 2D 13C HSQC (HSQC0) spectroscopy offers advantages over traditional 2D NMR for quantitative analysis of solutions containing a mixture of compounds because the signal intensities are directly proportional to the concentrations of the constituents. The HSQC0 spectrum is derived from a series of spectra collected with increasing repetition times within the basic HSQC block by extrapolating the repetition time to zero. Here we present an alternative approach to data collection, gradient-selective time-zero 1H-13C HSQC0 in combination with fast maximum likelihood reconstruction (FMLR) data analysis and the use of two concentration references for absolute concentration determination. Gradient-selective data acquisition results in cleaner spectra, and NMR data can be acquired in both constant-time and non-constant time mode. Semi-automatic data analysis is supported by the FMLR approach, which is used to deconvolute the spectra and extract peak volumes. The peak volumes obtained from this analysis are converted to absolute concentrations by reference to the peak volumes of two internal reference compounds of known concentration: DSS (4,4-dimethyl-4-silapentane-1-sulfonic acid) at the low concentration limit (which also serves as chemical shift reference) and MES (2-(N-morpholino)ethanesulfonic acid) at the high concentration limit. The linear relationship between peak volumes and concentration is better defined with two references than with one, and the measured absolute concentrations of individual compounds in the mixture are more accurate. We compare results from semi-automated gsHSQC0 with those obtained by the original manual phase-cycled HSQC0 approach. The new approach is suitable for automatic metabolite profiling by simultaneous quantification of multiple metabolites in a complex mixture. PMID:22029275

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

PubMed Central

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

2017-01-01

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

Mn and Btex Reference Value Arrays (Final Reports)

EPA Science Inventory

These final reports are a summary of reference value arrays with critical supporting documentation for the chemicals manganese, benzene, toluene, ethylbenzene, and xylene. Each chemical is covered in a separate document, and each is a statement of the status of the available inha...

CADDIS Volume 2. Sources, Stressors and Responses: Unspecified Toxic Chemicals

EPA Pesticide Factsheets

Intro to the unspecified toxic chemicals module, when to list toxic chemicals as a candidate cause, ways to measure toxic chemicals, simple and detailed conceptual diagrams for toxic chemicals, toxic chemicals module references and literature reviews.

Isotope shifts in francium isotopes Fr 206 - 213 and Fr 221

DOE PAGES

Collister, R.; Gwinner, G.; Tandecki, M.; ...

2014-11-07

We present the isotope shifts of the 7s 1/2 to 7p 1/2 transition for francium isotopes ²⁰⁶⁻²¹³Fr with reference to ²²¹Fr collected from two experimental periods. The shifts are measured on a sample of atoms prepared within a magneto-optical trap by a fast sweep of radio-frequency sidebands applied to a carrier laser. King plot analysis, which includes literature values for 7s 1/2 to 7p 3/2 isotope shifts, provides a field shift constant ratio of 1.0520(10) and a difference between the specific mass shift constants of 170(100) GHz amu between the D₁ and D₂ transitions, of sufficient precision to differentiate betweenmore » ab initio calculations.« less

[Changes in functional state during occupational activities in workers at objects for chemical weapons destruction].

PubMed

2010-01-01

The authors studied functional state before and after the working shift in workers at objects for chemical weapons destruction, analyzed changes in central and peripheral hemodynamics parameters, vegetative regulation of heart rhythm, stabilographic and psychophysiologic values.

APPROACHES FOR INCORPORATING NON-CHEMICAL STRESSORS INTO CUMULATIVE RISK ASSESSMENTS

EPA Science Inventory

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

Peptides containing internal residues of pyroglutamic acid: proton NMR characteristics

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

Khan, S.A.

1986-05-01

The proton NMR characteristics of internal pyroglutamic acid (Glp; 5-oxoproline) residues in seven tripeptides of the general structure Boc-Xxx-Glp-Yyy-NH/sub 2/ were studied. In general, the chemical shifts of several diagnostic protons moved downfield on going from the Glu-containing peptides (Boc-Xxx-Glu-Yyy-NH/sub 2/) to the corresponding Glp-containing peptides. The C-2 proton of the Xxx residue was shifted by about 1.1 ppm. The N-2 proton of the Yyy residue was shifted by about 0.5 ppm. The C-2 proton of the Glx residue itself was shifted by about 0.5 ppm. One of the Glx C-3 protons was also shifted by about 0.5 ppm, butmore » the other remained essentially unchanged. Finally, the Glx C-4 protons were shifted by about 0.3 ppm. Internal Glu residues are readily converted chemically into internal Glp residues. This conversion also occurs as a side reaction during HP cleavage of the protecting group from Glu(OBzl) residues. The spontaneous fragmentation of serum proteins C3, C4 and lambda/sub 2/-macroglobulin under denaturing conditions is probably due to regioselective hydrolysis of an internal Glp residue formed in each of these proteins upon denaturation. These proton NMR characteristics may be useful in establishing the presence of internal Glp residues in synthetic and natural peptides.« less

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

PubMed

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

2009-01-01

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

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

PubMed

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

2010-07-14

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

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

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

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

2015-09-15

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

Molecular structure activity on pharmaceutical applications of Phenacetin using spectroscopic investigation

NASA Astrophysics Data System (ADS)

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

2017-01-01

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

Chemometric Analysis of Gas Chromatography – Mass Spectrometry Data using Fast Retention Time Alignment via a Total Ion Current Shift Function

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

Nadeau, Jeremy S.; Wright, Bob W.; Synovec, Robert E.

2010-04-15

A critical comparison of methods for correcting severely retention time shifted gas chromatography-mass spectrometry (GC-MS) data is presented. The method reported herein is an adaptation to the Piecewise Alignment Algorithm to quickly align severely shifted one-dimensional (1D) total ion current (TIC) data, then applying these shifts to broadly align all mass channels throughout the separation, referred to as a TIC shift function (SF). The maximum shift varied from (-) 5 s in the beginning of the chromatographic separation to (+) 20 s toward the end of the separation, equivalent to a maximum shift of over 5 peak widths. Implementing themore » TIC shift function (TIC SF) prior to Fisher Ratio (F-Ratio) feature selection and then principal component analysis (PCA) was found to be a viable approach to classify complex chromatograms, that in this study were obtained from GC-MS separations of three gasoline samples serving as complex test mixtures, referred to as types C, M and S. The reported alignment algorithm via the TIC SF approach corrects for large dynamic shifting in the data as well as subtle peak-to-peak shifts. The benefits of the overall TIC SF alignment and feature selection approach were quantified using the degree-of-class separation (DCS) metric of the PCA scores plots using the type C and M samples, since they were the most similar, and thus the most challenging samples to properly classify. The DCS values showed an increase from an initial value of essentially zero for the unaligned GC-TIC data to a value of 7.9 following alignment; however, the DCS was unchanged by feature selection using F-Ratios for the GC-TIC data. The full mass spectral data provided an increase to a final DCS of 13.7 after alignment and two-dimensional (2D) F-Ratio feature selection.« less

Biological monitoring of benzene exposure for process operators during ordinary activity in the upstream petroleum industry.

PubMed

Bråtveit, Magne; Kirkeleit, Jorunn; Hollund, Bjørg Eli; Moen, Bente E

2007-07-01

This study characterized the exposure of crude oil process operators to benzene and related aromatics during ordinary activity and investigated whether the operators take up benzene at this level of exposure. We performed the study on a fixed, integrated oil and gas production facility on Norway's continental shelf. The study population included 12 operators and 9 referents. We measured personal exposure to benzene, toluene, ethylbenzene and xylene during three consecutive 12-h work shifts using organic vapour passive dosimeter badges. We sampled blood and urine before departure to the production facility (pre-shift), immediately after the work shift on Day 13 of the work period (post-shift) and immediately before the following work shift (pre-next shift). We also measured the exposure to hydrocarbons during short-term tasks by active sampling using Tenax tubes. The arithmetic mean exposure over the 3 days was 0.042 ppm for benzene (range <0.001-0.69 ppm), 0.05 ppm for toluene, 0.02 ppm for ethylbenzene and 0.03 ppm for xylene. Full-shift personal exposure was significantly higher when the process operators performed flotation work during the shift versus other tasks. Work in the flotation area was associated with short-term (6-15 min) arithmetic mean exposure to benzene of 1.06 ppm (range 0.09-2.33 ppm). The concentrations of benzene in blood and urine did not differ between operators and referents at any time point. When we adjusted for current smoking in regression analysis, benzene exposure was significantly associated with the post-shift concentration of benzene in blood (P = 0.01) and urine (P = 0.03), respectively. Although these operators perform tasks with relatively high short-term exposure to benzene, the full-shift mean exposure is low during ordinary activity. Some evidence indicates benzene uptake within this range of exposure.

NMR Spectroscopy Using a Chiral Lanthanide Shift Reagent to Assess the Optical Purity of 1-Phenylethylamine

NASA Astrophysics Data System (ADS)

Viswanathan, Tito; Toland, Alan

1995-10-01

Enantiomeric forms of 1-phenylethylamine cannot be distinguished by 1H or 13C-NMR because the groups attached to the stereocenter are in an enantiopic environment. However, the chemical shifts of the protons in the groups attached to the stereocenter can be differentially altered to appear as distinct peaks in the NMR spectrum. This is accomplished by the use of a commercially available chiral lanthanide shift reagent, Yb(tfC)3. The NMR spectrum after the addition of a chiral shift reagent allows one to assess the optical purity of the sample.

Dosimetric impact of applicator displacement during high dose rate (HDR) Cobalt-60 brachytherapy for cervical cancer: A planning study

NASA Astrophysics Data System (ADS)

Yong, J. S.; Ung, N. M.; Jamalludin, Z.; Malik, R. A.; Wong, J. H. D.; Liew, Y. M.; Ng, K. H.

2016-02-01

We investigated the dosimetric impact of applicator displacement on dose specification during high dose rate (HDR) Cobalt-60 (Co-60) brachytherapy for cervical cancer through a planning study. Eighteen randomly selected HDR full insertion plans were restrospectively studied. The tandem and ovoids were virtually shifted translationally and rotationally in the x-, y- and z-axis directions on the treatment planning system. Doses to reference points and volumes of interest in the plans with shifted applicators were compared with the original plans. The impact of dose displacement on 2D (point-based) and 3D (volume-based) treatment planning techniques was also assessed. A ±2 mm translational y-axis applicator shift and ±4° rotational x-axis applicator shift resulted in dosimetric changes of more than 5% to organs at risk (OAR) reference points. Changes to the maximum doses to 2 cc of the organ (D2cc) in 3D planning were statistically significant and higher than the reference points in 2D planning for both the rectum and bladder (p<0.05). Rectal D2cc was observed to be the most sensitive to applicator displacement among all dose metrics. Applicator displacement that is greater than ±2 mm translational y-axis and ±4° rotational x-axis resulted in significant dose changes to the OAR. Thus, steps must be taken to minimize the possibility of applicator displacement during brachytherapy.

CADDIS Volume 2. Sources, Stressors and Responses: Unspecified Toxic Chemicals - Simple Conceptual Diagram

EPA Pesticide Factsheets

Intro to the unspecified toxic chemicals module, when to list toxic chemicals as a candidate cause, ways to measure toxic chemicals, simple and detailed conceptual diagrams for toxic chemicals, toxic chemicals module references and literature reviews.

CADDIS Volume 2. Sources, Stressors and Responses: Unspecified Toxic Chemicals - Detailed Conceptual Diagram

EPA Pesticide Factsheets

Intro to the unspecified toxic chemicals module, when to list toxic chemicals as a candidate cause, ways to measure toxic chemicals, simple and detailed conceptual diagrams for toxic chemicals, toxic chemicals module references and literature reviews.

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

PubMed

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

2011-01-01

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

Atmospheric aerosols: A literature summary of their physical characteristics and chemical composition

NASA Technical Reports Server (NTRS)

Harris, F. S., Jr.

1976-01-01

This report contains a summary of 199 recent references on the characterization of atmospheric aerosols with respect to their composition, sources, size distribution, and time changes, and with particular reference to the chemical elements measured by modern techniques, especially activation analysis.

The Wellington Indo-Fijians: Language Shift among Teenage New Immigrants.

ERIC Educational Resources Information Center

Shameem, Nikhat

1994-01-01

The Indo-Fijian settlers, who speak Fiji Hindi, a preliterate language, migrated to New Zealand following the 1987 Fiji military coup. This article looks at the maintenance of Fiji Hindi among teenage Indi-Fijian immigrants and the factors contributing to a shift from Fiji Hindi to the use of English in all domains. (40 references) (LR)

Extended working hours: Impacts on workers

Treesearch

D. Mitchell; T. Gallagher

2010-01-01

Some logging business owners are trying to manage their equipment assets by increasing the scheduled machine hours. The intent is to maximize the total tons produced by a set of equipment. This practice is referred to as multi-shifting, double-shifting, or extended working hours. One area often overlooked is the impact that working non-traditional hours can have on...

Board of Regents of the Nevada System of Higher Education, on behalf of the University of Nevada, Reno

DOEpatents

Adams, Jesse D.; Sulchek, Todd A.; Feigin, Stuart C.

2017-07-11

A disclosed chemical detection system for detecting a target material, such as an explosive material, can include a cantilevered probe, a probe heater coupled to the cantilevered probe, and a piezoelectric element disposed on the cantilevered probe. The piezoelectric element can be configured as a detector and/or an actuator. Detection can include, for example, detecting a movement of the cantilevered probe or a property of the cantilevered probe. The movement or a change in the property of the cantilevered probe can occur, for example, by adsorption of the target material, desorption of the target material, reaction of the target material and/or phase change of the target material. Examples of detectable movements and properties include temperature shifts, impedance shifts, and resonant frequency shifts of the cantilevered probe. The overall chemical detection system can be incorporated, for example, into a handheld explosive material detection system.

The HSP90 binding mode of a radicicol-like E-oxime from docking, binding free energy estimations, and NMR 15N chemical shifts

PubMed Central

Spichty, Martin; Taly, Antoine; Hagn, Franz; Kessler, Horst; Barluenga, Sofia; Winssinger, Nicolas; Karplus, Martin

2009-01-01

We determine the binding mode of a macrocyclic radicicol-like oxime to yeast HSP90 by combining computer simulations and experimental measurements. We sample the macrocyclic scaffold of the unbound ligand by parallel tempering simulations and dock the most populated conformations to yeast HSP90. Docking poses are then evaluated by the use of binding free energy estimations with the linear interaction energy method. Comparison of QM/MM-calculated NMR chemical shifts with experimental shift data for a selective subset of back-bone 15N provides an additional evaluation criteria. As a last test we check the binding modes against available structure-activity-relationships. We find that the most likely binding mode of the oxime to yeast HSP90 is very similar to the known structure of the radicicol-HSP90 complex. PMID:19482409

Probing Structural Changes among Analogous Inhibitor-Bound Forms of HIV-1 Protease and a Drug-Resistant Mutant in Solution by Nuclear Magnetic Resonance.

PubMed

Khan, Shahid N; Persons, John D; Paulsen, Janet L; Guerrero, Michel; Schiffer, Celia A; Kurt-Yilmaz, Nese; Ishima, Rieko

2018-03-13

In the era of state-of-the-art inhibitor design and high-resolution structural studies, detection of significant but small protein structural differences in the inhibitor-bound forms is critical to further developing the inhibitor. Here, we probed differences in HIV-1 protease (PR) conformation among darunavir and four analogous inhibitor-bound forms and compared them with a drug-resistant mutant using nuclear magnetic resonance chemical shifts. Changes in amide chemical shifts of wild-type (WT) PR among these inhibitor-bound forms, ΔCSP, were subtle but detectable and extended >10 Å from the inhibitor-binding site, asymmetrically between the two subunits of PR. Molecular dynamics simulations revealed differential local hydrogen bonding as the molecular basis of this remote asymmetric change. Inhibitor-bound forms of the drug-resistant mutant also showed a similar long-range ΔCSP pattern. Differences in ΔCSP values of the WT and the mutant (ΔΔCSPs) were observed at the inhibitor-binding site and in the surrounding region. Comparing chemical shift changes among highly analogous inhibitors and ΔΔCSPs effectively eliminated local environmental effects stemming from different chemical groups and enabled exploitation of these sensitive parameters to detect subtle protein conformational changes and to elucidate asymmetric and remote conformational effects upon inhibitor interaction.

Has Chemical Education Reached Equilibrium?

NASA Astrophysics Data System (ADS)

Moore, John W.

1997-06-01

The other day I got to thinking about whether something akin to Le Chatelier's principle operates in chemical education. That is, whenever someone alters the conditions under which we interact with students, there is a shift in the system that attempts to minimize or counteract the change.

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

PubMed

Stevens, Joanna S; Walczak, Monika; Jaye, Cherno; Fischer, Daniel A

2016-10-24

The dramatic colour and phase alteration with the solid-state, temperature-dependent reaction between squaric acid and 4,4'-bipyridine has been probed in situ with X-ray absorption spectroscopy. The electronic and chemical sensitivity to the local atomic environment through chemical shifts in the near-edge X-ray absorption fine structure (NEXAFS) revealed proton transfer from the acid to the bipyridine base through the change in nitrogen protonation state in the high-temperature form. Direct detection of proton transfer coupled with structural analysis elucidates the nature of the solid-state process, with intermolecular proton transfer occurring along an acid-base chain followed by a domino effect to the subsequent acid-base chains, leading to the rapid migration along the length of the crystal. NEXAFS thereby conveys the ability to monitor the nature of solid-state chemical reactions in situ, without the need for a priori information or long-range order. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

PubMed

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

1985-02-01

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

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

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

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

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

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

DOE PAGES

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

2017-12-06

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

Human biomonitoring reference values for some non-persistent chemicals in blood and urine derived from the Canadian Health Measures Survey 2009-2013.

PubMed

Khoury, Cheryl; Werry, Kate; Haines, Douglas; Walker, Mike; Malowany, Morie

2018-05-01

The Canadian Health Measures Survey collects nationally representative human biomonitoring data on a suite of chemicals and their metabolites, including many non-persistent chemicals. Data has been collected on non-persistent chemicals, including acrylamide, chlorophenols, environmental phenols and triclocarban, organophosphate insecticides, phthalates, polycyclic aromatic hydrocarbon, pyrethroid insecticides, and volatile organic compounds from 2009 to 2013. Using a systematic approach building on the reference interval concept proposed by the International Federation of Clinical Chemistry and Laboratory Medicine and the International Union of Pure and Applied Chemistry, we derive human biomonitoring reference values (RV 95 s) for these classes of non-persistent chemicals in blood and urine for the general Canadian population. RV 95 s were derived for biomarkers of non-persistent chemicals with widespread detection in Canadians (>66% detection rate). Samples with urinary creatinine levels outside the recommended range of 0.3-3.0 μg/L were excluded. Reference populations were constructed by applying smoking and fasting as exclusion criteria where appropriate. Age and sex were evaluated as possible partitioning criteria and separate RV 95 s were derived for sub-populations in cases where partitioning was deemed necessary. Reference values were derived for 40 biomarkers and represent the first set of RV 95 s for non-persistent chemicals in the general Canadian population. These values provide a measure of the upper margin of background exposure in the general population and can be compared against individual and population human biomonitoring data. RV 95 s can be used to by public health officials to identify individuals with high exposures, and by risk assessors and risk managers to identify atypical exposures or subpopulations with elevated exposures. Crown Copyright © 2018. Published by Elsevier GmbH. All rights reserved.

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

PubMed

Straka, Michal; Lantto, Perttu; Vaara, Juha

2008-03-27

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

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

PubMed

Peng, Dungeng; Ogura, Hiroshi; Ma, Li-Hua; Evans, John P; de Montellano, Paul R Ortiz; La Mar, Gerd N

2013-04-01

Solution 2D (1)H NMR was carried out on the azide-ligated substrate complex of human heme oxygenase, hHO, to provide information on the active site molecular structure, chromophore electronic/magnetic properties, and the distal H-bond network linked to the exogenous ligand by catalytically relevant oriented water molecules. While 2D NMR exhibited very similar patterns of two-dimensional nuclear Overhauser spectroscopy cross peaks of residues with substrate and among residues as the previously characterized cyanide complex, significant, broadly distributed chemical shift differences were observed for both labile and non-labile protons. The anisotropy and orientation of the paramagnetic susceptibility tensor, χ, were determined for both the azide and cyanide complexes. The most significant difference observed is the tilt of the major magnetic axes from the heme normal, which is only half as large for the azide than cyanide ligand, with each ligand tilted toward the catalytically cleaved α-meso position. The difference in chemical shifts is quantitatively correlated with differences in dipolar shifts in the respective complexes for all but the distal helix. The necessity of considering dipolar shifts, and hence determination of the orientation/anisotropy of χ, in comparing chemical shifts involving paramagnetic complexes, is emphasized. The analysis shows that the H-bond network cannot detect significant differences in H-bond acceptor properties of cyanide versus azide ligands. Lastly, significant retardation of distal helix labile proton exchange upon replacing cyanide with azide indicates that the dynamic stability of the distal helix is increased upon decreasing the steric interaction of the ligand with the distal helix. Copyright © 2013. Published by Elsevier Inc.

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

Collister, R.; Gwinner, G.; Tandecki, M.

We present the isotope shifts of the 7s 1/2 to 7p 1/2 transition for francium isotopes ²⁰⁶⁻²¹³Fr with reference to ²²¹Fr collected from two experimental periods. The shifts are measured on a sample of atoms prepared within a magneto-optical trap by a fast sweep of radio-frequency sidebands applied to a carrier laser. King plot analysis, which includes literature values for 7s 1/2 to 7p 3/2 isotope shifts, provides a field shift constant ratio of 1.0520(10) and a difference between the specific mass shift constants of 170(100) GHz amu between the D₁ and D₂ transitions, of sufficient precision to differentiate betweenmore » ab initio calculations.« less

Shift Verification and Validation

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

Pandya, Tara M.; Evans, Thomas M.; Davidson, Gregory G

2016-09-07

This documentation outlines the verification and validation of Shift for the Consortium for Advanced Simulation of Light Water Reactors (CASL). Five main types of problems were used for validation: small criticality benchmark problems; full-core reactor benchmarks for light water reactors; fixed-source coupled neutron-photon dosimetry benchmarks; depletion/burnup benchmarks; and full-core reactor performance benchmarks. We compared Shift results to measured data and other simulated Monte Carlo radiation transport code results, and found very good agreement in a variety of comparison measures. These include prediction of critical eigenvalue, radial and axial pin power distributions, rod worth, leakage spectra, and nuclide inventories over amore » burn cycle. Based on this validation of Shift, we are confident in Shift to provide reference results for CASL benchmarking.« less

PHYTOTOX: DATABASE DEALING WITH THE EFFECT OF ORGANIC CHEMICALS ON TERRESTRIAL VASCULAR PLANTS

EPA Science Inventory

A new database, PHYTOTOX, dealing with the direct effects of exogenously supplied organic chemicals on terrestrial vascular plants is described. The database consists of two files, a Reference File and Effects File. The Reference File is a bibliographic file of published research...

Graphical Arrays of Chemical-Specific Health Effect Reference Values for Inhalation Exposures (2009 Final Report)

EPA Science Inventory

This document provides graphical arrays and tables of key information on the derivation of human inhalation health effect reference values for specific chemicals, allowing comparisons across durations, populations, and intended use. A number of program offices within the Agency, ...

Integrated Model of Chemical Perturbations of a Biological ...

EPA Pesticide Factsheets

We demonstrate a computational network model that integrates 18 in vitro, high-throughput screening assays measuring estrogen receptor (ER) binding, dimerization, chromatin binding, transcriptional activation and ER-dependent cell proliferation. The network model uses activity patterns across the in vitro assays to predict whether a chemical is an ER agonist or antagonist, or is otherwise influencing the assays through a manner dependent on the physics and chemistry of the technology platform (“”assay interference”). The method is applied to a library of 1812 commercial and environmental chemicals, including 45 ER positive and negative reference chemicals. Among the reference chemicals, the network model correctly identified the agonists and antagonists with the exception of very weak compounds whose activity was outside the concentration range tested. The model agonist score also correlated with the expected potency class of the active reference chemicals. Of the 1812 chemicals evaluated, 52 (2.8%) were predicted to be strongly ER active in agonist or antagonist mode. This dataset and model were also used to begin a systematic investigation of assay interference. The most prominent cause of false-positive activity (activity in an assay that is likely not due to interaction of the chemical with ER) is cytotoxicity. The model provides the ability to prioritize a large set of important environmental chemicals with human exposure potential for additional in v

Phase shifting interferometer

DOEpatents

Sommargren, Gary E.

1999-01-01

An interferometer which has the capability of measuring optical elements and systems with an accuracy of .lambda./1000 where .lambda. is the wavelength of visible light. Whereas current interferometers employ a reference surface, which inherently limits the accuracy of the measurement to about .lambda./50, this interferometer uses an essentially perfect spherical reference wavefront generated by the fundamental process of diffraction. Whereas current interferometers illuminate the optic to be tested with an aberrated wavefront which also limits the accuracy of the measurement, this interferometer uses an essentially perfect spherical measurement wavefront generated by the fundamental process of diffraction. This interferometer is adjustable to give unity fringe visibility, which maximizes the signal-to-noise, and has the means to introduce a controlled prescribed relative phase shift between the reference wavefront and the wavefront from the optics under test, which permits analysis of the interference fringe pattern using standard phase extraction algorithms.

Phase shifting interferometer

DOEpatents

Sommargren, G.E.

1999-08-03

An interferometer is disclosed which has the capability of measuring optical elements and systems with an accuracy of {lambda}/1000 where {lambda} is the wavelength of visible light. Whereas current interferometers employ a reference surface, which inherently limits the accuracy of the measurement to about {lambda}/50, this interferometer uses an essentially perfect spherical reference wavefront generated by the fundamental process of diffraction. Whereas current interferometers illuminate the optic to be tested with an aberrated wavefront which also limits the accuracy of the measurement, this interferometer uses an essentially perfect spherical measurement wavefront generated by the fundamental process of diffraction. This interferometer is adjustable to give unity fringe visibility, which maximizes the signal-to-noise, and has the means to introduce a controlled prescribed relative phase shift between the reference wavefront and the wavefront from the optics under test, which permits analysis of the interference fringe pattern using standard phase extraction algorithms. 11 figs.

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

NASA Astrophysics Data System (ADS)

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

2015-05-01

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

6-Aminopenicillanic acid revisited: A combined solid state NMR and in silico refinement

NASA Astrophysics Data System (ADS)

Aguiar, Daniel Lima Marques de; San Gil, Rosane Aguiar da Silva; Alencastro, Ricardo Bicca de; Souza, Eugenio Furtado de; Borré, Leandro Bandeira; Vaiss, Viviane da Silva; Leitão, Alexandre Amaral

2016-09-01

13C/15N (experimental and ab initio) solid-state NMR was used to achieve an affordable way to improve hydrogen refinement of 6-aminopenicillanic acid (6-APA) structure. The lattice effect on the isotropic chemical shifts was probed by using two different magnetic shielding calculations: isolated molecules and periodic crystal structure. The electron density difference maps of optimized and non-optimized structures were calculated in order to investigate the interactions inside the 6-APA unit cell. The 13C and 15N chemical shifts assignments were unambiguously stablished. In addition, some of the literature 13C resonances ambiguities could be properly solved.

Combining Nuclear Magnetic Resonance Spectroscopy and Density Functional Theory Calculations to Characterize Carvedilol Polymorphs.

PubMed

Rezende, Carlos A; San Gil, Rosane A S; Borré, Leandro B; Pires, José Ricardo; Vaiss, Viviane S; Resende, Jackson A L C; Leitão, Alexandre A; De Alencastro, Ricardo B; Leal, Katia Z

2016-09-01

The experiments of carvedilol form II, form III, and hydrate by (13)C and (15)N cross-polarization magic-angle spinning (CP MAS) are reported. The GIPAW (gauge-including projector-augmented wave) method from DFT (density functional theory) calculations was used to simulate (13)C and (15)N chemical shifts. A very good agreement was found for the comparison between the global results of experimental and calculated nuclear magnetic resonance (NMR) chemical shifts for carvedilol polymorphs. This work aims a comprehensive understanding of carvedilol crystalline forms employing solution and solid-state NMR as well as DFT calculations. Copyright © 2016. Published by Elsevier Inc.

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

NASA Astrophysics Data System (ADS)

Wachter-Jurcsak, Nanette; Zamani, Hossein

1999-05-01

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

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

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

Cort, John R.; Cho, Herman M.

2009-10-01

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

Bonding in Some Zintl Phases: A Study by Tin-119 Mössbauer Spectroscopy

NASA Astrophysics Data System (ADS)

Asbrand, M.; Berry, F. J.; Eisenmann, B.; Kniep, R.; Smart, L. E.; Thied, R. C.

1995-09-01

The 119Sn Mössbauer parameters for a range of Zintl phase compounds are reported. The compounds containing tetrahedrally coordinated tin of composition M5SnX3 (M = Na, K; X = P, As, Sb) have chemical isomer shifts close to that of grey-tin and can be considered to be covalently bonded species. The layer structures of composition KSnX (X = As, Sb) and double-layer compounds M Sn2X2 (M = Na, Sr; X = As, Sb) have tin in a distorted octahedral environment. The chemical isomer shifts are closer to that of white-tin and can be interpreted in terms of metallic bonding.

Improving the analysis of NMR spectra tracking pH-induced conformational changes: removing artefacts of the electric field on the NMR chemical shift.

PubMed

Kukić, Predrag; Farrell, Damien; Søndergaard, Chresten R; Bjarnadottir, Una; Bradley, John; Pollastri, Gianluca; Nielsen, Jens Erik

2010-03-01

pH-induced chemical shift perturbations (CSPs) can be used to study pH-dependent conformational transitions in proteins. Recently, an elegant principal component analysis (PCA) algorithm was developed and used to study the pH-dependent structural transitions in bovine beta-lactoglobulin (betaLG) by analyzing its NMR pH-titration spectra. Here, we augment this analysis method by filtering out changes in the NMR chemical shift that stem from effects that are electrostatic in nature. Specifically, we examine how many CSPs can be explained by purely electrostatic effects arising from titrational events in betaLG. The results show that around 20% of the amide nuclei CSPs in betaLG originate exclusively from "through-space" electric field effects. A PCA of NMR data where electric field artefacts have been removed gives a different picture of the pH-dependent structural transitions in betaLG. The method implemented here is well suited to be applied on a whole range of proteins, which experience at least one pH-dependent conformational change. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

Obtaining molecular and structural information from 13C-14N systems with 13C FIREMAT experiments.

PubMed

Strohmeier, Mark; Alderman, D W; Grant, David M

2002-04-01

The effect of dipolar coupling to 14N on 13C FIREMAT (five pi replicated magic angle turning) experiments is investigated. A method is developed for fitting the 13C FIREMAT FID employing the full theory to extract the 13C-14N dipolar and 13C chemical shift tensor information. The analysis requires prior knowledge of the electric field gradient (EFG) tensor at the 14N nucleus. In order to validate the method the analysis is done for the amino acids alpha-glycine, gamma-glycine, l-alanine, l-asparagine, and l-histidine on FIREMAT FIDs recorded at 13C frequencies of 50 and 100 MHz. The dipolar and chemical shift data obtained with this analysis are in very good agreement with the previous single-crystal 13C NMR results and neutron diffraction data on alpha-glycine, l-alanine, and l-asparagine. The values for gamma-glycine and l-histidine obtained with this new method are reported for the first time. The uncertainties in the EFG tensor on the resultant 13C chemical shift and dipolar tensor values are assessed. (c) 2002 Elsevier Science (USA).

The Impact of a Science Education Game on Students' Learning and Perception of Inhalants as Body Pollutants.

PubMed

Klisch, Yvonne; Miller, Leslie M; Wang, Shu; Epstein, Joel

2012-04-01

This study investigated the knowledge gains and attitude shifts attributable to a unique online science education game, Uncommon Scents. The game was developed to teach middle school students about the biological consequences of exposure to toxic chemicals in an environmental science context, as well as the risks associated with abusing these chemicals as inhalants. Middle school students ( n = 444) grades six through eight participated in the study consisting of a pre-test, three game-play sessions, and a delayed post-test. After playing the game, students demonstrated significant gains in science content knowledge, with game usability ratings emerging as the strongest predictor of post-test content knowledge scores. The intervention also resulted in a shift to more negative attitudes toward inhalants, with the most negative shift occurring among eighth grade students and post-test knowledge gains as the strongest predictor of attitude change across all grade levels. These findings suggest that the environmental science approach used in Uncommon Scents is an efficacious strategy for delivering both basic science content and influencing perceived harm relating to the inhalation of toxic chemicals from common household products.

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

NASA Astrophysics Data System (ADS)

Goudarzi, Nasser

2016-04-01

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

Probing hydrogen bonding in cocrystals and amorphous dispersions using (14)N-(1)H HMQC solid-state NMR.

PubMed

Tatton, Andrew S; Pham, Tran N; Vogt, Frederick G; Iuga, Dinu; Edwards, Andrew J; Brown, Steven P

2013-03-04

Cocrystals and amorphous solid dispersions have generated interest in the pharmaceutical industry as an alternative to more established solid delivery forms. The identification of intermolecular hydrogen bonding interactions in a nicotinamide palmitic acid cocrystal and a 50% w/w acetaminophen-polyvinylpyrrolidone solid dispersion are reported using advanced solid-state magic-angle spinning (MAS) NMR methods. The application of a novel (14)N-(1)H HMQC experiment, where coherence transfer is achieved via through-space couplings, is shown to identify specific hydrogen bonding motifs. Additionally, (1)H isotropic chemical shifts and (14)N electric field gradient (EFG) parameters, both accessible from (14)N-(1)H HMQC experiments, are shown to be sensitive to changes in hydrogen bonding geometry. Numerous indicators of molecular association are accessible from this experiment, including NH cross-peaks occurring from intermolecular hydrogen bonds and changes in proton chemical shifts or electric field gradient parameters. First-principles calculations using the GIPAW approach that yield accurate estimates of isotropic chemical shifts, and EFG parameters were used to assist in assignment. It is envisaged that (14)N-(1)H HMQC solid state NMR experiments could become a valuable screening technique of solid delivery forms in the pharmaceutical industry.

The Impact of a Science Education Game on Students' Learning and Perception of Inhalants as Body Pollutants

NASA Astrophysics Data System (ADS)

Klisch, Yvonne; Miller, Leslie M.; Wang, Shu; Epstein, Joel

2012-04-01

This study investigated the knowledge gains and attitude shifts attributable to a unique online science education game, Uncommon Scents. The game was developed to teach middle school students about the biological consequences of exposure to toxic chemicals in an environmental science context, as well as the risks associated with abusing these chemicals as inhalants. Middle school students (n = 444) grades six through eight participated in the study consisting of a pre-test, three game-play sessions, and a delayed post-test. After playing the game, students demonstrated significant gains in science content knowledge, with game usability ratings emerging as the strongest predictor of post-test content knowledge scores. The intervention also resulted in a shift to more negative attitudes toward inhalants, with the most negative shift occurring among eighth grade students and post-test knowledge gains as the strongest predictor of attitude change across all grade levels. These findings suggest that the environmental science approach used in Uncommon Scents is an efficacious strategy for delivering both basic science content and influencing perceived harm relating to the inhalation of toxic chemicals from common household products.

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

NASA Astrophysics Data System (ADS)

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

2009-02-01

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

Combined Approach for the Structural Characterization of Alkali Fluoroscandates: Solid-State NMR, Powder X-ray Diffraction, and Density Functional Theory Calculations.

PubMed

Rakhmatullin, Aydar; Polovov, Ilya B; Maltsev, Dmitry; Allix, Mathieu; Volkovich, Vladimir; Chukin, Andrey V; Boča, Miroslav; Bessada, Catherine

2018-02-05

The structures of several fluoroscandate compounds are presented here using a characterization approach combining powder X-ray diffraction and solid-state NMR. The structure of K 5 Sc 3 F 14 was fully determined from Rietveld refinement performed on powder X-ray diffraction data. Moreover, the local structures of NaScF 4 , Li 3 ScF 6 , KSc 2 F 7 , and Na 3 ScF 6 compounds were studied in detail from solid-state 19 F and 45 Sc NMR experiments. The 45 Sc chemical shift ranges for six- and seven-coordinated scandium environments were defined. The 19 F chemical shift ranges for bridging and terminal fluorine atoms were also determined. First-principles calculations of the 19 F and 45 Sc NMR parameters were carried out using plane-wave basis sets and periodic boundary conditions (CASTEP), and the results were compared with the experimental data. A good agreement between the calculated shielding constants and experimental chemical shifts was obtained. This demonstrates the good potential of computational methods in spectroscopic assignments of solid-state 45 Sc NMR spectroscopy.

There is Diversity in Disorder-"In all Chaos there is a Cosmos, in all Disorder a Secret Order".

PubMed

Nielsen, Jakob T; Mulder, Frans A A

2016-01-01

The protein universe consists of a continuum of structures ranging from full order to complete disorder. As the structured part of the proteome has been intensively studied, stably folded proteins are increasingly well documented and understood. However, proteins that are fully, or in large part, disordered are much less well characterized. Here we collected NMR chemical shifts in a small database for 117 protein sequences that are known to contain disorder. We demonstrate that NMR chemical shift data can be brought to bear as an exquisite judge of protein disorder at the residue level, and help in validation. With the help of secondary chemical shift analysis we demonstrate that the proteins in the database span the full spectrum of disorder, but still, largely segregate into two classes; disordered with small segments of order scattered along the sequence, and structured with small segments of disorder inserted between the different structured regions. A detailed analysis reveals that the distribution of order/disorder along the sequence shows a complex and asymmetric distribution, that is highly protein-dependent. Access to ratified training data further suggests an avenue to improving prediction of disorder from sequence.

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

PubMed

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

2013-11-01

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

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

NASA Astrophysics Data System (ADS)

Krykunov, Mykhaylo; Ziegler, Tom

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

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

PubMed Central

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

2009-01-01

The authors investigated the performance of the iterative Steiglitz–McBride (SM) algorithm on an autoregressive moving average (ARMA) model of signals from a fast, sparsely sampled, multiecho, chemical shift imaging (CSI) acquisition using simulation, phantom, ex vivo, and in vivo experiments with a focus on its potential usage in magnetic resonance (MR)-guided interventions. The ARMA signal model facilitated a rapid calculation of the chemical shift, apparent spin-spin relaxation time (T2*), and complex amplitudes of a multipeak system from a limited number of echoes (≤16). Numerical simulations of one- and two-peak systems were used to assess the accuracy and uncertainty in the calculated spectral parameters as a function of acquisition and tissue parameters. The measured uncertainties from simulation were compared to the theoretical Cramer–Rao lower bound (CRLB) for the acquisition. Measurements made in phantoms were used to validate the T2* estimates and to validate uncertainty estimates made from the CRLB. We demonstrated application to real-time MR-guided interventions ex vivo by using the technique to monitor a percutaneous ethanol injection into a bovine liver and in vivo to monitor a laser-induced thermal therapy treatment in a canine brain. Simulation results showed that the chemical shift and amplitude uncertainties reached their respective CRLB at a signal-to-noise ratio (SNR)≥5 for echo train lengths (ETLs)≥4 using a fixed echo spacing of 3.3 ms. T2* estimates from the signal model possessed higher uncertainties but reached the CRLB at larger SNRs and∕or ETLs. Highly accurate estimates for the chemical shift (<0.01 ppm) and amplitude (<1.0%) were obtained with ≥4 echoes and for T2* (<1.0%) with ≥7 echoes. We conclude that, over a reasonable range of SNR, the SM algorithm is a robust estimator of spectral parameters from fast CSI acquisitions that acquire ≤16 echoes for one- and two-peak systems. Preliminary ex vivo and in vivo experiments corroborated the results from simulation experiments and further indicate the potential of this technique for MR-guided interventional procedures with high spatiotemporal resolution ∼1.6×1.6×4 mm3 in ≤5 s. PMID:19378736

Asbestos: Geology, Mineralogy, Mining, and Uses

USGS Publications Warehouse

Virta, Robert L.

2002-01-01

The term asbestos is a generic designation referring usually to six types of naturally occurring mineral fibers that are or have been commercially exploited. These fibers belong to two mineral groups: serpentines and amphiboles. The serpentine group contains a single asbestiform variety: chrysotile; five asbestiform varieties of amphiboles are known: anthophyllite asbestos, grunerite asbestos (amosite), riebeckite asbestos (crocidolite), tremolite asbestos, and actinolite asbestos. These fibrous minerals share several properties which qualify them as asbestiform fibers: they are found in bundles of fibers which can be easily separated from the host matrix or cleaved into thinner fibers; the fibers exhibit high tensile strengths, they show high length: diameter (aspect) ratios, from a minimum of 20 up to greater than 1000; they are sufficiently flexible to be spun; and macroscopically, they resemble organic fibers such as cellulose. Since asbestos fibers are all silicates, they exhibit several other common properties, such as incombustibility, thermal stability, resistance to biodegradation, chemical inertia toward most chemicals, and low electrical conductivity. The term asbestos has traditionally been attributed only to those varieties that are commercially exploited. The industrial applications of asbestos fibers have now shifted almost exclusively to chrysotile. Two types of amphiboles, commonly designated as amosite and crocidolite are no longer mined. The other three amphibole varieties, anthophyllite asbestos, actinolite asbestos, and tremolite asbestos, have no significant industrial applications presently.

Theoretical Modeling of (99)Tc NMR Chemical Shifts.

PubMed

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

2016-09-06

Technetium-99 (Tc) displays a rich chemistry due to its wide range of accessible oxidation states (from -I to +VII) and ability to form coordination compounds. Determination of Tc speciation in complex mixtures is a major challenge, and (99)Tc nuclear magnetic resonance (NMR) spectroscopy is widely used to probe chemical environments of Tc in odd oxidation states. However, interpretation of (99)Tc NMR data is hindered by the lack of reference compounds. Density functional theory (DFT) calculations can help to fill this gap, but to date few computational studies have focused on (99)Tc NMR of compounds and complexes. This work evaluates the effectiveness of both pure generalized gradient approximation and their corresponding hybrid functionals, both with and without the inclusion of scalar relativistic effects, to model the (99)Tc NMR spectra of Tc(I) carbonyl compounds. With the exception of BLYP, which performed exceptionally well overall, hybrid functionals with inclusion of scalar relativistic effects are found to be necessary to accurately calculate (99)Tc NMR spectra. The computational method developed was used to tentatively assign an experimentally observed (99)Tc NMR peak at -1204 ppm to fac-Tc(CO)3(OH)3(2-). This study examines the effectiveness of DFT computations for interpretation of the (99)Tc NMR spectra of Tc(I) coordination compounds in high salt alkaline solutions.

Field Characterization of Potential Reference Sediments in the Gulf of Mexico: Chemical and Biological Quality

EPA Science Inventory

Lewis, Michael A., Jed G. Campbell, Peggy S. Harris, Darrin D. Dantin, Steve S. Foss, Robert L. Quarles, James C. Moore and Cynthia A. Chancy. Submitted. Characterization of Potential Reference Areas in the Gulf of Mexico: Near-Coastal Sediment Chemical and Biological Quality. En...

A multiscale simulation technique for molecular electronics: design of a directed self-assembled molecular n-bit shift register memory device.

PubMed

Lambropoulos, Nicholas A; Reimers, Jeffrey R; Crossley, Maxwell J; Hush, Noel S; Silverbrook, Kia

2013-12-20

A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology.

A multiscale simulation technique for molecular electronics: design of a directed self-assembled molecular n-bit shift register memory device

NASA Astrophysics Data System (ADS)

Lambropoulos, Nicholas A.; Reimers, Jeffrey R.; Crossley, Maxwell J.; Hush, Noel S.; Silverbrook, Kia

2013-12-01

A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology.

Host shifts and evolutionary radiations of butterflies

PubMed Central

Fordyce, James A.

2010-01-01

Ehrlich and Raven proposed a model of coevolution where major host plant shifts of butterflies facilitate a burst of diversification driven by their arrival to a new adaptive zone. One prediction of this model is that reconstructions of historical diversification of butterflies should indicate an increase in diversification rate following major host shifts. Using reconstructed histories of 15 butterfly groups, I tested this prediction and found general agreement with Ehrlich and Raven's model. Butterfly lineages with an inferred major historical host shift showed evidence of diversification rate variation, with a significant acceleration following the host shift. Lineages without an inferred major host shift generally agreed with a constant-rate model of diversification. These results are consistent with the view that host plant associations have played a profound role in the evolutionary history of butterflies, and show that major shifts to chemically distinct plant groups leave a historical footprint that remains detectable today. PMID:20610430

Development and Validation of a Computational Model for Androgen Receptor Activity

PubMed Central

2016-01-01

Testing thousands of chemicals to identify potential androgen receptor (AR) agonists or antagonists would cost millions of dollars and take decades to complete using current validated methods. High-throughput in vitro screening (HTS) and computational toxicology approaches can more rapidly and inexpensively identify potential androgen-active chemicals. We integrated 11 HTS ToxCast/Tox21 in vitro assays into a computational network model to distinguish true AR pathway activity from technology-specific assay interference. The in vitro HTS assays probed perturbations of the AR pathway at multiple points (receptor binding, coregulator recruitment, gene transcription, and protein production) and multiple cell types. Confirmatory in vitro antagonist assay data and cytotoxicity information were used as additional flags for potential nonspecific activity. Validating such alternative testing strategies requires high-quality reference data. We compiled 158 putative androgen-active and -inactive chemicals from a combination of international test method validation efforts and semiautomated systematic literature reviews. Detailed in vitro assay information and results were compiled into a single database using a standardized ontology. Reference chemical concentrations that activated or inhibited AR pathway activity were identified to establish a range of potencies with reproducible reference chemical results. Comparison with existing Tier 1 AR binding data from the U.S. EPA Endocrine Disruptor Screening Program revealed that the model identified binders at relevant test concentrations (<100 μM) and was more sensitive to antagonist activity. The AR pathway model based on the ToxCast/Tox21 assays had balanced accuracies of 95.2% for agonist (n = 29) and 97.5% for antagonist (n = 28) reference chemicals. Out of 1855 chemicals screened in the AR pathway model, 220 chemicals demonstrated AR agonist or antagonist activity and an additional 174 chemicals were predicted to have potential weak AR pathway activity. PMID:27933809

"I Am Chelsea Manning": Comparison of Gendered Representation of Private Manning in U.S. and International News Media.

PubMed

Hackl, Andrea M; Becker, Amy B; Todd, Maureen E

2016-01-01

On August 22, 2013, Bradley Manning released a statement requesting to be referred to as female. In the following days, the news media discussed whether language should shift toward a female representation. Using quantitative content analysis and qualitative contextual analysis, this study analyzed whether U.S. and international newspapers (N = 197) acknowledged Manning's request to be referred to as "Chelsea" in the two weeks after the statement. Results suggest that the mainstream press was hesitant in shifting toward a female representation. A comparison of international and U.S. newspapers suggests that the U.S. press lagged behind international coverage using a female depiction.

Phase-shifting point diffraction interferometer focus-aid enhanced mask

DOEpatents

Naulleau, Patrick

2000-01-01

A phase-shifting point diffraction interferometer system (PS/PDI) employing a PS/PDI mask that includes a PDI focus aid is provided. The PDI focus aid mask includes a large or secondary reference pinhole that is slightly displaced from the true or primary reference pinhole. The secondary pinhole provides a larger capture tolerance for interferometrically performing fine focus. With the focus-aid enhanced mask, conventional methods such as the knife-edge test can be used to perform an initial (or rough) focus and the secondary (large) pinhole is used to perform interferometric fine focus. Once the system is well focused, high accuracy interferometry can be performed using the primary (small) pinhole.

Developing a list of reference chemicals for testing alternatives to whole fish toxicity tests.

PubMed

Schirmer, Kristin; Tanneberger, Katrin; Kramer, Nynke I; Völker, Doris; Scholz, Stefan; Hafner, Christoph; Lee, Lucy E J; Bols, Niels C; Hermens, Joop L M

2008-11-11

This paper details the derivation of a list of 60 reference chemicals for the development of alternatives to animal testing in ecotoxicology with a particular focus on fish. The chemicals were selected as a prerequisite to gather mechanistic information on the performance of alternative testing systems, namely vertebrate cell lines and fish embryos, in comparison to the fish acute lethality test. To avoid the need for additional experiments with fish, the U.S. EPA fathead minnow database was consulted as reference for whole organism responses. This database was compared to the Halle Registry of Cytotoxicity and a collation of data by the German EPA (UBA) on acute toxicity data derived from zebrafish embryos. Chemicals that were present in the fathead minnow database and in at least one of the other two databases were subject to selection. Criteria included the coverage of a wide range of toxicity and physico-chemical parameters as well as the determination of outliers of the in vivo/in vitro correlations. While the reference list of chemicals now guides our research for improving cell line and fish embryo assays to make them widely applicable, the list could be of benefit to search for alternatives in ecotoxicology in general. One example would be the use of this list to validate structure-activity prediction models, which in turn would benefit from a continuous extension of this list with regard to physico-chemical and toxicological data.

Advanced gasifier and water gas shift technologies for low cost coal conversion to high hydrogen syngas

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

Kramer, Andrew Kramer

The Gas Technology Institute (GTI) and team members RTI International (RTI), Coanda Research and Development, and Nexant, are developing and maturing a portfolio of technologies to meet the United States Department of Energy (DOE) goals for lowering the cost of producing high hydrogen syngas from coal for use in carbon capture power and coal-to-liquids/chemicals. This project matured an advanced pilot-scale gasifier, with scalable and commercially traceable components, to readiness for use in a first-of-a-kind commercially-relevant demonstration plant on the scale of 500-1,000 tons per day (TPD). This was accomplished through cold flow simulation of the gasifier quench zone transition regionmore » at Coanda and through an extensive hotfire gasifier test program on highly reactive coal and high ash/high ash fusion temperature coals at GTI. RTI matured an advanced water gas shift process and catalyst to readiness for testing at pilot plant scale through catalyst development and testing, and development of a preliminary design basis for a pilot scale reactor demonstrating the catalyst. A techno-economic analysis was performed by Nexant to assess the potential benefits of the gasifier and catalyst technologies in the context of power production and methanol production. This analysis showed an 18%reduction in cost of power and a 19%reduction in cost of methanol relative to DOE reference baseline cases.« less

When the universe expands too fast: relentless dark matter

NASA Astrophysics Data System (ADS)

D'Eramo, Francesco; Fernandez, Nicolas; Profumo, Stefano

2017-05-01

We consider a modification to the standard cosmological history consisting of introducing a new species phi whose energy density red-shifts with the scale factor a like ρphi propto a-(4+n). For 0n>, such a red-shift is faster than radiation, hence the new species dominates the energy budget of the universe at early times while it is completely negligible at late times. If equality with the radiation energy density is achieved at low enough temperatures, dark matter can be produced as a thermal relic during the new cosmological phase. Dark matter freeze-out then occurs at higher temperatures compared to the standard case, implying that reproducing the observed abundance requires significantly larger annihilation rates. Here, we point out a completely new phenomenon, which we refer to as relentless dark matter: for large enough n, unlike the standard case where annihilation ends shortly after the departure from thermal equilibrium, dark matter particles keep annihilating long after leaving chemical equilibrium, with a significant depletion of the final relic abundance. Relentless annihilation occurs for n >= 2 and n >= 4 for s-wave and p-wave annihilation, respectively, and it thus occurs in well motivated scenarios such as a quintessence with a kination phase. We discuss a few microscopic realizations for the new cosmological component and highlight the phenomenological consequences of our calculations for dark matter searches.

Synthesis, antimicrobial evaluation and theoretical prediction of NMR chemical shifts of thiazole and selenazole derivatives with high antifungal activity against Candida spp.

NASA Astrophysics Data System (ADS)

Łączkowski, Krzysztof Z.; Motylewska, Katarzyna; Baranowska-Łączkowska, Angelika; Biernasiuk, Anna; Misiura, Konrad; Malm, Anna; Fernández, Berta

2016-03-01

Synthesis and investigation of antimicrobial activities of novel thiazoles and selenazoles is presented. Their structures were determined using NMR, FAB(+)-MS, HRMS and elemental analyses. To support the experiment, theoretical calculations of the 1H NMR shifts were carried out for representative systems within the DFT B3LYP/6-311++G** approximation which additionally confirmed the structure of investigated compounds. Among the derivatives, compounds 4b, 4h, 4j and 4l had very strong activity against reference strains of Candida albicans ATCC and Candida parapsilosis ATCC 22019 with MIC = 0.49-7.81 μg/ml. In the case of compounds 4b, 4c, 4h - 4j and 4l, the activity was very strong against of Candida spp. isolated from clinical materials, i.e. C. albicans, Candida krusei, Candida inconspicua, Candida famata, Candida lusitaniae, Candida sake, C. parapsilosis and Candida dubliniensis with MIC = 0.24-15.62 μg/ml. The activity of several of these was similar to the activity of commonly used antifungal agent fluconazole. Additionally, compounds 4m - 4s were found to be active against Gram-positive bacteria, both pathogenic staphylococci Staphylococcus aureus ATCC with MIC = 31.25-125 μg/ml and opportunistic bacteria, such as Staphylococcus epidermidis ATCC 12228 and Micrococcus luteus ATCC 10240 with MIC = 7.81-31.25 μg/ml.

Postmodernism versus Professionalism in Higher Education. Thematic Reflections on Higher Education

ERIC Educational Resources Information Center

Milliken, John

2004-01-01

A global paradigm shift is taking place at the beginning of the Twenty-First Century, which is resulting in massive changes in the frames of reference about the ways of life, work, and society and how they are viewed and organized. This shift is essentially a sweeping set of worldwide changes in the public domain which challenges the prevailing…

40 CFR 60.1185 - What types of operator certification must the chief facility operator and shift supervisor obtain...

Code of Federal Regulations, 2010 CFR

2010-07-01

.... (c) Each chief facility operator and shift supervisor must take one of three actions: (1) Obtain a... in your State. (2) Schedule a full certification exam with the American Society of Mechanical Engineers (QRO-1-1994) (incorporated by reference in § 60.17(h)(1)). (3) Schedule a full certification exam...

The Shifting Politics of the Private in Education: Debates and Developments in Researching Private School Outreach in India

ERIC Educational Resources Information Center

Ashley, Laura Day

2013-01-01

This paper addresses the politics of researching private education with special reference to the Indian context. Due to a recent increase in privatised forms of education globally and recognition of the private sector by governments, international agencies and researchers as a policy and academic interest, this is shifting ground. The evolving…

Effect of a Surprising Downward Shift in Reinforcer Value on Stimulus Over-Selectivity in a Simultaneous Discrimination Procedure

ERIC Educational Resources Information Center

Reynolds, Gemma; Reed, Phil

2013-01-01

Stimulus over-selectivity refers to the phenomenon whereby behavior is controlled by a subset of elements in the environment at the expense of other equally salient aspects of the environment. The experiments explored whether this cue interference effect was reduced following a surprising downward shift in reinforcer value. Experiment 1 revealed…

Tests of the Dynamic Field Theory and the Spatial Precision Hypothesis: Capturing a Qualitative Developmental Transition in Spatial Working Memory

PubMed Central

Schutte, Anne R.; Spencer, John P.

2009-01-01

This study tested a dynamic field theory (DFT) of spatial working memory and an associated spatial precision hypothesis (SPH). Between three and six years of age there is a qualitative shift in how children use reference axes to remember locations: 3-year-olds’ spatial recall responses are biased toward reference axes after short memory delays, whereas 6-year-olds’ responses are biased away from reference axes. According to the DFT and the SPH, quantitative improvements over development in the precision of excitatory and inhibitory working memory processes lead to this qualitative shift. Simulations of the DFT in Experiment 1 predict that improvements in precision should cause the spatial range of targets attracted toward a reference axis to narrow gradually over development with repulsion emerging and gradually increasing until responses to most targets show biases away from the axis. Results from Experiment 2 with 3- to 5-year-olds support these predictions. Simulations of the DFT in Experiment 3 quantitatively fit the empirical results and offer insights into the neural processes underlying this developmental change. PMID:19968430

A Vision of the Chemical Engineering Curriculum of the Future

ERIC Educational Resources Information Center

Armstrong, Robert C.

2006-01-01

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

Using Arago's spot to monitor optical axis shift in a Petzval refractor.

PubMed

Bruns, Donald G

2017-03-10

Measuring the change in the optical alignment of a camera attached to a telescope is necessary to perform astrometric measurements. Camera movement when the telescope is refocused changes the plate constants, invalidating the calibration. Monitoring the shift in the optical axis requires a stable internal reference source. This is easily implemented in a Petzval refractor by adding an illuminated pinhole and a small obscuration that creates a spot of Arago on the camera. Measurements of the optical axis shift for a commercial telescope are given as an example.

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

NASA Astrophysics Data System (ADS)

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.

CON4EI: Selection of the reference chemicals for hazard identification and labelling of eye irritating chemicals.

PubMed

Adriaens, E; Alépée, N; Kandarova, H; Drzewieckac, A; Gruszka, K; Guest, R; Willoughby, J A; Verstraelen, S; Van Rompay, A R

2017-10-01

Assessment of the acute eye irritation potential is part of the international regulatory requirements for testing of chemicals. In the past, several prospective and retrospective validation studies have taken place in the area of serious eye damage/eye irritation testing. Success in terms of complete replacement of the regulatory in vivo Draize rabbit eye test has not yet been achieved. A very important aspect to ensure development of successful alternative test methods and/or strategies for serious eye damage/eye irritation testing is the selection of appropriate reference chemicals. A set of 80 reference chemicals was selected for the CEFIC-LRI-AIMT6-VITO CON4EI (CONsortium for in vitro Eye Irritation testing strategy) project, in collaboration with Cosmetics Europe, from the Draize Reference Database published by Cosmetics Europe based on key criteria that were set in their paper (e.g. balanced by important driver of classification and physical state). The most important goals of the CON4EI project were to identify the performance of eight in vitro alternative tests in terms of driver of classification and to identify similarities/differences between the methods in order the build a successful testing strategy that can discriminate between all UN GHS categories. This paper provides background on selection of the test chemicals. Copyright © 2017 Elsevier Ltd. All rights reserved.

Reprint of "CON4EI: Selection of the reference chemicals for hazard identification and labelling of eye irritating chemicals".

PubMed

Adriaens, E; Alépée, N; Kandarova, H; Drzewieckac, A; Gruszka, K; Guest, R; Willoughby, J A; Verstraelen, S; Van Rompay, A R

2018-06-01

Assessment of the acute eye irritation potential is part of the international regulatory requirements for testing of chemicals. In the past, several prospective and retrospective validation studies have taken place in the area of serious eye damage/eye irritation testing. Success in terms of complete replacement of the regulatory in vivo Draize rabbit eye test has not yet been achieved. A very important aspect to ensure development of successful alternative test methods and/or strategies for serious eye damage/eye irritation testing is the selection of appropriate reference chemicals. A set of 80 reference chemicals was selected for the CEFIC-LRI-AIMT6-VITO CON4EI (CONsortium for in vitro Eye Irritation testing strategy) project, in collaboration with Cosmetics Europe, from the Draize Reference Database published by Cosmetics Europe based on key criteria that were set in their paper (e.g. balanced by important driver of classification and physical state). The most important goals of the CON4EI project were to identify the performance of eight in vitro alternative tests in terms of driver of classification and to identify similarities/differences between the methods in order the build a successful testing strategy that can discriminate between all UN GHS categories. This paper provides background on selection of the test chemicals. Copyright © 2018. Published by Elsevier Ltd.

A Joined-Wing Flight Experiment

DTIC Science & Technology

2008-02-01

and fuselage, reference geometry and ventral fins, reference geometry and winglets and finally reference geometry and main gear strut-fins. He...the addition of winglets or strut fins, unless the center of mass was shifted forward [30]. Throughout his analysis it became clear that VA-1...With the addition of winglets or fins placed over the main wheel struts, 02.0≈Δ βN C . The addition of the winglets or strut fins introduces a spiral

A multi-technique approach to assess chemical speciation of phosphate in soils

NASA Astrophysics Data System (ADS)

Belchior Abdala, Dalton; Rodrigues, Marcos; Herrera, Wilfrand; Pavinato, Paulo Sergio

2017-04-01

Soil scientists see chemical characterization of phosphorus (e.g., chemical speciation) as a winning strategy to increase phosphorus use efficiency in agriculture, to understand the fate of applied P fertilizer in soils and to devise strategies to minimize P losses to the environment. Phosphorus (P) is majorly presented in soils as phosphate, bound to mineral components of soils such as Al-, Ca- and Fe-(hydr)oxides or associated with organic molecules, being thus generally referred to as organic phosphates. In addition, because of the turnover of P between plants and microbes, it delivers P back to soils as a mixture of species with high spatial and chemical heterogeneity, adding complexity to the determination of the P species contained in environmental samples. Therefore, due to the variety of forms that phosphate can present in soils, its precise chemical characterization can only be achieved using a set of analytical techniques. Although established methodologies (e. g., soil test P, sequential chemical fractionation, P isotherms) have been useful to subsidize information for the establishment of policies and guidelines for soil management and P fertilizers use, they have failed to provide detailed information on P chemistry and reactivity in soils in a more satisfactory manner, which are critical to predict P bioavailability to plants and loss potential to the environment. More recently, the association of wet chemistry analysis with spectroscopy and microscopy techniques has arguably represented the most successful means to chemically speciate phosphate in soils. This is because using qualitative (chemical speciation), quantitative (chemical fractionation) and spatial (microscopy) data allows for triangulation of information, thereby reducing bias and increasing validity of the results. The analysis framework that we propose in this study includes the use of (i) sequential chemical fractionation of soil P to determine the partitioning of P within the different P pools considered in the fractionation protocol, (ii) two synchrotron-based X-ray absorption spectroscopic techniques, XANES and EXAFS, for chemical characterization of the P forms and mineralogy of Fe-(hydr)oxides present in a sample, and (iii) Scanning Electron Microscopy and Energy-Dispersive spectroscopy, SEM/EDS, to provide complimentary information to corroborate and aid in the interpretation of our P XANES data. It was shown that the combination of techniques can assist us not only in the determination of the P chemical species present in a given material, but also to better understand the complex and dynamic processes to which P is subjected in soils. The association of spectroscopy (XANES and EXAFS) and microscopy (SEM/EDS) with wet chemistry data in this study was key to shift our understanding of the relationship between P and other soil mineral components from a macroscopic into a microscopic one. This represents a strong driving force to integrate the results of multi-analytical techniques into a more complete understanding of the systems under study. In addition, we provide a library of reference spectra for P K-edge XANES containing P sorbed to single and binary mixtures of mineral analogues intended to assist in the identification of P sorbed species commonly found in soils and sediments. Key-words: P K-edge XANES, Fe K-edge EXAFS, sequential chemical fractionation, soil phosphorus

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

PubMed

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

2008-12-11

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

Identifying known unknowns using the US EPA's CompTox ...

EPA Pesticide Factsheets

Chemical features observed using high-resolution mass spectrometry can be tentatively identified using online chemical reference databases by searching molecular formulae and monoisotopic masses and then rank-ordering of the hits using appropriate relevance criteria. The most likely candidate “known unknowns,” which are those chemicals unknown to an investigator but contained within a reference database or literature source, rise to the top of a chemical list when rank-ordered by the number of associated data sources. The U.S. EPA’s CompTox Chemistry Dashboard is a curated and freely available resource for chemistry and computational toxicology research, containing more than 720,000 chemicals of relevance to environmental health science. In this research, the performance of the Dashboard for identifying “known unknowns” was evaluated against that of the online ChemSpider database, one of the primary resources used by mass spectrometrists, using multiple previously studied datasets reported in the peer-reviewed literature totaling 162 chemicals. These chemicals were examined using both applications via molecular formula and monoisotopic mass searches followed by rank-ordering of candidate compounds by associated references or data sources. A greater percentage of chemicals ranked in the top position when using the Dashboard, indicating an advantage of this application over ChemSpider for identifying known unknowns using data source ranking. Addition

Medial Entorhinal Grid Cells and Head Direction Cells Rotate with a T-Maze More Often During Less Recently Experienced Rotations

PubMed Central

Gupta, Kishan; Beer, Nathan J.; Keller, Lauren A.; Hasselmo, Michael E.

2014-01-01

Prior studies of head direction (HD) cells indicate strong landmark control over the preferred firing direction of these cells, with few studies exhibiting shifts away from local reference frames over time. We recorded spiking activity of grid and HD cells in the medial entorhinal cortex of rats, testing correlations of local environmental cues with the spatial tuning curves of these cells' firing fields as animals performed continuous spatial alternation on a T-maze that shared the boundaries of an open-field arena. The environment was rotated into configurations the animal had either seen or not seen in the past recording week. Tuning curves of both cell types demonstrated commensurate shifts of tuning with T-maze rotations during less recent rotations, more so than recent rotations. This strongly suggests that animals are shifting their reference frame away from the local environmental cues over time, learning to use a different reference frame more likely reliant on distal or idiothetic cues. In addition, grid fields demonstrated varying levels of “fragmentation” on the T-maze. The propensity for fragmentation does not depend on grid spacing and grid score, nor animal trajectory, indicating the cognitive treatment of environmental subcompartments is likely driven by task demands. PMID:23382518

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Thiol-thione tautomeric analysis, spectroscopic (FT-IR, Laser-Raman, NMR and UV-vis) properties and DFT computations of 5-(3-pyridyl)-4H-1,2,4-triazole-3-thiol molecule.

PubMed

Gökce, Halil; Öztürk, Nuri; Ceylan, Ümit; Alpaslan, Yelda Bingöl; Alpaslan, Gökhan

2016-06-15

In this study, the 5-(3-pyridyl)-4H-1,2,4-triazole-3-thiol molecule (C7H6N4S) molecule has been characterized by using FT-IR, Laser-Raman, NMR and UV-vis spectroscopies. Quantum chemical calculations have been performed to investigate the molecular structure (thione-thiol tautomerism), vibrational wavenumbers, electronic transition absorption wavelengths in DMSO solvent and vacuum, proton and carbon-13 NMR chemical shifts and HOMOs-LUMOs energies at DFT/B3LYP/6-311++G(d,p) level for all five tautomers of the title molecule. The obtained results show that the calculated vibrational wavenumbers, NMR chemical shifts and UV-vis wavelengths are in a good agreement with experimental data. Copyright © 2016 Elsevier B.V. All rights reserved.

The combustion of Al-CuO powder mixture under shock wave initiation of the reaction

NASA Astrophysics Data System (ADS)

Ananev, S. Yu; Yankovsky, B. D.; Dolgoborodov, A. Yu

2018-01-01

The results of experiments on monitoring of manifestations of chemical transformation of Al-CuO powder mixture as a result of shock loading are given. Speeds of shift and expansion of chemical transformation area in free space are determined. The data about structure of combustion area of are received. The temperature of combustion area is measured. The duration of chemical transformation is determined.

Expert system application for prioritizing preventive actions for shift work: shift expert.

PubMed

Esen, Hatice; Hatipoğlu, Tuğçen; Cihan, Ahmet; Fiğlali, Nilgün

2017-09-19

Shift patterns, work hours, work arrangements and worker motivations have increasingly become key factors for job performance. The main objective of this article is to design an expert system that identifies the negative effects of shift work and prioritizes mitigation efforts according to their importance in preventing these negative effects. The proposed expert system will be referred to as the shift expert. A thorough literature review is conducted to determine the effects of shift work on workers. Our work indicates that shift work is linked to demographic variables, sleepiness and fatigue, health and well-being, and social and domestic conditions. These parameters constitute the sections of a questionnaire designed to focus on 26 important issues related to shift work. The shift expert is then constructed to provide prevention advice at the individual and organizational levels, and it prioritizes this advice using a fuzzy analytic hierarchy process model, which considers comparison matrices provided by users during the prioritization process. An empirical study of 61 workers working on three rotating shifts is performed. After administering the questionnaires, the collected data are analyzed statistically, and then the shift expert produces individual and organizational recommendations for these workers.

Research on effects of phase error in phase-shifting interferometer

NASA Astrophysics Data System (ADS)

Wang, Hongjun; Wang, Zhao; Zhao, Hong; Tian, Ailing; Liu, Bingcai

2007-12-01

Referring to phase-shifting interferometry technology, the phase shifting error from the phase shifter is the main factor that directly affects the measurement accuracy of the phase shifting interferometer. In this paper, the resources and sorts of phase shifting error were introduction, and some methods to eliminate errors were mentioned. Based on the theory of phase shifting interferometry, the effects of phase shifting error were analyzed in detail. The Liquid Crystal Display (LCD) as a new shifter has advantage as that the phase shifting can be controlled digitally without any mechanical moving and rotating element. By changing coded image displayed on LCD, the phase shifting in measuring system was induced. LCD's phase modulation characteristic was analyzed in theory and tested. Based on Fourier transform, the effect model of phase error coming from LCD was established in four-step phase shifting interferometry. And the error range was obtained. In order to reduce error, a new error compensation algorithm was put forward. With this method, the error can be obtained by process interferogram. The interferogram can be compensated, and the measurement results can be obtained by four-step phase shifting interferogram. Theoretical analysis and simulation results demonstrate the feasibility of this approach to improve measurement accuracy.

Conditional heteroscedasticity as a leading indicator of ecological regime shifts.

PubMed

Seekell, David A; Carpenter, Stephen R; Pace, Michael L

2011-10-01

Regime shifts are massive, often irreversible, rearrangements of nonlinear ecological processes that occur when systems pass critical transition points. Ecological regime shifts sometimes have severe consequences for human well-being, including eutrophication in lakes, desertification, and species extinctions. Theoretical and laboratory evidence suggests that statistical anomalies may be detectable leading indicators of regime shifts in ecological time series, making it possible to foresee and potentially avert incipient regime shifts. Conditional heteroscedasticity is persistent variance characteristic of time series with clustered volatility. Here, we analyze conditional heteroscedasticity as a potential leading indicator of regime shifts in ecological time series. We evaluate conditional heteroscedasticity by using ecological models with and without four types of critical transition. On approaching transition points, all time series contain significant conditional heteroscedasticity. This signal is detected hundreds of time steps in advance of the regime shift. Time series without regime shifts do not have significant conditional heteroscedasticity. Because probability values are easily associated with tests for conditional heteroscedasticity, detection of false positives in time series without regime shifts is minimized. This property reduces the need for a reference system to compare with the perturbed system.

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

NASA Astrophysics Data System (ADS)

Ishii, Yoshitaka

2001-05-01

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

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

PubMed

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

2011-11-07

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

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

McChesney, J.D.

The chemical substances utilized in consumer products, and for pharmaceutical and agricultural uses are generally referred to as specialty chemicals. These may be flavor or fragrance substances, intermediates for synthesis of drugs or agrochemicals or the drugs or agrochemicals themselves, insecticides or insect pheromones or antifeedants, plant growth regulators, etc. These are in contrast to chemicals which are utilized in large quantities for fuels or preparation of plastics, lubricants, etc., which are usually referred to as industrial chemicals. The specific utilization of specialty chemicals is associated with a specific important physiochemical or biological property. They may possess unique properties asmore » lubricants or waxes or have a very desirable biological activity such as a drug, agrochemical or perfume ingredient. These unique properties convey significant economic value to the specific specialty chemical. The economic commercial production of specialty chemicals commonly requires the isolation of a precursor or the specialty chemical itself from a natural source. The discovery, development and commercialization of specialty chemicals is presented and reviewed. The economic and sustainable production of specialty chemicals is discussed.« less