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Sample records for chemical shift calculations

  1. Calculations of proton chemical shifts in olefins and aromatics

    CERN Document Server

    Escrihuela, M C

    2000-01-01

    induced reagents on alpha,beta unsaturated ketones has also been investigated in order to deduce molecular structures and to obtain the assignment of the spectra of these molecules. A semi-empirical calculation of the partial atomic charges in organic compounds based on molecular dipole moments (CHARGE3) was developed into a model capable of predicting proton chemical shifts in a wide variety of organic compounds to a reasonable degree of accuracy. The model has been modified to include condensed aromatic hydrocarbons and substituted benzenes, alkenes, halo-monosubstituted benzenes and halo-alkenes. Within the aromatic compounds the influence of the pi electron densities and the ring current have been investigated, along with the alpha, beta and gamma effects. The model gives the first accurate calculation of the proton chemical shifts of condensed aromatic compounds and the proton substituent chemical shifts (SCS) in the benzene ring. For the data set of 55 proton chemical shifts spanning 3 ppm the rms error...

  2. Calculations of NMR chemical shifts with APW-based methods

    Science.gov (United States)

    Laskowski, Robert; Blaha, Peter

    2012-01-01

    We present a full potential, all electron augmented plane wave (APW) implementation of first-principles calculations of NMR chemical shifts. In order to obtain the induced current we follow a perturbation approach [Pickard and Mauri, Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.63.245101 63, 245101 (2001)] and extended the common APW + local orbital (LO) basis by several LOs at higher energies. The calculated all-electron current is represented in traditional APW manner as Fourier series in the interstitial region and with a spherical harmonics representation inside the nonoverlapping atomic spheres. The current is integrated using a “pseudocharge” technique. The implementation is validated by comparison of the computed chemical shifts with some “exact” results for spherical atoms and for a set of solids and molecules with available published data.

  3. Ab Initio Calculation of Nuclear Magnetic Resonance Chemical Shift Anisotropy Tensors 1. Influence of Basis Set on the Calculation of 31P Chemical Shifts

    Energy Technology Data Exchange (ETDEWEB)

    Alam, T.M.

    1998-09-01

    The influence of changes in the contracted Gaussian basis set used for ab initio calculations of nuclear magnetic resonance (NMR) phosphorous chemical shift anisotropy (CSA) tensors was investigated. The isotropic chemical shitl and chemical shift anisotropy were found to converge with increasing complexity of the basis set at the Hartree-Fock @IF) level. The addition of d polarization function on the phosphorous nucIei was found to have a major impact of the calculated chemical shi~ but diminished with increasing number of polarization fimctions. At least 2 d polarization fimctions are required for accurate calculations of the isotropic phosphorous chemical shift. The introduction of density fictional theory (DFT) techniques through tie use of hybrid B3LYP methods for the calculation of the phosphorous chemical shift tensor resulted in a poorer estimation of the NMR values, even though DFT techniques result in improved energy and force constant calculations. The convergence of the W parametem with increasing basis set complexity was also observed for the DFT calculations, but produced results with consistent large deviations from experiment. The use of a HF 6-31 l++G(242p) basis set represents a good compromise between accuracy of the simulation and the complexity of the calculation for future ab initio calculations of 31P NMR parameters in larger complexes.

  4. Ab Initio Calculations of Deuterium Isotope Effects on Chemical Shifts of Salt-Bridged Lysines

    DEFF Research Database (Denmark)

    Ullah, Saif; Ishimoto, Takayoshi; Williamson, Mike P.;

    2011-01-01

    Deuterium isotope effects measure the change in chemical shift on substitution of a proton by deuterium. They have been calculated by direct treatment of the H/D nuclear quantum effect using a multicomponent ab initio molecular orbital method based on a non-Born−Oppenheimer approximation. This me......Deuterium isotope effects measure the change in chemical shift on substitution of a proton by deuterium. They have been calculated by direct treatment of the H/D nuclear quantum effect using a multicomponent ab initio molecular orbital method based on a non-Born−Oppenheimer approximation...

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

    Energy Technology Data Exchange (ETDEWEB)

    Swails, Jason [Rutgers University, Department of Chemistry and Chemical Biology and BioMaPS Institute (United States); Zhu, Tong; He, Xiao, E-mail: xiaohe@phy.ecnu.edu.cn [East China Normal University, State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science (China); Case, David A., E-mail: case@biomaps.rutgers.edu [Rutgers University, Department of Chemistry and Chemical Biology and BioMaPS Institute (United States)

    2015-10-15

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

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

    Directory of Open Access Journals (Sweden)

    Karl-Heinz Böhm

    2014-04-01

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

  7. First-principles calculation of core-level binding energy shift in surface chemical processes

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Combined with third generation synchrotron radiation light sources, X-ray photoelectron spectroscopy (XPS) with higher energy resolution, brilliance, enhanced surface sensitivity and photoemission cross section in real time found extensive applications in solid-gas interface chemistry. This paper reports the calculation of the core-level binding energy shifts (CLS) using the first-principles density functional theory. The interplay between the CLS calculations and XPS measurements to uncover the structures, adsorption sites and chemical reactions in complex surface chemical processes are highlight. Its application on clean low index (111) and vicinal transition metal surfaces, molecular adsorption in terms of sites and configuration, and reaction kinetics are domonstrated.

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

    DEFF Research Database (Denmark)

    Lægsgaard, Jesper

    2001-01-01

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

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

    Science.gov (United States)

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

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

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

    Science.gov (United States)

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

    2008-08-14

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

  11. Protein Chemical Shift Prediction

    CERN Document Server

    Larsen, Anders S

    2014-01-01

    The protein chemical shifts holds a large amount of information about the 3-dimensional structure of the protein. A number of chemical shift predictors based on the relationship between structures resolved with X-ray crystallography and the corresponding experimental chemical shifts have been developed. These empirical predictors are very accurate on X-ray structures but tends to be insensitive to small structural changes. To overcome this limitation it has been suggested to make chemical shift predictors based on quantum mechanical(QM) calculations. In this thesis the development of the QM derived chemical shift predictor Procs14 is presented. Procs14 is based on 2.35 million density functional theory(DFT) calculations on tripeptides and contains corrections for hydrogen bonding, ring current and the effect of the previous and following residue. Procs14 is capable at performing predictions for the 13CA, 13CB, 13CO, 15NH, 1HN and 1HA backbone atoms. In order to benchmark Procs14, a number of QM NMR calculatio...

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

    NARCIS (Netherlands)

    Tamiola, Kamil; Mulder, Frans A. A.

    2012-01-01

    NMR spectroscopy offers the unique possibility to relate the structural propensities of disordered proteins and loop segments of folded peptides to biological function and aggregation behaviour. Backbone chemical shifts are ideally suited for this task, provided that appropriate reference data are a

  13. Observed and calculated 1H and 13C chemical shifts induced by the in situ oxidation of model sulfides to sulfoxides and sulfones.

    Science.gov (United States)

    Dracínský, Martin; Pohl, Radek; Slavetínská, Lenka; Budesínský, Milos

    2010-09-01

    A series of model sulfides was oxidized in the NMR sample tube to sulfoxides and sulfones by the stepwise addition of meta-chloroperbenzoic acid in deuterochloroform. Various methods of quantum chemical calculations have been tested to reproduce the observed (1)H and (13)C chemical shifts of the starting sulfides and their oxidation products. It has been shown that the determination of the energy-minimized conformation is a very important condition for obtaining realistic data in the subsequent calculation of the NMR chemical shifts. The correlation between calculated and observed chemical shifts is very good for carbon atoms (even for the 'cheap' DFT B3LYP/6-31G* method) and somewhat less satisfactory for hydrogen atoms. The calculated chemical shifts induced by oxidation (the Delta delta values) agree even better with the experimental values and can also be used to determine the oxidation state of the sulfur atom (-S-, -SO-, -SO(2)-).

  14. On the calculation of Mossbauer isomer shift

    NARCIS (Netherlands)

    Filatov, Michael

    2007-01-01

    A quantum chemical computational scheme for the calculation of isomer shift in Mossbauer spectroscopy is suggested. Within the described scheme, the isomer shift is treated as a derivative of the total electronic energy with respect to the radius of a finite nucleus. The explicit use of a finite nuc

  15. Effect of spectra recording conditions on the example of chemical shifts calculation in CMR spectra of 1-pentylbenzoylformate

    OpenAIRE

    Mizyuk, Volodymyr; Shibanov, Volodymyr

    2011-01-01

    The concept of "compatible" and "incompatible" CMR spectra has been introduced. Application of compatibility increments (IC) allows to calculate the chemical shifts of C and C3 atoms of pentyloxyl fragment in 1-pentylbenzoylformate with a sufficiently good accuracy. Введено поняття "сумісних " і "несумісних " ЯМР спектрів. Застосування "інкрементів узгодження " дало можливість з достатньою точністю розрахувати хімічні зсуви атомів С2 і С пентилоксильного фрагменту в 1-пентилбензоїлформіаті....

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

    Science.gov (United States)

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

    2016-04-01

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

  17. Effects of structural differences on the NMR chemical shifts in cinnamic acid derivatives: Comparison of GIAO and GIPAW calculations

    Science.gov (United States)

    Szeleszczuk, Łukasz; Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika; Wawer, Iwona

    2016-06-01

    In this article we report the results of combined theoretical and experimental structural studies on cinnamic acid derivatives (CADs), one of the main groups of secondary metabolites present in various medicinal plant species and food products of plant origin. The effects of structural differences in CADs on their spectroscopic properties were studied in detail by both: solid-state NMR and GIAO/GIPAW calculations. Theoretical computations were used in order to perform signal assignment in 13C CP/MAS NMR spectra of the cinnamic, o-coumaric, m-coumaric, p-coumaric, caffeic, ferulic, sinapic and 3,4-dimethoxycinnamic acids, and to evaluate the accuracy of GIPAW and GIAO methodology.

  18. Accessible surface area from NMR chemical shifts

    International Nuclear Information System (INIS)

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

  19. A Short History of Three Chemical Shifts

    Science.gov (United States)

    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…

  20. On the calculation of Mössbauer isomer shift.

    Science.gov (United States)

    Filatov, Michael

    2007-08-28

    A quantum chemical computational scheme for the calculation of isomer shift in Mossbauer spectroscopy is suggested. Within the described scheme, the isomer shift is treated as a derivative of the total electronic energy with respect to the radius of a finite nucleus. The explicit use of a finite nucleus model in the calculations enables one to incorporate straightforwardly the effects of relativity and electron correlation. The results of benchmark calculations carried out for several iron complexes as well as for a number of atoms and atomic ions are presented and compared with the available experimental and theoretical data. PMID:17764223

  1. Plakilactones G and H from a marine sponge. Stereochemical determination of highly flexible systems by quantitative NMR-derived interproton distances combined with quantum mechanical calculations of 13C chemical shifts

    Directory of Open Access Journals (Sweden)

    Simone Di Micco

    2013-12-01

    Full Text Available In this paper the stereostructural investigation of two new oxygenated polyketides, plakilactones G and H, isolated from the marine sponge Plakinastrella mamillaris collected at Fiji Islands, is reported. The stereostructural studies began on plakilactone H by applying an integrated approach of the NOE-based protocol and quantum mechanical calculations of 13C chemical shifts. In particular, plakilactone H was used as a template to extend the application of NMR-derived interproton distances to a highly flexible molecular system with simultaneous assignment of four non-contiguous stereocenters. Chemical derivatization and quantum mechanical calculations of 13C on plakilactone G along with a plausible biogenetic interconversion between plakilactone G and plakilactone H allowed us to determine the absolute configuration in this two new oxygenated polyketides.

  2. Protein Structure Determination Using Chemical Shifts

    DEFF Research Database (Denmark)

    Christensen, Anders Steen

    In this thesis, a protein structure determination using chemical shifts is presented. The method is implemented in the open source PHAISTOS protein simulation framework. The method combines sampling from a generative model with a coarse-grained force field and an energy function that includes...... chemical shifts. The method is benchmarked on folding simulations of five small proteins. In four cases the resulting structures are in excellent agreement with experimental data, the fifth case fail likely due to inaccuracies in the energy function. For the Chymotrypsin Inhibitor protein, a structure...

  3. Ab Initio Prediction of 29Si-NMR Chemical Shifts

    Institute of Scientific and Technical Information of China (English)

    CHU Shidong; LI Yingxia; SONG Ni; GUAN Huashi

    2002-01-01

    The ability of several ab initio models to predict experimental 29Si-NMR chemical shift is examined. The shielding values of trimethylsilyl chloride (A), t-butyldimethylsilyl chloride (B) and allyltrimethylsilane (C) are calculated by GIAO, CSGT and IGAIM methods, using HF/6-31G*, B3LYP/6-31G*, HF/6-311+G**, B3LYP/6-311+G** and MPWlPW91/6-311+G** models respectively. The 29Si chemical shifts calculated by GIAO method using HF/6-311+G**model are highly in agreement with those obtained experimentally. All of the models above reproduce the trends of chemical shifts in all cases studied, suggesting that the models are of practical value.

  4. Chemical shift prediction for denatured proteins

    Energy Technology Data Exchange (ETDEWEB)

    Prestegard, James H., E-mail: jpresteg@ccrc.uga.edu; Sahu, Sarata C.; Nkari, Wendy K.; Morris, Laura C.; Live, David; Gruta, Christian

    2013-02-15

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

  5. First principles calculation of Mossbauer isomer shift

    NARCIS (Netherlands)

    Filatov, Michael

    2009-01-01

    Mossbauer spectroscopy is a widely used analytic too] which provides information about local electronic Structure of solid materials on an atomic scale. The isomer shift of resonance nuclear gamma transition is a sensitive parameter which depends on the charge and spin state of the resonating atom a

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

    International Nuclear Information System (INIS)

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

  7. Bayesian inference of protein structure from chemical shift data

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen; Christensen, Anders Steen; Hamelryck, Thomas Wim;

    2015-01-01

    Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model......, and a bias is introduced which might result in incorrect structures. In the inferential structure determination framework, both the unknown structure and the disagreement between experimental and back-calculated data are formulated as a joint probability distribution, thus utilizing the full information...... content of the data. Here, we present the formulation of such a probability distribution where the error in chemical shift prediction is described by either a Gaussian or Cauchy distribution. The methodology is demonstrated and compared to a set of empirically weighted potentials through Markov chain...

  8. Using Angle calculations to demonstrate vowel shifts

    DEFF Research Database (Denmark)

    Fabricius, Anne

    2008-01-01

    This paper gives an overview of the long-term trends of diachronic changes evident within the short vowel system of RP during the 20th century. more specifically, it focusses on changing juxtapositions of the TRAP, STRUT and LOT, FOOT vowel centroid positions. The paper uses geometric calculation...

  9. Random coil chemical shift for intrinsically disordered proteins

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Brander, Søren; Poulsen, Flemming Martin

    2011-01-01

    Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins. The quality of the secondary chemical shifts is dependent on an appropriate choice of random coil chemical shifts. We report random coil chemical....... Temperature has a non-negligible effect on the (13)C random coil chemical shifts, so temperature coefficients are reported for the random coil chemical shifts to allow extrapolation to other temperatures. The pH dependence of the histidine random coil chemical shifts is investigated in a titration series......, which allows the accurate random coil chemical shifts to be obtained at any pH. By correcting the random coil chemical shifts for the effects of temperature and pH, systematic biases of the secondary chemical shifts are minimized, which will improve the reliability of detection of transient secondary...

  10. Calculation of isotope shifts and relativistic shifts in CI, CII, CIII and CIV

    OpenAIRE

    Berengut, J. C.; Flambaum, V. V.; Kozlov, M. G.

    2005-01-01

    We present an accurate ab initio method of calculating isotope shifts and relativistic shifts in atomic spectra. We test the method on neutral carbon and three carbon ions. The relativistic shift of carbon lines may allow them to be included in analyses of quasar absorption spectra that seek to measure possible variations in the fine structure constant, alpha, over the lifetime of the Universe. Carbon isotope shifts can be used to measure isotope abundances in gas clouds: isotope abundances a...

  11. Multiconfiguration calculations of electronic isotope shift factors in Al I

    CERN Document Server

    Filippin, Livio; Ekman, Jörgen; Fritzsche, Stephan; Godefroid, Michel; Jönsson, Per

    2016-01-01

    The present work reports results from systematic multiconfiguration Dirac-Hartree-Fock calculations of electronic isotope shift factors for a set of transitions between low-lying states in neutral aluminium. These electronic quantities together with observed isotope shifts between different pairs of isotopes provide the changes in mean-square charge radii of the atomic nuclei. Two computational approaches are adopted for the estimation of the mass- and field shift factors. Within these approaches, different models for electron correlation are explored in a systematic way to determine a reliable computational strategy and estimate theoretical uncertainties of the isotope shift factors.

  12. Improving 3D structure prediction from chemical shift data

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-09-15

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

  13. Magnetic shift of the chemical freezeout and electric charge fluctuations

    CERN Document Server

    Fukushima, Kenji

    2016-01-01

    We discuss the effect of a strong magnetic field on the chemical freezeout points in the ultra-relativistic heavy-ion collision. As a result of the inverse magnetic catalysis or the magnetic inhibition, the crossover onset to hot and dense matter out of quarks and gluons should be shifted to a lower temperature. To quantify this shift we employ the hadron resonance gas model and an empirical condition for the chemical freezeout. We point out that the charged particle abundances are significantly affected by the magnetic field so that the electric charge fluctuation is largely enhanced especially at high baryon density. The charge conservation partially cancels the enhancement but our calculation shows that the electric charge fluctuation could serve as a magnetometer.

  14. Inferential protein structure determination and refinement using fast, electronic structure based backbone amide chemical shift predictions

    CERN Document Server

    Christensen, Anders S

    2015-01-01

    This report covers the development of a new, fast method for calculating the backbone amide proton chemical shifts in proteins. Through quantum chemical calculations, structure-based forudsiglese the chemical shift for amidprotonen in protein has been parameterized. The parameters are then implemented in a computer program called Padawan. The program has since been implemented in protein folding program Phaistos, wherein the method andvendes to de novo folding of the protein structures and to refine the existing protein structures.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    Deuterium isotope effects on 13C-NMR chemical shifts are investigated in a series of 10-hydroxybenzo[h]quinolines (HBQ’s) The OH proton is deuteriated. The isotope effects on 13C chemical shifts in these hydrogen bonded systems are rather unusual. The formal four-bond effects are found...... to be negative, indicating transmission via the hydrogen bond. In addition unusual long-range effects are seen. Structures, NMR chemical shifts and changes in nuclear shieldings upon deuteriation are calculated using DFT methods. Two-bond deuterium isotope effects on 13C chemical shifts are correlated...... with calculated OH stretching frequencies. Isotope effects on chemical shifts are calculated for systems with OH exchanged by OD. Hydrogen bond potentials are discussed. New and more soluble nitro derivatives are synthesized....

  16. Calculations of the shifts of an X-ray line in the nonrelativistic and relativistic approximations

    International Nuclear Information System (INIS)

    A technique is suggested for calculation of chemical shifts of hard X-ray lines accompanying the formation of one or several vacancies in electron shells when the electrons are either removed from an atom or transit in other states. The containing both additive and non-additive terms with respect to the number of removed electrons are obtained. Such expressions have been derived first in the non-relativistic approximation and then generalized for the relativistic case. The application is discussed of the expressions obtained for interpretation of experimental values of chemical shifts and for extracting information from these results concerning valency configurations and charged states of atoms in compounds

  17. Detection of initiation sites in protein folding of the four helix bundle ACBP by chemical shift analysis

    DEFF Research Database (Denmark)

    Modig, K.; Jürgensen, Vibeke Würtz; Lindorff-Larsen, K.;

    2007-01-01

    A simple alternative method for obtaining "random coil" chemical shifts by intrinsic referencing using the protein's own peptide sequence is presented. These intrinsic random coil backbone shifts were then used to calculate secondary chemical shifts, that provide important information on the resi......A simple alternative method for obtaining "random coil" chemical shifts by intrinsic referencing using the protein's own peptide sequence is presented. These intrinsic random coil backbone shifts were then used to calculate secondary chemical shifts, that provide important information...... on the residual secondary structure elements in the acid-denatured state of an acylcoenzyme A binding protein. This method reveals a clear correlation between the carbon secondary chemical shifts and the amide secondary chemical shifts 3-5 residues away in the primary sequence. These findings strongly suggest...... transient formation of short helix-like segments, and identify unique sequence segments important for protein folding....

  18. Probabilistic Approach to Determining Unbiased Random-coil Carbon-13 Chemical Shift Values from the Protein Chemical Shift Database

    International Nuclear Information System (INIS)

    We describe a probabilistic model for deriving, from the database of assigned chemical shifts, a set of random coil chemical shift values that are 'unbiased' insofar as contributions from detectable secondary structure have been minimized (RCCSu). We have used this approach to derive a set of RCCSu values for 13Cα and 13Cβ for 17 of the 20 standard amino acid residue types by taking advantage of the known opposite conformational dependence of these parameters. We present a second probabilistic approach that utilizes the maximum entropy principle to analyze the database of 13Cα and 13Cβ chemical shifts considered separately; this approach yielded a second set of random coil chemical shifts (RCCSmax-ent). Both new approaches analyze the chemical shift database without reference to known structure. Prior approaches have used either the chemical shifts of small peptides assumed to model the random coil state (RCCSpeptide) or statistical analysis of chemical shifts associated with structure not in helical or strand conformation (RCCSstruct-stat). We show that the RCCSmax-ent values are strikingly similar to published RCCSpeptide and RCCSstruct-stat values. By contrast, the RCCSu values differ significantly from both published types of random coil chemical shift values. The differences (RCCSpeptide-RCCSu) for individual residue types show a correlation with known intrinsic conformational propensities. These results suggest that random coil chemical shift values from both prior approaches are biased by conformational preferences. RCCSu values appear to be consistent with the current concept of the 'random coil' as the state in which the geometry of the polypeptide ensemble samples the allowed region of (φ,ψ)-space in the absence of any dominant stabilizing interactions and thus represent an improved basis for the detection of secondary structure. Coupled with the growing database of chemical shifts, this probabilistic approach makes it possible to refine

  19. Spreadsheet Templates for Chemical Equilibrium Calculations.

    Science.gov (United States)

    Joshi, Bhairav D.

    1993-01-01

    Describes two general spreadsheet templates to carry out all types of one-equation chemical equilibrium calculations encountered by students in undergraduate chemistry courses. Algorithms, templates, macros, and representative examples are presented to illustrate the approach. (PR)

  20. Improved chemical shift prediction by Rosetta conformational sampling

    Energy Technology Data Exchange (ETDEWEB)

    Tian Ye [Sanford Burnham Medical Research Institute (United States); Opella, Stanley J. [University of California San Diego, Department of Chemistry and Biochemistry (United States); Marassi, Francesca M., E-mail: fmarassi@sbmri.org [Sanford Burnham Medical Research Institute (United States)

    2012-11-15

    Chemical shift frequencies represent a time-average of all the conformational states populated by a protein. Thus, chemical shift prediction programs based on sequence and database analysis yield higher accuracy for rigid rather than flexible protein segments. Here we show that the prediction accuracy can be significantly improved by averaging over an ensemble of structures, predicted solely from amino acid sequence with the Rosetta program. This approach to chemical shift and structure prediction has the potential to be useful for guiding resonance assignments, especially in solid-state NMR structural studies of membrane proteins in proteoliposomes.

  1. Counterion influence on chemical shifts in strychnine salts

    Energy Technology Data Exchange (ETDEWEB)

    Metaxas, Athena E.; Cort, John R.

    2013-05-01

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

  2. Counterion influence on chemical shifts in strychnine salts.

    Science.gov (United States)

    Metaxas, Athena E; Cort, John R

    2013-05-01

    The highly toxic plant alkaloid strychnine is often isolated in the form of the anion salt of its protonated tertiary amine. Here, we characterize the relative influence of different counterions on (1)H and (13)C chemical shifts in several strychnine salts in D2O, methanol-d4 (CD3OD), and chloroform-d (CDCl3) solvents. In organic solvents but not in water, substantial variation in chemical shifts of protons near the tertiary amine was observed among different salts. These secondary shifts reveal differences in the way each anion influences electronic structure within the protonated amine. The distributions of secondary shifts allow salts to be easily distinguished from each other as well as from the free base form. 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 with 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. PMID:23495106

  3. Method for evaluating chemical shifts of x-ray emission lines in molecules and solids

    Science.gov (United States)

    Lomachuk, Yuriy V.; Titov, Anatoly V.

    2013-12-01

    A method of evaluating chemical shifts of x-ray emission lines for period four and heavier elements is developed. This method is based on the relativistic pseudopotential model and one-center restoration approach [Int. J. Quantum Chem.IJQCB20020-760810.1002/qua.20418 104, 223 (2005)] to recover a proper electronic structure in heavy-atom cores after the pseudopotential simulation of chemical compounds. The approximations of instantaneous transition and frozen core are presently applied to derive an expression for chemical shift as a difference between mean values of certain effective operator. The method allows one to avoid evaluation of small quantities (chemical shifts ˜0.01-1 eV) as differences of very large values (transition energies ˜1-100 keV in various compounds). The results of our calculations of chemical shifts for the Kα1, Kα2, and L transitions of group-14 metal cations with respect to neutral atoms are presented. Calculations of Kα1-line chemical shifts for the Pb core transitions in PbO and PbF2 with respect to those in the Pb atom are also performed and discussed. The accuracy of approximations used is estimated and the quality of the calculations is analyzed.

  4. Effects of structural differences on the NMR chemical shifts in isostructural dipeptides.

    Science.gov (United States)

    Altheimer, Benjamin D; Mehta, Manish A

    2014-04-10

    Porous crystalline dipeptides have gained recent attention for their potential as gas-storage materials. Within this large class is a group of dipeptides containing alanine, valine, and isoleucine with very similar crystal structures. We report the (13)C (carbonyl and Cα) and (15)N (amine and amide) solid-state NMR isotropic chemical shifts in a series of seven such isostructural porous dipeptides as well as shift tensor data for the carbonyl and amide sites. Using their known crystal structures and aided by ab initio quantum chemical calculations for the resonance assignments, we elucidate trends relating local structure, hydrogen-bonding patterns, and chemical shift. We find good correlation between the backbone dihedral angles and the Cα1 and Cα2 shifts. For the C1 shift tensor, the δ11 value shifts downfield as the hydrogen-bond distance increases, δ22 shifts upfield, and δ33 shows little variation. The C2 shift tensor shows no appreciable correlation with structural parameters. For the N2 tensor, δ11 shows little dependence on the hydrogen-bond length, whereas δ22 and δ33 both show a decrease in shielding as the hydrogen bond shortens. Our analysis teases apart some, but not all, structural contributors to the observed differences the solid-state NMR chemical shifts.

  5. RIS3: A program for relativistic isotope shift calculations

    Science.gov (United States)

    Nazé, C.; Gaidamauskas, E.; Gaigalas, G.; Godefroid, M.; Jönsson, P.

    2013-09-01

    An atomic spectral line is characteristic of the element producing the spectrum. The line also depends on the isotope. The program RIS3 (Relativistic Isotope Shift) calculates the electron density at the origin and the normal and specific mass shift parameters. Combining these electronic quantities with available nuclear data, isotope-dependent energy level shifts are determined. Program summaryProgram title:RIS3 Catalogue identifier: ADEK_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADEK_v2_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.: 5147 No. of bytes in distributed program, including test data, etc.: 32869 Distribution format: tar.gz Programming language: Fortran 77. Computer: HP ProLiant BL465c G7 CTO. Operating system: Centos 5.5, which is a Linux distribution compatible with Red Hat Enterprise Advanced Server. Classification: 2.1. Catalogue identifier of previous version: ADEK_v1_0 Journal reference of previous version: Comput. Phys. Comm. 100 (1997) 81 Subprograms used: Cat Id Title Reference ADZL_v1_1 GRASP2K VERSION 1_1 to be published. Does the new version supersede the previous version?: Yes Nature of problem: Prediction of level and transition isotope shifts in atoms using four-component relativistic wave functions. Solution method: The nuclear motion and volume effects are treated in first order perturbation theory. Taking the zero-order wave function in terms of a configuration state expansion |Ψ>=∑μcμ|Φ(γμPJMj)>, where P, J and MJ are, respectively, the parity and angular quantum numbers, the electron density at the nucleus and the normal and specific mass shift parameters may generally be expressed as ∑cμcν where V is the relevant operator. The matrix elements, in turn, can be expressed as sums over radial integrals multiplied

  6. Calculating Shocks In Flows At Chemical Equilibrium

    Science.gov (United States)

    Eberhardt, Scott; Palmer, Grant

    1988-01-01

    Boundary conditions prove critical. Conference paper describes algorithm for calculation of shocks in hypersonic flows of gases at chemical equilibrium. Although algorithm represents intermediate stage in development of reliable, accurate computer code for two-dimensional flow, research leading up to it contributes to understanding of what is needed to complete task.

  7. Method of evaluating chemical shifts of X-ray emission lines in molecules and solids

    CERN Document Server

    Lomachuk, Yuriy V

    2013-01-01

    Method of evaluating chemical shifts of X-ray emission lines for sufficiently heavy atoms (beginning from period 4 elements) in chemical compounds is developed. This method is based on the pseudopotential model and one-center restoration method (to reconstruct the proper electronic structure in heavy-atom cores). The approximations of instantaneous transition and frozen inner core spinors of the atom are used for derivation of an expression for chemical shift as a difference between mean values of some effective operator. The method allows one to avoid evaluating small values (chemical shifts ~ 0.01{\\div}1 eV) as differences of very large values (transition energies ~ 1{\\div}100 keV in various compounds). The results of our calculations of chemical shifts for the K_{\\alpha1,2} and L transitions of the group 14 metal cations with respect to neutral atoms are presented. The calculations of chemical shift of K_{\\alpha1}-line in the Pb-core transition within PbO and PbF_2 with respect to the neutral Pb are also p...

  8. From NMR chemical shifts to amino acid types: Investigation of the predictive power carried by nuclei

    International Nuclear Information System (INIS)

    An approach to automatic prediction of the amino acid type from NMR chemical shift values of its nuclei is presented here, in the frame of a model to calculate the probability of an amino acid type given the set of chemical shifts. The method relies on systematic use of all chemical shift values contained in the BioMagResBank (BMRB). Two programs were designed, one (BMRB stats) for extracting statistical chemical shift parameters from the BMRB and another one (RESCUE2) for computing the probabilities of each amino acid type, given a set of chemical shifts. The Bayesian prediction scheme presented here is compared to other methods already proposed: PROTYP (Grzesiek and Bax, J. Biomol. NMR, 3, 185-204, 1993) RESCUE (Pons and Delsuc, J. Biomol. NMR, 15, 15-26, 1999) and PLATON (Labudde et al., J. Biomol. NMR, 25, 41-53, 2003) and is found to be more sensitive and more specific. Using this scheme, we tested various sets of nuclei. The two nuclei carrying the most information are Cβ and Hβ, in agreement with observations made in Grzesiek and Bax, 1993. Based on four nuclei: Hβ, Cβ, Cα and C', it is possible to increase correct predictions to a rate of more than 75%. Taking into account the correlations between the nuclei chemical shifts has only a slight impact on the percentage of correct predictions: indeed, the largest correlation coefficients display similar features on all amino acids

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

    DEFF Research Database (Denmark)

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

    2006-01-01

    Investigation of all O-methyl ethers of 1,2,3-benzenetriol and 4-methyl-1,2,3-benzenetriol (3-16) by 1H NMR spectroscopy and density-functional calculations disclosed practically useful conformational effects on 1H NMR chemical shifts in the aromatic ring. While the conversion of phenol (2) to an...

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

    DEFF Research Database (Denmark)

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

    2013-01-01

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

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

    Science.gov (United States)

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

    2006-12-01

    Investigation of all O-methyl ethers of 1,2,3-benzenetriol and 4-methyl-1,2,3-benzenetriol (3-16) by 1H NMR spectroscopy and density-functional calculations disclosed practically useful conformational effects on 1H NMR chemical shifts in the aromatic ring. While the conversion of phenol (2) to anisole (1) causes only small positive changes of 1H NMR chemical shifts (Delta delta Hmeta > Hpara, the experimental O-methylation induced shifts in ortho-disubstituted phenols are largest for Hpara, Delta delta equals; 0.19 +/- 0.02 ppm (n = 11). The differences are due to different conformational behavior of the OH and OCH3 groups; while the ortho-disubstituted OH group remains planar in polyphenols due to hydrogen bonding and conjugative stabilization, the steric congestion in ortho-disubstituted anisoles outweighs the conjugative effects and forces the Ar-OCH3 torsion out of the ring plane, resulting in large stereoelectronic effects on the chemical shift of Hpara. Conformational searches and geometry optimizations for 3-16 at the B3LYP/6-31G** level, followed by B3LYP/6-311++G(2d,2p) calculations for all low-energy conformers, gave excellent correlation between computed and observed 1H NMR chemical shifts, including agreement between computed and observed chemical shift changes caused by O-methylation. The observed regularities can aid structure elucidation of partly O-methylated polyphenols, including many natural products and drugs, and are useful in connection with chemical shift predictions by desktop computer programs. PMID:17137372

  12. THE PERMANENT DETECTION OF SHIFTS IN THE PROBLEM OF CALCULATION AUTOMATION OF THE CORRECTION RAIL CURVES

    Directory of Open Access Journals (Sweden)

    V. V. Lahuta

    2008-01-01

    Full Text Available The numerical method of solution of a differential equation of railway shifts is presented allowing to calculate the quantity of shifts in any point of a railway curve during its straightening. Shifts calculated between the points of measurement of bend arrows can be used as control ones.

  13. Deuterium isotope effects on 13C chemical shifts of negatively charged NH.N systems

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Pietrzak, Mariusz; Grech, Eugeniusz;

    2013-01-01

    ” and equilibrium cases. NMR assignments of the former have been revised. The NH proton is deuteriated. The isotope effects on 13C chemical shifts are rather unusual in these strongly hydrogen bonded systems between a NH and a negatively charged nitrogen atom. The formal four-bond effects are found to be negative...... indicating transmission via the hydrogen bond. In addition, unusual long range effects are seen. Structures, 1H and 13C NMR chemical shifts and changes in nuclear shieldings upon deuteriation are calculated using density functional theory methods......Deuterium isotope effects on 13C chemical shifts are investigated in anions of 1,8-bis(4-toluenesulphonamido)naphthalenes together with N,N-(naphthalene-1,8-diyl)bis(2,2,2-trifluoracetamide) all with bis(1,8-dimethylamino)napthaleneH+ as counter ion. These compounds represent both “static...

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

    Directory of Open Access Journals (Sweden)

    Anders S Christensen

    Full Text Available 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 ((h3J(NC' spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding.

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

    CERN Document Server

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

    2013-01-01

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

  16. Reactivity of Tourmaline by Quantum Chemical Calculations

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    ZnAb initio calculations on reactivity of tourmaline were performed using both Gaussian and density function theory discrete variation method (DFT-DVM). The HF, B3LYP methods and basis sets STO-3G(3d,3p),6-31G(3d,3p) and 6-311++G(3df,3pd) were used in the calculations. The experimental results show energy value obtained from B3LYP and 6-31++1G(3df,3pd) basis sets is more accurate than those from other methods. The highest occupied molecular orbital (HOMO) of the tourmaline cluster mainly consists of O atom of hydroxyl group with relative higher energy level, suggesting that chemical bond between those of electron acceptor and this site may readily form, indicating the higher reactivity of hydroxyl group. The lowest unoccupied molecular orbital (LUMO) of the tourmaline cluster are dominantly composed of Si, O of tetrahedron and Na with relative lower energy level, suggesting that these atoms may tend to form chemical bond with those of electron donor. The results also prove that the O atoms of the tourmaline cluster have stronger reactivity than other atoms.

  17. Chemical-shift MRI of exogenous lipoid pneumonia

    Energy Technology Data Exchange (ETDEWEB)

    Cox, J.E.; Choplin, R.H.; Chiles, C. [Wake Forest Univ., Winston-Salem, NC (United States)

    1996-05-01

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

  18. Pulse NMR in solids: chemical shift, lead fluoride, and thorium hydride

    International Nuclear Information System (INIS)

    The fluorine chemical shift of a single crystal CaF2 was measured up to 4 kilobar at room temperature using multiple pulse NMR. The pressure dependence of the shift is found to be --1.7 +- 1 ppM/kbar, while an overlap model predicts a shift of --0.46 ppM/kbar.The chemical shift tensor is separated into ''geometrical'' and ''chemical'' contributions, and comparison of the proposed model calculations with recent data on hydroxyl proton chemical shift tensors shows that the geometrical portion accounts for the qualitative features of the measured tensors. A study of fluoride ion motion in β-PbF2 doped with NaF was conducted by measurement of the 19F transverse relaxation time (T2), spin lattice relaxation time (T1) and the spin lattice relaxation time in the rotating frame (T/sub 1r). Two samples of Th4H15, prepared under different conditions but both having the proper ratio of H/Th (to within 1 percent), were studied. The structure of the Th4H15 suggested by x-ray measurements is confirmed through a moment analysis of the rigid lattice line shape

  19. Molecular orbital calculations using chemical graph theory

    CERN Document Server

    Dias, Jerry Ray

    1993-01-01

    Professor John D. Roberts published a highly readable book on Molecular Orbital Calculations directed toward chemists in 1962. That timely book is the model for this book. The audience this book is directed toward are senior undergraduate and beginning graduate students as well as practicing bench chemists who have a desire to develop conceptual tools for understanding chemical phenomena. Although, ab initio and more advanced semi-empirical MO methods are regarded as being more reliable than HMO in an absolute sense, there is good evidence that HMO provides reliable relative answers particularly when comparing related molecular species. Thus, HMO can be used to rationalize electronic structure in 1t-systems, aromaticity, and the shape use HMO to gain insight of simple molecular orbitals. Experimentalists still into subtle electronic interactions for interpretation of UV and photoelectron spectra. Herein, it will be shown that one can use graph theory to streamline their HMO computational efforts and to arrive...

  20. Substituent effects in the 13C NMR chemical shifts of alpha-mono-substituted acetonitriles.

    Science.gov (United States)

    Reis, Adriana K C A; Rittner, Roberto

    2007-03-01

    13C chemical shifts empirical calculations, through a very simple additivity relationship, for the alpha-methylene carbon of some alpha-mono-substituted acetonitriles, Y-CH(2)-CN (Y=H, F, Cl, Br, I, OMe, OEt, SMe, SEt, NMe(2), NEt(2), Me and Et), lead to similar, or even better, results in comparison to the reported values obtained through Quantum Mechanics methods. The observed deviations, for some substituents, are very similar for both approaches. This divergence between experimental and calculated, either empirically or theoretically, values are smaller than for the corresponding acetones, amides, acetic acids and methyl esters, which had been named non-additivity effects (or intramolecular interaction chemical shifts, ICS) and attributed to some orbital interactions. Here, these orbital interactions do not seem to be the main reason for the non-additivity effects in the empirical calculations, which must be due solely to the magnetic anisotropy of the heavy atom present in the substituent. These deviations, which were also observed in the theoretical calculations, were attributed in that case to the non-inclusion of relativistic effects and spin-orbit coupling in the Hamiltonian. Some divergence is also observed for the cyano carbon chemical shifts, probably due to the same reasons.

  1. From NMR chemical shifts to amino acid types: Investigation of the predictive power carried by nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Marin, Antoine; Malliavin, Therese E. [Institut de Biologie Physico-Chimique, Laboratoire de Biochimie Theorique, CNRS UPR 9080 (France)], E-mail: therese.malliavin@ibpc.fr; Nicolas, Pierre; Delsuc, Marc-Andre [INRA - Domaine de Vilvert, Unite Mathematique Informatique et Genome (France)

    2004-09-15

    An approach to automatic prediction of the amino acid type from NMR chemical shift values of its nuclei is presented here, in the frame of a model to calculate the probability of an amino acid type given the set of chemical shifts. The method relies on systematic use of all chemical shift values contained in the BioMagResBank (BMRB). Two programs were designed, one (BMRB stats) for extracting statistical chemical shift parameters from the BMRB and another one (RESCUE2) for computing the probabilities of each amino acid type, given a set of chemical shifts. The Bayesian prediction scheme presented here is compared to other methods already proposed: PROTYP (Grzesiek and Bax, J. Biomol. NMR, 3, 185-204, 1993) RESCUE (Pons and Delsuc, J. Biomol. NMR, 15, 15-26, 1999) and PLATON (Labudde et al., J. Biomol. NMR, 25, 41-53, 2003) and is found to be more sensitive and more specific. Using this scheme, we tested various sets of nuclei. The two nuclei carrying the most information are C{sub {beta}} and H{sub {beta}}, in agreement with observations made in Grzesiek and Bax, 1993. Based on four nuclei: H{sub {beta}}, C{sub {beta}}, C{sub {alpha}} and C', it is possible to increase correct predictions to a rate of more than 75%. Taking into account the correlations between the nuclei chemical shifts has only a slight impact on the percentage of correct predictions: indeed, the largest correlation coefficients display similar features on all amino acids.

  2. Relativistic calculations of the isotope shifts in highly charged Li-like ions

    CERN Document Server

    Zubova, N A; Shabaev, V M; Tupitsyn, I I; Volotka, A V; Plunien, G; Brandau, C; Stöhlker, Th

    2014-01-01

    Relativistic calculations of the isotope shifts of energy levels in highly charged Li-like ions are performed. The nuclear recoil (mass shift) contributions are calculated by merging the perturbative and large-scale configuration-interaction Dirac-Fock-Sturm (CI-DFS) methods. The nuclear size (field shift) contributions are evaluated by the CI-DFS method including the electron-correlation, Breit, and QED corrections. The nuclear deformation and nuclear polarization corrections to the isotope shifts in Li-like neodymium, thorium, and uranium are also considered. The results of the calculations are compared with the theoretical values obtained with other methods.

  3. Lamb shift calculations for high-Z lithium like ions

    International Nuclear Information System (INIS)

    We present ab initio calculations of the complete gauge invariant set of the self energy and vacuum polarization screening diagrams for the 2p2p1/2-2s transition in Li like ions. Various contributions to the transition energy are collected. The accuracy of theoretical predictions is discussed

  4. Substituent effects on 61Ni NMR chemical shifts

    OpenAIRE

    Bühl, Michael; Peters, Dietmund; Herges, Rainer

    2009-01-01

    Ni-61 chemical shifts of Ni(all-trans-cdt) L (cdt = cyclododecatriene, L = none, CO, PMe3), Ni(CO)(4), Ni(C2H4)(2)(PMe3), Ni(cod)(2) (cod = cyclooctadiene) and Ni(PX3)(4) (X = Me, F, Cl) are computed at the GIAO (gauge-including atomic orbitals), BPW91, B3LYP and BHandHLYP levels, using BP86-optimised geometries and an indirect referencing scheme. For this set of compounds, substituent effects on delta(Ni-61) are better described with hybrid functionals than with the pure BPW91 functional. On...

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

    Science.gov (United States)

    Fukushima, Kenji; Hidaka, Yoshimasa

    2016-09-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

  7. Calculating absorption shifts for retinal proteins: computational challenges.

    Science.gov (United States)

    Wanko, M; Hoffmann, M; Strodel, P; Koslowski, A; Thiel, W; Neese, F; Frauenheim, T; Elstner, M

    2005-03-01

    Rhodopsins can modulate the optical properties of their chromophores over a wide range of wavelengths. The mechanism for this spectral tuning is based on the response of the retinal chromophore to external stress and the interaction with the charged, polar, and polarizable amino acids of the protein environment and is connected to its large change in dipole moment upon excitation, its large electronic polarizability, and its structural flexibility. In this work, we investigate the accuracy of computational approaches for modeling changes in absorption energies with respect to changes in geometry and applied external electric fields. We illustrate the high sensitivity of absorption energies on the ground-state structure of retinal, which varies significantly with the computational method used for geometry optimization. The response to external fields, in particular to point charges which model the protein environment in combined quantum mechanical/molecular mechanical (QM/MM) applications, is a crucial feature, which is not properly represented by previously used methods, such as time-dependent density functional theory (TDDFT), complete active space self-consistent field (CASSCF), and Hartree-Fock (HF) or semiempirical configuration interaction singles (CIS). This is discussed in detail for bacteriorhodopsin (bR), a protein which blue-shifts retinal gas-phase excitation energy by about 0.5 eV. As a result of this study, we propose a procedure which combines structure optimization or molecular dynamics simulation using DFT methods with a semiempirical or ab initio multireference configuration interaction treatment of the excitation energies. Using a conventional QM/MM point charge representation of the protein environment, we obtain an absorption energy for bR of 2.34 eV. This result is already close to the experimental value of 2.18 eV, even without considering the effects of protein polarization, differential dispersion, and conformational sampling.

  8. Elucidating the Link between NMR Chemical Shifts and Electronic Structure in d(0) Olefin Metathesis Catalysts.

    Science.gov (United States)

    Halbert, Stéphanie; Copéret, Christophe; Raynaud, Christophe; Eisenstein, Odile

    2016-02-24

    The nucleophilic carbon of d(0) Schrock alkylidene metathesis catalysts, [M] = CHR, display surprisingly low downfield chemical shift (δ(iso)) and large chemical shift anisotropy. State-of-the-art four-component relativistic calculations of the chemical shift tensors combined with a two-component analysis in terms of localized orbitals allow a molecular-level understanding of their orientations, the magnitude of their principal components (δ11 > δ22 > δ33) and associated δ(iso). This analysis reveals the dominating influence of the paramagnetic contribution yielding a highly deshielded alkylidene carbon. The largest paramagnetic contribution, which originates from the coupling of alkylidene σ(MC) and π*(MC) orbitals under the action of the magnetic field, is analogous to that resulting from coupling σ(CC) and π*(CC) in ethylene; thus, δ11 is in the MCH plane and is perpendicular to the MC internuclear direction. The higher value of carbon-13 δ(iso) in alkylidene complexes relative to ethylene is thus due to the smaller energy gap between σ(MC) and π*(MC) vs this between σ(CC) and π*(CC) in ethylene. This effect also explains why the highest value of δ(iso) is observed for Mo and the lowest for Ta, the values for W and Re being in between. In the presence of agostic interaction, the chemical shift tensor principal components orientation (δ22 or δ33 parallel or perpendicular to π(MX)) is influenced by the MCH angle because it determines the orientation of the alkylidene CHR fragment relative to the MC internuclear axis. The orbital analysis shows how the paramagnetic terms, understood with a localized bond model, determine the chemical shift tensor and thereby δ(iso). PMID:26787258

  9. Elucidating the Link between NMR Chemical Shifts and Electronic Structure in d(0) Olefin Metathesis Catalysts.

    Science.gov (United States)

    Halbert, Stéphanie; Copéret, Christophe; Raynaud, Christophe; Eisenstein, Odile

    2016-02-24

    The nucleophilic carbon of d(0) Schrock alkylidene metathesis catalysts, [M] = CHR, display surprisingly low downfield chemical shift (δ(iso)) and large chemical shift anisotropy. State-of-the-art four-component relativistic calculations of the chemical shift tensors combined with a two-component analysis in terms of localized orbitals allow a molecular-level understanding of their orientations, the magnitude of their principal components (δ11 > δ22 > δ33) and associated δ(iso). This analysis reveals the dominating influence of the paramagnetic contribution yielding a highly deshielded alkylidene carbon. The largest paramagnetic contribution, which originates from the coupling of alkylidene σ(MC) and π*(MC) orbitals under the action of the magnetic field, is analogous to that resulting from coupling σ(CC) and π*(CC) in ethylene; thus, δ11 is in the MCH plane and is perpendicular to the MC internuclear direction. The higher value of carbon-13 δ(iso) in alkylidene complexes relative to ethylene is thus due to the smaller energy gap between σ(MC) and π*(MC) vs this between σ(CC) and π*(CC) in ethylene. This effect also explains why the highest value of δ(iso) is observed for Mo and the lowest for Ta, the values for W and Re being in between. In the presence of agostic interaction, the chemical shift tensor principal components orientation (δ22 or δ33 parallel or perpendicular to π(MX)) is influenced by the MCH angle because it determines the orientation of the alkylidene CHR fragment relative to the MC internuclear axis. The orbital analysis shows how the paramagnetic terms, understood with a localized bond model, determine the chemical shift tensor and thereby δ(iso).

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

    Science.gov (United States)

    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. PMID:26584373

  11. Computational Assignment of Chemical Shifts for Protein Residues

    CERN Document Server

    Bratholm, Lars A

    2013-01-01

    Fast and accurate protein structure prediction is one of the major challenges in structural biology, biotechnology and molecular biomedicine. These fields require 3D protein structures for rational design of proteins with improved or novel properties. X-ray crystallography is the most common approach even with its low success rate, but lately NMR based approaches have gained popularity. The general approach involves a set of distance restraints used to guide a structure prediction, but simple NMR triple-resonance experiments often provide enough structural information to predict the structure of small proteins. Previous protein folding simulations that have utilised experimental data have weighted the experimental data and physical force field terms more or less arbitrarily, and the method is thus not generally applicable to new proteins. Furthermore a complete and near error-free assignment of chemical shifts obtained by the NMR experiments is needed, due to the static, or deterministic, assignment. In this ...

  12. Core correlation effects in multiconfiguration calculations of isotope shifts in Mg I

    CERN Document Server

    Filippin, Livio; Ekman, Jörgen; Jönsson, Per

    2016-01-01

    The present work reports results from systematic multiconfiguration Dirac-Hartree-Fock calculations of isotope shifts for several well-known transitions in neutral magnesium. Relativistic normal and specific mass shift factors as well as the electronic probability density at the origin are calculated. Combining these electronic quantities with available nuclear data, energy and transition level shifts are determined for the $^{26}$Mg$-^{24}$Mg pair of isotopes. Different models for electron correlation are adopted. It is shown that although valence and core-valence models provide accurate values for the isotope shifts, the inclusion of core-core excitations in the computational strategy significantly improves the accuracy of the transition energies and normal mass shift factors.

  13. Light-shift calculation in the ns-states of hydrogenic systems

    NARCIS (Netherlands)

    Jungmann, Klaus-Peter; Yakhontov, Victor

    1996-01-01

    We present the results of the light-shift calculations in the as-states of hydrogenic systems in the presence of a weak laser field. This is done by means of analytical calculations of the scalar dynamic polarizabilities (DP) of the corresponding levels. In contrast to the usual technique, our analy

  14. Pitfalls of adrenal imaging with chemical shift MRI

    International Nuclear Information System (INIS)

    Chemical shift (CS) MRI of the adrenal glands exploits the different precessional frequencies of fat and water protons to differentiate the intracytoplasmic lipid-containing adrenal adenoma from other adrenal lesions. The purpose of this review is to illustrate both technical and interpretive pitfalls of adrenal imaging with CS MRI and emphasize the importance of adherence to strict technical specifications and errors that may occur when other imaging features and clinical factors are not incorporated into the diagnosis. When performed properly, the specificity of CS MRI for the diagnosis of adrenal adenoma is over 90%. Sampling the in-phase and opposed-phase echoes in the correct order and during the same breath-hold are essential requirements, and using the first echo pair is preferred, if possible. CS MRI characterizes more adrenal adenomas then unenhanced CT but may be non-diagnostic in a proportion of lipid-poor adenomas; CT washout studies may be able to diagnose these lipid-poor adenomas. Other primary and secondary adrenal tumours and supra-renal disease entities may contain lipid or gross fat and mimic adenoma or myelolipoma. Heterogeneity within an adrenal lesion that contains intracytoplasmic lipid could be due to myelolipoma, lipomatous metaplasia of adenoma, or collision tumour. Correlation with previous imaging, other imaging features, clinical history, and laboratory investigations can minimize interpretive errors

  15. Applications of Chemical Shift Imaging to Marine Sciences

    Directory of Open Access Journals (Sweden)

    Haakil Lee

    2010-08-01

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

  16. Diagnostic value of chemical shift artifact in distinguishing benign lymphadenopathy

    International Nuclear Information System (INIS)

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

  17. Using Neural Networks for 13C NMR Chemical Shift Prediction-Comparison with Traditional Methods

    Science.gov (United States)

    Meiler, Jens; Maier, Walter; Will, Martin; Meusinger, Reinhard

    2002-08-01

    Interpretation of 13C chemical shifts is essential for structure elucidation of organic molecules by NMR. In this article, we present an improved neural network approach and compare its performance to that of commonly used approaches. Specifically, our recently proposed neural network ( J. Chem. Inf. Comput. Sci. 2000, 40, 1169-1176) is improved by introducing an extended hybrid numerical description of the carbon atom environment, resulting in a standard deviation (std. dev.) of 2.4 ppm for an independent test data set of ˜42,500 carbons. Thus, this neural network allows fast and accurate 13C NMR chemical shift prediction without the necessity of access to molecule or fragment databases. For an unbiased test dataset containing 100 organic structures the accuracy of the improved neural network was compared to that of a prediction method based on the HOSE code ( hierarchically ordered spherical description of environment) using S PECI NFO. The results show the neural network predictions to be of quality (std. dev.=2.7 ppm) comparable to that of the HOSE code prediction (std. dev.=2.6 ppm). Further we compare the neural network predictions to those of a wide variety of other 13C chemical shift prediction tools including incremental methods (C HEMD RAW, S PECT OOL), quantum chemical calculation (G AUSSIAN, C OSMOS), and HOSE code fragment-based prediction (S PECI NFO, ACD/CNMR, P REDICTI T NMR) for the 47 13C-NMR shifts of Taxol, a natural product including many structural features of organic substances. The smallest standard deviations were achieved here with the neural network (1.3 ppm) and S PECI NFO (1.0 ppm).

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

    Science.gov (United States)

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

    2016-10-01

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

  19. Theoretical Modeling of (99)Tc NMR Chemical Shifts.

    Science.gov (United States)

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

    2016-09-01

    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. PMID:27518482

  20. 19-Fluorine nuclear magnetic resonance chemical shift variability in trifluoroacetyl species

    OpenAIRE

    Sloop, Joseph

    2013-01-01

    Joseph C SloopSchool of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA, USAAbstract: This review examines the variability of chemical shifts observed in 19-fluorine (19F) nuclear magnetic resonance spectra for the trifluoroacetyl (TFA) functional group. The range of 19F chemical shifts reported spectra for the TFA group varies generally from −85 to −67 ppm relative to CFCl3. The literature revealed several factors that impact chemical shifts of the TFA...

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

    International Nuclear Information System (INIS)

    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

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

    Science.gov (United States)

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

    2016-09-01

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

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

    Science.gov (United States)

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

    2013-01-24

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

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

    Science.gov (United States)

    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. PMID:21806118

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

    DEFF Research Database (Denmark)

    Boomsma, Wouter; Tian, Pengfei; Frellsen, J.;

    2014-01-01

    Significance Chemical shifts are the most fundamental parameters measured in nuclear magnetic resonance spectroscopy. Since these parameters are exquisitely sensitive to the local atomic environment, they can provide detailed information about the three-dimensional structures of proteins. It has...... their thermal fluctuations, thereby broadening the scope of chemical shifts in structural biology....

  6. Carbon-13 magnetic resonance chemical shift additivity relationships of clinically used furocoumarins and furchromones

    International Nuclear Information System (INIS)

    The natural abundance carbon-13 nuclear magnetic resonance spectra of various clinically used furocoumarins and furochromones have been studied. The assignments of carbon chemical shift values were based on the theory of chemical shift, additivity rules, SFORD spectra and model compounds. (author)

  7. Carbon Footprint Calculations: An Application of Chemical Principles

    Science.gov (United States)

    Treptow, Richard S.

    2010-01-01

    Topics commonly taught in a general chemistry course can be used to calculate the quantity of carbon dioxide emitted into the atmosphere by various human activities. Each calculation begins with the balanced chemical equation for the reaction that produces the CO[subscript 2] gas. Stoichiometry, thermochemistry, the ideal gas law, and dimensional…

  8. Calculations of hydrogen atom multiphoton energy level shifts, transition amplitudes and ionization probabilities

    International Nuclear Information System (INIS)

    Analyses of the resonant multiphoton ionization of atoms require knowledge of ac Stark energy shifts and of multiphoton, bound-to-bound state, transition amplitudes. In this paper, we consider the three-photon photoionization of hydrogen atoms at frequencies that are at and surrounding the two-photon 1s to 2s resonance. AC energy shift sums of both the 1s and 2s states are calculated as a function of the laser frequency along with two-photon 1s → 2s resonant transition amplitude sums. These quantities are calculated using an extended version of a method, which has often been employed in a variety of ways, of calculating these sums by expressing them in terms of solutions to a variety of differential equations that are derived from the different sums being evaluated. We demonstrate how exact solutions are obtained to these differential equations, which lead to exact evaluations of the corresponding sums. A variety of different cases are analysed, some involving analytic continuation, some involving real number analysis and some involving complex number analysis. A dc Stark sum calculation of the 2s state is carried out to illustrate the case where analytic continuation, pole isolation and pole subtraction are required and where the calculation can be carried out analytically; the 2s state, ac Stark shift sum calculations involve a case where no analytic continuation is required, but where the solution to the differential equation produces complex numbers owing to the finite photoionization lifetime of the 2s state. Results from these calculations are then used to calculate three-photon ionization probabilities of relevance to an analysis of the multiphoton ionization data published by Kyrala and Nichols (1991 Phys. Rev. A 44, R1450)

  9. Isotope shifts in beryllium-, boron-, carbon-, and nitrogen-like ions from relativistic configuration interaction calculations

    Energy Technology Data Exchange (ETDEWEB)

    Nazé, C.; Verdebout, S. [Service de Chimie Quantique et Photophysique, CP160/09, Université Libre de Bruxelles, Avenue F.D. Roosevelt 50, B 1050 Brussels (Belgium); Rynkun, P.; Gaigalas, G. [Vilnius University, Institute of Theoretical Physics and Astronomy, LT-01108 Vilnius (Lithuania); Godefroid, M., E-mail: mrgodef@ulb.ac.be [Service de Chimie Quantique et Photophysique, CP160/09, Université Libre de Bruxelles, Avenue F.D. Roosevelt 50, B 1050 Brussels (Belgium); Jönsson, P. [Group for Materials Science and Applied Mathematics, Malmö University, 205-06 Malmö (Sweden)

    2014-09-15

    Energy levels, normal and specific mass shift parameters as well as electronic densities at the nucleus are reported for numerous states along the beryllium, boron, carbon, and nitrogen isoelectronic sequences. Combined with nuclear data, these electronic parameters can be used to determine values of level and transition isotope shifts. The calculation of the electronic parameters is done using first-order perturbation theory with relativistic configuration interaction wavefunctions that account for valence, core–valence, and core–core correlation effects as zero-order functions. Results are compared with experimental and other theoretical values, when available.

  10. Chemical Bond Calculations of Crystal Growth of KDP and ADP

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    A novel method was proposed to calculate the crystal morphology (or growth habit) on the basis of chemical bond analysis. All constituent chemical bonds were distinguished as relevant and independent bonds according to their variations during the crystallization process. By employing the current method, the influence of specific growth conditions on the crystal morphology can be considered in the structure analysis process. The ideal morphologies of both KDP (KH2PO4) and ADP (NH4H2PO4) crystals were calculated and compared with our obtained crystallites at room temperature, which validates the present calculation method very well.

  11. Method of evaluating chemical shifts of X-ray emission lines in molecules and solids

    OpenAIRE

    Lomachuk, Yuriy V.; Titov, Anatoly V.

    2013-01-01

    Method of evaluating chemical shifts of X-ray emission lines for sufficiently heavy atoms (beginning from period 4 elements) in chemical compounds is developed. This method is based on the pseudopotential model and one-center restoration method (to reconstruct the proper electronic structure in heavy-atom cores). The approximations of instantaneous transition and frozen inner core spinors of the atom are used for derivation of an expression for chemical shift as a difference between mean valu...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-01-15

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

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

    Science.gov (United States)

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

    2015-11-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-11-15

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

  15. Modern ab initio valence bond theory calculations reveal charge shift bonding in protic ionic liquids.

    Science.gov (United States)

    Patil, Amol Baliram; Bhanage, Bhalchandra Mahadeo

    2016-06-21

    The nature of bonding interactions between the cation and the anion of an ionic liquid is at the heart of understanding ionic liquid properties. A particularly interesting case is a special class of ionic liquids known as protic ionic liquids. The extent of proton transfer in protic ionic liquids has been observed to vary according to the interacting species. Back proton transfer renders protic ionic liquids volatile and to be considered as inferior ionic liquids. We try to address this issue by employing modern ab initio valence bond theory calculations. The results indicate that the bonding in the cation and the anion of a prototypical ionic liquid, ethylammonium nitrate, is fundamentally different. It is neither characteristic of covalent/polar covalent bonding nor ionic bonding but rather charge shift bonding as a resonance hybrid of two competing ionic molecular electronic structure configurations. An investigation of other analogous protic ionic liquids reveals that this charge shift bonding seems to be a typical characteristic of protic ionic liquids while the ionic solid analogue compound ammonium nitrate has less charge shift bonding character as compared to protic ionic liquids. Further the extent of charge shift bonding character has been found to be congruent with the trends in many physicochemical properties such as melting point, conductivity, viscosity, and ionicity of the studied ionic liquids indicating that percentage charge shift character may serve as a key descriptor for large scale computational screening of ionic liquids with desired properties.

  16. Development of continuous-energy eigenvalue sensitivity coefficient calculation methods in the shift Monte Carlo Code

    Energy Technology Data Exchange (ETDEWEB)

    Perfetti, C.; Martin, W. [Univ. of Michigan, Dept. of Nuclear Engineering and Radiological Sciences, 2355 Bonisteel Boulevard, Ann Arbor, MI 48109-2104 (United States); Rearden, B.; Williams, M. [Oak Ridge National Laboratory, Reactor and Nuclear Systems Div., Bldg. 5700, P.O. Box 2008, Oak Ridge, TN 37831-6170 (United States)

    2012-07-01

    Three methods for calculating continuous-energy eigenvalue sensitivity coefficients were developed and implemented into the Shift Monte Carlo code within the SCALE code package. The methods were used for two small-scale test problems and were evaluated in terms of speed, accuracy, efficiency, and memory requirements. A promising new method for calculating eigenvalue sensitivity coefficients, known as the CLUTCH method, was developed and produced accurate sensitivity coefficients with figures of merit that were several orders of magnitude larger than those from existing methods. (authors)

  17. Mineral Moessbauer spectroscopy: correlations between chemical shift and quadrupole splitting parameters

    International Nuclear Information System (INIS)

    The variety of coordination numbers, symmetries, distortions and ligand environments in thermally-stable iron-bearing minerals provide wide ranges of chemical shift (δ) and quadrupole splitting (Δ) parameters, which serve to characterize the crystal chemistries and site occupancies of Fe2+ and Fe3+ ions in minerals of terrestrial and extraterrestrial origins. Correlations between ferrous and ferric chemical shifts enable thermally-induced electron delocalization behavior in mixed-valence Fe2+-Fe3+ minerals to be identified, while chemical shift versus quadrupole splitting correlations serve to identify nanophase ferric oxides and oxyhydroxides in oxidized minerals and in meteorites subjected to aqueous oxidation before and after they arrived on Earth. (orig.)

  18. Chemical Potential Calculations In Dense Liquids Using Metadynamics

    CERN Document Server

    Perego, Claudio; Parrinello, Michele

    2016-01-01

    The calculation of chemical potential has traditionally been a challenge in atomistic simulations. One of the most used approaches is Widom's insertion method in which the chemical potential is calculated by periodically attempting to insert an extra particle in the system. In dense systems this method fails since the insertion probability is very low. In this paper we show that in a homogeneous fluid the insertion probability can be increased using metadynamics. We test our method on a supercooled high density binary Lennard-Jones fluid. We find that we can obtain efficiently converged results even when Widom's method fails.

  19. Sequential Voronoi diagram calculations using simple chemical reactions

    CERN Document Server

    Costello, Ben de Lacy; Adamatzky, Andy

    2012-01-01

    In our recent paper [de Lacy Costello et al. 2010] we described the formation of complex tessellations of the plane arising from the various reactions of metal salts with potassium ferricyanide and ferrocyanide loaded gels. In addition to producing colourful tessellations these reactions are naturally computing generalised Voronoi diagrams of the plane. The reactions reported previously were capable of the calculation of three distinct Voronoi diagrams of the plane. As diffusion coupled with a chemical reaction is responsible for the calculation then this is achieved in parallel. Thus an increase in the complexity of the data input does not utilise additional computational resource. Additional benefits of these chemical reactions is that a permanent record of the Voronoi diagram calculation (in the form of precipitate free bisectors) is achieved, so there is no requirement for further processing to extract the calculation results. Previously it was assumed that the permanence of the results was also a potenti...

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

    Energy Technology Data Exchange (ETDEWEB)

    Li, Dawei; Brüschweiler, Rafael, E-mail: bruschweiler.1@osu.edu [The Ohio State University, Campus Chemical Instrument Center (United States)

    2015-07-15

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

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

    Science.gov (United States)

    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.

  2. Supramolecular chemical shift reagents inducing conformational transitions: NMR analysis of carbohydrate homooligomer mixtures

    DEFF Research Database (Denmark)

    Beeren, Sophie; Meier, Sebastian

    2015-01-01

    We introduce the concept of supramolecular chemical shift reagents as a tool to improve signal resolution for the NMR analysis of homooligomers. Non-covalent interactions with the shift reagent can constrain otherwise flexible analytes inducing a conformational transition that results in signal...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-04-15

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

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

    International Nuclear Information System (INIS)

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

  5. New Regularization-Renormalization Method in Quantum Electrodynamics and Qualitative Calculation on Lamb Shift

    CERN Document Server

    Ni, G; Ni, Guang-jiong; Wang, Haibin

    1997-01-01

    A simple but effective method for regularization-renormalization (R-R) is proposed for handling the Feynman diagram integral (FDI) at one loop level in quantum electrodynamics (QED). The divergence is substituted by some constants to be fixed via experiments. So no counter term, no bare parameter and no arbitrary running mass scale is involved. Then the Lamb Shift in Hydrogen atom can be calculated qualitatively and simply as $\\Delta E(2S_{1/2})- \\Delta E(2P_{1/2})=996.7 MHz$ versus the experimental value $1057.85 MHz$.

  6. A comparison of chemical shift sensitivity of trifluoromethyl tags: optimizing resolution in {sup 19}F NMR studies of proteins

    Energy Technology Data Exchange (ETDEWEB)

    Ye, Libin; Larda, Sacha Thierry; Frank Li, Yi Feng [University of Toronto, UTM, Department of Chemistry (Canada); Manglik, Aashish [Stanford University School of Medicine, Department of Molecular and Cellular Physiology (United States); Prosser, R. Scott, E-mail: scott.prosser@utoronto.ca [University of Toronto, UTM, Department of Chemistry (Canada)

    2015-05-15

    The elucidation of distinct protein conformers or states by fluorine ({sup 19}F) NMR requires fluorinated moieties whose chemical shifts are most sensitive to subtle changes in the local dielectric and magnetic shielding environment. In this study we evaluate the effective chemical shift dispersion of a number of thiol-reactive trifluoromethyl probes [i.e. 2-bromo-N-(4-(trifluoromethyl)phenyl)acetamide (BTFMA), N-(4-bromo-3-(trifluoromethyl)phenyl)acetamide (3-BTFMA), 3-bromo-1,1,1-trifluoropropan-2-ol (BTFP), 1-bromo-3,3,4,4,4-pentafluorobutan-2-one (BPFB), 3-bromo-1,1,1-trifluoropropan-2-one (BTFA), and 2,2,2-trifluoroethyl-1-thiol (TFET)] under conditions of varying polarity. In considering the sensitivity of the {sup 19}F NMR chemical shift to the local environment, a series of methanol/water mixtures were prepared, ranging from relatively non-polar (MeOH:H{sub 2}O = 4) to polar (MeOH:H{sub 2}O = 0.25). {sup 19}F NMR spectra of the tripeptide, glutathione ((2S)-2-amino-4-{[(1R)-1-[(carboxymethyl)carbamoyl] -2-sulfanylethyl]carbamoyl}butanoic acid), conjugated to each of the above trifluoromethyl probes, revealed that the BTFMA tag exhibited a significantly greater range of chemical shift as a function of solvent polarity than did either BTFA or TFET. DFT calculations using the B3LYP hybrid functional and the 6-31G(d,p) basis set, confirmed the observed trend in chemical shift dispersion with solvent polarity.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-07-01

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

  8. Calculations of the vibrational frequency and isotopic shift of UF6 and U2F6

    Institute of Scientific and Technical Information of China (English)

    Zhang Yun-Guang; Zha Xin-Wei

    2012-01-01

    Molecular structure,vibrational frequency and infrared intensity of UF6 are investigated by using the revised Perdew-Burke-Enzerhof function with the triple-zeta polarized basis set.The calculation results are in good agreement with the experimental values and indicate the existence of a stable U2F6 molecule with a multiple bonded U2 unit.The calculation results also predict that the D3d symmetry of U2F6 is more stable than D3h.The optimized geometries,vibrational frequencies,and infrared intensities are also reported for U2F6 molecules in D3d symmetry.In addition,the isotopic shift of vibrational frequencies of the two molecules under isotopic substitution of uranium atom are also investigated with the same method.The U2F6 molecule is predicted to be better than UF6 for laser uranic isotope separation.

  9. Effect of shifting cultivation on soil physical and chemical properties in Bandarban hill district, Bangladesh

    Institute of Scientific and Technical Information of China (English)

    Khandakar Showkat Osman; M. Jashimuddin; S. M. Sirajul Haque; Sohag Miah

    2013-01-01

    This study reports the effects of shifting cultivation at slashing stage on soil physicochemical properties at Bandarban Sadar Upazila in Chittagong Hill Tracts of Bangladesh. At this initial stage of shifting cultivation no general trend was found for moisture content, maximum water holding capacity, field capacity, dry and moist bulk density, parti-cle density for some chemical properties between shifting cultivated land and forest having similar soil texture. Organic matter was significantly (p≤0.05) lower in 1-year and 3-year shifting cultivated lands and higher in 2-year shifting cultivation than in adjacent natural forest. Significant differences were also found for total N, exchangeable Ca, Mg and K and in CEC as well as for available P. Slashed area showed higher soil pH. Deterioration in land quality starts from burning of slashing materials and continues through subsequent stages of shifting cultivation.

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

    Science.gov (United States)

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

    2015-02-01

    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.

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

    International Nuclear Information System (INIS)

    Chemical shifts of nuclei in or attached to a protein backbone are exquisitely sensitive to their local environment. A computer program, SPARTA, is described that uses this correlation with local structure to predict protein backbone chemical shifts, given an input three-dimensional structure, by searching a newly generated database for triplets of adjacent residues that provide the best match in φ/ψ/χ1 torsion angles and sequence similarity to the query triplet of interest. The database contains 15N, 1HN, 1Hα, 13Cα, 13Cβ and 13C' chemical shifts for 200 proteins for which a high resolution X-ray (≤2.4 A) structure is available. The relative importance of the weighting factors for the φ/ψ/χ1 angles and sequence similarity was optimized empirically. The weighted, average secondary shifts of the central residues in the 20 best-matching triplets, after inclusion of nearest neighbor, ring current, and hydrogen bonding effects, are used to predict chemical shifts for the protein of known structure. Validation shows good agreement between the SPARTA-predicted and experimental shifts, with standard deviations of 2.52, 0.51, 0.27, 0.98, 1.07 and 1.08 ppm for 15N, 1HN, 1Hα, 13Cα, 13Cβ and 13C', respectively, including outliers

  12. RefDB: A database of uniformly referenced protein chemical shifts

    International Nuclear Information System (INIS)

    RefDB is a secondary database of reference-corrected protein chemical shifts derived from the BioMagResBank (BMRB). The database was assembled by using a recently developed program (SHIFTX) to predict protein 1H, 13C and 15N chemical shifts from X-ray or NMR coordinate data of previously assigned proteins. The predicted shifts were then compared with the corresponding observed shifts and a variety of statistical evaluations performed. In this way, potential mis-assignments, typographical errors and chemical referencing errors could be identified and, in many cases, corrected. This approach allows for an unbiased, instrument-independent solution to the problem of retrospectively re-referencing published protein chemical shifts. Results from this study indicate that nearly 25% of BMRB entries with 13C protein assignments and 27% of BMRB entries with 15N protein assignments required significant chemical shift reference readjustments. Additionally, nearly 40% of protein entries deposited in the BioMagResBank appear to have at least one assignment error. From this study it evident that protein NMR spectroscopists are increasingly adhering to recommended IUPAC 13C and 15N chemical shift referencing conventions, however, approximately 20% of newly deposited protein entries in the BMRB are still being incorrectly referenced. This is cause for some concern. However, the utilization of RefDB and its companion programs may help mitigate this ongoing problem. RefDB is updated weekly and the database, along with its associated software, is freely available at http://redpoll.pharmacy.ualberta.ca and the BMRB website

  13. MCDF calculations of the specific mass shift in helium-like ions

    Energy Technology Data Exchange (ETDEWEB)

    Bhatti, Muhammad I.; Bucardo, Manuel [Department of Physics and Geology, University of Texas Pan American, Edinburg, TX (United States); Perger, Warren F. [Departments of Electrical Engineering and Physics, Michigan Technological University, Houghton, MI (United States)

    2001-02-14

    An extension of the GRASP92 (Parpia F A, Froese Fischer C and Grant I P 1996 Comput. Phys. Commun. 94 249) multi-configuration Dirac-Fock (MCDF) program described previously (Perger W F and Idrees M 1995 Phys. Commun. 85 389-97) is used for the calculation of the specific mass shift (SMS) of the helium {sup 1}S ground state isoelectronic sequence. We also employ a multi-configuration Hartree-Fock (MCHF) method to calculate the ground state SMS for comparison with MCDF results. The SMS matrix elements for two-electron systems obtained from the relativistic program are shown to exhibit a trend: the larger the atomic number Z, the larger the relativistic contributions to the SMS matrix elements for the ions. The SMS matrix elements approximately vary as Z{sup 3} along the isoelectronic sequence from Z 2 to 92. In addition, it is shown that the relativistic effects increase approximately as Z{sup 3}/A{sup 2} in the SMS values for all the ions considered confirming some previous observations (Parpia F A, Tong M and Froese Fischer C 1992 Phys. Rev. A 46 3717-24). Excellent agreement is found between the present ab initio calculations and the available semi-relativistic calculations for the small values of Z along the helium-like ions. Furthermore, a large set of configuration state functions used in the calculations has revealed larger disagreements for high-Z ions between both relativistic (MCDF-optimized-level) and nonrelativistic (MCHF) calculations suggesting that the SMS for helium-like ions with Z>40 relativistic and correlation effects are increasingly important. (author)

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

    Energy Technology Data Exchange (ETDEWEB)

    Labudde, D.; Leitner, D.; Krueger, M.; Oschkinat, H. [Forschungsinstitut fuer Molekulare Pharmakologie (Germany)], E-mail: oschkinat@fmp-berlin.de

    2003-01-15

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

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

    International Nuclear Information System (INIS)

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

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

    DEFF Research Database (Denmark)

    Hansen, Poul Erik

    2015-01-01

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

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

    DEFF Research Database (Denmark)

    Hansen, Poul Erik

    2015-01-01

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

  18. Effect of pH, urea, peptide length, and neighboring amino acids on alanine alpha-proton random coil chemical shifts.

    Science.gov (United States)

    Carlisle, Elizabeth A; Holder, Jessica L; Maranda, Abby M; de Alwis, Adamberage R; Selkie, Ellen L; McKay, Sonya L

    2007-01-01

    Accurate random coil alpha-proton chemical shift values are essential for precise protein structure analysis using chemical shift index (CSI) calculations. The current study determines the chemical shift effects of pH, urea, peptide length and neighboring amino acids on the alpha-proton of Ala using model peptides of the general sequence GnXaaAYaaGn, where Xaa and Yaa are Leu, Val, Phe, Tyr, His, Trp or Pro, and n = 1-3. Changes in pH (2-6), urea (0-1M), and peptide length (n = 1-3) had no effect on Ala alpha-proton chemical shifts. Denaturing concentrations of urea (8M) caused significant downfield shifts (0.10 +/- 0.01 ppm) relative to an external DSS reference. Neighboring aliphatic residues (Leu, Val) had no effect, whereas aromatic amino acids (Phe, Tyr, His and Trp) and Pro caused significant shifts in the alanine alpha-proton, with the extent of the shifts dependent on the nature and position of the amino acid. Smaller aromatic residues (Phe, Tyr, His) caused larger shift effects when present in the C-terminal position (approximately 0.10 vs. 0.05 ppm N-terminal), and the larger aromatic tryptophan caused greater effects in the N-terminal position (0.15 ppm vs. 0.10 C-terminal). Proline affected both significant upfield (0.06 ppm, N-terminal) and downfield (0.25 ppm, C-terminal) chemical shifts. These new Ala correction factors detail the magnitude and range of variation in environmental chemical shift effects, in addition to providing insight into the molecular level interactions that govern protein folding.

  19. Classical calculation of relativistic frequency-shifts in an ideal Penning trap

    CERN Document Server

    Ketter, Jochen; Höcker, Martin; Schuh, Marc; Streubel, Sebastian; Blaum, Klaus

    2013-01-01

    The ideal Penning trap consists of a uniform magnetic field and an electrostatic quadrupole potential. In the classical low-energy limit, the three characteristic eigenfrequencies of a charged particle trapped in this configuration do not depend on the amplitudes of the three eigenmotions. No matter how accurate the experimental realization of the ideal Penning trap, its harmonicity is ultimately compromised by special relativity. Using a classical formalism of first-order perturbation theory, we calculate the relativistic frequency-shifts associated with the motional degrees of freedom for a spinless particle stored in an ideal Penning trap, and we compare the results with the simple but surprisingly accurate model of relativistic mass-increase.

  20. Distinguishing between cystic teratomas and endometriomas of the ovary using chemical shift gradient echo magnetic resonance imaging

    Energy Technology Data Exchange (ETDEWEB)

    Ishijima Hideyuki; Ishizaka Hiroshi; Inoue Tomio [Gunma University Hospital, Gunma (Japan). Depts. of Diagnostic Radiaology and Nuclear Medicine

    1996-02-01

    The purpose of this study was to evaluate the efficacy of chemical shift gradient echo magnetic resonance imaging (MRI) in distinguishing between cystic teratomas and endometriomas of the ovary, using a 1.5 T magnet. The study included 22 patients with 31 ovarian lesions (15 cystic teratomas and 16 endometriomas), which showed high signal intensity on T1-weighted spin echo images. Chemical shift gradient echo images with three different echo times (TE = 2.5, 4.5 and 6.5 ms) were obtained in all cases. Indices were calculated on the basis of the signal intensities of lesions on the chemical shift gradient echo images. All endometriomas had signal intensity indices of less than 2.1, while all cystic teratomas had signal intensity indices of 18.1 or greater. It was concluded that the method used in this study presents the following advantages: the acquisition time is short; it needs no special software; and it does not depend on magnetic field homogeneity. 11 refs., 4 figs.

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

    Directory of Open Access Journals (Sweden)

    Ricardo Infante-Castillo

    2012-01-01

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

  2. Ontogenetic shift in response to prey-derived chemical cues in prairie rattlesnakes Crotalus viridis viridis

    Institute of Scientific and Technical Information of China (English)

    Anthony J.SAVIOLA; David CHISZAR; Stephen P.MACKESSY

    2012-01-01

    Snakes often have specialized diets that undergo a shift from one prey type to another depending on the life stage of the snake.Crotalus viridis viridis (prairie rattlesnake) takes different prey at different life stages,and neonates typically prey on ectotherms,while adults feed almost entirely on small endotherms.We hypothesized that elevated rates of tongue flicking to chemical stimuli should correlate with particular prey consumed,and that this response shifts from one prey type to another as individuals age.To examine if an ontogenetic shift in response to chemical cues occurred,we recorded the rate of tongue flicking for 25 neonate,20 subadult,and 20 adult (average SVL=280.9,552,789.5 mm,respectively) wild-caught C.v.viridis to chemical stimuli presented on a cotton-tipped applicator; water-soluble cues from two ectotherms (prairie lizard,Sceloporus undulatus,and house gecko,Hemidactylusfrenatus),two endotherms (deer mouse,Peromyscus maniculatus and lab mouse,Mus musculus),and water controls were used.Neonates tongue flicked significantly more to chemical cues of their common prey,S.undulatus,than to all other chemical cues; however,the response to this lizard's chemical cues decreased in adult rattlesnakes.Subadults tongue flicked with a higher rate of tongue flicking to both S.undulatus and P.maniculatus than to all other treatments,and adults tongue flicked significantly more to P.maniculatus than to all other chemical cues.In addition,all three sub-classes demonstrated a greater response for natural prey chemical cues over chemical stimuli of prey not encountered in the wild (M.musculus and H.frenatus).This shift in chemosensory response correlated with the previously described ontogenetic shifts in C.v.viridis diet.Because many vipers show a similar ontogenetic shift in diet and venom composition,we suggest that this shift in prey cue discrimination is likely a general phenomenon among viperid snakes.

  3. Three-body calculation of the $1s$ level shift in kaonic deuterium with realistic $\\bar{K}N$ potentials

    CERN Document Server

    Révai, János

    2016-01-01

    The $1s$ level shift in kaonic deuterium was calculated using Coulomb Sturmian expansion of Faddeev equations. The convergence of the method yields an $\\sim\\ 1\\ eV$ accuracy for the level shifts. We used three different, realistic, multichannel $\\bar{K}N$ interactions reproducing all known experimental two-body $\\bar{K}N$ data. The different results suggest, that the level shift should be in the range $\\Delta E\\sim(800\\pm30)-(480\\pm20){\\rm i}\\ \\ eV$. The (almost) exact level shifts were compared with values, given by the commonly used approximations.

  4. Proton Magnetic Resonance and Human Thyroid Neoplasia III. Ex VivoChemical-Shift Microimaging

    Science.gov (United States)

    Rutter, Allison; Künnecke, Basil; Dowd, Susan; Russell, Peter; Delbridge, Leigh; Mountford, Carolyn E.

    1996-03-01

    Magnetic-resonance chemical-shift microimaging, with a spatial resolution of 40 × 40 μm, is a modality which can detect alterations to cellular chemistry and hence markers of pathological processes in human tissueex vivo.This technique was used as a chemical microscope to assess follicular thyroid neoplasms, lesions which are unsatisfactorily investigated using standard histopathological techiques or water-based magnetic-resonance imaging. The chemical-shift images at the methyl frequency (0.9 ppm) identify chemical heterogeneity in follicular tumors which are histologically homogeneous. The observed changes to cellular chemistry, detectable in foci of approximately 100 cells or less, support the existence of a preinvasive state hitherto unidentified by current pathological techniques.

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

    Science.gov (United States)

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

    2016-01-01

    Previous studies have reported significant region-dependent differences in the fiber-type composition of human skeletal muscle. It is therefore hypothesized that there is a difference between the deep and superficial parts of muscle energy metabolism during exercise. We hypothesized that the inorganic phosphate (Pi)/phosphocreatine (PCr) ratio of the superficial parts would be higher, compared with the deep parts, as the work rate increases, because the muscle fiber-type composition of the fast-type may be greater in the superficial parts compared with the deep parts. This study used two-dimensional 31Phosphorus Chemical Shift Imaging (31P-CSI) to detect differences between the deep and superficial parts of the human leg muscles during dynamic knee extension exercise. Six healthy men participated in this study (age 27±1 year, height 169.4±4.1 cm, weight 65.9±8.4 kg). The experiments were carried out with a 1.5-T superconducting magnet with a 5-in. diameter circular surface coil. The subjects performed dynamic one-legged knee extension exercise in the prone position, with the transmit-receive coil placed under the right quadriceps muscles in the magnet. The subjects pulled down an elastic rubber band attached to the ankle at a frequency of 0.25, 0.5 and 1 Hz for 320 s each. The intracellular pH (pHi) was calculated from the median chemical shift of the Pi peak relative to PCr. No significant difference in Pi/PCr was observed between the deep and the superficial parts of the quadriceps muscles at rest. The Pi/PCr of the superficial parts was not significantly increased with increasing work rate. Compared with the superficial areas, the Pi/PCr of the deep parts was significantly higher (p<0.05) at 1 Hz. The pHi showed no significant difference between the two parts. These results suggest that muscle oxidative metabolism is different between deep and superficial parts of quadriceps muscles during dynamic exercise. PMID:26782194

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

    Science.gov (United States)

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

    2016-01-01

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

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

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Poulsen, Flemming Martin

    2011-01-01

    Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues...... use random coil peptides containing glutamine instead of glycine to determine the random coil chemical shifts and the neighbor correction factors. The resulting correction factors correlate to changes in the populations of the major wells in the Ramachandran plot, which demonstrates that changes...... in the conformational ensemble are an important source of neighbor effects in disordered proteins. Glutamine derived random coil chemical shifts and correction factors modestly improve our ability to predict (13)C chemical shifts of intrinsically disordered proteins compared to existing datasets, and may thus improve...

  8. Automated assignment of NMR chemical shifts based on a known structure and 4D spectra.

    Science.gov (United States)

    Trautwein, Matthias; Fredriksson, Kai; Möller, Heiko M; Exner, Thomas E

    2016-08-01

    Apart from their central role during 3D structure determination of proteins the backbone chemical shift assignment is the basis for a number of applications, like chemical shift perturbation mapping and studies on the dynamics of proteins. This assignment is not a trivial task even if a 3D protein structure is known and needs almost as much effort as the assignment for structure prediction if performed manually. We present here a new algorithm based solely on 4D [(1)H,(15)N]-HSQC-NOESY-[(1)H,(15)N]-HSQC spectra which is able to assign a large percentage of chemical shifts (73-82 %) unambiguously, demonstrated with proteins up to a size of 250 residues. For the remaining residues, a small number of possible assignments is filtered out. This is done by comparing distances in the 3D structure to restraints obtained from the peak volumes in the 4D spectrum. Using dead-end elimination, assignments are removed in which at least one of the restraints is violated. Including additional information from chemical shift predictions, a complete unambiguous assignment was obtained for Ubiquitin and 95 % of the residues were correctly assigned in the 251 residue-long N-terminal domain of enzyme I. The program including source code is available at https://github.com/thomasexner/4Dassign . PMID:27484442

  9. Chemical shifts in transition metal dithiocarbamates from infrared and X-ray photoelectron spectroscopies

    Science.gov (United States)

    Payne, R.; Magee, R. J.; Liesegang, J.

    1982-11-01

    Measurements of the IR stretching frequencies of the NC and MS bonds in transition-metal (M) dithiocarbamates show significant correlation with measurement of core level XPS chemical shifts. This is believed to be the first demonstration of such a correlation for a series of solid-phase compounds.

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

    Science.gov (United States)

    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…

  11. Database proton NMR chemical shifts for RNA signal assignment and validation

    International Nuclear Information System (INIS)

    The Biological Magnetic Resonance Data Bank contains NMR chemical shift depositions for 132 RNAs and RNA-containing complexes. We have analyzed the 1H NMR chemical shifts reported for non-exchangeable protons of residues that reside within A-form helical regions of these RNAs. The analysis focused on the central base pair within a stretch of three adjacent base pairs (BP triplets), and included both Watson–Crick (WC; G:C, A:U) and G:U wobble pairs. Chemical shift values were included for all 43 possible WC-BP triplets, as well as 137 additional triplets that contain one or more G:U wobbles. Sequence-dependent chemical shift correlations were identified, including correlations involving terminating base pairs within the triplets and canonical and non-canonical structures adjacent to the BP triplets (i.e. bulges, loops, WC and non-WC BPs), despite the fact that the NMR data were obtained under different conditions of pH, buffer, ionic strength, and temperature. A computer program (RNAShifts) was developed that enables convenient comparison of RNA 1H NMR assignments with database predictions, which should facilitate future signal assignment/validation efforts and enable rapid identification of non-canonical RNA structures and RNA-ligand/protein interaction sites.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-03-15

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

  13. The statistical shift of the chemical potential causing anomalous conductivity in hydrogenated microcrystalline silicon

    NARCIS (Netherlands)

    Lof, R.W.; Schropp, R.E.I.

    2010-01-01

    The behavior of the electrical conductivity in hydrogenated microcrystalline silicon (μ c-Si:H) that is frequently observed is explained by considering the statistical shift in the chemical potential as a function of the crystalline fraction (Xc), the dangling bond density (N db), and the doping den

  14. LDA+DMFT calculations of the Knight shift and relaxation rate in VOMoO{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Kiani, Amin; Pavarini, Eva [Institute for Advanced Simulation and JARA, Forschungszentrum Juelich, 52425 Juelich (Germany)

    2013-07-01

    By using the LDA+DMFT approach and the local vertex approximation, we calculate the magnetic linear response function of strongly correlated transition-metal oxides. From the susceptibility we obtain Knight shift and relaxation rate. We present results for the frustrated system VOMoO{sub 4}. In particular we investigate how the Knight shift and the relaxation time behave in different temperature and correlation regimes.

  15. Noninvasive Temperature Mapping With MRI Using Chemical Shift Water-Fat Separation

    OpenAIRE

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

    2010-01-01

    Tissues containing both water and lipids, e.g., breast, confound standard MR proton reference frequency-shift methods for mapping temperatures due to the lack of temperature-induced frequency shift in lipid protons. Generalized Dixon chemical shift–based water-fat separation methods, such as GE’s iterative decomposition of water and fat with echo asymmetry and least-squares estimation method, can result in complex water and fat images. Once separated, the phase change over time of the water s...

  16. Quantification of fat using chemical shift imaging and 1H-MR spectroscopy in phantom model

    International Nuclear Information System (INIS)

    Objective: To evaluate the accuracy of chemical shift imaging (CSI) and MR spectroscopy (MRS) for fat quantification in phantom model. Methods: Eleven phantoms were made according to the volume percentage of fat ranging from 0 to 100% with an interval of 10%. The fat concentration in the phantoms were measured respectively by CSI and MRS and compared using one-sample t test. The correlation between the two methods was also analyzed. The concentration of saturated fatty acids (FS), unsaturated fatty acids (FU) and the poly, unsaturation degree (PUD) were calculated by using MRS. Results: The fat concentration was (48.0±1.0)%, (57.0±0.5)%, (67.3±0.6)%, (77.3± 0.6)%, (83.3±0.6)% and (91.0±1.0)% respectively with fat volume of 50% to 100% by CSI. The fat concentration was (8.3±0.6)%, (16.3±0.7)%, (27.7±0.6)%, (36.0±1.0)%, (43.5± 0.6)% and (56.5±1.0)% respectively with fat volume of 10% to 60% by MRS, the fat concentration were underestimated by CSI and MRS (P<0.05), and had high linear correlation with the real concentration in phantoms (CSI: r=0.998, MRS: r=0.996, P<0.01). There was also a linear correlation between two methods (r=0.992, P<0.01) but no statistically significant difference (paired- samples t test, t=-0.125, P=0.903). By using MRS, the relative ratio of FS and FU in fat were 0. 15 and 0.85, the PUD was 0.0325, respectively, and highly consistent with these in phantoms. Conclusion: Both CSI and MRS are efficient and accurate methods in fat quantification at 7.0 T MR. (authors)

  17. Calculating the mean time to capture for tethered ligands and its effect on the chemical equilibrium of bound ligand pairs.

    Science.gov (United States)

    Shen, Lu; Decker, Caitlin G; Maynard, Heather D; Levine, Alex J

    2016-09-01

    We present here the calculation of the mean time to capture of a tethered ligand to the receptor. This calculation is then used to determine the shift in the partitioning between (1) free, (2) singly bound, and (3) doubly bound ligands in chemical equilibrium as a function of the length of the tether. These calculations are used in the research article Fibroblast Growth Factor 2 Dimer with Superagonist in vitro Activity Improves Granulation Tissue Formation During Wound Healing (Decker et al., in press [1]) to explain quantitatively how changes in polymeric linker length in the ligand dimers modifies the efficacy of these molecules relative to that of free ligands. PMID:27408925

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-07-15

    A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, {>=}90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed ({phi}, {psi}) torsion angles of ca 12 Masculine-Ordinal-Indicator . TALOS-N also reports sidechain {chi}{sup 1} rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts.

  19. Relationship between electrophilicity index, Hammett constant and nucleus-independent chemical shift

    Indian Academy of Sciences (India)

    M Elango; R Parthasarathi; G Karthik Narayanan; A Md Sabeelullah; U Sarkar; N S Venkatasubramaniyan; V Subramanian; P K Chattaraj

    2005-01-01

    Inter-relationships between the electrophilicity index (), Hammett constant (ó) and nucleusindependent chemical shift (NICS (1) - NICS value one å ngstrom above the ring centre) have been investigated for a series of meta- and para-substituted benzoic acids. Good linear relationships between Hammett constant vs electrophilicity and Hammett constant vs NICS (1) values have been observed. However, the variation of NICS (1) against shows only a low correlation coefficient.

  20. Phase correction method for least-squares wavefront calculation in statistical generalized phase-shifting digital holography

    Science.gov (United States)

    Yoshikawa, Nobukazu; Kajihara, Kazuki

    2015-09-01

    When phase-shifting digital holography with a continuous fringe-scanning scheme is implemented using a PC-based measurement system without any synchronous circuit, nonuniform phase-shifted interference fringes are captured because of the fluctuation in the image-capturing interval. To cope with the nonuniform phase shifts, a statistical generalized phase-shifting approach is employed. Because the algorithm is designed to use an arbitrary phase shift, the nonuniform phase shifts do not obstruct object-wave retrieval. Moreover, multiple interference fringes can be obtained in a short time owing to the continuous fringe-scanning scheme. However, the wavefront calculation method is not designed for sequentially recorded interference fringes. To use multiple interference fringes appropriately, we develop a least-squares wavefront calculation method combined with corrections for the initial phase and the direction of phase rotation. We verify the proposed method by numerical simulations and optical experiments. The results show that the object wave with the same initial phase can be correctly reconstructed by using both phase correction methods simultaneously.

  1. Predictions of the fluorine NMR chemical shifts of perfluorinated carboxylic acids, CnF(2n+1)COOH (n = 6-8).

    Science.gov (United States)

    Liu, Zizhong; Goddard, John D

    2009-12-17

    Perfluorinated carboxylic acids (PFCAs) are a class of persistent environmental pollutants. Commercially available PFCAs are mixtures of linear and branched isomers, possibly with impurities. Different isomers have different physical and chemical properties and toxicities. However, little is known about the properties and the finer details of the structures of the individual branched isomers. Full geometry optimizations for the linear n-alkane (C(6)-C(27)) PFCAs indicated that all have helical structures. The helical angle increases slightly with increasing chain length, from 16.3 degrees in C(6)F(13)COOH to 17.0 degrees in C(27)F(55)COOH. This study predicts (19)F NMR parameters for 69 linear and branched isomers of the perfluoro carboxylic acids C(6)F(13)COOH, C(7)F(15)COOH, and C(8)F(17)COOH. B3LYP-GIAO/6-31++G(d,p)//B3LYP/6-31G(d,p) was used for the NMR calculations with analysis of the chemical shifts by the natural bond orbital method. The predictions of the (19)F chemical shifts revealed the differences among the CF(3), CF(2), and CF groups. In general, the absolute values for the chemical shifts for the CF(3) group are smaller than 90 ppm, for the CF larger than 160 ppm, and for the CF(2) between 110 and 130 ppm. The chemical shifts of the branched isomers are smaller in magnitude than the linear ones. The decrease is correlated with the steric hindrance of the CF(3) groups, the more hindered the CF(3), the greater the decrease in the (19)F chemical shifts. The predicted (19)F chemical shifts are similar to those for analogous perfluoro compounds with other terminal functional groups such as -SO(3)H or -SO(3)NH(2)CH(2)CH(3).

  2. Molecular structure and vibrational bands and 13C chemical shift assignments of both enmein-type diterpenoids by DFT study

    Science.gov (United States)

    Wang, Tao; Wu, Yi fang; Wang, Xue liang

    2014-01-01

    We report here theoretical and experimental studies on the molecular structure and vibrational and NMR spectra of both natural enmein type diterpenoids molecule (6, 7-seco-ent-kaurenes enmein type), isolated from the leaves of Isodon japonica (Burm.f.) Hara var. galaucocalyx (maxin) Hara. The optimized geometry, total energy, NMR chemical shifts and vibrational wavenumbers of epinodosinol and epinodosin have been determined using B3LYP method with 6-311G (d,p) basis set. A complete vibrational assignment is provided for the observed IR spectra of studied compounds. The calculated wavenumbers and 13C c.s. are in an excellent agreement with the experimental values. Quantum chemical calculations at the B3LYP/6-311G (d,p) level of theory have been carried out on studied compounds to obtain a set of molecular electronic properties (MEP,HOMO, LUMO and gap energies ΔEg). Electrostatic potential surfaces have been mapped over the electron density isosurfaces to obtain information about the size, shape, charge density distribution and chemical reactivity of the molecules.

  3. Fast calculation method of computer generated hologram animation for viewpoint parallel shift and rotation using Fourier transform optical system.

    Science.gov (United States)

    Watanabe, Ryosuke; Yamaguchi, Kazuhiro; Sakamoto, Yuji

    2016-01-20

    Computer generated hologram (CGH) animations can be made by switching many CGHs on an electronic display. Some fast calculation methods for CGH animations have been proposed, but one for viewpoint movement has not been proposed. Therefore, we designed a fast calculation method of CGH animations for viewpoint parallel shifts and rotation. A Fourier transform optical system was adopted to expand the viewing angle. The results of experiments were that the calculation time of our method was over 6 times faster than that of the conventional method. Furthermore, the degradation in CGH animation quality was found to be sufficiently small.

  4. Interference of lateralized distractors on arithmetic problem solving: a functional role for attention shifts in mental calculation.

    Science.gov (United States)

    Masson, Nicolas; Pesenti, Mauro

    2016-07-01

    Solving arithmetic problems has been shown to induce shifts of spatial attention in simple probe-detection tasks, subtractions orienting attention to the left side and additions to the right side of space. Whether these attentional shifts constitute epiphenomena or are critically linked to the calculation process is still unknown. In the present study, we investigate participants' performance on addition and subtraction solving while they have to detect central or lateralized targets. The results show that lateralized distractors presented in the hemifield congruent to the operation to be solved interfere with arithmetical solving: participants are slower to solve subtractions or additions when distractors are located on the left or on the right, respectively. These results converge with previous data to show that attentional shifts underlie not only number processing but also mental arithmetic. They extend them as they reveal the reverse effect of the one previously reported by showing that inducing attention shifts interferes with the solving of arithmetic problems. They also demonstrate that spatial attentional shifts are part of the calculation procedure of solving mentally arithmetic problems. Their functional role is to access, from the first operand, the representation of the result in a direction congruent to the operation. PMID:25991551

  5. Interference of lateralized distractors on arithmetic problem solving: a functional role for attention shifts in mental calculation.

    Science.gov (United States)

    Masson, Nicolas; Pesenti, Mauro

    2016-07-01

    Solving arithmetic problems has been shown to induce shifts of spatial attention in simple probe-detection tasks, subtractions orienting attention to the left side and additions to the right side of space. Whether these attentional shifts constitute epiphenomena or are critically linked to the calculation process is still unknown. In the present study, we investigate participants' performance on addition and subtraction solving while they have to detect central or lateralized targets. The results show that lateralized distractors presented in the hemifield congruent to the operation to be solved interfere with arithmetical solving: participants are slower to solve subtractions or additions when distractors are located on the left or on the right, respectively. These results converge with previous data to show that attentional shifts underlie not only number processing but also mental arithmetic. They extend them as they reveal the reverse effect of the one previously reported by showing that inducing attention shifts interferes with the solving of arithmetic problems. They also demonstrate that spatial attentional shifts are part of the calculation procedure of solving mentally arithmetic problems. Their functional role is to access, from the first operand, the representation of the result in a direction congruent to the operation.

  6. Clouds in Super-Earth Atmospheres: Chemical Equilibrium Calculations

    Science.gov (United States)

    Mbarek, Rostom; Kempton, Eliza M.-R.

    2016-08-01

    Recent studies have unequivocally proven the existence of clouds in super-Earth atmospheres. Here we provide a theoretical context for the formation of super-Earth clouds by determining which condensates are likely to form under the assumption of chemical equilibrium. We study super-Earth atmospheres of diverse bulk composition, which are assumed to form by outgassing from a solid core of chondritic material, following Schaefer & Fegley. The super-Earth atmospheres that we study arise from planetary cores made up of individual types of chondritic meteorites. They range from highly reducing to oxidizing and have carbon to oxygen (C:O) ratios that are both sub-solar and super-solar, thereby spanning a range of atmospheric composition that is appropriate for low-mass exoplanets. Given the atomic makeup of these atmospheres, we minimize the global Gibbs free energy of formation for over 550 gases and condensates to obtain the molecular composition of the atmospheres over a temperature range of 350-3000 K. Clouds should form along the temperature-pressure boundaries where the condensed species appear in our calculation. We find that the composition of condensate clouds depends strongly on both the H:O and C:O ratios. For the super-Earth archetype GJ 1214b, KCl and ZnS are the primary cloud-forming condensates at solar composition, in agreement with previous work. However, for oxidizing atmospheres, K2SO4 and ZnO condensates are favored instead, and for carbon-rich atmospheres with super-solar C:O ratios, graphite clouds appear. For even hotter planets, clouds form from a wide variety of rock-forming and metallic species.

  7. Automated prediction of 15N, 13Cα, 13Cβ and 13C' chemical shifts in proteins using a density functional database

    International Nuclear Information System (INIS)

    A database of peptide chemical shifts, computed at the density functional level, has been used to develop an algorithm for prediction of 15N and 13C shifts in proteins from their structure; the method is incorporated into a program called SHIFTS (version 4.0). The database was built from the calculated chemical shift patterns of 1335 peptides whose backbone torsion angles are limited to areas of the Ramachandran map around helical and sheet configurations. For each tripeptide in these regions of regular secondary structure (which constitute about 40% of residues in globular proteins) SHIFTS also consults the database for information about sidechain torsion angle effects for the residue of interest and for the preceding residue, and estimates hydrogen bonding effects through an empirical formula that is also based on density functional calculations on peptides. The program optionally searches for alternate side-chain torsion angles that could significantly improve agreement between calculated and observed shifts. The application of the program on 20 proteins shows good consistency with experimental data, with correlation coefficients of 0.92, 0.98, 0.99 and 0.90 and r.m.s. deviations of 1.94, 0.97, 1.05, and 1.08 ppm for 15N, 13Cα, 13Cβ and 13C', respectively. Reference shifts fit to protein data are in good agreement with 'random-coil' values derived from experimental measurements on peptides. This prediction algorithm should be helpful in NMR assignment, crystal and solution structure comparison, and structure refinement

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

    Science.gov (United States)

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

    2016-02-01

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

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

    Science.gov (United States)

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

    2016-02-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-02-15

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

  11. Calculation of the density shift and broadening of the transition lines in pionic helium: Computational problems

    Energy Technology Data Exchange (ETDEWEB)

    Bakalov, Dimitar, E-mail: dbakalov@inrne.bas.bg [Bulgarian Academy of Sciences, INRNE (Bulgaria)

    2015-08-15

    The potential energy surface and the computational codes, developed for the evaluation of the density shift and broadening of the spectral lines of laser-induced transitions from metastable states of antiprotonic helium, fail to produce convergent results in the case of pionic helium. We briefly analyze the encountered computational problems and outline possible solutions of the problems.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-09-15

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

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

    Science.gov (United States)

    Görling, Benjamin; Bräse, Stefan; Luy, Burkhard

    2016-01-01

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

  14. Model analysis of influences of the high-temperature reactor on location shifting in chemical industry

    International Nuclear Information System (INIS)

    An analysis is presented of the influences of High-Temperature Reactor on probable location shifting of big chemical plants, in the future. This is done by a spatial location model, that includes an investigation on 116 industrial locations within the first six countries of Common Market. The results of a computerized program show differences in location qualities when furnished either with traditional or with nuclear energy systems. In addition to location factor energy some other important factors, as subventions, taxes, labour, and transport costs are analysed, and their influence on industrial location is quantified. (orig.)

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

    Directory of Open Access Journals (Sweden)

    Benjamin Görling

    2016-09-01

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

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

    Science.gov (United States)

    Görling, Benjamin; Bräse, Stefan; Luy, Burkhard

    2016-01-01

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

  17. Three model space experiments on chemical reactions. [Gibbs adsorption, equilibrium shift and electrodeposition

    Science.gov (United States)

    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.

  18. Liver fat quantification: Comparison of dual-echo and triple-echo chemical shift MRI to MR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Satkunasingham, Janakan; Besa, Cecilia [Department of Radiology, Body MRI, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Bane, Octavia [Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Shah, Ami [Department of Radiology, Body MRI, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Oliveira, André de; Gilson, Wesley D.; Kannengiesser, Stephan [Siemens AG, Healthcare Sector, Erlangen (Germany); Taouli, Bachir, E-mail: bachir.taouli@mountsinai.org [Department of Radiology, Body MRI, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States)

    2015-08-15

    Highlights: • We present a large cohort of patients who underwent dual and triple echo chemical shift imaging against multi-echo T{sub 2} corrected MR spectroscopy (MRS) for liver fat quantification. • Our data suggests that a triple-echo sequence is highly accurate for detection of liver fat, even in the presence of T{sub 2}{sup *} shortening, with minor discrepancies when compared with the advanced fat quantification method. - Abstract: Purpose: To assess the diagnostic value of MRI using dual-echo (2PD) and triple-echo (3PD) chemical shift imaging for liver fat quantification against multi-echo T{sub 2} corrected MR spectroscopy (MRS) used as the reference standard, and examine the effect of T{sub 2}{sup *} imaging on accuracy of MRI for fat quantification. Materials and methods: Patients who underwent 1.5 T liver MRI that incorporated 2PD, 3PD, multi-echo T{sub 2}{sup *} and MRS were included in this IRB approved prospective study. Regions of interest were placed in the liver to measure fat fraction (FF) with 2PD and 3PD and compared with MRS-FF. A random subset of 25 patients with a wide range of MRS-FF was analyzed with an advanced FF calculation method, to prove concordance with the 3PD. The statistical analysis included correlation stratified according to T{sub 2}{sup *}, Bland-Altman analysis, and calculation of diagnostic accuracy for detection of MRS-FF > 6.25%. Results: 220 MRI studies were identified in 217 patients (mean BMI 28.0 ± 5.6). 57/217 (26.2%) patients demonstrated liver steatosis (MRS-FF > 6.25%). Bland-Altman analysis revealed strong agreement between 3PD and MRS (mean ± 1.96 SD: −0.5% ± 4.6%) and weaker agreement between 2PD and MRS (4.7% ± 16.0%). Sensitivity of 3PD for diagnosing FF> 6.25% was higher than that of 2PD. 3PD-FF showed minor discrepancies (coefficient of variation <10%) from FF measured with the advanced method. Conclusion: Our large series study validates the use of 3PD chemical shift sequence for detection of

  19. Liver fat quantification: Comparison of dual-echo and triple-echo chemical shift MRI to MR spectroscopy

    International Nuclear Information System (INIS)

    Highlights: • We present a large cohort of patients who underwent dual and triple echo chemical shift imaging against multi-echo T2 corrected MR spectroscopy (MRS) for liver fat quantification. • Our data suggests that a triple-echo sequence is highly accurate for detection of liver fat, even in the presence of T2* shortening, with minor discrepancies when compared with the advanced fat quantification method. - Abstract: Purpose: To assess the diagnostic value of MRI using dual-echo (2PD) and triple-echo (3PD) chemical shift imaging for liver fat quantification against multi-echo T2 corrected MR spectroscopy (MRS) used as the reference standard, and examine the effect of T2* imaging on accuracy of MRI for fat quantification. Materials and methods: Patients who underwent 1.5 T liver MRI that incorporated 2PD, 3PD, multi-echo T2* and MRS were included in this IRB approved prospective study. Regions of interest were placed in the liver to measure fat fraction (FF) with 2PD and 3PD and compared with MRS-FF. A random subset of 25 patients with a wide range of MRS-FF was analyzed with an advanced FF calculation method, to prove concordance with the 3PD. The statistical analysis included correlation stratified according to T2*, Bland-Altman analysis, and calculation of diagnostic accuracy for detection of MRS-FF > 6.25%. Results: 220 MRI studies were identified in 217 patients (mean BMI 28.0 ± 5.6). 57/217 (26.2%) patients demonstrated liver steatosis (MRS-FF > 6.25%). Bland-Altman analysis revealed strong agreement between 3PD and MRS (mean ± 1.96 SD: −0.5% ± 4.6%) and weaker agreement between 2PD and MRS (4.7% ± 16.0%). Sensitivity of 3PD for diagnosing FF> 6.25% was higher than that of 2PD. 3PD-FF showed minor discrepancies (coefficient of variation <10%) from FF measured with the advanced method. Conclusion: Our large series study validates the use of 3PD chemical shift sequence for detection of liver fat in the clinical environment, even in the presence of

  20. A unified equation for calculating methane vapor pressures in the CH4-H2O system with measured Raman shifts

    Science.gov (United States)

    Lu, W.; Chou, I.-Ming; Burruss, R.C.; Song, Y.

    2007-01-01

    A unified equation has been derived by using all available data for calculating methane vapor pressures with measured Raman shifts of C-H symmetric stretching band (??1) in the vapor phase of sample fluids near room temperature. This equation eliminates discrepancies among the existing data sets and can be applied at any Raman laboratory. Raman shifts of C-H symmetric stretching band of methane in the vapor phase of CH4-H2O mixtures prepared in a high-pressure optical cell were also measured at temperatures between room temperature and 200 ??C, and pressures up to 37 MPa. The results show that the CH4 ??1 band position shifts to higher wavenumber as temperature increases. We also demonstrated that this Raman band shift is a simple function of methane vapor density, and, therefore, when combined with equation of state of methane, methane vapor pressures in the sample fluids at elevated temperatures can be calculated from measured Raman peak positions. This method can be applied to determine the pressure of CH4-bearing systems, such as methane-rich fluid inclusions from sedimentary basins or experimental fluids in hydrothermal diamond-anvil cell or other types of optical cell. ?? 2007 Elsevier Ltd. All rights reserved.

  1. Signal processing method based on group delay calculation for distributed Bragg wavelength shift in optical frequency domain reflectometry.

    Science.gov (United States)

    Wada, Daichi; Igawa, Hirotaka; Murayama, Hideaki; Kasai, Tokio

    2014-03-24

    A signal processing method based on group delay calculations is introduced for distributed measurements of long-length fiber Bragg gratings (FBGs) based on optical frequency domain reflectometry (OFDR). Bragg wavelength shifts in interfered signals of OFDR are regarded as group delay. By calculating group delay, the distribution of Bragg wavelength shifts is obtained with high computational efficiency. We introduce weighted averaging process for noise reduction. This method required only 3.5% of signal processing time which was necessary for conventional equivalent signal processing based on short-time Fourier transform. The method also showed high sensitivity to experimental signals where non-uniform strain distributions existed in a long-length FBG.

  2. Comparison of experimental and theoretical calculations of backscattering amplitude and phase shift functions for a number of fcc metals

    International Nuclear Information System (INIS)

    Extended x-ray absorption fine structure (EXAFS) spectra have been acquired experimentally for a number of fcc metals with atomic number Z between 28 (Ni) and 90 (Th). The backscattering amplitude and phase shift functions have been extracted from the data and compared with calculations based on a single scattering theory, using for the ejected electron, the exact curved wave function. The calculated functions obtained with the curved wave formalism provide increased accuracy, particularly at low k, i.e. k < 4 A/sup -1/, compared to those obtained with the plane wave approximation

  3. Qualitative Study of Substituent Effects on NMR 15N and 17O Chemical Shifts

    Science.gov (United States)

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

    2009-08-01

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

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

    Science.gov (United States)

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

    2009-09-10

    A qualitative approach to analyze the electronic origin of substituent effects on the paramagnetic part of chemical shifts is described and applied to few model systems, where its potentiality can be appreciated. The formulation of this approach is based on the following grounds. The influence of different inter- or intramolecular interactions on a second-order property can be qualitatively predicted if it can be known how they affect the main virtual excitations entering into that second-order property. A set of consistent approximations are introduced in order to analyze the behavior of occupied and virtual orbitals that define some experimental trends of magnetic shielding constants. This approach is applied first to study the electronic origin of methyl-beta substituent effects on both (15)N and (17)O chemical shifts, and afterward it is applied to a couple of examples of long-range substituent effects originated in charge transfer interactions such as the conjugative effect in aromatic compounds and sigma-hyperconjugative interactions in saturated multicyclic compounds. PMID:19685922

  5. Doppler-shifted auroral H β emission: a comparison between observations and calculations

    Directory of Open Access Journals (Sweden)

    K. Aarsnes

    Full Text Available Two sounding rockets equipped with photometers and particle detectors have been flown into proton auroras. The measured altitude dependence of the proton flux is compared with calculations based upon known energy-range relations for protons in air. Expressions suitable for numerical calculations of Doppler profiles at arbitrary angles to the geomagnetic field and at different heights within an aurora are developed. Profiles due to some typical proton spectra have been calculated and it is shown that altitude profiles at some wavelengths are more sensitive to the shape of the proton spectrum than are profiles at other wavelengths. Variations in the Hβ Doppler profile versus height for several angles with the magnetic field is studied. Profiles, as generated by the actually measured protons in the energy range 1 keV to 1 MeV, have been calculated and are compared with direct optical measurements made by ground and rocket photometers. The rocket photometers took measurements at different wavelengths within the Doppler profile. The correspondence between calculations and measurements is generally good. The total Hβ is calculated and fair agreement with the measured intensity is found.

  6. Quantum chemical calculations for polymers and organic compounds

    Science.gov (United States)

    Lopez, J.; Yang, C.

    1982-01-01

    The relativistic effects of the orbiting electrons on a model compound were calculated. The computational method used was based on 'Modified Neglect of Differential Overlap' (MNDO). The compound tetracyanoplatinate was used since empirical measurement and calculations along "classical" lines had yielded many known properties. The purpose was to show that for large molecules relativity effects could not be ignored and that these effects could be calculated and yield data in closer agreement to empirical measurements. Both the energy band structure and molecular orbitals are depicted.

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

    DEFF Research Database (Denmark)

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

    2011-01-01

    of ¿-gauche effect. To overcome this, we reference the chemical shifts to those in a more disordered state resulting in residue specific random coil chemical shifts. The (13)C secondary chemical shifts of the methyl groups of valine, leucine, and isoleucine show sequence specific effects, which allow...

  8. Water-fat imaging and general chemical shift imaging with spectrum modeling

    Science.gov (United States)

    An, Li

    Water-fat chemical shift imaging (CSI) has been an active research area in magnetic resonance imaging (MRI) since the early 1980's. There are two main reasons for water- fat imaging. First, water-fat imaging can serve as a fat- suppression method. Removing the usually bright fatty signals not only extends the useful dynamic range of an image, but also allows better visualization of lesions or injected contrast, and removes chemical shift artifacts, which may contribute to improved diagnosis. Second, quantification of water and fat provides useful chemical information for characterizing tissues such as bone marrow, liver, and adrenal masses. A milestone in water- fat imaging is the Dixon method that can produce separate water and fat images with only two data acquisitions. In practice, however, the Dixon method is not always successful due to field inhomogeneity problems. In recent years, many variations of the Dixon method have been proposed to overcome the field inhomogeneity problem. In general, these methods can at best separate water and fat without identifying the two because the water and fat magnetization vectors are sampled symmetrically, only parallel and anti-parallel. Furthermore, these methods usually depend on two-dimensional phase unwrapping which itself is sensitive to noise and artifacts, and becomes unreliable when the images have disconnected tissues in the field-of-view (FOV). We will first introduce the basic principles of nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) in chapter 1, and briefly review the existing water-fat imaging techniques in chapter 2. In chapter 3, we will introduce a new method for water-fat imaging. With three image acquisitions, a general direct phase encoding (DPE) of the chemical shift information is achieved, which allows an unambiguous determination of water and fat on a pixel by pixel basis. Details of specific implementations and noise performance will be discussed. Representative results

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

    Science.gov (United States)

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

    2015-06-01

    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 SiO2 (200 nm)/Si substrates with a backgate electrode and top source/drain Au electrodes, and C 1s line profiles under biasing at the backgate and drain electrodes were measured. When applying -30 V to the backgate, there is C 1s core level shift of 0.1 eV; this shift can be attributed to a chemical potential shift corresponding to band bending by the field effect, resulting in p-type doping.

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

    International Nuclear Information System (INIS)

    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 SiO2 (200 nm)/Si substrates with a backgate electrode and top source/drain Au electrodes, and C 1s line profiles under biasing at the backgate and drain electrodes were measured. When applying −30 V to the backgate, there is C 1s core level shift of 0.1 eV; this shift can be attributed to a chemical potential shift corresponding to band bending by the field effect, resulting in p-type doping

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

    Energy Technology Data Exchange (ETDEWEB)

    Nagamura, Naoka, E-mail: NAGAMURA.Naoka@nims.go.jp; Kitada, Yuta; Honma, Itaru [Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Tsurumi, Junto; Matsui, Hiroyuki; Takeya, Jun [Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561 (Japan); Horiba, Koji [Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Oshima, Masaharu [Synchrotron Radiation Research Organization, The University of Tokyo, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan)

    2015-06-22

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

  12. A technique for calculating ionospheric Doppler shifts from standard ionograms suitable for scientific, HF communication, and OTH radar applications

    Science.gov (United States)

    Lynn, K. J. W.

    2009-12-01

    High-resolution Doppler ionograms taken at 5 min intervals were obtained from a KEL IPS 71 ionosonde operating over a full ionosonde sweep range. The ionograms were converted into true height profiles using the program POLAN. POLAN also produced an equivalent parabolic layer model of best fit to the true height profile. A parabolic layer model of the ionosphere is defined by three parameters, namely, peak height, maximum electron density/critical frequency, and parabolic thickness. Equations for calculating Doppler shift from a time-varying parabolic layer model have long been known but have seen remarkably little use in the absence of suitable input data and a means of verifying the results. This paper shows that these equations can provide an accurate means of calculating ionospheric Doppler shift based on standard ionospheric ionograms taken at a 5 min rate over a 24 h period when compared with actual Doppler measurements. Apart from its scientific interest, the demonstrated technique will prove particularly valuable in deriving Doppler shift and associated signal fading for the real-time control of over-the-horizon radar and HF communication links.

  13. DFT Studies on Thermal Stabilities,Electronic Structures, and 13C Chemical Shifts of C24O2 Based on Fullerene C24(D6)

    Institute of Scientific and Technical Information of China (English)

    WANG Zhen; ZHANG Jing

    2011-01-01

    Quantum chemical calculations on some possible equilibrium geometries of C2402 isomers derived from C24 (D6) and C240 have been performed using density functional theory (DFT) method. The geometric and electronic structures as well as the relative energies and thermal stabilities of various C2402 isomers at the ground state have been calculated at the B3LYP/6-31G(d) level of theory. And the 1,4,2,5-C2402 isomer was found to be the most stable geometry where two oxygen atoms were added to the longest carbon-carbon bonds in the same pentagon from a thermodynamic point of view. Based on the optimized neutral geometries, the vertical ionization potential and vertical electron affinity have been obtained. Meanwhile, the vibrational frequencies,IR spectrum, and 13C chemical shifts of various C2402 isomers have been calculated and analyzed.

  14. Aromatic Character Studies on Divalent 3, 5 and 7-membered Rings C2H2M,C4H4M and C6H6M(M=C,Si,Ge,Sn and Pb)via Nucleus-independent Chemical Shifts (NICS) Calculation%通过核独立化学位移(NICS)计算研究二价三、五、七元环C2H2M,C4H4M and C6H6M(M=C,Si,Ge,Sn and Pb)的芳香族特性

    Institute of Scientific and Technical Information of China (English)

    Vessally E; Nikoorazm M; Ramazani A

    2008-01-01

    The aromatic character of divalent three, five and seven-membered rings C2H2M,C4H4 and C6H6M(M=C,Si, Ge, Sn and Pb) is investigated through magnetic and geometric criteria by Density Functional Theory (DFT) method using 6-311++G (3df,2p) basis set of the GAUSSIAN 98 program. The result of Nucleus-independent Chemical Shifts (NICS) (0.5) calculations show an aromatic character for singlet state of C2H2M,(M=C, Si, Ge, Sn and Sn) and nonaromatic character for triplet states of C2H2M (except M =Ge and Pb). NICS (0.5) calculations show nonaromatic character for the singlet state of C4H4C and antiaromatic character for C4H4M (M=Si, Ge, Sn and Pb). In contrast, NICS (0.5) calculations indicate antiaromatic character for the triplet state of C4H4C and nonaromatic character to C4H4M (M=Si, Ge, Sn and Pb). NICS (0.5) calculations show a slightly homoaromatic character for the singlet state of C6H6M and anti-aromatic character for triplet state of C6H6M.

  15. A Successive Shift Box-Counting Method for Calculating Fractal Dimensions and Its Application in Identification of Faults

    Institute of Scientific and Technical Information of China (English)

    沈晓华; 邹乐君; 李宏升; 沈忠悦; 杨树峰

    2002-01-01

    Fractal dimensions of a terrain quantitatively describe the self-organized structure of the terrain geometry. However, the local topographic variation cannot be illustrated by the conventional box-counting method. This paper proposes a successive shift box-counting method, in which the studied object is divided into small sub-objects that are composed of a series of grids according to its characteristic scaling. The terrain fractal dimensions in the grids are calculated with the successive shift box-counting method and the scattered points with values of fractal dimensions are obtained. The present research shows that the planar variation of fractal dimensions is well consistent with fault traces and geological boundaries.

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

    Science.gov (United States)

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

    2016-09-01

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

  17. Chemical shift measurements of chlorine K X-ray spectra using a high-resolution PIXE system

    International Nuclear Information System (INIS)

    A high-efficiency high-resolution wavelength-dispersive spectrograph with a von-Hamos configuration was developed for chemical state identification of elements in environmental samples using PIXE analysis. To evaluate the performance of this system, chlorine K X-ray spectra for NaCl, NH4Cl and polyvinylchloride (PVC) targets were measured and compared. Also, to study the applicability to environmental mixed samples, mixtures of NaCl and NH4Cl with different mixing ratios were measured. Through observation of Cl Kα1 X-ray from NaCl, the energy resolution of the system was determined to be 1.1 eV. For the NaCl sample, a Kβx line was observed at an energy, which is higher than that of the Kβ main peak by 2 eV, whereas no Kβx emission was observed for the NH4Cl sample. The chemical shift of the Kβ main peak for PVC relative to that for NaCl was about 1.2 eV. For NaCl-NH4Cl mixture targets, the relative intensity of Kβx satellite to the Kβ main line provided an indication of mixing ratio. Energies and relative intensity of Cl Kβ X-ray satellites for NaCl and NH4Cl samples calculated by a simple molecular-orbital method agreed only qualitatively with the experimental results

  18. Improving the chemical shift dispersion of multidimensional NMR spectra of intrinsically disordered proteins

    Energy Technology Data Exchange (ETDEWEB)

    Bermel, Wolfgang [Bruker BioSpin GmbH (Germany); Bruix, Marta [Consejo Superior de Investigaciones Cientificas, Instituto de Quimica Fisica ' ' Rocasolano' ' (Spain); Felli, Isabella C., E-mail: felli@cerm.unifi.it [University of Florence, Department of Chemistry ' Ugo Shiff' (Italy); Kumar, M.V. Vasantha [University of Florence, Magnetic Resonance Center (Italy); Pierattelli, Roberta, E-mail: pierattelli@cerm.unifi.it [University of Florence, Department of Chemistry ' Ugo Shiff' (Italy); Serrano, Soraya [Consejo Superior de Investigaciones Cientificas, Instituto de Quimica Fisica ' ' Rocasolano' ' (Spain)

    2013-03-15

    Intrinsically disordered proteins (IDPs) have recently attracted the attention of the scientific community challenging the well accepted structure-function paradigm. In the characterization of the dynamic features of proteins nuclear magnetic resonance spectroscopy (NMR) is a strategic tool of investigation. However the peculiar properties of IDPs, with the lack of a unique 3D structure and their high flexibility, have a strong impact on NMR observables (low chemical shift dispersion, efficient solvent exchange broadening) and thus on the quality of NMR spectra. Key aspects to be considered in the design of new NMR experiments optimized for the study of IDPs are discussed. A new experiment, based on direct detection of {sup 13}C{sup {alpha}}, is proposed.

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-09-21

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

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

    CERN Document Server

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

    2011-01-01

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

  2. Quantum Chemical Calculations Resolved Identification of Methylnitrocatechols in Atmospheric Aerosols.

    Science.gov (United States)

    Frka, Sanja; Šala, Martin; Kroflič, Ana; Huš, Matej; Čusak, Alen; Grgić, Irena

    2016-06-01

    Methylnitrocatechols (MNCs) are secondary organic aerosol (SOA) tracers and major contributors to atmospheric brown carbon; however, their formation and aging processes in atmospheric waters are unknown. To investigate the importance of aqueous-phase electrophilic substitution of 3-methylcatechol with nitronium ion (NO2(+)), we performed quantum calculations of their favorable pathways. The calculations predicted the formation of 3-methyl-5-nitrocatechol (3M5NC), 3-methyl-4-nitrocatechol (3M4NC), and a negligible amount of 3-methyl-6-nitrocatechol (3M6NC). MNCs in atmospheric PM2 samples were further inspected by LC/(-)ESI-MS/MS using commercial as well as de novo synthesized authentic standards. We detected 3M5NC and, for the first time, 3M4NC. In contrast to previous reports, 3M6NC was not observed. Agreement between calculated and observed 3M5NC/3M4NC ratios cannot unambiguously confirm the electrophilic mechanism as the exclusive formation pathway of MNCs in aerosol water. However, the examined nitration by NO2(+) is supported by (1) the absence of 3M6NC in the ambient aerosols analyzed and (2) the constant 3M5NC/3M4NC ratio in field aerosol samples, which indicates their common formation pathway. The magnitude of error one could make by incorrectly identifying 3M4NC as 3M6NC in ambient aerosols was also assessed, suggesting the importance of evaluating the literature regarding MNCs with special care. PMID:27136117

  3. Quantum Chemical Calculations Resolved Identification of Methylnitrocatechols in Atmospheric Aerosols.

    Science.gov (United States)

    Frka, Sanja; Šala, Martin; Kroflič, Ana; Huš, Matej; Čusak, Alen; Grgić, Irena

    2016-06-01

    Methylnitrocatechols (MNCs) are secondary organic aerosol (SOA) tracers and major contributors to atmospheric brown carbon; however, their formation and aging processes in atmospheric waters are unknown. To investigate the importance of aqueous-phase electrophilic substitution of 3-methylcatechol with nitronium ion (NO2(+)), we performed quantum calculations of their favorable pathways. The calculations predicted the formation of 3-methyl-5-nitrocatechol (3M5NC), 3-methyl-4-nitrocatechol (3M4NC), and a negligible amount of 3-methyl-6-nitrocatechol (3M6NC). MNCs in atmospheric PM2 samples were further inspected by LC/(-)ESI-MS/MS using commercial as well as de novo synthesized authentic standards. We detected 3M5NC and, for the first time, 3M4NC. In contrast to previous reports, 3M6NC was not observed. Agreement between calculated and observed 3M5NC/3M4NC ratios cannot unambiguously confirm the electrophilic mechanism as the exclusive formation pathway of MNCs in aerosol water. However, the examined nitration by NO2(+) is supported by (1) the absence of 3M6NC in the ambient aerosols analyzed and (2) the constant 3M5NC/3M4NC ratio in field aerosol samples, which indicates their common formation pathway. The magnitude of error one could make by incorrectly identifying 3M4NC as 3M6NC in ambient aerosols was also assessed, suggesting the importance of evaluating the literature regarding MNCs with special care.

  4. Calculation of transition probabilities and ac Stark shifts in two-photon laser transitions of antiprotonic helium

    OpenAIRE

    HORI, MASAKI; Korobov, Vladimir I.

    2010-01-01

    Numerical ab initio variational calculations of the transition probabilities and ac Stark shifts in two-photon transitions of antiprotonic helium atoms driven by two counter-propagating laser beams are presented. We found that sub-Doppler spectroscopy is in principle possible by exciting transitions of the type (n,L)->(n-2,L-2) between antiprotonic states of principal and angular momentum quantum numbers n~L-1~35, first by using highly monochromatic, nanosecond laser beams of intensities 10^4...

  5. Microscopic Theoretical Calculations ofR-Line Thermal Shifts and Broadenings of MgO:Cr3+

    Institute of Scientific and Technical Information of China (English)

    MA DongPing; LIU YanYun; MA Ning; CHEN JuRong

    2002-01-01

    By taking into account all the irreducible representations and their components in t he electron-phononinteraction (EPI) as well as all the levels and the admixtures of basic wavefunctions within d3 elect ronic configuration,the values of all the parameters in the expressions of thermal shift (TS) and thermal broadening (TB) due to EPI forthe ground level, R level and R line of MgO:Cr3+ have microscopically been evaluated; and then, TS and TB of R lineand various contributions to them have uniformly been calculated. The results arc in very good agreement with theexperimental data. It is found that all the three terms of TS due to EPI are red shifts; the Raman term is the largestone, and the optical-branch term and neighbor-level term are important for TS; the contribution to TS from thermalexpansion is bluc shift, which is also important. The R-line TS of MgO:Cr3+ comes from the first-order term of EPI. Theelastic Raman scattering of acoustic phonons plays a dominant role in R-line TB of MgO:Cr3+. For both TS and TB,it is very important to take into account all the admixtures of basic wavefunctions within d3 electronic configuration.

  6. Calculation of transition probabilities and ac Stark shifts in two-photon laser transitions of antiprotonic helium

    International Nuclear Information System (INIS)

    Numerical ab initio variational calculations of the transition probabilities and ac Stark shifts in two-photon transitions of antiprotonic helium atoms driven by two counter-propagating laser beams are presented. We found that sub-Doppler spectroscopy is, in principle, possible by exciting transitions of the type (n,L)→(n-2,L-2) between antiprotonic states of principal and angular momentum quantum numbers n∼L-1∼35, first by using highly monochromatic, nanosecond laser beams of intensities 104-105 W/cm2, and then by tuning the virtual intermediate state close (e.g., within 10-20 GHz) to the real state (n-1,L-1) to enhance the nonlinear transition probability. We expect that ac Stark shifts of a few MHz or more will become an important source of systematic error at fractional precisions of better than a few parts in 109. These shifts can, in principle, be minimized and even canceled by selecting an optimum combination of laser intensities and frequencies. We simulated the resonance profiles of some two-photon transitions in the regions n=30-40 of the p4He+ and p3He+ isotopes to find the best conditions that would allow this.

  7. Reference potential approach to the quantum-mechanical inverse problem: I. Calculation of phase shift and Jost function

    CERN Document Server

    Selg, M

    2005-01-01

    Elegant and mathematically rigorous methods of the quantum inverse theory are difficult to put into practice because there is always some lack of needful input information. In this situation, one may try to construct a reference potential, whose spectral characteristics would be in a reasonable agreement with the available data of the system's properties. Since the reference potential is fixed, it is always possible to calculate all its spectral characteristics, including phase shift for scattering states and Jost function, the main key to solve the inverse problem. Thereafter, one can calculate a Bargmann potential whose Jost function differs from the initial one only by a rational factor. This way it is possible, at least in principle, to construct a more reliable potential for the system. The model system investigated in this paper is diatomic xenon molecule in ground electronic state. Its reference potential is built up of several smoothly joined Morse type components, which enables to solve the related e...

  8. Exact trajectory in semiclassical line broadening and line shifting calculation test for H2-He Q(1) line

    International Nuclear Information System (INIS)

    The semiclassical model RB (Robert, D. and Bonamy, J. (Journal de Physique (Paris), 1979, 40, 923 for calculation of line width and line shift has been used in many applications. It contains an approximate 'parabolic' trajectory. Bykov, A.D. et al, Atmospheric and Oceanic Optics (1992) 5, 587, have recently proposed an analytical expression for an exact treatment of the classical path. This paper analyses the consequence of introducing the exact trajectory within the RB model for the H2-He Q(1) line chosen as a simple test. Moreover, a comparison with results of exact close-coupling calculations is also given for this molecular system. (Copyright (c) 1999 Elsevier Science B.V., Amsterdam. All rights reserved.)

  9. Fast algorithm for calculating chemical kinetics in turbulent reacting flow

    International Nuclear Information System (INIS)

    The design of a very fast, automatic black-box code for homogeneous, gas-phase chemical kinetics problems requires an understanding of the physical and numerical sources of computational inefficiency. Some major sources reviewed in this paper are stiffness of the governing ordinary differential equations and its detection, choice of appropriate method (i.e., integration algorithm plus stepsize control strategy), nonphysical initial conditions, and too frequent evaluation of thermochemical and kinetic properties. Specific techniques are recommended (and some advised against) for improving or overcoming the identified problem areas. It is argued that, because reactive species increase exponentially with time during induction and early heat release, and all species exhibit asymptotic, exponential decay with time during late heat release and equilibration, exponential-fitted integration algorithms are inherently more accurate for kinetics modeling than classical, polynomial-interpolant methods for the same computational work

  10. Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria

    Science.gov (United States)

    Jorgensen, William L.; Thomas, Laura L.

    2009-01-01

    An overview is provided on the computation of free energy changes in solution using perturbation theory, overlap sampling, and related approximate methods. As a specific application, extensive results are provided for free energies of hydration of substituted benzenes using the OPLS-AA force field in explicit TIP4P water. For a similar amount of computer time, the double-wide sampling and overlap sampling methods yield very similar results in the free-energy perturbation calculations. With standard protocols, the average statistical uncertainty in computed differences in free energies of hydration is 0.1 – 0.2 kcal/mol. Application of the power-series expansion in the Peierls equation was also tested. Use of the first-order term is generally reliable, while inclusion of the slowly-convergent, second-order fluctuation term causes deterioration in the results for strongly hydrogen-bonded solutes. PMID:19936324

  11. Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Xianwei [Center for Optics and Optoelectronics Research, College of Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310023 (China); State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062 (China); Zhang, John Z. H.; He, Xiao, E-mail: xiaohe@phy.ecnu.edu.cn [State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062 (China); NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062 (China)

    2015-11-14

    Recent advance in biophysics has made it possible to directly measure site-specific electric field at internal sites of proteins using molecular probes with C = O or C≡N groups in the context of vibrational Stark effect. These measurements directly probe changes of electric field at specific protein sites due to, e.g., mutation and are very useful in protein design. Computational simulation of the Stark effect based on force fields such as AMBER and OPLS, while providing good insight, shows large errors in comparison to experimental measurement due to inherent difficulties associated with point charge based representation of force fields. In this study, quantum mechanical calculation of protein’s internal electrostatic properties and vibrational Stark shifts was carried out by using electrostatically embedded generalized molecular fractionation with conjugate caps method. Quantum calculated change of mutation-induced electric field and vibrational Stark shift is reported at the internal probing site of enzyme human aldose reductase. The quantum result is in much better agreement with experimental data than those predicted by force fields, underscoring the deficiency of traditional point charge models describing intra-protein electrostatic properties.

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

    CERN Document Server

    Ota, Y; Ohba, I; Yoshida, N; Mikami, Shuji; Ohba, Ichiro; Ota, Yukihiro; Yoshida, Noriyuki

    2006-01-01

    Recently, Yu, Brown, and Chuang [Phys. Rev. A {\\bf 71}, 032341 (2005)] investigated the entanglement attainable from unitary transformed thermal states in liquid-state nuclear magnetic resonance (NMR). Their research gave an insight into the role of the entanglement in a liquid-state NMR quantum computer. Moreover, they attempted to reveal the role of mixed-state entanglement in quantum computing. However, they assumed that the Zeeman energy of each nuclear spin which corresponds to a qubit takes a common value for all; there is no chemical shift. In this paper, we research a model with the chemical shifts and analytically derive the physical parameter region where unitary transformed thermal states are entangled, by the positive partial transposition (PPT) criterion with respect to any bipartition. We examine the effect of the chemical shifts on the boundary between the separability and the nonseparability, and find it is negligible.

  13. Clouds in Super-Earth Atmospheres: Chemical Equilibrium Calculations

    CERN Document Server

    Mbarek, Rostom

    2016-01-01

    Recent studies have unequivocally proven the existence of clouds in super-Earth atmospheres (Kreidberg et al. 2014). Here we provide a theoretical context for the formation of super-Earth clouds by determining which condensates are likely to form under the assumption of chemical equilibrium. We study super-Earth atmospheres of diverse bulk composition, which are assumed to form by outgassing from a solid core of chondritic material, following Schaefer & Fegley (2010). The super-Earth atmospheres that we study arise from planetary cores made up of individual types of chondritic meteorites. They range from highly reducing to oxidizing and have carbon to oxygen (C:O) ratios that are both subsolar and super-solar, thereby spanning a range of atmospheric composition that is appropriate for low-mass exoplanets. Given the atomic makeup of these atmospheres, we minimize the global Gibbs free energy of formation for over 550 gases and condensates to obtain the molecular composition of the atmospheres over a temper...

  14. All-atom Molecular Dynamic Simulations Combined with the Chemical Shifts Study on the Weak Interactions of Ethanol-water System

    Institute of Scientific and Technical Information of China (English)

    ZHANG Rong; LUO San-Lai; WU Wen-Juan

    2008-01-01

    All-atom molecular dynamics(MD)simulation combined with chemical shifts was performed to investigate the interactions over the entire concentration range of the ethanol(EtOH)-water system.The results of the simulation were adopted to explain the NMR experiments by hydrogen bonding analysis.The strong hydrogen bonds and weak C-H…O contacts coexist in the mixtures through the analysis of the radial distribution functions.And the liquid structures in the whole concentration of EtOH-water mixtures can be classified into three regions by the statistic analysis of the hydrogen-bonding network in the MD simulations.Moreover,the chemical shifts of the hydrogen atom are in agreement witb the statistical results of the average number hydrogen bonds in the MD simulations.Interestingly,the excess relative extent Eηrel calculated by the MD simulations and chemical shifts in the EtOH aqueous solutions shows the largest deviation at XEtOH≈0.18.The excess properties present good agreement with the excess enthalpy in the concentration dependence.

  15. SUBSTITUENT CHEMICAL SHIFT (SCS) AND THE SEQUENCE STRUCTURE OF ETHYLENE-VINYL ALCOHOL COPOLYMERS

    Institute of Scientific and Technical Information of China (English)

    ZHOU Zinan; TIAN Wenjing; WU Shengrong; DAI Yingkun; FENG Zhiliu; SHEN Lianfang; YUAN Hanzhen

    1992-01-01

    Three ethylene-vinyl alcohol copolymers were studied by means of the substituent chemical shift(SCS) method. The SCS parameters of hydroxy (-OH)in two different solvents were obtained: in deuterium oxide/phenol (20/80 W/W ) the parameters are S1 = 42.77 ± 0.08ppm, S2 = 7.15 ±0.06 ppm,S3(s )=-4.08±0.02ppm, S3(t)=-3.09±0.20ppm,S4=0.48±0.03ppm, S5 =0.26±0.05ppm. In o-dichlorobenzen-d4 S1(s)=44.79±0.61ppm, S2=7.40±0.00ppm, S3 (s)=-4.51±0.17ppm, S3 (t)= -3.13± 0.00 ppm, S4 =0 . 63±0.04ppm, S5=0.36±0.00ppm. Simultaneously the 13CNMR spectra of EVA copolymers were assigned by using the SCS parameters obtained.

  16. Chemical shift assignment of the alternative scaffold protein IscA.

    Science.gov (United States)

    Popovic, Matija; Pastore, Annalisa

    2016-04-01

    The IscA protein (11.5 kDa) is an essential component of the iron sulphur cluster biogenesis machine. In bacteria, the machine components are clustered in operons, amongst which the most important is the isc operon. Bacterial IscA has direct homologues also in eukaryotes. Like the protein IscU, IscA is thought to assist cluster formation as an alternative scaffold protein which receives the cluster before transferring it further to the final acceptors. Several crystal structures have been published. They all report an IscA dimeric form, although the packing of the protomers in the dimers differs amongst structures. No solution studies have currently been reported. Here we report the (1)H, (13)C and (15)N backbone and side-chain chemical shift assignments of the cluster-free E. coli IscA as a starting point for further studies of the structure and functions of this still poorly characterized protein. We show that IscA exists in solution as an equilibrium between different species. Spectrum assignment was thus challenging given the heterogeneous nature of the sample but doable through judicious choice of selective labelling and concentration dependent studies.

  17. The study on temporal lobe epilepsy with single-voxel proton MR spectroscopy and chemical shift imaging

    International Nuclear Information System (INIS)

    Objective: To investigate the value of different proton MR spectroscopy techniques including single-voxel spectroscopy (SVS) and chemical shift imaging (CSI) in diagnosing patients with temporal lobe epilepsy. Methods: Sixty cases (40 normal, 20 temporal lobe epilepsy) experienced SVS and CSI. The volume of interest (VOI) of SVS was placed over the anterior hippocampus formation (HF) region, including part of the head and body of the HF. The VOI of CSI encompassed bilateral HF and the head, body and tail of HF. The VOI was divided into 5 voxels from anterior to posterior. The metabolite data of both SVS and CSI were obtained and the ratios of NAA/Cr and NAA/(Cho+Cr) were recorded or calculated. Results: The ipsilateral hippocampus to the seizure of TLE patients had lower ratios of NAA/(Cho+Cr) and NAA/Cr, and the differences compared with those of the normal group and contralateral subgroup were statistically significant (F=41.958, P1HMRS study improved the diagnostic yield of MR evaluation in TLE patients. There was a correlation between the ratio of NAA/(Cho+Cr) and the location of HF. Regional variation must be considered when interpreting proton spectra of the HF. (author)

  18. 129Xe-NMR of xenon adsorbed on zeolites: determination of the dimensions of the void space from the chemical shift δ(129Xe)

    International Nuclear Information System (INIS)

    The chemical shift δS of xenon adsorbed on zeolite and extrapolated to zero concentration depends only on the internal void space of the solid. The smaller the channels or cavities, or the more restricted the diffusion, the greater δS becomes. We have calculated the theoretical values of the mean free path l-bar of xenon adsorbed in various zeolites. We deduce from them the dependence of the δS on l-bar. It is now possible to determine the dimensions of any void space in which xenon can be adsorbed. 4 refs.; 2 figs.; 3 tabs

  19. Correlation of 1H NMR Chemical Shift for Aqueous Solutions by Statistical Associating Fluid Theory Association Model

    Institute of Scientific and Technical Information of China (English)

    许波; 李浩然; 王从敏; 许映杰; 韩世钧

    2005-01-01

    1H NMR chemical shifts of binary aqueous mixtures of acylamide, alcohol, dimethyl sulphoxide (DMSO), and acetone are correlated by statistical associating fluid theory (SAFT) association model. The comparison between SAFT association model and Wilson equation shows that the former is better for dealing with aqueous solutions. Finally, the specialties of both models are discussed.

  20. Calculations of physical and chemical reactions with DNA in aqueous solution from Auger cascades

    International Nuclear Information System (INIS)

    Monte Carlo calculations are performed of the physical and chemical interactions in liquid water by electrons produced during Auger cascades resulting from the decay of various radionuclides. Estimates are also made of the number of direct physical and indirect chemical interactions that would be produced on DNA located near the decay site. 13 refs., 8 figs

  1. The HSP90 binding mode of a radicicol-like E-oxime from docking, binding free energy estimations, and NMR 15N chemical shifts

    Science.gov (United States)

    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

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

    Science.gov (United States)

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

    2016-01-01

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

  3. Ab-inito calculation of energy level alignment and vacuum level shift at CuPc/C60 interfaces

    Science.gov (United States)

    Sai, Na; Zhu, Xiaoyang; Chelikowsky, James; Leung, Kevin

    2012-02-01

    The alignment of the donor and acceptor enegy levels is of crucial importance for organic photovotaic performance. We investigate the interfaical electronic structure and energy level alignment of copper phthalocyanine (CuPc)/fullerene (C60) using ab-inito density functional theory calculations including van der Waals interactions and hybrid density functionals. We show that energy level alignment critically depends on the standing-up and lying-down orientation of the CuPc molecules relative to C60 at the interface. We calculate the magnitude of the interface dipole at different molecular orientations and compare them to the vacuum level shift observed in photoemission spectroscopy. The validity of existing theoretical models which invoke charge transfer on this organic interface will be discussed in light of our predictions. Sandia National Laboratories is a multiprogram laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Deparment of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  4. Relativistic many-body calculation of energies, lifetimes, polarizabilities, blackbody radiative shift and hyperfine constants in Lu2+

    CERN Document Server

    Safronova, U I; Johnson, W R

    2016-01-01

    Energy levels of 30 low-lying states of Lu2+ and allowed electric-dipole matrix elements between these states are evaluated using a relativistic all-order method in which all single, double and partial triple excitations of Dirac-Fock wave functions are included to all orders of perturbation theory. Matrix elements are critically evaluated for their accuracy and recommended values of the matrix elements are given together with uncertainty estimates. Line strengths, transition rates and lifetimes of the metastable 5d(3/2) and 5d(5/2) states are calculated. Recommended values are given for static polarizabilities of the 6s, 5d and 6p states and tensor polarizabilities of the 5d and 6p(3/2) states. Uncertainties of the polarizability values are estimated in all cases. The blackbody radiation shift of the 6s(1/2)-5d(5/2) transition frequency of the Lu2+ ion is calculated with the aid of the recommended scalar polarizabilities of the 6s(1/2) and 5d(5/2) states. Finally, A and B hyperfine constants are determined f...

  5. Relativistic many-body calculation of energies, lifetimes, polarizabilities, blackbody radiative shift, and hyperfine constants in Lu2 +

    Science.gov (United States)

    Safronova, U. I.; Safronova, M. S.; Johnson, W. R.

    2016-09-01

    Energy levels of 30 low-lying states of Lu2 + and allowed electric-dipole matrix elements between these states are evaluated using a relativistic all-order method in which all single, double, and partial triple excitations of Dirac-Fock wave functions are included to all orders of perturbation theory. Matrix elements are critically evaluated for their accuracy and recommended values of the matrix elements are given together with uncertainty estimates. Line strengths, transition rates, and lifetimes of the metastable 5 d3 /2 and 5 d5 /2 states are calculated. Recommended values are given for static polarizabilities of the 6 s , 5 d , and 6 p states and tensor polarizabilities of the 5 d and 6 p3 /2 states. Uncertainties of the polarizability values are estimated in all cases. The blackbody radiation shift of the 6 s1 /2-5 d5 /2 transition frequency of the Lu2 + ion is calculated with the aid of the recommended scalar polarizabilities of the 6 s1 /2 and 5 d5 /2 states. Finally, A and B hyperfine constants are determined for states of 2+175Lu with n ≤9 . This work provides recommended values of transition matrix elements, polarizabilities, and hyperfine constants of Lu2 +, critically evaluated for accuracy, for benchmark tests of high-precision theoretical methodology and planning of future experiments.

  6. Determination of the Optimal Energy Denominator Shift Parameter of KRb Electronic States in Quantum Chemical Computations Using Perturbation Theory

    Science.gov (United States)

    Shundalau, M. B.; Minko, A. A.

    2016-01-01

    The influence of the energy denominator shift (EDS) parameter and the quantitative and qualitative compositions of electronic states included in CASSCF(2,14)/XMCQDPT2 ab initio calculations of the ground state equilibrium internuclear distance and dissociation energy of polar KRb was determined.

  7. Chemical-shift tensors of heavy nuclei in network solids: a DFT/ZORA investigation of (207)Pb chemical-shift tensors using the bond-valence method.

    Science.gov (United States)

    Alkan, Fahri; Dybowski, C

    2015-10-14

    Cluster models are used in calculation of (207)Pb NMR magnetic-shielding parameters of α-PbO, β-PbO, Pb3O4, Pb2SnO4, PbF2, PbCl2, PbBr2, PbClOH, PbBrOH, PbIOH, PbSiO3, and Pb3(PO4)2. We examine the effects of cluster size, method of termination of the cluster, charge on the cluster, introduction of exact exchange, and relativistic effects on calculation of magnetic-shielding tensors with density functional theory. Proper termination of the cluster for a network solid, including approximations such as compensation of charge by the bond-valence (BV) method, is essential to provide results that agree with experiment. The inclusion of relativistic effects at the spin-orbit level for such heavy nuclei is an essential factor in achieving agreement with experiment. PMID:26345261

  8. Anomalous chemical shifts in X-ray photoelectron spectra of sulfur-containing compounds of silver (I) and (II)

    International Nuclear Information System (INIS)

    Highlights: • Ag 3d5/2 binding energy for Ag(II)SO4 is as large as 370.1 eV. • This is the largest value ever measured for a silver (II) compound. • Large shift is connected with the extreme oxidizing nature of Ag(II) species. • Ag(I)2S2O7 exhibits both positive and negative shifts with respect to metallic Ag. • Two distinct Ag(I) sites are responsible for large BE difference of 3.6 eV. - Abstract: Anomalous chemical shifts, i.e. cases when binding energy decreases with the increase of the oxidation state, have been well-documented for selected compounds of silver, and well understood based on analysis of initial- and final-state effects in the XPS spectra. Here we report two examples of even more exotic behaviour of chemical shifts for two silver compounds. The first one is Ag2S2O7 which exhibits both positive and negative substantial shifts with respect to metallic Ag for two distinct Ag(I) sites in its crystal structure, which differ by as much as 3.6 eV. Another is AgSO4, a rare example of oxo silver (II) salt, which exhibits “normal” chemical shift but the Ag 3d5/2 binding energy takes the largest value measured for a silver (II) compound (370.1 eV). This property is connected predominantly with the extremely strongly oxidizing nature of Ag(II) species

  9. Halogen effect on structure and 13C NMR chemical shift of 3,6-disubstituted-N-alkyl carbazoles

    DEFF Research Database (Denmark)

    Radula-Janik, Klaudia; Kupka, Teobald; Ejsmont, Krzysztof;

    2013-01-01

    ). The decreasing electronegativity of the halogen substituent (F, Cl, Br and I) was reflected in both nonrelativistic and relativistic NMR results as decreased values of chemical shifts of carbon atoms attached to halogen (C3 and C6) leading to a strong sensitivity to halogen atom type at 3 and 6 positions....... The relativistic effect of Br and I atoms on nuclear shieldings was modeled using the spin-orbit ZORA method. Significant heavy atom shielding effects for the carbon atom directly bonded with bromine and iodine were observed (~ -10 and ~ -30 ppm while the other carbon shifts were practically unaffected...

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

    Directory of Open Access Journals (Sweden)

    Chen eSong

    2015-07-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

  12. Predicting 15N chemical shifts in proteins using the preceding residue-specific individual shielding surfaces from φ, ψi-1, and χ1torsion angles

    International Nuclear Information System (INIS)

    Empirical shielding surfaces are most commonly used to predict chemical shifts in proteins from known backbone torsion angles, φ and ψ. However, the prediction of 15N chemical shifts using this technique is significantly poorer, compared to that for the other nuclei such as 1Hα, 13Cα, and 13Cβ. In this study, we investigated the effects from the preceding residue and the side-chain geometry, χ1, on 15N chemical shifts by statistical methods. For an amino acid sequence XY, the 15N chemical shift of Y is expressed as a function of the amino acid types of X and Y, as well as the backbone torsion angles, φ and ψi-1. Accordingly, 380 empirical 'Preceding Residue Specific Individual (PRSI)' 15N chemical shift shielding surfaces, representing all the combinations of X and Y (except for Y=Pro), were built and used to predict 15N chemical shift from φ and ψi-1. We further investigated the χ1 effects, which were found to account for differences in 15N chemical shifts by ∼5 ppm for amino acids Val, Ile, Thr, Phe, His, Tyr, and Trp. Taking the χ1 effects into account, the χ1-calibrated PRSI shielding surfaces (XPRSI) were built and used to predict 15N chemical shifts for these amino acids. We demonstrated that 15N chemical shift predictions are significantly improved by incorporating the preceding residue and χ1 effects. The present PRSI and XPRSI shielding surfaces were extensively compared with three recently published programs, SHIFTX (Neal et al., 2003), SHIFTS (Xu and Case, 2001 and 2002), and PROSHIFT (Meiler, 2003) on a set of ten randomly selected proteins. A set of Java programs using XPRSI shielding surfaces to predict 15N chemical shifts in proteins were developed and are freely available for academic users at http://www.pronmr.com or by sending email to one of the authors Yunjun Wang

  13. Cuticular hydrocarbon divergence in the jewel wasp Nasonia : evolutionary shifts in chemical communication channels?

    NARCIS (Netherlands)

    Buellesbach, J.; Gadau, J.; Beukeboom, L. W.; Echinger, F.; Raychoudhury, R.; Werren, J. H.; Schmitt, T.

    2013-01-01

    The evolution and maintenance of intraspecific communication channels constitute a key feature of chemical signalling and sexual communication. However, how divergent chemical communication channels evolve while maintaining their integrity for both sender and receiver is poorly understood. In this s

  14. Calculation of complex chemical equilibrium compositions of composite rocket propellants combustion products

    Directory of Open Access Journals (Sweden)

    NIKOLA KILIBARDA

    2000-11-01

    Full Text Available An adequate method for calculating chemical equilibrium in a predominantly gaseous, multi-component reactive mixture was investigated and successfully applied. This method involves the stated equilibrium reaction scheme, including, first, the formation of chemical species, of which concentrations prevail in the mixture, then the formation of gaseous atomic species by dissociation of previous ones, and, finally, the formation of complex chemical species from the atomic species. A computer program, which permits calculations of equilibrium compositions by the iteration procedure, has been developed. The results of calculations have been compared with data obtained by the programs OPHELIE, MICROPEP, and the program SPP, as documented in the NASA-Lewis Code, which is presently the world-wide standard. All comparisons gave satisfactory agreement.

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

    Science.gov (United States)

    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.

  16. Extracting chemical information from plane wave calculations by a 3D 'fuzzy atoms' analysis

    Science.gov (United States)

    Bakó, I.; Stirling, A.; Seitsonen, A. P.; Mayer, I.

    2013-03-01

    Bond order and valence indices have been calculated by the method of the three-dimensional 'fuzzy atoms' analysis, using the numerical molecular orbitals obtained from plane wave DFT calculations, i.e., without introducing any external atom-centered functions. Weight functions of both Hirshfeld and Becke types have been applied. The results are rather close to the similar 'fuzzy atoms' ones obtained by using atom-centered basis sets and agree well with the chemical expectations, stressing the power of the genuine chemical concepts.

  17. Differential dynamic engagement within 24 SH3 domain: peptide complexes revealed by co-linear chemical shift perturbation analysis.

    Directory of Open Access Journals (Sweden)

    Elliott J Stollar

    Full Text Available 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.

  18. Chemical shift of Mn and Cr K-edges in X-ray absorption spectroscopy with synchrotron radiation

    Indian Academy of Sciences (India)

    D Joseph; A K Yadav; S N Jha; D Bhattacharyya

    2013-11-01

    Mn and Cr K X-ray absorption edges were measured in various compounds containing Mn in Mn2+, Mn3+ and Mn4+ oxidation states and Cr in Cr3+ and Cr6+ oxidation states. Few compounds possess tetrahedral coordination in the 1st shell surrounding the cation while others possess octahedral coordination. Measurements have been carried out at the energy dispersive EXAFS beamline at INDUS-2 Synchrotron Radiation Source at Raja Ramanna Centre for Advanced Technology, Indore. Energy shifts of ∼8–16 eV were observed for Mn K edge in the Mn-compounds while a shift of 13–20 eV was observed for Cr K edge in Cr-compounds compared to values in elementalMn and Cr, respectively. The different chemical shifts observed for compounds having the same oxidation state of the cation but different anions or ligands show the effect of different chemical environments surrounding the cations in determining their X-ray absorption edges in the above compounds. The above chemical effect has been quantitatively described by determining the effective charges on Mn and Cr cations in the above compounds.

  19. Identification of zinc-ligated cysteine residues based on 13Calpha and 13Cbeta chemical shift data.

    Science.gov (United States)

    Kornhaber, Gregory J; Snyder, David; Moseley, Hunter N B; Montelione, Gaetano T

    2006-04-01

    Although a significant number of proteins include bound metals as part of their structure, the identification of amino acid residues coordinated to non-paramagnetic metals by NMR remains a challenge. Metal ligands can stabilize the native structure and/or play critical catalytic roles in the underlying biochemistry. An atom's chemical shift is exquisitely sensitive to its electronic environment. Chemical shift data can provide valuable insights into structural features, including metal ligation. In this study, we demonstrate that overlapped 13Cbeta chemical shift distributions of Zn-ligated and non-metal-ligated cysteine residues are largely resolved by the inclusion of the corresponding 13Calpha chemical shift information, together with secondary structural information. We demonstrate this with a bivariate distribution plot, and statistically with a multivariate analysis of variance (MANOVA) and hierarchical logistic regression analysis. Using 287 13Calpha/13Cbeta shift pairs from 79 proteins with known three-dimensional structures, including 86 13Calpha and 13Cbeta shifts for 43 Zn-ligated cysteine residues, along with corresponding oxidation state and secondary structure information, we have built a logistic regression model that distinguishes between oxidized cystines, reduced (non-metal ligated) cysteines, and Zn-ligated cysteines. Classifying cysteines/cystines with a statistical model incorporating all three phenomena resulted in a predictor of Zn ligation with a recall, precision and F-measure of 83.7%, and an accuracy of 95.1%. This model was applied in the analysis of Bacillus subtilis IscU, a protein involved in iron-sulfur cluster assembly. The model predicts that all three cysteines of IscU are metal ligands. We confirmed these results by (i) examining the effect of metal chelation on the NMR spectrum of IscU, and (ii) inductively coupled plasma mass spectrometry analysis. To gain further insight into the frequency of occurrence of non-cysteine Zn

  20. Bonding and chemical shifts in aluminosilicate glasses: importance of Madelung effects

    CERN Document Server

    Cruguel, H; Kerjan, O; Bart, F; Gautier-Soyer, M

    2003-01-01

    A detailed study of the XPS binding energy shifts of Si 2p, O 1s and Zr 3d in a series of aluminosilicate glasses (a three oxide glass: SiO sub 2 -Al sub 2 O sub 3 -CaO, three four-oxide glasses: SiO sub 2 -Al sub 2 O sub 3 -CaO-TiO sub 2 , ZrO sub 2 or CeO sub 2 , along with a six-oxide glass SiO sub 2 -Al sub 2 O sub 3 -CaO-TiO sub 2 -ZrO sub 2 -CeO sub 2) is presented. Their composition is such that these glasses have the same mean electronegativity, so that no changes in the atomic charges is expected. The binding energy shifts are interpreted in terms of initial and final state effects, and the balance of charge transfer contribution and electrostatic effects is discussed. Referred to the ternary glass, the binding energy shifts of the Si 2p, O 1s and Zr 3d lines in the complex glasses are due to an initial state effect, as the extraatomic relaxation is similar along the glass series. These shifts originate from electrostatic Madelung effects, likely coming from a structural change induced by the presenc...

  1. A Simple Method to Calculate the Temperature Dependence of the Gibbs Energy and Chemical Equilibrium Constants

    Science.gov (United States)

    Vargas, Francisco M.

    2014-01-01

    The temperature dependence of the Gibbs energy and important quantities such as Henry's law constants, activity coefficients, and chemical equilibrium constants is usually calculated by using the Gibbs-Helmholtz equation. Although, this is a well-known approach and traditionally covered as part of any physical chemistry course, the required…

  2. Systematic Approach to Calculate the Concentration of Chemical Species in Multi-Equilibrium Problems

    Science.gov (United States)

    Baeza-Baeza, Juan Jose; Garcia-Alvarez-Coque, Maria Celia

    2011-01-01

    A general systematic approach is proposed for the numerical calculation of multi-equilibrium problems. The approach involves several steps: (i) the establishment of balances involving the chemical species in solution (e.g., mass balances, charge balance, and stoichiometric balance for the reaction products), (ii) the selection of the unknowns (the…

  3. An atomic electronegative distance vector and carbon-13 nuclear magnetic resonance chemical shifts of alcohols and alkanes

    Institute of Scientific and Technical Information of China (English)

    LIU, Shu-Shea; XIA, Zhi-Ning; CAI, Shao-Xi; LIU, Yan

    2000-01-01

    A novel atomic electronegative distance vector (AEDV) has been developed to express the chemical environment of various chemically equivalent carbon atoms in alcohols and alkanes.Combining AEDV and γ parameter, four five-parameter Iinear relationship equations of chemical shift for four types of carbon atoms are created by using multiple linear regression.Correlation coefficients are R = 0.9887, 0.9972, 0.9978 and 0.9968 and roots of mean square error are RMS = 0.906, 0.821, 1.091and 1.091of four types of carbons, i.e., type1,2, 3, and 4 for primary, secondary, tertiary, and quaternary carbons, respectively. The stability and prediction capacity for external samples of four models have been tested by cross- validation.

  4. Computer program for calculation of complex chemical equilibrium compositions and applications. Part 1: Analysis

    Science.gov (United States)

    Gordon, Sanford; Mcbride, Bonnie J.

    1994-01-01

    This report presents the latest in a number of versions of chemical equilibrium and applications programs developed at the NASA Lewis Research Center over more than 40 years. These programs have changed over the years to include additional features and improved calculation techniques and to take advantage of constantly improving computer capabilities. The minimization-of-free-energy approach to chemical equilibrium calculations has been used in all versions of the program since 1967. The two principal purposes of this report are presented in two parts. The first purpose, which is accomplished here in part 1, is to present in detail a number of topics of general interest in complex equilibrium calculations. These topics include mathematical analyses and techniques for obtaining chemical equilibrium; formulas for obtaining thermodynamic and transport mixture properties and thermodynamic derivatives; criteria for inclusion of condensed phases; calculations at a triple point; inclusion of ionized species; and various applications, such as constant-pressure or constant-volume combustion, rocket performance based on either a finite- or infinite-chamber-area model, shock wave calculations, and Chapman-Jouguet detonations. The second purpose of this report, to facilitate the use of the computer code, is accomplished in part 2, entitled 'Users Manual and Program Description'. Various aspects of the computer code are discussed, and a number of examples are given to illustrate its versatility.

  5. Efficient chemical equilibrium calculations for geochemical speciation and reactive transport modelling

    Science.gov (United States)

    Leal, Allan M. M.; Blunt, Martin J.; LaForce, Tara C.

    2014-04-01

    Chemical equilibrium calculations are essential for many environmental problems. It is also a fundamental tool for chemical kinetics and reactive transport modelling, since these applications may require hundreds to billions equilibrium calculations in a single simulation. Therefore, an equilibrium method for such critical applications must be very efficient, robust and accurate. In this work we demonstrate the potential effectiveness of a novel Gibbs energy minimisation algorithm for reactive transport simulations. The algorithm includes strategies to converge from poor initial guesses; capabilities to specify non-linear equilibrium constraints such as pH of an aqueous solution and activity or fugacity of a species; a rigorous phase stability test to determine the unstable phases; and a strategy to boost the convergence speed of the calculations to quadratic rates, requiring only few iterations to converge. We use this equilibrium method to solve geochemical problems relevant to carbon storage in saline aquifers, where aqueous, gaseous and minerals phases are present. The problems are formulated to mimic the ones found in kinetics and transport simulations, where a sequence of equilibrium calculations are performed, each one using the previous solution as the initial guess. The efficiency and convergence rates of the calculations are presented, which require an average of 1-2 iterations. These results indicate that critical applications such as chemical kinetics and reactive transport modelling can potentially benefit by using this multiphase equilibrium algorithm.

  6. The PubChemQC Project: a large chemical database from the first principle calculations

    CERN Document Server

    Nakata, Maho

    2015-01-01

    In this research, we have been constructing a large database of molecules by {\\it ab initio} calculations. Currently, we have over 1.53 million entries of 6-31G* B3LYP optimized geometries and ten excited states by 6-31+G* TDDFT calculations. To calculate molecules, we only refer the InChI (International Chemical Identifier) representation of chemical formula by the International Union of Pure and Applied Chemistry (IUPAC), thus, no reference to experimental data. These results are open to public at http://pubchemqc.riken.jp/. The molecular data have been taken from the PubChem Project (http://pubchem.ncbi.nlm.nih.gov/) which is one of the largest in the world (approximately 63 million molecules are listed) and free (public domain) database. Our final goal is, using these data, to develop a molecular search engine or molecular expert system to find molecules which have desired properties.

  7. FragIt: A Tool to Prepare Input Files for Fragment Based Quantum Chemical Calculations

    CERN Document Server

    Steinmann, Casper; Hansen, Anne S; Jensen, Jan H

    2012-01-01

    Near linear scaling fragment based quantum chemical calculations are becoming increasingly popular for treating large systems with high accuracy and is an active field of research. However, it remains difficult to set up these calculations without expert knowledge. To facilitate the use of such methods, software tools need to be available for support, setup and lower the barrier of entry for usage by non-experts. We present a fragmentation methodology and accompanying tools called FragIt to help setup these calculations. It uses the SMARTS language to find chemically appropriate substructures in structures and is used to prepare input files for the fragment molecular orbital method in the GAMESS program package. We present patterns of fragmentation for proteins and polysaccharides, specifically D-galactopyranose for use in cyclodextrins.

  8. The PubChemQC project: A large chemical database from the first principle calculations

    Science.gov (United States)

    Maho, Nakata

    2015-12-01

    In this research, we have been constructing a large database of molecules by ab initio calculations. Currently, we have over 1.53 million entries of 6-31G* B3LYP optimized geometries and ten excited states by 6-31+G* TDDFT calculations. To calculate molecules, we only refer the InChI (International Chemical Identifier) representation of chemical formula by the International Union of Pure and Applied Chemistry (IUPAC), thus, no reference to experimental data. These results are open to public at http://pubchemqc.riken.jp/. The molecular data have been taken from the PubChem Project (http://pubchem.ncbi.nlm.nih.gov/) which is one of the largest in the world (approximately 63 million molecules are listed) and free (public domain) database. Our final goal is, using these data, to develop a molecular search engine or molecular expert system to find molecules which have desired properties.

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

    Science.gov (United States)

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

    2014-06-14

    The behaviour of metal-organic cages upon guest encapsulation can be difficult to elucidate in solution. Paramagnetic metal centres introduce additional dispersion of signals that is useful for characterisation of host-guest complexes in solution using nuclear magnetic resonance (NMR). However, paramagnetic centres also complicate spectral assignment due to line broadening, signal integration error, and large changes in chemical shifts, which can be difficult to assign even for known compounds. Quantum chemical predictions can provide information that greatly facilitates the assignment of NMR signals and identification of species present. Here we explore how the prediction of paramagnetic NMR spectra may be used to gain insight into the spin crossover (SCO) properties of iron(II)-based metal organic coordination cages, specifically examining how the structure of the local metal coordination environment affects SCO. To represent the tetrahedral metal-organic cage, a model system is generated by considering an isolated metal-ion vertex: fac-ML3(2+) (M = Fe(II), Co(II); L = N-phenyl-2-pyridinaldimine). The sensitivity of the (1)H paramagnetic chemical shifts to local coordination environments is assessed and utilised to shed light on spin crossover behaviour in iron complexes. Our data indicate that expansion of the metal coordination sphere must precede any thermal SCO. An attempt to correlate experimental enthalpies of SCO with static properties of bound guests shows that no simple relationship exists, and that effects are likely due to nuanced dynamic response to encapsulation. PMID:24752730

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

    Science.gov (United States)

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

    2016-06-01

    For a better understanding of nuclear magnetic resonance (NMR) detected pressure responses of folded as well as unstructured proteins the availability of data from well-defined model systems are indispensable. In this work we report the pressure dependence of chemical shifts of the backbone atoms (1)H(α), (13)C(α) and (13)C' in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of these nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The polynomial pressure coefficients B 1 and B 2 are dependent on the type of amino acid studied. The coefficients of a given nucleus show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure are also weakly correlated. PMID:27335085

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

    Science.gov (United States)

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

    2016-06-01

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

  12. Ab Initio Calculation of 19F NMR Chemical Shielding for Alkaline-earth-metal Fluorides

    Institute of Scientific and Technical Information of China (English)

    CAI,Shu-Hui(蔡淑惠); CHEN,Zhong,(陈忠); LU,Xin(吕鑫); CHEN,Zhi-Wei(陈志伟); WAN,Hui-Lin(万惠霖)

    2001-01-01

    Gauge-independent atomic orbital (GIAO) method atHartree-Fock (HF) and density functional theory (DFr) lev-els,respectively,was employed to calculate 19F NMR chemi-cal shieldings of solid state alkaline-earth-metal fluorides MF2 (M = Mg,Ca,Sr,Ba).The results show that,although thecalculated19F chemical shieldings tend to be larger than the experinental values,they have a fairly good linear relation-ship with the observed ones.The calculated results based on different combinations of basis sets show that the B3LYP (ahybrid of DFT with HF) predictions are greatly superior tothe I-IF predictions.When a basis set of metal atom with ef- fecfive core potential (ECP) has well representation of valencewavefunction,especially wavefuncfion of d component,andproper definition of core electron nmnher,it can be applied toobtain 19F chemical shielding which is dose to that of all-elec-tron calculation.Tne variation of 19F chemical shielding of al-kaline-earth-metal fluorides correlates well with the latticefactor A/R2.``

  13. Nucleus-independent chemical shift criterion for aromaticity in Π-extended tetraoxa[8]circulenes

    DEFF Research Database (Denmark)

    Baryshnikov, Gleb V.; Minaev, Boris F.; Pittelkow, Michael;

    2013-01-01

    Recently synthesized p-extended symmetrical tetraoxa[8]circulenes that exhibit electroluminescent properties were calculated at the density functional theory (DFT) level using the quantum theory of atoms in molecules (QTAIM) approach to electron density distribution analysis. Nucleus-independent ...

  14. Quantum chemical calculation of the equilibrium structures of small metal atom clusters

    Science.gov (United States)

    Kahn, L. R.

    1981-01-01

    A decomposition of the molecular energy is presented that is motivated by the atom superposition and electron delocalization physical model of chemical binding. The energy appears in physically transparent form consisting of a classical electrostatic interaction, a zero order two electron exchange interaction, a relaxation energy, and the atomic energies. Detailed formulae are derived in zero and first order of approximation. The formulation extends beyond first order to any chosen level of approximation leading, in principle, to the exact energy. The structure of this energy decomposition lends itself to the fullest utilization of the solutions to the atomic sub problems to simplify the calculation of the molecular energy. If nonlinear relaxation effects remain minor, the molecular energy calculation requires at most the calculation of two center, two electron integrals. This scheme thus affords the prospects of substantially reducing the computational effort required for the calculation of molecular energies.

  15. Forming NCO(-) in Dense Molecular Clouds: Possible Gas-Phase Chemical Paths From Quantum Calculations.

    Science.gov (United States)

    Yurtsever, E; Gianturco, F A; Wester, R

    2016-07-14

    The existence of NCO(-) anions in the interstellar medium (ISM) has been suggested and searched for over the years but without any formal definitive sighting of that molecule. We discuss in this work the possible formation of either NCO(-) directly or of NCO neutral as a precursor to NCO(-) formation by electron attachment. We follow simple, gas-phase chemical reactions for which the general features are obtained from accurate quantum calculations. The results are shedding some additional light on the likely presence of this anion in the ISM environment, drawing further information from the specific features of the considered reactions on the additional chemical options that exist for its formation. PMID:26696323

  16. Gradient-echo in-phase and opposed-phase chemical shift imaging: Role in evaluating bone marrow

    International Nuclear Information System (INIS)

    Chemical shift imaging (CSI) provides valuable information for assessing the bone marrow, while adding little to total examination time. In this article, we review the uses of CSI for evaluating bone marrow abnormalities. CSI can be used for differentiating marrow-replacing lesions from a range of non-marrow-replacing processes, although the sequence is associated with technical limitations and pitfalls. Particularly at 3 T, susceptibility artefacts are prevalent, and optimal technical parameters must be implemented with appropriate choices for echo times

  17. A multiple pulse zero crossing NMR technique, and its application to F-19 chemical shift measurements in solids

    Science.gov (United States)

    Burum, D. P.; Elleman, D. D.; Rhim, W.-K.

    1978-01-01

    A simple multiple-pulse 'zero crossing technique' for accurately determining the first moment of a solid-state NMR spectrum is introduced. This technique was applied to obtain the F-19 chemical shift versus pressure curves up to 5 kbar for single crystals of CaF2 (0.29 + or - 0.02 ppm/kbar) and BaF2 (0.62 + or - 0.05 ppm/kbar). Results at ambient temperature and pressure are also reported for a number of other fluorine compounds. Because of its high data rate, this technique is potentially several orders of magnitude more sensitive than similar CW methods.

  18. 13C Magic angle spinning NMR analysis and quantum chemical modeling of the bathochromic shift of astaxanthin in alpha-crustacyanin, the blue carotenoprotein complex in the carapace of the lobster Homarus gammarus.

    Science.gov (United States)

    Weesie, R J; Jansen, F J; Merlin, J C; Lugtenburg, J; Britton, G; de Groot, H J

    1997-06-17

    Selective isotope enrichment, 13C magic angle spinning (MAS) NMR, and semiempirical quantum chemical modeling, have been used to analyze ligand-protein interactions associated with the bathochromic shift of astaxanthin in alpha-crustacyanin, the blue carotenoprotein complex from the carapace of the lobster Homarus gammarus. Spectra of alpha-crustacyanin were obtained after reconstitution with astaxanthins labeled with 13C at positions 4,4', 12,12', 13,13', or 20,20'. The data reveal substantial downfield shifts of 4.9 and 7.0 ppm at positions 12 and 12' in the complex, respectively. In contrast, at the 13 and 13' positions, small upfield shifts of 1.9 ppm were observed upon binding to the protein. These data are in line with previously obtained results for positions 14,14' (3.9 and 6.8 ppm downfield) and 15,15' (0.6 ppm upfield) and confirm the unequal perturbation of both halves after binding of the chromophore. However, these results also show that the main perturbation is of symmetrical origin, since the chemical shift differences exhibit a similar pattern in both halves of the astaxanthin molecule. A small downfield shift of 2.4 ppm was detected for the 4 and 4' positions. Finally, the 20,20' methyl groups are shifted 0.4 ppm upfield by the protein. The full data set provides convincing evidence that charge polarization is of importance for the bathochromic shift. The NMR shifts are compared with calculated charge densities for astaxanthin subjected to variations in protonation states of the ring-functional groups, as models of ligand-protein interactions. Taking into account the color shift and other available optical data, the current model for the mechanisms of interaction with the protein was refined. The results point toward a mechanism in which the astaxanthin is charged and subject to strong electrostatic polarizations originating from both keto groups, most likely a double protonation. PMID:9200677

  19. Computational tool for phase-shift calculation in an interference pattern by fringe displacements based on a skeletonized image

    Science.gov (United States)

    Rivera-Ortega, Uriel; Pico-Gonzalez, Beatriz

    2016-01-01

    In this manuscript an algorithm based on a graphic user interface (GUI) designed in MATLAB for an automatic phase-shifting estimation between two digitalized interferograms is presented. The proposed algorithm finds the midpoint locus of the dark and bright interference fringes in two skeletonized fringe patterns and relates their displacements with the corresponding phase-shift. In order to demonstrate the usefulness of the proposed GUI, its application to simulated and experimental interference patterns will be shown. The viability of this GUI makes it a helpful and easy-to-use computational tool for educational or research purposes in optical phenomena for undergraduate or graduate studies in the field of physics.

  20. Analytical calculation of the frequency shift in phase oscillators driven by colored noise: implications for electrical engineering and neuroscience.

    Science.gov (United States)

    Galán, Roberto F

    2009-09-01

    We provide an analytical expression for the mean frequency shift in phase oscillators as a function of the standard deviation, sigma and the autocorrelation time, tau of small random perturbations. We show that the frequency shift is negative and proportional to sigma;{2} . Its absolute value increases monotonically with tau , approaching an asymptote determined by the L2 -norm of the phase-response curve. We validate our theoretical predictions with computer simulations and discuss their implications for the design of electronic oscillators and for the encoding of information in biological neural networks.

  1. Effective method for calculating the phase shifts for the scattering of slow particles with nonzero orbital angular momentum

    Energy Technology Data Exchange (ETDEWEB)

    Bruk, Y.M.

    1986-09-01

    Pais's functional equation for the phase shifts for scattering with nonzero angular momentum is solved for particles with low energies. It is shown that for short-range potentials with screening (in particular, of Yukawa or Thomas-Fermi type), Pais's equation reduces to transcendent equations. For potentials about/r /sup n/, n > 0, simple algebraic equations are obtained for finding the phase shifts delta /sub l/, l is identical to 0. The possibility of using Pais's approximation to find resonance situations in the case of the scattering of slow particles with nonzero angular momentum is discussed.

  2. Study of molecular structure, vibrational, electronic and NMR spectra of oncocalyxone A using DFT and quantum chemical calculations

    Science.gov (United States)

    Joshi, Bhawani Datt; Srivastava, Anubha; Honorato, Sara Braga; Tandon, Poonam; Pessoa, Otília Deusdênia Loiola; Fechine, Pierre Basílio Almeida; Ayala, Alejandro Pedro

    2013-09-01

    Oncocalyxone A (C17H18O5) is the major secondary metabolite isolated from ethanol extract from the heartwood of Auxemma oncocalyx Taub popularly known as “pau branco”. Oncocalyxone A (Onco A) has many pharmaceutical uses such as: antitumor, analgesic, antioxidant and causative of inhibition of platelet activation. We have performed the optimized geometry, total energy, conformational study, molecular electrostatic potential mapping, frontier orbital energy gap and vibrational frequencies of Onco A employing ab initio Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d, p) basis set. Stability of the molecule arising from hyperconjugative interactions and/or charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV-vis spectrum of the compound was recorded in DMSO and MeOH solvent. The TD-DFT calculations have been performed to explore the influence of electronic absorption spectra in the gas phase, as well as in solution environment using IEF-PCM and 6-31G basis set. The 13C NMR chemical shifts have been calculated with the B3LYP/6-311++G(d, p) basis set and compared with the experimental values. These methods have been used as tools for structural characterization of Onco A.

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

    Science.gov (United States)

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

    2015-11-17

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

  4. Application of multivariate image analysis in QSPR study of 13C chemical shifts of naphthalene derivatives: a comparative study.

    Science.gov (United States)

    Garkani-Nejad, Zahra; Poshteh-Shirani, Marziyeh

    2010-11-15

    A new implemented QSPR method, whose descriptors achieved from bidimensional images, was applied for predicting (13)C NMR chemical shifts of 25 mono substituted naphthalenes. The resulted descriptors were subjected to principal component analysis (PCA) and the most significant principal components (PCs) were extracted. MIA-QSPR (multivariate image analysis applied to quantitative structure-property relationship) modeling was done by means of principal component regression (PCR) and principal component-artificial neural network (PC-ANN) methods. Eigen value ranking (EV) and correlation ranking (CR) were used here to select the most relevant set of PCs as inputs for PCR and PC-ANN modeling methods. The results supported that the correlation ranking-principal component-artificial neural network (CR-PC-ANN) model could predict the (13)C NMR chemical shifts of all 10 carbon atoms in mono substituted naphthalenes with R(2) ≥ 0.922 for training set, R(2) ≥ 0.963 for validation set and R(2) ≥ 0.936 for the test set. Comparison of the results with other existing factor selection method revealed that less accurate results were obtained by the eigen value ranking procedure. PMID:21035668

  5. Influence of Hartree-Fock exchange on the calculated Mössbauer isomer shifts and quadrupole splittings in ferrocene derivatives using density functional theory.

    Science.gov (United States)

    Nemykin, Victor N; Hadt, Ryan G

    2006-10-01

    Influence of molecular geometry, type of exchange-correlation functional, and contraction scheme of basis set applied at the iron nuclei have been tested in the calculation of 57Fe Mössbauer isomer shifts and quadrupole splittings for a wide range of ligand types, as well as oxidation and spin states, in inorganic and organometallic systems. It has been found that uncontraction of the s-part of Wachter's full-electron basis set at the iron nuclei does not appreciably improve the calculated isomer shifts. The observed correlations for all tested sets of geometries are close to each other and predominantly depend on the employed exchange-correlation functional with B3LYP functional being slightly better as compared to BPW91. Both hybrid (B3LYP) and pure (BPW91) exchange-correlation functionals are suitable for the calculation of isomer shifts in organometallic compounds. Surprisingly, it has been found that the hybrid B3LYP exchange-correlation functional completely fails in accurate prediction of quadrupole splittings in ferrocenes, while performance of the pure BPW91 functional for the same systems was excellent. This observation has been explained on the basis of relationship between the amount of Hartree-Fock exchange involved in the applied exchange-correlation functional and the calculated HOMO-LUMO energy gap in ferrocenes. On the basis of this explanation, use of only pure exchange-correlation functionals has been suggested for accurate prediction of Mössbauer spectra parameters in ferrocenes.

  6. First-order perturbative calculation of the frequency-shifts caused by static cylindrically-symmetric electric and magnetic imperfections of a Penning trap

    CERN Document Server

    Ketter, Jochen; Höcker, Martin; Streubel, Sebastian; Blaum, Klaus

    2014-01-01

    The ideal Penning trap consists of a uniform magnetic field and an electrostatic quadrupole potential. Cylindrically-symmetric deviations thereof are parametrized by the coefficients Bn and Cn, respectively. Relativistic mass-increase aside, the three characteristic eigenfrequencies of a charged particle stored in an ideal Penning trap are independent of the three motional amplitudes. This three-fold harmonicity is a highly-coveted virtue for precision experiments that rely on the measurement of at least one eigenfrequency in order to determine fundamental properties of the stored particle, such as its mass. However, higher-order contributions to the ideal fields result in amplitude-dependent frequency-shifts. In turn, these frequency-shifts need to be understood for estimating systematic experimental errors, and eventually for correcting them by means of calibrating the imperfections. The problem of calculating the frequency-shifts caused by small imperfections of a near-ideal trap yields nicely to perturbat...

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

    CERN Document Server

    Heuvel, Willem Van den

    2012-01-01

    We present a theory for the temperature-dependent nuclear magnetic shielding tensor of molecules with arbitrary electronic structure. The theory is a generalization of Ramsey's theory for closed-shell molecules. The shielding tensor is defined as a second derivative of the Helmholtz free energy of the electron system in equilibrium with the applied magnetic field and the nuclear magnetic moments. This derivative is analytically evaluated and expressed as a sum over states formula. Special consideration is given to a system with an isolated degenerate ground state for which the size of the degeneracy and the composition of the wave functions are arbitrary. In this case the paramagnetic part of the shielding tensor is expressed in terms of the $g$ and $A$ tensors of the EPR spin Hamiltonian of the degenerate state. As an illustration of the proposed theory, we provide an explicit formula for the paramagnetic shift of the central lanthanide ion in endofullerenes Ln@C$_{60}$, with Ln=Ce$^{3+}$, Nd$^{3+}$, Sm$^{3+...

  8. Calculation of the temperature-induced frequency shifts of Raman modes as a function of pressure in phase I of S-triazine

    International Nuclear Information System (INIS)

    The temperature-induced frequency shifts 1/ω(δω/δΤ) are calculated for the Raman modes I and IV as a function of pressure in phase I (P< PC) of s-triazine. For this calculation, the Raman frequencies measured for the modes I and IV at various pressures are used in phase I of s-triazine according to the spectroscopic modifications of the Pippard relations. By determining the mode Gruneisen parameters of the Raman modes studied here, a linear variation of the temperature-induced 1/ω(δω/δΤ) with the pressure-induced frequency shifts 1/ω(δω/δP) is established in phase I (P< PC) of s-triazine.

  9. Unquenched quark-model calculation of excited $\\rho$ resonances and P-wave $\\pi\\pi$ phase shifts

    CERN Document Server

    Coito, Susana; van Beveren, Eef

    2015-01-01

    The $\\rho(770)$ vector resonance, its radial recurrences, and the corresponding P-wave $\\pi\\pi$ phase shifts are investigated in an unquenched quark model with all classes of relevant decay channels included, viz. pseudoscalar-pseudoscalar, vector-pseudoscalar, vector-vector, vector-scalar, axialvector-pseudoscalar, and axialvector-vector, totalling 26 channels. Two of the few model parameters are fixed at previously used values, whereas the other three are adjusted to the $\\rho(770)$ resonance and the lower P-wave $\\pi\\pi$ phases. Preliminary results indicate the model's capacity to reproduce these phases as well as the $\\rho$ mass and width. However, at higher energies the phase shifts tend to rise too sharply. A possible remedy is an extension of the model so as to handle resonances in the final states for most of the included decay channels. Work in progress.

  10. Calculation of chemical quantities for the radioactive liquid waste treatment facility

    Energy Technology Data Exchange (ETDEWEB)

    Del Signore, John C. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); McClenahan, Robert L. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2007-03-01

    The Radioactive Liquid Waste Treatment Facility (RLWTF) receives, stores, and treats both low-level and transuranic radioactive liquid wastes (RLW). Treatment of RLW requires the use of different chemicals. Examples include the use of calcium oxide to precipitate metals and radioactive elements from the radioactive liquid waste, and the use of hydrochloric acid to clean membrane filters that are used in the treatment process. The RL WTF is a Hazard Category 2 nuclear facility, as set forth in the LANL Final Safety Analysis Report of October 1995, and a DOE letter of March 11, 1999. A revised safety basis is being prepared for the RLWTF, and will be submitted to the NNSA in early 2007. This set of calculations establishes maximum chemical quantities that will be used in the 2007 safety basis.

  11. Calculation of chemical reaction energies using the AM05 density functional

    CERN Document Server

    Muller, Richard P; Janssen, Curtis L

    2009-01-01

    We present results that compare the accuracy of the AM05 density functional to a set of chemical reaction energies. The reactions were generated from the singlet species in the well-known G2 test suite. Our results show that, in general, the AM05 functional performs as well as the other "pure" density functionals, but none of these perform as well as the hybrid B3LYP functional. These results are nonetheless encouraging because the AM05 functional arises from very simple assumptions, and does not require the calculation of the Hartree-Fock exchange integrals.

  12. An implicit flux-split algorithm to calculate hypersonic flowfields in chemical equilibrium

    Science.gov (United States)

    Palmer, Grant

    1987-01-01

    An implicit, finite-difference, shock-capturing algorithm that calculates inviscid, hypersonic flows in chemical equilibrium is presented. The flux vectors and flux Jacobians are differenced using a first-order, flux-split technique. The equilibrium composition of the gas is determined by minimizing the Gibbs free energy at every node point. The code is validated by comparing results over an axisymmetric hemisphere against previously published results. The algorithm is also applied to more practical configurations. The accuracy, stability, and versatility of the algorithm have been promising.

  13. NMR chemical shift analysis of the conformational transition between the monomer and tetramer of melittin in an aqueous solution.

    Science.gov (United States)

    Miura, Yoshinori

    2016-05-01

    It is known that melittin in an aqueous solution undergoes a conformational transition between the monomer and tetramer by variation in temperature. The transition correlates closely with isomers of the proline residue; monomeric melittin including a trans proline peptide bond (trans-monomer) is involved directly in the transition, whereas monomeric melittin having a cis proline peptide bond (cis-monomer) is virtually not. The transition has been explored by using nuclear magnetic resonance spectroscopy in order to clarify the stability of the tetrameric conformation and the cooperativity of the transition. In the light of temperature dependence of chemical shifts of resonances from the isomeric monomers, we qualitatively estimate the temperature-, salt-, and concentration-dependence of the relative equilibrium populations of the trans-monomer and tetramer, and show that the tetramer has a maximum conformational stability at 30-45 °C and that the transition cooperativity is very low. PMID:26658745

  14. Backbone and stereospecific (13)C methyl Ile (δ1), Leu and Val side-chain chemical shift assignments of Crc.

    Science.gov (United States)

    Sharma, Rakhi; Sahu, Bhubanananda; Ray, Malay K; Deshmukh, Mandar V

    2015-04-01

    Carbon catabolite repression (CCR) allows bacteria to selectively assimilate a preferred compound among a mixture of several potential carbon sources, thus boosting growth and economizing the cost of adaptability to variable nutrients in the environment. The RNA-binding catabolite repression control (Crc) protein acts as a global post-transcriptional regulator of CCR in Pseudomonas species. Crc triggers repression by inhibiting the expression of genes involved in transport and catabolism of non-preferred substrates, thus indirectly favoring assimilation of preferred one. We report here a nearly complete backbone and stereospecific (13)C methyl side-chain chemical shift assignments of Ile (δ1), Leu and Val of Crc (~ 31 kDa) from Pseudomonas syringae Lz4W. PMID:24496608

  15. The chemically driven phase transformation in a memristive abacus capable of calculating decimal fractions.

    Science.gov (United States)

    Xu, Hanni; Xia, Yidong; Yin, Kuibo; Lu, Jianxin; Yin, Qiaonan; Yin, Jiang; Sun, Litao; Liu, Zhiguo

    2013-01-01

    The accurate calculation of decimal fractions is still a challenge for the binary-coded computations that rely on von Neumann paradigm. Here, we report a kind of memristive abacus based on synaptic Ag-Ge-Se device, in which the memristive long-term potentiation and depression are caused by a chemically driven phase transformation. The growth and the rupture of conductive Ag₂Se dendrites are confirmed via in situ transmission electron microscopy. By detecting the change in memristive synaptic weight, the quantity of input signals applied onto the device can be "counted". This makes it possible to achieve the functions of abacus that is basically a counting frame. We demonstrate through experimental studies that this kind of memristive abacus can calculate decimal fractions in the light of the abacus algorithms. This approach opens up a new route to do decimal arithmetic in memristive devices without encoding binary-coded decimal.

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

    Science.gov (United States)

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

    2015-05-01

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

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

    Science.gov (United States)

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

    2016-08-31

    The thickness-dependent surface states of MoS2 thin films grown by the chemical vapor deposition process on the SiO2-Si substrates are investigated by X-ray photoelectron spectroscopy. Raman and high-resolution transmission electron microscopy suggest the thicknesses of MoS2 films to be ranging from 3 to 10 layers. Both the core levels and valence band edges of MoS2 shift downward ∼0.2 eV as the film thickness increases, which can be ascribed to the Fermi level variations resulting from the surface states and bulk defects. Grainy features observed from the atomic force microscopy topographies, and sulfur-vacancy-induced defect states illustrated at the valence band spectra imply the generation of surface states that causes the downward band bending at the n-type MoS2 surface. Bulk defects in thick MoS2 may also influence the Fermi level oppositely compared to the surface states. When Au contacts with our MoS2 thin films, the Fermi level downshifts and the binding energy reduces due to the hole-doping characteristics of Au and easy charge transfer from the surface defect sites of MoS2. The shift of the onset potentials in hydrogen evolution reaction and the evolution of charge-transfer resistances extracted from the impedance measurement also indicate the Fermi level varies with MoS2 film thickness. The tunable Fermi level and the high chemical stability make our MoS2 a potential catalyst. The observed thickness-dependent properties can also be applied to other transition-metal dichalcogenides (TMDs), and facilitates the development in the low-dimensional electronic devices and catalysts. PMID:27488185

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

    Science.gov (United States)

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

    2016-08-31

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

  19. Microscopic structures of ionic liquids 1-ethyl-3-methylimidazolium tetrafluoroborate in water probed by the relative chemical shift

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The relative chemical shifts (△δ) △δwere put forward to investigate the microscopic structure of 1-ethyl-3-methyl-imidazolium tetrafluoroborate (EmimBF4) during the dilution process with water.The concentration-dependent △δ(C2)H-(C4)H,△δ(C2)H-(C5)H and △δ(C4)H-(C5)H were analyzed.The results reveal that the variations of the microscopic structures of three aromatic protons are inconsistent.The strength of the H-bond between water and three aromatic protons follows the order:(C2)H···O > (C4)H···O > (C5)H···O.The concentration-dependent △δ(C6)H-(C7)H and △δ(C6)H-(C8)H indicate the formation of the H-bonds of (Calkyl)H···O is impossible,and more water is located around (C6)H than around (C7)H or (C8)H.The concentration-dependent △δ(C2)H-(C4)H and △δ(C2)H-(C5)H both increase rapidly when xwater > 0.9 or so,suggesting the ionic pairs of EmimBF4 are dissociated rapidly.The turning points of concentration-dependent △δ(C2)H-(C4)H and △δ(C2)H-(C5)H indicate that some physical properties of the EmimBF4/water mixtures also change at the corresponding concentration point.The microscopic structures of EmimBF4 in water could be clearly detected by the relative chemical shifts.

  20. Zero discharge tanning: a shift from chemical to biocatalytic leather processing.

    Science.gov (United States)

    Thanikaivelan, Palanisamy; Rao, Jonnalagadda Raghava; Nair, Balachandran Unni; Ramasami, Thirumalachari

    2002-10-01

    Beam house processes (Beam house processes generally mean liming-reliming processes, which employ beam.) contribute more than 60% of the total pollution from leather processing. The use of lime and sodium sulfide is of environmental concern (1, 2). Recently, the authors have developed an enzyme-based dehairing assisted with a very low amount of sodium sulfide, which completely avoids the use of lime. However, the dehaired pelt requires opening up of fiber bundles for further processing, where lime is employed to achieve this through osmotic swelling. Huge amounts of lime sludge and total solids are the main drawbacks of lime. An alternative bioprocess, based on alpha-amylase for fiber opening, has been attempted after enzymatic unhairing. This totally eliminates the use of lime in leather processing. This method enables subsequent processes and operations in leather making feasible without a deliming process. A control experiment was run in parallel using conventional liming-reliming processes. It has been found that the extent of opening up of fiber bundles using alpha-amylase is comparable to that of the control. This has been substantiated through scanning electron microscopic, stratigraphic chrome distribution analysis, and softness measurements. Performance of the leathers is shown to be on a par with leathers produced by the conventional process through physical and hand evaluation. Importantly, softness of the leathers is numerically proven to be comparable with that of control. The process also demonstrates reduction in chemical oxygen demand load by 45% and total solids load by 20% compared to the conventional process. The total dry sludge from the beam house processes is brought down from 152 to 8 kg for processing 1 ton of raw hides.

  1. Free energy calculations, enhanced by a Gaussian ansatz, for the "chemical work" distribution.

    Science.gov (United States)

    Boulougouris, Georgios C

    2014-05-15

    The evaluation of the free energy is essential in molecular simulation because it is intimately related with the existence of multiphase equilibrium. Recently, it was demonstrated that it is possible to evaluate the Helmholtz free energy using a single statistical ensemble along an entire isotherm by accounting for the "chemical work" of transforming each molecule, from an interacting one, to an ideal gas. In this work, we show that it is possible to perform such a free energy perturbation over a liquid vapor phase transition. Furthermore, we investigate the link between a general free energy perturbation scheme and the novel nonequilibrium theories of Crook's and Jarzinsky. We find that for finite systems away from the thermodynamic limit the second law of thermodynamics will always be an inequality for isothermal free energy perturbations, resulting always to a dissipated work that may tend to zero only in the thermodynamic limit. The work, the heat, and the entropy produced during a thermodynamic free energy perturbation can be viewed in the context of the Crooks and Jarzinsky formalism, revealing that for a given value of the ensemble average of the "irreversible" work, the minimum entropy production corresponded to a Gaussian distribution for the histogram of the work. We propose the evaluation of the free energy difference in any free energy perturbation based scheme on the average irreversible "chemical work" minus the dissipated work that can be calculated from the variance of the distribution of the logarithm of the work histogram, within the Gaussian approximation. As a consequence, using the Gaussian ansatz for the distribution of the "chemical work," accurate estimates for the chemical potential and the free energy of the system can be performed using much shorter simulations and avoiding the necessity of sampling the computational costly tails of the "chemical work." For a more general free energy perturbation scheme that the Gaussian ansatz may not be

  2. Quantum Monte Carlo, time-dependent density functional theory, and density functional theory calculations of diamondoid excitation energies and Stokes shifts

    CERN Document Server

    Marsusi, F; Drummond, N D

    2011-01-01

    We have computed the absorption and emission energies and hence Stokes shifts of small diamondoids as a function of size using different theoretical approaches, including density functional theory and quantum Monte Carlo (QMC) calculations. The absorption spectra of these molecules were also investigated by time-dependent density functional theory (TD-DFT) and compared with experiment. We have analyzed the structural distortion and formation of a self-trapped exciton in the excited state, and we have studied the effects of these on the Stokes shift as a function of size. Compared to recent experiments, QMC overestimates the excitation energies by about 0.8(1) eV on average. Benefiting from a cancellation of errors, the optical gaps obtained in DFT calculations with the B3LYP functional are in better agreement with experiment. It is also shown that TD-B3LYP calculations can reproduce most of the features found in the experimental spectra. According to our calculations, the structures of diamondoids in the exci...

  3. 短波信道探测中多普勒频移的计算%Calculation of Doppler shift in HF channel sounding

    Institute of Scientific and Technical Information of China (English)

    刘月亮; 蒋宇中; 张四起

    2012-01-01

    For the purpose of exact measurement of Doppler shift, based on the pulse compression technique, this paper di the theoretical deduction of the calculation of Doppler shift, in which the signal modulated by Zadoff-Chu sequence was used a the sounding signal and a simplified Watterson model was used as the HF channel. It obtained a calculation formula of Dopple shift, carried out the simulation, of the calculation result of the formula for the case of two paths. The simulation results shoi that the calculation result of the formula is right when the Doppler difference of the two paths is less than ± 0. 3 Hz. On the ba sis of this,made the simulation of Doppler shift* s effect on the pulse compression of Zadoff-Chu sequence. The results shoi that the effect of the Doppler shift which is less than 10 Hz is negligible, which affirms that Zadoff-Chu sequence is an appro priate sequence for HF channel sounding.%为准确获取短波信道探测信号的多普勒频移,把被Zadoff-Chu序列调制的信号作为探测信号,以简化的Watterson模型作为短波信道,采用脉冲压缩技术,对多普勒频移的计算进行了理论推导,得出了一种多普勒频移的计算公式,对两条路径时公式的计算结果进行了仿真.结果表明,在两条路径的多普勒频移相差小于±0.3 Hz时,计算结果较为准确.在此基础上,仿真分析了多普勒频移对Zadoff-Chu序列的脉冲压缩的影响.分析表明,小于10 Hz的多普勒频移对Zadoff-Chu序列的脉冲压缩的影响可以忽略不计,将该序列应用在短波信道探测中比较合适.

  4. Dissociative electron transfer in polychlorinated aromatics. Reduction potentials from convolution analysis and quantum chemical calculations.

    Science.gov (United States)

    Romańczyk, Piotr P; Rotko, Grzegorz; Kurek, Stefan S

    2016-08-10

    Formal potentials of the first reduction leading to dechlorination in dimethylformamide were obtained from convolution analysis of voltammetric data and confirmed by quantum chemical calculations for a series of polychlorinated benzenes: hexachlorobenzene (-2.02 V vs. Fc(+)/Fc), pentachloroanisole (-2.14 V), and 2,4-dichlorophenoxy- and 2,4,5-trichlorophenoxyacetic acids (-2.35 V and -2.34 V, respectively). The key parameters required to calculate the reduction potential, electron affinity and/or C-Cl bond dissociation energy, were computed at both DFT-D and CCSD(T)-F12 levels. Comparison of the obtained gas-phase energies and redox potentials with experiment enabled us to verify the relative energetics and the performance of various implicit solvent models. Good agreement with the experiment was achieved for redox potentials computed at the DFT-D level, but only for the stepwise mechanism owing to the error compensation. For the concerted electron transfer/C-Cl bond cleavage process, the application of a high level coupled cluster method is required. Quantum chemical calculations have also demonstrated the significant role of the π*ring and σ*C-Cl orbital mixing. It brings about the stabilisation of the non-planar, C2v-symmetric C6Cl6˙(-) radical anion, explains the experimentally observed low energy barrier and the transfer coefficient close to 0.5 for C6Cl5OCH3 in an electron transfer process followed by immediate C-Cl bond cleavage in solution, and an increase in the probability of dechlorination of di- and trichlorophenoxyacetic acids due to substantial population of the vibrational excited states corresponding to the out-of-plane C-Cl bending at ambient temperatures. PMID:27477334

  5. Dissociative electron transfer in polychlorinated aromatics. Reduction potentials from convolution analysis and quantum chemical calculations.

    Science.gov (United States)

    Romańczyk, Piotr P; Rotko, Grzegorz; Kurek, Stefan S

    2016-08-10

    Formal potentials of the first reduction leading to dechlorination in dimethylformamide were obtained from convolution analysis of voltammetric data and confirmed by quantum chemical calculations for a series of polychlorinated benzenes: hexachlorobenzene (-2.02 V vs. Fc(+)/Fc), pentachloroanisole (-2.14 V), and 2,4-dichlorophenoxy- and 2,4,5-trichlorophenoxyacetic acids (-2.35 V and -2.34 V, respectively). The key parameters required to calculate the reduction potential, electron affinity and/or C-Cl bond dissociation energy, were computed at both DFT-D and CCSD(T)-F12 levels. Comparison of the obtained gas-phase energies and redox potentials with experiment enabled us to verify the relative energetics and the performance of various implicit solvent models. Good agreement with the experiment was achieved for redox potentials computed at the DFT-D level, but only for the stepwise mechanism owing to the error compensation. For the concerted electron transfer/C-Cl bond cleavage process, the application of a high level coupled cluster method is required. Quantum chemical calculations have also demonstrated the significant role of the π*ring and σ*C-Cl orbital mixing. It brings about the stabilisation of the non-planar, C2v-symmetric C6Cl6˙(-) radical anion, explains the experimentally observed low energy barrier and the transfer coefficient close to 0.5 for C6Cl5OCH3 in an electron transfer process followed by immediate C-Cl bond cleavage in solution, and an increase in the probability of dechlorination of di- and trichlorophenoxyacetic acids due to substantial population of the vibrational excited states corresponding to the out-of-plane C-Cl bending at ambient temperatures.

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

    Energy Technology Data Exchange (ETDEWEB)

    Mao, Kanmi [Iowa State Univ., Ames, IA (United States)

    2011-01-01

    . Furthermore, conformational details of two types of PFP were confirmed by theoretical calculation, operated by Dr. Takeshi Kobayashi. Finally, the arrangement of two surfactants, cetyltrimetylammoium bromide (CTAB) and cetylpyridinium bromide (CPB), mixed inside the MSN pores, was studied by solid-state NMR (Chapter 6). By analyzing the 1H-1H DQMAS and NOESY correlation spectra, the CTAB and CPB molecules were shown to co-exist inside the pores without forming significant monocomponent domains. A 'folded-over' conformation of CPB headgroups was proposed according to the results from 1H-29Si 2D HETCOR.

  7. Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropy

    International Nuclear Information System (INIS)

    The solution structure of d(CGCGAATTCGCG)2 has been determined on the basis of an exceptionally large set of residual dipolar couplings. In addition to the heteronuclear 13C-1H and 15N-1H and qualitative homonuclear 1H-1H dipolar couplings, previously measured in bicelle medium, more than 300 quantitative 1H-1H and 22 31P-1H dipolar restraints were obtained in liquid crystalline Pf1 medium, and 22 31P chemical shift anisotropy restraints. High quality DNA structures can be obtained solely on the basis of these new restraints, and these structures are in close agreement with those calculated previously on the basis of 13C-1H and 15N-1H dipolar couplings. In the newly calculated structures, 31P-1H dipolar and 3JsubH3'Psub couplings and 31P CSA data restrain the phosphodiester backbone torsion angles. The final structure represents a quite regular B-form helix with a modest bending of ∼10 deg., which is essentially independent of whether or not electrostatic terms are used in the calculation. Combined, the number of homo- and heteronuclear dipolar couplings significantly exceeds the number of degrees of freedom in the system. Results indicate that the dipolar coupling data cannot be fit by a single structure, but are compatible with the presence of rapid equilibria between C2'-endo and C3'-endo deoxyribose puckers (sugar switching). The C2'-H2'/H2'' dipolar couplings in B-form DNA are particularly sensitive to sugar pucker and yield the largest discrepancies when fit to a single structure. To resolve these discrepancies, we suggest a simplified dipolar coupling analysis that yields N/S equilibria for the ribose sugar puckers, which are in good agreement with previous analyses of NMR JHH couplings, with a population of the minor C3'-endo form higher for pyrimidines than for purines

  8. High accuracy NMR chemical shift corrected for bulk magnetization as a tool for structural elucidation of dilutable microemulsions. Part 1 - Proof of concept.

    Science.gov (United States)

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

    2016-02-01

    In microemulsions, changes in droplet size and shape and possible transformations occur under various conditions. They are difficult to characterize by most analytical tools because of their nano-sized structure and dynamic nature. Several methods are usually combined to obtain reliable information, guiding the scientist in understanding their physical behavior. We felt that there is a need for a technique that complements those in use today in order to provide more information on the microemulsion behavior, mainly as a function of dilution with water. The improvement of NMR chemical shift measurements independent of bulk magnetization effects makes it possible to study the very weak intermolecular chemical shift effects. In the present study, we used NMR high resolution magic angle spinning to measure the chemical shift very accurately, free of bulk magnetization effects. The chemical shift of microemulsion components is measured as a function of the water content in order to validate the method in an interesting and promising, U-type dilutable microemulsion, which had been previously studied by a variety of techniques. Phase transition points of the microemulsion (O/W, bicontinuous, W/O) and changes in droplet shape were successfully detected using high-accuracy chemical shift measurements. We analyzed the results and found them to be compatible with the previous studies, paving the way for high-accuracy chemical shifts to be used for the study of other microemulsion systems. We detected two transition points along the water dilution line of the concentrate (reverse micelles) corresponding to the transition from swollen W/O nano-droplets to bicontinuous to the O/W droplets along with the changes in the droplets' sizes and shapes. The method seems to be in excellent agreement with other previously studied techniques and shows the advantage of this easy and valid technique.

  9. Efficiency enhancement calculations of state-of-the-art solar cells by luminescent layers with spectral shifting, quantum cutting, and quantum tripling function

    OpenAIRE

    Kate, ten, F.J.W.; Jong, de, T.; Hintzen, HTJM Bert; Kolk, van der, J.P.

    2013-01-01

    Solar cells of which the efficiency is not limited by the Shockley-Queisser limit can be obtained by integrating a luminescent spectral conversion layer into the cell structure. We have calculated the maximum efficiency of state-of-the-art c-Si, pc-Si, a-Si, CdTe, GaAs, CIS, CIGS, CGS, GaSb, and Ge solar cells with and without an integrated spectral shifting, quantum cutting, or quantum tripling layer using their measured internal quantum efficiency (IQE) curves. Our detailed balance limit ca...

  10. Study on the electronic structure of nickel hydroxide by quantum chemical DV-Xα calculation

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The electronic structures of atom clusters Ni7O12H122+and Ni7O12H-9 of β-Ni(OH)2 were calculated by quantum chemical DV-Xα method.By analyzing the state densities,orbital populations,net charges and electric charge density differences of the selected clusters,it was indicated that β-Ni(OH)2 was not typical ionic crystal,and the bonds between Ni and O atoms had obvious covalent characteristics.The bonds between H atom and other atoms in the crystal structure were weaker,which ensured that H atoms can easily deintercalate and intercalate into β-Ni(OH)2-The structure of β-Ni(OH)2 was not changed by moderate de-intercalation of H atoms.However,with the excessive de-intercalation of H atoms,the structure of β-Ni(OH)2 changed and the electrochemical active properties were reduced.

  11. An Analytical Investigation of Three General Methods of Calculating Chemical-Equilibrium Compositions

    Science.gov (United States)

    Zeleznik, Frank J.; Gordon, Sanford

    1960-01-01

    The Brinkley, Huff, and White methods for chemical-equilibrium calculations were modified and extended in order to permit an analytical comparison. The extended forms of these methods permit condensed species as reaction products, include temperature as a variable in the iteration, and permit arbitrary estimates for the variables. It is analytically shown that the three extended methods can be placed in a form that is independent of components. In this form the Brinkley iteration is identical computationally to the White method, while the modified Huff method differs only'slightly from these two. The convergence rates of the modified Brinkley and White methods are identical; and, further, all three methods are guaranteed to converge and will ultimately converge quadratically. It is concluded that no one of the three methods offers any significant computational advantages over the other two.

  12. Overcoming computational uncertainties to reveal chemical sensitivity in single molecule conduction calculations.

    Science.gov (United States)

    Solomon, Gemma C; Reimers, Jeffrey R; Hush, Noel S

    2005-06-01

    In the calculation of conduction through single molecule's approximations about the geometry and electronic structure of the system are usually made in order to simplify the problem. Previously [G. C. Solomon, J. R. Reimers, and N. S. Hush, J. Chem. Phys. 121, 6615 (2004)], we have shown that, in calculations employing cluster models for the electrodes, proper treatment of the open-shell nature of the clusters is the most important computational feature required to make the results sensitive to variations in the structural and chemical features of the system. Here, we expand this and establish a general hierarchy of requirements involving treatment of geometrical approximations. These approximations are categorized into two classes: those associated with finite-dimensional methods for representing the semi-infinite electrodes, and those associated with the chemisorption topology. We show that ca. 100 unique atoms are required in order to properly characterize each electrode: using fewer atoms leads to nonsystematic variations in conductivity that can overwhelm the subtler changes. The choice of binding site is shown to be the next most important feature, while some effects that are difficult to control experimentally concerning the orientations at each binding site are actually shown to be insignificant. Verification of this result provides a general test for the precision of computational procedures for molecular conductivity. Predictions concerning the dependence of conduction on substituent and other effects on the central molecule are found to be meaningful only when they exceed the uncertainties of the effects associated with binding-site variation.

  13. Quantum chemical calculations of bond dissociation energies for COOH scission and electronic structure in some acids

    Institute of Scientific and Technical Information of China (English)

    Zeng Hui; Zhao Jun; Xiao Xun

    2013-01-01

    Quantum chemical calculations are performed to investigate the equilibrium C-COOH bond distances and the bond dissociation energies (BDEs) for 15 acids.These compounds are studied by utilizing the hybrid density functional theory (DFT) (B3LYP,B3PW91,B3P86,PBE1PBE) and the complete basis set (CBS-Q) method in conjunction with the 6-31 lG** basis as DFT methods have been found to have low basis sets sensitivity for small and medium molecules in our previous work.Comparisons between the computational results and the experimental values reveal that CBS-Q method,which can produce reasonable BDEs for some systems in our previous work,seems unable to predict accurate BDEs here.However,the B3P86 calculated results accord very well with the experimental values,within an average absolute error of 2.3 kcal/mol.Thus,B3P86 method is suitable for computing the reliable BDEs of C-COOH bond for carboxylic acid compounds.In addition,the energy gaps between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of studied compounds are estimated,based on which the relative thermal stabilities of the studied acids are also discussed.

  14. Quantum chemical calculations of bond dissociation energies for COOH scission and electronic structure in some acids

    International Nuclear Information System (INIS)

    Quantum chemical calculations are performed to investigate the equilibrium C—COOH bond distances and the bond dissociation energies (BDEs) for 15 acids. These compounds are studied by utilizing the hybrid density functional theory (DFT) (B3LYP, B3PW91, B3P86, PBE1PBE) and the complete basis set (CBS—Q) method in conjunction with the 6-311G** basis as DFT methods have been found to have low basis sets sensitivity for small and medium molecules in our previous work. Comparisons between the computational results and the experimental values reveal that CBS—Q method, which can produce reasonable BDEs for some systems in our previous work, seems unable to predict accurate BDEs here. However, the B3P86 calculated results accord very well with the experimental values, within an average absolute error of 2.3 kcal/mol. Thus, B3P86 method is suitable for computing the reliable BDEs of C—COOH bond for carboxylic acid compounds. In addition, the energy gaps between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of studied compounds are estimated, based on which the relative thermal stabilities of the studied acids are also discussed. (atomic and molecular physics)

  15. Ultrafast magnetic-resonance-imaging velocimetry of liquid-liquid systems: overcoming chemical-shift artifacts using compressed sensing.

    Science.gov (United States)

    Tayler, Alexander B; Benning, Martin; Sederman, Andrew J; Holland, Daniel J; Gladden, Lynn F

    2014-06-01

    We present simultaneous measurement of dispersed and continuous phase flow fields for liquid-liquid systems obtained using ultrafast magnetic resonance imaging. Chemical-shift artifacts, which are otherwise highly problematic for this type of measurement, are overcome using a compressed sensing based image reconstruction algorithm that accounts for off-resonant signal components. This scheme is combined with high-temporal-resolution spiral imaging (188 frames per second), which is noted for its robustness to flow. It is demonstrated that both quantitative signal intensity and phase preconditioning are preserved throughout the image reconstruction algorithm. Measurements are acquired of oil droplets of varying viscosity rising through stagnant water. From these data it is apparent that the internal droplet flow fields are heavily influenced by the droplet shape oscillations, and that the accurate modeling of droplet shape is of critical importance in the modeling of droplet-side hydrodynamics. The application of the technique to three-component systems is also demonstrated, as is the measurement of local concentration maps of a mutually soluble species (acetone in polydimethylsiloxane-water).

  16. Chemical shifts assignments of the archaeal MC1 protein and a strongly bent 15 base pairs DNA duplex in complex.

    Science.gov (United States)

    Loth, Karine; Landon, Céline; Paquet, Françoise

    2015-04-01

    MC1 is the most abundant architectural protein present in Methanosarcina thermophila CHTI55 in laboratory growth conditions and is structurally unrelated to other DNA-binding proteins. MC1 functions are to shape and to protect DNA against thermal denaturation by binding to it. Therefore, MC1 has a strong affinity for any double-stranded DNA. However, it recognizes and preferentially binds to bent DNA, such as four-way junctions and negatively supercoiled DNA minicircles. Combining NMR data, electron microscopy data, biochemistry, molecular modelisation and docking approaches, we proposed recently a new type of DNA/protein complex, in which the monomeric protein MC1 binds on the concave side of a strongly bent 15 base pairs DNA. We present here the NMR chemical shifts assignments of each partner in the complex, (1)H (15)N MC1 protein and (1)H (13)C (15)N bent duplex DNA, as first step towards the first experimental 3D structure of this new type of DNA/protein complex.

  17. ¹³C solid-state NMR analysis of the most common pharmaceutical excipients used in solid drug formulations, Part I: Chemical shifts assignment.

    Science.gov (United States)

    Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika Agnieszka; Szeleszczuk, Łukasz; Wawer, Iwona

    2016-04-15

    Solid-state NMR is an excellent and useful method for analyzing solid-state forms of drugs. In the (13)C CP/MAS NMR spectra of the solid dosage forms many of the signals originate from the excipients and should be distinguished from those of active pharmaceutical ingredient (API). In this work the most common pharmaceutical excipients used in the solid drug formulations: anhydrous α-lactose, α-lactose monohydrate, mannitol, sucrose, sorbitol, sodium starch glycolate type A and B, starch of different origin, microcrystalline cellulose, hypromellose, ethylcellulose, methylcellulose, hydroxyethylcellulose, sodium alginate, magnesium stearate, sodium laurilsulfate and Kollidon(®) were analyzed. Their (13)C CP/MAS NMR spectra were recorded and the signals were assigned, employing the results (R(2): 0.948-0.998) of GIPAW calculations and theoretical chemical shifts. The (13)C ssNMR spectra for some of the studied excipients have not been published before while for the other signals in the spectra they were not properly assigned or the assignments were not correct. The results summarize and complement the data on the (13)C ssNMR analysis of the most common pharmaceutical excipients and are essential for further NMR studies of API-excipient interactions in the pharmaceutical formulations. PMID:26845204

  18. ¹³C solid-state NMR analysis of the most common pharmaceutical excipients used in solid drug formulations, Part I: Chemical shifts assignment.

    Science.gov (United States)

    Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika Agnieszka; Szeleszczuk, Łukasz; Wawer, Iwona

    2016-04-15

    Solid-state NMR is an excellent and useful method for analyzing solid-state forms of drugs. In the (13)C CP/MAS NMR spectra of the solid dosage forms many of the signals originate from the excipients and should be distinguished from those of active pharmaceutical ingredient (API). In this work the most common pharmaceutical excipients used in the solid drug formulations: anhydrous α-lactose, α-lactose monohydrate, mannitol, sucrose, sorbitol, sodium starch glycolate type A and B, starch of different origin, microcrystalline cellulose, hypromellose, ethylcellulose, methylcellulose, hydroxyethylcellulose, sodium alginate, magnesium stearate, sodium laurilsulfate and Kollidon(®) were analyzed. Their (13)C CP/MAS NMR spectra were recorded and the signals were assigned, employing the results (R(2): 0.948-0.998) of GIPAW calculations and theoretical chemical shifts. The (13)C ssNMR spectra for some of the studied excipients have not been published before while for the other signals in the spectra they were not properly assigned or the assignments were not correct. The results summarize and complement the data on the (13)C ssNMR analysis of the most common pharmaceutical excipients and are essential for further NMR studies of API-excipient interactions in the pharmaceutical formulations.

  19. The value of 15-minute delayed contrast-enhanced CT to differentiate hyperattenuating adrenal masses compared with chemical shift MR imaging

    Energy Technology Data Exchange (ETDEWEB)

    Koo, Hyun Jung; Choi, Hyuck Jae; Cho, Kyoung-Sik [Asan Medical Center, University of Ulsan College of Medicine, Department of Radiology and Research Institute of Radiology, Seoul (Korea, Republic of); Kim, Hwa Jung; Kim, Sun-Ok [Asan Medical Center, University of Ulsan College of Medicine, Cancer Center, Department of Clinical Epidemiology and Biostatistics, Seoul (Korea, Republic of)

    2014-06-15

    To investigate the diagnostic performance of 15-min delayed contrast-enhanced computed tomography (15-DECT) compared with that of chemical shift magnetic resonance (CSMR) imaging in differentiating hyperattenuating adrenal masses and to perform subgroup analysis in underlying malignancy and non-malignancy. This study included 478 adrenal masses in 453 patients examined with 15-DECT and 235 masses in 217 patients examined with CSMR. Relative percentage washout (RPW) and absolute percentage washout (APW) on 15-DECT, and signal intensity index (SII) and adrenal-to-spleen ratio (ASR) on CSMR were measured. Sensitivity, specificity and accuracy of 15-DECT and CSMR were analysed for characterisation of adrenal adenoma. Subgroup analyses were performed in patients with and without underlying malignancy. Attenuation and size of the masses on unenhanced CT correlated with the risk of non-adenoma. RPW calculated from 15-DECT showed the highest diagnostic performance for characterising hyperattenuating adrenal masses regardless of underlying malignancy, and the sensitivity, specificity and accuracy were 91.7 %, 74.8 % and 88.1 %, respectively in all patients. The risk of non-adenoma increased approximately threefold as mass size increased 1 cm or as its attenuation value increased by 10 Hounsfield units. 15-DECT was more accurate than CSMR in characterising hyperattenuating adrenal masses regardless of underlying malignancy. (orig.)

  20. The calculation of the chemical exergies of coal-based fuels by using the higher heating values

    International Nuclear Information System (INIS)

    This paper demonstrates the application of exergy to gain a better understanding of coal properties, especially chemical exergy and specific chemical exergy. In this study, a BASIC computer program was used to calculation of the chemical exergies of the coal-based fuels. Calculations showed that the chemical composition of the coal influences strongly the values of the chemical exergy. The exergy value of a coal is closely related to the H:C and O:C ratios. High proportions of hydrogen and/or oxygen, compared to carbon, generally reduce the exergy value of the coal. High contents of the moisture and/or the ash cause to low values of the chemical exergy. The aim of this paper is to calculate the chemical exergy of coals by using equations given in the literature and to detect and to evaluate quantitatively the effect of irreversible phenomena increased the thermodynamic imperfection of the processes. In this paper, the calculated exergy values of the fuels will be useful for energy experts studied in the coal mining area and coal-fired powerplants

  1. Prediction of (195) Pt NMR chemical shifts of dissolution products of H2 [Pt(OH)6 ] in nitric acid solutions by DFT methods: how important are the counter-ion effects?

    Science.gov (United States)

    Tsipis, Athanassios C; Karapetsas, Ioannis N

    2016-08-01

    (195) Pt NMR chemical shifts of octahedral Pt(IV) complexes with general formula [Pt(NO3 )n (OH)6 - n ](2-) , [Pt(NO3 )n (OH2 )6 - n ](4 - n) (n = 1-6), and [Pt(NO3 )6 - n  - m (OH)m (OH2 )n ](-2 + n - m) formed by dissolution of platinic acid, H2 [Pt(OH)6 ], in aqueous nitric acid solutions are calculated employing density functional theory methods. Particularly, the gauge-including atomic orbitals (GIAO)-PBE0/segmented all-electron relativistically contracted-zeroth-order regular approximation (SARC-ZORA)(Pt) ∪ 6-31G(d,p)(E)/Polarizable Continuum Model computational protocol performs the best. Excellent second-order polynomial plots of δcalcd ((195) Pt) versus δexptl ((195) Pt) chemical shifts and δcalcd ((195) Pt) versus the natural atomic charge QPt are obtained. Despite of neglecting relativistic and spin orbit effects the good agreement of the calculated δ (195) Pt chemical shifts with experimental values is probably because of the fact that the contribution of relativistic and spin orbit effects to computed σ(iso) (195) Pt magnetic shielding of Pt(IV) coordination compounds is effectively cancelled in the computed δ (195) Pt chemical shifts, because the relativistic corrections are expected to be similar in the complexes and the proper reference standard used. To probe the counter-ion effects on the (195) Pt NMR chemical shifts of the anionic [Pt(NO3 )n (OH)6 - n ](2-) and cationic [Pt(NO3 )n (OH2 )6 - n ](4 - n) (n = 0-3) complexes we calculated the (195) Pt NMR chemical shifts of the neutral (PyH)2 [Pt(NO3 )n (OH)6 - n ] (n = 1-6; PyH = pyridinium cation, C5 H5 NH(+) ) and [Pt(NO3 )n (H2 O)6 - n ](NO3 )4 - n (n = 0-3) complexes. Counter-anion effects are very important for the accurate prediction of the (195) Pt NMR chemical shifts of the cationic [Pt(NO3 )n (OH2 )6 - n ](4 - n) complexes, while counter-cation effects are less important for the anionic [Pt(NO3 )n (OH)6

  2. The Effects of Consistent Chemical Kinetics Calculations on the Pressure-Temperature Profiles and Emission Spectra of Hot Jupiters

    CERN Document Server

    Drummond, Benjamin; Baraffe, Isabelle; Amundsen, David S; Mayne, Nathan J; Venot, Olivia; Goyal, Jayesh

    2016-01-01

    In this work we investigate the impact of calculating non-equilibrium chemical abundances consistently with the temperature structure for the atmospheres of highly-irradiated, close-in gas giant exoplanets. Chemical kinetics models have been widely used in the literature to investigate the chemical compositions of hot Jupiter atmospheres which are expected to be driven away from chemical equilibrium via processes such as vertical mixing and photochemistry. All of these models have so far used pressure--temperature (P-T) profiles as fixed model input. This results in a decoupling of the chemistry from the radiative and thermal properties of the atmosphere, despite the fact that in nature they are intricately linked. We use a one-dimensional radiative-convective equilibrium model, ATMO, which includes a sophisticated chemistry scheme to calculate P-T profiles which are fully consistent with non-equilibrium chemical abundances, including vertical mixing and photochemistry. Our primary conclusion is that, in case...

  3. Chemical shift as a probe of molecular interfaces: NMR studies of DNA binding by the three amino-terminal zinc finger domains from transcription factor IIIA

    Energy Technology Data Exchange (ETDEWEB)

    Foster, Mark P.; Wuttke, Deborah S.; Clemens, Karen R.; Jahnke, Wolfgang; Radhakrishnan, Ishwar; Tennant, Linda; Reymond, Martine; Chung, John; Wright, Peter E. [Scripps Research Institute, Department of Molecular Biology and Skaggs Institute for Chemical Biology (United States)

    1998-07-15

    We report the NMR resonance assignments for a macromolecular protein/DNA complex containing the three amino-terminal zinc fingers (92 amino acid residues) of Xenopus laevis TFIIIA (termed zf1-3) bound to the physiological DNA target (15 base pairs), and for the free DNA. Comparisons are made of the chemical shifts of protein backbone{sup 1} H{sup N}, {sup 15}N,{sup 13} C{sup {alpha}} and{sup 13} C{sup {beta}} and DNA base and sugar protons of the free and bound species. Chemical shift changes are analyzed in the context of the structures of the zf1-3/DNA complex to assess the utility of chemical shift change as a probe of molecular interfaces. Chemical shift perturbations that occur upon binding in the zf1-3/DNA complex do not correspond directly to the structural interface, but rather arise from a number of direct and indirect structural and dynamic effects.

  4. Probing the solvent shell with 195Pt chemical shifts: density functional theory molecular dynamics study of Pt(II) and Pt(IV) anionic complexes in aqueous solution.

    Science.gov (United States)

    Truflandier, Lionel A; Autschbach, Jochen

    2010-03-17

    Ab initio molecular dynamics (aiMD) simulations based on density functional theory (DFT) were performed on a set of five anionic platinum complexes in aqueous solution. (195)Pt nuclear magnetic shielding constants were computed with DFT as averages over the aiMD trajectories, using the two-component relativistic zeroth-order regular approximation (ZORA) in order to treat relativistic effects on the Pt shielding tensors. The chemical shifts obtained from the aiMD averages are in good agreement with experimental data. For Pt(II) and Pt(IV) halide complexes we found an intermediate solvent shell interacting with the complexes that causes pronounced solvent effects on the Pt chemical shifts. For these complexes, the magnitude of solvent effects on the Pt shielding constant can be correlated with the surface charge density. For square-planar Pt complexes the aiMD simulations also clearly demonstrate the influence of closely coordinated non-equatorial water molecules on the Pt chemical shift, relating the structure of the solution around the complex to the solvent effects on the metal NMR chemical shift. For the complex [Pt(CN)(4)](2-), the solvent effects on the Pt shielding constant are surprisingly small. PMID:20166712

  5. Experimental and Quantum Chemical Calculations of Imidazolium Appended Naphthalene Hybrid in Different Biomimicking Aqueous Interfaces.

    Science.gov (United States)

    Yenupuri, Tej Varma; Mydlova, Lucia; Agarwal, Devesh S; Sharma, Ritika; Sakhuja, Rajeev; Makowska-Janusik, Malgorzata; Pant, Debi D

    2016-08-25

    The effect of solvent polarity and micellar headgroup on a newly designed imidazolium based ionic liquid (IL) conjugated with naphthalene, 1,2-dimethyl-3-((6-(octyloxy)naphthalen-2-yl)methyl)-1H-imidazol-3-ium chloride (IN-O8-Cl), was studied using steady state and time-resolved fluorescence techniques. We observed that the dipole moment in the excited state is remarkably higher than the ground state. The effect of micellar surface charge on the photophysics of IN-O8-Cl in aqueous phase at room temperature was investigated. Formation of premicellar aggregates in sodium dodecylsulfate (SDS) was perceived; further the microenvironment of IN-O8-Cl was examined using steady-state fluorescence spectroscopy. Micropolarity of the micellar environment of SDS was found to be lower than that of cetyltrimethylammonium bromide (CTAB) and triton X-100 (TX100) following the order SDS < TX-100 < CTAB. The binding constant (Kb) and edge excitation red shift (EERS) from the emission maximum suggest that the probe binds strongly to the micelles. Multiexponential behavior was observed in time-resolved fluorescence lifetime studies in all micellar environments. We have observed an increase in rotational correlation time as we move from pure aqueous phase to solution containing surfactants of different head charge. Varieties of spectral parameters were used to justify the region in which the probe is present. The experimentally obtained dipole moment data were justified and explained by the DFT calculations of the electronic properties of IN-O8-Cl molecules in gas phase and in selected solvents. PMID:27486828

  6. The Molecular Structure of Phenetole Studied by Microwave Spectroscopy and Quantum Chemical Calculations

    Science.gov (United States)

    Ferres, Lynn; Stahl, Wolfgang; Nguyen, Ha Vinh Lam

    2016-06-01

    A pulsed molecular beam Fourier transform microwave spectrometer operating in the frequency range 2 - 26.5 GHz was used to measure the spectrum of phenetole (ethyl phenyl ether or ethoxybenzene, C6H5OC2H5). The conformational landscape is completely determined by the orientations of the phenyl ring and the ethyl group. A two-dimensional potential energy surface was calculated at the MP2/6-311++G(d,p) level of theory. Two conformers were found: The trans conformer has a Cs symmetry, and the gauche conformer has the ethyl group tilted out of the phenyl plane by about 70°. Totally 186 rotational transitions were assigned to the more stable planar trans conformer, and fitted using a semi-rigid rotor model to measurement accuracy of 2 kHz. Highly accurate rotational and centrifugal distortion constants were determined. Several method and basis set combinations were applied to check for convergence and to compare with the experimentally deduced molecular parameters. The inertial defect of the observed conformer Δc = (Ic - Ia - Ib) = -6.718 uÅ2 confirms that the heavy atom skeleton is planar with two pairs of hydrogen atoms out of plane. All lines in the spectrum could be assigned to the trans conformer, which confirms that the gauche conformer cannot be observed under our measurement conditions. In agreement with the rather high torsional barrier of the methyl group (V3 = 1168 wn) calculated by quantum chemical methods, all assigned lines appeared sharp and no signs of splittings were observed for the methyl internal rotation.

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Kohl, Chad A. [Mayo Clinic, Department of Radiology, Phoenix, AZ (United States); Radiology Ltd., Tucson, AZ (United States); Chivers, F.S.; Lorans, Roxanne; Roberts, Catherine C.; Kransdorf, Mark J. [Mayo Clinic, Department of Radiology, Phoenix, AZ (United States)

    2014-08-15

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

  9. Combining ambiguous chemical shift mapping with structure-based backbone and NOE assignment from 15N-NOESY

    KAUST Repository

    Jang, Richard

    2011-01-01

    Chemical shift mapping is an important technique in NMRbased 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. However, automated methods are necessary for high-throughput drug screening. 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-toone mapping. On the three proteins, it achieves an average accuracy of 94% or better. Copyright © 2011 ACM.

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

    Indian Academy of Sciences (India)

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

    2014-05-01

    Uranium L3 X-ray absorption edge was measured in various compounds containing uranium in U4+, U5+ and U6+ oxidation states. The measurements have been carried out at the Energy Dispersive EXAFS beamline (BL-08) at INDUS-2 synchrotron radiation source at RRCAT, Indore. Energy shifts of ∼ 2–3 eV were observed for U L3 edge in the U-compounds compared to their value in elemental U. The different chemical shifts observed for the compounds having the same oxidation state of the cation but different anions or ligands show the effect of different chemical environments surrounding the cations in determining their X-ray absorption edges in the above compounds. The above chemical effect has been quantitatively described by determining the effective charges on U cation in the above compounds.

  11. CEQCSY: a new code for chemical equilibrium calculation in multiphased systems

    International Nuclear Information System (INIS)

    As part of the CEC Chemval/mirage project, a method is presented for calculating the thermodynamic equilibrium state of a multiphase system, by minimizing its Gibbs free energy constrained by mass balances. Compared to the other algorithms available in the literature, the method has three main characteristics: - the sets of equations corresponding to the conditions of homogeneous and heterogeneous equilibria are simultaneously solved, - a mathematical criterion for bringing a new multicomponent phase in the system is rigorously demontrated. - It enables a detailed representation of the multisite solid solutions with constraints called site closure relation. The code CEQCSY (Chemical Equilibrium in Complex SYstem) uses this formalism, and works with the thermodynamic data base from the EQ3/6 code. This choice makes easier several compared tests with EQ6: quartz dissolution in water, water-atmospheric air equilibrium, theoretical re-equilibrium of seawater, hydrothermal alteration of granite including solid solutions. The test results demonstrate the high efficiency and velocity of the code CEQCSY, when working on equilibrium state of multiphase systems. This high velocity was the aim of this work, in order to couple with thermic, hydrodynamic or mechanic codes

  12. Antioxidative effect of schisanhenol on human low density lipoprotein and its quantum chemical calculation

    Institute of Scientific and Technical Information of China (English)

    Ling-hong YU; Geng-tao LIU; You-min SUN; Hong-yu ZHANG

    2004-01-01

    AIM: To investigate the effect of schisanhenol (Sal) on copper ion-induced oxidative modulation of human low density lipoprotein (LDL). METHODS: The antioxidative activity of eight schisandrins (DCL) on microsome lipid peroxidation induced by Vit C/NADPH system was first observed, and then, the effect of Sal on Cu2+-induced human LDL oxidation was studied. The generation of malondialdehyde (MDA), lipofuscin, reactive oxygen species (ROS), consumption of α-tocopherol as well as electrophoretic mobility of LDL were determined as criteria of LDL oxidation. Finally, the quantum chemical method was used to calculate the theoretical parameters of eight DCL for elucidating the difference of their antioxidant ability. RESULTS: Sal was shown to be the most active one among eight schizandrins in inhibiting microsome lipid oxidation induced by Vit C/NADPH. Sal 100, 50, and 10 μrnol/L inhibited production of MDA, lipofuscin and ROS as well as the consumption of α-tocopherol in Cu2+-induced oxidation of human LDL in a dose-dependent manner. Sal also reduced electrophoretic mobility of the oxidized human LDL. Further study of quantum chemistry found that Sal was the strongest one among eight DCL to scavenge O-2, R·, RO·, and ROO· radicals. CONCLUSION: Sal has antioxidative effect on human LDL oxidation.The mechanism of Sal against LDL oxidation may be through scavenging free radicals.

  13. The (impossible?) formation of acetaldehyde on the grain surfaces: insights from quantum chemical calculations

    CERN Document Server

    Enrique-Romero, Joan; Ceccarelli, Cecilia; Balucani, Nadia

    2016-01-01

    Complex Organic Molecules (COMs) have been detected in the interstellar medium (ISM). However, it is not clear whether their synthesis occurs on the icy surfaces of interstellar grains or via a series of gas-phase reactions. As a test case of the COMs synthesis in the ISM, we present new quantum chemical calculations on the formation of acetaldehyde (CH3CHO) from the coupling of the HCO and CH3 radicals, both in gas phase and on water ice surfaces. The binding energies of HCO and CH3 on the amorphous water ice were also computed (2333 and 734 K, respectively). Results indicate that, in gas phase, the products could be either CH3CHO, CH4 + CO, or CH3OCH, depending on the relative orientation of the two radicals. However, on the amorphous water ice, only the CH4 + CO product is possible due to the geometrical constraints imposed by the water ice surface. Therefore, acetaldehyde cannot be synthesized by the CH3 + HCO coupling on the icy grains. We discuss the implications of these results and other cases, such a...

  14. Octafluorodirhenate(III) Revisited: Solid-State Preparation, Characterization, and Multiconfigurational Quantum Chemical Calculations.

    Science.gov (United States)

    Mariappan Balasekaran, Samundeeswari; Todorova, Tanya K; Pham, Chien Thang; Hartmann, Thomas; Abram, Ulrich; Sattelberger, Alfred P; Poineau, Frederic

    2016-06-01

    A simple method for the high-yield preparation of (NH4)2[Re2F8]·2H2O has been developed that involves the reaction of (n-Bu4N)2[Re2Cl8] with molten ammonium bifluoride (NH4HF2). Using this method, the new salt [NH4]2[Re2F8]·2H2O was prepared in ∼90% yield. The product was characterized in solution by ultraviolet-visible light (UV-vis) and (19)F nuclear magnetic resonance ((19)F NMR) spectroscopies and in the solid-state by elemental analysis, powder X-ray diffraction (XRD), and infrared (IR) spectroscopy. Multiconfigurational CASSCF/CASPT2 quantum chemical calculations were performed to investigate the molecular and electronic structure, as well as the electronic absorption spectrum of the [Re2F8](2-) anion. The metal-metal bonding in the Re2(6+) unit was quantified in terms of effective bond order (EBO) and compared to that of its [Re2Cl8](2-) and [Re2Br8](2-) analogues.

  15. Thermodynamic Calculation in Elimination of Water Pollutants at Hydro-geo-chemical Barriers

    Institute of Scientific and Technical Information of China (English)

    VELIKOV, B.; VELIKOV, B; PANAYOTOVA, M.; PANAYOTOVA, M

    2001-01-01

    Thermodynamic saturation coefficients (Ks) and transformation indices (It) can be used to evaluate the possibility of forming hydro-geo-chemical precipitation barriers and assess the solid phase (rodk) stability in aquifers. Calculations are made on the basis of data on water pH, Eh, conductivity (X) and some relevant ion concentrations. The dependencies of Ks and It on water pH and Eh values can be expressed graphically to estimate the barriers parameters. Barrier generation leads to a decrease in concentrations of pollutants due mainly to precipitation, co-preciptitation and/or sorption processes. Using the diagram Ks, It-f (pH, Eh), supplemented with representative data on concentrations of pollutants before and after the barrier, the elimination and migration of pollutants can be roughly evaluated (predicted) only on the basis of determining pH and Eh values of water and concentrations of ions participating in the barrier formation. The proposed method is applied to assess the migration and elimination of pollutants (U, 226Ra, β-emitters, SO42-) in Bulgarian uranium mine surroundings.

  16. A model for reliability analysis and calculation applied in an example from chemical industry

    Directory of Open Access Journals (Sweden)

    Pejović Branko B.

    2010-01-01

    Full Text Available The subject of the paper is reliability design in polymerization processes that occur in reactors of a chemical industry. The designed model is used to determine the characteristics and indicators of reliability, which enabled the determination of basic factors that result in a poor development of a process. This would reduce the anticipated losses through the ability to control them, as well as enabling the improvement of the quality of production, which is the major goal of the paper. The reliability analysis and calculation uses the deductive method based on designing of a scheme for fault tree analysis of a system based on inductive conclusions. It involves the use standard logical symbols and rules of Boolean algebra and mathematical logic. The paper eventually gives the results of the work in the form of quantitative and qualitative reliability analysis of the observed process, which served to obtain complete information on the probability of top event in the process, as well as objective decision making and alternative solutions.

  17. Environmental capacity of chemical oxygen demand in the Bohai Sea: modeling and calculation

    Institute of Scientific and Technical Information of China (English)

    ZHAO Xixi; WANG Xiulin; SHI Xiaoyong; LI Keqiang; DING Dongsheng

    2011-01-01

    A three-dimensional advection-diffusion model coupled with the degradation process is established for describing the transport of chemical oxygen demand (COD). Comparison of the simulated distribution of COD at the surface in the Bohai Sea in August, 2001 with field observations, shows that the model simulates the dataset reasonably well. The Laizhou Bay, Bohai Bay, and Liaodong Bay were contaminated heavily near shore. Based on the optimal discharge flux method, the Environmental Capacity (EC) and allocated capacities of COD in the Bohai Sea are calculated. For seawater of Grades I to IV of the Chinese National Standard, the ECs of COD in the Bohai Sea were 77×104t/a, 116×l04t/a, 154×l04t/a and 193×104t/a, respectively. The Huanghe (Yellow) River pollutant discharge accounted for the largest percentage of COD at 14.3%, followed by that of from the Liugu River (11.5%), and other nine local rivers below 10%. The COD level in 2005 was worse than that of Grade II seawater and was beyond the environmental capacity. In average, 35% COD reduction is called to meet the standard of Grade I seawater.

  18. The (impossible?) formation of acetaldehyde on the grain surfaces: insights from quantum chemical calculations

    Science.gov (United States)

    Enrique-Romero, J.; Rimola, A.; Ceccarelli, C.; Balucani, N.

    2016-06-01

    Complex Organic Molecules (COMs) have been detected in the interstellar medium (ISM). However, it is not clear whether their synthesis occurs on the icy surfaces of interstellar grains or via a series of gas-phase reactions. As a test case of the COMs synthesis in the ISM, we present new quantum chemical calculations on the formation of acetaldehyde (CH3CHO) from the coupling of the HCO and CH3 radicals, both in gas phase and on water ice surfaces. The binding energies of HCO and CH3 on the amorphous water ice were also computed (2333 and 734 K, respectively). Results indicate that, in gas phase, the products could be either CH3CHO, CH4 + CO, or CH3OCH, depending on the relative orientation of the two radicals. However, on the amorphous water ice, only the CH4 + CO product is possible due to the geometrical constraints imposed by the water ice surface. Therefore, acetaldehyde cannot be synthesized by the CH3 + HCO coupling on the icy grains. We discuss the implications of these results and other cases, such as ethylene glycol and dimethyl ether, in which similar situations can occur, suggesting that formation of these molecules on the grain surfaces might be unlikely.

  19. Chemical-state analysis of organic semiconductors using soft X-ray absorption spectroscopy combined with first-principles calculation.

    Science.gov (United States)

    Natsume, Yutaka; Kohno, Teiichiro; Minakata, Takashi; Konishi, Tokuzo; Gullikson, Eric M; Muramatsu, Yasuji

    2012-02-16

    The chemical states of organic semiconductors were investigated by total-electron-yield soft X-ray absorption spectroscopy (TEY-XAS) and first-principles calculations. The organic semiconductors, pentacene (C(22)H(14)) and pentacenequinone (C(22)H(12)O(2)), were subjected to TEY-XAS and the experimental spectra obtained were compared with the 1s core-level excited spectra of C and O atoms, calculated by a first-principles planewave pseudopotential method. Excellent agreement between the measured and the calculated spectra were obtained for both materials. Using this methodology, we examined the chemical states of the aged pentacene, and confirmed that both C-OH and C═O chemical bonds are generated by exposure to air. This result implies that not only oxygen but also humidity causes pentacene oxidation.

  20. Multilayer MoS2 prepared by one-time and repeated chemical vapor depositions: anomalous Raman shifts and transistors with high ON/OFF ratio

    Science.gov (United States)

    Wu, Chong-Rong; Chang, Xiang-Rui; Chang, Shu-Wei; Chang, Chung-En; Wu, Chao-Hsin; Lin, Shih-Yen

    2015-11-01

    We show that multilayer molybdenum disulfide (MoS2) grown with the chemical vapor deposition (CVD) may exhibit quite distinct behaviors of Raman shifts from those of exfoliated ones. The anomalous Raman shifts depend on CVD growth modes and are attributed to the modified dielectric screening and interlayer coupling of MoS2 in various growth conditions. With repeated CVD growths, we demonstrated the precise control over the layer number of MoS2. A decently large drain current, high ON/OFF ratio of 105, and enhanced field-effect mobility can be achieved in transistors fabricated on the six-layer MoS2.

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

    Science.gov (United States)

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

    2016-01-01

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

  2. Octafluorodirhenate(III) Revisited: Solid-State Preparation, Characterization, and Multiconfigurational Quantum Chemical Calculations

    Energy Technology Data Exchange (ETDEWEB)

    Mariappan Balasekaran, Samundeeswari; Todorova, Tanya K.; Pham, Chien Thang; Hartmann, Thomas; Abram, Ulrich; Sattelberger, Alfred P.; Poineau, Frederic

    2016-06-06

    A simple method for the high-yield preparation of (NH4)2[Re2F8]· 2H2O has been developed that involves the reaction of (n-Bu4N)2[Re2Cl8] with molten ammonium bifluoride (NH4HF2). Using this method, the new salt [NH4]2[Re2F8]·2H2O was prepared in ~90% yield. The product was characterized in solution by ultraviolet-visible light (UV-vis) and 19F nuclear magnetic resonance (19F NMR) spectroscopies and in the solid-state by elemental analysis, powder X-ray diffraction (XRD), and infrared (IR) spectroscopy. Multiconfigurational CASSCF/CASPT2 quantum chemical calculations were performed to investigate the molecular and electronic structure, as well as the electronic absorption spectrum of the [Re2F8] 2- anion. The metal-metal bonding in the Re2 6+ unit was quantified in terms of effective bond order (EBO) and compared to that of its [Re2Cl8] 2- and [Re2Br8] 2- analogues.

  3. Calculation of Equation of State of QCD at Finite Chemical Potential and Temperature

    Institute of Scientific and Technical Information of China (English)

    QIAO Qing-Peng; ZONG Hong-Shi; TANG Jian; HOU Feng-Yao; LI Xue-Qian; SUN Wei-Min; L(U) Xiao-Fu

    2008-01-01

    In this paper, using path integral techniques we derive a model-independent formula for the pressure density (μ, T) (or equivalently the partition function) of Quantum Chromodynamics (QCD), which gives the equation of state (EOS) of QCD at finite chemical potential and temperature. In this formula the pressure density (μ, T) consists of two terms: the first term (μ,T) T=0) is a #-independent (but T-dependent) constant; the second term is totally determined by G[μ, T] (p ωn) (the dressed quark propagator at finite μ and finite T), which contains all the nontrivial μ-dependence. Then, in the framework of the rainbow-ladder approximation of the Dyson-Schwinger (DS) approach and under the approximation of neglecting the μ-dependence of the dressed gluon propagator, we show that G[μ, T] (p, ωn) can be obtained from G[T] (p, ωn) (the dressed quark propagator at μ = 0) by the substitution ωn →ωn + iμ. This result facilitates numerical calculations considerably. By this result, once G[T](p, ωn) is known, one can determine the EOS of QCD under the above approximations (up to the additive term (μ, T)[T=0). Finally, a comparison of the present EOS of QCD and the EOS obtained in the previous literatures in the framework of the rainbow-ladder approximation of the DS approach is given. It is found that the EOS given in the previous literatures does not satisfy the thermodynamic relation p(μ, T) = T.

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

    Energy Technology Data Exchange (ETDEWEB)

    Joseph, D., E-mail: djoseph@barc.gov.in [Nuclear Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Basu, S.; Jha, S.N.; Bhattacharyya, D. [Applied Spectroscopy Division, Bhabha Atomic Research Centre, Mumbai 400085 (India)

    2012-03-01

    Cu K X-ray absorption edges were measured in compounds such as CuO, Cu(CH{sub 3}CO{sub 2}){sub 2}, Cu(CO{sub 3}){sub 2}, and CuSO{sub 4} where Cu is present in oxidation state of 2+, using the energy dispersive EXAFS beamline at INDUS-2 Synchrotron radiation source at RRCAT, Indore. Energy shifts of {approx}4-7 eV were observed for Cu K X-ray absorption edge in the above compounds compared to its value in elemental copper. The difference in the Cu K edge energy shifts in the different compounds having same oxidation state of Cu shows the effect of different chemical environments surrounding the cation in the above compounds. The above chemical effect has been quantitatively described by determining the effective charges on Cu cations in the above compounds.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-12-15

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

  6. Deciphering Noncovalent Interactions Accompanying 7,7,8,8-Tetracyanoquinodimethane Encapsulation within Biphene[n]arenes: Nucleus-Independent Chemical Shifts Approach.

    Science.gov (United States)

    Lande, Dipali N; Rao, Soniya S; Gejji, Shridhar P

    2016-07-18

    Binding of novel biphene[n]arene hosts to antiaromatic 7,7,8,8-tetracyanoquinodimethane (TCNQ) are investigated by DFT. Biphene[4]arene favors the inclusion complex through noncovalent interactions, such as hydrogen bonding, π-π stacking, C-H⋅⋅⋅π, and C-H⋅⋅⋅H-C dihydrogen bonding. Donor-acceptor complexation renders aromatic character to the guest through charge transfer. The formation of TCNQ anionic radicals through supramolecular π stacking significantly influences its chemical and photophysical behavior. Electron density reorganization consequent to encapsulation of TCNQ reflects in the shift of characteristic vibrations in the IR spectra. The accompanying aromaticities arising from the induced ring currents are analyzed by employing nucleus-independent chemical shifts based profiles. PMID:27028656

  7. Quantum-chemical calculations and electron diffraction study of the equilibrium molecular structure of vitamin K3

    Science.gov (United States)

    Khaikin, L. S.; Tikhonov, D. S.; Grikina, O. E.; Rykov, A. N.; Stepanov, N. F.

    2014-05-01

    The equilibrium molecular structure of 2-methyl-1,4-naphthoquinone (vitamin K3) having C s symmetry is experimentally characterized for the first time by means of gas-phase electron diffraction using quantum-chemical calculations and data on the vibrational spectra of related compounds.

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

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, J.S.; Vigneron, D.B.; Murphy-Boesch, J.; Nelson, S.J.; Kessler, H.B.; Coia, L.; Curran, W.; Brown, T.R. (Fox Chase Cancer Center, Philadelphia, PA (United States))

    1991-08-01

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

  9. Measurement of sample temperatures under magic-angle spinning from the chemical shift and spin-lattice relaxation rate of 79Br in KBr powder

    OpenAIRE

    Thurber, Kent R.; Tycko, Robert

    2008-01-01

    Accurate determination of sample temperatures in solid state nuclear magnetic resonance (NMR) with magic-angle spinning (MAS) can be problematic, particularly because frictional heating and heating by radio-frequency irradiation can make the internal sample temperature significantly different from the temperature outside the MAS rotor. This paper demonstrates the use of 79Br chemical shifts and spin-lattice relaxation rates in KBr powder as temperature-dependent parameters for the determinati...

  10. Orientational constraints as three-dimensional structural constraints from chemical shift anisotropy: the polypeptide backbone of gramicidin A in a lipid bilayer.

    OpenAIRE

    Mai, W.; Hu, W; Wang, C; Cross, T A

    1993-01-01

    Chemical shifts observed from samples that are uniformly aligned with respect to the magnetic field can be used as very high-resolution structural constraints. This constraint takes the form of an orientational constraint rather than the more familiar distance constraint. The accuracy of these constraints is dependent upon the quality of the tensor characterization. Both tensor element magnitudes and tensor orientations with respect to the molecular frame need to be considered. Here these con...

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

    Science.gov (United States)

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

    2015-07-01

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

  12. The Navy/NASA Engine Program (NNEP89): Interfacing the program for the calculation of complex Chemical Equilibrium Compositions (CEC)

    Science.gov (United States)

    Gordon, Sanford

    1991-01-01

    The NNEP is a general computer program for calculating aircraft engine performance. NNEP has been used extensively to calculate the design and off-design (matched) performance of a broad range of turbine engines, ranging from subsonic turboprops to variable cycle engines for supersonic transports. Recently, however, there has been increased interest in applications for which NNEP is not capable of simulating, such as the use of alternate fuels including cryogenic fuels and the inclusion of chemical dissociation effects at high temperatures. To overcome these limitations, NNEP was extended by including a general chemical equilibrium method. This permits consideration of any propellant system and the calculation of performance with dissociation effects. The new extended program is referred to as NNEP89.

  13. Mechanistic insights into enzymatic and homogeneous transition metal catalysis from quantum-chemical calculations

    OpenAIRE

    Crawford, Luke

    2015-01-01

    Catalysis is a key area of chemistry. Through catalysis it is possible to achieve better synthetic routes, exploit molecules normally considered to be inactive and also attain novel chemical transformations. The development of new catalysts is crucial to furthering chemistry as a field. Computational chemistry, arising from applying the equations of quantum and classical mechanics to solving chemical problems, offers an essential route to investigating the underlying atomistic detail of ca...

  14. Characteristics of the complexing of chitosan with sodium dodecyl sulfate, according to IR spectroscopy data and quantum-chemical calculations

    Science.gov (United States)

    Shilova, S. V.; Romanova, K. A.; Galyametdinov, Yu. G.; Tret'yakova, A. Ya.; Barabanov, V. P.

    2016-06-01

    The complexing of protonated chitosan with dodecyl sulfate ions in water solutions is studied using IR spectroscopy data and quantum-chemical calculations. It is established that the electrostatic interaction between the protonated amino groups of chitosan and dodecyl sulfate ions is apparent in the IR spectrum as a band at 833 cm-1. The need to consider the effect the solvent has on the formation of hydrogen-bound ion pairs [CTS+ ṡ C12H25O 3 - ] is shown via a quantum-chemical simulation of the equilibrium geometry and the energy characteristics of complexing and hydration.

  15. Structural and stability investigation of the anticancer drug Cyclophosphamide via quantum chemical calculations :A nanotube drug delivery

    Directory of Open Access Journals (Sweden)

    Z. Felegari

    2014-12-01

    Full Text Available Cyclophosphamide is a medicine used to interfere with the growth and spread of tumor cells and treat cancers and autoimmune disorders.This work reports the study of anticancer drugs with density functional theory (DFT and electronic structures.Its structure was optimized with B3LYP/6-311G* level in the gas phase and different solvents (SCRF calculation. NBO analysis,NMR parameter,thermodynamic properties,HOMO and LUMO,HOMO-LUMO band gap, and the electronic chemical potential (µ were calculated. The results indicated that the Cyclophosphamide in water solvent is more stable than the gas phase orother solvents.

  16. Quantum chemical calculation of the equilibrium structures of small metal atom clusters

    Science.gov (United States)

    Kahn, L. R.

    1982-01-01

    Metal atom clusters are studied based on the application of ab initio quantum mechanical approaches. Because these large 'molecular' systems pose special practical computational problems in the application of the quantum mechanical methods, there is a special need to find simplifying techniques that do not compromise the reliability of the calculations. Research is therefore directed towards various aspects of the implementation of the effective core potential technique for the removal of the metal atom core electrons from the calculations.

  17. Evaluation of photodissociation coefficient calculations for use in atmospheric chemical models. Doctoral thesis

    Energy Technology Data Exchange (ETDEWEB)

    Petropaviovskikh, I.

    1995-07-01

    The chemistry of the atmosphere is strongly influenced by solar radiation, In addition to the obvious heating effect, solar radiation at visible and ultra-violet (UV) wavelengths drives atmospheric chemistry by photodissociating relatively stable molecules into usually highly reactive fragments. Photodissociation coefficients (J-values) describe quantitatively the frequency of atmospheric photolysis reactions, and therefore it is important to calculate them accurately. The author has examined a number of outstanding problems in the calculation of J-values.

  18. Transport-induced shifts in condensate dew-point and composition in multicomponent systems with chemical reaction

    Science.gov (United States)

    Rosner, D. E.; Nagarajan, R.

    1985-01-01

    Partial heterogeneous condensation phenomena in multicomponent reacting systems are analyzed taking into consideration the chemical element transport phenomena. It is demonstrated that the dew-point surface temperature in chemically reactive systems is not a purely thermodynamic quantity, but is influenced by the multicomponent diffusion and Soret-mass diffusion phenomena. Several distinct dew-points are shown to exist in such systems and, as a result of transport constraints, the 'sharp' locus between two chemically distinct condensates is systematically moved to a difference mainstream composition.

  19. Rule of additivity as forecasting numerical values energy of occupied molecular orbital (homo with quantum chemical calculations

    Directory of Open Access Journals (Sweden)

    Andrei Sikachina

    2015-11-01

    Full Text Available In the published article is considering extending the application of the rule of additivity, namely for the theoretical calculation of the energy value of the highest occupied molecular orbital. The author received and verified data for the reference-type basic functional groups of organic compounds on the example of organic phosphine derivatives (with the help of quantum chemical PCGAMESS2009 package for compounds having a tendency to be paired and non-binding.

  20. Chemical reaction calculation simulation of redox behavior of metal ions and the like in the nitric acid solution

    International Nuclear Information System (INIS)

    It is known that corrosion rate of stainless steel in nitric acid solution is affected by the valence change of oxidizing metallic ions. In this study, we conducted redox reaction analyses using chemical reaction calculation model to clarify the mechanism of valence change. We obtained that the oxidization of metallic ions in the solution is not only caused by nitric acid but also nitrogen oxides. (author)

  1. Structure analysis and spectroscopic characterization of 2-Fluoro-3-Methylpyridine-5-Boronic Acid with experimental (FT-IR, Raman, NMR and XRD) techniques and quantum chemical calculations

    Science.gov (United States)

    Alver, Özgür; Dikmen, Gökhan

    2016-03-01

    Possible stable conformers, geometrical molecular structures, vibrational properties as well as band assignments, nuclear magnetic shielding tensors of 2-Fluoro-3-Methylpyridine-5-Boronic Acid (2F3MP5BA) were studied experimentally and theoretically using FT-IR, Raman, (CP/MAS) NMR and XRD spectroscopic methods. FT-IR and Raman spectra were evaluated in the region of 3500-400 cm-1, and 3200-400 cm-1, respectively. The optimized geometric structures, vibrational wavenumbers and nuclear magnetic shielding tensors were examined using Becke-3-Lee-Yang-Parr (B3LYP) hybrid density functional theory method with 6-311++G(d, p) basis set. 1H, 13C NMR chemical shifts were calculated using the gauge invariant atomic orbital (GIAO) method. 1H, 13C, APT and HETCOR NMR experiments of title molecule were carried out in DMSO solution. 13C CP/MAS NMR measurement was done with 4 mm zirconium rotor and glycine was used as an external standard. Single crystal of 2F3MP5BA was also prepared for XRD measurements. Assignments of vibrational wavenumbers were also strengthened by calculating the total energy distribution (TED) values using scaled quantum mechanical (SQM) method.

  2. Spectroscopic [FT-IR and FT-Raman] and molecular modeling (MM) study of benzene sulfonamide molecule using quantum chemical calculations

    Science.gov (United States)

    Vinod, K. S.; Periandy, S.; Govindarajan, M.

    2016-07-01

    The spectroscopic and molecular modeling (MM) study includes, FT-IR, FT-Raman and 13C NMR and 1H NMR spectra of the Benzene sulfonamide were recorded for the analysis. The observed experimental and theoretical frequencies (IR and Raman) were assigned according to their distinctive region. The present study of this title molecule have been carried out by hybrid computational calculations of HF and DFT (B3LYP) methods with 6-311+G(d,p) and 6-311++G(d,p) basis sets and the corresponding results are tabulated. The structural modifications of the compound due to the substitutions of NH2 and SO2 were investigated. The minimum energy conformers of the compound were studied using conformational analysis. The alternations of the vibrational pattern of the base structure related to the substitutions were analyzed. The thermodynamic parameters (such as zero-point vibrational energy, thermal energy, specific heat capacity, rotational constants, entropy, and dipole moment) of Benzene sulfonamide have been calculated. The donor acceptor interactions of the compound and the corresponding UV transitions are found out using NBO analysis. The NMR spectra were simulated by using the gauge independent atomic orbital (GIAO) method with B3LYP methods and the 6-311++G(d,p) basis set and their spectra were simulated and the chemical shifts related to TMS were compared. A quantum computational study on the electronic and optical properties absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies, were performed by HF and DFT methods. The energy gap of the present compound was calculated related to HOMO and LUMO energies which confirm the occurring of charge transformation between the base and ligand group. Besides frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) was performed. The thermodynamic properties (heat capacity, entropy, and enthalpy) of the title compound at different temperatures were calculated in gas phase and

  3. Calculation of Propulsive Nozzle Flowfields in Multidiffusing Chemically Reacting Environments. Ph.D. Thesis - Purdue Univ.

    Science.gov (United States)

    Kacynski, Kenneth John

    1994-01-01

    An advanced engineering model has been developed to aid in the analysis and design of hydrogen/oxygen chemical rocket engines. The complete multispecies, chemically reacting and multidiffusing Navier-Stokes equations are modelled, including the Soret thermal diffusion and the Dufour energy transfer terms. In addition to the spectrum of multispecies aspects developed, the model developed in this study is also conservative in axisymmetric flow for both inviscid and viscous flow environments and the boundary conditions employ a viscous, chemically reacting, reference plane characteristics method. Demonstration cases are presented for a 1030:1 area ratio nozzle, a 25 lbf film cooled nozzle, and a transpiration cooled plug and spool rocket engine. The results indicate that the thrust coefficient predictions of the 1030:1 and the 25 lbf film cooled nozzle are within 0.2 to 0.5 percent, respectively, of experimental measurements when all of the chemical reaction and diffusion terms are considered. Further, the model's predictions agree very well with the heat transfer measurements made in all of the nozzle test cases. The Soret thermal diffusion term is demonstrated to have a significant effect on the predicted mass fraction of hydrogen along the wall of the nozzle in both the laminar flow 1030:1 nozzle and the turbulent flow plug and spool nozzle analysis cases performed. Further, the Soret term was shown to represent an important fraction of the diffusion fluxes occurring in a transpiration cooled rocket engine.

  4. Double-echo gradient chemical shift MR imaging fails to differentiate minimal fat renal angiomyolipomas from other homogeneous solid renal tumors

    Energy Technology Data Exchange (ETDEWEB)

    Ferré, R., E-mail: kn638@yahoo.fr [Department of Radiology, Necker Hospital, 149 rue de Sèvres, 75730 Paris (France); Cornelis, F. [Department of Radiology, Pellegrin Hospital, Place Amélie Raba Léon, 33076 Bordeaux (France); Verkarre, V. [Department of Pathology, Necker Hospital, 149 rue de Sèvres, 75730 Paris (France); Eiss, D.; Correas, J.M. [Department of Radiology, Necker Hospital, 149 rue de Sèvres, 75730 Paris (France); Grenier, N. [Department of Radiology, Pellegrin Hospital, Place Amélie Raba Léon, 33076 Bordeaux (France); Hélénon, O. [Department of Radiology, Necker Hospital, 149 rue de Sèvres, 75730 Paris (France)

    2015-03-15

    Highlights: •Diagnosis of AMLs with minimal fat (mfAMLs) is still challenging with MRI. •Drop of signal on opposed-phase MR imaging is not specific of mfAMLs. •Double-echo gradient-echo sequences cannot accurately differentiate renal mfAMLs from other renal tumors. -- Abstract: Objectives: The purpose of this retrospective study was to evaluate the diagnostic performance of double-echo gradient chemical shift (GRE) magnetic resonance (MR) imaging for the differentiation of angiomyolipomas with minimal fat (mfAML) from other homogeneous solid renal tumors. Methods: Between 2005 and 2010 in two institutions, all histologically proven homogenous solid renal tumors imaged with computed tomography and MR imaging, including GRE sequences, have been retrospectively selected. A total of 118 patients (mean age: 61 years; range: 20–87) with 119 tumors were included. Two readers measured independently the signal intensity (SI) on GRE images and calculated SI index (SII) and tumor-to-spleen ratio (TSR) on in-phase and opposed-phase images. Intra- and interreader agreement was obtained. Cut-off values were derived from the receiver operating characteristic (ROC) curve analysis. Results: Twelve mfAMLs in 11 patients were identified (mean size: 2.8 cm; range: 1.2–3.5), and 107 non-AML tumors (3.2 cm; 1–7.8) in 107 patients. The intraobserver reproducibility of SII and TSR was excellent with an intraclass correlation coefficient equal to 0.99 [0.98–0.99]. The coefficient of correlation between the readers was 0.99. The mean values of TSR for mfAMLs and non-mfAMLs were −7.0 ± 22.8 versus −8.2 ± 21.2 for reader 1 and −6.7 ± 22.8 versus −8.4 ± 20.9 for reader 2 respectively. No significant difference was noticed between the two groups for SII (p = 0.98) and TSR (p = 0.86). Only 1 out of 12 mfAMLs and 11 of 107 non-AML tumors presented with a TSR inferior to −30% (p = 0.83). Conclusion: In a routine practice, GRE sequences cannot be a confident tool to

  5. Chemical profiling and classification of illicit heroin by principal component analysis, calculation of inter sample correlation and artificial neural networks.

    Science.gov (United States)

    Esseiva, Pierre; Anglada, Frederic; Dujourdy, Laurence; Taroni, Franco; Margot, Pierre; Pasquier, Eric Du; Dawson, Michael; Roux, Claude; Doble, Philip

    2005-08-15

    Artificial neural networks (ANNs) were utilised to validate illicit drug classification in the profiling method used at "Institut de Police Scientifique" of the University of Lausanne (IPS). This method established links between samples using a combination of principal component analysis (PCA) and calculation of a correlation value between samples. Heroin seizures sent to the IPS laboratory were analysed using gas chromatography (GC) to separate the major alkaloids present in illicit heroin. Statistical analysis was then performed on 3371 samples. Initially, PCA was performed as a preliminary screen to identify samples of a similar chemical profile. A correlation value was then calculated for each sample previously identified with PCA. This correlation value was used to determine links between drug samples. These links were then recorded in an Ibase((R)) database. From this database the notion of "chemical class" arises, where samples with similar chemical profiles are grouped together. Currently, about 20 "chemical classes" have been identified. The normalised peak areas of six target compounds were then used to train an ANN to classify each sample into its appropriate class. Four hundred and sixty-eight samples were used as a training data set. Sixty samples were treated as blinds and 370 as non-linked samples. The results show that in 96% of cases the neural network attributed the seizure to the right "chemical class". The application of a neural network was found to be a useful tool to validate the classification of new drug seizures in existing chemical classes. This tool should be increasingly used in such situations involving profile comparisons and classifications.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-06-15

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

  7. Chemical shift magnetic resonance imaging in differentiation of benign from malignant vertebral collapse in a rural tertiary care hospital in North India

    Science.gov (United States)

    Mittal, Puneet; Gupta, Ranjana; Mittal, Amit; Joshi, Sandeep

    2016-01-01

    Introduction: Magnetic resonance imaging (MRI) is the modality of the first choice for evaluation of vertebral compression/collapse. Many MRI qualitative features help to differentiate benign from malignant collapse. We conducted this study to look for a quantitative difference in chemical shift values in benign and malignant collapse using dual-echo gradient echo in-phase/out-phase imaging. Materials and Methods: MRI examinations of a total of 38 patients were retrospectively included in the study who had vertebral compression/collapse with marrow edema in which final diagnosis was available at the time of imaging/follow-up. Signal intensity value in the region of abnormal marrow signal and adjacent normal vertebra was measured on in phase/out phase images. Signal intensity ratio (SIR) was measured by dividing signal intensity value on opposite phase images to that on in phase images. SIR was compared in normal vertebrae and benign and malignant vertebral collapse. Results: There were 21 males and 17 females with mean age of 52.4 years (range 28–76 years). Out of total 38 patients, 18 were of benign vertebral collapse and 20 of malignant vertebral collapse. SIR in normal vertebrae was 0.30 ± 0.14, 0.67 ± 0.18 in benign vertebral collapse, and 1.20 ± 0.27 in malignant vertebral collapse with significant difference in SIR of normal vertebrae versus benign collapse (P < 0.01) and in benign collapse versus malignant collapse (P < 0.01). Assuming a cutoff of <0.95 for benign collapse and ≥0.95 for malignant collapse, chemical shift imaging had a sensitivity of 90% and specificity of 94.4%. Conclusion: Chemical shift imaging is a rapid and useful sequence in differentiating benign from malignant vertebral collapse with good specificity and sensitivity.

  8. Secondary structural analysis of proteins based on 13C chemical shift assignments in unresolved solid-state NMR spectra enhanced by fragmented structure database

    International Nuclear Information System (INIS)

    Magic-angle-spinning solid-state 13C NMR spectroscopy is useful for structural analysis of non-crystalline proteins. However, the signal assignments and structural analysis are often hampered by the signal overlaps primarily due to minor structural heterogeneities, especially for uniformly-13C,15N labeled samples. To overcome this problem, we present a method for assigning 13C chemical shifts and secondary structures from unresolved two-dimensional 13C–13C MAS NMR spectra by spectral fitting, named reconstruction of spectra using protein local structures (RESPLS). The spectral fitting was conducted using databases of protein fragmented structures related to 13Cα, 13Cβ, and 13C′ chemical shifts and cross-peak intensities. The experimental 13C–13C inter- and intra-residue correlation spectra of uniformly isotope-labeled ubiquitin in the lyophilized state had a few broad peaks. The fitting analysis for these spectra provided sequence-specific Cα, Cβ, and C′ chemical shifts with an accuracy of about 1.5 ppm, which enabled the assignment of the secondary structures with an accuracy of 79 %. The structural heterogeneity of the lyophilized ubiquitin is revealed from the results. Test of RESPLS analysis for simulated spectra of five different types of proteins indicated that the method allowed the secondary structure determination with accuracy of about 80 % for the 50–200 residue proteins. These results demonstrate that the RESPLS approach expands the applicability of the NMR to non-crystalline proteins exhibiting unresolved 13C NMR spectra, such as lyophilized proteins, amyloids, membrane proteins and proteins in living cells.

  9. Computer program for calculation of complex chemical equilibrium compositions and applications. Supplement 1: Transport properties

    Science.gov (United States)

    Gordon, S.; Mcbride, B.; Zeleznik, F. J.

    1984-01-01

    An addition to the computer program of NASA SP-273 is given that permits transport property calculations for the gaseous phase. Approximate mixture formulas are used to obtain viscosity and frozen thermal conductivity. Reaction thermal conductivity is obtained by the same method as in NASA TN D-7056. Transport properties for 154 gaseous species were selected for use with the program.

  10. Large-scale quantum mechanical scattering calculations for molecular energy transfer and chemical reactions

    International Nuclear Information System (INIS)

    The authors discuss two projects involving quantal collision theory calculations on supercomputers. In the first project the authors are considering HF-HF collisions and calculating rotational energy transfer for collisions of rigid molecules and vibrational-to-vibrational (V-V) energy transfer for collisions including all degrees of freedom. They examined several potential energy surfaces, and they parametrized a new one that should be more accurate for the cross correlation of the forces. For rotational energy transfer they also compared the results to classical trajectory calculations. The quantal calculations were carried out by integrating the close coupling equations with scattering boundary conditions using an extensively vectorized R matrix propagation code on the Control Data Corporation Cyber 205 computer. In the second project they are considering atom-diatom reactive collisions for low initial rotational states and both the ground and first excited vibrational state. The three arrangement channels (A =BC, AB+C, and AC+B) are coupled by the Fock scheme, and the reactive amplitude density (obtained by operating on the initial state with the reactance operator or the total wave function with the interaction potential) is expanded in a square-integrable basis set. This leads to a large system of coupled algebraic equations which are constructed and solved using a large-memory Cray-2 computer. Variational improvements have been tested successfully for nonreactive collisions and will soon be implemented for reactive collisions

  11. A Steady-State Approximation to the Two-Dimensional Master Equation for Chemical Kinetics Calculations.

    Science.gov (United States)

    Nguyen, Thanh Lam; Stanton, John F

    2015-07-16

    In the field of chemical kinetics, the solution of a two-dimensional master equation that depends explicitly on both total internal energy (E) and total angular momentum (J) is a challenging problem. In this work, a weak-E/fixed-J collisional model (i.e., weak-collisional internal energy relaxation/free-collisional angular momentum relaxation) is used along with the steady-state approach to solve the resulting (simplified) two-dimensional (E,J)-grained master equation. The corresponding solutions give thermal rate constants and product branching ratios as functions of both temperature and pressure. We also have developed a program that can be used to predict and analyze experimental chemical kinetics results. This expedient technique, when combined with highly accurate potential energy surfaces, is cable of providing results that may be meaningfully compared to experiments. The reaction of singlet oxygen with methane proceeding through vibrationally excited methanol is used as an illustrative example. PMID:25815602

  12. Other compounds isolated from Simira glaziovii and the {sup 1}H and {sup 13}C NMR chemical shift assignments of new 1-epi-castanopsol

    Energy Technology Data Exchange (ETDEWEB)

    Araujo, Marcelo F. de; Vieira, Ivo J. Curcino [Universidade Federal Rural do Rio de Janeiro, Seropedica, RJ (Brazil). Dept. de Quimica; Braz-Filho, Raimundo [Universidade Estadual do Norte Fluminense (UENF), Campos dos Goytacases, RJ (Brazil). Centro de Ciencias Tecnologicas. Lab. de Ciencias Quimicas; Carvalho, Mario G. de, E-mail: mgeraldo@ufrrj.br [Universidade Federal do Rio de Janeiro (NPPN/UFRJ), RJ (Brazil). Centro de Ciencias da Saude. Nucleo de Pesquisa em Produtos Naturais

    2012-07-01

    A new triterpene, 1-epi-castanopsol, besides eleven known compounds: sitosterol, stigmasterol, campesterol, lupeol, lupenone, simirane B, syringaresinol, scopoletin, isofraxidin, 6,7,8-trimethoxycoumarin and harman, were isolated from the wood of Simira glaziovii. The structures of the known compounds were defined by 1D, 2D {sup 1}H, {sup 13}C NMR spectra data analyses and comparison with literature data. The detailed spectral data analyses allowed the definition of the structure of the new 1-epi isomer of castanopsol and performance of {sup 1}H and {sup 13}C NMR chemical shift assignments. (author)

  13. Liver steatosis (LS) evaluated through chemical-shift magnetic resonance imaging liver enzymes in morbid obesity; effect of weight loss obtained with intragastric balloon gastric banding.

    Science.gov (United States)

    Folini, Laura; Veronelli, Annamaria; Benetti, Alberto; Pozzato, Carlo; Cappelletti, Marco; Masci, Enzo; Micheletto, Giancarlo; Pontiroli, Antonio E

    2014-01-01

    The aim of this study was to evaluate in morbid obesity clinical and metabolic effects related to weight loss on liver steatosis (LS), measured through chemical-shift magnetic resonance imaging (MRI) and liver enzymes. Forty obese subjects (8 M/32 W; BMI 42.8 ± 7.12 kg/m(2), mean ± SD) were evaluated for LS through ultrasound (US-LS), chemical-shift MRI (MRI-LS), liver enzymes [aspartate aminotransferase (AST), alanine aminotransferase (ALT), γ-glutamyltransferase (GGT), alkaline phosphatase (ALP)], anthropometric parameters [weight, BMI, waist circumference (WC)], lipids, insulin, insulin resistance (HOMA-IR), glycated hemoglobin (HbA1c), oral glucose tolerance test, and body composition [fat mass (FM) and fat-free mass (FFM) at bio-impedance analysis (BIA)]. Anthropometric measures, MRI-LS, BIA, and biochemical parameters were reevaluated 6 months later in 18 subjects undergoing restrictive bariatric approach, i.e., intragastric balloon (BIB, n = 13) or gastric banding (LAGB, n = 5), and in 13 subjects receiving hypocaloric diet. At baseline, US-LS correlates only with MRI-LS, and the latter correlates with ALT, AST, and GGT. After 6 months, subjects undergoing BIB or LAGB had significant changes of BMI, weight, WC, ALT, AST, GGT, ALP, HbA1c, insulin, HOMA-IR, FM, FFM, and MRI-LS. Diet-treated obese subjects had no significant change of any parameter under study; change of BMI, fat mass, and fat-free mass was significantly greater in LAGB/BIB subjects than in diet-treated subjects. Change of MRI-LS showed a significant correlation with changes in weight, BMI, WC, GGT, ALP, and basal MRI-LS. Significant weight loss after BIB or LAGB is associated with decrease in chemical-shift MRI-LS and with reduction in liver enzymes; chemical-shift MRI and liver enzymes allow monitoring of LS in follow-up studies.

  14. Chloromethane Complexation by Cryptophanes : Host-Guest Chemistry Investigated by NMR and Quantum Chemical Calculations

    OpenAIRE

    Takacs, Zoltan

    2012-01-01

    Host–guest complexes are widely investigated because of their importance in many industrial applications. The investigation of their physico–chemical properties helps understanding the inclusion phenomenon. The hosts investigated in this work are cryptophane molecules possessing a hydrophobic cavity. They can encapsulate small organic guests such as halo–methanes (CH2Cl2, CHCl3). The encapsulation process was investigated from both the guest and the host point of view. With the help of Nuclea...

  15. Chemical solver to compute molecule and grain abundances and non-ideal MHD resistivities in prestellar core-collapse calculations

    Science.gov (United States)

    Marchand, P.; Masson, J.; Chabrier, G.; Hennebelle, P.; Commerçon, B.; Vaytet, N.

    2016-07-01

    We develop a detailed chemical network relevant to calculate the conditions that are characteristic of prestellar core collapse. We solve the system of time-dependent differential equations to calculate the equilibrium abundances of molecules and dust grains, with a size distribution given by size-bins for these latter. These abundances are used to compute the different non-ideal magneto-hydrodynamics resistivities (ambipolar, Ohmic and Hall), needed to carry out simulations of protostellar collapse. For the first time in this context, we take into account the evaporation of the grains, the thermal ionisation of potassium, sodium, and hydrogen at high temperature, and the thermionic emission of grains in the chemical network, and we explore the impact of various cosmic ray ionisation rates. All these processes significantly affect the non-ideal magneto-hydrodynamics resistivities, which will modify the dynamics of the collapse. Ambipolar diffusion and Hall effect dominate at low densities, up to nH = 1012 cm-3, after which Ohmic diffusion takes over. We find that the time-scale needed to reach chemical equilibrium is always shorter than the typical dynamical (free fall) one. This allows us to build a large, multi-dimensional multi-species equilibrium abundance table over a large temperature, density and ionisation rate ranges. This table, which we make accessible to the community, is used during first and second prestellar core collapse calculations to compute the non-ideal magneto-hydrodynamics resistivities, yielding a consistent dynamical-chemical description of this process. The multi-dimensional multi-species equilibrium abundance table and a copy of the code are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/592/A18

  16. Quantum Chemical Calculations and Experimental Studies on 2,3-Diphenyl-tetrazole-5-thione

    Institute of Scientific and Technical Information of China (English)

    赵朴素; 卑凤利; 杨绪杰; 汪信; 陆路德; 建方方; 侯玉霞

    2004-01-01

    2,3-Diphenyl-tetrazole-5-thione has been synthesized and characterized by X-ray diffraction analysis and FTIR spectra. The extended MO calculations by using density functional theory (DFT) and self-consistent field molecular orbital Hartree-Fock theory with 6-31gG* basis set were carried out. The optimized structure and atomic charge distributions have been investi- gated, showing the exocyclic sulfur atom has the biggest negative charge value and this site is the most likely site of protonation and methylation as well as the potential coordination site with metallic ions. The predicted harmonic vibration frequencies are compared to the experimental values. On the basis of vibrational analyses, the thermodynamic properties of this compound at different temperature have been calculated, revealing the correlations between C0p, m, S0m, H0m and temperature.

  17. 13C-NMR chemical shift databases as a quick tool to evaluate structural models of humic substances

    DEFF Research Database (Denmark)

    Nyrop Albers, Christian; Hansen, Poul Erik

    2010-01-01

    Models for humic and fulvic acids are discussed based on 13C liquid state NMR spectra combined with results from elemental analysis and titration studies. The analysis of NMR spectra is based on a full reconstruction of the NMR spectrum done with help of 13C-NMR data bases by adding up chemical s...

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

    Science.gov (United States)

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

    2016-01-01

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

  19. Quantum chemical calculations on structure of Mo8 O4-26

    Institute of Scientific and Technical Information of China (English)

    吴争平; 尹周澜; 陈启元; 张平民

    2002-01-01

    Two possible structures of Mo8O4-26 were optimized using the Polak-Ribiere method of Molecular Mechanics Optimization and the termination condition is RMS (Root-mean-square) gradient of 0.42kJ/mol. Based on the calculations of the molecular dynamics, Lengevin dynamics and Monte Carlo dynamics simulation, the structure models of Mo8O4-26 with the lowest energy were acquired respectively according to the energy of the systems calculated using the ZIDO/1 and PM3 methods. The total energy, energies of some frontier molecular orbitals and atomic charges of Mo8O4-26 were computed at the HF/3-21G and HF/STO-3G levels. The calculation results show that the contortion of the structure with eight MoO6 is smaller than that of the structure with six MoO6 and two MoO4. The total energies of the two structures are nearly equal because the contortion of the structure with six MoO6 and two MoO4 would make the exclusion force decreased.

  20. Comparison of trajectory models in calculations of N2-broadened half-widths and N2-induced line shifts for the rotational band of H216O and comparison with measurements

    International Nuclear Information System (INIS)

    In this work, Complex Robert-Bonamy calculations of half-widths and line shifts were done for N2-broadening of water for 1639 transitions in the rotational band using two models for the trajectories. The first is a model correct to second order in time, the Robert-Bonamy parabolic approximation. The second is the solution of Hamilton's equations. Both models use the isotropic part of the atom-atom potential to determine the trajectories. The present calculations used an intermolecular potential expanded to 20th order to assure the convergence of the half-widths and line shifts. The aim of the study is to assess if the difference in the half-widths and line shifts determined from the two trajectory models is greater than the accuracy requirements of the spectroscopic and remote sensing communities. The results of the calculations are compared with measurements of the half-widths and line shifts. It is shown that the effects of the trajectory model greatly exceed the needs of current remote sensing measurements and that line shape parameters calculated using trajectories determined by solving Hamilton's equations agree better with measurement.

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

    DEFF Research Database (Denmark)

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

    2000-01-01

    compared to single voxel methods. In the present study, the optimal voxel size is calculated from segmented human brain data and accompanying field maps. The optimal voxel size is found to be approximately 8 cc, but a wide range of values, 4-64 cc, can be chosen with little increase in estimated...

  2. An interactive computer code for calculation of gas-phase chemical equilibrium (EQLBRM)

    Science.gov (United States)

    Pratt, B. S.; Pratt, D. T.

    1984-01-01

    A user friendly, menu driven, interactive computer program known as EQLBRM which calculates the adiabatic equilibrium temperature and product composition resulting from the combustion of hydrocarbon fuels with air, at specified constant pressure and enthalpy is discussed. The program is developed primarily as an instructional tool to be run on small computers to allow the user to economically and efficiency explore the effects of varying fuel type, air/fuel ratio, inlet air and/or fuel temperature, and operating pressure on the performance of continuous combustion devices such as gas turbine combustors, Stirling engine burners, and power generation furnaces.

  3. Final Technical Report: A Paradigm Shift in Chemical Processing: New Sustainable Chemistries for Low-VOC Coatings

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Kenneth F.

    2006-07-26

    The project employed new processes to make emulsion polymers from reduced levels of petroleum-derived chemical feedstocks. Most waterborne paints contain spherical, emulsion polymer particles that serve as the film-forming binder phase. Our goal was to make emulsion polymer particles containing 30 percent feedstock that would function as effectively as commercial emulsions made from higher level feedstock. The processes developed yielded particles maintained their film formation capability and binding capacity while preserving the structural integrity of the particles after film formation. Rohm and Haas Company (ROH) and Archer Daniels Midland Company (ADM) worked together to employ novel polymer binders (ROH) and new, non-volatile, biomass-derived coalescing agents (ADM). The University of Minnesota Department of Chemical Engineering and Material Science utilized its unique microscopy capabilities to characterize films made from the New Emulsion Polymers (NEP).

  4. Unified Electrostatic Understanding on the Solvation-Induced Changes in the CN Stretching Frequency and the NMR Chemical Shifts of a Nitrile.

    Science.gov (United States)

    Torii, Hajime

    2016-09-15

    Understanding on the spectroscopic properties of a functional group is essential to use it to detect changes in the structural and/or dynamical properties through the situations of intermolecular interactions. The present study is devoted to elucidating the factors that control the solvation-induced changes in the C≡N stretching frequency and the (13)C and (15)N NMR chemical shifts of the nitrile group. It is shown that the nonelectrostatic contribution of the hydration-induced changes in the C≡N stretching frequency as previously thought, as well as the specific effect of hydrogen bonding on the (13)C and (15)N chemical shifts, actually originate from the spatially inhomogeneous nature of the electrostatic situation generated by the hydrogen-bond donating water molecule, especially by the OH bond dipole. On this basis, a unified electrostatic interaction model that encompasses the cases of both hydration and dipolar solvation is constructed. The responses of electrons in these two cases are also discussed. PMID:27547990

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-15

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

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2010-03-17

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Alizai, Hamza; Nardo, Lorenzo; Karampinos, Dimitrios C.; Joseph, Gabby B.; Yap, Samuel P.; Baum, Thomas; Krug, Roland; Majumdar, Sharmila; Link, Thomas M. [University of California, San Francisco, Musculoskeletal and Quantitative Imaging Research Group, Department of Radiology and Biomedical Imaging, San Francisco, CA (United States)

    2012-07-15

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

  9. Lattice dynamics and chemical bonding in Sb2Te3 from first-principles calculations

    International Nuclear Information System (INIS)

    Pressure effects on the lattice dynamics and the chemical bonding of the three-dimensional topological insulator, Sb2Te3, have been studied from a first-principles perspective in its rhombohedral phase. Where it is possible to compare, theory agrees with most of the measured phonon dispersions. We find that the inclusion of relativistic effects, in terms of the spin-orbit interaction, affects the vibrational features to some extend and creates large fluctuations on phonon density of state in high frequency zone. By investigations of structure and electronic structure, we analyze in detail the semiconductor to metal transition at ∼2 GPa followed by an electronic topological transition at a pressure of ∼4.25 GPa

  10. Elucidating electronic transitions from σ orbitals of liquid n- and branched alkanes by far-ultraviolet spectroscopy and quantum chemical calculations.

    Science.gov (United States)

    Morisawa, Yusuke; Tachibana, Shin; Ehara, Masahiro; Ozaki, Yukihiro

    2012-12-01

    Attenuated total reflection far-ultraviolet (ATR-FUV) spectra containing Rydberg states of n-alkanes (C(m)H(2m+2); m varies in the range 5-9) and branched alkanes observed in the liquid phase were investigated by quantum chemical calculations with the aim of elucidating electronic transitions from σ orbitals of liquid n- and branched alkanes. New assignments are proposed based on the time-dependent density functional theory (TD-DFT) and symmetry-adapted cluster configuration interaction (SAC-CI) calculations, and the differences in these spectra are analyzed in detail. The FUV spectra of n-alkanes show a broad asymmetric feature near 8.3 eV. The strong band at ∼8.3 eV shows a red shift with a significant increase in intensity as the carbon chain length increases, which is attributed to the overlapping transitions from the third (or fourth) highest occupied molecular orbitals HOMO-2 (or HOMO-3) and HOMO-1 to Rydberg 3p(y) by the TD-DFT and SAC-CI calculations. This band was previously assigned to the overlap of two peaks arising from the transition from the HOMO to 3p and from the HOMO-1 to 3s based on their term values. Although the most intense transition, T1, is from HOMO-2 for m = 5 and 6 and HOMO-3 for m varying in the range of 7-9, the shape of Kohn-Sham molecular orbital for T1 is similar among the all-alkanes investigated. The theoretical result also has demonstrated that the red shift originates in both stabilization of the Rydberg 3p(y) and destabilization of the occupied orbitals. The intensity of the shoulder at 7.7 eV drastically increases in the spectra of the branched alkanes, especially for those with quaternary carbon atoms such as 2,2-dimethyl butane. This increase in intensity is caused by a reduction in symmetry in the branched alkanes, which leads the forbidden transitions to Rydberg 3s to allowed transitions. In this way, the present study has provided new insight into the existence of their Rydberg transitions and the shape of the relevant

  11. Parameters for the RM1 Quantum Chemical Calculation of Complexes of the Trications of Thulium, Ytterbium and Lutetium.

    Directory of Open Access Journals (Sweden)

    Manoel A M Filho

    Full Text Available The RM1 quantum chemical model for the calculation of complexes of Tm(III, Yb(III and Lu(III is advanced. Subsequently, we tested the models by fully optimizing the geometries of 126 complexes. We then compared the optimized structures with known crystallographic ones from the Cambridge Structural Database. Results indicate that, for thulium complexes, the accuracy in terms of the distances between the lanthanide ion and its directly coordinated atoms is about 2%. Corresponding results for ytterbium and lutetium are both 3%, levels of accuracy useful for the design of lanthanide complexes, targeting their countless applications.

  12. Parameters for the RM1 Quantum Chemical Calculation of Complexes of the Trications of Thulium, Ytterbium and Lutetium.

    Science.gov (United States)

    Filho, Manoel A M; Dutra, José Diogo L; Rocha, Gerd B; Simas, Alfredo M; Freire, Ricardo O

    2016-01-01

    The RM1 quantum chemical model for the calculation of complexes of Tm(III), Yb(III) and Lu(III) is advanced. Subsequently, we tested the models by fully optimizing the geometries of 126 complexes. We then compared the optimized structures with known crystallographic ones from the Cambridge Structural Database. Results indicate that, for thulium complexes, the accuracy in terms of the distances between the lanthanide ion and its directly coordinated atoms is about 2%. Corresponding results for ytterbium and lutetium are both 3%, levels of accuracy useful for the design of lanthanide complexes, targeting their countless applications. PMID:27223475

  13. Parameters for the RM1 Quantum Chemical Calculation of Complexes of the Trications of Thulium, Ytterbium and Lutetium.

    Science.gov (United States)

    Filho, Manoel A M; Dutra, José Diogo L; Rocha, Gerd B; Simas, Alfredo M; Freire, Ricardo O

    2016-01-01

    The RM1 quantum chemical model for the calculation of complexes of Tm(III), Yb(III) and Lu(III) is advanced. Subsequently, we tested the models by fully optimizing the geometries of 126 complexes. We then compared the optimized structures with known crystallographic ones from the Cambridge Structural Database. Results indicate that, for thulium complexes, the accuracy in terms of the distances between the lanthanide ion and its directly coordinated atoms is about 2%. Corresponding results for ytterbium and lutetium are both 3%, levels of accuracy useful for the design of lanthanide complexes, targeting their countless applications.

  14. The hyperfine structure in the rotational spectra of bromofluoromethane: Lamb-dip technique and quantum-chemical calculations

    OpenAIRE

    Cazzoli, Gabriele; Puzzarini, Cristina; Stopkowicz, Stella; Gauss, Jürgen

    2008-01-01

    Abstract The hyperfine structure in the rotational spectra of six isotopic species of bromofluoromethane, namely CH2{79}BrF, CH2{81}BrF, CDH{79}BrF, CDH{81}BrF, CD2{79}BrF, and CD2{81}BrF, has been investigated using the Lamb-dip technique in the submillimeter-wave frequency range. Measurements as well as assignment procedures have been supported by high-level quantum-chemical calculations of the hyperfine parameters at the coupled-cluster level. For all species, the accuracy of th...

  15. A quantitative analysis of weak intermolecular interactions & quantum chemical calculations (DFT) of novel chalcone derivatives

    Science.gov (United States)

    Chavda, Bhavin R.; Gandhi, Sahaj A.; Dubey, Rahul P.; Patel, Urmila H.; Barot, Vijay M.

    2016-05-01

    The novel chalcone derivatives have widespread applications in material science and medicinal industries. The density functional theory (DFT) is used to optimized the molecular structure of the three chalcone derivatives (M-I, II, III). The observed discrepancies between the theoretical and experimental (X-ray data) results attributed to different environments of the molecules, the experimental values are of the molecule in solid state there by subjected to the intermolecular forces, like non-bonded hydrogen bond interactions, where as isolated state in gas phase for theoretical studies. The lattice energy of all the molecules have been calculated using PIXELC module in Coulomb -London -Pauli (CLP) package and is partitioned into corresponding coulombic, polarization, dispersion and repulsion contributions. Lattice energy data confirm and strengthen the finding of the X-ray results that the weak but significant intermolecular interactions like C-H…O, Π- Π and C-H… Π plays an important role in the stabilization of crystal packing.

  16. In Vivo Anti-Leukemia, Quantum Chemical Calculations and ADMET Investigations of Some Quaternary and Isothiouronium Surfactants

    Directory of Open Access Journals (Sweden)

    Ahmed A. El-Henawy

    2013-04-01

    Full Text Available Anti-leukemia screening of previously prepared isothiouronium and quaternary salts was performed, and some salts exhibited promising activity as anticancer agents. Quantum chemical calculations were utilized to explore the electronic structure and stability of these compounds. Computational studies have been carried out at the PM3 semiempirical molecular orbitals level, to establish the HOMO-LUMO, IP and ESP mapping of these compounds. The ADMET properties were also studied to gain a clear view of the potential oral bioavailability of these compounds. The surface properties calculated included critical micelle concentration (CMC, maximum surface excess (Γmax, minimum surface area (Amin, free energy of micellization (ΔGomic and adsorption (ΔGoads.

  17. An Approach to Calculate Mineralś Bulk Moduli KS from Chemical Composition and Density ρ

    Science.gov (United States)

    Breuer, S.; Schilling, F. R.; Mueller, B.; Drüppel, K.

    2015-12-01

    The elastic properties of minerals are fundamental parameters for technical and geotechnical applications and an important research topic towards a better understanding of the Eart&hacute;s interior. Published elastic properties, chemical composition, and density data of 86 minerals (total of 258 data including properties of minerals at various p, T conditions) were collected into a database. It was used to test different hypotheses about relationships between these properties (e.g. water content in minerals and their Poisson's ratio). Furthermore, a scheme to model the average elastic properties, i.e. the bulk modulus KS, based on mineral density and composition was developed. Birc&hacute;s law, a linearity between density ρ and wave velocity (e.g. vp.), is frequently used in seismic and seismology to derive density of the Eart&hacute;s interior from seismic velocities. Applying the compiled mineral data contradicts the use of a simple velocity-density relation (e.g. Gardneŕs relation, 1974). The presented model-approach to estimate the mineralś bulk moduli Ks (as Voigt-Reuss-Hill average) is based on the idea of pressure-temperature (p-T) dependent ionś bulk moduli. Using a multi-exponential regression to ascertain the ionś bulk moduli and by applying an exponential scaling with density ρ, their bulk moduli could be modelled. As a result, > 88 % of the 258 bulk moduli data are predicted with an uncertainty of < 20 % compared to published values. Compared to other models (e.g. Anderson et al. 1970 and Anderson & Nafe 1965), the here presented approach to model the bulk moduli only requires the density ρ and chemical composition of the mineral and is not limited to a specific group of minerals, composition, or structure. In addition to this, by using the pressure and temperature dependent density ρ(p, T), it is possible to predict bulk moduli for varying p-T conditions. References:Gardner, G.H.F, Gardner, L.W. and Gregory, A.R. (1974). Geophysics, 39, No. 6

  18. Paradigm shift in LUNG SBRT dose calculation associated with Heterogeneity correction; Cambio de paradigma en SBRT pulmonar asociada al calculo de dosis con correccion de heterogeneidad

    Energy Technology Data Exchange (ETDEWEB)

    Zucca Aparicio, D.; Perez Moreno, J. M.; Fernandez Leton, P.; Garcia Ruiz-Zorrilla, J.; Pinto Monedero, M.; Marti Asensjo, J.; Alonso Iracheta, L.

    2015-07-01

    Treatment of lung injury SBRT requires great dosimetric accuracy, the increasing clinical importance of dose calculation heterogeneities introducing algorithms that adequately model the transport of particles narrow beams in media of low density, as with Monte Carlo calculation. (Author)

  19. Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table.

    Science.gov (United States)

    Aquilante, Francesco; Autschbach, Jochen; Carlson, Rebecca K; Chibotaru, Liviu F; Delcey, Mickaël G; De Vico, Luca; Fdez Galván, Ignacio; Ferré, Nicolas; Frutos, Luis Manuel; Gagliardi, Laura; Garavelli, Marco; Giussani, Angelo; Hoyer, Chad E; Li Manni, Giovanni; Lischka, Hans; Ma, Dongxia; Malmqvist, Per Åke; Müller, Thomas; Nenov, Artur; Olivucci, Massimo; Pedersen, Thomas Bondo; Peng, Daoling; Plasser, Felix; Pritchard, Ben; Reiher, Markus; Rivalta, Ivan; Schapiro, Igor; Segarra-Martí, Javier; Stenrup, Michael; Truhlar, Donald G; Ungur, Liviu; Valentini, Alessio; Vancoillie, Steven; Veryazov, Valera; Vysotskiy, Victor P; Weingart, Oliver; Zapata, Felipe; Lindh, Roland

    2016-02-15

    In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization. PMID:26561362

  20. NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary

    International Nuclear Information System (INIS)

    An algorithm, CYLIB, is presented for converting molecular topology descriptions from the PDB Chemical Component Dictionary into CYANA residue library entries. The CYANA structure calculation algorithm uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atoms with fixed relative positions. Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of ligands but the process is time-consuming and error-prone. An automated method is necessary in order to handle the large number of different potential ligand molecules to be studied in drug design projects. Here, we present an algorithm for this purpose, and show that CYANA structure calculations can be performed with almost all small molecule ligands and non-standard amino acid residues in the PDB Chemical Component Dictionary

  1. NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary

    Energy Technology Data Exchange (ETDEWEB)

    Yilmaz, Emel Maden; Güntert, Peter, E-mail: guentert@em.uni-frankfurt.de [Goethe University Frankfurt am Main, Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry (Germany)

    2015-09-15

    An algorithm, CYLIB, is presented for converting molecular topology descriptions from the PDB Chemical Component Dictionary into CYANA residue library entries. The CYANA structure calculation algorithm uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atoms with fixed relative positions. Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of ligands but the process is time-consuming and error-prone. An automated method is necessary in order to handle the large number of different potential ligand molecules to be studied in drug design projects. Here, we present an algorithm for this purpose, and show that CYANA structure calculations can be performed with almost all small molecule ligands and non-standard amino acid residues in the PDB Chemical Component Dictionary.

  2. Correlations of the chemical shift on fasly rotating biological solids by means of NMR spectroscopy; Korrelationen der chemischen Verschiebung an schnell rotierenden biologischen Festkoerpern mittels NMR-Spektroskopie

    Energy Technology Data Exchange (ETDEWEB)

    Herbst, Christian

    2010-04-27

    The basic aim of the thesis was the development and improvement of homo- and heteronuclear feedback sequences for the generation of correlation spectra of the chemical shift. In a first step the possibility of the acquisition of {sup 13}C-{sup 13} correlation spectra of the chemical shift by means of inversion pulses with low RF power factor was studied. Furthermore it was shown that broad-band phase-modulated inversion and universal rotational pulses can be constructed by means of global optimization procedures like the genetic algorithms under regardment of the available RF field strength. By inversion, universal rotational, and 360 pulses as starting values of the optimization efficient homonuclear CN{sub n}{sup {nu}} and RN{sub n}{sup {nu}} mixing sequences as well as heteronuclear RN{sub n}{sup {nu}{sub s},{nu}{sub k}} feedback sequences were generated. The satisfactory power of the numerically optimized sequences was shown by means of the simulation as well by means of correlation experiments of the chemical shift of L-histidine, L-arginine, and the (CUG){sub 97}-RNA. This thesis deals furthermore with the possibility to acquire simultaneously different signals with several receivers. By means of numerically optimized RN{sub n}{sup {nu}{sub s},{nu}{sub k}} pulse sequences both {sup 15}N-{sup 13}C and {sup 13}C-{sup 15}N correlation spectra were simultaneously generated. Furthermore it could be shown that the simultaneous acquisition of 3D-{sup 15}N-{sup 13}C-{sup 13}C and {sup 13}C-{sup 15}N-({sup 1}H)-{sup 1}H correlation spectra is possible. By this in only one measurement process resonance assignments can be met and studies of the global folding performed. A further application of several receivers is the simultaneous acquisition of CHHC, NHHN, NHHC, as well as CHHN spectra. By such experiments it is possible to characterize the hydrogen-bonding pattern and the glycosidic torsion angle {sup {chi}} in RNA. This was demonstrated by means of the (CUG){sub 97

  3. Calculation of the relative chemical stabilities of proteins as a function of temperature and redox chemistry in a hot spring.

    Directory of Open Access Journals (Sweden)

    Jeffrey M Dick

    Full Text Available Uncovering the chemical and physical links between natural environments and microbial communities is becoming increasingly amenable owing to geochemical observations and metagenomic sequencing. At the hot spring known as Bison Pool in Yellowstone National Park, the cooling of the water in the outflow channel is associated with an increase in oxidation potential estimated from multiple field-based measurements. Representative groups of proteins whose sequences were derived from metagenomic data also exhibit an increase in average oxidation state of carbon in the protein molecules with distance from the hot-spring source. The energetic requirements of reactions to form selected proteins used in the model were computed using amino-acid group additivity for the standard molal thermodynamic properties of the proteins, and the relative chemical stabilities of the proteins were investigated by varying temperature, pH and oxidation state, expressed as activity of dissolved hydrogen. The relative stabilities of the proteins were found to track the locations of the sampling sites when the calculations included a function for hydrogen activity that increases with temperature and is higher, or more reducing, than values consistent with measurements of dissolved oxygen, sulfide and oxidation-reduction potential in the field. These findings imply that spatial patterns in the amino acid compositions of proteins can be linked, through energetics of overall chemical reactions representing the formation of the proteins, to the environmental conditions at this hot spring, even if microbial cells maintain considerably different internal conditions. Further applications of the thermodynamic calculations are possible for other natural microbial ecosystems.

  4. 1H chemical shift imaging of the brain in guanidino methyltransferase deficiency, a creatine deficiency syndrome; guanidinoacetate accumulation in the gray matter

    International Nuclear Information System (INIS)

    MR spectroscopy results in a mild case of guanidinoacetate methyltransferase (GAMT) deficiency are presented. The approach differs from previous MRS studies in the acquisition of a chemical shift imaging spectral map showing gray and white matter with the corresponding spectra in one overview. MR spectroscopy revealed guanidinoacetate (GAA) in the absence of creatine. New is that GAA signals are more prominent in gray matter than in white. In the prevailing view, that enzyme deficiency is localized in liver and pancreas and that all GAA is transported into the brain from the blood and the cerebrospinal fluid, this would be compatible with a more limited uptake and/or better clearance of GAA from the white matter compared to the grey matter. (orig.)

  5. Examination of anticipated chemical shift and shape distortion effect on materials commonly used in prosthetic socket fabrication when measured using MRI: a validation study.

    Science.gov (United States)

    Safari, Mohammad Reza; Rowe, Philip; Buis, Arjan

    2013-01-01

    The quality of lower-limb prosthetic socket fit is influenced by shape and volume consistency during the residual limb shape-capturing process (i.e., casting). Casting can be quantified with magnetic resonance imaging (MRI) technology. However, chemical shift artifact and image distortion may influence the accuracy of MRI when common socket/casting materials are used. We used a purpose-designed rig to examine seven different materials commonly used in socket fabrication during exposure to MRI. The rig incorporated glass marker tubes filled with water doped with 1 g/L copper sulfate (CS) and 9 plastic sample vials (film containers) to hold the specific material specimens. The specimens were scanned 9 times in different configurations. The absolute mean difference of the glass marker tube length was 1.39 mm (2.98%) (minimum = 0.13 mm [0.30%], maximum = 5.47 mm [14.03%], standard deviation = 0.89 mm). The absolute shift for all materials was <1.7 mm. This was less than the measurement tolerance of +/-2.18 mm based on voxel (three-dimensional pixel) dimensions. The results show that MRI is an accurate and repeatable method for dimensional measurement when using matter containing water. Additionally, silicone and plaster of paris plus 1 g/L CS do not show a significant shape distortion nor do they interfere with the MRI image of the residual limb.

  6. Examination of anticipated chemical shift and shape distortion effect on materials commonly used in prosthetic socket fabrication when measured using MRI: A validation study

    Directory of Open Access Journals (Sweden)

    Mohammad Reza Safari, PhD

    2013-02-01

    Full Text Available The quality of lower-limb prosthetic socket fit is influenced by shape and volume consistency during the residual limb shape-capturing process (i.e., casting. Casting can be quantified with magnetic resonance imaging (MRI technology. However, chemical shift artifact and image distortion may influence the accuracy of MRI when common socket/casting materials are used. We used a purpose-designed rig to examine seven different materials commonly used in socket fabrication during exposure to MRI. The rig incorporated glass marker tubes filled with water doped with 1 g/L copper sulfate (CS and 9 plastic sample vials (film containers to hold the specific material specimens. The specimens were scanned 9 times in different configurations. The absolute mean difference of the glass marker tube length was 1.39 mm (2.98% (minimum = 0.13 mm [0.30%], maximum = 5.47 mm [14.03%], standard deviation = 0.89 mm. The absolute shift for all materials was <1.7 mm. This was less than the measurement tolerance of +/–2.18 mm based on voxel (three-dimensional pixel dimensions. The results show that MRI is an accurate and repeatable method for dimensional measurement when using matter containing water. Additionally, silicone and plaster of paris plus 1 g/L CS do not show a significant shape distortion nor do they interfere with the MRI image of the residual limb.

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

    DEFF Research Database (Denmark)

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

    2004-01-01

    An approach is presented that allows a detailed, quantitative characterization of conformational exchange processes in proteins on the mus-ms time scale. The approach relies on a combined analysis of NMR relaxation rates and chemical shift changes and requires that the chemical shift...... variabilis (A.v. PCu) (Ma, L.; Hass, M. A. S.; Vierick, N.; Kristensen, S. M.; Ulstrup, J.; Led, J. J. Biochemistry 2003, 42, 320-330). The R-1 and R-2 relaxation rates of the backbone N-15 nuclei were measured at a series of pH and temperatures on an 15N labeled sample of A.v. PCu, and the 15 N chemical...... quantitatively by the correlation between the R-ex terms and the corresponding chemical shift differences of the exchanging species. By this approach, the R-ex terms of N-15 nuclei belonging to contiguous regions in the protein could be assigned to the same exchange process. Furthermore, the analysis...

  8. 31P-MR spectroscopy of all regions of the human heart at 1.5 T with acquisition-weighted chemical shift imaging

    International Nuclear Information System (INIS)

    Aim: Aim of this study was to show whether or not acquisition-weighted chemical shift imaging (AW-CSI) allows the determination of PCr and ATP in the lateral and posterior wall of the human heart at 1.5 T. Methods: 12 healthy volunteers were examined using a conventional chemical shift imaging (CSI) and an AW-CSI. The sequences differed only in the number of repetitions for each point in k space. A hanning function was used as filter function leading to 7 repetitions in the center of the k space and 0 in the corners. Thus, AW-CSI had the same resolution as the CSI sequence. The results for both sequences were analyzed using identically positioned voxels in the septal, anterior, lateral and posterior wall. Results: The determined averaged AW-CSI signal to noise ratios were higher for PCr by a factor of 1.3 and for ATP by 1.4 than those of CSI. The PCr/ATP ratios were higher by a factor of 1.2 - 1.3 and showed a smaller standard deviation in all locations for AW-CSI. The mean PCr/ATP ratios determined by AW-CSI of septal, lateral and posterior wall were almost identical (1.72 - 1.76), while it was higher in the anterior wall (1.9). Conclusions: The reduced contamination in AW-CSI improves the signal to noise ratio and the determination of the PCr/ATP ratio in cardiac 31P spectroscopy compared to CSI with the same resolution. The results in volunteers indicate that AW-CSI renders 31P spectroscopy of the lateral and posterior wall of the human heart feasible for patient studies at 1.5 T. (orig.)

  9. A chemical solver to compute molecule and grain abundances and non-ideal MHD resistivities in prestellar core collapse calculations

    CERN Document Server

    Marchand, Pierre; Chabrier, Gilles; Hennebelle, Patrick; Commerçon, Benoit; Vaytet, Neil

    2016-01-01

    We develop a detailed chemical network relevant to the conditions characteristic of prestellar core collapse. We solve the system of time-dependent differential equations to calculate the equilibrium abundances of molecules and dust grains, with a size distribution given by size-bins for these latter. These abundances are used to compute the different non-ideal magneto-hydrodynamics resistivities (ambipolar, Ohmic and Hall), needed to carry out simulations of protostellar collapse. For the first time in this context, we take into account the evaporation of the grains, the thermal ionisation of Potassium, Sodium and Hydrogen at high temperature, and the thermionic emission of grains in the chemical network, and we explore the impact of various cosmic ray ionisation rates. All these processes significantly affect the non-ideal magneto-hydrodynamics resistivities, which will modify the dynamics of the collapse. Ambipolar diffusion and Hall effect dominate at low densities, up to n_H = 10^12 cm^-3, after which Oh...

  10. 1,3- and 1,5-Sigmatropic Shifts:Insights into the Structure-Reactivity Relationship from ab initio Calculations

    Institute of Scientific and Technical Information of China (English)

    ZOU,Jian-Wei; ZHANG,Bing; YU,Qing-Sen

    2004-01-01

    @@ Thermal [ 1,n]-sigmatropic rearrangements of hydrogen shift have been of considerable theoretical and experimental interests during the past several decades.[1,2] In this paper, a group of intramolecular proton transfers in hydrocarbons and heteroatom substituted analogues, including twelve 1,3- and twelve corresponding 1,5-sigmatropic rearrangements (Scheme 1), have been investigated at the QCISD(T)/6-3 1 1G(d,p)∥B3LYP/6-311++G(d,p) level of theory.

  11. Molecular size evaluation of linear and branched paraffins from the gasoline pool by DFT quantum chemical calculations

    Energy Technology Data Exchange (ETDEWEB)

    Federico Jimenez-Cruz; Georgina C. Laredo [Instituto Mexicano del Petroleo, Mexico (Mexico). Programa de Tratamiento de Crudo Maya

    2004-11-01

    A good approach of the critical molecular dimensions of 35 linear and branched C5-C8 paraffins by DFT quantum chemical calculations at B3LYP/6-31G{asterisk}{asterisk} level of theory in gas phase is described. In this context, we found that either the determined molecular width or width-height average values can be used as critical measures in the analysis for selection of molecular sieves materials, depending on their pore size and shape. The molecular width values for linear and monosubstituted paraffins are 4.2 and 5.5 {angstrom}, respectively. In the case of disubstituted paraffins, the values are 5.5 for 2,3-, 2,4-, 2,5- and 3,4-disubstituted and for 2,2- and 3,3-disubstituted are 6.7-7.1 {angstrom}. The values for ethyl-substituted are 6.1-6.7 {angstrom} and for trisubstituted isoparaffins are 6.7. In order to select a porous material for selective separation of isoparaffins and paraffins, the zeolite diffusivity can be correlated with the critical diameter of the paraffins according to the geometry-limited diffusion concept and the effective minimum dimensions of the molecules. The calculated values of CPK molecular volume of the titled paraffins showed a good discrimination between the number of carbons and molecular size. 25 refs., 4 figs., 2 tabs.

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

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy, E-mail: ramamoor@umich.edu [Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055 (United States)

    2015-05-28

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

  13. Isotope shifts of the three lowest 1S states of the B+ ion calculated with a finite-nuclear-mass approach and with relativistic and quantum electrodynamics corrections

    Science.gov (United States)

    Bubin, Sergiy; Komasa, Jacek; Stanke, Monika; Adamowicz, Ludwik

    2010-03-01

    We present very accurate quantum mechanical calculations of the three lowest S-states [1s22s2(S10), 1s22p2(S10), and 1s22s3s(S10)] of the two stable isotopes of the boron ion, B10+ and B11+. At the nonrelativistic level the calculations have been performed with the Hamiltonian that explicitly includes the finite mass of the nucleus as it was obtained by a rigorous separation of the center-of-mass motion from the laboratory frame Hamiltonian. The spatial part of the nonrelativistic wave function for each state was expanded in terms of 10 000 all-electron explicitly correlated Gaussian functions. The nonlinear parameters of the Gaussians were variationally optimized using a procedure involving the analytical energy gradient determined with respect to the nonlinear parameters. The nonrelativistic wave functions of the three states were subsequently used to calculate the leading α2 relativistic corrections (α is the fine structure constant; α =1/c, where c is the speed of light) and the α3 quantum electrodynamics (QED) correction. We also estimated the α4 QED correction by calculating its dominant component. A comparison of the experimental transition frequencies with the frequencies obtained based on the energies calculated in this work shows an excellent agreement. The discrepancy is smaller than 0.4 cm-1.

  14. Isotope shifts of the three lowest 1S states of the B+ ion calculated with a finite-nuclear-mass approach and with relativistic and quantum electrodynamics corrections.

    Science.gov (United States)

    Bubin, Sergiy; Komasa, Jacek; Stanke, Monika; Adamowicz, Ludwik

    2010-03-21

    We present very accurate quantum mechanical calculations of the three lowest S-states [1s(2)2s(2)((1)S(0)), 1s(2)2p(2)((1)S(0)), and 1s(2)2s3s((1)S(0))] of the two stable isotopes of the boron ion, (10)B(+) and (11)B(+). At the nonrelativistic level the calculations have been performed with the Hamiltonian that explicitly includes the finite mass of the nucleus as it was obtained by a rigorous separation of the center-of-mass motion from the laboratory frame Hamiltonian. The spatial part of the nonrelativistic wave function for each state was expanded in terms of 10,000 all-electron explicitly correlated Gaussian functions. The nonlinear parameters of the Gaussians were variationally optimized using a procedure involving the analytical energy gradient determined with respect to the nonlinear parameters. The nonrelativistic wave functions of the three states were subsequently used to calculate the leading alpha(2) relativistic corrections (alpha is the fine structure constant; alpha=1/c, where c is the speed of light) and the alpha(3) quantum electrodynamics (QED) correction. We also estimated the alpha(4) QED correction by calculating its dominant component. A comparison of the experimental transition frequencies with the frequencies obtained based on the energies calculated in this work shows an excellent agreement. The discrepancy is smaller than 0.4 cm(-1).

  15. Detailed calculation of spectral noise caused by measurement errors of Mach-Zehnder interferometer optical path phases in a spatial heterodyne spectrometer with a phase shift scheme.

    Science.gov (United States)

    Takada, Kazumasa; Seino, Mitsuyoshi; Chiba, Akito; Okamoto, Katsunari

    2013-04-20

    We calculate the root mean square (rms) value of the spectral noise caused by optical path phase measurement errors in a spatial heterodyne spectrometer (SHS) featuring a complex Fourier transformation. In our calculation the deviated phases of each Mach-Zehnder interferometer in the in-phase and quadrature states are treated as statistically independent random variables. We show that the rms value is proportional to the rms error of the phase measurement and that the proportionality coefficient is given analytically. The relationship enables us to estimate the potential performance of the SHS such as the sidelobe suppression ratio for a given measurement error. PMID:23669661

  16. Efficiency enhancement calculations of state-of-the-art solar cells by luminescent layers with spectral shifting, quantum cutting, and quantum tripling function

    NARCIS (Netherlands)

    Ten Kate, O.M.; De Jong, M.; Hintzen, H.T.; Van der Kolk, E.

    2013-01-01

    Solar cells of which the efficiency is not limited by the Shockley-Queisser limit can be obtained by integrating a luminescent spectral conversion layer into the cell structure. We have calculated the maximum efficiency of state-of-the-art c-Si, pc-Si, a-Si, CdTe, GaAs, CIS, CIGS, CGS, GaSb, and Ge

  17. Self-consistent Green’s-function technique for bulk and surface impurity calculations: Surface core-level shifts by complete screening

    DEFF Research Database (Denmark)

    Aldén, M.; Abrikosov, I. A.; Johansson, B.;

    1994-01-01

    We have implemented an efficient self-consistent Green's-function technique, based on the tight-binding linear-muffin-tin-orbitals method, for calculating the electronic structure and total energy of a substitutional impurity located either in the bulk or at the surface. The technique makes use o...

  18. The Balance Calculating System of Chemical Engineering Counting and Its Selection Methods%化工计算衡算体系及其选择技巧

    Institute of Scientific and Technical Information of China (English)

    张南哲

    2015-01-01

    化工计算是化学工程学的基础,在化工计算中衡算体系的划定是一项重要环节。以物料衡算为例,说明了化工计算衡算体系划分的多样化和重要性,指出了选择衡算体系的基本原则和一些具体的方法和技巧。恰当选择化工衡算体系不仅可以简化计算、提高衡算效率,而且可以避免错误的出现。%Chemical calculations are the basis of chemical engineering. In chemical engineering calculation, division of balance calculating system is an important part. Took the material balance as an example, the diversification and the importance of balance chemical calculation division were explained, the basic principles to choose the balance calculating and some specific methods and skills were pointed out. Proper selection of the balance calculating system can not only simplify the calculation and improve the efficiency, but also avoid the errors.

  19. The overall phase shift and lens effect calculation using Gaussian boundary conditions and paraxial ray approximation for an end-pumped solid-state laser

    Indian Academy of Sciences (India)

    H Nadgaran; P Elahi

    2006-03-01

    In this work, the inhomogeneous equation of heat conduction was exactly solved by applying inhomogeneous boundary conditions for laser crystals of aspect ratio=1 (aspect ratio=radius of the laser rod/length of the laser rod). We have shown that the paraxial ray approximation leads the solution to be a function of 2, that is, the approximation is equivalent to a situation in which a homogeneous pump source is used. The solution was then used to derive expressions for the overall phase shift, focal length of the thermal lens and the end effect induced curvature of the end face. The expressions were then applied to Nd:YAG laser medium. The result shows a meaningful correction of the order of 0.001 cm to the focal length of Nd:YAG rod for 3 W source power and beam waist of 100 m.

  20. Production of lightning NOx and its vertical distribution calculated from three-dimensional cloud-scale chemical transport model simulations

    KAUST Repository

    Ott, Lesley E.

    2010-02-18

    A three-dimensional (3-D) cloud-scale chemical transport model that includes a parameterized source of lightning NOx on the basis of observed flash rates has been used to simulate six midlatitude and subtropical thunderstorms observed during four field projects. Production per intracloud (PIC) and cloud-to-ground (PCG) flash is estimated by assuming various values of PIC and PCG for each storm and determining which production scenario yields NOx mixing ratios that compare most favorably with in-cloud aircraft observations. We obtain a mean PCG value of 500 moles NO (7 kg N) per flash. The results of this analysis also suggest that on average, PIC may be nearly equal to PCG, which is contrary to the common assumption that intracloud flashes are significantly less productive of NO than are cloud-to-ground flashes. This study also presents vertical profiles of the mass of lightning NOx after convection based on 3-D cloud-scale model simulations. The results suggest that following convection, a large percentage of lightning NOx remains in the middle and upper troposphere where it originated, while only a small percentage is found near the surface. The results of this work differ from profiles calculated from 2-D cloud-scale model simulations with a simpler lightning parameterization that were peaked near the surface and in the upper troposphere (referred to as a “C-shaped” profile). The new model results (a backward C-shaped profile) suggest that chemical transport models that assume a C-shaped vertical profile of lightning NOx mass may place too much mass near the surface and too little in the middle troposphere.

  1. Electronic structures of TiO2-TCNE, -TCNQ, and -2,6-TCNAQ surface complexes studied by ionization potential measurements and DFT calculations: Mechanism of the shift of interfacial charge-transfer bands

    Science.gov (United States)

    Fujisawa, Jun-ichi; Hanaya, Minoru

    2016-06-01

    Interfacial charge-transfer (ICT) transitions between inorganic semiconductors and π-conjugated molecules allow direct charge separation without loss of energy. This feature is potentially useful for efficient photovoltaic conversions. Charge-transferred complexes of TiO2 nanoparticles with 7,7,8,8-tetracyanoquinodimethane (TCNQ) and its analogues (TCNX) show strong ICT absorption in the visible region. The ICT band was reported to be significantly red-shifted with extension of the π-conjugated system of TCNX. In order to clarify the mechanism of the red-shift, in this work, we systematically study electronic structures of the TiO2-TCNX surface complexes (TCNX; TCNE, TCNQ, 2,6-TCNAQ) by ionization potential measurements and density functional theory (DFT) calculations.

  2. Calculation of activation energies for transport and recombination in mesoporous TiO2/dye/electrolyte films--taking into account surface charge shifts with temperature.

    Science.gov (United States)

    O'Regan, Brian C; Durrant, James R

    2006-05-01

    Transient photovoltage and photocurrent measurements have been employed to determine the recombination and transport kinetics in operating dye-sensitized photovoltaic cells as a function of potential and temperature. Photocurrent transients have been taken at the open circuit potential, as opposed to the standard measurement at short circuit. Kinetic results have been used to calculate the activation energy as function of the Fermi level position in the TiO(2). In the calculation of activation energies, we have explicitly taken into account the temperature dependence of the offset between the electrolyte redox potential and the conduction band edge. This new method gives activation energies that decrease linearly as the Fermi level position moves toward the conduction band edge, as expected, but not found in previous studies. The results are consistent with the presence of a distribution of traps below the TiO(2) conduction band, the detrapping from which limits both the transport and the recombination of electrons. PMID:16640403

  3. High resolution spectroscopy and chemical shift imaging of hyperpolarized 129Xe dissolved in the human brain in vivo at 1.5 tesla

    Science.gov (United States)

    Rao, Madhwesha; Stewart, Neil J.; Norquay, Graham; Griffiths, Paul D.

    2016-01-01

    Purpose Upon inhalation, xenon diffuses into the bloodstream and is transported to the brain, where it dissolves in various compartments of the brain. Although up to five chemically distinct peaks have been previously observed in 129Xe rat head spectra, to date only three peaks have been reported in the human head. This study demonstrates high resolution spectroscopy and chemical shift imaging (CSI) of 129Xe dissolved in the human head at 1.5 Tesla. Methods A 129Xe radiofrequency coil was built in‐house and 129Xe gas was polarized using spin‐exchange optical pumping. Following the inhalation of 129Xe gas, NMR spectroscopy was performed with spectral resolution of 0.033 ppm. Two‐dimensional CSI in all three anatomical planes was performed with spectral resolution of 2.1 ppm and voxel size 20 mm × 20 mm. Results Spectra of hyperpolarized 129Xe dissolved in the human head showed five distinct peaks at 188 ppm, 192 ppm, 196 ppm, 200 ppm, and 217 ppm. Assignment of these peaks was consistent with earlier studies. Conclusion High resolution spectroscopy and CSI of hyperpolarized 129Xe dissolved in the human head has been demonstrated. For the first time, five distinct NMR peaks have been observed in 129Xe spectra from the human head in vivo. Magn Reson Med 75:2227–2234, 2016. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. PMID:27080441

  4. Chemical Bonding of AlH3 Hydride by Al-L2,3 Electron Energy-Loss Spectra and First-Principles Calculations

    Directory of Open Access Journals (Sweden)

    Kazutaka Ikeda

    2012-03-01

    Full Text Available In a previous study, we used transmission electron microscopy and electron energy-loss (EEL spectroscopy to investigate dehydrogenation of AlH3 particles. In the present study, we systematically examine differences in the chemical bonding states of Al-containing compounds (including AlH3 by comparing their Al-L2,3 EEL spectra. The spectral chemical shift and the fine peak structure of the spectra were consistent with the degree of covalent bonding of Al. This finding will be useful for future nanoscale analysis of AlH3 dehydrogenation toward the cell.

  5. Non-covalent interactions in ionic liquid ion pairs and ion pair dimers: a quantum chemical calculation analysis.

    Science.gov (United States)

    Marekha, Bogdan A; Kalugin, Oleg N; Idrissi, Abdenacer

    2015-07-14

    Ionic liquids (ILs) being composed of bulky multiatomic ions reveal a plethora of non-covalent interactions which determine their microscopic structure. In order to establish the main peculiarities of these interactions in an IL-environment, we have performed quantum chemical calculations for a set of representative model molecular clusters. These calculations were coupled with advanced methods of analysis of the electron density distribution, namely, the quantum theory of atoms in molecules (QTAIM) and the non-covalent interaction (NCI; J. Am. Chem. Soc., 2010, 132, 6499) approaches. The former allows for profound quantitative characterization of non-covalent interactions between atoms while the latter gives an overview of spatial extent, delocalization, and relative strength of such interactions. The studied systems consist of 1-butyl-3-methylimidazolium (Bmim(+)) cations and different perfluorinated anions: tetrafluoroborate (BF4(-)), hexafluorophosphate (PF6(-)), trifluoromethanesulfonate (TfO(-)), and bis(trifluoromethanesulfonyl)imide (TFSI(-)). IL ion pairs and ion pair dimers were considered as model structures for the neat ILs and large aggregates. Weak electrostatic hydrogen bonding was found between the anions and the imidazolium ring hydrogen atoms of cations. Weaker but still appreciable hydrogen bonding was also noted for hydrogen atoms adjacent to the imidazolium ring alkyl groups of Bmim(+). The relative strength of the hydrogen bonding is higher in BmimTfO and BmimBF4 ILs than in BmimPF6 and BmimTFSI, whereas BmimTfO and BmimTFSI reveal higher sensitivity of hydrogen bonding at the different hydrogen atoms of the imidazolium ring. PMID:26059822

  6. Measurement of sample temperatures under magic-angle spinning from the chemical shift and spin-lattice relaxation rate of 79Br in KBr powder

    Science.gov (United States)

    Thurber, Kent R.; Tycko, Robert

    2009-01-01

    Accurate determination of sample temperatures in solid state nuclear magnetic resonance (NMR) with magic-angle spinning (MAS) can be problematic, particularly because frictional heating and heating by radio-frequency irradiation can make the internal sample temperature significantly different from the temperature outside the MAS rotor. This paper demonstrates the use of 79Br chemical shifts and spin-lattice relaxation rates in KBr powder as temperature-dependent parameters for the determination of internal sample temperatures. Advantages of this method include high signal-to-noise, proximity of the 79Br NMR frequency to that of 13C, applicability from 20 K to 320 K or higher, and simultaneity with adjustment of the MAS axis direction. We show that spin-lattice relaxation in KBr is driven by a quadrupolar mechanism. We demonstrate a simple approach to including KBr powder in hydrated samples, such as biological membrane samples, hydrated amyloid fibrils, and hydrated microcrystalline proteins, that allows direct assessment of the effects of frictional and radio-frequency heating under experimentally relevant conditions. PMID:18930418

  7. Comprehensive signal assignment of 13C-labeled lignocellulose using multidimensional solution NMR and 13C chemical shift comparison with solid-state NMR.

    Science.gov (United States)

    Komatsu, Takanori; Kikuchi, Jun

    2013-09-17

    A multidimensional solution NMR method has been developed using various pulse programs including HCCH-COSY and (13)C-HSQC-NOESY for the structural characterization of commercially available (13)C labeled lignocellulose from potatoes (Solanum tuberosum L.), chicory (Cichorium intybus), and corn (Zea mays). This new method allowed for 119 of the signals in the (13)C-HSQC spectrum of lignocelluloses to be assigned and was successfully used to characterize the structures of lignocellulose samples from three plants in terms of their xylan and xyloglucan structures, which are the major hemicelluloses in angiosperm. Furthermore, this new method provided greater insight into fine structures of lignin by providing a high resolution to the aromatic signals of the β-aryl ether and resinol moieties, as well as the diastereomeric signals of the β-aryl ether. Finally, the (13)C chemical shifts assigned in this study were compared with those from solid-state NMR and indicated the presence of heterogeneous dynamics in the polysaccharides where rigid cellulose and mobile hemicelluloses moieties existed together. PMID:24010724

  8. Determination of the Orientation and Dynamics of Ergosterol in Model Membranes Using Uniform 13C Labeling and Dynamically Averaged 13C Chemical Shift Anisotropies as Experimental Restraints

    Science.gov (United States)

    Soubias, O.; Jolibois, F.; Massou, S.; Milon, A.; Réat, V.

    2005-01-01

    A new strategy was established to determine the average orientation and dynamics of ergosterol in dimyristoylphosphatidylcholine model membranes. It is based on the analysis of chemical shift anisotropies (CSAs) averaged by the molecular dynamics. Static 13C CSA tensors were computed by quantum chemistry, using the gauge-including atomic-orbital approach within Hartree-Fock theory. Uniformly 13C-labeled ergosterol was purified from Pichia pastoris cells grown on labeled methanol. After reconstitution into dimyristoylphosphatidylcholine lipids, the complete 1H and 13C assignment of ergosterol's resonances was performed using a combination of magic-angle spinning two-dimensional experiments. Dynamically averaged CSAs were determined by standard side-band intensity analysis for isolated 13C resonances (C3 and ethylenic carbons) and by off-magic-angle spinning experiments for other carbons. A set of 18 constraints was thus obtained, from which the sterol's molecular order parameter and average orientation could be precisely defined. The validity of using computed CSAs in this strategy was verified on cholesterol model systems. This new method allowed us to quantify ergosterol's dynamics at three molar ratios: 16 mol % (Ld phase), 30 mol % (Lo phase), and 23 mol % (mixed phases). Contrary to cholesterol, ergosterol's molecular diffusion axis makes an important angle (14°) with the inertial axis of the rigid four-ring system. PMID:15923221

  9. Determination of NH proton chemical shift anisotropy with 14N-1H heteronuclear decoupling using ultrafast magic angle spinning solid-state NMR

    Science.gov (United States)

    Pandey, Manoj Kumar; Nishiyama, Yusuke

    2015-12-01

    The extraction of chemical shift anisotropy (CSA) tensors of protons either directly bonded to 14N nuclei (I = 1) or lying in their vicinity using rotor-synchronous recoupling pulse sequence is always fraught with difficulty due to simultaneous recoupling of 14N-1H heteronuclear dipolar couplings and the lack of methods to efficiently decouple these interactions. This difficulty mainly arises from the presence of large 14N quadrupolar interactions in comparison to the rf field that can practically be achieved. In the present work it is demonstrated that the application of on-resonance 14N-1H decoupling with rf field strength ∼30 times weaker than the 14N quadrupolar coupling during 1H CSA recoupling under ultrafast MAS (90 kHz) results in CSA lineshapes that are free from any distortions from recoupled 14N-1H interactions. With the use of extensive numerical simulations we have shown the applicability of our proposed method on a naturally abundant L-Histidine HCl·H2O sample.

  10. Scan time reduction in {sup 23}Na-Magnetic Resonance Imaging using the chemical shift imaging sequence. Evaluation of an iterative reconstruction method

    Energy Technology Data Exchange (ETDEWEB)

    Weingaertner, Sebastian; Konstandin, Simon; Schad, Lothar R. [Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Wetterling, Friedrich [Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Dublin Univ. (Ireland) Trinity Inst. of Neuroscience; Fatar, Marc [Heidelberg Univ., Mannheim (Germany). Dept. of Neurology; Neumaier-Probst, Eva [Heidelberg Univ., Mannheim (Germany). Dept. of Neuroradiology

    2015-07-01

    To evaluate potential scan time reduction in {sup 23}Na-Magnetic Resonance Imaging with the chemical shift imaging sequence (CSI) using undersampled data of high-quality datasets, reconstructed with an iterative constrained reconstruction, compared to reduced resolution or reduced signal-to-noise ratio. CSI {sup 23}Na-images were retrospectively undersampled and reconstructed with a constrained reconstruction scheme. The results were compared to conventional methods of scan time reduction. The constrained reconstruction scheme used a phase constraint and a finite object support, which was extracted from a spatially registered {sup 1}H-image acquired with a double-tuned coil. The methods were evaluated using numerical simulations, phantom images and in-vivo images of a healthy volunteer and a patient who suffered from cerebral ischemic stroke. The constrained reconstruction scheme showed improved image quality compared to a decreased number of averages, images with decreased resolution or circular undersampling with weighted averaging for any undersampling factor. Brain images of a stroke patient, which were reconstructed from three-fold undersampled k-space data, resulted in only minor differences from the original image (normalized root means square error < 12%) and an almost identical delineation of the stroke region (mismatch < 6%). The acquisition of undersampled {sup 23}Na-CSI images enables up to three-fold scan time reduction with improved image quality compared to conventional methods of scan time saving.

  11. Quantum Chemical Calculations on the Interaction between Flavonol and Functional Monomers (Methacrylic Acid and 4-Vinylpyridine in Molecularly Imprinted Polymers

    Directory of Open Access Journals (Sweden)

    Luis Enrique Gómez-Pineda

    2010-06-01

    Full Text Available Quantum chemical calculations were performed to characterize the interaction of the flavonol molecule (FL with methacrylic acid (MAA and 4-vinylpyridine (4VPy in the formation of imprinted polymers. The polarizable continuum model (PCM was used to gain insight on the type of interaction between the reactant molecules under vacuum conditions and in the presence of different solvents. The effect of solvent on the pre-polymerization complex formation was evaluated through the stability energy, in which chloroform behaves as the best solvent for the synthesis of the imprinted polymers since it facilitates the reaction by lowering its degree of stabilization. The reactivity was analyzed in terms of the electrostatic surface potential (ESP and Mulliken charge. By means of these results, it has been possible to determine two potential recognition sites for the interaction of the MAA monomer and one for the 4VPy in relation to the strength of interaction with FL. In this concern, the interaction of the system FL-MAA is stronger than FL-4VPy.

  12. Shifting Attention

    Science.gov (United States)

    Ingram, Jenni

    2014-01-01

    This article examines the shifts in attention and focus as one teacher introduces and explains an image that represents the processes involved in a numeric problem that his students have been working on. This paper takes a micro-analytic approach to examine how the focus of attention shifts through what the teacher and students do and say in the…

  13. Synthesis, antimicrobial evaluation and theoretical prediction of NMR chemical shifts of thiazole and selenazole derivatives with high antifungal activity against Candida spp.

    Science.gov (United States)

    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.

  14. Calculation of liquid-liquid equilibrium of aqueous two-phase systems using a chemical-theory-based excess Gibbs energy model

    Directory of Open Access Journals (Sweden)

    Pessôa Filho P. A.

    2004-01-01

    Full Text Available Mixtures containing compounds that undergo hydrogen bonding show large deviations from ideal behavior. These deviations can be accounted for through chemical theory, according to which the formation of a hydrogen bond can be treated as a chemical reaction. This chemical equilibrium needs to be taken into account when applying stability criteria and carrying out phase equilibrium calculations. In this work, we illustrate the application of the stability criteria to establish the conditions under which a liquid-phase split may occur and the subsequent calculation of liquid-liquid equilibrium using a chemical-theory-modified Flory-Huggins equation to describe the non ideality of aqueous two-phase systems composed of poly(ethylene glycol and dextran. The model was found to be able to correlate ternary liquid-liquid diagrams reasonably well by simple adjustment of the polymer-polymer binary interaction parameter.

  15. Determination of the Tautomeric Equilibria of Pyridoyl Benzoyl -Diketones in the Liquid and Solid State through the use of Deuterium Isotope Effects on 1H and 13C NMR Chemical Shifts and Spin Coupling Constants

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Borisov, Eugeny V.; Lindon, John C.

    2015-01-01

    The tautomeric equilibria for 2-pyridoyl-, 3-pyridoyl-, and 4-pyridoyl-benzoyl methane have been investigated using deuterium isotope effects on 1H and 13C chemical shifts both in the liquid and the solid state. Equilibria are established both in the liquid and the solid state. In addition, in th...

  16. SAFT缔合模型关联含水体系的1H NMR%Correlation of 1H NMR Chemical Shift for Aqueous Solutions by Statistical Associating Fluid Theory Association Model

    Institute of Scientific and Technical Information of China (English)

    许波; 李浩然; 王从敏; 许映杰; 韩世钧

    2005-01-01

    1H NMR chemical shifts of binary aqueous mixtures of acylamide, alcohol, dimethyl sulphoxide (DMSO), and acetone are correlated by statistical associating fluid theory (SAFT) association model. The comparison between SAFT association model and Wilson equation shows that the former is better for dealing with aqueous solutions. Finally, the specialties of both models are discussed.

  17. The use of chemical shift temperature gradients to establish the paramagnetic susceptibility tensor orientation: Implication for structure determination/refinement in paramagnetic metalloproteins

    Energy Technology Data Exchange (ETDEWEB)

    Xia Zhicheng; Nguyen, Bao D.; La Mar, Gerd N. [University of California, Department of Chemistry (United States)

    2000-06-15

    The use of dipolar shifts as important constraints in refining molecular structure of paramagnetic metalloproteins by solution NMR is now well established. A crucial initial step in this procedure is the determination of the orientation of the anisotropic paramagnetic susceptibility tensor in the molecular frame which is generated interactively with the structure refinement. The use of dipolar shifts as constraints demands knowledge of the diamagnetic shift, which, however, is very often not directly and easily accessible. We demonstrate that temperature gradients of dipolar shifts can serve as alternative constraints for determining the orientation of the magnetic axes, thereby eliminating the need to estimate the diamagnetic shifts. This approach is tested on low-spin, ferric sperm whale cyanometmyoglobin by determining the orientation, anisotropies and anisotropy temperature gradients by the alternate routes of using dipolar shifts and dipolar shift gradients as constraints. The alternate routes ultimately lead to very similar orientation of the magnetic axes, magnetic anisotropies and magnetic anisotropy temperature gradients which, by inference, would lead to an equally valid description of the molecular structure. It is expected that the use of the dipolar shift temperature gradients, rather than the dipolar shifts directly, as constraints will provide an accurate shortcut in a solution structure determination of a paramagnetic metalloprotein.

  18. The use of a hot cyclone for separation of heavy metals during combustion, evaluation by chemical equilibrium calculations

    International Nuclear Information System (INIS)

    This degree-project is a part of a project financed by the European Communities non Nuclear energy program. The aim of the project is to reach a sustainable use of biofuels as energy source. A requirement for sustainable use of biomass fuel in combustion and gasification plants is that the ash produced can be recycled back to the forest and farmlands in a safe and controlled way. Recycling is important because most of the nutrients (Ca, Mg, P, Na and K) are ending up in the ash. However, the ashes also contain heavy metals and organic pollutants that should not be recycled. To solve this problem, a new technique for separation of the heavy metals during combustion is under development. This technique builds on evaporation of heavy metals and particle separation with a hot cyclone. The idea is that the heavy metal will pass the cyclone as gas species while the nutrients will be separated in the cyclone from the flue gas. The heavy metals are then collected in the more efficient cleaning device downstream in the process. In the present study, the technique has been evaluated by chemical equilibrium calculations and the results were compared with some previously performed full-scale experiments. The results show that by this technique a separation of Cd and Pb will be possible. Concerning the elements As, Cu and Cr, it may be possible to separate them to some extent while the element Ni and V will not be separated. At least 60-70% of Na and K and 90% of Ca, Mg and P will be separated in the cyclone 21 refs, 12 figs, 2 tabs

  19. Free Energy Minimization Calculation of Complex Chemical Equilibria. Reduction of Silicon Dioxide with Carbon at High Temperature.

    Science.gov (United States)

    Wai, C. M.; Hutchinson, S. G.

    1989-01-01

    Discusses the calculation of free energy in reactions between silicon dioxide and carbon. Describes several computer programs for calculating the free energy minimization and their uses in chemistry classrooms. Lists 16 references. (YP)

  20. Origin of the chemical shift in X-ray absorption near-edge spectroscopy at the Mn K-Edge in manganese oxide compounds

    NARCIS (Netherlands)

    de Vries, AH; Hozoi, L; Broer, R; Broer-Braam, H.B.

    2003-01-01

    The absorption edge in Mn K-edge X-ray absorption spectra of manganese oxide compounds shows a shift of several electronvolts in going from MnO through LaMnO3 to CaMnO3. On the other hand, in X-ray photoelectron spectra much smaller shifts are observed. To identify the mechanisms that cause the obse

  1. Improved techniques for outgoing wave variational principle calculations of converged state-to-state transition probabilities for chemical reactions

    Science.gov (United States)

    Mielke, Steven L.; Truhlar, Donald G.; Schwenke, David W.

    1991-01-01

    Improved techniques and well-optimized basis sets are presented for application of the outgoing wave variational principle to calculate converged quantum mechanical reaction probabilities. They are illustrated with calculations for the reactions D + H2 yields HD + H with total angular momentum J = 3 and F + H2 yields HF + H with J = 0 and 3. The optimization involves the choice of distortion potential, the grid for calculating half-integrated Green's functions, the placement, width, and number of primitive distributed Gaussians, and the computationally most efficient partition between dynamically adapted and primitive basis functions. Benchmark calculations with 224-1064 channels are presented.

  2. Cardiac high-energy phosphate metabolism alters with age as studied in 196 healthy males with the help of 31-phosphorus 2-dimensional chemical shift imaging.

    Directory of Open Access Journals (Sweden)

    Regina Esterhammer

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

  3. Cardiac high-energy phosphate metabolism alters with age as studied in 196 healthy males with the help of 31-phosphorus 2-dimensional chemical shift imaging.

    Science.gov (United States)

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

    2014-01-01

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

  4. Tough Shift

    DEFF Research Database (Denmark)

    Brewer, Robert S.; Verdezoto, Nervo; Holst, Thomas;

    2015-01-01

    people to change their behavior at home. Leveraging prior research on encouraging reductions in residential energy use through game play, we introduce ShareBuddy: a casual mobile game intended to encourage players not only to reduce, but also to shift their electricity use. We conducted two field studies...... real-world resource use into a game....

  5. Power Shift

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@ "We are entering a new era of world history: the end of Western domination and the arrival of the Asian century. The question is: will Washington wake up to this reality?" This is the central premise of Kishore Mahbubani's provocative new book The New Asian Hemisphere: The Irresistible Shift of Global Power to the East.

  6. CHEMICALS

    CERN Multimedia

    Medical Service

    2002-01-01

    It is reminded that all persons who use chemicals must inform CERN's Chemistry Service (TIS-GS-GC) and the CERN Medical Service (TIS-ME). Information concerning their toxicity or other hazards as well as the necessary individual and collective protection measures will be provided by these two services. Users must be in possession of a material safety data sheet (MSDS) for each chemical used. These can be obtained by one of several means : the manufacturer of the chemical (legally obliged to supply an MSDS for each chemical delivered) ; CERN's Chemistry Service of the General Safety Group of TIS ; for chemicals and gases available in the CERN Stores the MSDS has been made available via EDH either in pdf format or else via a link to the supplier's web site. Training courses in chemical safety are available for registration via HR-TD. CERN Medical Service : TIS-ME :73186 or service.medical@cern.ch Chemistry Service : TIS-GS-GC : 78546

  7. Oxygen 17 NMR in the evaluation of oxygen bounding with central ion using hydrolysis products of niobium, tantalum, arsenic, antimony pentafluorides as an example. Symbasis in the change of 17O and 19F chemical shifts

    International Nuclear Information System (INIS)

    Hydrolysis products of niobium, tantalum, antimony and arsenic pentafluorides in acetonitrile solution were studied by the methods of 17O and 19F NMR. In 17O NMR spectra of niobium and tantalum pentafluorides hydrolysis products resonance signals of oxo-, hydroxo- and aquafluorocomplexes were defined. Considerable shift of 17O NMR resonance signals towards weak field making up about 300 m.p., may indicate a higher covalency (Π-character) of Nb-O bond compared to Ta-O one. Symbasis in the change of chemical shifts in 17O NMR and 19F NMR of the relevant hexafluorides and hydrolysis products was detected implying similarity of chemical bond nature in oxygen and fluorine

  8. The protein amide {sup 1}H{sup N} chemical shift temperature coefficient reflects thermal expansion of the N-H{center_dot}{center_dot}{center_dot}O=C hydrogen bond

    Energy Technology Data Exchange (ETDEWEB)

    Hong Jingbo; Jing Qingqing; Yao Lishan, E-mail: yaols@qibebt.ac.cn [Chinese Academy of Sciences, Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology (China)

    2013-01-15

    The protein amide {sup 1}H{sup N} chemical shift temperature coefficient can be determined with high accuracy by recording spectra at different temperatures, but the physical mechanism responsible for this temperature dependence is not well understood. In this work, we find that this coefficient strongly correlates with the temperature coefficient of the through-hydrogen-bond coupling, {sup 3h}J{sub NC Prime }, based on NMR measurements of protein GB3. Parallel tempering molecular dynamics simulation suggests that the hydrogen bond distance variation at different temperatures/replicas is largely responsible for the {sup 1}H{sup N} chemical shift temperature dependence, from which an empirical equation is proposed to predict the hydrogen bond thermal expansion coefficient, revealing responses of individual hydrogen bonds to temperature changes. Different expansion patterns have been observed for various networks formed by {beta} strands.

  9. Relativistic calculation of the beta decay probabilities in the optimized Dirac-Kohn-Sham atom model and a chemical environment effect

    Energy Technology Data Exchange (ETDEWEB)

    Glushkov, Alexander [Odessa University (Ukraine); Russian Academy of Sciences, Troitsk (Russian Federation); Khetselius, Olga; Dubrovskaya, Yuliya [Odessa University (Ukraine); Lovett, Ludmila [UK National Academy of Sciences and Bookdata Co., London (United Kingdom)

    2009-07-01

    New theoretical scheme for calculating the beta decay characteristics and an account for chemical environment effect on the beta decay ones is developed. As method of calculation of the relativistic fields and electron wave functions, the gauge invariant Dirac-Fock and Dirac-Kohn-Sham approaches are used. The results of calculating the decay probabilities for the beta decays: {sup 33}P-{sup 33}S, {sup 35}S-{sup 35}Cl, {sup 63}Ni-{sup 63}Cu, {sup 241}Pu-{sup 241}Am are presented. Comparison of the Fermi function values is carried out for different approximations of an exchange effect account, calculation with using wave functions on the boundary of the charged spherical nucleus and with using squires of the amplitudes of expansion of these functions near zero.

  10. Free-energy calculations using classical molecular simulation: application to the determination of the melting point and chemical potential of a flexible RDX model.

    Science.gov (United States)

    Sellers, Michael S; Lísal, Martin; Brennan, John K

    2016-03-21

    We present an extension of various free-energy methodologies to determine the chemical potential of the solid and liquid phases of a fully-flexible molecule using classical simulation. The methods are applied to the Smith-Bharadwaj atomistic potential representation of cyclotrimethylene trinitramine (RDX), a well-studied energetic material, to accurately determine the solid and liquid phase Gibbs free energies, and the melting point (Tm). We outline an efficient technique to find the absolute chemical potential and melting point of a fully-flexible molecule using one set of simulations to compute the solid absolute chemical potential and one set of simulations to compute the solid-liquid free energy difference. With this combination, only a handful of simulations are needed, whereby the absolute quantities of the chemical potentials are obtained, for use in other property calculations, such as the characterization of crystal polymorphs or the determination of the entropy. Using the LAMMPS molecular simulator, the Frenkel and Ladd and pseudo-supercritical path techniques are adapted to generate 3rd order fits of the solid and liquid chemical potentials. Results yield the thermodynamic melting point Tm = 488.75 K at 1.0 atm. We also validate these calculations and compare this melting point to one obtained from a typical superheated simulation technique.

  11. Computer Program for Calculation of Complex Chemical Equilibrium Compositions, Rocket Performance, Incident and Reflected Shocks, and Chapman-Jouguet Detonations. Interim Revision, March 1976

    Science.gov (United States)

    Gordon, S.; Mcbride, B. J.

    1976-01-01

    A detailed description of the equations and computer program for computations involving chemical equilibria in complex systems is given. A free-energy minimization technique is used. The program permits calculations such as (1) chemical equilibrium for assigned thermodynamic states (T,P), (H,P), (S,P), (T,V), (U,V), or (S,V), (2) theoretical rocket performance for both equilibrium and frozen compositions during expansion, (3) incident and reflected shock properties, and (4) Chapman-Jouguet detonation properties. The program considers condensed species as well as gaseous species.

  12. Determination of structural, spectrometric and nonlinear optical features of 2-(4-hydroxyphenylazo)benzoic acid by experimental techniques and quantum chemical calculations

    Science.gov (United States)

    Cinar, Mehmet; Yildiz, Nihat; Karabacak, Mehmet; Kurt, Mustafa

    2013-03-01

    The optimized geometrical structure, vibrational and electronic transitions, chemical shifts and nonlinear optical properties of 2-(4-hydroxyphenylazo)benzoic acid (HABA) compound were presented in this study. The ground state geometrical structure and vibrational wavenumbers were carried out by using density functional (DFT/B3LYP) method with 6-311++G(d,p) basis set. The vibrational spectra of title compound were recorded in solid state with FT-IR and FT-Raman spectrometry in the range of 4000-400 cm-1 and 4000-10 cm-1; respectively. The fundamental assignments were done on the basis of the recorded spectra and total energy distribution (TED) of the vibrational modes. The 1H and 13C NMR spectra were recorded in deuterated DMSO solution, and gauge-invariant atomic orbitals (GIAOs) method was used to predict the isotropic chemical shifts. The UV-Vis absorption spectra of the compound were observed in the range of 200-800 nm in ethanol, methanol and water solvents. To investigate the nonlinear optical properties, the polarizability, anisotropy of polarizability and molecular first hyperpolarizability were computed. A detailed description of spectroscopic behaviors of compound was given based on the comparison of experimental measurements and theoretical computations.

  13. A Series of Diamagnetic Pyridine Monoimine Rhenium Complexes with Different Degrees of Metal-to-Ligand Charge Transfer: Correlating (13) C NMR Chemical Shifts with Bond Lengths in Redox-Active Ligands.

    Science.gov (United States)

    Sieh, Daniel; Kubiak, Clifford P

    2016-07-18

    A set of pyridine monoimine (PMI) rhenium(I) tricarbonyl chlorido complexes with substituents of different steric and electronic properties was synthesized and fully characterized. Spectroscopic (NMR and IR) and single-crystal X-ray diffraction analyses of these complexes showed that the redox-active PMI ligands are neutral and that the overall electronic structure is little affected by the choices of the substituent at the ligand backbone. One- and two-electron reduction products were prepared from selected starting compounds and could also be characterized by multiple spectroscopic methods and X-ray diffraction. The final product of a one-electron reduction in THF is a diamagnetic metal-metal-bonded dimer after loss of the chlorido ligand. Bond lengths in and NMR chemical shifts of the PMI ligand backbone indicate partial electron transfer to the ligand. Two-electron reduction in THF also leads to the loss of the chlorido ligand and a pentacoordinate complex is obtained. The comparison with reported bond lengths and (13) C NMR chemical shifts of doubly reduced free pyridine monoaldimine ligands indicates that both redox equivalents in the doubly reduced rhenium complex investigated here are located in the PMI ligand. With diamagnetic complexes varying over three formal reduction stages at the PMI ligand we were, for the first time, able to establish correlations of the (13) C NMR chemical shifts with the relevant bond lengths in redox-active ligands over a full redox series. PMID:27319753

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

    Energy Technology Data Exchange (ETDEWEB)

    Yoshimura, Yuichi; Kulminskaya, Natalia V.; Mulder, Frans A. A., E-mail: fmulder@chem.au.dk [Aarhus University, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO) (Denmark)

    2015-02-15

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

  15. Synthesis, crystal structure analysis, spectral characterization, quantum chemical calculations, antioxidant and antimicrobial activity of 3-(4-chlorophenyl)-3a,4,7,7a-tetrahydro-4,7-methanobenzo[d]isoxazole

    Science.gov (United States)

    Eryılmaz, Serpil; Gül, Melek; İnkaya, Ersin; İdil, Önder; Özdemir, Namık

    2016-10-01

    In this paper, 3-(4-chlorophenyl)-3a,4,7,7a-tetrahydro-4,7-methanobenzo[d]isoxazole was synthesized via 1,3 dipolar cycloaddition, characterized by spectroscopic analysis such as FT-IR, 1H NMR, 13C NMR, UV-Vis, LC-MS/MS, Elemental Analysis, and X-ray Single Crystal diffraction technique. The Density Functional Theory (DFT/B3LYP) method with 6-311G(d,p) basis set in the ground state was applied for quantum chemical calculations and molecular geometric parameters of the compound were compared with the X-ray analysis results. FT-IR, NMR and UV-Vis spectral analysis were analysed to determine the compliance with the vibrational frequencies, 1H NMR and 13C NMR chemical shifts and absorption wavelength values. The frontier molecular orbitals (FMOs), some global reactivity descriptors, molecular electrostatic potential (MEP), thermodynamic properties, non-linear optical (NLO) behaviour of the compound were examined with the same method in gas phase, theoretically. Moreover, antioxidant activity was determined with three different methods - DPPH radical scavenging, reducing and metal chelating, antimicrobial activity were carried out with Gram positive, Gram negative and Eukaryote for the title compound.

  16. 化学反应焓变计算的解析%Understanding of the Calculation of Enthalpy Change in Chemical Reaction

    Institute of Scientific and Technical Information of China (English)

    梁营

    2011-01-01

    物理化学概念公式多,理论逻辑性强。化学反应焓变的计算内容繁多、计算思路新颖,如何很好理解其内涵,掌握其计算方法对学好物理化学具有重要作用,对学好其它热力学函数的计算具有指导作用。文章详细讨论了化学反应过程中焓变计算公式的引出,假设的模型和计算公式的误差情况。%There are many concepts and formulas in physical chemistry and its logic in theory is very strong.There are more contents and new calculation train of thought in the calculation of chemical reaction enthalpy.How to understand the contents well and grasp the calculation method is important for learning physical chemistry well,also play a vital role for learning other thermodynamical functions.The derivation,the assumption model and the errors of calculation of enthalpy change in chemical reactions were discussed in detail in the paper.

  17. Accurate electronic and chemical properties of 3d transition metal oxides using a calculated linear response U and a DFT + U(V) method

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Zhongnan; Kitchin, John R., E-mail: jkitchin@andrew.cmu.edu [Department of Chemical Engineering, Carnegie Mellon University, 5000 Forbes Ave., Pittsburgh, Pennsylvania 15213 (United States); Joshi, Yogesh V.; Raman, Sumathy [Exxon-Mobil Research and Engineering, 1545 Route 22 E St. 1, Annandale, New Jersey 08801 (United States)

    2015-04-14

    We validate the usage of the calculated, linear response Hubbard U for evaluating accurate electronic and chemical properties of bulk 3d transition metal oxides. We find calculated values of U lead to improved band gaps. For the evaluation of accurate reaction energies, we first identify and eliminate contributions to the reaction energies of bulk systems due only to changes in U and construct a thermodynamic cycle that references the total energies of unique U systems to a common point using a DFT + U(V ) method, which we recast from a recently introduced DFT + U(R) method for molecular systems. We then introduce a semi-empirical method based on weighted DFT/DFT + U cohesive energies to calculate bulk oxidation energies of transition metal oxides using density functional theory and linear response calculated U values. We validate this method by calculating 14 reactions energies involving V, Cr, Mn, Fe, and Co oxides. We find up to an 85% reduction of the mean average error (MAE) compared to energies calculated with the Perdew-Burke-Ernzerhof functional. When our method is compared with DFT + U with empirically derived U values and the HSE06 hybrid functional, we find up to 65% and 39% reductions in the MAE, respectively.

  18. Quantum chemical calculations and analysis of FTIR, FT-Raman and UV-Vis spectra of temozolomide molecule

    Science.gov (United States)

    Bhat, Sheeraz Ahmad; Ahmad, Shabbir

    2015-11-01

    A combined experimental and theoretical study of the structure, vibrational and electronic spectra of temozolomide molecule, which is largely used in the treatment of brain tumours, is presented. FTIR (4000-400 cm-1) and FT-Raman spectra (4000‒50 cm-1) have been recorded and analysed using anharmonic frequency calculations using VPT2, VSCF and CC-VSCF levels of theory within B3LYP/6-311++G(d,p) framework. Anharmonic methods give accurate frequencies of fundamental modes, overtones as well as Fermi resonances and account for coupling of different modes. The anharmonic frequencies calculated using VPT2 and CC-VSCF methods show better agreement with the experimental data. Harmonic frequencies including solvent effects are also computed using IEF-PCM model. The magnitudes of coupling between pair of modes have been calculated using coupling integral based on 2MR-QFF approximation. Intermolecular interactions are discussed for three possible dimers of temozolomide. UV-Vis spectrum, examined in ethanol solvent, is compared with the calculated spectrum at TD-DFT/6-311++G(d,p) level of theory. The electronic properties, such as excitation energy, frontier molecular orbital energies and the assignments of the absorption bands are also discussed.

  19. Accurate pKa Calculation of the Conjugate Acids of Alkanolamines, Alkaloids and Nucleotide Bases by Quantum Chemical Methods

    NARCIS (Netherlands)

    Gangarapu, S.; Marcelis, A.T.M.; Zuilhof, H.

    2013-01-01

    The pKa of the conjugate acids of alkanolamines, neurotransmitters, alkaloid drugs and nucleotide bases are calculated with density functional methods (B3LYP, M08-HX and M11-L) and ab initio methods (SCS-MP2, G3). Implicit solvent effects are included with a conductor-like polarizable continuum mode

  20. Center Manifold and Lie Symmetry Calculations on a Quasi-chemical Model for Growth-death Kinetics in Food

    OpenAIRE

    DeCoste, Rachelle; Piscitelle, Louis

    2007-01-01

    Food scientists at the U.S. Army's Natick Solider Center have developed a model for the lifecyle of the bacteria Staphylococcus aureus in intermediate moisture bread. In this article, we study this model using dynamical systems and Lie symmetry methods. We calculate center manifolds and Lie symmetries for different cases of parameter values and compare our results to those of the food scientists.

  1. Effect of aromatic molecules on the aggregation of C-phycocyanin: quantum chemical calculations on phycocyanobilin and phycoerythrobilin

    Energy Technology Data Exchange (ETDEWEB)

    Kumbar, M. (Adelphi Univ., Garden City, NY); MacColl, R.

    1975-08-01

    The energies of the highest occupied and lowest empty molecular orbitals were calculated for the chromophore groups of the proteins phycocyanin and phycoerythrin. These tetrapyrrole groups on the algal proteins are shown to provide them with the potential of acting as efficient electron donors and acceptors. In addition, the ..pi.. electron charges and bond orders were also computed. 4 figures, 1 table.

  2. Shifting densities

    OpenAIRE

    Mille, Matthieu

    2000-01-01

    In this paper, the author adopt a time-geography approach to examine the temporal variation of urban density by analysing spatial load changes at different times of the day at the communal and community level. The evolution of means of transport coupled with the abandon of the notion of direct proximity to the urban dwelling place provide the basis for this new approach to the study of urban densities. The shift towards spatial specialisation within cities has lead to radical changes in the f...

  3. Simulation of the f—d transitions of lanthanide ions in YPO4 using quantum-chemical calculations

    Science.gov (United States)

    Hu, Liu-Sen; Wen, Jun; Yin, Min; Xia, Shang-Da

    2012-01-01

    We constructed an effective one-electron Hamiltonian by using the 4f/5d energies and eigenvectors obtained from the first-principles calculation with the relativistic self-consistent discrete variational Slater software package (DV-Xα). From the effective Hamiltonian, we obtained the crystal-field and spin-orbit interaction parameters for the 4f and 5d electrons of lanthanide ions (Ce3+, Pr3+, Nd3+ and Eu3+) doped in YPO4, and these parameters were used to calculate the 4fN-4fN-15d transition. Comparison with experiments shows that the obtained parameters are reasonable and the excitation spectra can be well predicted.

  4. Excitons in poly(para phenylene vinylene): a quantum-chemical perspective based on high-level ab initio calculations.

    Science.gov (United States)

    Mewes, Stefanie A; Mewes, Jan-Michael; Dreuw, Andreas; Plasser, Felix

    2016-01-28

    Excitonic effects play a fundamental role in the photophysics of organic semiconductors such as poly(para phenylene vinylene) (PPV). The emergence of these effects is examined for PPV oligomers based on high level ab initio excited-state calculations. The computed many-body wavefunctions are subjected to our recently developed exciton analysis protocols to provide a qualitative and quantitative characterization of excitonic effects. The discussion is started by providing high-level benchmark calculations using the algebraic-diagrammatic construction for the polarization propagator in third order of perturbation theory (ADC(3)). These calculations support the general adequacy of the computationally more efficient ADC(2) method in the case of singly excited states but also reveal the existence of low-energy doubly excited states. In a next step, a series of oligomers with chains of two to eight phenyl rings is studied at the ADC(2) level showing that the confinement effects are dominant for small oligomers, while delocalized exciton bands emerge for larger systems. In the case of the largest oligomer, the first twenty singlet and triplet excited states are computed and a detailed analysis in terms of the Wannier and Frenkel models is presented. The presence of different Wannier bands becomes apparent, showing a general trend that exciton sizes are lowered with increasing quasi-momentum within the bands. PMID:26700493

  5. Calculation and Interpretation of the Standard Chemical Exergies of Elements Using the Chemical Reference Species%使用化学参考物质计算和阐明元素的标准化学放射本能

    Institute of Scientific and Technical Information of China (English)

    B(I)LGEN Sel(c)uk

    2009-01-01

    Exergy is the amount of work obtainable when some matter is brought to a state of thermodynamic equilibrium with the common components of the natural surroundings by means of reversible processes, involving interaction only with the above mentioned components of nature. This paper presents standard chemical exergy values for 85 elements. Reference species in the atmosphere (air), dissolved in the hydrosphere (oceans), and contained in the lithosphere (minerals) are used for these calculations. Standard chemical exergy values of elements were calculated from tabulated values obtained for standard conditions (an ambient temperature of 298.15 K and an atmospheric pressure of 0.1 MPa). Very low concentrations of elements in the atmosphere and oceans and the abundance of elements in the Earth's crust are no longer used in determining reference states for chemical elements. Liquid and gas mixtures generally are not useful as reference states. As a result of the work in this paper, a table of the chemical exergy values of many elements in the periodic table under standard conditions was tabulated.

  6. New Phase Shifting Algorithms Insensitive to Linear Phase Shift Errors

    Directory of Open Access Journals (Sweden)

    J. Novák

    2002-01-01

    Full Text Available This article describes and analyses multistep algorithms for evaluating of the wave field phase in interferometric measurements using the phase shifting technique. New phase shifting algorithms are proposed, with a constant but arbitrary phase shift between captured frames of the intensity of the interference field. The phase evaluation process then does not depend on linear phase shift errors. A big advantage of the described algorithms is their ability to determine the phase shift value at every point of the detector plane. A detailed analysis of these algorithms with respect to main factors that affect interferometric measurements is then carried out. The dependency of these algorithms on phase shift values is also studied several phase calculation algorithms are proposed. These are compared with respect to the resulting phase errors.

  7. The Use of Quantum Chemical Semiempirical Methods to Calculate the Lattice Energies of Organic Molecular Crystals. Part I: The Three Polymorphs of Glycine

    Science.gov (United States)

    Raabe, Gerhard

    2000-07-01

    A method to calculate the lattice energies of organic molecular crystals is described. It is based on the semiempirical quantum chemical MINDO/3 approximation but might also be used within the framework of any other quantum chemical method. The lattice energy is approximated by the sum of dispersion-, induction-, exchange repulsion-, and electrostatic energy. Different, however, from other schemes employed in this field, like for example the atom-atom-potential method, the variables in the expression for the lattice energy have not been fitted to reproduce experimental values and, therefore, the single contributions retain their original physical meaning. Moreover, the method offers the advantage that it may be directly applied to all compounds that can be treated within the framework of the underlying quantum chemical method. Thus, time consuming readjustment of the entire parameter set upon extension of the group of target molecules by another class of compounds becomes obsolete. As an example, the lattice energies of the three polymorphs of glycine are calculated.

  8. Site-specific protein backbone and side-chain NMR chemical shift and relaxation analysis of human vinexin SH3 domain using a genetically encoded {sup 15}N/{sup 19}F-labeled unnatural amino acid

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Pan [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China); School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Xi, Zhaoyong; Wang, Hu [School of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026 (China); Shi, Chaowei [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China); School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Xiong, Ying, E-mail: yxiong73@ustc.edu.cn [School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Tian, Changlin, E-mail: cltian@ustc.edu.cn [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China)

    2010-11-19

    Research highlights: {yields} Chemical synthesis of {sup 15}N/{sup 19}F-trifluomethyl phenylalanine. {yields} Site-specific incorporation of {sup 15}N/{sup 19}F-trifluomethyl phenylalanine to SH3. {yields} Site-specific backbone and side chain chemical shift and relaxation analysis. {yields} Different internal motions at different sites of SH3 domain upon ligand binding. -- Abstract: SH3 is a ubiquitous domain mediating protein-protein interactions. Recent solution NMR structural studies have shown that a proline-rich peptide is capable of binding to the human vinexin SH3 domain. Here, an orthogonal amber tRNA/tRNA synthetase pair for {sup 15}N/{sup 19}F-trifluoromethyl-phenylalanine ({sup 15}N/{sup 19}F-tfmF) has been applied to achieve site-specific labeling of SH3 at three different sites. One-dimensional solution NMR spectra of backbone amide ({sup 15}N){sup 1}H and side-chain {sup 19}F were obtained for SH3 with three different site-specific labels. Site-specific backbone amide ({sup 15}N){sup 1}H and side-chain {sup 19}F chemical shift and relaxation analysis of SH3 in the absence or presence of a peptide ligand demonstrated different internal motions upon ligand binding at the three different sites. This site-specific NMR analysis might be very useful for studying large-sized proteins or protein complexes.

  9. Host–guest complexes of mixed glycol-bipyridine cryptands: prediction of ion selectivity by quantum chemical calculations, part V

    OpenAIRE

    Svetlana Begel; Ralph Puchta; Rudi van Eldik

    2013-01-01

    The selectivity of the cryptands [2.2.bpy] and [2.bpy.bpy] for the endohedral complexation of alkali, alkaline-earth and earth metal ions was predicted on the basis of the DFT (B3LYP/LANL2DZp) calculated structures and complex-formation energies. The cavity size in both cryptands lay between that for [2.2.2] and [bpy.bpy.bpy], such that the complexation of K+, Sr2+ and Tl3+ is most favorable. While the [2.2.bpy] is moderately larger, preferring Rb+ complexation and demonstrating equal priorit...

  10. WATEQF; a FORTRAN IV version of WATEQ : a computer program for calculating chemical equilibrium of natural waters

    Science.gov (United States)

    Plummer, L. Niel; Jones, Blair F.; Truesdell, Alfred Hemingway

    1976-01-01

    WATEQF is a FORTRAN IV computer program that models the thermodynamic speciation of inorganic ions and complex species in solution for a given water analysis. The original version (WATEQ) was written in 1973 by A. H. Truesdell and B. F. Jones in Programming Language/one (PL/1.) With but a few exceptions, the thermochemical data, speciation, coefficients, and general calculation procedure of WATEQF is identical to the PL/1 version. This report notes the differences between WATEQF and WATEQ, demonstrates how to set up the input data to execute WATEQF, provides a test case for comparison, and makes available a listing of WATEQF. (Woodard-USGS)

  11. Size-Dependent Raman Shifts for nanocrystals.

    Science.gov (United States)

    Gao, Yukun; Zhao, Xinmei; Yin, Penggang; Gao, Faming

    2016-04-22

    Raman spectroscopy is a very sensitive tool for probing semiconductor nanocrystals. The underlying mechanism behind the size-dependent Raman shifts is still quite controversial. Here we offer a new theoretical method for the quantum confinement effects on the Raman spectra of semiconductor nanocrystals. We propose that the shift of Raman spectra in nanocrystals can result from two overlapping effects: the quantum effect shift and surface effect shift. The quantum effect shift is extracted from an extended Kubo formula, the surface effect shift is determined via the first principles calculations. Fairly good prediction of Raman shifts can be obtained without the use of any adjustable parameter. Closer analysis shows that the size-dependent Raman shifts in Si nanocrystals mainly result from the quantum effect shifts. For nanodiamond, the proportion of surface effect shift in Raman shift is up to about 40%. Such model can also provide a good baseline for using Raman spectroscopy as a tool to measure size.

  12. The calculation of radiation fields of chemical contamination of nature with the use of a digital model

    International Nuclear Information System (INIS)

    Danger of contamination of the environment by convection of air and fluid transport in porous media arise while disposing of waste radioactive isotopes and chemical industry waste in underground deep-seated horizons. As a result there is eventually observed the formation of radioactive fields of local character. A lot of methods using for defining of radioactive fields of objects of the similar type, basically are based on the registration particles and quantum, emitted by nuclear of the corresponding elements in their radioactive decay. This is especially important for objects intended for placement in the mass of low permeable rocks, such as rock type. On the base of complex using of modern information basis created the model of induced radiation field of environment

  13. Standard Gibbs free energies of reactions of ozone with free radicals in aqueous solution: quantum-chemical calculations.

    Science.gov (United States)

    Naumov, Sergej; von Sonntag, Clemens

    2011-11-01

    Free radicals are common intermediates in the chemistry of ozone in aqueous solution. Their reactions with ozone have been probed by calculating the standard Gibbs free energies of such reactions using density functional theory (Jaguar 7.6 program). O(2) reacts fast and irreversibly only with simple carbon-centered radicals. In contrast, ozone also reacts irreversibly with conjugated carbon-centered radicals such as bisallylic (hydroxycylohexadienyl) radicals, with conjugated carbon/oxygen-centered radicals such as phenoxyl radicals, and even with nitrogen- oxygen-, sulfur-, and halogen-centered radicals. In these reactions, further ozone-reactive radicals are generated. Chain reactions may destroy ozone without giving rise to products other than O(2). This may be of importance when ozonation is used in pollution control, and reactions of free radicals with ozone have to be taken into account in modeling such processes.

  14. The structure and molecular parameters of camphene determined by Fourier transform microwave spectroscopy and quantum chemical calculations

    Science.gov (United States)

    Neeman, Elias M.; Dréan, Pascal; Huet, Thérèse R.

    2016-04-01

    Camphene (C10H16) is a bicyclic monoterpene of atmospheric interest. The structure of the unique stable conformer was optimized using density functional theory and ab initio calculations. The rotational spectrum of camphene was recorded in a supersonic jet expansion with a Fourier transform microwave spectrometer over the range 2-20 GHz. Signals from the parent species and from the ten 13C isotopomers were observed in natural abundance. The rotational and centrifugal distortion parameters were fitted to a Watson's Hamiltonian in the A-reduction. Complex line-shapes resulting from a magnetic interaction associated with the pairs of hydrogen nuclei in the methylene groups was observed and modeled. The rotational constants were used together with equilibrium structure to determine the r0 and the rm(1) gas-phase geometries of the carbon skeleton. The present work provides the first spectroscopic characterization of camphene in the gas phase.

  15. Host–guest complexes of mixed glycol-bipyridine cryptands: prediction of ion selectivity by quantum chemical calculations, part V

    Directory of Open Access Journals (Sweden)

    Svetlana Begel

    2013-06-01

    Full Text Available The selectivity of the cryptands [2.2.bpy] and [2.bpy.bpy] for the endohedral complexation of alkali, alkaline-earth and earth metal ions was predicted on the basis of the DFT (B3LYP/LANL2DZp calculated structures and complex-formation energies. The cavity size in both cryptands lay between that for [2.2.2] and [bpy.bpy.bpy], such that the complexation of K+, Sr2+ and Tl3+ is most favorable. While the [2.2.bpy] is moderately larger, preferring Rb+ complexation and demonstrating equal priority for Sr2+ and Ba2+, the slightly smaller [2.bpy.bpy] yields more stable cryptates with Na+ and Ca2+. Although the CH2-units containing molecular bars fixed at the bridgehead nitrogen atoms determine the flexibility of the cryptands, the twist angles associated with the bipyridine and glycol building blocks also contribute considerably.

  16. A chiral rhenium complex with predicted high parity violation effects: synthesis, stereochemical characterization by VCD spectroscopy and quantum chemical calculations

    CERN Document Server

    Saleh, Nidal; Roisnel, Thierry; Guy, Laure; Bast, Radovan; Saue, Trond; Darquié, Benoît; Crassous, Jeanne

    2015-01-01

    With their rich electronic, vibrational, rotational and hyperfine structure, molecular systems have the potential to play a decisive role in precision tests of fundamental physics. For example, electroweak nuclear interactions should cause small energy differences between the two enantiomers of chiral molecules, a signature of parity symmetry breaking. Enantioenriched oxorhenium(VII) complexes S-(-)- and R-(+)-3 bearing a chiral 2-methyl-1-thio-propanol ligand have been prepared as potential candidates for probing molecular parity violation effects via high resolution laser spectroscopy of the Re=O stretching. Although the rhenium atom is not a stereogenic centre in itself, experimental vibrational circular dichroism (VCD) spectra revealed a surrounding chiral environment, evidenced by the Re=O bond stretching mode signal. The calculated VCD spectrum of the R enantiomer confirmed the position of the sulfur atom cis to the methyl, as observed in the solid-state X-ray crystallographic structure, and showed the ...

  17. Design, synthesis, characterization, quantum-chemical calculations and anti-inflammatory activity of novel series of thiophene derivatives

    Science.gov (United States)

    Helal, M. H.; Salem, M. A.; Gouda, M. A.; Ahmed, N. S.; El-Sherif, A. A.

    2015-08-01

    Interaction of 1-(4-morpholinophenyl)ethanone 1 with either malononitrile or ethyl cyanoacetate 2 afforded Knoevenagel-Cope product 3. In subsequent treatment of 3 with sulfur, the 2-aminothiophene derivatives (4a, 4b) are formed under basic conditions. The solvent-free reaction of thiophene derivative 4a with ethyl cyanoacetate afforded thieno[2,3-d][1,3]oxazine derivative 6. The base catalyzed condensation of 2-aminothiophene derivative (4a) with ethyl cyanoacetate afforded N-(thieno-2-yl) cyanoacetamide derivative 7. The latter was used to synthesize different heterocyclic derivatives comprising, pyridine and coumarin rings. Also, several substituted thieno[2,3-d]pyrimidines have been prepared from reaction of 2-aminothiophene-3-carbonitrile 4b with some electrophilic reagents. The structure of the newly compounds were confirmed on the basis of elemental analysis and spectral data. The molecular modeling of the synthesized compounds has been drawn and their molecular parameters were calculated. Also, valuable information is obtained from calculation of the molecular parameters including electronegativity, net dipole moment of the compounds, total energy, electronic energy, binding energy, HOMO and LUMO energy. Evaluation of anti-inflammatory activity of the tested compounds was performed in albino rats by producing carrageenan induced paw oedema and measuring the zone of inflammation at different time intervals i.e. 1, 2, 3 and 4 h after carrageenan injection. Results indicated that most of the tested compounds showed moderate to good activity comparable to indomethacin. Also, compound 16 with additional morpholine ring beside the thiophene ring inhibits carrageenan induced paw oedema more than the standard indomethacin drug at all the time scales studied. Thus, compound 16 is considered as a promising compound for further modification to obtain clinically useful anti-inflammatory agent.

  18. Molecular structure, electronic properties, NLO, NBO analysis and spectroscopic characterization of Gabapentin with experimental (FT-IR and FT-Raman) techniques and quantum chemical calculations.

    Science.gov (United States)

    Sinha, Leena; Karabacak, Mehmet; Narayan, V; Cinar, Mehmet; Prasad, Onkar

    2013-05-15

    Gabapentin (GP), structurally related to the neurotransmitter GABA (gamma-aminobutyric acid), mimics the activity of GABA and is also widely used in neurology for the treatment of peripheral neuropathic pain. It exists in zwitterionic form in solid state. The present communication deals with the quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of GP using density functional (DFT/B3LYP) method with 6-311++G(d,p) basis set. In view of the fact that amino acids exist as zwitterions as well as in the neutral form depending on the environment (solvent, pH, etc.), molecular properties of both the zwitterionic and neutral form of GP have been analyzed. The fundamental vibrational wavenumbers as well as their intensities were calculated and compared with experimental FT-IR and FT-Raman spectra. The fundamental assignments were done on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanical (SQM) method. The electric dipole moment, polarizability and the first hyperpolarizability values of the GP have been calculated at the same level of theory and basis set. The nonlinear optical (NLO) behavior of zwitterionic and neutral form has been compared. Stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using natural bond orbital analysis. Ultraviolet-visible (UV-Vis) spectrum of the title molecule has also been calculated using TD-DFT method. The thermodynamic properties of both the zwitterionic and neutral form of GP at different temperatures have been calculated. PMID:23545435

  19. Molecular structure, electronic properties, NLO, NBO analysis and spectroscopic characterization of Gabapentin with experimental (FT-IR and FT-Raman) techniques and quantum chemical calculations

    Science.gov (United States)

    Sinha, Leena; Karabacak, Mehmet; Narayan, V.; Cinar, Mehmet; Prasad, Onkar

    2013-05-01

    Gabapentin (GP), structurally related to the neurotransmitter GABA (gamma-aminobutyric acid), mimics the activity of GABA and is also widely used in neurology for the treatment of peripheral neuropathic pain. It exists in zwitterionic form in solid state. The present communication deals with the quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of GP using density functional (DFT/B3LYP) method with 6-311++G(d,p) basis set. In view of the fact that amino acids exist as zwitterions as well as in the neutral form depending on the environment (solvent, pH, etc.), molecular properties of both the zwitterionic and neutral form of GP have been analyzed. The fundamental vibrational wavenumbers as well as their intensities were calculated and compared with experimental FT-IR and FT-Raman spectra. The fundamental assignments were done on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanical (SQM) method. The electric dipole moment, polarizability and the first hyperpolarizability values of the GP have been calculated at the same level of theory and basis set. The nonlinear optical (NLO) behavior of zwitterionic and neutral form has been compared. Stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using natural bond orbital analysis. Ultraviolet-visible (UV-Vis) spectrum of the title molecule has also been calculated using TD-DFT method. The thermodynamic properties of both the zwitterionic and neutral form of GP at different temperatures have been calculated.

  20. Monomeric and dimeric structures analysis and spectroscopic characterization of 3,5-difluorophenylboronic acid with experimental (FT-IR, FT-Raman, 1H and 13C NMR, UV) techniques and quantum chemical calculations

    Science.gov (United States)

    Karabacak, Mehmet; Kose, Etem; Atac, Ahmet; Asiri, Abdullah M.; Kurt, Mustafa

    2014-01-01

    The spectroscopic properties of 3,5-difluorophenylboronic acid (3,5-DFPBA, C6H3F2B(OH)2) were investigated by FT-IR, FT-Raman UV-Vis, 1H and 13C NMR spectroscopic techniques. FT-IR (4000-400 cm-1) and FT-Raman spectra (3500-10 cm-1) in the solid phase and 1H and 13C NMR spectra in DMSO solution were recorded. The UV spectra that dissolved in ethanol and water were recorded in the range of 200-400 nm for each solution. The structural and spectroscopic data of the molecule have been obtained for possible three conformers from DFT (B3LYP) with 6-311++G(d,p) basis set calculations. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. Hydrogen-bonded dimer of title molecule, optimized by counterpoise correction, was also studied B3LYP at the 6-311++G(d,p) level and the effects of molecular association through O-H⋯O hydrogen bonding have been discussed. 1H and 13C NMR chemical shifts were calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, oscillator strength, wavelengths, HOMO and LUMO energies, were performed by time-dependent density functional theory (TD-DFT) results complements with the experimental findings. Total and partial density of state (TDOS and PDOS) and also overlap population density of state (OPDOS) diagrams analysis were presented. The effects due to the substitutions of boric acid group and halogen were investigated. The results of the calculations were applied to simulate spectra of the title compound, which show excellent agreement with observed spectra. Besides, frontier molecular orbitals (FMO), molecular electrostatic potential (MEP), nonlinear optical properties (NLO) and thermodynamic features were performed.

  1. Identification of GABA A receptor modulators in Kadsura longipedunculata and assignment of absolute configurations by quantum-chemical ECD calculations

    Science.gov (United States)

    Zaugg, Janine; Ebrahimi, Samad Nejad; Smiesko, Martin; Baburin, Igor; Hering, Steffen; Hamburger, Matthias

    2011-01-01

    A petroleum ether extract of Kadsura longipedunculata enhanced the GABA-induced chloride current (IGABA) by 122.5 ± 0.3% (n = 2) when tested at 100 μg/ml in Xenopus laevis oocytes expressing GABA A receptors (α1β2γ2S subtype) in two-microelectrode voltage clamp measurements. Thirteen compounds were subsequently identified by HPLC-based activity profiling as responsible for GABA A receptor activity and purified in preparative scale. 6-Cinnamoyl-6,7-dihydro-7-myrceneol and 5,6-dihydrocuparenic acid were thereby isolated for the first time. The determination of the absolute stereochemistry of these compounds was achieved by comparison of experimental and calculated ECD spectra. All but one of the 13 isolated compounds from K. longipedunculata potentiated IGABA through GABA A receptors composed of α1β2γ2S subunits in a concentration-dependent manner. Potencies ranged from 12.8 ± 3.1 to 135.6 ± 85.7 μM, and efficiencies ranged from 129.7 ± 36.8% to 885.8 ± 291.2%. The phytochemical profiles of petroleum ether extracts of Kadsura japonica fruits (114.1 ± 2.6% potentiation of IGABA at 100 μg/ml, n = 2), and Schisandra chinensis fruits (inactive at 100 μg/ml) were compared by HPLC-PDA-ESIMS with that of K. longipedunculata. PMID:21889177

  2. Combining Nuclear Magnetic Resonance Spectroscopy and Density Functional Theory Calculations to Characterize Carvedilol Polymorphs.

    Science.gov (United States)

    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. PMID:26372719

  3. Combining Nuclear Magnetic Resonance Spectroscopy and Density Functional Theory Calculations to Characterize Carvedilol Polymorphs.

    Science.gov (United States)

    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.

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

    DEFF Research Database (Denmark)

    Jankowska, Marzena; Kupka, Teobald; Stobiński, Leszek;

    2016-01-01

    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 4-component Dirac-Coulomb Hamiltonian using Dyall’s acv4z basis sets. The relativistic corrections to the nuclear magnetic...

  5. Kinetic measurements and quantum chemical calculations on low spin Ni(II)/(III) macrocyclic complexes in aqueous and sulphato medium

    Indian Academy of Sciences (India)

    Anuradha Sankaran; E J Padma Malar; Venkatapuram Ramanujam Vijayaraghavan

    2015-07-01

    Cu(II) ion catalyzed kinetics of oxidation of H2O2 by [NiIIIL2] (L2 = 1,8-bis(2-hydroxyethyl)-1,3,6,8,10,13-hexaazacyclotetradecane) was studied in aqueous acidic medium in the presence of sulphate ion. The rate of oxidation of H2O2 by [NiIIIL2] is faster than that by [NiIIIL1] (L1 = 1,4,8,11-tetraazacyclote-tradecane) in sulphate medium. DFT calculations at BP86/def2-TZVP level lead to different modes of bonding between [NiL]II/III and water ligands (L = L1 and L2). In aqueous medium, two water molecules interact with [NiL]II through weak hydrogen bonds with L and are tilted by ∼23° from the vertical axis forming the dihydrate [NiL]2+.2H2O. However, there is coordinate bond formation between [NiL1]III and two water molecules in aqueous medium and an aqua and a sulphato ligand in sulphate medium leading to the octahedral complexes [NiL1(H2O)2]3+ and [NiL1(SO4)(H2O)]+. In the analogous [NiL2]III, the water molecules are bound by hydrogen bonds resulting in [NiL2]3+.2H2O and [NiL2(SO4)]+.H2O. As the sulphato complex [NiL2(SO4)]+.H2O is less stable than [NiL1(SO4)(H2O)]+ in view of the weak H-bonding interactions in the former it can react faster. Thus the difference in the mode of bonding between Ni(III) and the water ligand can explain the rate of oxidation of H2O2 by [NiIIIL] complexes.

  6. Influence of Chemical Effect on the Kβ/Kα Intensity Ratios and Kβ Energy Shift of Co, Ni, Cu, and Zn Complexes

    Institute of Scientific and Technical Information of China (English)

    G. Apaydma, V. Ayhkg; Z. Biyiklioglu; E. Tirasoglu; H. Kantekin

    2008-01-01

    Chemical effects on the Kβ/Kα intensity ratios and ΔE energy differences for Co, Ni, Cu, and Zn complexes were investigated. The samples were excited by 59.5 keV γ-rays from a 241 Am annular radioactive source. K X-rays emitted by samples were counted by an Ultra-LEGe detector with a resolution of 150 eV at 5.9 keV. We observed the effects of different ligands on the Kβ/Kα intensity ratios and ΔE energy differences for Co, Ni, Cu, and Zn complexes. We tried to investigate chemical effects on central atoms using the behaviors of different ligands in these complexes. The experimental values of Kβ/Kα were compared with the theoretical and other experimental values of pure Co, Ni, Cu, and Zn.

  7. 4D Non-uniformly sampled HCBCACON and {sup 1}J(NC{sup {alpha}})-selective HCBCANCO experiments for the sequential assignment and chemical shift analysis of intrinsically disordered proteins

    Energy Technology Data Exchange (ETDEWEB)

    Novacek, Jiri [Masaryk University, Faculty of Science, NCBR, and CEITEC (Czech Republic); Haba, Noam Y.; Chill, Jordan H. [Bar Ilan University, Department of Chemistry (Israel); Zidek, Lukas, E-mail: lzidek@chemi.muni.cz; Sklenar, Vladimir [Masaryk University, Faculty of Science, NCBR, and CEITEC (Czech Republic)

    2012-06-15

    A pair of 4D NMR experiments for the backbone assignment of disordered proteins is presented. The experiments exploit {sup 13}C direct detection and non-uniform sampling of the indirectly detected dimensions, and provide correlations of the aliphatic proton (H{sup {alpha}}, and H{sup {beta}}) and carbon (C{sup {alpha}}, C{sup {beta}}) resonance frequencies to the protein backbone. Thus, all the chemical shifts regularly used to map the transient secondary structure motifs in the intrinsically disordered proteins (H{sup {alpha}}, C{sup {alpha}}, C{sup {beta}}, C Prime , and N) can be extracted from each spectrum. Compared to the commonly used assignment strategy based on matching the C{sup {alpha}} and C{sup {beta}} chemical shifts, inclusion of the H{sup {alpha}} and H{sup {beta}} provides up to three extra resonance frequencies that decrease the chance of ambiguous assignment. The experiments were successfully applied to the original assignment of a 12.8 kDa intrinsically disordered protein having a high content of proline residues (26 %) in the sequence.

  8. Hash: a program to accurately predict protein H{sup {alpha}} shifts from neighboring backbone shifts

    Energy Technology Data Exchange (ETDEWEB)

    Zeng Jianyang, E-mail: zengjy@gmail.com [Tsinghua University, Institute for Interdisciplinary Information Sciences (China); Zhou Pei [Duke University Medical Center, Department of Biochemistry (United States); Donald, Bruce Randall [Duke University, Department of Computer Science (United States)

    2013-01-15

    Chemical shifts provide not only peak identities for analyzing nuclear magnetic resonance (NMR) data, but also an important source of conformational information for studying protein structures. Current structural studies requiring H{sup {alpha}} chemical shifts suffer from the following limitations. (1) For large proteins, the H{sup {alpha}} chemical shifts can be difficult to assign using conventional NMR triple-resonance experiments, mainly due to the fast transverse relaxation rate of C{sup {alpha}} that restricts the signal sensitivity. (2) Previous chemical shift prediction approaches either require homologous models with high sequence similarity or rely heavily on accurate backbone and side-chain structural coordinates. When neither sequence homologues nor structural coordinates are available, we must resort to other information to predict H{sup {alpha}} chemical shifts. Predicting accurate H{sup {alpha}} chemical shifts using other obtainable information, such as the chemical shifts of nearby backbone atoms (i.e., adjacent atoms in the sequence), can remedy the above dilemmas, and hence advance NMR-based structural studies of proteins. By specifically exploiting the dependencies on chemical shifts of nearby backbone atoms, we propose a novel machine learning algorithm, called Hash, to predict H{sup {alpha}} chemical shifts. Hash combines a new fragment-based chemical shift search approach with a non-parametric regression model, called the generalized additive model, to effectively solve the prediction problem. We demonstrate that the chemical shifts of nearby backbone atoms provide a reliable source of information for predicting accurate H{sup {alpha}} chemical shifts. Our testing results on different possible combinations of input data indicate that Hash has a wide rage of potential NMR applications in structural and biological studies of proteins.

  9. 化工销售物流损耗计算与优化研究%The study on chemical products sales logistics loss calculation and optimization

    Institute of Scientific and Technical Information of China (English)

    许高阳; 索寒生

    2012-01-01

    化工物流损耗不仅给企业造成较大的经济损失,而且会给社会带来健康和安全隐患.根据中国石化化工销售物流的特点,在运输上,给出了损耗的计算方法与本公司、承运单位和保险公司的赔付规则,在仓储上,针对自有仓储与外租仓储2种场景,给出了入库、出库和库存保管环节的损耗计算方法.建立了以货损率为约束条件的数学规划模型.并结合具体场景,提出了减少物流损耗的对策.%Chemical logistics loss not only cause greater economic losses, and would bring a health and safety hazard. According to the characteristics of Sinopec Chemical Products Sales Logistics, this paper provides the chemical products logistics loss calculation methods and payout rules for the company, carrier unit and the insurance company in transportation. In warehousing, this article gives the storage, a library and inventory loss calculation method for its own warehouse and outside. An integer programming model is established, based on cargo damage rate constraints. It also gives the countermeasures to reduce logistics loss combined with specific scenes.

  10. Exploring the dynamics of reaction N((2)D)+C2H4 with crossed molecular-beam experiments and quantum-chemical calculations.

    Science.gov (United States)

    Lee, Shih-Huang; Chin, Chih-Hao; Chen, Wei-Kan; Huang, Wen-Jian; Hsieh, Chu-Chun

    2011-05-14

    We conducted the title reaction using a crossed molecular-beam apparatus, quantum-chemical calculations, and RRKM calculations. Synchrotron radiation from an undulator served to ionize selectively reaction products by advantage of negligibly small dissociative ionization. We observed two products with gross formula C(2)H(3)N and C(2)H(2)N associated with loss of one and two hydrogen atoms, respectively. Measurements of kinetic-energy distributions, angular distributions, low-resolution photoionization spectra, and branching ratios of the two products were carried out. Furthermore, we evaluated total branching ratios of various exit channels using RRKM calculations based on the potential-energy surface of reaction N((2)D)+C(2)H(4) established with the method CCSD(T)/6-311+G(3df,2p)//B3LYP/6-311G(d,p)+ZPE[B3LYP/6-311G(d,p)]. The combination of experimental and computational results allows us to reveal the reaction dynamics. The N((2)D) atom adds to the C=C π-bond of ethene (C(2)H(4)) to form a cyclic complex c-CH(2)(N)CH(2) that directly ejects a hydrogen atom or rearranges to other intermediates followed by elimination of a hydrogen atom to produce C(2)H(3)N; c-CH(2)(N)CH+H is the dominant product channel. Subsequently, most C(2)H(3)N radicals, notably c-CH(2)(N)CH, further decompose to CH(2)CN+H. This work provides results and explanations different from the previous work of Balucani et al. [J. Phys. Chem. A, 2000, 104, 5655], indicating that selective photoionization with synchrotron radiation as an ionization source is a good choice in chemical dynamics research.

  11. THEORETICAL-ANALYSIS OF THE O(1S) BINDING-ENERGY SHIFTS IN ALKALINE-EARTH OXIDES - CHEMICAL OR ELECTROSTATIC CONTRIBUTIONS

    NARCIS (Netherlands)

    PACCHIONI, G; BAGUS, PS

    1994-01-01

    We report results from ab initio cluster-model calculations on the O(1s) binding energy (BE) in the alkaline-earth oxides, MgO, CaO, SrO, and BaO; all these oxides have a cubic lattice structure. We have obtained values for both the initial- and final-state BE's. A simple point-charge model, where a

  12. Of owl or ostrich. The U.S. policy of calculated ambiguity to deter the use of chemical and biological weapons

    Energy Technology Data Exchange (ETDEWEB)

    Lakamp, M.A.

    1998-12-01

    The United States has adopted a policy of calculated ambiguity regarding the role of nuclear weapons in response to a potential chemical or biological weapons (CBW) attack. Many factors affect decisions about the role nuclear weapons play in US counterproliferation strategy. This thesis describes the policy of calculated ambiguity and offers some observations about its prospects and pitfalls. The thesis presents evidence that suggests nuclear weapons could play a positive role in the US counterproliferation strategy, at least in some circumstances. It also explains how such a role could conflict with the US nonproliferation strategy. Such a role would also violate the nuclear taboo and be seen by a majority of countries as illegal and immoral. The United States has chosen a policy of calculated ambiguity in an attempt to retain the deterrent value of nuclear weapons without paying the political, legal, and moral costs of explicit reliance on nuclear weapons to deter the use of CBW. This may have short-term benefits, but ultimately may damage the national interest.

  13. Some Phthalocyanine and Naphthalocyanine Derivatives as Corrosion Inhibitors for Aluminium in Acidic Medium: Experimental, Quantum Chemical Calculations, QSAR Studies and Synergistic Effect of Iodide Ions.

    Science.gov (United States)

    Dibetsoe, Masego; Olasunkanmi, Lukman O; Fayemi, Omolola E; Yesudass, Sasikumar; Ramaganthan, Baskar; Bahadur, Indra; Adekunle, Abolanle S; Kabanda, Mwadham M; Ebenso, Eno E

    2015-08-28

    The effects of seven macrocyclic compounds comprising four phthalocyanines (Pcs) namely 1,4,8,11,15,18,22,25-octabutoxy-29H,31H-phthalocyanine (Pc1), 2,3,9,10,16,17,23,24-octakis(octyloxy)-29H,31H-phthalocyanine (Pc2), 2,9,16,23-tetra-tert-butyl-29H,31H-phthalocyanine (Pc3) and 29H,31H-phthalocyanine (Pc4), and three naphthalocyanines namely 5,9,14,18,23,27,32,36-octabutoxy-2,3-naphthalocyanine (nPc1), 2,11,20,29-tetra-tert-butyl-2,3-naphthalocyanine (nPc2) and 2,3-naphthalocyanine (nP3) were investigated on the corrosion of aluminium (Al) in 1 M HCl using a gravimetric method, potentiodynamic polarization technique, quantum chemical calculations and quantitative structure activity relationship (QSAR). Synergistic effects of KI on the corrosion inhibition properties of the compounds were also investigated. All the studied compounds showed appreciable inhibition efficiencies, which decrease with increasing temperature from 30 °C to 70 °C. At each concentration of the inhibitor, addition of 0.1% KI increased the inhibition efficiency compared to the absence of KI indicating the occurrence of synergistic interactions between the studied molecules and I(-) ions. From the potentiodynamic polarization studies, the studied Pcs and nPcs are mixed type corrosion inhibitors both without and with addition of KI. The adsorption of the studied molecules on Al surface obeys the Langmuir adsorption isotherm, while the thermodynamic and kinetic parameters revealed that the adsorption of the studied compounds on Al surface is spontaneous and involves competitive physisorption and chemisorption mechanisms. The experimental results revealed the aggregated interactions between the inhibitor molecules and the results further indicated that the peripheral groups on the compounds affect these interactions. The calculated quantum chemical parameters and the QSAR results revealed the possibility of strong interactions between the studied inhibitors and metal surface. QSAR analysis on the

  14. Some Phthalocyanine and Naphthalocyanine Derivatives as Corrosion Inhibitors for Aluminium in Acidic Medium: Experimental, Quantum Chemical Calculations, QSAR Studies and Synergistic Effect of Iodide Ions.

    Science.gov (United States)

    Dibetsoe, Masego; Olasunkanmi, Lukman O; Fayemi, Omolola E; Yesudass, Sasikumar; Ramaganthan, Baskar; Bahadur, Indra; Adekunle, Abolanle S; Kabanda, Mwadham M; Ebenso, Eno E

    2015-01-01

    The effects of seven macrocyclic compounds comprising four phthalocyanines (Pcs) namely 1,4,8,11,15,18,22,25-octabutoxy-29H,31H-phthalocyanine (Pc1), 2,3,9,10,16,17,23,24-octakis(octyloxy)-29H,31H-phthalocyanine (Pc2), 2,9,16,23-tetra-tert-butyl-29H,31H-phthalocyanine (Pc3) and 29H,31H-phthalocyanine (Pc4), and three naphthalocyanines namely 5,9,14,18,23,27,32,36-octabutoxy-2,3-naphthalocyanine (nPc1), 2,11,20,29-tetra-tert-butyl-2,3-naphthalocyanine (nPc2) and 2,3-naphthalocyanine (nP3) were investigated on the corrosion of aluminium (Al) in 1 M HCl using a gravimetric method, potentiodynamic polarization technique, quantum chemical calculations and quantitative structure activity relationship (QSAR). Synergistic effects of KI on the corrosion inhibition properties of the compounds were also investigated. All the studied compounds showed appreciable inhibition efficiencies, which decrease with increasing temperature from 30 °C to 70 °C. At each concentration of the inhibitor, addition of 0.1% KI increased the inhibition efficiency compared to the absence of KI indicating the occurrence of synergistic interactions between the studied molecules and I(-) ions. From the potentiodynamic polarization studies, the studied Pcs and nPcs are mixed type corrosion inhibitors both without and with addition of KI. The adsorption of the studied molecules on Al surface obeys the Langmuir adsorption isotherm, while the thermodynamic and kinetic parameters revealed that the adsorption of the studied compounds on Al surface is spontaneous and involves competitive physisorption and chemisorption mechanisms. The experimental results revealed the aggregated interactions between the inhibitor molecules and the results further indicated that the peripheral groups on the compounds affect these interactions. The calculated quantum chemical parameters and the QSAR results revealed the possibility of strong interactions between the studied inhibitors and metal surface. QSAR analysis on the

  15. Some Phthalocyanine and Naphthalocyanine Derivatives as Corrosion Inhibitors for Aluminium in Acidic Medium: Experimental, Quantum Chemical Calculations, QSAR Studies and Synergistic Effect of Iodide Ions

    Directory of Open Access Journals (Sweden)

    Masego Dibetsoe

    2015-08-01

    Full Text Available The effects of seven macrocyclic compounds comprising four phthalocyanines (Pcs namely 1,4,8,11,15,18,22,25-octabutoxy-29H,31H-phthalocyanine (Pc1, 2,3,9,10,16,17,23,24-octakis(octyloxy-29H,31H-phthalocyanine (Pc2, 2,9,16,23-tetra-tert-butyl-29H,31H-phthalocyanine (Pc3 and 29H,31H-phthalocyanine (Pc4, and three naphthalocyanines namely 5,9,14,18,23,27,32,36-octabutoxy-2,3-naphthalocyanine (nPc1, 2,11,20,29-tetra-tert-butyl-2,3-naphthalocyanine (nPc2 and 2,3-naphthalocyanine (nP3 were investigated on the corrosion of aluminium (Al in 1 M HCl using a gravimetric method, potentiodynamic polarization technique, quantum chemical calculations and quantitative structure activity relationship (QSAR. Synergistic effects of KI on the corrosion inhibition properties of the compounds were also investigated. All the studied compounds showed appreciable inhibition efficiencies, which decrease with increasing temperature from 30 °C to 70 °C. At each concentration of the inhibitor, addition of 0.1% KI increased the inhibition efficiency compared to the absence of KI indicating the occurrence of synergistic interactions between the studied molecules and I− ions. From the potentiodynamic polarization studies, the studied Pcs and nPcs are mixed type corrosion inhibitors both without and with addition of KI. The adsorption of the studied molecules on Al surface obeys the Langmuir adsorption isotherm, while the thermodynamic and kinetic parameters revealed that the adsorption of the studied compounds on Al surface is spontaneous and involves competitive physisorption and chemisorption mechanisms. The experimental results revealed the aggregated interactions between the inhibitor molecules and the results further indicated that the peripheral groups on the compounds affect these interactions. The calculated quantum chemical parameters and the QSAR results revealed the possibility of strong interactions between the studied inhibitors and metal surface. QSAR

  16. Understanding the structure and dynamic of odorants in the gas phase using a combination of microwave spectroscopy and quantum chemical calculations

    Science.gov (United States)

    Mouhib, Halima

    2014-07-01

    This tutorial is an introduction for PhD students and researchers who intend to start their future work in the field of microwave spectroscopy to investigate structural and dynamical aspects of isolated molecular systems in the gas phase. Although the presented case studies are related to odorants, i.e., volatile molecules that possess a noticeable scent, the background and applications of the method can be transferred to any other resembling molecular system. In the early days, microwave spectroscopy was mainly related to the structure determination of very small systems such as OCS or ammonia, where the bond lengths could be determined with high accuracy by measuring the different isotopic species of the molecules. Nowadays, the method is far more advanced and is also used to tackle various fundamental molecular problems in different fields such as physical chemistry and molecular physics. Interesting questions that can be investigated concern, e.g., the molecular structure, i.e., the different conformations, not only of the isolated molecule but also of van der Waals complexes with water, noble gases or other molecules. The dynamical and intra- or intermolecular effects can be straightforwardly observed without the influence of the environment as in the condensed phase. This evolution was only achieved by using quantum chemical methods as a complementary tool to elude the necessity of isotopologues for structure determination, which cannot be realized for large systems (>5 atoms). The combination of microwave spectroscopy and quantum chemical calculations is the method of choice when it comes to sampling the conformational space of molecules. This is particularly the case when small energy differences make it difficult to determine the conformers of the lowest energy using computational methods alone. Although quantum chemical calculations are important for the validation of microwave spectra, the focus of the tutorial is set on the experimental part of the

  17. Iboga alkaloids from Peschiera affinis (Apocynaceae) - unequivocal {sup 1}H and {sup 13}C chemical shift assignments: antioxidant activity; Alcaloides iboga de Peschiera affinis (Apocynaceae) - atribuicao inequivoca dos deslocamentos quimicos dos atomos de hidrogenio e carbono: atividade antioxidante

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Allana Kellen L.; Magalhaes, Ticiane S.; Monte, Francisco Jose Q.; Mattos, Marcos Carlos de; Oliveira, Maria Conceicao F. de; Almeida, Maria Mozarina B.; Lemos, Telma L.G.; Braz-Filho, Raimundo [Universidade Federal do Ceara (UFC), Fortaleza, CE (Brazil). Dept. de Quimica Organica e Inorganica], e-mail: tlemos@dqoi.ufc.br

    2009-07-01

    Six known alkaloids iboga type and the triterpene {alpha}- and {beta}-amyrin acetate were isolated from the roots and stems of Peschiera affinis. Their structures were characterized on the basis of spectral data mainly NMR and mass spectra. 1D and 2D NMR spectra were also used to unequivocal {sup 1}H and {sup 13}C chemical shift assignments of alkaloids. The ethanolic extract of roots, alkaloidic and no-alkaloidic fractions and iso-voacristine hydroxyindolenine and voacangine were evaluated for their antioxidative properties using an autographic assay based on {beta}-carotene bleaching on TLC plates, and also spectrophotometric detection by reduction of the stable DPPH (2,2-diphenyl-1-picrylhydrazyl) free radical. (author)

  18. Molecular level investigations of phosphate sorption on corundum (α-Al2O3) by 31P solid state NMR, ATR-FTIR and quantum chemical calculation

    Science.gov (United States)

    Li, Wei; Pierre-Louis, Andro-Marc; Kwon, Kideok D.; Kubicki, James D.; Strongin, Daniel R.; Phillips, Brian L.

    2013-04-01

    Phosphate sorption at the corundum (α-Al2O3)/water interface was investigated as a function of phosphate concentration (0.1-1 mM) and pH (3-11) by 31P solid state NMR spectroscopy, ATR-FTIR, and quantum chemical calculation. The 31P NMR spectra indicate that under these experimental conditions phosphate adsorbs onto corundum mainly as inner-sphere complexes that yield a peak at δP = -2.8 ppm with full width at half maximum (FWHM) of 9.2 ppm, with a small amount aluminum phosphate surface precipitates as suggested by an NMR signal observed from δP = -12 to -20 ppm. We employed 31P{27Al} rotational echo adiabatic passage double resonance (REAPDOR) to further analyze the phosphate adsorption samples prepared at pH 5 and 9 in order to determine the phosphate/Al coordination. To aid interpretation of the NMR data, a series of bidentate and monodentate structural models of phosphate adsorbed on corundum (0 0 1) and (0 1 2) surfaces were calculated using density function theory (DFT). By comparing the experimental REAPDOR curves and those simulated from these models, we can assign the dominant peaks to bidentate binuclear surface complexes. Formation of bidentate binuclear surface complexes is supported by the ATR/FTIR spectra combined with DFT calculation, which further suggests a mixture of non-protonated bidentate and mono-protonated bidentate surface complexes on the corundum surface at pH 5. At pH 9, both NMR and ATR/FTIR indicate the formation of bidentate surface complexes on corundum surface.

  19. Automated two-point dixon screening for the evaluation of hepatic steatosis and siderosis: comparison with R2*-relaxometry and chemical shift-based sequences

    International Nuclear Information System (INIS)

    To evaluate the automated two-point Dixon screening sequence for the detection and estimated quantification of hepatic iron and fat compared with standard sequences as a reference. One hundred and two patients with suspected diffuse liver disease were included in this prospective study. The following MRI protocol was used: 3D-T1-weighted opposed- and in-phase gradient echo with two-point Dixon reconstruction and dual-ratio signal discrimination algorithm (''screening'' sequence); fat-saturated, multi-gradient-echo sequence with 12 echoes; gradient-echo T1 FLASH opposed- and in-phase. Bland-Altman plots were generated and correlation coefficients were calculated to compare the sequences. The screening sequence diagnosed fat in 33, iron in 35 and a combination of both in 4 patients. Correlation between R2* values of the screening sequence and the standard relaxometry was excellent (r = 0.988). A slightly lower correlation (r = 0.978) was found between the fat fraction of the screening sequence and the standard sequence. Bland-Altman revealed systematically lower R2* values obtained from the screening sequence and higher fat fraction values obtained with the standard sequence with a rather high variability in agreement. The screening sequence is a promising method with fast diagnosis of the predominant liver disease. It is capable of estimating the amount of hepatic fat and iron comparable to standard methods. (orig.)

  20. Automated two-point dixon screening for the evaluation of hepatic steatosis and siderosis: comparison with R2*-relaxometry and chemical shift-based sequences

    Energy Technology Data Exchange (ETDEWEB)

    Henninger, B.; Rauch, S.; Schocke, M.; Jaschke, W.; Kremser, C. [Medical University of Innsbruck, Department of Radiology, Innsbruck (Austria); Zoller, H. [Medical University of Innsbruck, Department of Internal Medicine, Innsbruck (Austria); Kannengiesser, S. [Siemens AG, Healthcare Sector, MR Applications Development, Erlangen (Germany); Zhong, X. [Siemens Healthcare, MR R and D Collaborations, Atlanta, GA (United States); Reiter, G. [Siemens AG, Healthcare Sector, MR R and D Collaborations, Graz (Austria)

    2015-05-01

    To evaluate the automated two-point Dixon screening sequence for the detection and estimated quantification of hepatic iron and fat compared with standard sequences as a reference. One hundred and two patients with suspected diffuse liver disease were included in this prospective study. The following MRI protocol was used: 3D-T1-weighted opposed- and in-phase gradient echo with two-point Dixon reconstruction and dual-ratio signal discrimination algorithm (''screening'' sequence); fat-saturated, multi-gradient-echo sequence with 12 echoes; gradient-echo T1 FLASH opposed- and in-phase. Bland-Altman plots were generated and correlation coefficients were calculated to compare the sequences. The screening sequence diagnosed fat in 33, iron in 35 and a combination of both in 4 patients. Correlation between R2* values of the screening sequence and the standard relaxometry was excellent (r = 0.988). A slightly lower correlation (r = 0.978) was found between the fat fraction of the screening sequence and the standard sequence. Bland-Altman revealed systematically lower R2* values obtained from the screening sequence and higher fat fraction values obtained with the standard sequence with a rather high variability in agreement. The screening sequence is a promising method with fast diagnosis of the predominant liver disease. It is capable of estimating the amount of hepatic fat and iron comparable to standard methods. (orig.)

  1. Using NMR chemical shift imaging to monitor swelling and molecular transport in drug-loaded tablets of hydrophobically modified poly(acrylic acid): methodology and effects of polymer (in)solubility.

    Science.gov (United States)

    Knöös, Patrik; Topgaard, Daniel; Wahlgren, Marie; Ulvenlund, Stefan; Piculell, Lennart

    2013-11-12

    A new technique has been developed using NMR chemical shift imaging (CSI) to monitor water penetration and molecular transport in initially dry polymer tablets that also contain small low-molecular weight compounds to be released from the tablets. Concentration profiles of components contained in the swelling tablets could be extracted via the intensities and chemical shift changes of peaks corresponding to protons of the components. The studied tablets contained hydrophobically modified poly(acrylic acid) (HMPAA) as the polymer component and griseofulvin and ethanol as hydrophobic and hydrophilic, respectively, low-molecular weight model compounds. The water solubility of HMPAA could be altered by titration with NaOH. In the pure acid form, HMPAA tablets only underwent a finite swelling until the maximum water content of the polymer-rich phase, as confirmed by independent phase studies, had been reached. By contrast, after partial neutralization with NaOH, the polyacid became fully miscible with water. The solubility of the polymer affected the water penetration, the polymer release, and the releases of both ethanol and griseofulvin. The detailed NMR CSI concentration profiles obtained highlighted the clear differences in the disintegration/dissolution/release behavior for the two types of tablet and provided insights into their molecular origin. The study illustrates the potential of the NMR CSI technique to give information of importance for the development of pharmaceutical tablets and, more broadly, for the general understanding of any operation that involves the immersion and ultimate disintegration of a dry polymer matrix in a solvent. PMID:24106807

  2. Cerebral gliomas: prospective comparison of multivoxel 2D chemical-shift imaging proton MR spectroscopy, echoplanar perfusion and diffusion-weighted MRI

    International Nuclear Information System (INIS)

    Developments in MRI have made it possible to use diffusion-weighted MRI, perfusion MRI and proton MR spectroscopy (MRS) to study lesions in the brain. We evaluated whether these techniques provide useful, complementary information for grading gliomas, in comparison with conventional MRI. We studied 17 patients with histologically verified gliomas, adding multivoxel proton MRS, echoplanar diffusion and perfusion MRI the a routine MRI examination. The maximum relative cerebral blood volume (CBV), minimum apparent diffusion coefficient (ADC) and metabolic peak area ratios in proton MRS were calculated in solid parts of tumours on the same slice from each imaging data set. The mean minimum ADC of the 13 high-grade gliomas (0.92±0.27 x 10-3 mm2/s) was lower than that of the four low-grade gliomas (1.28±0.15 x 10-3 mm2/s) (P<0.05). Means of maximum choline (Cho)/N-acetylaspartate (NAA), Cho/creatine (Cr), Cho/Cr in normal brain (Cr-n) and minimum NAA/Cr ratios were 5.90±2.62, 4.73±2.22, 2.66±0.68 and 0.40±0.06, respectively, in the high-grade gliomas, and 1.65±1.37, 1.84±1.20, 1.61±1.29 and 1.65±1.61, respectively, in the low-grade gliomas. Significant differences were found on spectroscopy between the high- and low-grade gliomas (P<0.05). Mean maximum relative CBV in the high-grade gliomas (6.10±3.98) was higher than in the low-grade gliomas (1.74±0.57) (P<0.05). Echoplanar diffusion, perfusion MRI and multivoxel proton MRS can offer diagnostic information, not available with conventional MRI, in the assessment of glioma grade. (orig.)

  3. Calculated rate constants of the chemical reactions involving the main byproducts SO2F, SOF2, SO2F2 of SF6 decomposition in power equipment

    Science.gov (United States)

    Fu, Yuwei; Rong, Mingzhe; Yang, Kang; Yang, Aijun; Wang, Xiaohua; Gao, Qingqing; Liu, Dingxin; Murphy, Anthony B.

    2016-04-01

    SF6 is widely used in electrical equipment as an insulating gas. In the presence of an electric arc, partial discharge (PD) or spark, SF6 dissociation products (such as SF2, SF3 and SF4) react with the unavoidable gas impurities (such as water vapor and oxygen), electrodes and surrounding solid insulation materials, forming several toxic and corrosive byproducts. The main stable decomposition products are SO2F, SO2F2 and SOF2, which have been confirmed experimentally to have a direct relationship with discharge faults, and are thus expected to be useful in the fault diagnosis of power equipment. Various studies have been performed of the main SF6 decomposition species and their concentrations under different types of faults. However, most of the experiments focused on the qualitative analysis of the relationship between the stable products and discharge faults. Although some theoretical research on the formation of main SF6 derivatives have been carried out using chemical kinetics models, the basic data (chemical reactions and their rate constants) adopted in the model are inaccurate and incomplete. The complex chemical reactions of SF6 with the impurities are ignored in most cases. The rate constants of some reactions obtained at ambient temperature or in a narrow temperature range are adopted in the models over a far greater range, for example up to 12 000 K, due to the difficulty in the experimental measurement and theoretical estimation of rate coefficients, particularly at high temperatures. Therefore, improved theoretical models require not only the consideration of additional SF6 decomposition reactions in the presence of impurities but also on improved values of rate constants. This paper is devoted to determining the rate constants of the chemical reactions relating to the main byproducts of SF6 decomposition in SF6 gas-insulated power equipment: SO2F, SOF2 and SO2F2. Quantum chemistry calculations with density functional theory, conventional

  4. PACKAGE (Plasma Analysis, Chemical Kinetics and Generator Efficiency): a computer program for the calculation of partial chemical equilibrium/partial chemical rate controlled composition of multiphased mixtures under one dimensional steady flow

    Energy Technology Data Exchange (ETDEWEB)

    Yousefian, V.; Weinberg, M.H.; Haimes, R.

    1980-02-01

    The NASA CEC Code was the starting point for PACKAGE, whose function is to evaluate the composition of a multiphase combustion product mixture under the following chemical conditions: (1) total equilibrium with pure condensed species; (2) total equilibrium with ideal liquid solution; (3) partial equilibrium/partial finite rate chemistry; and (4) fully finite rate chemistry. The last three conditions were developed to treat the evolution of complex mixtures such as coal combustion products. The thermodynamic variable pairs considered are either pressure (P) and enthalpy, P and entropy, at P and temperature. Minimization of Gibbs free energy is used. This report gives detailed discussions of formulation and input/output information used in the code. Sample problems are given. The code development, description, and current programming constraints are discussed. (DLC)

  5. The calculation of accurate 17O hyperfine coupling constants in the hydroxyl radical: A difficult problem for current quantum chemical methods

    Science.gov (United States)

    Wetmore, Stacey D.; Eriksson, Leif A.; Boyd, Russell J.

    1998-12-01

    The hyperfine coupling constants (HFCCs) in the hydroxyl radical are investigated through comparison of results obtained from a variety of quantum chemical methods. The couplings obtained from the multi-reference configuration interaction (MRCI) wave function, built upon the restricted open-shell Hartree-Fock (ROHF) reference determinant, are investigated in terms of the basis set, the configuration selection energy threshold, and the size of the reference space. Overall results which converge to the experimental couplings are obtained for hydrogen, but not for oxygen. In particular, the MRCI method shows no improvement over density functional theory (the B3LYP functional), for the calculation of Aiso(17O). On the other hand, results in excellent agreement with experiment are obtained through the use of the quadratic configuration interaction (QCISD) method based on the unrestricted HF (UHF) reference determinant with the identical basis sets. Examination of UHF and ROHF based coupled-cluster methods, CCSD and CCSD(T), indicates that once a high enough level of electron correlation is included, the oxygen HFCC is independent of the form of the reference determinant. Unlike the ROHF-CCSD method, which yields reliable results once the effects of triple excitations have been taken into account, the MRCI wave function cannot easily be adjusted to account for the inadequacies of the ROHF reference determinant in order to accurately predict 17O HFCCs.

  6. Vibronic coupling in molecular crystals: A Franck-Condon Herzberg-Teller model of H-aggregate fluorescence based on quantum chemical cluster calculations

    Science.gov (United States)

    Wykes, M.; Parambil, R.; Beljonne, D.; Gierschner, J.

    2015-09-01

    Here, we present a general approach to treating vibronic coupling in molecular crystals based on atomistic simulations of large clusters. Such clusters comprise model aggregates treated at the quantum chemical level embedded within a realistic environment treated at the molecular mechanics level. As we calculate ground and excited state equilibrium geometries and vibrational modes of model aggregates, our approach is able to capture effects arising from coupling to intermolecular degrees of freedom, absent from existing models relying on geometries and normal modes of single molecules. Using the geometries and vibrational modes of clusters, we are able to simulate the fluorescence spectra of aggregates for which the lowest excited state bears negligible oscillator strength (as is the case, e.g., ideal H-aggregates) by including both Franck-Condon (FC) and Herzberg-Teller (HT) vibronic transitions. The latter terms allow the adiabatic excited state of the cluster to couple with vibrations in a perturbative fashion via derivatives of the transition dipole moment along nuclear coordinates. While vibronic coupling simulations employing FC and HT terms are well established for single-molecules, to our knowledge this is the first time they are applied to molecular aggregates. Here, we apply this approach to the simulation of the low-temperature fluorescence spectrum of para-distyrylbenzene single-crystal H-aggregates and draw comparisons with coarse-grained Frenkel-Holstein approaches previously extensively applied to such systems.

  7. Vibronic coupling in molecular crystals: A Franck-Condon Herzberg-Teller model of H-aggregate fluorescence based on quantum chemical cluster calculations

    Energy Technology Data Exchange (ETDEWEB)

    Wykes, M., E-mail: mikewykes@gmail.com; Parambil, R.; Gierschner, J. [Madrid Institute for Advanced Studies, IMDEA Nanoscience, Calle Faraday 9, Campus Cantoblanco, 28049 Madrid (Spain); Beljonne, D. [Laboratory for Chemistry of Novel Materials, University of Mons, Place du Parc 20, 7000 Mons (Belgium)

    2015-09-21

    Here, we present a general approach to treating vibronic coupling in molecular crystals based on atomistic simulations of large clusters. Such clusters comprise model aggregates treated at the quantum chemical level embedded within a realistic environment treated at the molecular mechanics level. As we calculate ground and excited state equilibrium geometries and vibrational modes of model aggregates, our approach is able to capture effects arising from coupling to intermolecular degrees of freedom, absent from existing models relying on geometries and normal modes of single molecules. Using the geometries and vibrational modes of clusters, we are able to simulate the fluorescence spectra of aggregates for which the lowest excited state bears negligible oscillator strength (as is the case, e.g., ideal H-aggregates) by including both Franck-Condon (FC) and Herzberg-Teller (HT) vibronic transitions. The latter terms allow the adiabatic excited state of the cluster to couple with vibrations in a perturbative fashion via derivatives of the transition dipole moment along nuclear coordinates. While vibronic coupling simulations employing FC and HT terms are well established for single-molecules, to our knowledge this is the first time they are applied to molecular aggregates. Here, we apply this approach to the simulation of the low-temperature fluorescence spectrum of para-distyrylbenzene single-crystal H-aggregates and draw comparisons with coarse-grained Frenkel-Holstein approaches previously extensively applied to such systems.

  8. Oxygen-aromatic contacts in intra-strand base pairs: analysis of high-resolution DNA crystal structures and quantum chemical calculations.

    Science.gov (United States)

    Jain, Alok; Krishna Deepak, R N V; Sankararamakrishnan, Ramasubbu

    2014-07-01

    Three-dimensional structures of biomolecules are stabilized by a large number of non-covalent interactions and some of them such as van der Waals, electrostatic and hydrogen bond interactions are well characterized. Delocalized π-electron clouds of aromatic residues are known to be involved in cation-π, CH-π, OH-π and π-π interactions. In proteins, many examples have been found in which the backbone carbonyl oxygen of one residue makes close contact with the aromatic center of aromatic residues. Quantum chemical calculations suggest that such contacts may provide stability to the protein secondary structures. In this study, we have systematically analyzed the experimentally determined high-resolution DNA crystal structures and identified 91 examples in which the aromatic center of one base is in close contact (interactions between the bases in base pairs with oxygen-aromatic contacts are energetically favorable. Decomposition of interaction energies indicates that dispersion forces are the major cause for energetically stable interaction in these base pairs. We speculate that oxygen-aromatic contacts in intra-strand base pairs in a DNA structure may have biological significance. PMID:24816369

  9. Hyperfine structure in the J = 1-0 transitions of DCO+, DNC, and HN13C: astronomical observations and quantum-chemical calculations

    CERN Document Server

    van der Tak, Floris; Harding, Michael; Gauss, Jürgen

    2009-01-01

    We have observed the rotational ground-state (J = 1-0) transitions of DCO+, HN13C and DNC with the IRAM 30m telescope toward the dark cloud LDN 1512 which has exceptionally narrow lines permitting hyperfine splitting to be resolved in part. The measured splittings of 50-300 kHz are used to derive nuclear quadrupole and spin-rotation parameters for these species. The measurements are supplemented by high-level quantum-chemical calculations using coupled-cluster techniques and large atomic-orbital basis sets. We find eQq = +151.12 (400) kHz and C_I = -1.12 (43) kHz for DCO+, eQq = 272.5 (51) kHz for HN13C, and eQq(D) = 265.9 (83) kHz and eQq(N) = 288.2 (71) kHz for DNC. The numbers for DNC are consistent with previous laboratory data, while our constants for DCO+ are somewhat smaller than previous results based on astronomical data. For both DCO+ and DNC, our results are more accurate than previous determinations. Our results are in good agreement with the corresponding best theoretical estimates. We also deriv...

  10. Lamb Shift in Nonrelativistic Quantum Electrodynamics.

    Science.gov (United States)

    Grotch, Howard

    1981-01-01

    The bound electron self-energy or Lamb shift is calculated in nonrelativistic quantum electrodynamics. Retardation is retained and also an interaction previously dropped in other nonrelativistic approaches is kept. Results are finite without introducing a cutoff and lead to a Lamb shift in hydrogen of 1030.9 MHz. (Author/JN)

  11. A comparative quantitative analysis of the IDEAL (iterative decomposition of water and fat with echo asymmetry and least-squares estimation) and the CHESS (chemical shift selection suppression) techniques in 3.0 T L-spine MRI

    Science.gov (United States)

    Kim, Eng-Chan; Cho, Jae-Hwan; Kim, Min-Hye; Kim, Ki-Hong; Choi, Cheon-Woong; Seok, Jong-min; Na, Kil-Ju; Han, Man-Seok

    2013-03-01

    This study was conducted on 20 patients who had undergone pedicle screw fixation between March and December 2010 to quantitatively compare a conventional fat suppression technique, CHESS (chemical shift selection suppression), and a new technique, IDEAL (iterative decomposition of water and fat with echo asymmetry and least squares estimation). The general efficacy and usefulness of the IDEAL technique was also evaluated. Fat-suppressed transverse-relaxation-weighed images and longitudinal-relaxation-weighted images were obtained before and after contrast injection by using these two techniques with a 1.5T MR (magnetic resonance) scanner. The obtained images were analyzed for image distortion, susceptibility artifacts and homogenous fat removal in the target region. The results showed that the image distortion due to the susceptibility artifacts caused by implanted metal was lower in the images obtained using the IDEAL technique compared to those obtained using the CHESS technique. The results of a qualitative analysis also showed that compared to the CHESS technique, fewer susceptibility artifacts and more homogenous fat removal were found in the images obtained using the IDEAL technique in a comparative image evaluation of the axial plane images before and after contrast injection. In summary, compared to the CHESS technique, the IDEAL technique showed a lower occurrence of susceptibility artifacts caused by metal and lower image distortion. In addition, more homogenous fat removal was shown in the IDEAL technique.

  12. Compressive Shift Retrieval

    Science.gov (United States)

    Ohlsson, Henrik; Eldar, Yonina C.; Yang, Allen Y.; Sastry, S. Shankar

    2014-08-01

    The classical shift retrieval problem considers two signals in vector form that are related by a shift. The problem is of great importance in many applications and is typically solved by maximizing the cross-correlation between the two signals. Inspired by compressive sensing, in this paper, we seek to estimate the shift directly from compressed signals. We show that under certain conditions, the shift can be recovered using fewer samples and less computation compared to the classical setup. Of particular interest is shift estimation from Fourier coefficients. We show that under rather mild conditions only one Fourier coefficient suffices to recover the true shift.

  13. Spectroscopy and quantum chemical modeling reveal a predominant contribution of excitonic interactions to the bathochromic shift in alpha-crustacyanin, the blue carotenoprotein in the carapace of the lobster Homarus gammarus.

    Science.gov (United States)

    van Wijk, Arjan A C; Spaans, Arnold; Uzunbajakava, Natallia; Otto, Cees; de Groot, Huub J M; Lugtenburg, Johan; Buda, Francesco

    2005-02-01

    To resolve the molecular basis of the coloration mechanism of alpha-crustacyanin, we used (13)C-labeled astaxanthins as chromophores for solid-state (13)C NMR and resonance Raman spectroscopy of [6,6',7,7']-(13)C(4) alpha-crustacyanin and [8,8',9,9',10,10',11,11',20,20']-(13)C(10) alpha-crustacyanin. We complement the experimental data with time-dependent density functional theory calculations on several models based on the structural information available for beta-crustacyanin. The data rule out major changes and strong polarization effects in the ground-state electron density of astaxanthin upon binding to the protein. Conformational changes in the chromophore and hydrogen-bond interactions between the astaxanthin and the protein can account only for about one-third of the total bathochromic shift in alpha-crustacyanin. The exciton coupling due to the proximity of two astaxanthin chromophores is found to be large, suggesting that aggregation effects in the protein represent the primary source of the color change. PMID:15686376

  14. Hyperfine structure in the J = 1-0 transitions of DCO^+, DNC, and HN13C: astronomical observations and quantum-chemical calculations

    Science.gov (United States)

    van der Tak, F. F. S.; Müller, H. S. P.; Harding, M. E.; Gauss, J.

    2009-11-01

    Context: Knowledge of the hyperfine structure of molecular lines is useful for estimating reliable column densities from observed emission, and essential for the derivation of kinematic information from line profiles. Aims: Deuterium bearing molecules are especially useful in this regard, because they are good probes of the physical and chemical structure of molecular cloud cores on the verge of star formation. However, the necessary spectroscopic data are often missing, especially for molecules which are too unstable for laboratory study. Methods: We have observed the ground-state (J = 1{-}0) rotational transitions of DCO^+, HN13C and DNC with the IRAM 30 m telescope toward the dark cloud LDN 1512 which has exceptionally narrow lines permitting hyperfine splitting to be resolved in part. The measured splittings of 50-300 kHz are used to derive nuclear quadrupole and spin-rotation parameters for these species. The measurements are supplemented by high-level quantum-chemical calculations using coupled-cluster techniques and large atomic-orbital basis sets. Results: We find eQq = + 151.12 (400) kHz and CI = -1.12 (43) kHz for DCO^+, eQq = 272.5 (51) kHz for HN13C, and eQq(D) =265.9 (83) kHz and eQq(N) = 288.2 (71) kHz for DNC. The numbers for DNC are consistent with previous laboratory data, while our constants for DCO+ are somewhat smaller than previous results based on astronomical data. For both DCO+ and DNC, our results are more accurate than previous determinations. Our results are in good agreement with the corresponding best theoretical estimates, which amount to eQq = 156.0 kHz and CI = -0.69 kHz for DCO^+, eQq = 279.5 kHz for HN13C, and eQq(D) = 257.6 kHz and eQq(N) = 309.6 kHz for DNC. We also derive updated rotational constants for HN13C: B = 43 545.6000 (47) MHz and D = 93.7 (20) kHz. Conclusions: The hyperfine splittings of the DCO^+, DNC and HN13C J = 1{-}0 lines range over 0.47-1.28 km s-1, which is comparable to typical line widths in pre

  15. Development of Prediction Models for the Reactivity of Organic Compounds with Ozone in Aqueous Solution by Quantum Chemical Calculations: The Role of Delocalized and Localized Molecular Orbitals.

    Science.gov (United States)

    Lee, Minju; Zimmermann-Steffens, Saskia G; Arey, J Samuel; Fenner, Kathrin; von Gunten, Urs

    2015-08-18

    Second-order rate constants (kO3) for the reaction of ozone with micropollutants are essential parameters for the assessment of micropollutant elimination efficiency during ozonation in water and wastewater treatment. Prediction models for kO3 were developed for aromatic compounds, olefins, and amines by quantum chemical molecular orbital calculations employing ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods. The kO3 values for aromatic compounds correlated well with the energy of a delocalized molecular orbital first appearing on an aromatic ring (i.e., the highest occupied molecular orbital (HOMO) or HOMO-n (n ≥ 0) when the HOMO is not located on the aromatic ring); the number of compounds tested (N) was 112, and the correlation coefficient (R(2)) values were 0.82-1.00. The kO3 values for olefins and amines correlated well with the energy of a localized molecular orbital (i.e., the natural bond orbital (NBO)) energy of the carbon-carbon π bond of olefins (N = 45, R(2) values of 0.82-0.85) and the NBO energy of the nitrogen lone-pair electrons of amines (N = 59, R(2) values of 0.81-0.83), respectively. Considering the performance of the kO3 prediction model and the computational costs, the HF/6-31G method is recommended for all aromatic groups and olefins investigated herein, whereas the HF/MIDI!, HF/6-31G*, or HF/6-311++G** methods are recommended for amines. Based on their mean absolute errors, the above models could predict kO3 within a factor of 4, on average, relative to the experimentally determined values. Overall, good correlations were also observed (R(2) values of 0.77-0.96) between kO3 predictions by quantum molecular orbital descriptors in this study and by the Hammett (σ) and Taft (σ*) constants from previously developed quantitative structure-activity relationship (QSAR) models. Hence, the quantum molecular orbital descriptors are an alternative to σ and σ*-values in QSAR applications and can also be utilized to

  16. Comparison of brown and white adipose tissue fat fractions in ob, seipin, and Fsp27 gene knockout mice by chemical shift-selective imaging and (1)H-MR spectroscopy.

    Science.gov (United States)

    Peng, Xin-Gui; Ju, Shenghong; Fang, Fang; Wang, Yu; Fang, Ke; Cui, Xin; Liu, George; Li, Peng; Mao, Hui; Teng, Gao-Jun

    2013-01-15

    Brown adipose tissue (BAT) plays a key role in thermogenesis to protect the body from cold and obesity. White adipose tissue (WAT) stores excess energy in the form of triglycerides. To better understand the genetic effect on regulation of WAT and BAT, we investigated the fat fraction (FF) in two types of adipose tissues in ob/ob, human BSCL2/seipin gene knockout (SKO), Fsp27 gene knockout (Fsp27(-/-)), and wild-type (WT) mice in vivo using chemical shift selective imaging and (1)H-MR spectroscopy. We reported that the visceral fat volume in WAT was significantly larger in ob/ob mice, but visceral fat volumes were lower in SKO and Fsp27(-/-) mice compared with WT mice. BAT FF was significantly higher in ob/ob mice than the WT group and similar to that of WAT. In contrast, WAT FFs in SKO and Fsp27(-/-) mice were lower and similar to that of BAT. The adipocyte size of WAT in ob/ob mice and the BAT adipocyte size in ob/ob, SKO, and Fsp27 mice were significantly larger compared with WT mice. However, the WAT adipocyte size was significantly smaller in SKO mice than in WT mice. Positive correlations were observed between the adipocyte size and FFs of WAT and BAT. These results suggested that smaller adipocyte size correlates with lower FFs of WAT and BAT. In addition, the differences in FFs in WAT and BAT measured by MR methods in different mouse models were related to the different regulation effects of ob, seipin, or Fsp27 gene on developing WAT and BAT.

  17. 磁共振化学位移成像评估椎体骨髓脂肪含量的应用%Application of assessing fat content of vertebral bone marrow with chemical-shift MRI

    Institute of Scientific and Technical Information of China (English)

    雷立存; 任庆云; 母建奎; 祁宇轩; 何丽; 刘斋

    2015-01-01

    Objective To investigate the feasibility for assessing the fat content of vertebral bone marrow in postmenopausal women with chemical-shift MRI technique..Methods Lumbar vertebral body.(L1-L4)(224 vertebral body) of 56 cases of postmeno-pausal women were selected and all patients were performed with chemical-shift MRI and dual-energy X-ray absorptiometry (DXA).to obtain signal decline index and bone density..The patients were divided into normal group,.osteopenia group and osteoporosis group according to DXA results,.and the difference of signal decline index among three groups was analyzed so as to investigate the law of signal decline index of vertebrae of groups with different bone density. Results 68 subjects in normal group,.72 subjects with osteopenia and 84 subjects with osteoporosis were determined according to DXA results. .The median of vertebrae signal decline index of the three groups (normal group, osteopenia group and osteoporosis group) were 60.57%(67.86%-45.34%),.58.22%.(69.29%-49.49%) and 56.80%.(67.52%-36.00%),.respectively. There was statistically significant difference (P0.05). Conclusion Measuring vertebrae signal decline index with chemical shift MRI can reflect the changes of fat content in patients with osteoporosis, and is of high value in clinical application.%目的:探讨磁共振化学位移成像技术评估绝经后女性椎体骨髓脂肪含量的可行性。方法选取56例绝经后女性患者的腰椎1~4椎体(共计224个椎体),所有患者均行磁共振化学位移成像和双能X线吸收法骨密度测定,得出每个椎体信号下降指数和骨密度值,按照骨密度T分数分为骨量正常组,骨量减少组和骨质疏松组,分析三组椎体信号下降指数的差异,探讨不同骨密度组椎体信号下降指数的变化规律。结果56例患者224个椎体按照T分数进行分组,骨量正常组68个,骨量减少组72个,骨质疏松组84个,骨量正常组,骨量减少组和

  18. Sensitivity of aerosol optical depth, single scattering albedo, and phase function calculations to assumptions on physical and chemical properties of aerosol

    Science.gov (United States)

    In coupled chemistry-meteorology simulations, the calculation of aerosol optical properties is an important task for the inclusion of the aerosol effects on the atmospheric radiative budget. However, the calculation of these properties from an aerosol profile is not uniquely defi...

  19. High resolution NMR theory and chemical applications

    CERN Document Server

    Becker, Edwin D

    1969-01-01

    High Resolution NMR: Theory and Chemical Applications focuses on the applications of nuclear magnetic resonance (NMR), as well as chemical shifts, lattices, and couplings. The book first offers information on the theory of NMR, including nuclear spin and magnetic moment, spin lattice relaxation, line widths, saturation, quantum mechanical description of NMR, and ringing. The text then ponders on instrumentation and techniques and chemical shifts. Discussions focus on the origin of chemical shifts, reference compounds, empirical correlations of chemical shifts, modulation and phase detection,

  20. Catalogue of methods of calculation, interpolation, smoothing, and reduction for the physical, chemical, and biological parameters of deep hydrology (CATMETH) (NODC Accession 7700442)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The document presents the methods, formulas and citations used by the BNDO to process physical, chemical, and biological data for deep hydrology including...

  1. The Issue of Calculating the Final Temperature of the Products of Rapid Exothermic Chemical Reactions with Significant Energy Release in a Closed Volume

    Directory of Open Access Journals (Sweden)

    Lazarev V.

    2016-02-01

    Full Text Available The theoretical problem solved in this article is the calculation of thermodynamic parameters such as final temperature, distribution of the liquid and dry saturated vapour phases of the substance that are considered to be in thermodynamic equilibrium, and pressure of the system of several reaction products after adding to the system a certain amount of heat or the thermal effect released during rapid exothermic reaction in a closed volume that occurs so fast that it can be considered to be adiabatic, and when the volume of liquid reagents is several orders of magnitude less than the volume of the reactor. The general multi-substance problem is reduced to a theoretical problem for one substance of calculation thermodynamic parameters of system after adding a certain amount of heat that gives theoretically rigorous isochoric calculation. In this article, we substantiate our view that isochoric pass of calculation is more robust compared to seemingly more natural isobaric pass of calculation, if the later involves quite not trivial calculation of the adiabatic compression of a two-phase system (liquid – dry saturated vapour that can pass itself into another kind of state (liquid – wet saturated vapour, which requires, apparently, more complex descriptions compared with isochoric calculation because the specific heat capacity of wet saturated vapour can be negative.

  2. Quantum mechanical calculations of vibrational population inversion in chemical reactions - Numerically exact L-squared-amplitude-density study of the H2Br reactive system

    Science.gov (United States)

    Zhang, Y. C.; Zhang, J. Z. H.; Kouri, D. J.; Haug, K.; Schwenke, D. W.

    1988-01-01

    Numerically exact, fully three-dimensional quantum mechanicl reactive scattering calculations are reported for the H2Br system. Both the exchange (H + H-prime Br to H-prime + HBr) and abstraction (H + HBR to H2 + Br) reaction channels are included in the calculations. The present results are the first completely converged three-dimensional quantum calculations for a system involving a highly exoergic reaction channel (the abstraction process). It is found that the production of vibrationally hot H2 in the abstraction reaction, and hence the extent of population inversion in the products, is a sensitive function of initial HBr rotational state and collision energy.

  3. Implementing OpenShift

    CERN Document Server

    Miller, Adam

    2013-01-01

    A standard tutorial-based approach to using OpenShift and deploying custom or pre-built web applications to the OpenShift Online cloud.This book is for software developers and DevOps alike who are interested in learning how to use the OpenShift Platform-as-a-Service for developing and deploying applications, how the environment works on the back end, and how to deploy their very own open source Platform-as-a-Service based on the upstream OpenShift Origin project.

  4. Orientation Preferences of Backbone Secondary Amide Functional Groups in Peptide Nucleic Acid Complexes: Quantum Chemical Calculations Reveal an Intrinsic Preference of Cationic D-Amino Acid-Based Chiral PNA Analogues for the P-form

    OpenAIRE

    Topham, Christopher M.; Smith, Jeremy C.

    2006-01-01

    Geometric descriptions of nonideal interresidue hydrogen bonding and backbone-base water bridging in the minor groove are established in terms of polyamide backbone carbonyl group orientation from analyses of residue junction conformers in experimentally determined peptide nucleic acid (PNA) complexes. Two types of interresidue hydrogen bonding are identified in PNA conformers in heteroduplexes with nucleic acids that adopt A-like basepair stacking. Quantum chemical calculations on the bindin...

  5. Quantum chemical calculation (electronic and topologic) and experimental (FT-IR, FT-Raman and UV) analysis of isonicotinic acid N-oxide

    Science.gov (United States)

    Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet

    2015-04-01

    In this work, the molecular conformation, vibrational and electronic analysis of isonicotinic acid N-oxide (iso-NANO) were presented in the ground state using experimental techniques (FT-IR, FT-Raman and UV) and density functional theory (DFT) employing B3LYP exchange correlation with the 6-311++G(d,p) basis set. The geometry optimization and energies associated possible two conformers (Rot-I and Rot-II) were computed. The vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. The obtained structures were analyzed with the Atoms in Molecules (AIMs) methodology. The computational results diagnose the most stable conformer of iso-NANO as the Rot-I form. Total density of state (TDOS) and partial density of state (PDOS) and also overlap population density of state (OPDOS) diagrams analysis for the most stable conformer (Rot-I) were calculated using the same method. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures were calculated. As a result, the optimized geometry and calculated spectroscopic data show a good agreement with the experimental results.

  6. Trends in adsorbate induced core level shifts

    Science.gov (United States)

    Nilsson, Viktor; Van den Bossche, Maxime; Hellman, Anders; Grönbeck, Henrik

    2015-10-01

    Photoelectron core level spectroscopy is commonly used to monitor atomic and molecular adsorption on metal surfaces. As changes in the electron binding energies are convoluted measures with different origins, calculations are often used to facilitate the decoding of experimental signatures. The interpretation could in this sense benefit from knowledge on trends in surface core level shifts for different metals and adsorbates. Here, density functional theory calculations have been used to systematically evaluate core level shifts for (111) and (100) surfaces of 3d, 4d, and 5d transition metals upon CO, H, O and S adsorption. The results reveal trends and several non-intuitive cases. Moreover, the difficulties correlating core level shifts with charging and d-band shifts are underlined.

  7. Making Shifts toward Proficiency

    Science.gov (United States)

    McGatha, Maggie B.; Bay-Williams, Jennifer M.

    2013-01-01

    The Leading for Mathematical Proficiency (LMP) Framework (Bay-Williams et al.) has three components: (1) The Standards for Mathematical Practice; (2) Shifts in classroom practice; and (3) Teaching skills. This article briefly describes each component of the LMP framework and then focuses more in depth on the second component, the shifts in…

  8. Shifting employment revisited

    NARCIS (Netherlands)

    Cremers, Jan; Gramuglia, Alessia

    2014-01-01

    The CLR-network examined in 2006 the phenomenon of undeclared labour, with specific regard to the construction sector. The resulting study, Shifting Employment: undeclared labour in construction (Shifting-study hereafter), gave evidence that this is an area particularly affected by undeclared activi

  9. OpenShift cookbook

    CERN Document Server

    Gulati, Shekhar

    2014-01-01

    If you are a web application developer who wants to use the OpenShift platform to host your next big idea but are looking for guidance on how to achieve this, then this book is the first step you need to take. This is a very accessible cookbook where no previous knowledge of OpenShift is needed.

  10. Shifted Independent Component Analysis

    DEFF Research Database (Denmark)

    Mørup, Morten; Madsen, Kristoffer Hougaard; Hansen, Lars Kai

    2007-01-01

    Delayed mixing is a problem of theoretical interest and practical importance, e.g., in speech processing, bio-medical signal analysis and financial data modelling. Most previous analyses have been based on models with integer shifts, i.e., shifts by a number of samples, and have often been carried...

  11. Bonding and Moessbauer Isomer Shifts in (Hg,Pb)—1223 Cuprate

    Institute of Scientific and Technical Information of China (English)

    高发明; 田永君; 谌岩; 李东春; 董海峰; 张思远

    2003-01-01

    By using the chemical bond theory of dielectric description,the chemical bond parameters of(Hg,Pb)-1223 were calculated.The results show that the(Ba,Sr)-O and Ca-0 types of bond have higher ionic character,while the Cu-O and(Hg,Pb)-0 types of bond have more covalent character.Moessbauer isomer shifts of 57Fe and 119Sn doped in(Hg,Pb)-1223 were calculated by using the chemical environmental factor,he,defined by covalency and electronic polarizability.Four valence state tin and three valence iron sites were identified in 57Fe and 119Sn doped(Hg,Pb)-1223 superconductor.It can be concluded that all of the Fe atoms substitute the Cu at square planar Cu(1) site,Whereas Sn prefers to substitute the square pyramidal Cu(2) site.

  12. Bonding and M?ssbauer Isomer Shifts in (Tl,Pb) - 1223 Cuprate

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    By using the chemical bond theory of dielectric description,the chemical bond parameters of (Tl,Pb) - 1223 was calculated.The results show that the Sr-O,Tl-O,and Ca-O types of bond have higher ionic character and the Cu-O types of bond have more covalent character.M?ssbauer isomer shifts of 57Fe and 119Sn doped in (Tl,Pb) -1223 were calculated by using the chemical environmental factor,he,defined by covalency and electronic polarizability.Four valence state tin and three valence iron sites were identified in 57Fe,and 119Sn doped (Tl,Pb) -1223 superconductor.We conclude that all of the Fe atoms substitute the Cu at square planar Cu (1) site,whereas Sn prefers to substitute the square pyramidal Cu (2) site.

  13. Sign (di)Lemma for Dimension Shifting

    Indian Academy of Sciences (India)

    Nitin Nitsure

    2009-04-01

    There is a surprising occurrence of some minus signs in the isomorphisms produced in the well-known technique of dimension shifting in calculating derived functors in homological algebra. We explicitly determine these signs. Getting these signs right is important in order to avoid basic contradictions. We illustrate the result – which we call as the sign lemma for dimension shifting – by some de Rham cohomology and Chern class considerations for compact Riemann surfaces.

  14. Electronic structure and conformational properties of the amide linkage Part 9. Geometrical and electronic structures of N-alkenyllactams as determined by PE spectroscopy and semiempirical quantum chemical calculations

    Science.gov (United States)

    Woydt, Michael; Rademacher, Paul

    1992-01-01

    N-Alkenyllactams with a ring size from five to seven were studied by semiempirical quantum chemical methods (MNDO and AM1) and photoelectron (PE) spectroscopy. While MNDO leads to a minimum-energy conformation with a clinal alkenyl group, AM1 reveals the antiperiplanar conformation as the most stable one. The following sequence of the three highest occupied MOs was found by AM1: antisymmetric combination of π CC and n N (π 3, HOMO), oxygen lone-pair MO (n o, HOMO-1) and symmetric combination of π CC and n N (π 2 HOMO-2). MNDO calculations give the following orbital sequence: π CC (HOMO), n N and n O. In the AM1 calculations, substantial through-bond interactions were found, while in the MNDO calculations through-space interactions are favoured. The PE spectra of the investigated compounds agree better with the AM1 than with the MNDO results.

  15. The Issue of Calculating the Final Temperature of the Products of Rapid Exothermic Chemical Reactions with Significant Energy Release in a Closed Volume

    Science.gov (United States)

    Lazarev, V.; Geidmanis, D.

    2016-02-01

    The theoretical problem solved in this article is the calculation of thermodynamic parameters such as final temperature, distribution of the liquid and dry saturated vapour phases of the substance that are considered to be in thermodynamic equilibrium, and pressure of the system of several reaction products after adding to the system a certain amount of heat or the thermal effect released during rapid exothermic reaction in a closed volume that occurs so fast that it can be considered to be adiabatic, and when the volume of liquid reagents is several orders of magnitude less than the volume of the reactor. The general multi-substance problem is reduced to a theoretical problem for one substance of calculation thermodynamic parameters of system after adding a certain amount of heat that gives theoretically rigorous isochoric calculation. In this article, we substantiate our view that isochoric pass of calculation is more robust compared to seemingly more natural isobaric pass of calculation, if the later involves quite not trivial calculation of the adiabatic compression of a two-phase system (liquid - dry saturated vapour) that can pass itself into another kind of state (liquid - wet saturated vapour), which requires, apparently, more complex descriptions compared with isochoric calculation because the specific heat capacity of wet saturated vapour can be negative. The solved theoretical problem relates to a practical problem that has been a driver for our research as part of a design of the reactor of the titanium reduction from magnesium and titanium tetrachloride supplied into atmosphere of the reactor at high temperatures when both reagents are in gaseous state. The reaction is known to be exothermic with a high thermal effect, and estimate of the final temperature and pressure of the products of reaction, for instance, designing the reactor allows eliminating the possibility of the reaction products to penetrate backwards into supply tracts of the reagents

  16. A review of reaction rates and thermodynamic and transport properties for the 11-species air model for chemical and thermal nonequilibrium calculations to 30000 K

    Science.gov (United States)

    Gupta, Roop N.; Yos, Jerrold M.; Thompson, Richard A.

    1989-01-01

    Reaction rate coefficients and thermodynamic and transport properties are provided for the 11-species air model which can be used for analyzing flows in chemical and thermal nonequilibrium. Such flows will likely occur around currently planned and future hypersonic vehicles. Guidelines for determining the state of the surrounding environment are provided. Approximate and more exact formulas are provided for computing the properties of partially ionized air mixtures in such environments.

  17. Quantum-chemical calculations of the products and energies of electron induced ionization of 2-Furanmethanol, Tetrahydro-and 3-Furanol

    Directory of Open Access Journals (Sweden)

    Papp P.

    2008-01-01

    Full Text Available A theoretical treatment is used to perform conformational studies of title compounds, which was previously successfully used within our group for characterization of fragmentation patterns of some bio-molecules. Now we present studies of electron impact ionization of 2 Furanmethanol, Tetrahydro (C5H10O2 and 3-Furanol, Tetrahydro (C4H8O2, both as important models for more complicated compounds like nucleic acids. In this paper geometry of the neutral and cationic conformers of these two molecules was optimized on the DFT level with B3LYP functional, and ionization energies were estimated. DFT calculated results are supplemented with G3MP2 calculations, and a set of higher-level ab initio methods were empirically corrected to obtain more reliable results.

  18. Molecular structure, spectroscopic characterization (FT-IR, FT-Raman, UV and NMR), HOMO and LUMO analysis of 3-ethynylthiophene with DFT quantum chemical calculations

    Science.gov (United States)

    Karabacak, Mehmet; Bilgili, Sibel; Mavis, Tugba; Eskici, Mustafa; Atac, Ahmet

    2013-11-01

    In this work, FT-IR, FT-Raman, UV and NMR spectra of 3-ethynylthiophene (3-ETP, C6H4S) were carried out by using density functional theory DFT/B3LYP method with the 6-311++G(d,p), 6-311+G(d,p), 6-311G(d,p), 6-31++G(d,p), 6-31+G(d,p), 6-31G(d,p) basis sets. FT-IR and FT-Raman spectra were recorded in the regions of 3500-400 cm-1 and 3500-50 cm-1, respectively. The geometrical parameters, energies and wavenumbers were obtained and the complete assignments of fundamental vibrations were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. The 1H, 13C and HMQC (1H-13C correlation) NMR spectra in chloroform (CDCl3) were recorded and calculated. The UV spectrum of investigated compound were recorded in the region of 200-400 nm in ethanol solution. The electronic properties, such as excitation energies, absorption wavelengths, HOMO and LUMO energies were performed by DFT/B3LYP approach and the results were compared with experimental observations. The thermodynamic properties such zero-point vibrational energy, thermal energy, specific heat capacity, rotational constants, entropy, and dipole moment of the studied compound were calculated. As a result, the calculated results were compared with the observed data and found to be in good agreement.

  19. The vibrational structure of (E,E’)-1,4-diphenyl-1,3-butadiene. Linear dichroism FTIR spectroscopy and quantum chemical calculations

    DEFF Research Database (Denmark)

    Hansen, Bjarke Knud Vilster; Møller, Søren; Spanget-Larsen, Jens

    2006-01-01

    The title compound (DPB) was investigated by FTIR spectroscopy in liquid solutions and by FTIR linear dichroism (LD) measurements on samples aligned in stretched polyethylene. The LD data provided experimental assignments of molecular transition moment directions and vibrational symmetries for mo...... of a nearly complete assignment of the IR active fundamentals of DPB, involving reassignment of a number of transitions. In addition, previously published Raman spectra of DPB were well predicted by the B3LYP/cc-pVTZ calculations....

  20. Electrostatic Interactions Are Key to C═O n-π* Shifts: An Experimental Proof.

    Science.gov (United States)

    Haldar, Tapas; Bagchi, Sayan

    2016-06-16

    Carbonyl n-π* transitions are known to undergo blue shift in polar and hydrogen-bonding solvents. Using semiempirical expressions, previous studies hypothesized several factors like change in dipole moment and hydrogen-bond strength upon excitation to cause the blue shift. Theoretically, ground-state electrostatics has been predicted to be the key to the observed shifts, however, an experimental proof has been lacking. Our experimental results demonstrate a consistent linear correlation between IR (ground-state phenomenon) and n-π* frequency shifts (involves both ground and excited electronic-states) of carbonyls in hydrogen-bonded and non-hydrogen-bonded environments. The carbonyl hydrogen-bonding status is experimentally verified from deviation in n-π*/fluorescence correlation. The IR/n-π* correlation validates the key role of electrostatic stabilization of the ground state toward n-π* shifts and demonstrates the electrostatic nature of carbonyl hydrogen bonds. n-π* shifts show linear sensitivity to calculated electrostatic fields on carbonyls. Our results portray the potential for n-π* absorption to estimate local polarity in biomolecules and to probe chemical reactions involving carbonyl activation/stabilization. PMID:27249517