Science.gov

Sample records for ion structure determination

  1. Oligossacharide structure determination on an ion trap

    SciTech Connect

    Asam, M.R.; Glish, G.L.

    1995-12-31

    Oligosaccharides are important elements in intra- and inter-cellular/molecular recognition mechanisms. Linkage types are part of the information that determine the tertiary structure of oligosaccharides and the tertiary structure is what determines specific recognition, so easily obtained linkage sequences will provide valuable information for computer and other modeling of cellular signaling interactions. Hofmeister et al. have shown that lithium cationized oligosaccharides have specific MS/MS dissociation patterns indicative of the carbohydrate linkage under low energy CID conditions in a hybrid mass spectrometer. The authors have used electrospray ionization on a quadrupole ion trap mass spectrometer to examine MS/MS disaccharide dissociation patterns under ion trap conditions. These studies have concentrated on disaccharides complexed with lithium and sodium.

  2. Structural determinants of ion permeation in CRAC channels

    PubMed Central

    McNally, Beth A.; Yamashita, Megumi; Engh, Anita; Prakriya, Murali

    2009-01-01

    CRAC channels generate Ca2+ signals critical for the activation of immune cells and exhibit an intriguing pore profile distinguished by extremely high Ca2+ selectivity, low Cs+ permeability, and small unitary conductance. To identify the ion conduction pathway and gain insight into the structural bases of these permeation characteristics, we introduced cysteine residues in the CRAC channel pore subunit, Orai1, and probed their accessibility to various thiol-reactive reagents. Our results indicate that the architecture of the ion conduction pathway is characterized by a flexible outer vestibule formed by the TM1-TM2 loop, which leads to a narrow pore flanked by residues of a helical TM1 segment. Residues in TM3, and specifically, E190, a residue considered important for ion selectivity, are not close to the pore. Moreover, the outer vestibule does not significantly contribute to ion selectivity, implying that Ca2+ selectivity is conferred mainly by E106. The ion conduction pathway is sufficiently narrow along much of its length to permit stable coordination of Cd2+ by several TM1 residues, which likely explains the slow flux of ions within the restrained geometry of the pore. These results provide a structural framework to understand the unique permeation properties of CRAC channels. PMID:20018736

  3. Structural foundations of optogenetics: Determinants of channelrhodopsin ion selectivity.

    PubMed

    Berndt, Andre; Lee, Soo Yeun; Wietek, Jonas; Ramakrishnan, Charu; Steinberg, Elizabeth E; Rashid, Asim J; Kim, Hoseok; Park, Sungmo; Santoro, Adam; Frankland, Paul W; Iyer, Shrivats M; Pak, Sally; Ährlund-Richter, Sofie; Delp, Scott L; Malenka, Robert C; Josselyn, Sheena A; Carlén, Marie; Hegemann, Peter; Deisseroth, Karl

    2016-01-26

    The structure-guided design of chloride-conducting channelrhodopsins has illuminated mechanisms underlying ion selectivity of this remarkable family of light-activated ion channels. The first generation of chloride-conducting channelrhodopsins, guided in part by development of a structure-informed electrostatic model for pore selectivity, included both the introduction of amino acids with positively charged side chains into the ion conduction pathway and the removal of residues hypothesized to support negatively charged binding sites for cations. Engineered channels indeed became chloride selective, reversing near -65 mV and enabling a new kind of optogenetic inhibition; however, these first-generation chloride-conducting channels displayed small photocurrents and were not tested for optogenetic inhibition of behavior. Here we report the validation and further development of the channelrhodopsin pore model via crystal structure-guided engineering of next-generation light-activated chloride channels (iC++) and a bistable variant (SwiChR++) with net photocurrents increased more than 15-fold under physiological conditions, reversal potential further decreased by another ∼ 15 mV, inhibition of spiking faithfully tracking chloride gradients and intrinsic cell properties, strong expression in vivo, and the initial microbial opsin channel-inhibitor-based control of freely moving behavior. We further show that inhibition by light-gated chloride channels is mediated mainly by shunting effects, which exert optogenetic control much more efficiently than the hyperpolarization induced by light-activated chloride pumps. The design and functional features of these next-generation chloride-conducting channelrhodopsins provide both chronic and acute timescale tools for reversible optogenetic inhibition, confirm fundamental predictions of the ion selectivity model, and further elucidate electrostatic and steric structure-function relationships of the light-gated pore.

  4. Structural foundations of optogenetics: Determinants of channelrhodopsin ion selectivity

    PubMed Central

    Berndt, Andre; Lee, Soo Yeun; Wietek, Jonas; Ramakrishnan, Charu; Steinberg, Elizabeth E.; Rashid, Asim J.; Kim, Hoseok; Park, Sungmo; Santoro, Adam; Frankland, Paul W.; Iyer, Shrivats M.; Pak, Sally; Ährlund-Richter, Sofie; Delp, Scott L.; Malenka, Robert C.; Josselyn, Sheena A.; Carlén, Marie; Hegemann, Peter; Deisseroth, Karl

    2016-01-01

    The structure-guided design of chloride-conducting channelrhodopsins has illuminated mechanisms underlying ion selectivity of this remarkable family of light-activated ion channels. The first generation of chloride-conducting channelrhodopsins, guided in part by development of a structure-informed electrostatic model for pore selectivity, included both the introduction of amino acids with positively charged side chains into the ion conduction pathway and the removal of residues hypothesized to support negatively charged binding sites for cations. Engineered channels indeed became chloride selective, reversing near −65 mV and enabling a new kind of optogenetic inhibition; however, these first-generation chloride-conducting channels displayed small photocurrents and were not tested for optogenetic inhibition of behavior. Here we report the validation and further development of the channelrhodopsin pore model via crystal structure-guided engineering of next-generation light-activated chloride channels (iC++) and a bistable variant (SwiChR++) with net photocurrents increased more than 15-fold under physiological conditions, reversal potential further decreased by another ∼15 mV, inhibition of spiking faithfully tracking chloride gradients and intrinsic cell properties, strong expression in vivo, and the initial microbial opsin channel-inhibitor–based control of freely moving behavior. We further show that inhibition by light-gated chloride channels is mediated mainly by shunting effects, which exert optogenetic control much more efficiently than the hyperpolarization induced by light-activated chloride pumps. The design and functional features of these next-generation chloride-conducting channelrhodopsins provide both chronic and acute timescale tools for reversible optogenetic inhibition, confirm fundamental predictions of the ion selectivity model, and further elucidate electrostatic and steric structure–function relationships of the light-gated pore. PMID

  5. Understanding chlorophylls: central magnesium ion and phytyl as structural determinants.

    PubMed

    Fiedor, Leszek; Kania, Agnieszka; Myśliwa-Kurdziel, Beata; Orzeł, Łukasz; Stochel, Grazyna

    2008-12-01

    Phytol, a C20 alcohol esterifying the C-17(3) propionate, and Mg2+ ion chelated in the central cavity, are conservative structural constituents of chlorophylls. To evaluate their intramolecular structural effects we prepared a series of metal- and phytyl-free derivatives of bacteriochlorophyll a and applied them as model chlorophylls. A detailed spectroscopic study on the model pigments reveals meaningful differences in the spectral characteristics of the phytylated and non-phytylated pigments. Their analysis in terms of solvatochromism and axial coordination shows how the central Mg and phytyl residue shape the properties of the pigment. Surprisingly, the presence/absence of the central Mg has no effect on the solvatochromism of (bacterio)chlorophyll pi-electron system and the hydrophobicity of phytyl does not interfere with the first solvation shell of the chromophore. However, both residues significantly influence the conformation of the pigment macrocycle and the removal of either residue increases the macrocycle flexibility. The chelation of Mg has a flattening effect on the macrocycle whereas bulky phytyl residue seems to control the conformation of the chromophore via steric interactions with ring V and its substituents. The analysis of spectroscopic properties of bacteriochlorophyllide (free acid) shows that esterification of the C-17(3) propionate is necessary in chlorophylls because the carboxyl group may act as a strong chelator of the central Mg. These observations imply that the truncated chlorophylls used in theoretical studies are not adequate as models of native chromophores, especially when fine effects are to be modeled.

  6. Affinity of molecular ions for DNA structures is determined by solvent-accessible surface area.

    PubMed

    Nakano, Miki; Tateishi-Karimata, Hisae; Tanaka, Shigenori; Sugimoto, Naoki

    2014-08-14

    It is considered that Hoogsteen base pairs and DNA triplex structures play important roles in cellular processes even though these structures are less than duplexes of Watson-Crick base pairs. Molecular ions clearly affect the stability of DNA structures in vivo; however, the mechanisms are unknown. Here, we investigated the effects of sodium ions, choline ions, and tetramethylammonium ions on DNA triplexes using molecular dynamics simulations. We found that nonpolar interactions, which are associated with van der Waals interactions, and solvent-accessible surface area were more important than polar or electrostatic interactions in determining the affinity of a molecular cation for the DNA groove areas. The free energy gain due to a cation that fit optimally within a DNA groove was larger than the free energy loss due to the effect of dehydration. Cations with shapes complementary to that of a particular DNA groove configuration stabilized triplex formation, but cations that disturbed hydrogen bonds between DNA bases were destabilizing. These stabilizing and destabilizing mechanisms of molecular cations were also applicable to a DNA duplex composed of Watson-Crick base pairs. The molecular-level view of cation interactions with DNA structures will guide the design of DNA devices, DNA-based drugs, and genetic therapies.

  7. Travelling wave ion mobility and negative ion fragmentation for the structural determination of N-linked glycans.

    PubMed

    Harvey, David J; Scarff, Charlotte A; Edgeworth, Matthew; Crispin, Max; Scanlan, Christopher N; Sobott, Frank; Allman, Sarah; Baruah, Kavitha; Pritchard, Laura; Scrivens, James H

    2013-08-01

    Travelling wave ion mobility was investigated for its ability to separate N-glycans from other compounds and for resolution of isomers. Charged glycans, exemplified by sialylated complex N-glycans released from bovine fetuin and ionised by electrospray, could be separated from residual glycopeptides allowing the minor, more highly sialylated compounds to be detected where their ions were obscured by ions from other compounds in different charge states. This technique was also found to be excellent for extracting the N-glycan profiles from contaminated samples. Structural identification of the glycans was performed by negative ion CID fragmentation, a method that provides a wealth of structurally diagnostic ions. However, fragment ions can also appear in the glycan profiles where they can be mistaken for glycan molecular ions. Fragments and molecular ions were frequently shown to have different drift time profiles, allowing them to be differentiated. Some separation of isomers was found but only for the smallest compounds. Differentiation from conformers was achieved by plotting drift time profiles of the fragments; these profiles matched those of the precursor ions where conformers were present. The techniques were applied to investigations of N-glycans released from the fungus Piptoporus betulinus where the technique was used to separate different carbohydrate types present in biological extracts. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Structure of the TRPV1 ion channel determined by electron cryo-microscopy.

    PubMed

    Liao, Maofu; Cao, Erhu; Julius, David; Cheng, Yifan

    2013-12-05

    Transient receptor potential (TRP) channels are sensors for a wide range of cellular and environmental signals, but elucidating how these channels respond to physical and chemical stimuli has been hampered by a lack of detailed structural information. Here we exploit advances in electron cryo-microscopy to determine the structure of a mammalian TRP channel, TRPV1, at 3.4 Å resolution, breaking the side-chain resolution barrier for membrane proteins without crystallization. Like voltage-gated channels, TRPV1 exhibits four-fold symmetry around a central ion pathway formed by transmembrane segments 5-6 (S5-S6) and the intervening pore loop, which is flanked by S1-S4 voltage-sensor-like domains. TRPV1 has a wide extracellular 'mouth' with a short selectivity filter. The conserved 'TRP domain' interacts with the S4-S5 linker, consistent with its contribution to allosteric modulation. Subunit organization is facilitated by interactions among cytoplasmic domains, including amino-terminal ankyrin repeats. These observations provide a structural blueprint for understanding unique aspects of TRP channel function.

  9. Structure of the TRPV1 ion channel determined by electron cryo-microscopy

    PubMed Central

    Liao, Maofu; Cao, Erhu; Julius, David; Cheng, Yifan

    2014-01-01

    Transient receptor potential (TRP) channels are sensors for a wide range of cellular and environmental signals, but elucidating how these channels respond to physical and chemical stimuli has been hampered by a lack of detailed structural information. Here, we exploit advances in electron cryo-microscopy to determine the structure of a mammalian TRP channel, TRPV1, at 3.4Å resolution, breaking the side-chain resolution barrier for membrane proteins without crystallization. Like voltage-gated channels, TRPV1 exhibits four-fold symmetry around a central ion pathway formed by transmembrane helices S5–S6 and the intervening pore loop, which is flanked by S1–S4 voltage sensor-like domains. TRPV1 has a wide extracellular ‘mouth’ with short selectivity filter. The conserved ‘TRP domain’ interacts with the S4–S5 linker, consistent with its contribution to allosteric modulation. Subunit organization is facilitated by interactions among cytoplasmic domains, including N-terminal ankyrin repeats. These observations provide a structural blueprint for understanding unique aspects of TRP channel function. PMID:24305160

  10. EXAFS determinations of uranium structures: The uranyl ion complexed with tartaric, citric, and malic acids

    SciTech Connect

    Allen, P.G.; Shuh, D.K.; Bucher, J.J.

    1996-01-31

    Studies of the coordination chemistry of uranium in aqueous solutions are increasingly important for understanding the behavior of uranium in the environment. Actinide speciation information is essential for assessing and developing long-term strategies addressing problems such as migration in nuclear waste repositories or improvements in the processing of nuclear waste and materials. Relative to the latter, one method for removing uranium contamination from soils involves extraction using a chelating agent such as Tiron, or citrate. These types of extractants are quite efficient at binding the uranyl ion and thus are suitable for removing uranium contamination when it is in the hexavalent uranyl ion form. Martell et al. and Markovits et al. have published a series of articles detailing the complexation of the uranyl ion with tartaric, malic, and citric acids as a function of pH. Using the functional dependencies of potentiometric titration results, they showed that, in the pH range 2-4, the uranyl ion forms a 2:2 dimeric species, (UO{sub 2}){sub 2-} (L){sub 2}, where L = tartrate, malate, or citrate ligands. The authors have reinvestigated the solution structures of the uranyl complexes formed in these systems with the structural technique extended X-ray absorption fine-structure (EXAFS) spectroscopy.

  11. Determination of molecular-ion structures through the use of accelerated beams

    SciTech Connect

    Gemmell, D.S.

    1987-01-01

    In this talk we report on recent research on molecular-ion structures using fast molecular-ion beams provided by Argonne's 5-MV Dynamitron accelerator. The method has become known as the ''Coulomb-explosion'' technique. When molecular-ion projectiles travelling at velocities of a few percent of the velocity of light strike a foil, the electrons that bind the molecular projectiles are almost always totally stripped off within the first few Angstroms of penetration into the solid target. This leaves a cluster of bare (or nearly bare) nuclei which separate rapidly as a result of their mutual Coulomb repulsion. This violent dissociation process in which the initial electrostatic potential energy is converted into kinetic energy of relative motion in the center-of-mass, has been termed a ''Coulomb explosion.'' 4 refs., 2 figs.

  12. Determination of molecular-ion structures through the use of accelerated beams

    NASA Astrophysics Data System (ADS)

    Gemmell, D. S.

    In this talk we report on recent research on molecular-ion structures using fast molecular-ion beams provided by Argonne's 5-MV Dynamitron accelerator. The method has become known as the Coulomb-explosion technique. When molecular-ion projectiles travelling at velocities of a few percent of the velocity of light strike a foil, the electrons that bind the molecular projectiles are almost always totally stripped off within the first few Angstroms of penetration into the solid target. This leaves a cluster of bare (or nearly bare) nuclei which separate rapidly as a result of their mutual Coulomb repulsion. This violent dissociation process in which the initial electrostatic potential energy is converted into kinetic energy of relative motion in the center-of-mass, was termed a Coulomb explosion.

  13. Impact Collision Ion Scattering Spectroscopy Applied to the Determination of Atomic Surface Structure

    NASA Astrophysics Data System (ADS)

    Daley, Richard Stephen

    1990-08-01

    The technique of impact collision ion scattering spectroscopy (ICISS) was used to investigate the atomic structure and low energy ion scattering dynamics from various surfaces. A new formalism for calculating the three-dimensional cross section for an ion to scatter sequentially and classically from two atoms has been developed. This method can be used to assist in the interpretation of ICISS data in terms of quantitative surface-structure models. Shadowing and blocking effects for energetic ions scattering from more than one atom are shown to be special cases of rainbow scattering. Even at keV energies and above, the cross section at the critical angle for scattering must be evaluated by quantum or semi-classical means to avoid the singularity in the classically calculated cross sections. In an ICISS investigation of the Ag(110) surface, a surface flux peak analysis demonstrated that the surface was not a complete monolayer, but rather contained 10-15% random vacancies. Subsurface Li^+ scattering results confirmed the oscillatory relaxation of the first two atomic layers of the surface, with Delta_{12} = -7.5% and Delta_{23} = 4.0%. Modeling of the neutralization mechanism for the He^+ scattering gave a best fit time-dependent Auger neutralization time constant of 0.84 +/- 0.08 fs. A neutralization study of 5 keV He^+ ions scattered from Au adatoms on the Si(111)- sqrt{3} x sqrt {3}-Au surface showed the He^+ ICISS data contained false shadowing features that were actually the result of local neutralization effects. Good agreement was obtained for a radially dependent ion-atom neutralization theory with rate R = Aexp (-ar) , where A and a are 15.5 fs^{ -1} and 1.94 A^{-1} , respectively. A detailed examination of the Si(111)- sqrt{3} x sqrt{3 })-Ag surface was also made. The 5 keV Li ^+ ICISS data gave evidence for Ag island formation at single monolayer coverages of silver, while the LEED, AES and LEIS data showed that at relatively high coverages of Ag (35 ML

  14. Surface structure and dipole moments of RbI(001) determined by high-resolution medium-energy ion scattering

    NASA Astrophysics Data System (ADS)

    Okazawa, T.; Hoshino, Y.; Nishimura, T.; Kido, Y.

    2001-11-01

    The surface structure of RbI(001) was determined directly by means of medium-energy ion scattering (MEIS) with a monolayer depth resolution. The rumpled surface structure determined here was compared with semi-classical shell-model calculations. On the basis of a simple model regarding the lattice site ion as a point charge accompanied by a dipole moment, we evaluated the dipole moments of the top- and second-layer I- and Rb+ ions self-consistently from the relaxed lattice positions determined by means of MEIS and from the polarizabilities estimated systematically from experimental refraction data. The balance between a short-range force and a long-range coulombic one determined the equilibrium positions of the top- and second-layer ions; these are consistent with those derived by means of MEIS within the experimental uncertainties of 0.02 Å. This indicates that the polarizablities derived from the refraction data and the interatomic (short-range) potentials of the Born-Mayer type are applicable.

  15. Gas Phase Spectra and Structural Determination of Glucose 6 Phosphate Using Cryogenic Ion Vibrational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Kregel, Steven J.; Voss, Jonathan; Marsh, Brett; Garand, Etienne

    2014-06-01

    Glucose-6-Phosphate (G6P) is one member of a class of simple phosphorylated sugars that are relevant in biological processes. We have acquired a gas phase infrared spectrum of G6P- using cryogenic ion vibrational spectroscopy (CIVS) in a home-built spectrometer. The experimental spectrum was compared with calculated vibrational spectra from a systematic conformer search. For both of the α and β anomers, results show that only the lowest energy conformers are present in the gas phase. If spectral signatures for similar sugars could be cataloged, it would allow for conformer-specific determination of mixture composition, for example, for glycolyzation processes.

  16. Role of the diamagnetic zinc(II) ion in determining the electronic structure of lanthanide single-ion magnets.

    PubMed

    Shanmugam, Maheswaran; Upadhyay, Apoorva; Das, Chinmoy; Vaidya, Shefali; Singh, Sourabh Kumar; Gupta, Tulika; Mondal, Ranajit; Langley, Stuart; Murray, Keith; Rajaraman, Gopalan

    2017-02-08

    Four complexes containing Dy(III) and Pr(III) ions and their Ln(III)-Zn(II) analogs were isolated and its structure solved as as [DyIII(HL)2(NO3)3] (1), [PrIII(HL)2(NO3)3] (2), [ZnDy(L)2(NO3)2(CH3COO)] (3) and [Zn2Pr(L)2(CH3COO)4 (NO3)] (4). Dc and ac magnetic data were collected for all the four complexes. 1 and 3 shows out-of-phase susceptibility signals which is a characteristic signature for a single-molecule magnet . Fivefold increase in the anisotropic barrier (Ueff) is observed for 3 (83 cm-1), compared to 1 (16 cm-1) experimentally and the role of the dipolar interaction in the magnetization relaxation dynamics of 3, ac measurements were performed in solution. The ueff found to be 89.2 cm-1 compared to the solid state sample. The observed Ueff difference between 1 and 3 is rationalized by detailed ab intio calculations. The charge density on the bridging atoms and dihedral angle found to be the key parameters to the observed magnetization relaxation behaviour in 1 and 3.

  17. Use of ion-assisted techniques for determining the structure of TiO2 nanotubes

    NASA Astrophysics Data System (ADS)

    Renz, Renata P.; Vargas, André L. M.; Hübler, Roberto

    2015-12-01

    In recent years, several researchers have reported obtaining titanium dioxide nanotubes presenting a variety of advanced and functional properties for high-performance applications, e.g., for solar and fuel cells, gas sensor, self-cleaning and biomedical devices. Electrochemical oxidation of titanium has been widely used as a method for fabrication of self-organized titanium oxide nanotubes (TiO2 NTs), since it is a simple and inexpensive process, which allows a great control over the size and configuration of the formed structure. Normally, the morphological and structural characterizations are based on images from scanning or transmission electron microscopy. The use of characterization techniques assisted by energetic ion beams, such as RBS or MEIS, can simultaneously evaluate the composition and structural properties of the nanotubes. In this work, titanium oxide nanotubes were obtained by electrochemical oxidation of commercially pure titanium via constant-voltage experiments varying the growth time and the potential applied in order to access the formation dynamics of the NTs, including inner and outer diameters as function of the length, and the formation of the end lace type porous layer. The characterizations made by RBS were compared by analysis of top and cross-sectional FEG-SEM images demonstrating a good compromise between them.

  18. Evaluation of ion mobility spectroscopy for determining charge-solvated versus salt-bridge structures of protonated trimers.

    PubMed

    Wong, Richard L; Williams, Evan R; Counterman, Anne E; Clemmer, David E

    2005-07-01

    The cross sections of five different protonated trimers consisting of two base molecules and trifluoroacetic acid were measured by using ion mobility spectrometry. The gas-phase basicities of these five base molecules span an 8-kcal/mol range. These cross sections are compared with those determined from candidate low-energy salt-bridge and charge-solvated structures identified by using molecular mechanics calculations using three different force fields: AMBER*, MMFF, and CHARMm. With AMBER*, the charge-solvated structures are all globular and the salt-bridge structures are all linear, whereas with CHARMm, these two forms of the protonated trimers can adopt either shape. Globular structures have smaller cross sections than linear structures. Conclusions about the structure of these protonated trimers are highly dependent on the force field used to generate low-energy candidate structures. With AMBER*, all of the trimers are consistent with salt-bridge structures, whereas with MMFF the measured cross sections are more consistent with charge-solvated structures, although the assignments are ambiguous for two of the protonated trimers. Conclusions based on structures generated by using CHARMm suggest a change in structure from charge-solvated to salt-bridge structures with increasing gas-phase basicity of the constituent bases, a result that is most consistent with structural conclusions based on blackbody infrared radiative dissociation experiments for these protonated trimers and theoretical calculations on the uncharged base-acid pairs.

  19. Structure Determination and Time-Resolved Raman Spectroscopy of Yttrium Ion Exchange into Microporous Titanosilicate ETS-4.

    PubMed

    Celestian, Aaron J; Chappell, Caleb J; Rucks, Melinda J; Norris, Pauline

    2016-11-07

    The ion exchange of yttrium, one of the five most critical rare-earth elements as outlined by the U.S. Department of Energy, into ETS-4 is a dynamic, multistep ion exchange process. The ion exchange process was followed using in situ time-resolved Raman spectroscopy, and the crystal structures of the pre-exchange and post-exchange forms were determined by single-crystal X-ray diffraction. In situ Raman spectroscopy is an ideal tool for this type of study, as it measures the spectral changes that are a result of molecular geometry changes at fast time intervals, even where symmetry and unit volume changes are minimally detected by X-ray diffraction. By tracking the stepwise changes in the peak positions and intensities in the spectra, where we focused primarily on the strong spectral features corresponding to titania quantum wires and three-membered-ring bending and breathing modes, we constructed molecular models to explain the changes in the Raman spectrum during ion exchange. The multistep ion exchange process started with rapid absorption of Y into the Na2 site, causing titania quantum wires to kink. After this initial uptake, the exchange process slowed, likely caused by hydration coordination changes within the channels. Next, Y exchange accelerated again, during which time the Y site moved closer to the framework O(2-). Crystal structures of the maximal Y exchanged ETS-4 material were determined and confirmed the splitting of the Y site. Inductively coupled plasma optical emission spectroscopy was also used to quantify the extent of Y exchange and to measure if there were indications of titania leaching from the framework.

  20. Ion-ion dynamic structure factor of warm dense mixtures

    SciTech Connect

    Gill, N. M.; Heinonen, R. A.; Starrett, C. E.; Saumon, D.

    2015-06-25

    In this study, the ion-ion dynamic structure factor of warm dense matter is determined using the recently developed pseudoatom molecular dynamics method [Starrett et al., Phys. Rev. E 91, 013104 (2015)]. The method uses density functional theory to determine ion-ion pair interaction potentials that have no free parameters. These potentials are used in classical molecular dynamics simulations. This constitutes a computationally efficient and realistic model of dense plasmas. Comparison with recently published simulations of the ion-ion dynamic structure factor and sound speed of warm dense aluminum finds good to reasonable agreement. Using this method, we make predictions of the ion-ion dynamical structure factor and sound speed of a warm dense mixture—equimolar carbon-hydrogen. This material is commonly used as an ablator in inertial confinement fusion capsules, and our results are amenable to direct experimental measurement.

  1. Ion-ion dynamic structure factor of warm dense mixtures

    DOE PAGES

    Gill, N. M.; Heinonen, R. A.; Starrett, C. E.; ...

    2015-06-25

    In this study, the ion-ion dynamic structure factor of warm dense matter is determined using the recently developed pseudoatom molecular dynamics method [Starrett et al., Phys. Rev. E 91, 013104 (2015)]. The method uses density functional theory to determine ion-ion pair interaction potentials that have no free parameters. These potentials are used in classical molecular dynamics simulations. This constitutes a computationally efficient and realistic model of dense plasmas. Comparison with recently published simulations of the ion-ion dynamic structure factor and sound speed of warm dense aluminum finds good to reasonable agreement. Using this method, we make predictions of the ion-ionmore » dynamical structure factor and sound speed of a warm dense mixture—equimolar carbon-hydrogen. This material is commonly used as an ablator in inertial confinement fusion capsules, and our results are amenable to direct experimental measurement.« less

  2. Solution structure investigation of Ru(II) complex ion pairs: quantitative NOE measurements and determination of average interionic distances.

    PubMed

    Zuccaccia, C; Bellachioma, G; Cardaci, G; Macchioni, A

    2001-11-07

    The structure of the Ru(II) ion pairs trans-[Ru(COMe)[(pz(2))CH(2)](CO)(PMe(3))(2)]X (X(-) = BPh(4)(-), 1a; BPh(3)Me(-), 1b; BPh(3)(n-Bu)(-), 1c; BPh(3)(n-Hex)(-), 1d; B(3, 5-(CF(3))(2)(C(6)H(3)))(4)(-), 1e; PF(6)(-), 1f; and BF(4)(-), 1g; pz = pyrazol-1-yl-ring) was investigated in solution from both a qualitative (chloroform-d, methylene chloride-d(2), nithromethane-d(3)) and quantitative (methylene chloride-d(2)) point of view by performing 1D- and 2D-NOE NMR experiments. In particular, the relative anion-cation localization (interionic structure) was qualitatively determined by (1)H-NOESY and (19)F, (1)H-HOESY (heteronuclear Overhauser effect spectroscopy) NMR experiments. The counteranion locates close to the peripheral protons of the bispyrazolyl ligand independent of its nature and that of the solvent. In complexes 1c and 1d bearing unsymmetrical counteranions, the aliphatic chain points away from the metal center as indicated by the absence of NOE between the terminal Me group and any cationic protons. An estimation of the average interionic distances in solution was obtained by the quantification of the NOE build-up versus the mixing time under the assumption that the interionic and intramolecular correlation times (tau(c)) are the same. Such an assumption was checked by the experimental measurements of tau(c) from both the dipolar contribution to the carbon-13 longitudinal relaxation time T(DD-1)and the comparison of the intramolecular and interionic cross relaxation rate constant (sigma) dependence on the temperature. Both the methodologies indicate that anion and cation have comparable tau(c) values. The determined correlation time values were compared with those obtained for the neutral trans-[Ru(COMe)[(pz(2))BH(2)](CO)(PMe(3))(2)] complex (2), isosteric with the cation of 1. They were significantly shorter (approximately 3.8 times), indicating that the main contribution to dipolar relaxation processes comes from the overall ion pair rotation. As a

  3. The structures of small gold cluster anions as determined by a combination of ion mobility measurements and density functional calculations

    NASA Astrophysics Data System (ADS)

    Furche, Filipp; Ahlrichs, Reinhart; Weis, Patrick; Jacob, Christoph; Gilb, Stefan; Bierweiler, Thomas; Kappes, Manfred M.

    2002-10-01

    A combined experimental and theoretical study of small gold cluster anions is performed. The experimental effort consists of ion mobility measurements that lead to the assignment of the collision cross sections for the different cluster sizes at room temperature. The theoretical study is based on ab initio molecular dynamics calculations with the goal to find energetically favorable candidate structures. By comparison of the theoretical results with the measured collision cross sections as well as vertical detachment energies (VDEs) from the literature, we assign structures for the small Aun- ions (n<13) and locate the transition from planar to three-dimensional structures. While a unique assignment based on the observed VDEs alone is generally not possible, the collision cross sections provide a direct and rather sensitive measure of the cluster structure. In contrast to what was expected from other metal clusters and previous theoretical studies, the structural transition occurs at an unusually large cluster size of twelve atoms.

  4. Effects of Carbon Structure and Surface Oxygen on the Carbon's Performance as the Anode in Lithium-Ion Battery Determined

    NASA Technical Reports Server (NTRS)

    Hung, Ching-Cheh

    2000-01-01

    Four carbon materials (C1, C2, C3, and C4) were tested electrochemically at the NASA Glenn Research Center at Lewis Field to determine their performance in lithium-ion batteries. They were formed as shown in the figure. This process caused very little carbon loss. Products C1 and C3 contained very little oxygen because of the final overnight heating at 540 C. Products C2 and C4, on the other hand, contained small amounts of basic oxide. The electrochemical test involved cycles of lithium intercalation and deintercalation using C/saturated LiI-50/50 (vol %) ethylene carbonate (EC) and dimethyl carbonate (DMC)/Li half cell. The cycling test, which is summarized in the table, resulted in three major conclusions. The capacity of the carbon with a basic oxide surface converges to a constant 1. value quickly (within 4 cycles), possibly because the oxide prevents solvent from entering the carbon structure and, therefore, prolongs the carbon s cycle life. Under certain conditions, the disordered carbon can store more lithium than its 2. precursor. These samples and their precursor can intercalate at 200 mA/g and deintercalate at 3. a rate of 2000 mA/g without significant capacity loss.

  5. Using radio-induced fluorescence to determine the horizontal structure of ion layers in the mesosphere and lower thermosphere

    NASA Astrophysics Data System (ADS)

    Bernhardt, Paul A.; Gondarenko, Natalia A.; Guzdar, Parvez N.; Huba, Joseph D.; Ossakow, S. L.; Djuth, Frank T.; Tepley, C. A.; Sulzer, Michael P.; Kagan, Ludmila; Kelley, M. C.

    2002-01-01

    Two-dimensional images of Sporadic-E layers have been produced using a new technique called radio induced fluorescence (RIF). This technique makes the ion layers glow when being stimulated by high power radio waves. Normally the ion-layers do not radiate visible emissions. Experiments on January 1998 at Arecibo Observatory in Puerto Rico have shown that the layers can be made to glow at 557.7 nm and other wavelengths by illuminating them with radio waves at 3.175 MHz with effective radiated powers of 80 megawatts. The regions of the sporadic-E layers that have electron densities greater than the critical density for reflection of the radio waves emit electrons that collide with and excite atmospheric atomic oxygen and molecular nitrogen. A charge-coupled-device (CCD) imager located on the ground is used to capture images of the glowing E-region structures. The camera exposure times were in the range of 15 to 45 seconds. The images obtained using this technique show a wide variety of structures in the sporadic-E layers. Some layers cover the 15 x 30 km region illuminated by the radio wave beam. Other layers show strong modulation of the E-region by neutral wind instabilities. Two-dimensional computer simulations of the coupling between neutral wind turbulence and the ion layers simulate the structure in the images.

  6. In Situ Mass Spectrometric Determination of Molecular Structural Evolution at the Solid Electrolyte Interphase in Lithium-Ion Batteries.

    PubMed

    Zhu, Zihua; Zhou, Yufan; Yan, Pengfei; Vemuri, Rama Sesha; Xu, Wu; Zhao, Rui; Wang, Xuelin; Thevuthasan, Suntharampillai; Baer, Donald R; Wang, Chong-Min

    2015-09-09

    Dynamic structural and chemical evolution at solid-liquid electrolyte interface is always a mystery for a rechargeable battery due to the challenge to directly probe a solid-liquid interface under reaction conditions. We describe the creation and usage of in situ liquid secondary ion mass spectroscopy (SIMS) for the first time to directly observe the molecular structural evolution at the solid-liquid electrolyte interface for a lithium (Li)-ion battery under dynamic operating conditions. We have discovered that the deposition of Li metal on copper electrode leads to the condensation of solvent molecules around the electrode. Chemically, this layer of solvent condensate tends to be depleted of the salt anions and with reduced concentration of Li(+) ions, essentially leading to the formation of a lean electrolyte layer adjacent to the electrode and therefore contributing to the overpotential of the cell. This observation provides unprecedented molecular level dynamic information on the initial formation of the solid electrolyte interphase (SEI) layer. The present work also ultimately opens new avenues for implanting the in situ liquid SIMS concept to probe the chemical reaction process that intimately involves solid-liquid interface, such as electrocatalysis, electrodeposition, biofuel conversion, biofilm, and biomineralization.

  7. Synthesis and determination of the structural and optical characteristics of cBN micropowder with Eu{sup 3+} ions

    SciTech Connect

    Leonchik, S. V. Karotki, A. V.

    2013-10-15

    Cubic boron-nitride micropowder with Eu{sup 3+} ions (cBN:Eu) is synthesized under conditions of high pressures and temperatures. The structural, morphological, chemical, and optical characteristics of the cBN:Eu micropowder are studied using X-ray diffraction, energy-dispersive X-ray spectral microanalysis, photoluminescence, and optical transmission methods. It is found that the cBN:Eu lattice parameter is {approx}3.615 A. The intense red luminescence of the cBN:Eu micropowder (red glow), measured in the visible region of the spectrum in the range from 550 to 750 nm, is attributed to intracenter 4f-electron transitions of the Eu{sup 3+} ions. The possible nature of the cBN:Eu micropowder luminescence is discussed.

  8. Crystal Structure Determination of Low-Dimensional ZnS Powders Using EPR of Mn2+ Ions

    NASA Astrophysics Data System (ADS)

    Vorona, I. P.; Grachev, V. G.; Ishchenko, S. S.; Baran, N. P.; Bacherikov, Yu. Yu.; Zhuk, A. G.; Nosenko, V. V.

    2016-03-01

    Structures of low-dimensional ZnS powders doped with Cu, Co, and Mn were studied using Mn2+ ions as a paramagnetic probe. Particle sizes were 5-7 μm for ZnS:Cu, 7-10 μm for ZnS:Co, and 50-200 nm for ZnS:Mn. Spin-Hamiltonian parameters describing electron paramagnetic resonance spectra were obtained. Analysis of the spectra revealed that ZnS:Cu powder has cubic structure, ZnS:Mn powder has hexagonal structure with orthorhombic distortion, whereas ZnS:Co powder is a mixture of cubic and hexagonal phases in a 1:10 ratio.

  9. In-situ Mass Spectrometric Determination of Molecular Structural Evolution at the Solid Electrolyte Interphase in Lithium-Ion Batteries

    SciTech Connect

    Zhu, Zihua; Zhou, Yufan; Yan, Pengfei; Vemuri, Venkata Rama Ses; Xu, Wu; Zhao, Rui; Wang, Xuelin; Thevuthasan, Suntharampillai; Baer, Donald R.; Wang, Chong M.

    2015-08-19

    Dynamic molecular evolution at solid/liquid electrolyte interface is always a mystery for a rechargeable battery due to the challenge to directly probe/observe the solid/liquid interface under reaction conditions, which in essence appears to be similarly true for all the fields involving solid/liquid phases, such as electrocatalysis, electrodeposition, biofuel conversion, biofilm, and biomineralization, We use in-situ liquid secondary ion mass spectroscopy (SIMS) for the first time to directly observe the molecular structural evolution at the solid electrode/liquid electrolyte interface for a lithium (Li)-ion battery under dynamic operating conditions. We have discovered that the deposition of Li metal on copper electrode leads to the condensation of solvent molecules around the electrode. Chemically, this layer of solvent condensate tends to deplete the salt anion and with low concentration of Li+ ions, which essentially leads to the formation of a lean electrolyte layer adjacent to the electrode and therefore contributes to the overpotential of the cell. This unprecedented molecular level dynamic observation at the solid electrode/liquid electrolyte interface provides vital chemical information that is needed for designing of better battery chemistry for enhanced performance, and ultimately opens new avenues for using liquid SIMS to probe molecular evolution at solid/liquid interface in general.

  10. Application of lanthanide induced shifts for the determination of solution structures of metal ion-extractant complexes

    SciTech Connect

    Kalina, D.G.

    1984-01-01

    An analysis of the induced shifts in the nuclear magnetic resonance (NMR) spectra of extractants complexed to paramagnetic lanthanide ions has been performed. The complexes of a number of monofunctional and bifunctional extractants have been examined and assigned solution structures by minimizing the differences between the observed shifts and those calculated using a computer analysis in which the potential configurations of the complexes were generated. Complexes of monofunctional extractants were calculated to have coordination geometries quite similar to those observed in related compounds by crystallographic techniques. For the bifunctional extractants, differentiation between monodentate and bidentate coordination seems possible. 23 references, 2 figures, 7 tables.

  11. Structural Determination of Glycopeptidolipids of Mycobacterium smegmatis by High Resolution Multiple-stage Linear Ion-trap Mass Spectrometry with Electrospray Ionization

    PubMed Central

    Hsu, Fong-Fu; Pacheco, Sophia; Turk, John; Purdy, Georgiana

    2012-01-01

    Glycopeptidolipids (GPLs) are abundant in the cell walls of different species of mycobacteria and consist of tripeptide-amino-alcohol core of D-Phe-D-allo-Thr-D-Ala-L-alaninol linked to 3-hydroxy or 3-methoxy C26–34 fatty acyl chain at the N-terminal of D-Phe via amide linkage; and a 6-deoxytalose (6-dTal) and an O-methyl rhamnose residues respectively attach to D-allo-Thr and the terminal L-alaninol. They are important cell-surface antigens that are implicated in the pathogenesis of opportunistic mycobacteria belonging to the Mycobacterium avium complex. In this contribution, we described multiple-stage linear ion-trap in conjunction with high resolution mass spectrometry towards structural characterization of complex GPLs as [M + Na]+ ions isolated from Mycobacterium smegmatis, a fast-growing and non-pathogenic mycobacterial species. Following resonance excitation in an ion-trap, MSn spectra of the [M + Na]+ ions of GPLs contained mainly b and y series ions that readily determine the peptide sequence. Fragment ions from MSn also afford locating the 6-dTal and O-methyl rhamnose residues linked to the D-allo-Thr and terminal L-alaninol of the peptide core, respectively, as well as recognizing the modifications of the glycosides, including their acetylation and methylation states and the presence of succinyl group. The GPL families consisting of 3-hydroxy fatty acyl and of 3-methoxy fatty acyl substituents are readily distinguishable. The MS profiles of the GPLs from cells are dependant on the conditions they were grown and several isobaric isomers were identified for many of the molecular species. These multiple-stage mass spectrometric approaches give detailed structures of GPL in complex mixtures of which the isomeric structures are difficult to define using other analytical methods. PMID:23019158

  12. Theoretical challenge to the X-ray structure determination of dichloronitronium ion ("inorganic phosgene") Cl 2NO +

    NASA Astrophysics Data System (ADS)

    Brumm, Martin; Frenking, Gernot; Koch, Wolfram

    1991-08-01

    Ab initio calculations predict that the N—O interatomic distance in Cl 2NO +, 1, is 1.16±0.03 Å and suggest that the experimental value of 1.30-1.32 Å obtained by X-ray structure determination is probably erroneous.

  13. Crystallographic Structure Determination of Both [5,6]- and [6,6]-Isomers of Lithium-Ion-Containing Diphenylmethano[60]fullerene.

    PubMed

    Okada, Hiroshi; Kawakami, Hiroki; Aoyagi, Shinobu; Matsuo, Yutaka

    2017-06-02

    Organic functionalization of lithium-ion-containing [60]fullerene, Li(+)@C60, was performed by using diphenyl(diazo)methane as a stable, readily available diazo compound to obtain lithium-ion-containing [5,6]- and [6,6]-diphenylmethano[60]fullerenes, Li(+)@C61Ph2. The bis(trifluoromethanesulfonyl)imide (TFSI) salts of [5,6]- and [6,6]-Li(+)@C61Ph2 were successfully separated by using a cation exchange column with eluent containing LiTFSI. Improved separation protocol and high crystallinity of ionic components in less polar solvents enabled separate crystallization of each isomer. Both [5,6]-open and [6,6]-closed structures of Li(+)@C61Ph2 were determined by synchrotron radiation X-ray crystallography. Elucidating the [5,6]-open methano[60]fullerene (fulleroid) structure will contribute to materials research on fulleroids.

  14. X-ray crystallographic and mass spectrometric structure determination and functional characterization of succinylated porin from Rhodobacter capsulatus: implications for ion selectivity and single-channel conductance.

    PubMed Central

    Przybylski, M.; Glocker, M. O.; Nestel, U.; Schnaible, V.; Blüggel, M.; Diederichs, K.; Weckesser, J.; Schad, M.; Schmid, A.; Welte, W.; Benz, R.

    1996-01-01

    The role of charges near the pore mouth has been discussed in theoretical work about ion channels. To introduce new negative charges in a channel protein, amino groups of porin from Rhodobacter capsulatus 37b4 were succinylated with succinic anhydride, and the precise extent and sites of succinylations and structures of the succinylporins determined by mass spectrometry and X-ray crystallography. Molecular weight and peptide mapping analyses using matrix-assisted laser desorption-ionization mass spectrometry identified selective succinylation of three lysine-epsilon-amino groups (Lys-46, Lys-298, Lys-300) and the N-terminal alpha-amino group. The structure of a tetra-succinylated porin (TS-porin) was determined to 2.4 A and was generally found unchanged in comparison to native porin to form a trimeric complex. All succinylated amino groups found in a mono/di-succinylated porin (MS-porin) and a TS-porin are localized at the inner channel surface and are solvent-accessible: Lys-46 is located at the channel constriction site, whereas Lys-298, Lys-300, and the N-terminus are all near the periplasmic entrance of the channel. The Lys-46 residue at the central constriction loop was modeled as succinyl-lysine from the electron density data and shown to bend toward the periplasmic pore mouth. The electrical properties of the MS-and TS-porins were determined by reconstitution into black lipid membranes, and showed a negative charge effect on ion transport and an increased cation selectivity through the porin channel. The properties of a typical general diffusion porin changed to those of a channel that contains point charges near the pore mouth. The single-channel conductance was no longer a linear function of the bulk aqueous salt concentration. The substantially higher cation selectivity of the succinylated porins compared with the native protein is consistent with the increase of negatively charged groups introduced. These results show tertiary structure

  15. How ions affect the structure of water.

    PubMed

    Hribar, Barbara; Southall, Noel T; Vlachy, Vojko; Dill, Ken A

    2002-10-16

    We model ion solvation in water. We use the MB model of water, a simple two-dimensional statistical mechanical model in which waters are represented as Lennard-Jones disks having Gaussian hydrogen-bonding arms. We introduce a charge dipole into MB waters. We perform (NPT) Monte Carlo simulations to explore how water molecules are organized around ions and around nonpolar solutes in salt solutions. The model gives good qualitative agreement with experiments, including Jones-Dole viscosity B coefficients, Samoilov and Hirata ion hydration activation energies, ion solvation thermodynamics, and Setschenow coefficients for Hofmeister series ions, which describe the salt concentration dependence of the solubilities of hydrophobic solutes. The two main ideas captured here are (1) that charge densities govern the interactions of ions with water, and (2) that a balance of forces determines water structure: electrostatics (water's dipole interacting with ions) and hydrogen bonding (water interacting with neighboring waters). Small ions (kosmotropes) have high charge densities so they cause strong electrostatic ordering of nearby waters, breaking hydrogen bonds. In contrast, large ions (chaotropes) have low charge densities, and surrounding water molecules are largely hydrogen bonded.

  16. Weighted difference of g factors of light Li-like and H-like ions for an improved determination of the fine-structure constant

    NASA Astrophysics Data System (ADS)

    Yerokhin, V. A.; Berseneva, E.; Harman, Z.; Tupitsyn, I. I.; Keitel, C. H.

    2016-08-01

    A weighted difference of the g factors of the Li- and H-like ion of the same element is studied and optimized in order to maximize the cancelation of nuclear effects. To this end, a detailed theoretical investigation is performed for the finite nuclear size correction to the one-electron g factor, the one- and two-photon exchange effects, and the QED effects. The coefficients of the Z α expansion of these corrections are determined, which allows us to set up the optimal definition of the weighted difference. It is demonstrated that, for moderately light elements, such weighted difference is nearly free from uncertainties associated with nuclear effects and can be utilized to extract the fine-structure constant from bound-electron g -factor experiments with an accuracy competitive with or better than its current literature value.

  17. Determination of the structural features of a long-lived electron-transfer state of 9-mesityl-10-methylacridinium ion.

    PubMed

    Hoshino, Manabu; Uekusa, Hidehiro; Tomita, Ayana; Koshihara, Shin-ya; Sato, Tokushi; Nozawa, Shunsuke; Adachi, Shin-ichi; Ohkubo, Kei; Kotani, Hiroaki; Fukuzumi, Shunichi

    2012-03-14

    Extensive efforts have been devoted to developing electron donor-acceptor systems that mimic the utilization of solar energy that occurs in photosynthesis. X-ray crystallographic analysis shows how absorbed photon energy is stabilized in those compounds by structural changes upon photoinduced electron transfer (ET). In this study, structural changes of a simple electron donor-acceptor dyad, 9-mesityl-10-methylacridinium cation (Acr(+)-Mes), upon photoinduced ET were directly observed by laser pump and X-ray probe crystallographic analysis. The N-methyl group in Acr(+) was bent, and a weak electrostatic interaction between Mes and a counteranion in the crystal (ClO(4)) was generated by photoinduced ET. These structural changes correspond to reduction and oxidation due to photoinduced ET and directly elucidate the mechanism in Acr(+)-Mes for mimicking photosynthesis efficiently.

  18. Pickup ion mediated plasmas: Shock wave structure

    NASA Astrophysics Data System (ADS)

    Mostafavi, P.; Zank, G. P.; Webb, G. M.

    2016-03-01

    Energetic particles such as pickup ions, solar energetic particles, or cosmic rays play an important role in determining shock structure. Cosmic-ray modified shocks were discussed by Axford et al. [2]. Jokipii and Williams [8] considered the effect of cosmic ray viscosity on the structure of cold thermal gas shocks mediated by cosmic rays. In the present paper, we consider a background thermal gas of arbitrary temperature to extend their work. The Zank et al. [7] model is used to determine the shock structure when energetic particle collisionless heat flux and viscosity is included.

  19. Structural Determination of Circulation.

    ERIC Educational Resources Information Center

    Blankenburg, William B.

    1981-01-01

    Analyzes the effects of both structural factors (demographics, economic conditions, and competition) and discretionary factors (content, design, and marketing techniques) and concludes that it is the former that determine a newspaper's circulation. (FL)

  20. Ion chromatographic determination of sulfur in fuels

    NASA Technical Reports Server (NTRS)

    Mizisin, C. S.; Kuivinen, D. E.; Otterson, D. A.

    1978-01-01

    The sulfur content of fuels was determined using an ion chromatograph to measure the sulfate produced by a modified Parr bomb oxidation. Standard Reference Materials from the National Bureau of Standards, of approximately 0.2 + or - 0.004% sulfur, were analyzed resulting in a standard deviation no greater than 0.008. The ion chromatographic method can be applied to conventional fuels as well as shale-oil derived fuels. Other acid forming elements, such as fluorine, chlorine and nitrogen could be determined at the same time, provided that these elements have reached a suitable ionic state during the oxidation of the fuel.

  1. Analysis of Native-Like Ions Using Structures for Lossless Ion Manipulations.

    PubMed

    Allen, Samuel J; Eaton, Rachel M; Bush, Matthew F

    2016-09-20

    Ion mobility separation of native-like protein and protein complex ions expands the structural information available through native mass spectrometry analysis. Here, we implement Structures for Lossless Ion Manipulations (SLIM) for the analysis of native-like ions. SLIM has been shown previously to operate with near lossless transmission of ions up to 3000 Da in mass. Here for the first time, SLIM was used to separate native-like protein and protein complex ions ranging in mass from 12 to 145 kDa. The resulting arrival-time distributions were monomodal and were used to determine collision cross section values that are within 3% of those determined from radio-frequency-confining drift cell measurements. These results are consistent with the retention of native-like ion structures throughout these experiments. The apparent resolving powers of native-like ions measured using SLIM are as high as 42, which is the highest value reported directly from experimental data for the native-like ion of a protein complex. Interestingly, the apparent resolving power depends strongly on the identity of the analyte, suggesting that the arrival-time distributions of these ions may have contributions from an ensemble of structures in the gas phase that is unique to each analyte. These results suggest that the broad range of emerging SLIM technologies may all be adaptable to the analysis of native-like ions, which will enable future applications in the areas of structural biology, biophysics, and biopharmaceutical characterization.

  2. Superconducting heavy-ion accelerating structures

    SciTech Connect

    Shepard, K.W.

    1996-08-01

    This paper briefly reviews the technical history of superconducting ion-accelerating structures. Various superconducting cavities currently used and being developed for use in ion linacs are discussed. Principal parameters and operational characteristics of superconducting structures in active use at various heavy-ion facilities are described.

  3. Electrostatic occlusion and quaternary structural ion pairing are key determinants of Cu(I)-mediated allostery in the copper-sensing operon repressor (CsoR).

    PubMed

    Chang, Feng-Ming James; Martin, Julia E; Giedroc, David P

    2015-04-21

    The copper-sensing operon repressor (CsoR) is an all-α-helical disc-shaped D2-symmetric homotetramer that forms a 2:1 tetramer/DNA operator complex and represses the expression of copper-resistance genes in a number of bacteria. A previous bioinformatics analysis of CsoR-family repressors distributes Cu(I)-sensing CsoRs in four of seven distinct clades on the basis of global sequence similarity. In this work, we define energetically important determinants of DNA binding in the apo-state (ΔΔGbind), and for allosteric negative coupling of Cu(I) binding to DNA binding (ΔΔGc) in a model clade IV CsoR from Geobacillus thermodenitrificans (Gt) of known structure, by selectively targeting for mutagenesis those charged residues uniquely conserved in clade IV CsoRs. These include a folded N-terminal "tail" and a number of Cu(I)-sensor and clade-specific residues that when mapped onto a model of Cu(I)-bound Gt CsoR define a path across one face of the tetramer. We find that Cu(I)-binding prevents formation of the 2:1 "sandwich" complex rather than DNA binding altogether. Folding of the N-terminal tail (residues R18, E22, R74) upon Cu-binding to the periphery of the tetramer inhibits assembly of the 2:1 apoprotein-DNA complex. In contrast, Ala substitution of residues that surround the central "hole" (R65, K101) in the tetramer, as well R48, impact DNA binding. We also identify a quaternary structural ion-pair, E73-K101″, that crosses the tetramer interface, charge-reversal of which restores DNA binding activity, allosteric regulation by Cu(I), and transcriptional derepression by Cu(I) in cells. These findings suggest an "electrostatic occlusion" model, in which basic residues important for DNA binding and/or allostery become sequestered via ion-pairing specifically in the Cu(I)-bound state, and this aids in copper-dependent disassembly of a repression complex.

  4. Structure elucidation of degradation products of the antibiotic amoxicillin with ion trap MS(n) and accurate mass determination by ESI TOF.

    PubMed

    Nägele, Edgar; Moritz, Ralf

    2005-10-01

    Today, it is necessary to identify relevant compounds appearing in discovery and development of new drug substances in the pharmaceutical industry. For that purpose, the measurement of accurate molecular mass and empirical formula calculation is very important for structure elucidation in addition to other available analytical methods. In this work, the identification and confirmation of degradation products in a finished dosage form of the antibiotic drug amoxicillin obtained under stress conditions will be demonstrated. Structure elucidation is performed utilizing liquid chromatography (LC) ion trap MS/MS and MS3 together with accurate mass measurement of the molecular ions and of the collision induced dissociation (CID) fragments by liquid chromatography electro spray ionization time-of-flight mass spectrometry (LC/ESI-TOF).

  5. Characterization of Ion Dynamics in Structures for Lossless Ion Manipulations

    PubMed Central

    2015-01-01

    Structures for Lossless Ion Manipulation (SLIM) represent a novel class of ion optical devices based upon electrodes patterned on planar surfaces, and relying on a combined action of radiofrequency and DC electric fields and specific buffer gas density conditions. Initial experimental studies have demonstrated the feasibility of the SLIM concept. This report offers an in-depth consideration of key ion dynamics properties in such devices based upon ion optics theory and computational modeling. The SLIM devices investigated are formed by two surfaces, each having an array of radiofrequency (RF) “rung” electrodes, bordered by DC “guard” electrodes. Ion motion is confined by the RF effective potential in the direction orthogonal to the boards and limited or controlled in the transversal direction by the guard DC potentials. Ions can be efficiently trapped and stored in SLIM devices where the confinement of ions can be “soft” in regard to the extent of collisional activation, similarly to RF-only multipole ion guides and traps. The segmentation of the RF rung electrodes and guards along the axis makes it possible to apply static or transient electric field profiles to stimulate ion transfer within a SLIM. In the case of a linear DC gradient applied to RF rungs and guards, a virtually uniform electric field can be created along the axis of the device, enabling high quality ion mobility separations. PMID:25152178

  6. Characterization of ion dynamics in structures for lossless ion manipulations.

    PubMed

    Tolmachev, Aleksey V; Webb, Ian K; Ibrahim, Yehia M; Garimella, Sandilya V B; Zhang, Xinyu; Anderson, Gordon A; Smith, Richard D

    2014-09-16

    Structures for Lossless Ion Manipulation (SLIM) represent a novel class of ion optical devices based upon electrodes patterned on planar surfaces, and relying on a combined action of radiofrequency and DC electric fields and specific buffer gas density conditions. Initial experimental studies have demonstrated the feasibility of the SLIM concept. This report offers an in-depth consideration of key ion dynamics properties in such devices based upon ion optics theory and computational modeling. The SLIM devices investigated are formed by two surfaces, each having an array of radiofrequency (RF) "rung" electrodes, bordered by DC "guard" electrodes. Ion motion is confined by the RF effective potential in the direction orthogonal to the boards and limited or controlled in the transversal direction by the guard DC potentials. Ions can be efficiently trapped and stored in SLIM devices where the confinement of ions can be "soft" in regard to the extent of collisional activation, similarly to RF-only multipole ion guides and traps. The segmentation of the RF rung electrodes and guards along the axis makes it possible to apply static or transient electric field profiles to stimulate ion transfer within a SLIM. In the case of a linear DC gradient applied to RF rungs and guards, a virtually uniform electric field can be created along the axis of the device, enabling high quality ion mobility separations.

  7. Characterization of Ion Dynamics in Structures for Lossless Ion Manipulations

    SciTech Connect

    Tolmachev, Aleksey V.; Webb, Ian K.; Ibrahim, Yehia M.; Garimella, Venkata BS; Zhang, Xinyu; Anderson, Gordon A.; Smith, Richard D.

    2014-08-23

    Structures for Lossless Ion Manipulation (SLIM) represent a novel class of ion optical devices based upon electrodes patterned on planar surfaces, and relying on a combined action of radio frequency and DC electric fields and specific buffer gas density conditions. Initial experimental studies have demonstrated the feasibility of the SLIM concept. This report offers an in-depth consideration of key ion dynamics properties in such devices based upon ion optics theory and computational modeling. The SLIM devices investigated are formed by two surfaces, each having an array of radio frequency (RF) "rung" electrodes, bordered by DC "guard" electrodes. Ion motion is confined by the RF effective potential in the direction orthogonal to the boards, and limited or controlled in the transversal direction by the guard DC potentials. Ions can be efficiently trapped and stored in SLIM devices where the confinement of ions can be ‘soft’ in regard to the extent of collisional activation, similarly to RF-only multipole ion guides and traps. The segmentation of the RF rung electrodes and guards along the axis makes it possible to apply electric field profiles to stimulate ion transfer within a SLIM. In the case of a linear DC gradient applied to RF rungs and guards, a virtually uniform electric field can be created along the axis of the device, enabling ion mobility separations.

  8. Determination of epichlorohydrin by ion chromatography.

    PubMed

    Sarzanini, C; Bruzzoniti, M C; Mentasti, E

    2000-07-07

    In this work we developed a new method for epichlorohydrin determination with suppressed ion chromatography. The technique is based on a reaction between the analyte and sulfur(IV) to form a product with a terminal sulfonate group that can be analyzed by anion-exchange chromatography. The reaction conditions were optimized as a function of temperature, type and concentrations of reagents and pH. Due to the characteristics of the product formed, the columns used were an lonPac AS 11 and AS II-HC with a NaOH eluent. The eluent concentration was optimized in order to achieve a complete separation of epichlorohydrin, chloride and nitrate ions, commonly occurring in drinking waters. In order to improve the detection limits, a preconcentration step, using reversed-phase materials, has been optimized. The method developed was suitable for epichlorohydrin determination in drinking water.

  9. The structure of the stable negative ion of calcium

    SciTech Connect

    Pegg, D.J.; Thompson, J.S.; Compton, R.N.; Alton, G.D.

    1988-01-01

    The structure of the Ca/sup /minus// ion has been determined using a crossed laser-ion beams apparatus. The photoelectron detachment spectrum shows that, contrary to earlier expectations, the Ca/sup /minus// ion is stably bound in the (4s/sup 2/4p)/sup 2/p state. The electron affinity of Ca was measured to be 0.043 /sup + -/ 0.007 eV.

  10. Kinetic structure of slow shocks - Effects of the electromagnetic ion/ion cyclotron instability

    NASA Technical Reports Server (NTRS)

    Omidi, N.; Winske, D.

    1992-01-01

    The structure of slow magnetosonic shocks in the low beta regime is analyzed with attention given to ion heating and the effects of waves upstream of the electromagnetic ion/ion cyclotron (EMIIC) instability. Shock formation is assessed by means of three methods - a relaxation method and two based on dynamic flow interactions - to determine the effects of initialization and boundary conditions on the formation. Good solutions are found with the piston method and the similar flow-flow method in which the plasma is injected from two boundaries to form two slow shocks. Plasma parameters and shock normal angle are found to be the key variables dictating the structure of the magnetosonic shocks. Four unique classes of resultant shock structures are described in which classical, steady, or nonsteady behavior is found. The analysis also yields insight into the relationship between EMIIC instability and ion dissipation.

  11. Determining structural performance

    NASA Technical Reports Server (NTRS)

    Ernst, Michael A.; Kiraly, Louis J.

    1987-01-01

    An overview is given of the methods and concepts developed to enhance and predict structural dynamic characteristics of advanced aeropropulsion systems. Aeroelasticity, Vibration Control, Dynamic Systems, and Computational Structural Methods are four disciplines that make up the research program at NASA/Lewis Research Center. The Aeroelasticity program develops analytical and experimental methods to minimize flutter and forced vibration of aerospace propulsion systems. Both frequency domain and time domain methods have been developed for applications on the turbofan, turbopump, and advanced turboprop. To improve life and performance, the Vibration Control program conceives, analyzes, develops, and demonstrates new methods to control vibrations in aerospace systems. Active and passive vibration control is accomplished with electromagnetic dampers, magnetic bearings, and piezoelectric crystals to control rotor vibrations. The Dynamic Systems program analyzes and verifies the dynamics of interacting systems, as well as develops concepts and methods for high-temperature dynamic seals. The Computational Structural Methods program uses computer science to improve solutions of structural problems.

  12. Exploring structural phase transitions of ion crystals

    PubMed Central

    Yan, L. L.; Wan, W.; Chen, L.; Zhou, F.; Gong, S. J.; Tong, X.; Feng, M.

    2016-01-01

    Phase transitions have been a research focus in many-body physics over past decades. Cold ions, under strong Coulomb repulsion, provide a repealing paradigm of exploring phase transitions in stable confinement by electromagnetic field. We demonstrate various conformations of up to sixteen laser-cooled 40Ca+ ion crystals in a home-built surface-electrode trap, where besides the usually mentioned structural phase transition from the linear to the zigzag, two additional phase transitions to more complicated two-dimensional configurations are identified. The experimental observation agrees well with the numerical simulation. Heating due to micromotion of the ions is analysed by comparison of the numerical simulation with the experimental observation. Our investigation implies very rich and complicated many-body behaviour in the trapped-ion systems and provides effective mechanism for further exploring quantum phase transitions and quantum information processing with ultracold trapped ions. PMID:26865229

  13. Ion nose spectral structures observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Ferradas, C. P.; Zhang, J.-C.; Spence, H. E.; Kistler, L. M.; Larsen, B. A.; Reeves, G.; Skoug, R.; Funsten, H.

    2016-12-01

    We present a statistical study of nose-like structures observed in energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet. Nose structures are spectral features named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. Using 22 months of observations from the Helium Oxygen Proton Electron instrument onboard Van Allen Probe A, we determine the number of noses observed, and the minimum L shell reached and energy of each nose on each pass through the inner magnetosphere. We find that multiple noses occur more frequently in heavy ions than in H+ and are most often observed during quiet times. The heavy-ion noses penetrate to lower L shells than H+ noses, and there is an energy-magnetic local time (MLT) dependence in the nose locations and energies that is similar for all species. The observations are interpreted by using a steady state model of ion drift in the inner magnetosphere. The model is able to explain the energy and MLT dependence of the different types of nose structures. Different ion charge-exchange lifetimes are the main cause for the deeper penetration of heavy-ion noses. The species dependence and preferred geomagnetic conditions of multiple-nose events indicate that they must be on long drift paths, leading to strong charge-exchange effects. The results provide important insight into the spatial distribution, species dependence, and geomagnetic conditions under which nose structures occur.

  14. Determining structural performance

    NASA Technical Reports Server (NTRS)

    Ernst, Michael A. (Editor); Brown, Gerald; Dirusso, Eliseo; Fleming, David; Janetzke, David; Kascak, Albert; Kaza, Krishna; Kielb, Robert; Kiraly, Louis J.; Lawrence, Charles

    1990-01-01

    An overview of the methods and concepts developed to enhance and predict structural dynamic characteristics of advanced aeropropulsion systems is presented. Aeroelasticity, vibration control, dynamic systems, and computational structural methods are four disciplines that make up the structural dynamic effort at LeRC. The aeroelasticity program develops analytical and experimental methods for minimizing flutter and forced vibration of aerospace propulsion systems. Both frequency domain and time domain methods were developed for applications on the turbofan, turbopump, and advanced turboprop. In order to improve life and performance, the vibration control program conceives, analyzes, develops, and demonstrates new methods for controlling vibrations in aerospace systems. Active and passive vibration control is accomplished with electromagnetic dampers, magnetic bearings, and piezoelectric crystals to control rotor vibrations. The dynamic systems program analyzes and verifies the dynamics of interacting systems, as well as develops concepts and methods for high-temperature dynamic seals. Work in this field involves the analysis and parametric identification of large, nonlinear, damped, stochastic systems. The computational structural methods program exploits modern computer science as an aid to the solutions of structural problems.

  15. Dynamic ion structure factor of warm dense matter.

    PubMed

    Vorberger, J; Donko, Z; Tkachenko, I M; Gericke, D O

    2012-11-30

    The dynamics of the ion structure in warm dense matter is determined by molecular dynamics simulations using an effective ion-ion potential. This potential is obtained from ab initio simulations and has a strong short-range repulsion added to a screened Coulomb potential. Models based on static or dynamic local field corrections are found to be insufficient to describe the data. An extended Mermin approach, a hydrodynamic model, and the method of moments with local constraints are capable of reproducing the numerical results but have rather limited predictive powers as they all need some numerical data as input. The method of moments is found to be the most promising.

  16. Rectangular Ion Funnel: A New Ion Funnel Interface for Structures for Lossless Ion Manipulations

    DOE PAGES

    Chen, Tsung-Chi; Webb, Ian K.; Prost, Spencer A.; ...

    2014-11-19

    A recent achievement in Structures for Lossless Ion Manipulations (SLIM) is the ability for near lossless ion focusing, transfer, and trapping in sub-atmospheric pressure regions. While lossless ion manipulations are advantageously applied to the applications of ion mobility separations and gas phase reactions, ion introduction through ring electrode ion funnels or more conventional ion optics to SLIM can involve discontinuities in electric fields or other perturbations that result in ion losses. In this work, we investigated a new funnel design that aims to seamlessly couple to SLIM at the funnel exit. This rectangular ion funnel (RIF) was initially evaluated bymore » ion simulations, fabricated utilizing printed circuit board technology and tested experimentally. The RIF was integrated to a SLIM-TOFMS system, and the operating parameters, including RF, DC bias of the RIF electrodes, and electric fields for effectively interfacing with a SLIM were characterized. The RIF provided a 2-fold sensitivity increase without significant discrimination over a wide m/z range along with greatly improved SLIM operational stability.« less

  17. Rectangular ion funnel: a new ion funnel interface for structures for lossless ion manipulations.

    PubMed

    Chen, Tsung-Chi; Webb, Ian K; Prost, Spencer A; Harrer, Marques B; Norheim, Randolph V; Tang, Keqi; Ibrahim, Yehia M; Smith, Richard D

    2015-01-06

    Structures for lossless ion manipulations (SLIM) have recently demonstrated the ability for near lossless ion focusing, transfer, and trapping in subatmospheric pressure regions. While lossless ion manipulations are advantageously applied to the applications of ion mobility separations and gas phase reactions, ion introduction through ring electrode ion funnels or more conventional ion optics to SLIM can involve discontinuities in electric fields or other perturbations that result in ion losses. In this work, we developed and investigated a new funnel design that aims to seamlessly couple to SLIM at the funnel exit. This rectangular ion funnel (RIF) was initially evaluated by ion simulations, fabricated utilizing printed circuit board technology, and tested experimentally. The RIF was integrated to a SLIM-time of flight (TOF) MS system, and the operating parameters, including RF, DC bias of the RIF electrodes, and electric fields for effectively interfacing with a SLIM, were characterized. The RIF provided a 2-fold sensitivity increase without significant discrimination over a wide m/z range and well matched to that of SLIM, along with greatly improved SLIM operational stability.

  18. Determining the Bohm criterion in plasmas with two ion species

    NASA Astrophysics Data System (ADS)

    Baalrud, S. D.; Hegna, C. C.

    2011-02-01

    A model that uniquely determines the flow speed of each ion species at the sheath edge of two ion species plasmas is developed. In this analysis, ion-ion two-stream instabilities can play an important role because they significantly enhance the friction between ion species. Two-stream instabilities arise when the difference in flow speeds between the ion species exceeds a critical value: V1-V2≡ΔV≥ΔVc. The resultant instability-enhanced friction rapidly becomes so strong that ΔV cannot significantly exceed ΔVc. Using the condition provided by ΔV =ΔVc and the generalized Bohm criterion, the speed of each ion species is uniquely determined as it leaves a quasineutral plasma and enters a sheath. Previous work [S. D. Baalrud et al., Phys. Rev. Lett. 103, 205002 (2009)] considered the cold ion limit (Ti→0), in which case ΔVc→0 and each ion species obtains a common "system" sound speed at the sheath edge. Finite ion temperatures are accounted for in this work. The result is that ΔVc depends on the density and thermal speed of each ion species; ΔVc has a minimum when the density ratio of the two ion species is near one, and becomes larger as the density ratio deviates from unity. As ΔVc increases, the speed of each ion species approaches its individual sound speed at the sheath edge.

  19. Resonant structures in heavy-ion reactions

    SciTech Connect

    Sanders, S.J.; Henning, W.; Ernst, H.; Geesaman, D.F.; Jachcinski, C.; Kovar, D.G.; Paul, M.; Schiffer, J.P.

    1980-01-01

    An investigation of heavy-ion resonance structures using the /sup 24/Mg(/sup 16/O, /sup 12/C)/sup 28/Si reaction is presented. The data are analyzed in the context of Breit-Wigner resonances added to a direct-reaction background.

  20. Principles of ion recognition in RNA: insights from the group II intron structures.

    PubMed

    Marcia, Marco; Pyle, Anna Marie

    2014-04-01

    Metal ions promote both RNA folding and catalysis, thus being essential in stabilizing the structure and determining the function of large RNA molecules, including group II introns. The latter are self-splicing metalloribozymes, containing a heteronuclear four-metal-ion center within the active site. In addition to these catalytic ions, group II introns bind many other structural ions, including delocalized ions that bind the RNA diffusively and well-ordered ions that bind the RNA tightly with high occupancy. The latter ions, which can be studied by biophysical methods, have not yet been analyzed systematically. Here, we compare crystal structures of the group IIC intron from Oceanobacillus iheyensis and classify numerous site-bound ions, which are primarily localized in the intron core and near long-range tertiary contacts. Certain ion-binding sites resemble motifs observed in known RNA structures, while others are idiosyncratic to the group II intron. Particularly interesting are (1) ions proximal to the active site, which may participate in splicing together with the catalytic four-metal-ion center, (2) organic ions that bind regions predicted to interact with intron-encoded proteins, and (3) unusual monovalent ions bound to GU wobble pairs, GA mismatches, the S-turn, the tetraloop-receptor, and the T-loop. Our analysis extends the general principles by which ions participate in RNA structural organization and it will aid in the determination and interpretation of future RNA structures.

  1. Principles of ion recognition in RNA: insights from the group II intron structures

    PubMed Central

    Marcia, Marco; Pyle, Anna Marie

    2014-01-01

    Metal ions promote both RNA folding and catalysis, thus being essential in stabilizing the structure and determining the function of large RNA molecules, including group II introns. The latter are self-splicing metalloribozymes, containing a heteronuclear four-metal-ion center within the active site. In addition to these catalytic ions, group II introns bind many other structural ions, including delocalized ions that bind the RNA diffusively and well-ordered ions that bind the RNA tightly with high occupancy. The latter ions, which can be studied by biophysical methods, have not yet been analyzed systematically. Here, we compare crystal structures of the group IIC intron from Oceanobacillus iheyensis and classify numerous site-bound ions, which are primarily localized in the intron core and near long-range tertiary contacts. Certain ion-binding sites resemble motifs observed in known RNA structures, while others are idiosyncratic to the group II intron. Particularly interesting are (1) ions proximal to the active site, which may participate in splicing together with the catalytic four-metal-ion center, (2) organic ions that bind regions predicted to interact with intron-encoded proteins, and (3) unusual monovalent ions bound to GU wobble pairs, GA mismatches, the S-turn, the tetraloop-receptor, and the T-loop. Our analysis extends the general principles by which ions participate in RNA structural organization and it will aid in the determination and interpretation of future RNA structures. PMID:24570483

  2. Chitosan Hydrogel Structure Modulated by Metal Ions

    NASA Astrophysics Data System (ADS)

    Nie, Jingyi; Wang, Zhengke; Hu, Qiaoling

    2016-10-01

    As one of the most important polysaccharide, chitosan (CS) has generated a great deal of interest for its desirable properties and wide applications. In the utilization of CS materials, hydrogel is a major and vital branch. CS has the ability to coordinate with many metal ions by a chelation mechanism. While most researchers focused on the applications of complexes between CS and metal ions, the complexes can also influence gelation process and structure of CS hydrogel. In the present work, such influence was studied with different metal ions, revealing two different kinds of mechanisms. Strong affinity between CS and metal ions leads to structural transition from orientation to multi-layers, while weak affinity leads to composite gel with in-situ formed inorganic particles. The study gave a better understanding of the gelation mechanism and provided strategies for the modulation of hydrogel morphology, which benefited the design of new CS-based materials with hierarchical structure and facilitated the utilization of polysaccharide resources.

  3. Chitosan Hydrogel Structure Modulated by Metal Ions

    PubMed Central

    Nie, Jingyi; Wang, Zhengke; Hu, Qiaoling

    2016-01-01

    As one of the most important polysaccharide, chitosan (CS) has generated a great deal of interest for its desirable properties and wide applications. In the utilization of CS materials, hydrogel is a major and vital branch. CS has the ability to coordinate with many metal ions by a chelation mechanism. While most researchers focused on the applications of complexes between CS and metal ions, the complexes can also influence gelation process and structure of CS hydrogel. In the present work, such influence was studied with different metal ions, revealing two different kinds of mechanisms. Strong affinity between CS and metal ions leads to structural transition from orientation to multi-layers, while weak affinity leads to composite gel with in-situ formed inorganic particles. The study gave a better understanding of the gelation mechanism and provided strategies for the modulation of hydrogel morphology, which benefited the design of new CS-based materials with hierarchical structure and facilitated the utilization of polysaccharide resources. PMID:27777398

  4. Electron Backstreaming Determination for Ion Thrusters

    NASA Technical Reports Server (NTRS)

    Wirz, Richard E.; Katz, Ira; Goebel, Dan M.; Anderson, John R.

    2008-01-01

    Electron backstreaming in ion thrusters is caused by the random flux of beam electrons past a potential barrier established by the accel grid. A technique that integrates this flux over the radial extent of the barrier reveals important aspects of electron backstreaming phenomena for individual beamlets, across the thruster beam, and throughout thruster life. For individual beamlets it was found that over 99% of the electron backstreaming occurs in a small annulus at the center of the beamlet that is less than 20% the area of the beamlet at the potential barrier established by the accel grid. For the thruster beam it was found that over 99% of the backstreaming current occurs inside of r = 6 cm for the over 28 cm diameter NSTAR grid. Initial validation against ELT data shows that the technique provides the correct behavior and magnitude of electron backstreaming limit, V(sub ebs). From the sensitivity analyses it is apparent that accel grid chamfering may be the dominant mechanism contributing to the sharp rise in the absolute value of V(sub ebs) observed in the ELT but does not explain the rise in ion transparency. Grid gap change also contributes to the absolute value of V(sub ebs) rise and large rises in ion transparency with thruster life for the center gridlet. Screen grid erosion contributes generally to rises in the absolute value of V(sub ebs) and ion transparency, but for the assumptions used herein, it appears to not have as much of an effect chamfering or grid gap change. Overall, it is apparent that accel grid chamfering, grid gap change, and screen grid erosion are important to the increase in electron backstreaming observed during the ELT.

  5. Electron Backstreaming Determination for Ion Thrusters

    NASA Technical Reports Server (NTRS)

    Wirz, Richard E.; Katz, Ira; Goebel, Dan M.; Anderson, John R.

    2008-01-01

    Electron backstreaming in ion thrusters is caused by the random flux of beam electrons past a potential barrier established by the accel grid. A technique that integrates this flux over the radial extent of the barrier reveals important aspects of electron backstreaming phenomena for individual beamlets, across the thruster beam, and throughout thruster life. For individual beamlets it was found that over 99% of the electron backstreaming occurs in a small annulus at the center of the beamlet that is less than 20% the area of the beamlet at the potential barrier established by the accel grid. For the thruster beam it was found that over 99% of the backstreaming current occurs inside of r = 6 cm for the over 28 cm diameter NSTAR grid. Initial validation against ELT data shows that the technique provides the correct behavior and magnitude of electron backstreaming limit, V(sub ebs). From the sensitivity analyses it is apparent that accel grid chamfering may be the dominant mechanism contributing to the sharp rise in the absolute value of V(sub ebs) observed in the ELT but does not explain the rise in ion transparency. Grid gap change also contributes to the absolute value of V(sub ebs) rise and large rises in ion transparency with thruster life for the center gridlet. Screen grid erosion contributes generally to rises in the absolute value of V(sub ebs) and ion transparency, but for the assumptions used herein, it appears to not have as much of an effect chamfering or grid gap change. Overall, it is apparent that accel grid chamfering, grid gap change, and screen grid erosion are important to the increase in electron backstreaming observed during the ELT.

  6. Structure analysis of bimetallic Co-Au nanoparticles formed by sequential ion implantation

    NASA Astrophysics Data System (ADS)

    Chen, Hua-jian; Wang, Yu-hua; Zhang, Xiao-jian; Song, Shu-peng; chen, Hong; Zhang, Ke; Xiong, Zu-zhao; Ji, Ling-ling; Dai, Hou-mei; Wang, Deng-jing; Lu, Jian-duo; Wang, Ru-wu; Zheng, Li-rong

    2016-08-01

    Co-Au alloy Metallic nanoparticles (MNPs) are formed by sequential ion implantation of Co and Au into silica glass at room temperature. The ion ranges of Au ions implantation process have been displayed to show the ion distribution. We have used the atomic force microscopy (AFM) and transmission electron microscopy (TEM) to investigate the formation of bimetallic nanoparticles. The extended X-ray absorption fine structure (EXAFS) has been used to study the local structural information of bimetallic nanoparticles. With the increase of Au ion implantation, the local environments of Co ions are changed enormously. Hence, three oscillations, respectively, Co-O, Co-Co and Co-Au coordination are determined.

  7. Ion nose spectral structures observed by the Van Allen Probes

    DOE PAGES

    Ferradas, C. P.; Zhang, J. -C.; Spence, H. E.; ...

    2016-11-22

    Here, we present a statistical study of nose-like structures observed in energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet. Nose structures are spectral features named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. Using 22 months of observations from the Helium Oxygen Proton Electron (HOPE) instrument onboard Van Allen Probe A, we determine the number of noses observed, and the minimum L-shell reached and energy of each nose on each pass through the inner magnetosphere. We find that multiple noses occur more frequentlymore » in heavy ions than in H+, and are most often observed during quiet times. The heavy-ion noses penetrate to lower L shells than H+ noses and there is an energy-magnetic local time (MLT) dependence in the nose locations and energies that is similar for all species. The observations are interpreted using a steady-state model of ion drift in the inner magnetosphere. The model is able to explain the energy and MLT dependence of the different types of nose structures. Different ion charge exchange lifetimes are the main cause for the deeper penetration of heavy-ion noses. The species dependence and preferred geomagnetic conditions of multiple-nose events indicate that they must be on long drift paths, leading to strong charge-exchange effects. The results provide important insight into the spatial distribution, species dependence, and geomagnetic conditions under which nose structures occur.« less

  8. Ion nose spectral structures observed by the Van Allen Probes

    SciTech Connect

    Ferradas, C. P.; Zhang, J. -C.; Spence, H. E.; Kistler, L. M.; Larsen, Brian Arthur; Reeves, Geoffrey D.; Skoug, Ruth M.; Funsten, Herbert O.

    2016-11-22

    Here, we present a statistical study of nose-like structures observed in energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet. Nose structures are spectral features named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. Using 22 months of observations from the Helium Oxygen Proton Electron (HOPE) instrument onboard Van Allen Probe A, we determine the number of noses observed, and the minimum L-shell reached and energy of each nose on each pass through the inner magnetosphere. We find that multiple noses occur more frequently in heavy ions than in H+, and are most often observed during quiet times. The heavy-ion noses penetrate to lower L shells than H+ noses and there is an energy-magnetic local time (MLT) dependence in the nose locations and energies that is similar for all species. The observations are interpreted using a steady-state model of ion drift in the inner magnetosphere. The model is able to explain the energy and MLT dependence of the different types of nose structures. Different ion charge exchange lifetimes are the main cause for the deeper penetration of heavy-ion noses. The species dependence and preferred geomagnetic conditions of multiple-nose events indicate that they must be on long drift paths, leading to strong charge-exchange effects. The results provide important insight into the spatial distribution, species dependence, and geomagnetic conditions under which nose structures occur.

  9. Solar wind compressible structures at ion scales

    NASA Astrophysics Data System (ADS)

    Perrone, D.; Alexandrova, O.; Rocoto, V.; Pantellini, F. G. E.; Zaslavsky, A.; Maksimovic, M.; Issautier, K.; Mangeney, A.

    2014-12-01

    In the solar wind turbulent cascade, the energy partition between fluid and kinetic degrees of freedom, in the vicinity of plasma characteristic scales, i.e. ion and electron Larmor radius and inertial lengths, is still under debate. In a neighborhood of the ion scales, it has been observed that the spectral shape changes and fluctuations become more compressible. Nowadays, a huge scientific effort is directed to the comprehension of the link between macroscopic and microscopic scales and to disclose the nature of compressive fluctuations, meaning that if space plasma turbulence is a mixture of quasi-linear waves (as whistler or kinetic Alfvèn waves) or if turbulence is strong with formation of coherent structures responsible for dissipation. Here we present an automatic method to identify compressible coherent structures around the ion spectral break, using Morlet wavelet decomposition of magnetic signal from Cluster spacecraft and reconstruction of magnetic fluctuations in a selected scale range. Different kind of coherent structures have been detected: from soliton-like one-dimensional structures to current sheet- or wave-like two-dimensional structures. Using a multi-satellite analysis, in order to characterize 3D geometry and propagation in plasma rest frame, we recover that these structures propagate quasi-perpendicular to the mean magnetic field, with finite velocity. Moreover, without using the Taylor hypothesis, the spatial scales of coherent structures have been estimated. Our observations in the solar wind can provide constraints on theoretical modeling of small scale turbulence and dissipation in collisionless magnetized plasmas.

  10. Ion-selective electrodes for gold and silver determination.

    PubMed

    Petrukhin, O M; Avdeeva, E N; Shavnya, Y V; Yankauskas, V P; Kazlauskas, R M; Bychkov, A S; Zolotov, Y A

    1987-01-01

    Some new ion-selective electrodes for silver and gold are described. They are based on the ion-associate species formed by the cyanide, chloride or thiourea complexes of the metals, with hydrophobic anions or cations, as appropriate. The electrodes have been applied to the determination of gold and silver in various technological process solutions in industry.

  11. Highly sensitive determination of hydrazine ion by ion-exclusion chromatography with ion-exchange enhancement of conductivity detection.

    PubMed

    Mori, Masanobu; Tanaka, Kazuhiko; Xu, Qun; Ikedo, Mikaru; Taoda, Hiroshi; Hu, Wenzhi

    2004-06-11

    An ion-exclusion chromatography method with ion-exchange enhancement of conductivity was developed for the selective separation and sensitive determination of hydrazine ion from alkali/alkaline earth metal cations and ammonium ion. Hydrazine ion was separated by ion-exclusion/penetration effect from other cations on a weakly basic anion-exchange column in the OH- form (TSKgel DEAE-5PW). Moreover, two different ion-exchange resin columns were inserted between the separating column and conductimetric detector in order to improve the sensitivity of hydrazine ion. The first enhancement column packed with a strongly basic anion-exchange resin in the SO4(2-) form (TSKgel SAX) for hydrazine ion can convert from N2H5OH to (N2H5)2SO4. Moreover, the second enhancement column packed with a strongly acidic cation-change resin in the H+ form (TSKgel SCX) can convert to H2SO4. As a result, the sensitivity of hydrazine ion using two conductivity enhancement columns could be 26.8-times greater than using the separating column alone. This method was effectiveness also for the enhancement of ammonium ion (6.1-times) and sodium ion (1.2-times). The calibration graph of hydrazine ion detected as H2SO4 was linear over the concentration range of 0.001-100 ppm (r2 = 0.9988). The detection limit of hydrazine ion in this system was 0.64 ppb. Therefore, hydrazine ion in real boiler water sample could be accurately determined, avoiding the interference of other cations.

  12. Determination of counter-ions in synthetic peptides by ion chromatography, capillary isotachophoresis and capillary electrophoresis.

    PubMed

    Mrozik, Wojciech; Markowska, Aleksandra; Guzik, Lukasz; Kraska, Bartłomiej; Kamysz, Wojciech

    2012-03-01

    The utility of three various analytical techniques [ion chromatography (IC), capillary electrophoresis (CE) and isotachophoresis (ITP)] was tested in the determination of counter-ions in synthetic peptides. The analyzed ions were acetates, trifluoroacetates and chlorides. IC provided the best results; CE, except limit of detection and limit of quantification, exhibited the comparable results. ITP was classified as the less useful because of the problem with the determination of the chloride ions. Nevertheless, all the three techniques were able to analyze trifluoroacetates and acetates ions with satisfactory results. Except analytical methods, three procedures using hydrochloric acid (HCl) (at two different concentrations) and acetic acid as sample solvents processed by lyophilization were tested. It has been found that the lyophilization not only by HCl but also by acetic acid is a simple and cheap procedure for removal of toxic trifluoroacetic counter-ions from peptides on satisfactory levels.

  13. Ion exchange determines iodine-131 concentration in aqueous samples

    NASA Technical Reports Server (NTRS)

    Fairman, W. D.; Sedlet, J.

    1967-01-01

    Inorganic radioiodide in aqueous media is analyzed by separating the radioactive iodine-131 as the iodide ion on a silver chloride column. The activity in the final precipitate may be determined by beta or gamma counting.

  14. Unraveling the Structure of Ultracold Mesoscopic Collinear Molecular Ions

    NASA Astrophysics Data System (ADS)

    Schurer, J. M.; Negretti, A.; Schmelcher, P.

    2017-08-01

    We present an in-depth many-body investigation of the so-called mesoscopic molecular ions that can buildup when an ion is immersed into an atomic Bose-Einstein condensate in one dimension. To this end, we employ the multilayer multiconfiguration time-dependent Hartree method for mixtures of ultracold bosonic species for solving the underlying many-body Schrödinger equation. This enables us to unravel the actual structure of such massive charged molecules from a microscopic perspective. Laying out their phase diagram with respect to atom number and interatomic interaction strength, we determine the maximal number of atoms bound to the ion and reveal spatial densities and molecular properties. Interestingly, we observe a strong interaction-induced localization, especially for the ion, that we explain by the generation of a large effective mass, similarly to ions in liquid Helium. Finally, we predict the dynamical response of the ion to small perturbations. Our results provide clear evidence for the importance of quantum correlations, as we demonstrate by benchmarking them with wave function ansatz classes employed in the literature.

  15. An ion selectivity filter in the extracellular domain of Cys-loop receptors reveals determinants for ion conductance.

    PubMed

    Hansen, Scott B; Wang, Hai-Long; Taylor, Palmer; Sine, Steven M

    2008-12-26

    Neurotransmitter binding to Cys-loop receptors promotes a prodigious transmembrane flux of several million ions/s, but to date, structural determinants of ion flux have been identified flanking the membrane-spanning region. Using x-ray crystallography, sequence analysis, and single-channel recording, we identified a novel determinant of ion conductance near the point of entry of permeant ions. Co-crystallization of acetylcholine-binding protein with sulfate anions revealed coordination of SO4(2-) with a ring of lysines at a position equivalent to 24 A above the lipid membrane in homologous Cys-loop receptors. Analysis of multiple sequence alignments revealed that residues equivalent to the ring of lysines are negatively charged in cation-selective receptors but are positively charged in anion-selective receptors. Charge reversal of side chains at homologous positions in the nicotinic receptor from the motor end plate decreases unitary conductance up to 80%. Selectivity filters stemming from transmembrane alpha-helices have similar pore diameters and compositions of amino acids. These findings establish that when the channel opens under a physiological electrochemical gradient, permeant ions are initially stabilized within the extracellular vestibule of Cys-loop receptors, and this stabilization is a major determinant of ion conductance.

  16. Squeezing of Ion Populations and Peaks in Traveling Wave Ion Mobility Separations and Structures for Lossless Ion Manipulations using Compression Ratio Ion Mobility Programming

    SciTech Connect

    Garimella, Venkata BS; Hamid, Ahmed M.; Deng, Liulin; Ibrahim, Yehia M.; Webb, Ian K.; Baker, Erin M.; Prost, Spencer A.; Norheim, Randolph V.; Anderson, Gordon A.; Smith, Richard D.

    2016-11-02

    In this work, we report an approach for spatial and temporal gas phase ion population manipulation, and demonstrate its application for the collapse of the ion distributions in ion mobility (IM) separations into tighter packets providing higher sensitivity measurements in conjunction with mass spectrometry (MS). We do this for ions moving from a conventionally traveling wave (TW)-driven region to a region where the TW is intermittently halted or ‘stuttered’. This approach causes the ion packets spanning a number of TW-created traveling traps (TT) to be redistributed into fewer TT, resulting in spatial compression. The degree of spatial compression is controllable and determined by the ratio of stationary time of the TW in the second region to its moving time. This compression ratio ion mobility programming (CRIMP) approach has been implemented using Structures for Lossless Ion Manipulations (SLIM) in conjunction with MS. CRIMP with the SLIM-MS platform is shown to provide increased peak intensities, reduced peak widths, and improved S/N ratios with MS detection. CRIMP also provides a foundation for extremely long path length and multi-pass IM separations in SLIM providing greatly enhanced IM resolution by reducing the detrimental effects of diffusional peak broadening due to increasing peak widths.

  17. Squeezing of Ion Populations and Peaks in Traveling Wave Ion Mobility Separations and Structures for Lossless Ion Manipulations Using Compression Ratio Ion Mobility Programming.

    PubMed

    Garimella, Sandilya V B; Hamid, Ahmed M; Deng, Liulin; Ibrahim, Yehia M; Webb, Ian K; Baker, Erin S; Prost, Spencer A; Norheim, Randolph V; Anderson, Gordon A; Smith, Richard D

    2016-12-06

    In this work we report an approach for spatial and temporal gas-phase ion population manipulation, wherein we collapse ion distributions in ion mobility (IM) separations into tighter packets providing higher sensitivity measurements in conjunction with mass spectrometry (MS). We do this for ions moving from a conventional traveling wave (TW)-driven region to a region where the TW is intermittently halted or "stuttered". This approach causes the ion packets spanning a number of TW-created traveling traps (TT) to be redistributed into fewer TT, resulting in spatial compression. The degree of spatial compression is controllable and determined by the ratio of stationary time of the TW in the second region to its moving time. This compression ratio ion mobility programming (CRIMP) approach has been implemented using "structures for lossless ion manipulations" (SLIM) in conjunction with MS. CRIMP with the SLIM-MS platform is shown to provide increased peak intensities, reduced peak widths, and improved signal-to-noise (S/N) ratios with MS detection. CRIMP also provides a foundation for extremely long path length and multipass IM separations in SLIM providing greatly enhanced IM resolution by reducing the detrimental effects of diffusional peak broadening and increasing peak widths.

  18. The structure and regulation of magnesium selective ion channels.

    PubMed

    Payandeh, Jian; Pfoh, Roland; Pai, Emil F

    2013-11-01

    The magnesium ion (Mg(2+)) is the most abundant divalent cation within cells. In man, Mg(2+)-deficiency is associated with diseases affecting the heart, muscle, bone, immune, and nervous systems. Despite its impact on human health, little is known about the molecular mechanisms that regulate magnesium transport and storage. Complete structural information on eukaryotic Mg(2+)-transport proteins is currently lacking due to associated technical challenges. The prokaryotic MgtE and CorA magnesium transport systems have recently succumbed to structure determination by X-ray crystallography, providing first views of these ubiquitous and essential Mg(2+)-channels. MgtE and CorA are unique among known membrane protein structures, each revealing a novel protein fold containing distinct arrangements of ten transmembrane-spanning α-helices. Structural and functional analyses have established that Mg(2+)-selectivity in MgtE and CorA occurs through distinct mechanisms. Conserved acidic side-chains appear to form the selectivity filter in MgtE, whereas conserved asparagines coordinate hydrated Mg(2+)-ions within the selectivity filter of CorA. Common structural themes have also emerged whereby MgtE and CorA sense and respond to physiologically relevant, intracellular Mg(2+)-levels through dedicated regulatory domains. Within these domains, multiple primary and secondary Mg(2+)-binding sites serve to staple these ion channels into their respective closed conformations, implying that Mg(2+)-transport is well guarded and very tightly regulated. The MgtE and CorA proteins represent valuable structural templates to better understand the related eukaryotic SLC41 and Mrs2-Alr1 magnesium channels. Herein, we review the structure, function and regulation of MgtE and CorA and consider these unique proteins within the expanding universe of ion channel and transporter structural biology.

  19. A new chemiluminescence method for the determination of nickel ion

    NASA Astrophysics Data System (ADS)

    Li, Li Na; Li, Nian Bing; Luo, Hong Qun

    2006-05-01

    A new chemiluminescence (CL) phenomenon described as the second-chemiluminescence (SCL) was observed and a strong CL signal was detected, when Ni(II) ion was injected into the mixture after the end of the reaction of potassium permanganate with alkaline luminol. The possible CL mechanism is proposed based on the kinetic curve of the CL reaction, CL spectra, UV-vis spectra and some other experiments. A flow-injection analysis for the determination of nickle(II) ion has been developed, based on the catalysis of nickel(II) ion on the CL reaction between potassium manganate produced on-line and luminol under alkaline condition. Under the optimum conditions, the SCL intensity is linear with the concentration of nickel(II) ion in the range of 8.0-200.0 μg l -1 and 0.2-2.0 mg l -1. The R.S.D. was 4.5% for 11 determinations of 250 μg l -1 nickel(II) ion and the detection limit (3 σ) for nickel(II) ion was 0.33 μg l -1. The method was applied to determine nickel(II) ion in synthetic samples with satisfactory results.

  20. Gravimetric determination of chlorhexidine using tetraphenylborate ion.

    PubMed

    Pinzauti, S; Dal Piaz, V; La Porta, E

    1976-08-01

    A precise and accurate gravimetric procedure was developed for the determination of chlorhexidine diacetate, digluconate, or dihydrochloride. Sodium tetraphenylborate solution was the precipitant in an acidic medium (pH 1). Tablets containing both chlorhexidine diacetate and benzocaine also were assayed.

  1. [Determination of iodide, thiocyanate and perchlorate ions in environmental water by two-dimensional ion chromatography].

    PubMed

    Lin, Li; Wang, Haibo; Shi, Yali

    2013-03-01

    A procedure for the determination of iodide, thiocyanate and perchlorate ions in environmental water by two-dimensional ion chromatography has been developed. At first the iodide, thiocyanate and perchlorate ions were separated from interfering ions by a column (IonPac AS16, 250 mm x 4 mm). The iodide ion, thiocyanate and perchlorate ions were then enriched with an enrichment column (MAC-200, 80 mm x 0.75 mm). In the 2nd-dimensional chromatography, iodide thiocyanate and perchlorate ions were separated and quantified by a capillary column (IonPac AS20 Capillary, 250 mm x 0.4 mm). The linear ranges were 0.05 -100 pg/L with correlation coefficients of 0. 999 9, and the detection limits were 0. 02 - 0.05 micro gg/L. The spiked recoveries of iodide, thiocyanate and perchlorate ions were in the range of 85.1% to 100.1%. The relative standard deviations of the recoveries were 1.7% to 4.9%.

  2. Determination of the diffusion coefficient of hydrogen ion in hydrogels.

    PubMed

    Schuszter, Gábor; Gehér-Herczegh, Tünde; Szűcs, Árpád; Tóth, Ágota; Horváth, Dezső

    2017-05-17

    The role of diffusion in chemical pattern formation has been widely studied due to the great diversity of patterns emerging in reaction-diffusion systems, particularly in H(+)-autocatalytic reactions where hydrogels are applied to avoid convection. A custom-made conductometric cell is designed to measure the effective diffusion coefficient of a pair of strong electrolytes containing sodium ions or hydrogen ions with a common anion. This together with the individual diffusion coefficient for sodium ions, obtained from PFGSE-NMR spectroscopy, allows the determination of the diffusion coefficient of hydrogen ions in hydrogels. Numerical calculations are also performed to study the behavior of a diffusion-migration model describing ionic diffusion in our system. The method we present for one particular case may be extended for various hydrogels and diffusing ions (such as hydroxide) which are relevant e.g. for the development of pH-regulated self-healing mechanisms and hydrogels used for drug delivery.

  3. Structure and selectivity in bestrophin ion channels

    SciTech Connect

    Yang, Tingting; Liu, Qun; Kloss, Brian; Bruni, Renato; Kalathur, Ravi C.; Guo, Youzhong; Kloppmann, Edda; Rost, Burkhard; Colecraft, Henry M.; Hendrickson, Wayne A.

    2014-09-25

    Human bestrophin 1 (hBest1) is a calcium-activated chloride channel from the retinal pigment epithelium, where it can suffer mutations associated with vitelliform macular degeneration, or Best disease. We describe the structure of a bacterial homolog (KpBest) of hBest1 and functional characterizations of both channels. KpBest is a pentamer that forms a five-helix transmembrane pore, closed by three rings of conserved hydrophobic residues, and has a cytoplasmic cavern with a restricted exit. From electrophysiological analysis of structure-inspired mutations in KpBest and hBest1, we find a subtle control of ion selectivity in the bestrophins, including reversal of anion/cation selectivity, and dramatic activation by mutations at the exit restriction. Lastly, a homology model of hBest1 shows the locations of disease-causing mutations and suggests possible roles in regulation.

  4. Structure and selectivity in bestrophin ion channels

    DOE PAGES

    Yang, Tingting; Liu, Qun; Kloss, Brian; ...

    2014-09-25

    Human bestrophin 1 (hBest1) is a calcium-activated chloride channel from the retinal pigment epithelium, where it can suffer mutations associated with vitelliform macular degeneration, or Best disease. We describe the structure of a bacterial homolog (KpBest) of hBest1 and functional characterizations of both channels. KpBest is a pentamer that forms a five-helix transmembrane pore, closed by three rings of conserved hydrophobic residues, and has a cytoplasmic cavern with a restricted exit. From electrophysiological analysis of structure-inspired mutations in KpBest and hBest1, we find a subtle control of ion selectivity in the bestrophins, including reversal of anion/cation selectivity, and dramatic activationmore » by mutations at the exit restriction. Lastly, a homology model of hBest1 shows the locations of disease-causing mutations and suggests possible roles in regulation.« less

  5. Determination of boron in silicates after ion exchange separation

    USGS Publications Warehouse

    Kramer, H.

    1955-01-01

    Existing methods for the determination of boron in silicates are not entirely satisfactory. Separation as the methyl ester is lengthy and frequently erratic. An accurate and rapid method applicable to glass, mineral, ore, and water samples uses ion exchange to remove interfering cations, and boron is determined titrimetrically in the presence of mannitol, using a pH meter to indicate the end point.

  6. On the ion chromatographic determination of S(IV)

    NASA Astrophysics Data System (ADS)

    Dasgupta, Purnendu K.

    Ion Chromatographie determination of S(IV) is described with special reference to the determination of SO 2(g) and/or aerosol S(IV) along with chloride, nitrate and sulfate in particulate matter. A method is presented for the baseline separation of the above species. The Chromatographic behavior of hydroxymethanesulfonate under various eluent conditions is discussed.

  7. Complete structural characterization of ceramides as [M-H](-) ions by multiple-stage linear ion trap mass spectrometry.

    PubMed

    Hsu, Fong-Fu

    2016-11-01

    Ceramide is a huge lipid family consisting of diversified structures including various modifications in the fatty acyl chain and the long chain base (LCB). In this contribution, negative-ion ESI linear ion-trap multiple-stage mass spectrometric method (LIT MS(n)) towards complete structural determination of ceramides in ten major families characterized as the [M-H](-) ions is described. Multiple sets of fragment ions reflecting the fatty acyl chain and LCB were observed in the CID MS(2) spectrum, while the sequential MS(3) and MS(4) spectra contain structural information for locating the double bond and the functional groups, permitting realization of the fragmentation processes. Thereby, differentiation of ceramide molecules varied by chain length, the LCB (sphingosine, phytosphigosine, 6-hydroxy-sphingosine), and by the modification (α-hydroxy-, β-hydroxy-, ω-hydroxy-FA) can be achieved; and many isomeric structures in the biological specimen can be revealed in detail.

  8. Crystal structure determination of Efavirenz

    SciTech Connect

    Popeneciu, Horea Dumitru, Ristoiu; Tripon, Carmen Borodi, Gheorghe Pop, Mihaela Maria

    2015-12-23

    Needle-shaped single crystals of the title compound, C{sub 14}H{sub 9}ClF{sub 3}NO{sub 2}, were obtained from a co-crystallization experiment of Efavirenz with maleic acid in a (1:1) ratio, using methanol as solvent. Crystal structure determination at room temperature revealed a significant anisotropy of the lattice expansion compared to the previously reported low-temperature structure. In both low- and room temperature structures the cyclopropylethynyl fragment in one of the asymmetric unit molecules is disordered. While at low-temperature only one C atom exhibits positional disorder, at room temperature the disorder is present for two C atoms of the cyclopropane ring.

  9. Novel gene complex structure determination

    SciTech Connect

    Gatewood, J.M.

    1997-08-01

    This is the final report of a one-year, Laboratory-Directed Research and Development (LORD) project at the Los Alamos National Laboratory. `Operative` chromatin containing exclusively the minor hasten variants was successfully isolated. Linker hasten H1 is quantitatively missing from operative chromatin. One of the aims of this proposal was to determine the proteins responsible for stabilizing operative chromatin. This chromatin is stabilized by microtubule proteins tar and tubulin. Another goal of this project was the structural characterization of operate chromatin nucleosomes. Using solution scattering, nucleosomes containing the minor variants were shown to be structurally distinct from major variant containing nucleosomes. The unusual structure and stabilization of operative chromatin by microtubule proteins provides a possible mechanism for direct interaction of transcription machinery with specific chromatin domains.

  10. Secondary structure determines protein topology

    PubMed Central

    Fleming, Patrick J.; Gong, Haipeng; Rose, George D.

    2006-01-01

    Using a test set of 13 small, compact proteins, we demonstrate that a remarkably simple protocol can capture native topology from secondary structure information alone, in the absence of long-range interactions. It has been a long-standing open question whether such information is sufficient to determine a protein's fold. Indeed, even the far simpler problem of reconstructing the three-dimensional structure of a protein from its exact backbone torsion angles has remained a difficult challenge owing to the small, but cumulative, deviations from ideality in backbone planarity, which, if ignored, cause large errors in structure. As a familiar example, a small change in an elbow angle causes a large displacement at the end of your arm; the longer the arm, the larger the displacement. Here, correct secondary structure assignments (α-helix, β-strand, β-turn, polyproline II, coil) were used to constrain polypeptide backbone chains devoid of side chains, and the most stable folded conformations were determined, using Monte Carlo simulation. Just three terms were used to assess stability: molecular compaction, steric exclusion, and hydrogen bonding. For nine of the 13 proteins, this protocol restricts the main chain to a surprisingly small number of energetically favorable topologies, with the native one prominent among them. PMID:16823044

  11. Data mining of metal ion environments present in protein structures

    PubMed Central

    Zheng, Heping; Chruszcz, Maksymilian; Lasota, Piotr; Lebioda, Lukasz; Minor, Wladek

    2010-01-01

    Analysis of metal-protein interaction distances, coordination numbers, B-factors (displacement parameters), and occupancies of metal binding sites in protein structures determined by X-ray crystallography and deposited in the PDB shows many unusual values and unexpected correlations. By measuring the frequency of each amino acid in metal ion binding sites, the positive or negative preferences of each residue for each type of cation were identified. Our approach may be used for fast identification of metal-binding structural motifs that cannot be identified on the basis of sequence similarity alone. The analysis compares data derived separately from high and medium resolution structures from the PDB with those from very high resolution small-molecule structures in the Cambridge Structural Database (CSD). For high resolution protein structures, the distribution of metal-protein or metal-water interaction distances agrees quite well with data from CSD, but the distribution is unrealistically wide for medium (2.0 – 2.5 Å) resolution data. Our analysis of cation B-factors versus average B-factors of atoms in the cation environment reveals substantial numbers of structures contain either an incorrect metal ion assignment or an unusual coordination pattern. Correlation between data resolution and completeness of the metal coordination spheres is also found. PMID:18614239

  12. Ion spectral structures observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Ferradas, C.; Zhang, J.; Spence, H. E.; Kistler, L. M.; Larsen, B.; Reeves, G. D.; Skoug, R. M.; Funsten, H. O.

    2015-12-01

    During the last decades several missions have recorded the presence of dynamic spectral features of energetic ions in the inner magnetosphere. Previous studies have reported single "nose-like" structures occurring alone and simultaneous nose-like structures (up to three). These ion structures are named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. They constitute the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. The HOPE mass spectrometer onboard the Van Allen Probes measures energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet, where these ion structures are observed. We present a statistical study of nose-like structures, using 2-years measurements from the HOPE instrument. The results provide important details about the spatial distribution (dependence on geocentric distance), spectral features of the structures (differences among species), and geomagnetic conditions under which these structures occur.

  13. Turn-on fluorescent chemosensor for determination of lutetium ion.

    PubMed

    Faridbod, F; Sedaghat, M; Hosseini, M; Ganjali, M R; Khoobi, M; Shafiee, A; Norouzi, P

    2015-02-25

    A turn-on fluorescent chemosensor is introduced for the detection of Lu(3+) ion using N-[3-methyl]-2-[pyridine-2-amido] phenyl] pyridine-2-carboxamide (L) molecule. Fluorescent emission intensity of L enhances after binding to Lu(3+) ions in ethanol-water solution (1:9, v/v). The observed enhancement is the result of a strong covalent binding between Lu(3+) ion and L (the binding constant value is 2.0×10(6) mol(-1) L). The proposed optical chemosensor can be applied for the analysis of Lu(3+) ion in a linear range of 3.3×10(-7) to 1.0×10(-5) mol L(-1). The limit of detection was obtained 8.6×10(-7) mol L(-1). The probe exhibits high selectivity toward Lu(3+) ion in comparison with common metal ions. The proposed fluorescent chemosensor was successfully used in the determination of Lu(3+) ion in some water samples. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. Determination of ethambutol in plasma using selected ion monitoring.

    PubMed

    Ohya, K; Shintani, S; Sano, M

    1980-12-12

    The determination of ethambutol in plasma is described. Using ethambutol-d4 as an internal standard, ethambutol and the internal standard were extracted with chloroform under alkaline conditions, and converted into their trifluoroacetyl derivatives with trifluoroacetic anhydride in benzene-pyridine (4:1). Selected ion monitoring was carried out by monitoring the peaks at m/z 294 and 296 corresponding to the fragment ion [M/2]+ of the derivatives. Ethambutol was determined by use of the peak height ratio of the peak at m/z 294 against that at m/z 296. The method was utilized for studying the bioavailability and pharmacokinetics of the drug.

  15. Determination of metal ions in biological purification of waste waters

    SciTech Connect

    Tikhomirova, L.N.; Spiridonova, N.N.; Mandzhgaladze, I.D.

    1994-12-01

    Chromium, nickel, copper, zinc, and manganese were determined in active sludge extracted for utilization from sewage purification works in biological purification of waste waters. The measurements were carried out by the atomic absorption method and with Merck colorimetric kits for rapid determination of metal ions. The results obtained by the rapid colorimetric method agree fairly well with those obtained by the atomic absorption method, which makes it possible to recommend rapid colorimetric methods for routine analysis of biological objects for the content of ions of heavy metals.

  16. Combining ion mobility spectrometry with hydrogen-deuterium exchange and top-down MS for peptide ion structure analysis.

    PubMed

    Khakinejad, Mahdiar; Kondalaji, Samaneh Ghassabi; Maleki, Hossein; Arndt, James R; Donohoe, Gregory C; Valentine, Stephen J

    2014-12-01

    The gas-phase conformations of electrosprayed ions of the model peptide KKDDDDIIKIIK have been examined by ion mobility spectrometry (IMS) and hydrogen deuterium exchange (HDX)-tandem mass spectrometry (MS/MS) techniques. [M+4H](4+) ions exhibit two conformers with collision cross sections of 418 Å(2) and 471 Å(2). [M+3H](3+) ions exhibit a predominant conformer with a collision cross section of 340 Å(2) as well as an unresolved conformer (shoulder) with a collision cross section of ~367 Å(2). Maximum HDX levels for the more compact [M+4H](4+) ions and the compact and partially-folded [M+3H](3+) ions are ~12.9, ~15.5, and ~14.9, respectively. Ion structures obtained from molecular dynamics simulations (MDS) suggest that this ordering of HDX level results from increased charge-site/exchange-site density for the more compact ions of lower charge. Additionally, a new model that includes two distance calculations (charge site to carbonyl group and carbonyl group to exchange site) for the computer-generated structures is shown to better correlate to the experimentally determined per-residue deuterium uptake. Future comparisons of IMS-HDX-MS data with structures obtained from MDS are discussed with respect to novel experiments that will reveal the HDX rates of individual residues.

  17. Combining Ion Mobility Spectrometry with Hydrogen-Deuterium Exchange and Top-Down MS for Peptide Ion Structure Analysis

    NASA Astrophysics Data System (ADS)

    Khakinejad, Mahdiar; Kondalaji, Samaneh Ghassabi; Maleki, Hossein; Arndt, James R.; Donohoe, Gregory C.; Valentine, Stephen J.

    2014-12-01

    The gas-phase conformations of electrosprayed ions of the model peptide KKDDDDIIKIIK have been examined by ion mobility spectrometry (IMS) and hydrogen deuterium exchange (HDX)-tandem mass spectrometry (MS/MS) techniques. [M+4H]4+ ions exhibit two conformers with collision cross sections of 418 Å2 and 471 Å2. [M+3H]3+ ions exhibit a predominant conformer with a collision cross section of 340 Å2 as well as an unresolved conformer (shoulder) with a collision cross section of ~367 Å2. Maximum HDX levels for the more compact [M+4H]4+ ions and the compact and partially-folded [M+3H]3+ ions are ~12.9, ~15.5, and ~14.9, respectively. Ion structures obtained from molecular dynamics simulations (MDS) suggest that this ordering of HDX level results from increased charge-site/exchange-site density for the more compact ions of lower charge. Additionally, a new model that includes two distance calculations (charge site to carbonyl group and carbonyl group to exchange site) for the computer-generated structures is shown to better correlate to the experimentally determined per-residue deuterium uptake. Future comparisons of IMS-HDX-MS data with structures obtained from MDS are discussed with respect to novel experiments that will reveal the HDX rates of individual residues.

  18. Structure determination of enterovirus 71

    SciTech Connect

    Plevka, Pavel; Perera, Rushika; Cardosa, Jane; Kuhn, Richard J.; Rossmann, Michael G.

    2013-02-20

    Enterovirus 71 is a picornavirus that causes hand, foot and mouth disease but may induce fatal neurological illness in infants and young children. Enterovirus 71 crystallized in a body-centered orthorhombic space group with two particles in general orientations in the crystallographic asymmetric unit. Determination of the particle orientations required that the locked rotation function excluded the twofold symmetry axes from the set of icosahedral symmetry operators. This avoided the occurrence of misleading high rotation-function values produced by the alignment of icosahedral and crystallographic twofold axes. Once the orientations and positions of the particles had been established, the structure was solved by molecular replacement and phase extension.

  19. Comprehensive Gas-Phase Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 2. Gas-Phase Hydrogen/Deuterium Exchange for Ion Population Estimation.

    PubMed

    Khakinejad, Mahdiar; Ghassabi Kondalaji, Samaneh; Tafreshian, Amirmahdi; Valentine, Stephen J

    2017-05-01

    Gas-phase hydrogen/deuterium exchange (HDX) using D2O reagent and collision cross-section (CCS) measurements are utilized to monitor the ion conformers of the model peptide acetyl-PAAAAKAAAAKAAAAKAAAAK. The measurements are carried out on a home-built ion mobility instrument coupled to a linear ion trap mass spectrometer containing electron transfer dissociation (ETD) capabilities. ETD is utilized to obtain per-residue deuterium uptake data for select ion conformers, and a new algorithm is presented for interpreting the HDX data. Using molecular dynamics (MD) production data and a hydrogen accessibility scoring (HAS)-number of effective collisions (NEC) model, hypothetical HDX behavior is attributed to various in-silico candidate (CCS match) structures. The HAS-NEC model is applied to all candidate structures, and non-negative linear regression is employed to determine structure contributions resulting in the best match to deuterium uptake. The accuracy of the HAS-NEC model is tested with the comparison of predicted and experimental isotopic envelopes for several of the observed c-ions. It is proposed that gas-phase HDX can be utilized effectively as a second criterion (after CCS matching) for filtering suitable MD candidate structures. In this study, the second step of structure elucidation, 13 nominal structures were selected (from a pool of 300 candidate structures) and each with a population contribution proposed for these ions. Graphical Abstract ᅟ.

  20. Comprehensive Gas-Phase Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 2. Gas-Phase Hydrogen/Deuterium Exchange for Ion Population Estimation

    NASA Astrophysics Data System (ADS)

    Khakinejad, Mahdiar; Ghassabi Kondalaji, Samaneh; Tafreshian, Amirmahdi; Valentine, Stephen J.

    2017-03-01

    Gas-phase hydrogen/deuterium exchange (HDX) using D2O reagent and collision cross-section (CCS) measurements are utilized to monitor the ion conformers of the model peptide acetyl-PAAAAKAAAAKAAAAKAAAAK. The measurements are carried out on a home-built ion mobility instrument coupled to a linear ion trap mass spectrometer containing electron transfer dissociation (ETD) capabilities. ETD is utilized to obtain per-residue deuterium uptake data for select ion conformers, and a new algorithm is presented for interpreting the HDX data. Using molecular dynamics (MD) production data and a hydrogen accessibility scoring (HAS)-number of effective collisions (NEC) model, hypothetical HDX behavior is attributed to various in-silico candidate (CCS match) structures. The HAS-NEC model is applied to all candidate structures, and non-negative linear regression is employed to determine structure contributions resulting in the best match to deuterium uptake. The accuracy of the HAS-NEC model is tested with the comparison of predicted and experimental isotopic envelopes for several of the observed c-ions. It is proposed that gas-phase HDX can be utilized effectively as a second criterion (after CCS matching) for filtering suitable MD candidate structures. In this study, the second step of structure elucidation, 13 nominal structures were selected (from a pool of 300 candidate structures) and each with a population contribution proposed for these ions.

  1. Comprehensive Gas-Phase Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 2. Gas-Phase Hydrogen/Deuterium Exchange for Ion Population Estimation

    NASA Astrophysics Data System (ADS)

    Khakinejad, Mahdiar; Ghassabi Kondalaji, Samaneh; Tafreshian, Amirmahdi; Valentine, Stephen J.

    2017-05-01

    Gas-phase hydrogen/deuterium exchange (HDX) using D2O reagent and collision cross-section (CCS) measurements are utilized to monitor the ion conformers of the model peptide acetyl-PAAAAKAAAAKAAAAKAAAAK. The measurements are carried out on a home-built ion mobility instrument coupled to a linear ion trap mass spectrometer containing electron transfer dissociation (ETD) capabilities. ETD is utilized to obtain per-residue deuterium uptake data for select ion conformers, and a new algorithm is presented for interpreting the HDX data. Using molecular dynamics (MD) production data and a hydrogen accessibility scoring (HAS)-number of effective collisions (NEC) model, hypothetical HDX behavior is attributed to various in-silico candidate (CCS match) structures. The HAS-NEC model is applied to all candidate structures, and non-negative linear regression is employed to determine structure contributions resulting in the best match to deuterium uptake. The accuracy of the HAS-NEC model is tested with the comparison of predicted and experimental isotopic envelopes for several of the observed c-ions. It is proposed that gas-phase HDX can be utilized effectively as a second criterion (after CCS matching) for filtering suitable MD candidate structures. In this study, the second step of structure elucidation, 13 nominal structures were selected (from a pool of 300 candidate structures) and each with a population contribution proposed for these ions.

  2. Ion Elevators and Escalators in Multilevel Structures for Lossless Ion Manipulations.

    PubMed

    Ibrahim, Yehia M; Hamid, Ahmed M; Cox, Jonathan T; Garimella, Sandilya V B; Smith, Richard D

    2017-02-07

    We describe two approaches based upon ion "elevator" and "escalator" components that allow moving ions to different levels in structures for lossless ion manipulations (SLIM). Guided by ion motion simulations, we designed elevator and escalator components based upon ion current measurements providing essentially lossless transmission in multilevel designs. The ion elevator design allowed ions to efficiently bridge a 4 mm gap between levels. The component was integrated in a SLIM and coupled to a QTOF mass spectrometer using an ion funnel interface to evaluate the m/z range transmitted as compared to transmission within a level (e.g., in a linear section). The analysis of singly charged ions of m/z 600-2700 produced similar mass spectra for both elevator and straight (linear motion) components. In the ion escalator design, traveling waves (TW) were utilized to transport ions efficiently between two SLIM levels. Ion current measurements and ion mobility (IM) spectrometry analysis illustrated that ions can be transported between TW-SLIM levels with no significant loss of either ions or IM resolution. These developments provide a path for the development of multilevel designs providing, e.g., much longer IM path lengths, more compact designs, and the implementation of much more complex SLIM devices in which, e.g., different levels may operate at different temperatures or with different gases.

  3. Average motion, structure and orientation of the distant magnetotail determined from remote sensing of the edge of the plasma sheet boundary layer with E greater than 35 keV ions

    NASA Technical Reports Server (NTRS)

    Owen, C. J.; Slavin, J. A.; Richardson, I. G.; Murphy, N.; Hynds, R. J.

    1995-01-01

    We study gradients of the energetic ion intesity observed at the edge of the plasma sheet boundary layer (PSBL) by the energetic ion anisotropy spectrometer (EPAS) on International Sun Earth Explorer 3 (ISEE 3). In particular, we have determined the velocity of the boundary relative to the spacecraft in the direction perpendicular to the tail axis and the angle which the boundary normal makes to the spacecraft spin axis for 1160 PSBL encounters at X(sub GSM) greater than -240 R(sub E). By asuming that, on average, the edge of the PSBL is parallel to the cross-tail current sheet, we are then able to determine a number of properties of the structure, orientation and motion of the deep geomagnetic tail. We conclude the following: (1) Most crossings of the edge of the PSBL are caused by transverse motuion of the entire tail induced by solar wind direction variations, although some are caused by reconfiguration of the tail due to geomagnetic activity. (2) The typical velocity of the PSBL (and hence of the tail) in the direction perpendicular to the tail axis is 50-85 km/s. (3) The average twist of the tail is near zero, with the edge of the PSBL (and by inference the cross-tail current sheet) lying parallel to the ecliptic plane (however, large twists are found in individual events and the distribution of twists is broad, with one standard deviation of approximately 50 deg. (4) The width of the distribution decreases with downtail distance. (5) The variation of the distributions with cross-tail position reveals that this decreas in width is most likely due to the edge of the PSBL being concave, or significantly flared at the tail flanks, in the near-Earth region. (6) During days on which the Interplanetary Magnetic Field (IMF) has 'away' sector structure, the north lobe of the trail is twisted on average towards dawn by 7.0 +/-2.4 deg. (7) During days on which the IMF has 'toward' sector structure, the north lobe is tilted towards duskby 3.8 +/- 2.3. (8) A subset of

  4. Determination of Dusty Particle Charge Taking into Account Ion Drag

    SciTech Connect

    Ramazanov, T. S.; Dosbolayev, M. K.; Jumabekov, A. N.; Amangaliyeva, R. Zh.; Orazbayev, S. A.; Petrov, O. F.; Antipov, S. N.

    2008-09-07

    This work is devoted to the experimental estimation of charge of dust particle that levitates in the stratum of dc glow discharge. Particle charge is determined on the basis of the balance between ion drag force, gravitational and electric forces. Electric force is obtained from the axial distribution of the light intensity of strata.

  5. Linkage Determination of Linear Oligosaccharides by MSn (n > 2) Collision-Induced Dissociation of Z1 Ions in the Negative Ion Mode

    NASA Astrophysics Data System (ADS)

    Konda, Chiharu; Bendiak, Brad; Xia, Yu

    2013-12-01

    Obtaining unambiguous linkage information between sugars in oligosaccharides is an important step in their detailed structural analysis. An approach is described that provides greater confidence in linkage determination for linear oligosaccharides based on multiple-stage tandem mass spectrometry (MSn, n >2) and collision-induced dissociation (CID) of Z1 ions in the negative ion mode. Under low energy CID conditions, disaccharides 18O-labeled on the reducing carbonyl group gave rise to Z1 product ions (m/z 163) derived from the reducing sugar, which could be mass-discriminated from other possible structural isomers having m/z 161. MS3 CID of these m/z 163 ions showed distinct fragmentation fingerprints corresponding to the linkage types and largely unaffected by sugar unit identities or their anomeric configurations. This unique property allowed standard CID spectra of Z1 ions to be generated from a small set of disaccharide samples that were representative of many other possible isomeric structures. With the use of MSn CID (n = 3 - 5), model linear oligosaccharides were dissociated into overlapping disaccharide structures, which were subsequently fragmented to form their corresponding Z1 ions. CID data of these Z1 ions were collected and compared with the standard database of Z1 ion CID using spectra similarity scores for linkage determination. As the proof-of-principle tests demonstrated, we achieved correct determination of individual linkage types along with their locations within two trisaccharides and a pentasaccharide.

  6. Linkage determination of linear oligosaccharides by MS(n) (n > 2) collision-induced dissociation of Z₁ ions in the negative ion mode.

    PubMed

    Konda, Chiharu; Bendiak, Brad; Xia, Yu

    2014-02-01

    Obtaining unambiguous linkage information between sugars in oligosaccharides is an important step in their detailed structural analysis. An approach is described that provides greater confidence in linkage determination for linear oligosaccharides based on multiple-stage tandem mass spectrometry (MS(n), n >2) and collision-induced dissociation (CID) of Z1 ions in the negative ion mode. Under low energy CID conditions, disaccharides (18)O-labeled on the reducing carbonyl group gave rise to Z1 product ions (m/z 163) derived from the reducing sugar, which could be mass-discriminated from other possible structural isomers having m/z 161. MS(3) CID of these m/z 163 ions showed distinct fragmentation fingerprints corresponding to the linkage types and largely unaffected by sugar unit identities or their anomeric configurations. This unique property allowed standard CID spectra of Z1 ions to be generated from a small set of disaccharide samples that were representative of many other possible isomeric structures. With the use of MS(n) CID (n = 3 - 5), model linear oligosaccharides were dissociated into overlapping disaccharide structures, which were subsequently fragmented to form their corresponding Z1 ions. CID data of these Z1 ions were collected and compared with the standard database of Z1 ion CID using spectra similarity scores for linkage determination. As the proof-of-principle tests demonstrated, we achieved correct determination of individual linkage types along with their locations within two trisaccharides and a pentasaccharide.

  7. Gas-Phase Transformation of Phosphatidylcholine Cations to Structurally Informative Anions via Ion/Ion Chemistry

    PubMed Central

    Stutzman, John R.; Blanksby, Stephen J.; McLuckey, Scott A.

    2013-01-01

    Gas-phase transformation of synthetic phosphatidylcholine (PC) monocations to structurally informative anions is demonstrated via ion/ion reactions with doubly deprotonated 1,4-phenylenedipropionic acid (PDPA). Two synthetic PC isomers, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (PC16:0/18:1) and 1-oleoyl-2-palmitoyl-sn-glycero-3-phosphocholine (PC18:1/16:0) were subjected to this ion/ion chemistry. The product of the ion/ion reaction is a negatively charged complex, [PC+PDPA-H]−. Collisional activation of the long-lived complex causes transfer of a proton and methyl cation to PDPA, generating [PC-CH3]−. Subsequent collisional activation of the demethylated PC anions produces abundant fatty acid carboxylate anions and low abundance acyl neutral losses as free acids and ketenes. Product ion spectra of [PC-CH3]− suggest favorable cleavage at the sn-2 position over the sn-1 due to distinct differences in the relative abundances. In contrast, collisional activation of PC cations is absent of abundant fatty acid chain-related product ions and typically indicates only the lipid class via formation of the phosphocholine cation. A solution phase method to produce the gas-phase adducted PC anion is also demonstrated. Product ion spectra derived from the solution phase method are similar to the results generated via ion/ion chemistry. This work demonstrates a gas-phase means to increase structural characterization of phosphatidylcholines via ion/ion chemistry. PMID:23469867

  8. Gas-phase transformation of phosphatidylcholine cations to structurally informative anions via ion/ion chemistry.

    PubMed

    Stutzman, John R; Blanksby, Stephen J; McLuckey, Scott A

    2013-04-02

    Gas-phase transformation of synthetic phosphatidylcholine (PC) monocations to structurally informative anions is demonstrated via ion/ion reactions with doubly deprotonated 1,4-phenylenedipropionic acid (PDPA). Two synthetic PC isomers, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (PC(16:0/18:1)) and 1-oleoyl-2-palmitoyl-sn-glycero-3-phosphocholine (PC(18:1/16:0)), were subjected to this ion/ion chemistry. The product of the ion/ion reaction is a negatively charged complex, [PC + PDPA - H](-). Collisional activation of the long-lived complex causes transfer of a proton and methyl cation to PDPA, generating [PC - CH3](-). Subsequent collisional activation of the demethylated PC anions produces abundant fatty acid carboxylate anions and low-abundance acyl neutral losses as free acids and ketenes. Product ion spectra of [PC - CH3](-) suggest favorable cleavage at the sn-2 position over the sn-1 due to distinct differences in the relative abundances. In contrast, collisional activation of PC cations is absent of abundant fatty acid chain-related product ions and typically indicates only the lipid class via formation of the phosphocholine cation. A solution phase method to produce the gas-phase adducted PC anion is also demonstrated. Product ion spectra derived from the solution phase method are similar to the results generated via ion/ion chemistry. This work demonstrates a gas-phase means to increase structural characterization of phosphatidylcholines via ion/ion chemistry.

  9. Flow injection determination of bromide ion in a developer using bromide ion-selective electrode detector.

    PubMed

    Masadome, T; Asano, Y; Nakamura, T

    1999-10-01

    A potentiometric flow injection determination method for bromide ion in a developer was proposed, by utilizing a flow-through type bromide ion-selective electrode detector. The sensing membrane of the electrode was Ag(2)S-AgBr membrane. The response of the electrode detector as a peak-shape signal was obtained for injected bromide ion in a developer. A linear relationship was found to exist between peak height and the concentration of the bromide ion in a developer in a concentration range from 1.0x10(-3) to 1.0x10(-2) mol l(-1). The relative standard deviation for 10 injections of a 6x10(-3) mol l(-1) bromide ion in a developer was 1.3% and the sampling rate was ca 17-20 samples h(-1). The present method was free from the interference of an organic reducing reagent, an organic substance in a developer sample solution for the determination of bromide ion in a developer.

  10. Ions in water: The microscopic structure of concentrated hydroxide solutions

    NASA Astrophysics Data System (ADS)

    Imberti, S.; Botti, A.; Bruni, F.; Cappa, G.; Ricci, M. A.; Soper, A. K.

    2005-05-01

    Neutron-diffraction data on aqueous solutions of hydroxides, at solute concentrations ranging from 1 solute per 12 water molecules to 1 solute per 3 water molecules, are analyzed by means of a Monte Carlo simulation (empirical potential structure refinement), in order to determine the hydration shell of the OH- in the presence of the smaller alkali metal ions. It is demonstrated that the symmetry argument between H+ and OH- cannot be used, at least in the liquid phase at such high concentrations, for determining the hydroxide hydration shell. Water molecules in the hydration shell of K+ orient their dipole moment at about 45° from the K+-water oxygen director, instead of radially as in the case of the Li+ and Na+ hydration shells. The K+-water oxygen radial distribution function shows a shallower first minimum compared to the other cation-water oxygen functions. The influence of the solutes on the water-water radial distribution functions is shown to have an effect on the water structure equivalent to an increase in the pressure of the water, depending on both ion concentration and ionic radius. The changes of the water structure in the presence of charged solutes and the differences among the hydration shells of the different cations are used to present a qualitative explanation of the observed cation mobility.

  11. Compact non-rock-salt structures in sodium fluoride cluster ions at specific sizes revealed by ion mobility mass spectrometry.

    PubMed

    Ohshimo, Keijiro; Takahashi, Tohru; Moriyama, Ryoichi; Misaizu, Fuminori

    2014-10-30

    Structures of small sodium fluoride cluster cations, Na(n)F(n-1)(+), have been determined for n = 5-23 by ion mobility mass spectrometry. In the mass spectrum of Na(n)F(n-1)(+) cluster ions measured after collisions in the ion-drift cell, cuboid ions with near-regular hexahedron such as n = 14 (3 × 3 × 3), 23 (3 × 3 × 5), 38 (3 × 5 × 5), 63 (5 × 5 × 5), and 88 (5 × 5 × 7) were predominantly observed as magic numbers. By comparison of the collision cross sections obtained from the ion mobility measurements with theoretical ones, we have experimentally shown that the ions of n = 7 and 10 have stable non-rock-salt type structures in which one sodium atom is encapsulated into the sodium fluoride cuboid lattice. The collision cross sections of n = 12 and 13 are almost equal to that of the n = 14 cuboid. A similar feature was also observed in collision cross sections of n = 21 and 22, which are equal to that of the n = 23 cuboid. These features indicate that the cluster ions of n = 12, 13, 21, and 22 have near-cuboid structures with some surface defects.

  12. Structures and physical properties of gaseous metal cationized biological ions.

    PubMed

    Burt, Michael B; Fridgen, Travis D

    2012-01-01

    Metal chelation can alter the activity of free biomolecules by modifying their structures or stabilizing higher energy tautomers. In recent years, mass spectrometric techniques have been used to investigate the effects of metal complexation with proteins, nucleobases and nucleotides, where small conformational changes can have significant physiological consequences. In particular, infrared multiple photon dissociation spectroscopy has emerged as an important tool for determining the structure and reactivity of gas-phase ions. Unlike other mass spectrometric approaches, this method is able to directly resolve structural isomers using characteristic vibrational signatures. Other activation and dissociation methods, such as blackbody infrared radiative dissociation or collision-induced dissociation can also reveal information about the thermochemistry and dissociative pathways of these biological ions. This information can then be used to provide information about the structures of the ionic complexes under study. In this article, we review the use of gas-phase techniques in characterizing metal-bound biomolecules. Particular attention will be given to our own contributions, which detail the ability of metal cations to disrupt nucleobase pairs, direct the self-assembly of nucleobase clusters and stabilize non-canonical isomers of amino acids.

  13. Ion imprinted polymeric nanoparticles for selective separation and sensitive determination of zinc ions in different matrices.

    PubMed

    Shamsipur, Mojtaba; Rajabi, Hamid Reza; Pourmortazavi, Seied Mahdi; Roushani, Mahmoud

    2014-01-03

    Preparation of Zn(2+) ion-imprinted polymer (Zn-IIP) nanoparticles is presented in this report. The Zn-IIP nanoparticles are prepared by dissolving stoichiometric amounts of zinc nitrate and selected chelating ligand, 3,5,7,20,40-pentahydroxyflavone, in 15 mL ethanol-acetonitrile (2:1; v/v) mixture as a porogen solvent in the presence of ethylene glycol-dimethacrylate (EGDMA) as cross-linking, methacrylic acid (MAA) as functional monomer, and 2,2-azobisisobutyronitrile (AIBN) as initiator. After polymerization, Cavities in the polymer particles corresponding to the Zn(2+) ions were created by leaching the polymer in HCl aqueous solution. The synthesized IIPs were characterized by scanning electron microscopy, X-ray diffraction, Fourier transform infrared spectroscopy, fluorescence spectroscopy and thermal analysis techniques. Also, the pH range for rebinding of Zn(2+) ion on the IIP and equilibrium binding time were optimized, using flame atomic absorption spectrometry. In selectivity study, it was found that imprinting results increased affinity of the material toward Zn(2+) ion over other competitor metal ions with the same charge and close ionic radius. The prepared IIPs were repeatedly used and regenerated for six times without any significant decrease in polymer binding affinities. Finally, the prepared sorbent was successfully applied to the selective recognition and determination of zinc ion in different real samples.

  14. Local structures of ions at ion-exchange resin/solution interface.

    PubMed

    Harada, Makoto; Okada, Tetsuo

    2005-08-26

    The local structures of Cl- and Br- in anion-exchange resins have been studied by X-ray absorption fine structure (XAFS), and separation selectivity is discussed on the basis of results. When two different anion-exchange resins having trimethylammonium and dimethylammonium groups as anion-exchange groups are employed for ion-exchange experiments, slightly higher Br- selectivity has been obtained with the former. XAFS has indicated that the average hydration numbers for a given anion is not affected by the structure of the ion-exchange group, but that the extent of ion-association between the anion and the ion-exchange groups depends on the type of the ion-exchange group. Shorter interaction distance (and in turn stronger ion-association) has been confirmed for the dimethylammonium-type resin, and is consistent with lower Br- selectivity of this resin.

  15. Determination of selected anions in water by ion chromatography

    USGS Publications Warehouse

    Fishman, Marvin J.; Pyen, Grace

    1979-01-01

    Ion chromatography is a rapid, sensitive, precise, and accurate method for the determination of major anions in rainwater and surface waters. Simultaneous analyses of a single sample for bromide, chloride, fluoride, nitrate, nitrite, orthophosphate, and sulfate require approximately 20 minutes to obtain a chromatogram. Minimum detection limits range from 0.01 mg/L for fluoride to 0.20 mg/L for chloride and sulfate. Relative standard deviations were less than 9% for all anions except nitrite in Standard Reference Water Samples. Only one reference sample contained nitrite and its concentration was near the minimum level of detection. Similar precision was found for chloride, nitrate, and sulfate at concentrations less than 5 mg/L in rainfall samples. Precision for fluoride ranged from 12 to 22%, but is attributed to the low concentrations in these samples. The other anions were not detected. To determine accuracy of results, several samples were spiked with known concentrations of fluoride, chloride, nitrate, and sulfate; recoveries ranged from 96 to 103%. Known amounts of bromide and phosphate were added, separately, to several other waters, which contained bromide or phosphate. Recovery of added bromide and phosphate ranged from approximately 95 to 104%. No recovery data were obtained for nitrite. Chloride, nitrate, nitrite, orthophosphate, and sulfate, in several samples, were also determined independently by automated colorimetric procedures. An automated ion-selective electrode method was used to determine fluoride. Results are in agreement with results obtained by ion chromatography. (USGS).

  16. Helical Pulse Line Structures for Ion Acceleration

    SciTech Connect

    Briggs, R.J.; Reginato, L.L.; Waldron, W.L.

    2005-05-01

    The basic concept of the ''Pulse Line Ion Accelerator'' is presented, where pulse power sources create a ramped traveling wave voltage pulse on a helical pulse line. Ions can surf on this traveling wave and achieve energy gains much larger than the peak applied voltage. Tapered and untapered lines are compared, and a transformer coupling technique for launching the wave is described.

  17. Ion Dynamics and Field Structure of Quasi-perpendicular Collisionless Shocks near the Critical Mach Number

    NASA Astrophysics Data System (ADS)

    Balikhin, M. A.; Malkov, M.; Sagdeev, R.; Dudnikova, G.

    2015-12-01

    The structure of subcritical (laminar) collisionless shocks has been understood long time ago. When the Mach number exceeds a critical value, some of the incident ions are reflected. This needs to be included into the description of the shock structure and entropy production at the shock front. We present an analytical model of ion reflection from a quasi-perpendicular collisionless shock and the formation of the foot region associated with this reflection. Reflected ions perturb the electrostatic and magnetic fields in the foot region which we self-consistently include in determining the fraction of reflected ions, depending on the Mach number of the shock. The subsequent motion of the shock reflected ions downstream and formation of the downstream field structure is analyzed. Models for thermalization of the downstream plasma and approaches to Rankine-Hugoniot relations will also be discussed. The obtained overall shock structure is compared with the Cluster observations.

  18. Structural determinants of glomerular permeability.

    PubMed

    Deen, W M; Lazzara, M J; Myers, B D

    2001-10-01

    Recent progress in relating the functional properties of the glomerular capillary wall to its unique structure is reviewed. The fenestrated endothelium, glomerular basement membrane (GBM), and epithelial filtration slits form a series arrangement in which the flow diverges as it enters the GBM from the fenestrae and converges again at the filtration slits. A hydrodynamic model that combines morphometric findings with water flow data in isolated GBM has predicted overall hydraulic permeabilities that are consistent with measurements in vivo. The resistance of the GBM to water flow, which accounts for roughly half that of the capillary wall, is strongly dependent on the extent to which the GBM surfaces are blocked by cells. The spatial frequency of filtration slits is predicted to be a very important determinant of the overall hydraulic permeability, in keeping with observations in several glomerular diseases in humans. Whereas the hydraulic resistances of the cell layers and GBM are additive, the overall sieving coefficient for a macromolecule (its concentration in Bowman's space divided by that in plasma) is the product of the sieving coefficients for the individual layers. Models for macromolecule filtration reveal that the individual sieving coefficients are influenced by one another and by the filtrate velocity, requiring great care in extrapolating in vitro observations to the living animal. The size selectivity of the glomerular capillary has been shown to be determined largely by the cellular layers, rather than the GBM. Controversial findings concerning glomerular charge selectivity are reviewed, and it is concluded that there is good evidence for a role of charge in restricting the transmural movement of albumin. Also discussed is an effect of albumin that has received little attention, namely, its tendency to increase the sieving coefficients of test macromolecules via steric interactions. Among the unresolved issues are the specific contributions of the

  19. Characteristic of Ion loss as Determined by Hybrid Simulations

    NASA Astrophysics Data System (ADS)

    Brecht, S. H.; Ledvina, S. A.

    2016-12-01

    One of the major objectives of the MAVEN mission is to determine the loss rate of oxygen ions from the atmosphere of Mars. It is thought that the oxygen ion loss represents a conduit for the loss of water from Mars. However, the actual measurements and estimates of global loss rates are very difficult because one needs an average over many orbits and full coverage of the loss regions of Mars; something that MAVEN will only accomplish with an extended mission. In the meantime global kinetic simulations are an avenue to gain further insight into the loss process and perhaps offer insight into the data analysis that will be performed on the MAVEN data. Hybrid particle codes provide self-consistent simulations of the ion dynamics occurring when the solar wind interacts with Mars. This paper reports the results of HALFSHEL hybrid code simulations of the solar wind interaction with Mars and the subsequent loss of oxygen ions in the form of O+ and O2+. Four simulations were performed representing different orientations of the crustal magnetic fields with the subsolar regions using a solar EUV flux representative of the moderate solar activity experienced by MAVEN. Loss rates will be presented as will evaluations of the distribution functions of the various loss ion species as accumulated at roughly 2 Rm for each of the four simulations. The results will be presented as faces on a box surrounding Mars so that one can evaluate regions such as that of the measured plasma plume. The plume feature has now been measured and is often seen in simulations. Finally, the losses and the subsequent velocity distributions will be compared between the various crustal magnetic field orientations. In summary, results from the HALFSHEL hybrid code will be presented. These results will address characteristics of the oxygen ions lost from Mars as a function of crustal magnetic field orientation. Further, they will be compared with respect to the regions surrounding Mars and the associated

  20. Characteristic of Ion loss as determined by hybrid simulations

    NASA Astrophysics Data System (ADS)

    Brecht, Stephen H.; Ledvina, Stephen

    2016-10-01

    One of the major objectives of the MAVEN mission is to determine the loss rate of oxygen ions from the atmosphere of Mars. It is thought that the oxygen ion loss represents a conduit for the loss of water from Mars. However, the actual measurements and estimates of global loss rates are very difficult because one needs an average over many orbits and full coverage of the loss regions of Mars; something that MAVEN will only accomplish with an extended mission. In the meantime global kinetic simulations are an avenue to gain further insight into the loss process and perhaps offer insight into the data analysis that will be performed on the MAVEN data. Hybrid particle codes provide self-consistent simulations of the ion dynamics occurring when the solar wind interacts with Mars.This paper reports the results of HALFSHEL hybrid code simulations of the solar wind interaction with Mars and the subsequent loss of oxygen ions in the form of O+ and O2+. Four simulations were performed representing different orientations of the crustal magnetic fields with the subsolar regions using a solar EUV flux representative of the moderate solar activity experienced by MAVEN. Loss rates will be presented as will evaluations of the distribution functions of the various loss ion species as accumulated at roughly 2 Rm for each of the four simulations. The results will be presented as faces on a box surrounding Mars so that one can evaluate regions such as that of the measured plasma plume. The plume feature has now been measured and is often seen in simulations. Finally, the losses and the subsequent velocity distributions will be compared between the various crustal magnetic field orientations.In summary, results from the HALFSHEL hybrid code will be presented. These results will address characteristics of the oxygen ions lost from Mars as a function of crustal magnetic field orientation. Further, they will be compared with respect to the regions surrounding Mars and the associated

  1. Ion aggregation in high salt solutions. II. Spectral graph analysis of water hydrogen-bonding network and ion aggregate structures.

    PubMed

    Choi, Jun-Ho; Cho, Minhaeng

    2014-10-21

    Graph theory in mathematics and computer science is the study of graphs that are structures with pairwise connections between any objects. Here, the spectral graph theory and molecular dynamics simulation method are used to describe both morphological variation of ion aggregates in high salt solutions and ion effects on water hydrogen-bonding network structure. From the characteristic value analysis of the adjacency matrices that are graph theoretical representations of ion clusters, ion networks, and water H-bond structures, we obtained the ensemble average eigenvalue spectra revealing intricate connectivity and topology of ion aggregate structure that can be classified as either ion cluster or ion network. We further show that there is an isospectral relationship between the eigenvalue spectra of ion networks in high KSCN solutions and those of water H-bonding networks. This reveals the isomorphic relationship between water H-bond structure and ion-ion network structure in KSCN solution. On the other hand, the ion clusters formed in high NaCl solutions are shown to be graph-theoretically and morphologically different from the ion network structures in KSCN solutions. These observations support the bifurcation hypothesis on large ion aggregate growth mechanism via either ion cluster or ion network formation. We thus anticipate that the present spectral graph analyses of ion aggregate structures and their effects on water H-bonding network structures in high salt solutions can provide important information on the specific ion effects on water structures and possibly protein stability resulting from protein-water interactions.

  2. Quasiclassical model of ion shell structure

    SciTech Connect

    Dyachkov, K.G.; Pankratov, P.M.

    1993-12-01

    An effective potential of the nl-electrons in atoms or ions obtained from the well-known screened hydrogenlike potential model is used to calculate ionization energies in the quasiclassical approximation. The method is suitable for the inner and outer shells of the ground and excited states. We consider here the outer shells of the lighter element ions. The approach yields good results for multicharged ions as well as for the weakly ionized s subshells and for less-than-half-filled p subshells. 18 refs., 1 fig., 2 tabs.

  3. Ion Trapping, Storage, and Ejection in Structures for Lossless Ion Manipulations.

    PubMed

    Zhang, Xinyu; Garimella, Sandilya V B; Prost, Spencer A; Webb, Ian K; Chen, Tsung-Chi; Tang, Keqi; Tolmachev, Aleksey V; Norheim, Randolph V; Baker, Erin S; Anderson, Gordon A; Ibrahim, Yehia M; Smith, Richard D

    2015-06-16

    A new Structures for Lossless Ion Manipulations (SLIM) module, having electrode arrays patterned on a pair of parallel printed circuit boards (PCB), was constructed and utilized to investigate capabilities for ion trapping at a pressure of 4 Torr. Positive ions were confined by application of RF voltages to a series of inner rung electrodes with alternating phase on adjacent electrodes, in conjunction with positive DC potentials on surrounding guard electrodes on each PCB. An axial DC field was also introduced by stepwise varying the DC potentials applied to the inner rung electrodes to control the ion transport and accumulation inside the ion trapping region. We show that ions can be trapped and accumulated with up to 100% efficiency, stored for at least 5 h with no significant losses, and then could be rapidly ejected from the SLIM trap. The present results provide a foundation for the development of much more complex SLIM devices that facilitate extended ion manipulations.

  4. Synthesis and application of ion-imprinted polymer nanoparticles for the determination of nickel ions

    NASA Astrophysics Data System (ADS)

    Abbasi, Shahryar; Roushani, Mahmoud; Khani, Hossein; Sahraei, Reza; Mansouri, Ghobad

    2015-04-01

    Novel Ni(II) ion-imprinted polymers (Ni-IIP) nanoparticles were prepared by using Ni(II) ion-1,5-diphenyl carbazide (DPC) complex as the template molecule and methacrylic acid, ethylene glycol dimethacrylate (EGDMA) and 2,2‧-azobisisobutyronitrile (AIBN) as the functional monomer, cross-linker and the radical initiator, respectively. The synthesized polymer particles were characterized physically and morphologically by using infrared spectroscopy (IR), thermo gravimetric analysis (TGA), X-ray diffraction (XRD) and scanning electron microscopic (SEM) techniques. Some parameters such as pH, weight of the polymer, adsorption time, elution time, eluent type and eluent volume which affects the efficiency of the polymer were studied. The preconcentration factor, relative standard deviation, and limit of detection of the method were found to be 100, 1.9%, and 0.002 μg mL-1, respectively. The prepared ion-imprinted polymer particles have an increased selectivity toward Ni(II) ions over a range of competing metal ions with the same charge and similar ionic radius. The method was applied to the determination of nickel in tomato and some water samples.

  5. Synthesis and application of ion-imprinted polymer nanoparticles for the determination of nickel ions.

    PubMed

    Abbasi, Shahryar; Roushani, Mahmoud; Khani, Hossein; Sahraei, Reza; Mansouri, Ghobad

    2015-04-05

    Novel Ni(II) ion-imprinted polymers (Ni-IIP) nanoparticles were prepared by using Ni(II) ion-1,5-diphenyl carbazide (DPC) complex as the template molecule and methacrylic acid, ethylene glycol dimethacrylate (EGDMA) and 2,2'-azobisisobutyronitrile (AIBN) as the functional monomer, cross-linker and the radical initiator, respectively. The synthesized polymer particles were characterized physically and morphologically by using infrared spectroscopy (IR), thermo gravimetric analysis (TGA), X-ray diffraction (XRD) and scanning electron microscopic (SEM) techniques. Some parameters such as pH, weight of the polymer, adsorption time, elution time, eluent type and eluent volume which affects the efficiency of the polymer were studied. The preconcentration factor, relative standard deviation, and limit of detection of the method were found to be 100, 1.9%, and 0.002 μg mL(-1), respectively. The prepared ion-imprinted polymer particles have an increased selectivity toward Ni(II) ions over a range of competing metal ions with the same charge and similar ionic radius. The method was applied to the determination of nickel in tomato and some water samples.

  6. Can the Transport Properties of Molten Salts and Ionic Liquids Be Used To Determine Ion Association?

    PubMed

    Harris, Kenneth R

    2016-12-01

    There have long been arguments supporting the concept of ion association in molten salts and ionic liquids, largely based on differences between the conductivity and that predicted from self-diffusion coefficients by the Nernst-Einstein equation for noninteracting ions. It is known from molecular dynamics simulations that even simple models based on charged hard spheres show such a difference due to the (anti)-correlation of ion motions. Formally this is expressed as a difference between the velocity cross-correlation coefficient of the oppositely charged ions and the mean of those for the two like-charged ions. This article examines molten salt and ionic liquid transport property data, comparing simple and model associated salts (ZnCl2, PbCl2, and TlCl) including weakly dissociated molecular liquids (H2O, HCOOH, H2SO4). Analysis employing Laity resistance coefficients (rij) shows that the common ion-association rationalization is flawed, consistent with recent direct measurements of the degree of ionicity in ionic liquid chlorides and with theoretical studies. However, the protic ionic liquids [PyrOMe][BF4] and [DBUH][CH3SO3] have larger than usual NE deviation parameters (>0.5), and large negative like-ion rii, analogous to those of ZnCl2. Structural, spectroscopic, and theoretical studies are suggested to determine whether these are indeed genuine examples of association.

  7. Determination of choline in infant formula by ion chromatography.

    PubMed

    Laikhtman, M; Rohrer, J S

    1999-01-01

    Choline was determined in infant formula by ion chromatography with suppressed conductivity detection. Samples were digested with 1M hydrochloric acid, filtered, diluted, and injected into the chromatographic system. Choline and the alkali and alkaline earth metals were separated on a high-resolution cation-exchange column and detected by suppressed conductivity. The method was linear between 2 and 200 mg/L (r2 = 0.9999), the concentration range of the diluted samples. This method accurately determined choline in powdered, concentrated, and ready-to-feed infant formulas. Recoveries of choline spikes into powdered infant formula at approximately 1, 0.8, 0.5, and 0.2 times the labeled value ranged from 85 to 114%. This method had good agreement for 8 blind duplicates. The values determined for these samples, which were used in an AOAC collaborative study of an enzymatic method, were consistent with the values determined by the enzymatic method.

  8. The determination of dopant ion valence distributions in insulating crystals using XANES measurements.

    PubMed

    Hughes-Currie, Rosa B; Ivanovskikh, Konstantin V; Wells, Jon-Paul R; Reid, Michael F; Gordon, Robert A

    2016-04-06

    Ytterbium-doped wide-bandgap fluoride crystals CaF2, SrF2 and NaMgF3 have been measured using x-ray absorption near edge structure (XANES) on the L3 edge to determine the ratio of trivalent to divalent Yb ions present in the crystals. This study improves upon previous XANES measurements of dopant ion valency by taking into account the x-ray emission transition probabilities for the divalent and trivalent species instead of simply assuming that the relative concentrations may be determined by the ratio of the x-ray excitation band areas. Trivalent to divalent ratios as high as 5 are inferred even at low total dopant ion concentrations of 0.05 mol% Yb.

  9. The determination of dopant ion valence distributions in insulating crystals using XANES measurements

    NASA Astrophysics Data System (ADS)

    Hughes-Currie, Rosa B.; Ivanovskikh, Konstantin V.; Wells, Jon-Paul R.; Reid, Michael F.; Gordon, Robert A.

    2016-04-01

    Ytterbium-doped wide-bandgap fluoride crystals CaF2, SrF2 and NaMgF3 have been measured using x-ray absorption near edge structure (XANES) on the L3 edge to determine the ratio of trivalent to divalent Yb ions present in the crystals. This study improves upon previous XANES measurements of dopant ion valency by taking into account the x-ray emission transition probabilities for the divalent and trivalent species instead of simply assuming that the relative concentrations may be determined by the ratio of the x-ray excitation band areas. Trivalent to divalent ratios as high as 5 are inferred even at low total dopant ion concentrations of 0.05 mol% Yb.

  10. Ion heating in an auroral potential structure

    NASA Astrophysics Data System (ADS)

    Anastasiadis, A.; Daglis, I. A.; Tsironis, C.

    2004-06-01

    We investigate the interaction of O+ ions with a one-dimensional potential well, using Hamiltonian formulation. Heating of plasma originating in the terrestrial ionosphere plays a catalytic role in solar-driven magnetic storms, which dissipate energy globally within the magnetosphere of the earth. An interesting candidate for ionospheric plasma heating is a potential well located at auroral arcs in the high-latitude magnetosphere. We consider a potential with an exponential form, having a characteristic length Lx. The oxygen ions drift towards the auroral arc in the presence of a constant magnetic field Bz and a constant electric field Ey. The orbits of individual ions for different initial conditions - phase angle and kinetic energy - are traced. Our results show that, depending upon the initial conditions, test particles can be either accelerated or decelerated. Furthermore, we perform a parametric study for the interactions of mono-energetic and Maxwellian type of initial ion distribution - using random phase angle injection of the particles - with respect to our main model parameter, the characteristic length of the potential Lx. We conclude that for characteristic lengths comparable to twice the ion gyroradius, the O+ population is accelerated.

  11. Structure-Functional Basis of Ion Transport in Sodium–Calcium Exchanger (NCX) Proteins

    PubMed Central

    Giladi, Moshe; Shor, Reut; Lisnyansky, Michal; Khananshvili, Daniel

    2016-01-01

    The membrane-bound sodium–calcium exchanger (NCX) proteins shape Ca2+ homeostasis in many cell types, thus participating in a wide range of physiological and pathological processes. Determination of the crystal structure of an archaeal NCX (NCX_Mj) paved the way for a thorough and systematic investigation of ion transport mechanisms in NCX proteins. Here, we review the data gathered from the X-ray crystallography, molecular dynamics simulations, hydrogen–deuterium exchange mass-spectrometry (HDX-MS), and ion-flux analyses of mutants. Strikingly, the apo NCX_Mj protein exhibits characteristic patterns in the local backbone dynamics at particular helix segments, thereby possessing characteristic HDX profiles, suggesting structure-dynamic preorganization (geometric arrangements of catalytic residues before the transition state) of conserved α1 and α2 repeats at ion-coordinating residues involved in transport activities. Moreover, dynamic preorganization of local structural entities in the apo protein predefines the status of ion-occlusion and transition states, even though Na+ or Ca2+ binding modifies the preceding backbone dynamics nearby functionally important residues. Future challenges include resolving the structural-dynamic determinants governing the ion selectivity, functional asymmetry and ion-induced alternating access. Taking into account the structural similarities of NCX_Mj with the other proteins belonging to the Ca2+/cation exchanger superfamily, the recent findings can significantly improve our understanding of ion transport mechanisms in NCX and similar proteins. PMID:27879668

  12. Structure-Functional Basis of Ion Transport in Sodium-Calcium Exchanger (NCX) Proteins.

    PubMed

    Giladi, Moshe; Shor, Reut; Lisnyansky, Michal; Khananshvili, Daniel

    2016-11-22

    The membrane-bound sodium-calcium exchanger (NCX) proteins shape Ca(2+) homeostasis in many cell types, thus participating in a wide range of physiological and pathological processes. Determination of the crystal structure of an archaeal NCX (NCX_Mj) paved the way for a thorough and systematic investigation of ion transport mechanisms in NCX proteins. Here, we review the data gathered from the X-ray crystallography, molecular dynamics simulations, hydrogen-deuterium exchange mass-spectrometry (HDX-MS), and ion-flux analyses of mutants. Strikingly, the apo NCX_Mj protein exhibits characteristic patterns in the local backbone dynamics at particular helix segments, thereby possessing characteristic HDX profiles, suggesting structure-dynamic preorganization (geometric arrangements of catalytic residues before the transition state) of conserved α₁ and α₂ repeats at ion-coordinating residues involved in transport activities. Moreover, dynamic preorganization of local structural entities in the apo protein predefines the status of ion-occlusion and transition states, even though Na⁺ or Ca(2+) binding modifies the preceding backbone dynamics nearby functionally important residues. Future challenges include resolving the structural-dynamic determinants governing the ion selectivity, functional asymmetry and ion-induced alternating access. Taking into account the structural similarities of NCX_Mj with the other proteins belonging to the Ca(2+)/cation exchanger superfamily, the recent findings can significantly improve our understanding of ion transport mechanisms in NCX and similar proteins.

  13. RNA Structure Determination Using SAXS Data

    PubMed Central

    Yang, Sichun; Parisien, Marc; Major, François; Roux, Benoît

    2011-01-01

    Exploiting the experimental information from small-angle x-ray solution scattering (SAXS) in conjunction with structure prediction algorithms can be advantageous in the case of ribonucleic acids (RNA), where global restraints on the 3D fold are often lacking. Traditional usage of SAXS data often starts by attempting to reconstruct the molecular shape ab initio, which is subsequently used to assess the quality of model Here, an alternative strategy is explored whereby the models from a very large decoy set are directly sorted according to their fit to the SAXS data is developed. For rapid computation of SAXS patterns, the method developed here makes use of a coarse-grained representation of RNA. It also accounts for the explicit treatment of the contribution to the scattering of water molecules and ions surrounding the RNA. The method, called Fast-SAXS-RNA, is first calibrated using a transfer RNA (tRNA-val) and then tested on the P4-P6 fragment of group I intron (P4-P6). Fast-SAXS-RNA is then used as a filter for decoy models generated by the MC-Fold and MC-Sym pipeline, a suite of RNA 3D all-atoms structure algorithms that encode and exploit RNA 3D architectural principles. The ability of Fast-SAXS-RNA to discriminate native folds is tested against three widely used RNA molecules in molecular modeling benchmarks: the tRNA, the P4-P6, and a synthetic hairpin suspected to assemble into a homodimer. For each molecule, a large pool of decoys are generated, scored, and ranked using Fast-SAXS-RNA. The method is able to identify low-RMSD models among top ranking structures, for both tRNA and P4-P6. For the hairpin, the approach correctly identifies the dimeric state as the solution structure over the monomeric state and alternative secondary structures. The method offers a powerful strategy for recognizing native RNA conformations as well as multimeric assemblies and alternative secondary structures, thus enabling high-throughput RNA structure determination using SAXS

  14. Cyclotetraphosphinophosphonium ions: synthesis, structures, and pseudorotation.

    PubMed

    Dyker, C Adam; Riegel, Susanne D; Burford, Neil; Lumsden, Michael D; Decken, Andreas

    2007-06-13

    The first derivatives of catenated cyclotetraphosphinophosphonium cations, [(PhP)4PPhMe]+ (8a), [(MeP)4PMe2]+ (8b), [(CyP)4PPh2]+ (8d), [(CyP)4PMe2]+ (8e), [(PhP)4PPh2]+ (8f), [(PhP)4PMe2]+ (8g), are synthesized as trifluoromethanesulfonate (triflate, OSO2CF3-) salts through the reaction of cyclopentaphosphines (PhP)5 (4a) or (MeP)5 (4b) with methyl triflate (MeOTf) or by a net phosphenium ion [PR2+, R = Ph, Me; from R2PCl and trimethylsilyltriflate (Me3SiOTf)] insertion into the P-P bond of either cyclotetraphosphine (CyP)4 (3c) or cyclopentaphosphines (PhP)5 (4a) or (MeP)5 (4b). Although more conveniently prepared from 4a, compound 8a[OTf] can also be formed from (PhP)4 (3a) and MeOTf, and derivatives 8f[OTf] and 8g[OTf] are also accessible through reactions of 3a and R2PCl/Me3SiOTf with R = Ph or Me, respectively. A tetrachlorogallate salt of [(PhP)4PPhtBu]+ (8c) has been synthesized by alkylation of 4a with tBuCl/GaCl3. 31P[1H] NMR parameters for all derivatives of 8 have been determined by iterative simulation of experimental data. Derivatives 8a[OTf], 8b[OTf], 8c[GaCl4], 8e[OTf], 8f[OTf], and 8g[OTf] and have been characterized by X-ray crystallography, showing the most favorable all-trans configuration of substituents for the phosphine centers, thus minimizing steric interactions. Each derivative adopts a unique envelope or twist conformation of C1 symmetry. The effective C2 symmetry observed for 8b, d, e, f, and g in solution, signified by their 31P[1H] NMR AA'BB'X spin systems, implies a rapid conformational exchange for derivatives of 8. The core frameworks of the cations in the solid state are viewed as snapshots of different conformational isomers within the solution-phase pseudorotation process.

  15. Structural Dynamics of Native-Like Ions in the Gas Phase: Results from Tandem Ion Mobility of Cytochrome c.

    PubMed

    Allen, Samuel J; Eaton, Rachel M; Bush, Matthew F

    2017-07-18

    Ion mobility (IM) is a gas-phase separation technique that is used to determine the collision cross sections of native-like ions of proteins and protein complexes, which are in turn used as restraints for modeling the structures of those analytes in solution. Here, we evaluate the stability of native-like ions using tandem IM experiments implemented using structures for lossless ion manipulations (SLIM). In this implementation of tandem IM, ions undergo a first dimension of IM up to a switch that is used to selectively transmit ions of a desired mobility. Selected ions are accumulated in a trap and then released after a delay to initiate the second dimension of IM. For delays ranging from 16 to 33 231 ms, the collision cross sections of native-like, 7+ cytochrome c ions increase monotonically from 15.1 to 17.1 nm(2). The largest products formed in these experiments at near-ambient temperature are still far smaller than those formed in energy-dependent experiments (∼21 nm(2)). However, the collision cross section increases by ∼2% between delay times of 16 and 211 ms, which may have implications for other IM experiments on these time scales. Finally, two subpopulations from the full population were each mobility selected and analyzed as a function of delay time, showing that the three populations can be differentiated for at least 1 s. Together, these results suggest that elements of native-like structure can have long lifetimes at near-ambient temperature in the gas phase but that gas-phase dynamics should be considered when interpreting results from IM.

  16. Determination of ion track radii in amorphous matrices via formation of nano-clusters by ion-beam irradiation

    SciTech Connect

    Buljan, M.; Karlusic, M.; Bogdanovic-Radovic, I.; Jaksic, M.; Radic, N.; Salamon, K.; Bernstorff, S.

    2012-09-03

    We report on a method for the determination of ion track radii, formed in amorphous materials by ion-beam irradiation. The method is based on the addition to an amorphous matrix of a small amount of foreign atoms, which easily diffuse and form clusters when the temperature is sufficiently increased. The irradiation causes clustering of these atoms, and the final separations of the formed clusters are dependent on the parameters of the ion-beam. Comparison of the separations between the clusters that are formed by ions with different properties in the same type of material enables the determination of ion-track radii.

  17. Determination of ion track radii in amorphous matrices via formation of nano-clusters by ion-beam irradiation

    NASA Astrophysics Data System (ADS)

    Buljan, M.; Karlušić, M.; Bogdanović-Radović, I.; Jakšić, M.; Salamon, K.; Bernstorff, S.; Radić, N.

    2012-09-01

    We report on a method for the determination of ion track radii, formed in amorphous materials by ion-beam irradiation. The method is based on the addition to an amorphous matrix of a small amount of foreign atoms, which easily diffuse and form clusters when the temperature is sufficiently increased. The irradiation causes clustering of these atoms, and the final separations of the formed clusters are dependent on the parameters of the ion-beam. Comparison of the separations between the clusters that are formed by ions with different properties in the same type of material enables the determination of ion-track radii.

  18. Simulation analysis for ion assisted fast ignition using structured targets

    NASA Astrophysics Data System (ADS)

    Sakagami, H.; Johzaki, T.; Sunahara, A.; Nagatomo, H.

    2016-05-01

    As the heating efficiency by fast electrons in the fast ignition scheme is estimated to be very low due to their large divergence angle and high energy. To mitigate this problem, low-density plastic foam, which can generate not only proton (H+) but also carbon (C6+) beams, can be introduced to currently used cone-guided targets and additional core heating by ions is expected. According to 2D PIC simulations, it is found that the ion beams also diverge by the static electric field and concave surface deformation. Thus structured targets are suggested to optimize ion beam characteristics, and their improvement and core heating enhancement by ion beams are confirmed.

  19. Ion Trapping, Storage, and Ejection in Structures for Lossless Ion Manipulations

    SciTech Connect

    Zhang, Xinyu; Garimella, Venkata BS; Prost, Spencer A.; Webb, Ian K.; Chen, Tsung-Chi; Tang, Keqi; Tolmachev, Aleksey V.; Norheim, Randolph V.; Baker, Erin Shammel; Anderson, Gordon A.; Ibrahim, Yehia M.; Smith, Richard D.

    2015-06-16

    A structure for lossless ion manipulation (SLIM) module was constructed with electrode arrays patterned on a pair of parallel printed circuit boards (PCB) separated by 5 mm and utilized to investigate capabilities for ion trapping at 4 Torr. Positive ions were confined by application of RF having alternating phases on a series of inner rung electrodes and by positive DC potentials on surrounding guard electrodes on each PCB. An axial DC field was also introduced by stepwise varying the DC potential of the inner rung electrodes so as to control the ion transport and accumulation inside the ion trap. We show that ions could be trapped and accumulated with 100% efficiency, stored for at least 5 hours with no losses, and could be rapidly ejected from the SLIM trap.

  20. Ion Trapping, Storage, and Ejection in Structures for Lossless Ion Manipulations

    PubMed Central

    Zhang, Xinyu; Garimella, Sandilya V. B.; Prost, Spencer A; Webb, Ian K; Chen, Tsung-Chi; Tang, Keqi; Tohnachev, Aleksey V.; Norheim, Randolph V.; Baker, Erin S.; Anderson, Gordon A; Ibrahim, Yehia M.; Smith, Richard D.

    2015-01-01

    A new Structures for Lossless lon Manipulations (SUM) module, having electrode arrays patterned on a pair of parallel printed circuit boards (PCB), was constructed and utilized to investigate capabilities for ion trapping at a pressure of 4 Torr. Positive ions were confined by application of RF voltages to a series of inner rung electrodes with alternating phase on adjacent electrodes, in conjunction with positive DC potentials on surrounding guard electrodes on each PCB. An axial DC :field was also introduced by stepwise varying the DC potentials applied to the inner rung electrodes to control the ion transport and accumulation inside the ion trapping region. We show that ions can be trapped and accumulated with up to 100% efficiency, stored for at least 5 h with no significant losses, and then could be rapidly ejected from the SUM trap. The present results provide a foundation for the development of much more complex SUM devices that facilitate extended ion manipulations. PMID:25971536

  1. Ion Trapping, Storage, and Ejection in Structures for Lossless Ion Manipulations

    DOE PAGES

    Zhang, Xinyu; Garimella, Sandilya V. B.; Prost, Spencer A.; ...

    2015-06-14

    Here, a structure for lossless ion manipulation (SLIM) module was constructed with electrode arrays patterned on a pair of parallel printed circuit boards (PCB) separated by 5 mm and utilized to investigate capabilities for ion trapping at 4 Torr. Positive ions were confined by application of RF having alternating phases on a series of inner rung electrodes and by positive DC potentials on surrounding guard electrodes on each PCB. An axial DC field was also introduced by stepwise varying the DC potential of the inner rung electrodes so as to control the ion transport and accumulation inside the ion trap.more » We show that ions could be trapped and accumulated with 100% efficiency, stored for at least 5 hours with no losses, and could be rapidly ejected from the SLIM trap.« less

  2. Ion Trapping, Storage, and Ejection in Structures for Lossless Ion Manipulations

    SciTech Connect

    Zhang, Xinyu; Garimella, Sandilya V. B.; Prost, Spencer A.; Webb, Ian K.; Chen, Tsung-Chi; Tang, Keqi; Tolmachev, Aleksey V.; Norheim, Randolph V.; Baker, Erin S.; Anderson, Gordon A.; Ibrahim, Yehia M.; Smith, Richard D.

    2015-06-14

    Here, a structure for lossless ion manipulation (SLIM) module was constructed with electrode arrays patterned on a pair of parallel printed circuit boards (PCB) separated by 5 mm and utilized to investigate capabilities for ion trapping at 4 Torr. Positive ions were confined by application of RF having alternating phases on a series of inner rung electrodes and by positive DC potentials on surrounding guard electrodes on each PCB. An axial DC field was also introduced by stepwise varying the DC potential of the inner rung electrodes so as to control the ion transport and accumulation inside the ion trap. We show that ions could be trapped and accumulated with 100% efficiency, stored for at least 5 hours with no losses, and could be rapidly ejected from the SLIM trap.

  3. Characterization of Traveling Wave Ion Mobility Separations in Structures for Lossless Ion Manipulations

    DOE PAGES

    Hamid, Ahmed M.; Ibrahim, Yehia M.; Garimella, Venkata BS; ...

    2015-10-28

    We report on the development and characterization of a new traveling wave-based Structure for Lossless Ion Manipulations (TW-SLIM) for ion mobility separations (IMS). The TW-SLIM module uses parallel arrays of rf electrodes on two closely spaced surfaces for ion confinement, where the rf electrodes are separated by arrays of short electrodes, and using these TWs can be created to drive ion motion. In this initial work, TWs are created by the dynamic application of dc potentials. The capabilities of the TW-SLIM module for efficient ion confinement, lossless ion transport, and ion mobility separations at different rf and TW parameters aremore » reported. The TW-SLIM module is shown to transmit a wide mass range of ions (m/z 200–2500) utilizing a confining rf waveform (~1 MHz and ~300 Vp-p) and low TW amplitudes (<20 V). Additionally, the short TW-SLIM module achieved resolutions comparable to existing commercially available low pressure IMS platforms and an ion mobility peak capacity of ~32 for TW speeds of <210 m/s. TW-SLIM performance was characterized over a wide range of rf and TW parameters and demonstrated robust performance. In conclusion, the combined attributes of the flexible design and low voltage requirements for the TW-SLIM module provide a basis for devices capable of much higher resolution and more complex ion manipulations.« less

  4. Characterization of Traveling Wave Ion Mobility Separations in Structures for Lossless Ion Manipulations

    SciTech Connect

    Hamid, Ahmed M.; Ibrahim, Yehia M.; Garimella, Venkata BS; Webb, Ian K.; Deng, Liulin; Chen, Tsung-Chi; Anderson, Gordon A.; Prost, Spencer A.; Norheim, Randolph V.; Tolmachev, Aleksey V.; Smith, Richard D.

    2015-10-28

    We report on the development and characterization of a new traveling wave-based Structure for Lossless Ion Manipulations (TW-SLIM) for ion mobility separations (IMS). The TW-SLIM module uses parallel arrays of rf electrodes on two closely spaced surfaces for ion confinement, where the rf electrodes are separated by arrays of short electrodes, and using these TWs can be created to drive ion motion. In this initial work, TWs are created by the dynamic application of dc potentials. The capabilities of the TW-SLIM module for efficient ion confinement, lossless ion transport, and ion mobility separations at different rf and TW parameters are reported. The TW-SLIM module is shown to transmit a wide mass range of ions (m/z 200–2500) utilizing a confining rf waveform (~1 MHz and ~300 Vp-p) and low TW amplitudes (<20 V). Additionally, the short TW-SLIM module achieved resolutions comparable to existing commercially available low pressure IMS platforms and an ion mobility peak capacity of ~32 for TW speeds of <210 m/s. TW-SLIM performance was characterized over a wide range of rf and TW parameters and demonstrated robust performance. In conclusion, the combined attributes of the flexible design and low voltage requirements for the TW-SLIM module provide a basis for devices capable of much higher resolution and more complex ion manipulations.

  5. Characterization of Traveling Wave Ion Mobility Separations in Structures for Lossless Ion Manipulations.

    PubMed

    Hamid, Ahmed M; Ibrahim, Yehia M; Garimella, Sandilya V B; Webb, Ian K; Deng, Liulin; Chen, Tsung-Chi; Anderson, Gordon A; Prost, Spencer A; Norheim, Randolph V; Tolmachev, Aleksey V; Smith, Richard D

    2015-11-17

    We report on the development and characterization of a traveling wave (TW)-based Structures for Lossless Ion Manipulations (TW-SLIM) module for ion mobility separations (IMS). The TW-SLIM module uses parallel arrays of rf electrodes on two closely spaced surfaces for ion confinement, where the rf electrodes are separated by arrays of short electrodes, and using these TWs can be created to drive ion motion. In this initial work, TWs are created by the dynamic application of dc potentials. The capabilities of the TW-SLIM module for efficient ion confinement, lossless ion transport, and ion mobility separations at different rf and TW parameters are reported. The TW-SLIM module is shown to transmit a wide mass range of ions (m/z 200-2500) utilizing a confining rf waveform (∼1 MHz and ∼300 Vp-p) and low TW amplitudes (<20 V). Additionally, the short TW-SLIM module achieved resolutions comparable to existing commercially available low pressure IMS platforms and an ion mobility peak capacity of ∼32 for TW speeds of <210 m/s. TW-SLIM performance was characterized over a wide range of rf and TW parameters and demonstrated robust performance. The combined attributes of the flexible design and low voltage requirements for the TW-SLIM module provide a basis for devices capable of much higher resolution and more complex ion manipulations.

  6. Recent progress and applications of ion-exclusion/ion-exchange chromatography for simultaneous determination of inorganic anions and cations.

    PubMed

    Nakatani, Nobutake; Kozaki, Daisuke; Mori, Masanobu; Tanaka, Kazuhiko

    2012-01-01

    One of the ultimate goals of ion chromatography is to determine both anions and cations found in samples with a single chromatographic run. In the present article, recent progress in ion-exclusion/ion-exchange chromatography for the simultaneous determinations of inorganic anions and cations are reviewed. Firstly, the principle and the control for the simultaneous separation and detection of analyte ions using ion-exclusion/cation-exchange chromatography with a weakly acidic cation-exchange column are outlined. Then, advanced chromatographic techniques in terms of analytical time, selectively and sensitivity are summarized. As a related method, ion-exclusion/anion-exchange chromatography with an anion-exchange column could be used for the simultaneous determination of inorganic nitrogen species, such as ammonium, nitrite and nitrate ions. Their usefulness and applications to water-quality monitoring and related techniques are also described.

  7. Facet-dependent stripping behavior of Cu2O microcrystals toward lead ions: a rational design for the determination of lead ions.

    PubMed

    Liu, Zhong-Gang; Sun, Yu-Feng; Chen, Wen-Kai; Kong, Yuan; Jin, Zhen; Chen, Xing; Zheng, Xiao; Liu, Jin-Huai; Huang, Xing-Jiu; Yu, Shu-Hong

    2015-06-03

    Facet-dependent stripping behavior in the determination of Pb(II): Well-defined Cu2O microcrystals with different structures show facet-dependent electrochemical behaviors toward heavy metal ions. This provides an important insight into the understanding the efficiency of facet-dependent properties of microcrystals on electroanalytical performance for the rational design of electrochemical analytical techniques for efficient detection of heavy metal ions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Naked-eye sensor for rapid determination of mercury ion.

    PubMed

    Liu, Jing; Wu, Dapeng; Yan, Xiaohui; Guan, Yafeng

    2013-11-15

    A naked-eye paper sensor for rapid determination of trace mercury ion in water samples was designed and demonstrated. The mercury-sensing rhodamine B thiolactone was immobilized in silica matrices and the silica matrices were impregnated firmly and uniformly in the filter paper. As water samples flow through the filter paper, the membrane color will change from white to purple red, which could be observed obviously with naked eye, when concentration of mercury ions equals to or exceeds 10nM, the maximum residue level in drinking water recommended by U.S. EPA. The color change can also be recorded by a flatbed scanner and then digitized, reducing the detection limit of Hg(2+) down to 1.2 nM. Moreover, this method is extremely specific for Hg(2+) and shows a high tolerance ratio of interferent coexisting ions. The presence of Na(+) (2 mM), K(+) (2 mM), Fe(3+) (0.1 mM), Zn(2+) (0.1 mM), Mg(2+) (0.1 mM), Ni(2+) (50 μM), Co(2+) (50 μM), Cd(2+) (50 μM), Pb(2+) (50 μM), Cu(2+) (50 μM) and Ag(+) (3.5 μM) did not interfere with the detection of Hg(2+) (25 nM). Finally, the present method was applied in the detection of Hg(2+) in mineral water, tap water and pond water.

  9. Structures, Lewis Acidities, Electrophilicities, and Protecting Group Abilities of Phenylfluorenylium and Tritylium Ions.

    PubMed

    Follet, Elsa; Mayer, Peter; Berionni, Guillaume

    2017-01-12

    The isolation, characterization, and the first X-ray structures of a fluorenylium ion and its Lewis adducts with nitrogen- and phosphorus-centered Lewis bases are reported. Kinetics of the reactions of a series of fluorenylium ions with reference π-, σ-, and n-nucleophiles of various sizes and nucleophilicities allowed the interplay between electronic and structural parameters on the electrophilicities of these planarized tertiary carbenium ions to be elucidated. Structure-reactivity correlations and extensive comparisons of their reactivities with those of di- and triarylcarbenium ions are described. Quantitative determination of the electrofugalities of fluorenylium ions revealed to which extent they are complementing tritylium ions as protecting groups and how their tuning is possible. Determination of the equilibrium constants of the Lewis adducts formation between pyridines of calibrated Lewis basicities and phenylfluorenylium and tritylium ions allowed the determination of their Lewis acidities and to showcase the potential of these carbon-centered Lewis acids in catalysis. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Method for fabricating MNOS structures utilizing hydrogen ion implantation

    NASA Astrophysics Data System (ADS)

    Saks, N. S.

    1984-05-01

    An improved method for reducing the density of electronic trapping states and fixed insulator charge in the thin oxide layer of an MNOS structure is discussed. The method includes the steps of implanting hydrogen ions in field region of the oxide layer and annealing the MNOS structure at 400 deg C to cause the ions to diffuse laterally into the gate region of the oxide layer.

  11. Structural Metals in the Group I Intron: A Ribozyme with a Multiple Metal Ion Core

    SciTech Connect

    Stahley,M.; Adams, P.; Wang, J.; Strobel, S.

    2007-01-01

    Metal ions play key roles in the folding and function for many structured RNAs, including group I introns. We determined the X-ray crystal structure of the Azoarcus bacterial group I intron in complex with its 5' and 3' exons. In addition to 222 nucleotides of RNA, the model includes 18 Mg2+ and K+ ions. Five of the metals bind within 12 Angstroms of the scissile phosphate and coordinate the majority of the oxygen atoms biochemically implicated in conserved metal-RNA interactions. The metals are buried deep within the structure and form a multiple metal ion core that is critical to group I intron structure and function. Eight metal ions bind in other conserved regions of the intron structure, and the remaining five interact with peripheral structural elements. Each of the 18 metals mediates tertiary interactions, facilitates local bends in the sugar-phosphate backbone or binds in the major groove of helices. The group I intron has a rich history of biochemical efforts aimed to identify RNA-metal ion interactions. The structural data are correlated to the biochemical results to further understand the role of metal ions in group I intron structure and function.

  12. [Determination of hydrazine ion in explosion dust of liquid explosive by ion chromatography].

    PubMed

    Wang, Yong; Geng, Qing; Zuo, Yuexian; Zhou, Xinwen; Lian, Hongzhen; Pan, Guangwen

    2013-09-01

    A method for the determination of hydrazine ion in explosion dust of liquid explosive has been established by ion chromatography. The hydrazine ion in an explosion dust sample was extracted with deionized water by sonification and centrifugation. The large molecules and solid particles in supernatant were removed by an OnGuard II RP column and a 0.22 microm filtration membrane, respectively. The filtrate was separated on an IonPac CS-12A column with isocratic elution of 5 mmol/L methanesulfonic acid (MSA). Then 0.1 mol/L NaOH solution was post-column added and the resultant solution was detected by an ampere detector with golden electrode. The results showed that, the calibration curve was linear in the range of 0.02 - 2.0 mg/L with a correlation coefficient (r2 ) of 0.999 7. The limits of detection (LOD, S/N = 3) and quantification (LOQ, S/N = 10) of hydrazine were 5.0 microg/L and 16.6 microg/L, respectively. The recoveries ranged between 95.4% and 99.1% with the relative standard deviations (RSDs, n = 5) of 2.1% - 3.3%. The hydrazine content in a real explosion dust sample of liquid explosive was 10.3 mg/kg by this method. The method is simple, accurate, and suitable for the quantitative detection of hydrazine ions in explosion dust of liquid explosive, and the method can meet the needs of the criminal evidence identification work.

  13. Spiking structure of amplitude characteristics for ion trajectories in hyperboloidal mass spectrometers: the theory.

    PubMed

    Sheretov, Ernst P; Philippov, Igor V; Karnav, Tatiana B; Kolotilin, Boris I; Ivanov, Vladimir W

    2002-01-01

    We present a theory that describes a 'spiking' structure of the amplitude characteristics for trajectories of ions within a hyperboloidal mass spectrometer (HMS) discovered and reported recently. This effect, as well as modulation parametric resonance, relates directly to a fine structure of the stability diagram for a HMS. A method of extremum characteristic solutions of the Hill equation (developed in our laboratory earlier) has been used in this work. Simple expressions determined the shape of narrow dips (or reversed peaks) in the amplitude of ion oscillation versus stability parameter curves and conditions of their appearance are presented. The results that were calculated from analytical expressions are compared with those obtained from direct computations of ion trajectories in a HMS. This effect with respect to a nature of 'black holes' or 'black canyons' observed earlier in investigations of trapping efficiency and ion trapping within ion traps is discussed.

  14. Determination of water-soluble atmospheric aerosols using ion chromatography.

    PubMed

    Fosco, Tinamarie; Schmeling, Martina

    2007-07-01

    A field study was established to investigate the chemical composition of atmospheric aerosols in Chicago, IL. One goal of this study was to determine the influence of precursor trace gases and local meteorology on concentrations of secondary aerosol ionic species. This paper describes the method details, shows the method is analytically valid, and reports overall as well as some specific results found during the field study. Two particulate air samples were collected per day onto quartz fiber filters at the Loyola University Chicago Air Station during the summer months in 2002-2004. In parallel, mixing ratios of ozone and nitrogen oxides were monitored and weather parameters were recorded. Particulates were extracted from the filter substrates and the subsequent solutions were analyzed by ion chromatography for anions, including low molecular weight organic acids, and cations. A washing procedure was implemented to reduce the high background values of the quartz fiber filters. Method validation showed that the collection method was efficient for all ions with exception of nitrate, whose efficiency of 70% indicated losses caused by volatilization. The extraction method also proved efficient for both field and laboratory samples, and the repeatability of the method was high with relative standard deviations less than 10% for all ions. Reproducibility of the results was determined by comparison of sulfate to sulfur analyzed by total reflection X-ray fluorescence spectrometry and proved to be high as well. Concentrations differed significantly between the three summer studies due to varying levels of precursor species as a consequence of distinct temperatures and wind direction profiles.

  15. Focused Ion Beam Fabrication of Microelectronic Structures

    DTIC Science & Technology

    1990-12-01

    writ- (5400 A thick, - 50 at. % Au), pumping out the organome- ing across preevaporated metal (Au, W, AL, and NiCr ) con- tallic gas and then sputtering ...surface interaction is multifaceted. Energetic ions (the relevant range in this field has been 1-300 keV) incident on a surface will: a) sputter off...main commercial applications of these columns, namely, photomask repair and integrated circuit restructuring, diagnostics and repair, exploit sputtering

  16. A method for the determination of potentiometric selectivity coefficients of ion selective electrodes in the presence of several interfering ions.

    PubMed

    Deyhimi, F

    1999-12-06

    In this work a new method is reported for the determination of potentiometric selectivity coefficients of ion-selective electrode in which, similar to real samples, several interfering ions are simultaneously present in test solutions and where the electrode shows its practical behavior. In order to illustrate this method, the potentiometric selectivity coefficients of a commercial liquid membrane ammonium selective electrode is determined for biologically important interfering ions: Li(+), Na(+) and K(+).

  17. Mobility-Selected Ion Trapping and Enrichment Using Structures for Lossless Ion Manipulations

    SciTech Connect

    Chen, Tsung-Chi; Ibrahim, Yehia M.; Webb, Ian K.; Garimella, Sandilya V. B.; Zhang, Xing; Hamid, Ahmed M.; Deng, Liulin; Karnesky, William E.; Prost, Spencer A.; Sandoval, Jeremy A.; Norheim, Randolph V.; Anderson, Gordon A.; Tolmachev, Aleksey V.; Baker, Erin Shammel; Smith, Richard D.

    2016-01-11

    The integration of ion mobility spectrometry (IMS) with mass spectrometry (MS) and the ability to trap ions in IMS-MS measurements is of great importance for performing reactions, accumulating ions, and increasing analytical measurement sensitivity. The development of Structures for Lossless Ion Manipulations (SLIM) offers the potential for ion manipulations in a more reliable and cost-effective manner, while opening opportunities for much more complex sequences of manipulations. Here, we demonstrate an ion separation and trapping module and a method based upon SLIM that consists of a linear mobility ion drift region, a switch/tee and a trapping region that allows the isolation and accumulation of mobility-separated species. The operation and optimization of the SLIM switch/tee and trap are described and demonstrated for the enrichment of the low abundance ions. Lastly, we observed a linear increase in ion intensity with the number of trapping/accumulation events using the SLIM trap, illustrating its potential for enhancing the sensitivity of low abundance or targeted species.

  18. Simulation of Electric Potentials and Ion Motion in Planar Electrode Structures for Lossless Ion Manipulations (SLIM)

    SciTech Connect

    Garimella, Sandilya V. B; Ibrahim, Yehia M.; Webb, Ian K.; Tolmachev, Aleksey V.; Zhang, Xinyu; Prost, Spencer A.; Anderson, Gordon A.; Smith, Richard D.

    2014-09-26

    Here we report a conceptual study and computational evaluation of novel planar electrode Structures for Lossless Ion Manipulations (SLIM). Planar electrode SLIM devices were designed that allow for flexible ion confinement, transport and storage using a combination of RF and DC fields. Effective potentials can be generated that provide near ideal regions for confining ions in the presence of a gas. Ion trajectory simulations using SIMION 8.1 demonstrated the capability for lossless ion motion in these devices over a wide m/z range and a range of electric fields at low pressures (e.g. a few torr). More complex ion manipulations, e.g. turning ions by 90° and dynamically switching selected ion species into orthogonal channels, are also feasible. Lastly, the performance of SLIM devices at ~4 torr pressure for performing ion mobility based separations (IMS) is computationally evaluated and compared to initial experimental results, and both of which agree closely with experimental and theoretical IMS performance for a conventional drift tube design.

  19. Simulation of Electric Potentials and Ion Motion in Planar Electrode Structures for Lossless Ion Manipulations (SLIM)

    PubMed Central

    Garimella, Sandilya V.B.; Ibrahim, Yehia M.; Webb, Ian K.; Tolmachev, Aleksey V.; Zhang, Xinyu; Prost, Spencer A.; Anderson, Gordon A.; Smith, Richard D.

    2014-01-01

    We report a conceptual study and computational evaluation of novel planar electrode Structures for Lossless Ion Manipulations (SLIM). Planar electrode SLIM devices were designed that allow for flexible ion confinement, transport and storage using a combination of RF and DC fields. Effective potentials can be generated that provide near ideal regions for confining and manipulating ions in the presence of a gas. Ion trajectory simulations using SIMION 8.1 demonstrated the capability for lossless ion motion in these devices over a wide m/z range and a range of electric fields at low pressures (e.g. a few torr). More complex ion manipulations, e.g. turning ions by 90° and dynamically switching selected ion species into orthogonal channels, are also shown feasible. The performance of SLIM devices at ~4 torr pressure for performing ion mobility based separations (IMS) is computationally evaluated and compared to initial experimental results, and both of which are also shown to agree closely with experimental and theoretical IMS performance for a conventional drift tube design. PMID:25257188

  20. Mobility-Selected Ion Trapping and Enrichment Using Structures for Lossless Ion Manipulations.

    PubMed

    Chen, Tsung-Chi; Ibrahim, Yehia M; Webb, Ian K; Garimella, Sandilya V B; Zhang, Xing; Hamid, Ahmed M; Deng, Liulin; Karnesky, William E; Prost, Spencer A; Sandoval, Jeremy A; Norheim, Randolph V; Anderson, Gordon A; Tolmachev, Aleksey V; Baker, Erin S; Smith, Richard D

    2016-02-02

    The integration of ion mobility spectrometry (IMS) with mass spectrometry (MS) and the ability to trap ions in IMS-MS measurements is of great importance for performing reactions, accumulating ions, and increasing analytical measurement sensitivity. The development of Structures for Lossless Ion Manipulations (SLIM) offers the potential for ion manipulations in an extended and more effective manner, while opening opportunities for many more complex sequences of manipulations. Here, we demonstrate an ion separation and trapping module and a method based upon SLIM that consists of a linear mobility ion drift region, a switch/tee and a trapping region that allows the isolation and accumulation of mobility-separated species. The operation and optimization of the SLIM switch/tee and trap are described and demonstrated for the enrichment of the low abundance ions. A linear improvement in ion intensity was observed with the number of trapping/accumulation events using the SLIM trap, illustrating its potential for enhancing the sensitivity of low abundance or targeted species.

  1. Simulation of electric potentials and ion motion in planar electrode structures for lossless ion manipulations (SLIM).

    PubMed

    Garimella, Sandilya V B; Ibrahim, Yehia M; Webb, Ian K; Tolmachev, Aleksey V; Zhang, Xinyu; Prost, Spencer A; Anderson, Gordon A; Smith, Richard D

    2014-11-01

    We report a conceptual study and computational evaluation of novel planar electrode structures for lossless ion manipulations (SLIM). Planar electrode SLIM components were designed that allow for flexible ion confinement, transport, and storage using a combination of radio frequency (rf) and DC fields. Effective potentials can be generated that provide near ideal regions for confining and manipulating ions in the presence of a gas. Ion trajectory simulations using SIMION 8.1 demonstrated the capability for lossless ion motion in these devices over a wide m/z range and a range of electric fields at low pressures (e.g., a few Torr). More complex ion manipulations (e.g., turning ions by 90(o) and dynamically switching selected ion species into orthogonal channels) are also shown feasible. The performance of SLIM devices at ~4 Torr pressure for performing ion mobility-based separations (IMS) is computationally evaluated and compared with initial experimental results, and both are also shown to agree closely with experimental and theoretical IMS performance for a conventional drift tube design.

  2. Mobility-Selected Ion Trapping and Enrichment Using Structures for Lossless Ion Manipulations

    DOE PAGES

    Chen, Tsung-Chi; Ibrahim, Yehia M.; Webb, Ian K.; ...

    2016-01-11

    The integration of ion mobility spectrometry (IMS) with mass spectrometry (MS) and the ability to trap ions in IMS-MS measurements is of great importance for performing reactions, accumulating ions, and increasing analytical measurement sensitivity. The development of Structures for Lossless Ion Manipulations (SLIM) offers the potential for ion manipulations in a more reliable and cost-effective manner, while opening opportunities for much more complex sequences of manipulations. Here, we demonstrate an ion separation and trapping module and a method based upon SLIM that consists of a linear mobility ion drift region, a switch/tee and a trapping region that allows the isolationmore » and accumulation of mobility-separated species. The operation and optimization of the SLIM switch/tee and trap are described and demonstrated for the enrichment of the low abundance ions. Lastly, we observed a linear increase in ion intensity with the number of trapping/accumulation events using the SLIM trap, illustrating its potential for enhancing the sensitivity of low abundance or targeted species.« less

  3. Simulation of Electric Potentials and Ion Motion in Planar Electrode Structures for Lossless Ion Manipulations (SLIM)

    DOE PAGES

    Garimella, Sandilya V. B; Ibrahim, Yehia M.; Webb, Ian K.; ...

    2014-09-26

    Here we report a conceptual study and computational evaluation of novel planar electrode Structures for Lossless Ion Manipulations (SLIM). Planar electrode SLIM devices were designed that allow for flexible ion confinement, transport and storage using a combination of RF and DC fields. Effective potentials can be generated that provide near ideal regions for confining ions in the presence of a gas. Ion trajectory simulations using SIMION 8.1 demonstrated the capability for lossless ion motion in these devices over a wide m/z range and a range of electric fields at low pressures (e.g. a few torr). More complex ion manipulations, e.g.more » turning ions by 90° and dynamically switching selected ion species into orthogonal channels, are also feasible. Lastly, the performance of SLIM devices at ~4 torr pressure for performing ion mobility based separations (IMS) is computationally evaluated and compared to initial experimental results, and both of which agree closely with experimental and theoretical IMS performance for a conventional drift tube design.« less

  4. Structural resolution of 4-substituted proline diastereomers with ion mobility spectrometry via alkali metal ion cationization.

    PubMed

    Flick, Tawnya G; Campuzano, Iain D G; Bartberger, Michael D

    2015-03-17

    The chirality of substituents on an amino acid can significantly change its mode of binding to a metal ion, as shown here experimentally by traveling wave ion mobility spectrometry-mass spectrometry (TWIMS-MS) of different proline isomeric molecules complexed with alkali metal ions. Baseline separation of the cis- and trans- forms of both hydroxyproline and fluoroproline was achieved using TWIMS-MS via metal ion cationization (Li(+), Na(+), K(+), and Cs(+)). Density functional theory calculations indicate that differentiation of these diastereomers is a result of the stabilization of differing metal-complexed forms adopted by the diastereomers when cationized by an alkali metal cation, [M + X](+) where X = Li, Na, K, and Cs, versus the topologically similar structures of the protonated molecules, [M + H](+). Metal-cationized trans-proline variants exist in a linear salt-bridge form where the metal ion interacts with a deprotonated carboxylic acid and the proton is displaced onto the nitrogen atom of the pyrrolidine ring. In contrast, metal-cationized cis-proline variants adopt a compact structure where the carbonyl of the carboxylic acid, nitrogen atom, and if available, the hydroxyl and fluorine substituent solvate the metal ion. Experimentally, it was observed that the resolution between alkali metal-cationized cis- and trans-proline variants decreases as the size of the metal ion increases. Density functional theory demonstrates that this is due to the decreasing stability of the compact charge-solvated cis-proline structure with increased metal ion radius, likely a result of steric hindrance and/or weaker binding to the larger metal ion. Furthermore, the unique structures adopted by the alkali metal-cationized cis- and trans-proline variants results in these molecules having significantly different quantum mechanically calculated dipole moments, a factor that can be further exploited to improve the diastereomeric resolution when utilizing a drift gas with a

  5. Determinants of Glycosaminoglycan (GAG) Structure

    PubMed Central

    Prydz, Kristian

    2015-01-01

    Proteoglycans (PGs) are glycosylated proteins of biological importance at cell surfaces, in the extracellular matrix, and in the circulation. PGs are produced and modified by glycosaminoglycan (GAG) chains in the secretory pathway of animal cells. The most common GAG attachment site is a serine residue followed by a glycine (-ser-gly-), from which a linker tetrasaccharide extends and may continue as a heparan sulfate, a heparin, a chondroitin sulfate, or a dermatan sulfate GAG chain. Which type of GAG chain becomes attached to the linker tetrasaccharide is influenced by the structure of the protein core, modifications occurring to the linker tetrasaccharide itself, and the biochemical environment of the Golgi apparatus, where GAG polymerization and modification by sulfation and epimerization take place. The same cell type may produce different GAG chains that vary, depending on the extent of epimerization and sulfation. However, it is not known to what extent these differences are caused by compartmental segregation of protein cores en route through the secretory pathway or by differential recruitment of modifying enzymes during synthesis of different PGs. The topic of this review is how different aspects of protein structure, cellular biochemistry, and compartmentalization may influence GAG synthesis. PMID:26308067

  6. Sensitivity of the interpretation of the experimental ion thermal diffusivity to the determination of the ion conductive heat flux

    SciTech Connect

    Stacey, W. M.

    2014-04-15

    A moments equation formalism for the interpretation of the experimental ion thermal diffusivity from experimental data is used to determine the radial ion thermal conduction flux that must be used to interpret the measured data. It is shown that the total ion energy flux must be corrected for thermal and rotational energy convection, for the work done by the flowing plasma against the pressure and viscosity, and for ion orbit loss of particles and energy, and expressions are presented for these corrections. Each of these factors is shown to have a significant effect on the interpreted ion thermal diffusivity in a representative DIII-D [J. Luxon, Nucl. Fusion 42, 614 (2002)] discharge.

  7. Structure Determination of Natural Products by Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Biemann, Klaus

    2015-07-01

    I review laboratory research on the development of mass spectrometric methodology for the determination of the structure of natural products of biological and medical interest, which I conducted from 1958 to the end of the twentieth century. The methodology was developed by converting small peptides to their corresponding polyamino alcohols to make them amenable to mass spectrometry, thereby making it applicable to whole proteins. The structures of alkaloids were determined by analyzing the fragmentation of a known alkaloid and then using the results to deduce the structures of related compounds. Heparin-like structures were investigated by determining their molecular weights from the mass of protonated molecular ions of complexes with highly basic, synthetic peptides. Mass spectrometry was also employed in the analysis of lunar material returned by the Apollo missions. A miniaturized gas chromatograph mass spectrometer was sent to Mars on board of the two Viking 1976 spacecrafts.

  8. Surface structure determines dynamic wetting

    PubMed Central

    Wang, Jiayu; Do-Quang, Minh; Cannon, James J.; Yue, Feng; Suzuki, Yuji; Amberg, Gustav; Shiomi, Junichiro

    2015-01-01

    Liquid wetting of a surface is omnipresent in nature and the advance of micro-fabrication and assembly techniques in recent years offers increasing ability to control this phenomenon. Here, we identify how surface roughness influences the initial dynamic spreading of a partially wetting droplet by studying the spreading on a solid substrate patterned with microstructures just a few micrometers in size. We reveal that the roughness influence can be quantified in terms of a line friction coefficient for the energy dissipation rate at the contact line, and that this can be described in a simple formula in terms of the geometrical parameters of the roughness and the line-friction coefficient of the planar surface. We further identify a criterion to predict if the spreading will be controlled by this surface roughness or by liquid inertia. Our results point to the possibility of selectively controlling the wetting behavior by engineering the surface structure. PMID:25683872

  9. Structure of apo acyl carrier protein and a proposal to engineer protein crystallization through metal ions

    SciTech Connect

    Qiu, Xiayang; Janson, Cheryl A.

    2010-11-16

    A topic of current interest is engineering surface mutations in order to improve the success rate of protein crystallization. This report explores the possibility of using metal-ion-mediated crystal-packing interactions to facilitate rational design. Escherichia coli apo acyl carrier protein was chosen as a test case because of its high content of negatively charged carboxylates suitable for metal binding with moderate affinity. The protein was successfully crystallized in the presence of zinc ions. The crystal structure was determined to 1.1 {angstrom} resolution with MAD phasing using anomalous signals from the co-crystallized Zn{sup 2+} ions. The case study suggested an integrated strategy for crystallization and structure solution of proteins via engineering surface Asp and Glu mutants, crystallizing them in the presence of metal ions such as Zn{sup 2+} and solving the structures using anomalous signals.

  10. Ion Beam Synthesis Of Metal - Silicon Carbide - Si Multilayer Structures

    NASA Astrophysics Data System (ADS)

    Lindner, J. K. N.; Tsang, W. M.; Stritzker, B.; Wong, S. P.

    2003-08-01

    High doses of Ti, Ni, Mo, or W ions were implanted at elevated temperatures either conventionally or using a MEVVA ion source into ion beam synthesized Si/SiC/Si or SiC/Si layer structures in order to create metallic layers contacting the SiC. The depth distribution of metal atoms and the formation of silicide and carbide phases as well as the formation of cavities at the lower SiC/Si interface are studied by Rutherford backscattering spectroscopy (RBS) and cross-sectional transmission electron microscopy (XTEM). A brief survey of the effects ocurring in the ion beam metallization of SiC films is given and the benefit of using ion beams for metallization of thin films is elucidated.

  11. Energy dependent track structure parametrisations for protons and carbon ions based on nanometric simulations

    NASA Astrophysics Data System (ADS)

    Alexander, Frauke; Villagrasa, Carmen; Rabus, Hans; Wilkens, Jan J.

    2015-09-01

    The BioQuaRT project within the European Metrology Research Programme aims at correlating ion track structure characteristics with the biological effects of radiation and develops measurement and simulation techniques for determining ion track structure on different length scales from about 2 nm to about 10 μm. Within this framework, we investigate methods to translate track-structure quantities derived on a nanometre scale to macroscopic dimensions. Input data sets were generated by simulations of ion tracks of protons and carbon ions in liquid water using the Geant 4 Monte Carlo toolkit with the Geant4-DNA processes. Based on the energy transfer points - recorded with nanometre resolution - we investigated parametrisations of overall properties of ion track structure. Three different track structure parametrisations have been developed using the distances to the 10 next neighbouring ionisations, the radial energy distribution and ionisation cluster size distributions. These parametrisations of nanometric track structure build a basis for deriving biologically relevant mean values which are essential in the clinical situation where each voxel is exposed to a mixed radiation field. Contribution to the Topical Issue "COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy", edited by Andrey Solov'yov, Nigel Mason, Gustavo García, Eugene Surdutovich.

  12. Ion time-of-flight determinations of doubly to singly ionized mercury ion ratios from a mercury electron bombardment discharge

    NASA Technical Reports Server (NTRS)

    Sellen, J. M., Jr.; Kemp, R. F.; Hall, D. F.

    1973-01-01

    Doubly to singly charged mercury ion ratios in electron bombardment ion thruster exhaust beams have been determined as functions of bombardment discharge potential, thrust beam current, thrust beam radial position, acceleration-deceleration voltage ratio, and propellant utilization fraction. A mathematical model for two-step ionization processes has been derived, and calculated ion ratios are compared to observed ratios. Production of Hg(++) appears to result primarily from sequential ionization of Hg(+) in the discharge. Experimental and analytical results are presented, and design, construction, and operation features of an electrostatic deflection ion time-of-flight analyzer for the determination of the above-mentioned ratios are reviewed.

  13. Extractive liquid-liquid spectrophotometric procedure for the determination of thiocyanate ions employing the ion pair reagent amiloride monohydrochloride.

    PubMed

    Bashammakh, A S; Bahaffi, S O; Al-Sibaai, A A; Al-Wael, H O; El-Shahawi, M S

    2007-05-29

    An accurate, inexpensive and less laborious liquid-liquid extractive spectrophotometric procedure for the determination of thiocyanate ions in aqueous media has been developed. The method has been based upon the formation of a yellow colored complex ion associate of the ion-pairing reagent 1-(3, 5-diamino-6-chloropyrazinecarboxyl) guanidine hydrochloride monohydrate, namely amiloride hydrochloride, DPG+.Cl- and the thiocyanate ions in aqueous media containing HNO3 (0.5 mol L(-1)) and subsequent extraction with 4-methyl-2-pentanone. The absorption electronic spectrum of the ion associate showed one well-defined peak at lambda(max) 366 nm. The stoichiometric mole ratio of DPG+.Cl- to the thiocyanate ions is 1:1. The effective molar absorptivity (epsilon) of the ion associate at lambda(max) 366 nm is 1.1+/-0.1x10(4) L mol(-1) cm(-1). The extraction constants (K(d), K(ex), and beta) enabled a simple and convenient use of the developed binary ion associate for the extractive spectrophotometric determination of traces of thiocyanate ions in the aqueous media. Beer's law and Ringbom's plots are obeyed in the concentration range 0.05-10 and 0.1-7 microg mL(-1) of the thiocyanate ions, respectively with a relative standard deviation of +/-2.3%. The calculated lower limits of detection (LOD) and quantitation (LOQ) of the developed procedure for the thiocyanate ions were found equal to 0.02 and 0.066 microg mL(-1), respectively. The developed method has been applied for the determination of trace amounts of thiocyanate ions in tap-, waste- and natural water samples and compared successfully with the reported methods at the 95% confidence level. The proposed method was also applied successfully for the determination of thiocyanate ions in saliva samples.

  14. Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels

    PubMed Central

    Sauguet, Ludovic; Poitevin, Frédéric; Murail, Samuel; Van Renterghem, Catherine; Moraga-Cid, Gustavo; Malherbe, Laurie; Thompson, Andrew W; Koehl, Patrice; Corringer, Pierre-Jean; Baaden, Marc; Delarue, Marc

    2013-01-01

    To understand the molecular mechanism of ion permeation in pentameric ligand-gated ion channels (pLGIC), we solved the structure of an open form of GLIC, a prokaryotic pLGIC, at 2.4 Å. Anomalous diffraction data were used to place bound anions and cations. This reveals ordered water molecules at the level of two rings of hydroxylated residues (named Ser6′ and Thr2′) that contribute to the ion selectivity filter. Two water pentagons are observed, a self-stabilized ice-like water pentagon and a second wider water pentagon, with one sodium ion between them. Single-channel electrophysiology shows that the side-chain hydroxyl of Ser6′ is crucial for ion translocation. Simulations and electrostatics calculations complemented the description of hydration in the pore and suggest that the water pentagons observed in the crystal are important for the ion to cross hydrophobic constriction barriers. Simulations that pull a cation through the pore reveal that residue Ser6′ actively contributes to ion translocation by reorienting its side chain when the ion is going through the pore. Generalization of these findings to the pLGIC family is proposed. PMID:23403925

  15. Protein Nitrogen Determination by Kjeldahl Digestion and Ion Chromatography.

    PubMed

    Wang, Hsiaoling; Pampati, Nagarani; McCormick, William M; Bhattacharyya, Lokesh

    2016-06-01

    We report development and validation of a simple, rapid, and accurate method for the quantitation of protein nitrogen, which combines Kjeldahl digestion and ion chromatography with suppressed conductivity detection and requires nanomolar amount of nitrogen in samples (≥10 μg protein). The mechanism of suppressed conductivity detection does not permit analysis of samples containing copper (present in Kjeldahl digestion solution) and aluminum (present in many vaccines as adjuvants) due to precipitation of their hydroxides within the suppressor. We overcame this problem by including 10 μM oxalic acid in Kjeldahl digests and in the eluent (30 mM methanesulfonic acid). The chromatography is performed using an IonPac CS-16 cation exchange column by isocratic elution. The method reduces the digestion time to less than 1 h and eliminates the distillation and titration steps of the Kjeldahl method, thereby reducing the analysis time significantly and improving precision and accuracy. To determine protein nitrogen in samples containing non-protein nitrogen, proteins are precipitated by a mixture of deoxycholate and trichloroacetic acid and the precipitates are analyzed after dissolving in KOH. The method is particularly useful for biological samples that are limited and can also be applied to food, environmental, and other materials.

  16. A novel ion selective sensor for promethium determination.

    PubMed

    Gupta, Vinod K; Jain, Rajeev; Hamdan, A J; Agarwal, Shilpi; Bharti, Arvind K

    2010-11-29

    This is a first promethium(145) ion-selective sensor based on the comparative study of two Schiff base ligands (X(1) and X(2)) as neutral ionophores. Effect of various plasticizers: 2-nitrophenyloctylether (o-NPOE), dibutyl phosphonate (DBP), dioctylphthalate (DOP), tri-(2-ethylhexyl) phosphate (TEHP), dibutyl butylphosphonate (DBBP), chloronaphthalene (CN) and anion excluders: potassium tetrakis (p-chloropheny1) borate (KTpClPB), sodiumtetraphenylborate (NaTPB) and oleic acid (OA) have been studied. The membrane with a composition of ionophore (X(1)/X(2)):KTpClPB:PVC:o-NPOE (w/w, %) in the ratio of 5:5:30:60 exhibited best performance. The best responsive membrane sensors (8 and 21) exhibited working concentration range of 4.5×10(-7)-1.0×10(-2) M and 3.5×10(-6)-1.0×10(-2) M with a detection limits of 3.2×10(-7) M and 2.3×10(-6) M and Nernstian slopes of 20.0±0.5, 19.5±0.5 mV decade(-1) of activity, respectively. The sensor no. 8 works satisfactorily in partially non-aqueous media up to 10% (v/v) content of methanol, ethanol and acetonitrile. Analytical application of the proposed sensor has been demonstrated in determination of promethium (III) ions in spiked water samples.

  17. Quadrupole ion trap studies of the structure and reactivity of transition metal ion pair complexes

    PubMed

    Vachet; Callahan

    2000-03-01

    Ion pairs are common species observed in the electrospray mass spectra of transition metal coordination complexes. To understand the nature of these ion pairs, a systematic study of the gas-phase chemistry of these species using ion-molecule reactions and collision-induced dissociation (CID) was carried out. Ion pair complexes of the type MLnX+ (where M is Mn(II), Fe(II), Co(II), Ni(II), Cu(II) or Zn(II), L is 1,10-phenanthroline, 2,2'-bipyridine, ethylenediamine, diethylenetriamine or 1,4,8,11-tetraazacyclotetradecane and X is Cl-, NO3-, acetylacetonate, ClO4-, acetate or SCN-) were studied. Ion-molecule reactions can distinguish whether the counterion in an ion pair is an inner- or outer-sphere ligand and can determine the coordination mode of the counterion. In addition, CID and ion-molecule reactions reveal some interesting chemistry of these complexes and unique coordination modes for some of the anions studied here were inferred from the ion-molecule reactions. For example, the thiocyanate ion is found to coordinate in a bidentate fashion in Zn(II) and Ni(II) complexes, contrasting behavior typically observed in solution. Also, certain Co(II) and Fe(II) ion pair complexes undergo oxidation reactions in which species such as dioxygen and nitric oxide from the counterions ClO4- and NO3- are transferred to the Co(II) and Fe(II) complexes, showing the inherent affinity of these metals for these molecules. These complexes were also studied by ion-molecule reactions and CID. Dioxygen in complexes formed by CID is demonstrated to be bidentate, suggesting the formation of a peroxo ligand with concurrent oxidation of the metal.

  18. Structural Heterogeneity of Doubly-Charged Peptide b-Ions

    PubMed Central

    Li, Xiaojuan; Huang, Yiqun; O’Connor, Peter B.; Lin, Cheng

    2011-01-01

    Performing collisionally activated dissociation (CAD) and electron capture dissociation (ECD) in tandem has shown great promise in providing comprehensive sequence information that was otherwise unobtainable by using either fragmentation method alone or in duet. However, the general applicability of this MS3 approach in peptide sequencing may be undermined by the formation of non-direct sequence ions, as sometimes observed under CAD, particularly when multiple stages of CAD are involved. In this study, varied-sized doubly-charged b-ions from three tachykinin peptides were investigated by ECD. Sequence scrambling was observed in ECD of all b-ions from neurokinin A (HKTDSFVGLM-NH2), suggesting the presence of N- and C-termini linked macro-cyclic conformers. On the contrary, none of the b-ions from eledoisin (pEPSKDAFIGLM-NH2) produced non-direct sequence ions under ECD, as it does not contain a free N-terminal amino group. ECD of several b-ions from Substance P (RPKPQQFFGLM-NH2) showed series of cm-Lys fragment ions which suggested that the macro-cyclic structure may also be formed by connecting the C-terminal carbonyl group and the ε-amino group of the lysine side chain. Theoretical investigation of selected Substance P b-ions revealed several low energy conformers, including both linear oxazolones and macro-ring structures, in corroboration with the experimental observation. This study showed that a b-ion may exist as a mixture of several forms, with their propensities influenced by its N-terminus, length, and certain side-chain groups. Further, the presence of several macro-cyclic structures may result in erroneous sequence assignment when the combined CAD and ECD methods are used in peptide sequencing. PMID:21472584

  19. Structure Change of PTFE by Low Energy Ion Irradiation

    NASA Astrophysics Data System (ADS)

    Watari, Kunio; Iwao, Toru; Yumoto, Motoshige

    The authors irradiate low energy nitrogen ion (100eV) on PTFE (poly-tetra-fluoro-ethylene) for surface modification. However, PTFE cannot anticipate adhesive strength improvement because it is collapse type polymer and weariness of surface occurs by ion irradiation. We paid attention to cross-linked structure to solve this problem. By this study introduce below, PTFE was changed collapse type polymer into cross-linked type polymer by rising temperature above the glass transition in the case of ion irradiation. As a result, the formation of the CF3 combination was restrained and collapse phenomenon was prevented by ion irradiation above the glass transition. In addition, it was suggested that cross-linked structure is effective for adhesive strength improvement by convolution of C1s spectrum and density profile.

  20. Fragment formula calculator (FFC): determination of chemical formulas for fragment ions in mass spectrometric data.

    PubMed

    Wegner, André; Weindl, Daniel; Jäger, Christian; Sapcariu, Sean C; Dong, Xiangyi; Stephanopoulos, Gregory; Hiller, Karsten

    2014-02-18

    The accurate determination of mass isotopomer distributions (MID) is of great significance for stable isotope-labeling experiments. Most commonly, MIDs are derived from gas chromatography/electron ionization mass spectrometry (GC/EI-MS) measurements. The analysis of fragment ions formed during EI, which contain only specific parts of the original molecule can provide valuable information on the positional distribution of the label. The chemical formula of a fragment ion is usually applied to derive the correction matrix for accurate MID calculation. Hence, the correct assignment of chemical formulas to fragment ions is of crucial importance for correct MIDs. Moreover, the positional distribution of stable isotopes within a fragment ion is of high interest for stable isotope-assisted metabolomics techniques. For example, (13)C-metabolic flux analyses ((13)C-MFA) are dependent on the exact knowledge of the number and position of retained carbon atoms of the unfragmented molecule. Fragment ions containing different carbon atoms are of special interest, since they can carry different flux information. However, the process of mass spectral fragmentation is complex, and identifying the substructures and chemical formulas for these fragment ions is nontrivial. For that reason, we developed an algorithm, based on a systematic bond cleavage, to determine chemical formulas and retained atoms for EI derived fragment ions. Here, we present the fragment formula calculator (FFC) algorithm that can calculate chemical formulas for fragment ions where the chemical bonding (e.g., Lewis structures) of the intact molecule is known. The proposed algorithm is able to cope with general molecular rearrangement reactions occurring during EI in GC/MS measurements. The FFC algorithm is able to integrate stable isotope labeling experiments into the analysis and can automatically exclude candidate formulas that do not fit the observed labeling patterns.1 We applied the FFC algorithm to create

  1. Krypton ion induced structural phase transition in zirconia thin film

    NASA Astrophysics Data System (ADS)

    Balasaritha, P.; Amirthapandian, S.; Magudapathy, P.; Krishnan, R.; Panigrahi, B. K.

    2017-05-01

    The ZrO2 thin film was grown using pulsed laser deposition (PLD) method and irradiated with 60 keV Kr+ ions. The as-prepared and ion irradiated ZrO2 thin films were characterised with high resolution transmission electron microscope(HRTEM). The as-prepared ZrO2 thin film was found to be monoclinic in structure. Upon 60 keV Kr+ ion implantation, the ZrO2 thin films transformed from monoclinic to tetragonal phase along with the formation of krypton bubbles.

  2. Ion Structure Near a Core-Shell Dielectric Nanoparticle

    NASA Astrophysics Data System (ADS)

    Ma, Manman; Gan, Zecheng; Xu, Zhenli

    2017-02-01

    A generalized image charge formulation is proposed for the Green's function of a core-shell dielectric nanoparticle for which theoretical and simulation investigations are rarely reported due to the difficulty of resolving the dielectric heterogeneity. Based on the formulation, an efficient and accurate algorithm is developed for calculating electrostatic polarization charges of mobile ions, allowing us to study related physical systems using the Monte Carlo algorithm. The computer simulations show that a fine-tuning of the shell thickness or the ion-interface correlation strength can greatly alter electric double-layer structures and capacitances, owing to the complicated interplay between dielectric boundary effects and ion-interface correlations.

  3. Structural Modification of Nanocrystalline Ceria using Ion Beams

    SciTech Connect

    Zhang, Yanwen; Edmondson, Philip D; Varga, Tamas; Moll, Sandra; Namavar, Fereydoon; Weber, William J

    2011-01-01

    Exceptional size-dependent electronic-ionic conductivity of nanostructured ceria can significantly alter materials properties in chemical, physical, electronic and optical applications. Using energetic ions, we have demonstrated effective modification of interface volume and grain size in nanocrystalline ceria from a few nm up to ~ 25 nm, which is the critical region for controlling size-dependent material property. The unique self-healing response of radiation damage at grain boundaries is applied to control the grain size at nanoscale as a function of ion dose and irradiation temperature. Structural modification by energetic ions is proposed to achieve disirable electronic-ionic conductivity.

  4. Determination of polydextrose in foods by ion chromatography: collaborative study.

    PubMed

    Craig, S A; Holden, J F; Khaled, M Y

    2001-01-01

    Eight collaborating laboratories assayed 7 blind duplicate pairs of foods for polydextrose content. The 7 test sample pairs ranged from low (2%) to high (95%) levels. The following foods were prepared with polydextrose mixed into the other ingredients and then baked, cooked, or otherwise prepared: milk chocolate candy, iced tea, sugar cookie, grape jelly, soft jellied candy, and powdered drink mix. Collaborators received a polydextrose standard to develop a calibration curve. The method determined polydextrose by ion chromatography, after removal of interfering food components (high molecular weight solubles). Repeatability standard deviations (RSDr) ranged from 3.93 to 9.04%; reproducibility standard deviations (RSDR) ranged from 4.48 to 14.06%. The average recovery was 94%.

  5. Textile-based sampling for potentiometric determination of ions.

    PubMed

    Lisak, Grzegorz; Arnebrant, Thomas; Ruzgas, Tautgirdas; Bobacka, Johan

    2015-06-02

    Potentiometric sensing utilizing textile-based micro-volume sampling was applied and evaluated for the determination of clinically (Na(+), K(+), Cl(-)) and environmentally (Cd(2+), Pb(2+) and pH) relevant analytes. In this technological design, calibration solutions and samples were absorbed into textiles while the potentiometric cells (ion-selective electrodes and reference electrode) were pressed against the textile. Once the liquid, by wicking action, reached the place where the potentiometric cell was pressed onto the textile, hence closing the electric circuit, the potentiometric response was obtained. Cotton, polyamide, polyester and their blends with elastane were applied for micro-volume sampling. The textiles were found to influence the determination of pH in environmental samples with pH close to neutral and Pb(2+) at low analyte concentrations. On the other hand, textile-based micro-volume sampling was successfully applied in measurements of Na(+) using solid-contact sodium-selective electrodes utilizing all the investigated textiles for sampling. It was found that in order to extend the application of textile-based sampling toward environmental analysis of ions it will be necessary to tailor the physio-chemical properties of the textile materials. In general, textile-based sampling opens new possibilities for direct chemical analysis of small-volume samples and provide a simple and low-cost method to screen various textiles for their effects on samples to identify which textiles are the most suitable for on-body sensing. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Modification of the crystal structure of gadolinium gallium garnet by helium ion irradiation

    SciTech Connect

    Ostafiychuk, B. K.; Yaremiy, I. P. Yaremiy, S. I.; Fedoriv, V. D.; Tomyn, U. O.; Umantsiv, M. M.; Fodchuk, I. M.; Kladko, V. P.

    2013-12-15

    The structure of gadolinium gallium garnet (GGG) single crystals before and after implantation by He{sup +} ions has been investigated using high-resolution X-ray diffraction methods and the generalized dynamic theory of X-ray scattering. The main types of growth defects in GGG single crystals and radiation-induced defects in the ion-implanted layer have been determined. It is established that the concentration of dislocation loops in the GGG surface layer modified by ion implantation increases and their radius decreases with an increase in the implantation dose.

  7. Highly ordered three-dimensional macroporous carbon spheres for determination of heavy metal ions

    SciTech Connect

    Zhang, Yuxiao; Zhang, Jianming; Liu, Yang; Huang, Hui; Kang, Zhenhui

    2012-04-15

    Highlights: Black-Right-Pointing-Pointer Highly ordered three dimensional macroporous carbon spheres (MPCSs) were prepared. Black-Right-Pointing-Pointer MPCS was covalently modified by cysteine (MPCS-CO-Cys). Black-Right-Pointing-Pointer MPCS-CO-Cys was first time used in electrochemical detection of heavy metal ions. Black-Right-Pointing-Pointer Heavy metal ions such as Pb{sup 2+} and Cd{sup 2+} can be simultaneously determined. -- Abstract: An effective voltammetric method for detection of trace heavy metal ions using chemically modified highly ordered three dimensional macroporous carbon spheres electrode surfaces is described. The highly ordered three dimensional macroporous carbon spheres were prepared by carbonization of glucose in silica crystal bead template, followed by removal of the template. The highly ordered three dimensional macroporous carbon spheres were covalently modified by cysteine, an amino acid with high affinities towards some heavy metals. The materials were characterized by physical adsorption of nitrogen, scanning electron microscopy, and transmission electron microscopy techniques. While the Fourier-transform infrared spectroscopy was used to characterize the functional groups on the surface of carbon spheres. High sensitivity was exhibited when this material was used in electrochemical detection (square wave anodic stripping voltammetry) of heavy metal ions due to the porous structure. And the potential application for simultaneous detection of heavy metal ions was also investigated.

  8. Determination of N-linked glycosylation in viral glycoproteins by negative ion mass spectrometry and ion mobility

    PubMed Central

    Bitto, David; Harvey, David J.; Halldorsson, Steinar; Doores, Katie J.; Pritchard, Laura K.; Huiskonen, Juha T.; Bowden, Thomas A.; Crispin, Max

    2016-01-01

    Summary Glycan analysis of virion-derived glycoproteins is challenging due to the difficulties in glycoprotein isolation and low sample abundance. Here, we describe how ion mobility mass spectrometry can be used to obtain spectra from virion samples. We also describe how negative ion fragmentation of glycans can be used to probe structural features of virion glycans. PMID:26169737

  9. Determination of N-linked Glycosylation in Viral Glycoproteins by Negative Ion Mass Spectrometry and Ion Mobility.

    PubMed

    Bitto, David; Harvey, David J; Halldorsson, Steinar; Doores, Katie J; Pritchard, Laura K; Huiskonen, Juha T; Bowden, Thomas A; Crispin, Max

    2015-01-01

    Glycan analysis of virion-derived glycoproteins is challenging due to the difficulties in glycoprotein isolation and low sample abundance. Here, we describe how ion mobility mass spectrometry can be used to obtain spectra from virion samples. We also describe how negative ion fragmentation of glycans can be used to probe structural features of virion glycans.

  10. Ion mobility–mass spectrometry for structural proteomics

    PubMed Central

    Zhong, Yueyang; Hyung, Suk-Joon; Ruotolo, Brandon T

    2012-01-01

    Ion mobility coupled to mass spectrometry has been an important tool in the fields of chemical physics and analytical chemistry for decades, but its potential for interrogating the structure of proteins and multiprotein complexes has only recently begun to be realized. Today, ion mobility– mass spectrometry is often applied to the structural elucidation of protein assemblies that have failed high-throughput crystallization or NMR spectroscopy screens. Here, we highlight the technology, approaches and data that have led to this dramatic shift in use, including emerging trends such as the integration of ion mobility–mass spectrometry data with more classical (e.g., ‘bottom-up’) proteomics approaches for the rapid structural characterization of protein networks. PMID:22292823

  11. Emerging approaches to probing ion channel structure and function.

    PubMed

    Li, Wei-Guang; Xu, Tian-Le

    2012-08-01

    Ion channels, as membrane proteins, are the sensors of the cell. They act as the first line of communication with the world beyond the plasma membrane and transduce changes in the external and internal environments into unique electrical signals to shape the responses of excitable cells. Because of their importance in cellular communication, ion channels have been intensively studied at the structural and functional levels. Here, we summarize the diverse approaches, including molecular and cellular, chemical, optical, biophysical, and computational, used to probe the structural and functional rearrangements that occur during channel activation (or sensitization), inactivation (or desensitization), and various forms of modulation. The emerging insights into the structure and function of ion channels by multidisciplinary approaches allow the development of new pharmacotherapies as well as new tools useful in controlling cellular activity.

  12. Structure of the hydrated and dimethyl sulfoxide solvated rubidium ions in solution.

    PubMed

    D'Angelo, Paola; Persson, Ingmar

    2004-05-31

    The structure of the hydrated and the dimethyl sulfoxide solvated rubidium ions in solution has been determined by means of large-angle X-ray scattering (LAXS) and extended X-ray absorption fine structure (EXAFS) studies. The models of the hydrated and dimethyl sulfoxide solvated rubidium ions fitting the experimental data best are square antiprisms with Rb-O bond distances of 2.98(2) and 2.98(3) A, respectively. The EXAFS data show a significant asymmetry in the Rb-O bond distance distribution with C(3) values of 0.0076 and 0.015 A(3), respectively. No second hydration sphere is observed around the hydrated rubidium ion. The dimethyl sulfoxide solvated rubidium ion displays a Rb-O-S bond angle of ca. 130 degrees, which is typical for a medium hard electron acceptor such as rubidium.

  13. Investigation of structural mimetics of natural phosphate ion binding motifs.

    PubMed

    Kataev, Evgeny A; Shumilova, Tatiana A

    2015-02-16

    Phosphates are ubiquitous in biology and nearly half of all proteins interact with their partners by means of recognition of phosphate residues. Therefore, a better understanding of the phosphate ion binding by peptidic structures is highly desirable. Two new receptors have been designed and synthesized and their anion binding properties in an acetonitrile solution have been determined. The structure of hosts mimics a part of the kinase active site that is responsible for the recognition of the phosphate residue. New hosts contain additional free amino groups with the aim to facilitate coordination of protonated anions, such as dihydrogen phosphate. According to spectrophotometric measurements, stepwise 1:1 and 1:2 binding modes have been observed for both receptors in the presence of acetate, hydrogen sulfate and dihydrogen phosphate. Compared with the acyclic receptor, the macrocyclic receptor has demonstrated a remarkably enhanced selectivity for dihydrogen phosphate over other anions. Fluorometric measurements have revealed different responses of the acyclic and macrocyclic receptors towards anions. However, in both cases, a 5-8 nm hypsochromic shift of fluorescence maximum has been observed upon interaction of acetate and dihydrogen phosphate with receptors.

  14. Ion flow and sheath structure near positively biased electrodes

    NASA Astrophysics Data System (ADS)

    Hood, R.; Scheiner, B.; Baalrud, S. D.; Hopkins, M. M.; Barnat, E. V.; Yee, B. T.; Merlino, R. L.; Skiff, F.

    2016-11-01

    What effect does a dielectric material surrounding a small positively biased electrode have on the ion flow and sheath structure near the electrode? Measurements of the ion velocity distribution function and plasma potential near positively biased electrodes were made using laser-induced fluorescence and an emissive probe. The results were compared with 2D particle-in-cell simulations. Both measurements and simulations showed that when the positive electrode was surrounded by the dielectric material, ions were accelerated toward the electrode to approximately 0.5 times the ion sound speed before being deflected radially by the electron sheath potential barrier of the electrode. The axial potential profile in this case contained a virtual cathode. In comparison, when the dielectric material was removed from around the electrode, both the ion flow and virtual cathode depth near the electrode were dramatically reduced. These measurements suggest that the ion presheath from the dielectric material surrounding the electrode may enclose the electron sheath of the electrode, resulting in a virtual cathode that substantially influences the ion flow profile in the region.

  15. Conductometric determination of ammonium ion with a mobile drop.

    PubMed

    Jaikang, Pheeraya; Grudpan, Kate; Kanyanee, Tinakorn

    2015-01-01

    A mobile drop based approach was utilized for the conductometric determination of aqueous ammonium ion. A liquid drop was manipulated by gravity to remain or move out of a conductivity measurement zone located on a hydrophobic path. A dilute sulfuric acid drop functioned as a micro gas absorber. Gaseous NH3 was liberated from a sample containing NH4(+) by adding NaOH and purged to flow over the absorber drop. As H(+) in the absorber drop was converted to NH4(+), the conductivity decreased. The rate of the conductivity decrease thus ultimately depended on the NH4(+) concentration in the sample. While the sample could be complex, the liberation of NH3 gas essentially freed the analyte of interest from the matrix and allowed the use of an otherwise nonselective detector. The system was applied to the determination of NH4(+) in some natural waters without prior filtration; the results agreed well with those from a manual indophenol blue method. The approach exhibited a limit of detection (LOD) of 5 μM and a relative standard deviation (RSD) of<5%. The mobile drop gave a constant volume of the gas absorbing solution and provided a cost-effective and simple analytical platform.

  16. Structural aspects of group I metal ion-nucleoside interactions

    NASA Astrophysics Data System (ADS)

    Theophanides, T.; Bariyanga, J.

    1989-12-01

    Lithium, sodium and potassium complexes of guanosine and inosine have been synthesized and characterized. The structures of the complexes have been studied by fast atom bombardment mass spectrometry (FAB-MS). The molecular structures of some defined complexes have been studied from spectral analysis. Detailed interpretation of the spectra suggests that the metal cation is linked to purine's N7 site. In addition, several ion clusters containing the matrix glycerol and the metal ions have been detected among the fragments of the mass spectra.

  17. Solitary structures with ion and electron thermal anisotropy

    NASA Astrophysics Data System (ADS)

    Khusroo, Murchana; Bora, Madhurjya P.

    2015-11-01

    The formation of electrostatic solitary structures is analysed for a magnetised plasma with ion and electron thermal anisotropies. The ion thermal anisotropy is modelled with the help of the Chew-Goldberger-Low (CGL) double adiabatic equations of state while the electrons are treated as inertia-less species with an anisotropic bi-Maxwellian velocity distribution function. A negative electron thermal anisotropy ≤ft({{T}e\\bot}/{{T}e\\parallel}>1\\right) is found to help form large amplitude solitary structures which are in agreement with observational data.

  18. Structural Basis for Allosteric Regulation of GPCRs by Sodium Ions

    SciTech Connect

    Liu, Wei; Chun, Eugene; Thompson, Aaron A.; Chubukov, Pavel; Xu, Fei; Katritch, Vsevolod; Han, Gye Won; Roth, Christopher B.; Heitman, Laura H.; IJzerman, Adriaan P.; Cherezov, Vadim; Stevens, Raymond C.

    2012-08-31

    Pharmacological responses of G protein-coupled receptors (GPCRs) can be fine-tuned by allosteric modulators. Structural studies of such effects have been limited due to the medium resolution of GPCR structures. We reengineered the human A{sub 2A} adenosine receptor by replacing its third intracellular loop with apocytochrome b{sub 562}RIL and solved the structure at 1.8 angstrom resolution. The high-resolution structure allowed us to identify 57 ordered water molecules inside the receptor comprising three major clusters. The central cluster harbors a putative sodium ion bound to the highly conserved aspartate residue Asp{sup 2.50}. Additionally, two cholesterols stabilize the conformation of helix VI, and one of 23 ordered lipids intercalates inside the ligand-binding pocket. These high-resolution details shed light on the potential role of structured water molecules, sodium ions, and lipids/cholesterol in GPCR stabilization and function.

  19. RNA folding: structure prediction, folding kinetics and ion electrostatics.

    PubMed

    Tan, Zhijie; Zhang, Wenbing; Shi, Yazhou; Wang, Fenghua

    2015-01-01

    Beyond the "traditional" functions such as gene storage, transport and protein synthesis, recent discoveries reveal that RNAs have important "new" biological functions including the RNA silence and gene regulation of riboswitch. Such functions of noncoding RNAs are strongly coupled to the RNA structures and proper structure change, which naturally leads to the RNA folding problem including structure prediction and folding kinetics. Due to the polyanionic nature of RNAs, RNA folding structure, stability and kinetics are strongly coupled to the ion condition of solution. The main focus of this chapter is to review the recent progress in the three major aspects in RNA folding problem: structure prediction, folding kinetics and ion electrostatics. This chapter will introduce both the recent experimental and theoretical progress, while emphasize the theoretical modelling on the three aspects in RNA folding.

  20. Structure and dynamics of aqueous solution of uranyl ions

    SciTech Connect

    Chopra, Manish; Choudhury, Niharendu

    2014-04-24

    The present work describes a molecular dynamics simulation study of structure and dynamics of aqueous solution of uranyl ions in water. Structural properties of the system in terms of radial distribution functions and dynamical characteristics as obtained through velocity autocorrelation function and mean square displacements have been analyzed. The results for radial distribution functions show the oxygen of water to form the first solvation shell at 2.4 Å around the uranium atom, whereas the hydrogen atoms of water are distributed around the uranium atom with the major peak at around 3.0 Å. Analyses of transport behaviors of ions and water through MSD indicates that the diffusion of the uranyl ion is much less as compared to that of the water molecules. It is also observed that the dynamical behavior of water molecules gets modified due to the presence of uranyl ion. The effect of increase in concentration of uranyl ions on the structure and dynamics of water molecules is also studied.

  1. Investigations on the structure of the extracted ion beam from an electron cyclotron resonance ion source

    SciTech Connect

    Spaedtke, P.; Lang, R.; Maeder, J.; Rossbach, J.; Tinschert, K.; Maimone, F.

    2012-02-15

    Using improved beam diagnostic tools, the structure of an ion beam extracted from an electron cyclotron resonance ion source (ECRIS) becomes visible. Especially viewing targets to display the beam profile and pepper pot devices for emittance measurements turned out to be very useful. On the contrary, diagnostic tools integrating over one space coordinate like wire harps for profile measurements or slit-slit devices, respectively slit-grid devices to measure the emittance might be applicable for beam transport investigations in a quadrupole channel, but are not very meaningful for investigations regarding the given ECRIS symmetry. Here we try to reproduce the experimentally found structure on the ion beam by simulation. For the simulation, a certain model has to be used to reproduce the experimental results. The model is also described in this paper.

  2. Structure of ceramic surfaces modified by ion-beam techniques

    SciTech Connect

    McHargue, C.J.; Naramoto, H.; White, C.W.; Williams, J.M.; Appleton, B.R.; Sklad, P.S.; Angelini, P.

    1982-01-01

    A wide variety of structures are produced by ion implantation in ceramics. Random (substitutional and interstitial site occupancy) solid solutions with concentrations of solute that exceed the solubility limit can be produced in Al/sub 2/O/sub 3/. The changes that occur during annealing are complex and sometimes unpredictable. Silicon carbide becomes amorphous in a manner analogous to Si for ion fluences that produce more than 0.2 dpa damage. Light (N) and heavy (Cr) ions produce similar results if the fluence is scaled to damage energy deposited. Because of mass differences in the ions, two damage regions are developed in TiB/sub 2/. The structure remains crystalline to very high damage levels. These structural alterations cause changes in the surface mechanical properties. Since virtually any chemical species can be implanted, one can independently control structural damage and chemical effects. When coupled with selective annealing, this technique has the potential for producing a wide range of surface structures and properties. 8 figures.

  3. Shock normal determination for multiple-ion shocks

    NASA Technical Reports Server (NTRS)

    Kessel, R. L.; Coates, A. J.; Motschmann, U.; Neubauer, F. M.

    1994-01-01

    We have adapted the single-ion Vinas and Scudder (1986) solution to the Rankine-Hugoniot (R-H) problem to a multiple-on solution. Using this technique, we can calculate a shock normal direction, shock speed, best estimate of the upstream and downstream magnetic field and plasma asymptotic states, and theta(sub Bn), the angle between the shock normal and the upstream magnetic field. We test the multi-ion solution with a theoretical case but are restricted to a perpendicular shock in order to close the multi-ion Rankine-Hugoniot equations. For this test case both single-ion and multi-ion solutions are equally valid. We examine parameter regimes to look for differences between single-ion and multi-ion solutions of the R-H equations, and we find that the largest differences occur for quasi-parallel shocks, small values of solar wind speed, large values of heavy ion density, and very strong and very weak shocks. For both the inbound and outbound crossing of comet Halley we have a slow solar wind speed, small values of water group ions and fairly weak shocks. We examine both the quasi-perpendicular inbound crossing and the quasi-parallel outbound crossing at comet Halley.

  4. Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure

    PubMed Central

    D'Atri, Valentina; Porrini, Massimiliano; Rosu, Frédéric; Gabelica, Valérie

    2015-01-01

    Ion mobility spectrometry experiments allow the mass spectrometrist to determine an ion's rotationally averaged collision cross section ΩEXP. Molecular modelling is used to visualize what ion three-dimensional structure(s) is(are) compatible with the experiment. The collision cross sections of candidate molecular models have to be calculated, and the resulting ΩCALC are compared with the experimental data. Researchers who want to apply this strategy to a new type of molecule face many questions: (1) What experimental error is associated with ΩEXP determination, and how to estimate it (in particular when using a calibration for traveling wave ion guides)? (2) How to generate plausible 3D models in the gas phase? (3) Different collision cross section calculation models exist, which have been developed for other analytes than mine. Which one(s) can I apply to my systems? To apply ion mobility spectrometry to nucleic acid structural characterization, we explored each of these questions using a rigid structure which we know is preserved in the gas phase: the tetramolecular G-quadruplex [dTGGGGT]4, and we will present these detailed investigation in this tutorial. © 2015 The Authors. Journal of Mass Spectrometry published by John Wiley & Sons Ltd. PMID:26259654

  5. Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure.

    PubMed

    D'Atri, Valentina; Porrini, Massimiliano; Rosu, Frédéric; Gabelica, Valérie

    2015-05-01

    Ion mobility spectrometry experiments allow the mass spectrometrist to determine an ion's rotationally averaged collision cross section Ω(EXP). Molecular modelling is used to visualize what ion three-dimensional structure(s) is(are) compatible with the experiment. The collision cross sections of candidate molecular models have to be calculated, and the resulting Ω(CALC) are compared with the experimental data. Researchers who want to apply this strategy to a new type of molecule face many questions: (1) What experimental error is associated with Ω(EXP) determination, and how to estimate it (in particular when using a calibration for traveling wave ion guides)? (2) How to generate plausible 3D models in the gas phase? (3) Different collision cross section calculation models exist, which have been developed for other analytes than mine. Which one(s) can I apply to my systems? To apply ion mobility spectrometry to nucleic acid structural characterization, we explored each of these questions using a rigid structure which we know is preserved in the gas phase: the tetramolecular G-quadruplex [dTGGGGT]4, and we will present these detailed investigation in this tutorial. © 2015 The Authors. Journal of Mass Spectrometry published by John Wiley & Sons Ltd.

  6. Structural properties of ion beam mixed tungsten/steel layers

    NASA Astrophysics Data System (ADS)

    Piatkowska, A.; Jagielski, J.; Kopcewicz, M.; Matz, W.; Zalar, A.; Mozetic, M.

    2003-05-01

    Structural properties of Kr ion beam mixed layers of tungsten deposited on high-speed steel have been studied by using Grazing incidence X-ray diffraction, conversion electron Mössbauer spectroscopy and Auger electron spectroscopy techniques. The results show that ion beam mixing at room temperature leads to the formation of an amorphous layer composed of the mixture of amorphous tungsten and amorphous Fe-W phase. The amorphous structure is stable upon annealing up to at least 450 °C. The ion beam mixing at the temperatures above 350 °C results in the formation of crystalline W 2C phase in addition to the amorphous Fe-W one persisting up to at least 450 °C.

  7. Enhanced Ion Acceleration from Micro-tube Structured Targets

    NASA Astrophysics Data System (ADS)

    Snyder, Joseph; Ji, Liangliang; Akli, Kramer

    2015-11-01

    We present an enhanced ion acceleration method that leverages recent advancements in 3D printing for target fabrication. Using the three-dimensional Particle-in-Cell simulation code Virtual Laser-Plasma Lab (VLPL), we model the interaction of a short pulse, high intensity laser with a micro-tube plasma (MTP) structured target. When compared to flat foils, the MTP target enhances the maximum proton energy by a factor of about 4. The ion enhancement is attributed to two main factors: high energy electrons extracted from the tube structure enhancing the accelerating field and light intensification within the MTP target increasing the laser intensity at the location of the foil. We also present results on ion energy scaling with micro-tube diameter and incident laser pulse intensity. This work was supported by the AFOSR under contract No. FA9550-14-1-0085.

  8. Plasma immersion ion implantation for surface treatment of complex branched structures

    NASA Astrophysics Data System (ADS)

    Kashin, Oleg A.; Lotkov, Alexander I.; Borisov, Dmitry P.; Slabodchikov, Vladimir A.; Kuznetsov, Vladimir M.; Kudryashov, Andrey N.; Krukovsky, Konstantin V.

    2016-11-01

    The paper presents experimental results demonstrating the capabilities of plasma immersion ion implantation of silicon (Si) for surface treatment of complex branched structures such are self-expanding intravascular nickel-titanium (NiTi) stents. Using NiTi stents of diameter 4 and 8 mm, it is shown that plasma immersion ion implantation can provide rather homogeneous doping of their outer and inner surfaces with Si atoms. Also presented are research data on the processes that determine the thickness, composition, and structure of surface layers subjected to this type of treatment.

  9. How unequivocally do ion chromatography experiments determine carbon cluster geometries?

    SciTech Connect

    Strout, D.L.; Book, L.D.; Millam, J.M.; Xu, C.; Scuseria, G.E.

    1994-09-01

    Ion chromatography experiments on carbon clusters have provided a powerful tool for characterizing the products of the laser ablation of graphite. Using this technique, several families of carbon clusters have been observed, and their role in a plausible fullerene formation process has been hypothesized. In this work, we have examined the experimental mobility results from a theoretical perspective. Our most interesting finding is the existence of a family of three-dimensional 2 + 4 cycloaddition products whose members match the experimental mobilities of the so-called `ring III` family over a range of cluster sizes, whereas previous studies have asserted that the `ring III` clusters are planar. In agreement with previous research, we find that the `ring I` and `ring II` families consist of monocyclic and bicycle rings, respectively. However, these families should be broadly defined so as to include ring structures with carbon branches, because short carbon branches have only a negligible effect on cluster mobility. 28 refs., 6 figs., 6 tabs.

  10. Ab initio simulations of the dynamic ion structure factor of warm dense lithium

    DOE PAGES

    Witte, B. B. L.; Shihab, M.; Glenzer, S. H.; ...

    2017-04-06

    Here, we present molecular dynamics simulations based on finite-temperature density functional theory that determine self-consistently the dynamic ion structure factor and the electronic form factor in lithium. Our comprehensive data set allows for the calculation of the dispersion relation for collective excitations, the calculation of the sound velocity, and the determination of the ion feature from the total electronic form factor and the ion structure factor. The results are compared with available experimental x-ray and neutron scattering data. Good agreement is found for both the liquid metal and warm dense matter domain. Finally, we study the impact of possible targetmore » inhomogeneities on x-ray scattering spectra.« less

  11. Intermittent structures at ion scales in the turbulent solar wind

    NASA Astrophysics Data System (ADS)

    Perrone, Denise; Alexandrova, Olga; Lion, Sonny; Roberts, Owen W.; Maksimovic, Milan; Escoubet, Philippe C.; Zouganelis, Yannis

    2017-04-01

    Understanding the physical mechanisms of dissipation, and the related heating, in turbulent collisionless plasmas (such as the solar wind) represents nowadays one of the key issues of plasma physics. Although the complex behavior of the solar wind has been matter of investigation of many years, some of the primary problems still remain a puzzle for the scientific community. Here, we study coherent structures responsible for solar wind intermittency around ion characteristic scales. We find that, in fast solar wind, intermittency is due to current sheets and Alfvén vortex-like structures. In slow solar wind, we observe as well compressive structures like magnetic solitons, holes and shocks. By using high-time resolution magnetic field data of multi-point measurements of Cluster spacecraft, we characterize the observed coherent structures in terms of topology and propagation speed. We show that all structures, both in fast and slow solar wind, are characterized by a strong wave-vector anisotropy in the perpendicular direction with respect to the local magnetic field and typical scales around ion characteristic scales. Moreover, some of them propagate in the plasma rest frame. Moreover, a further analysis on the ion velocity distribution shows a high variability; in particular, close to coherent structures the proton distribution function appears strongly deformed and far from the thermodynamic equilibrium. We discuss possible interpretation of the observed structures and their role in the heating process of the plasma.

  12. Precise determination of micromotion for trapped-ion optical clocks

    NASA Astrophysics Data System (ADS)

    Keller, J.; Partner, H. L.; Burgermeister, T.; Mehlstäubler, T. E.

    2015-09-01

    As relative systematic frequency uncertainties in trapped-ion spectroscopy are approaching the low 10-18 range, motional frequency shifts account for a considerable fraction of the uncertainty budget. Micromotion, a driven motion fundamentally connected to the principle of the Paul trap, is a particular concern in these systems. In this article, we experimentally investigate at this level three common methods for minimizing and determining the micromotion amplitude. We develop a generalized model for a quantitative application of the photon-correlation technique, which is applicable in the commonly encountered regime where the transition linewidth is comparable to the rf drive frequency. We show that a fractional frequency uncertainty due to the 2nd-order Doppler shift below |Δν/ν|=1 ×10-20 can be achieved. The quantitative evaluation is verified in an interleaved measurement with the conceptually simpler resolved sideband method. If not performed deep within the Lamb-Dicke regime, a temperature-dependent offset at the level of 10-19 is observed in resolved sideband measurements due to sampling of intrinsic micromotion. By direct comparison with photon-correlation measurements, we show that the simple to implement parametric heating method is sensitive to micromotion at the level of |Δν/ν|=1 ×10-20 as well.

  13. Cocaine abuse determination by ion mobility spectrometry using molecular imprinting.

    PubMed

    Sorribes-Soriano, A; Esteve-Turrillas, F A; Armenta, S; de la Guardia, M; Herrero-Martínez, J M

    2017-01-20

    A cocaine-based molecular imprinted polymer (MIP) has been produced by bulk polymerization and employed as selective solid-phase extraction support for the determination of cocaine in saliva samples by ion mobility spectrometry (IMS). The most appropriate conditions for washing and elution of cocaine from MIPs were studied and MIPs were characterized in terms of analyte binding capacity, reusability in water and saliva analysis, imprinting factor and selectivity were established and compared with non-imprinted polymers. The proposed MIP-IMS method provided a LOD of 18μgL(-1) and quantitative recoveries for blank saliva samples spiked from 75 to 500μgL(-1) cocaine. Oral fluid samples were collected from cocaine consumers and analysed by the proposed MIP-IMS methodology. Results, ranging from below the LOD to 51±2mgL(-1), were statistically comparable to those obtained by a confirmatory gas chromatography-mass spectrometry method. Moreover, results were compared to a qualitative lateral flow immunoassay procedure providing similar classification of the samples. Thus, MIP-IMS can be considered an useful alternative that provided fast, selective and sensitive results with a cost affordable instrumentation that does not require skilled operators. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. A New Ion Implant Monitor Electrical Test Structure.

    DTIC Science & Technology

    1986-01-01

    In this paper, a new Ion Implant Monitor test structure and measurement method is reported. A direct measurement of the sheet resistance of the...probe measurements. Voltage measurements are directly converted to sheet resistance , thus measurements may be performed rapidly.

  15. The gas phase structure of coulombically stretched polyethylene glycol ions.

    PubMed

    Larriba, Carlos; de la Mora, Juan Fernandez

    2012-01-12

    Prior ion-mobility mass-spectrometry (IMS-MS) studies of polyethylene glycol (PEG) ions have identified only two out of many sharply different observed structures: Linear shapes with several individually solvated singly charged cations at high charge states z (beads on a string), and single multiply charged globules at low z. The present study is devoted to assign all other existing structures of PEG ions, for the first time reaching masses of 100 kDa and charge states up to z = 10. There are at most z different structures at charge state z. All involve a single globule carrying n charges, tied to one or several appendices bearing z - n separate charges in a beads-on-a-string configuration. All sharp shape transitions observed at decreasing ion mass involve ejection of one elementary charge (sometimes two) from the shrinking globule into the growing linear appendage. This picture is supported by molecular dynamics simulations and approximate calculations of electrical mobilities for computed structures.

  16. Structure and dynamics of ion transport through gramicidin A.

    PubMed Central

    Mackay, D H; Berens, P H; Wilson, K R; Hagler, A T

    1984-01-01

    Molecular dynamics calculations in which all atoms were allowed to move were performed on a water-filled ion channel of the polypeptide dimer gramicidin A (approximately 600 atoms total) in the head-to-head Urry model conformation. Comparisons were made among nine simulations in which four different ions (lithium, sodium, potassium, and cesium) were each placed at two different locations in the channel as well as a reference simulation with only water present. Each simulation lasted for 5 ps and was carried out at approximately 300 K. The structure and dynamics of the peptide and interior waters were found to depend strongly on the ion tested and upon its location along the pore. Speculations on the solution and diffusion of ions in gramicidin are offered based on the observations in our model that smaller ions tended to lie off axis and to distort the positions of the carbonyl oxygens more to achieve proper solvation and that the monomer-monomer junction was more distortable than the center of the monomer. With the potential energy surface used, the unique properties of the linear chain of interior water molecules were found to be important for optimal solvation of the various ions. Strongly correlated motions persisting over 25 A among the waters in the interior single-file column were observed. PMID:6206901

  17. Prompt Gas Desorption Due to Ion Impact on Accelerator Structures

    NASA Astrophysics Data System (ADS)

    Vijay, Sagar; Seidl, Peter A.; Faltens, Andy; Lidia, Steven M.

    2011-10-01

    The repetition rate and peak current of high intensity ion accelerators for inertial fusion or other applications may be limited under certain conditions by the desorption of gas molecules and atoms due to stray ions striking the accelerator structure. We have measured the prompt yield of atoms in close proximity to the point of impact of the ions on a surface. Using the 300-keV, K+ ion beam of the Neutralized Drift Compression Experiment (NDCX-I), ions strike a metal target in a 5-10 microsecond bunch. The collector of a Bayert-Alpert style ionization gauge is used to detect the local pressure burst several centimeters away. Pressure transients are observed on a micro-second time scale due to the initial burst of desorbed gas, and on a much longer (~1 second) timescale, corresponding to the equilibration of the pressure after many ``bounces'' of atoms in the vacuum chamber. We report on these time dependent pressure measurements, modeling of the pressure transient, and implications for high-intensity ion accelerators. Work performed under auspices of U.S. DOE by LBNL under Contract DE-AC02-05CH1123.

  18. Determination of strong ion gap in healthy dogs.

    PubMed

    Fettig, Pamela K; Bailey, Dennis B; Gannon, Kristi M

    2012-08-01

    To determine and compare reference intervals of the strong ion gap (SIG) in a group of healthy dogs determined with 2 different equations. Prospective observational study. Tertiary referral and teaching hospital. Fifty-four healthy dogs. None. Serum biochemistry and blood gas analyses were performed for each dog. From these values, SIG was calculated using 2 different equations: SIG(1) = SID(a) {[Na (+)] + [K(+)] - [Cl(-)]+ [2 × Ca(2+)] + [2 × Mg(2+)] - [L-lactate]}- SID(e) {TCO(2) + A(-)} and SIG(2) = [albumin] × 4.9-anion gap. Reference intervals were established for each SIG equation using the mean ± 1.96 × standard deviation (SD). For SIG(1), the median was 7.13 mEq/L (range, 1.05-11.30 mEq/L) and the derived reference interval was 1.85-10.61 mEq/L. Median SIG(2) was -0.22 mEq/L (range, -5.34-6.61 mEq/L) and the mean SIG(2) was -0.09 mEq/L (95% confidence interval for the mean, -0.82-0.65 mEq/L). The derived reference interval was -5.36-5.18 mEq/L. The results of the SIG calculations were significantly different (P < 0.0001) between the 2 equations used. The 2 equations used to calculate SIG yielded significantly different results and cannot be used interchangeably. The authors believe SIG(2) to be a more accurate reflection of acid-base status in healthy dogs, and recommend that this calculation be used for future studies. © Veterinary Emergency and Critical Care Society 2012.

  19. Structure of a CLC chloride ion channel by cryo-electron microscopy

    PubMed Central

    Park, Eunyong; Campbell, Ernest B.; MacKinnon, Roderick

    2017-01-01

    CLC proteins transport chloride (Cl−) ions across cellular membranes to regulate muscle excitability, electrolyte movement across epithelia, and acidification of intracellular organelles. Some CLC proteins are channels that conduct Cl− ions passively, whereas others are secondary active transporters that exchange two Cl− ions for one H+. The structural basis underlying these distinctive transport mechanisms is puzzling because CLC channels and transporters are expected to share the same architecture based on sequence homology. To solve this puzzle we determined the structure of a mammalian CLC channel (CLC-K) using cryo-electron microscopy. A conserved loop in the Cl− transport pathway shows a structure markedly different from that of CLC transporters. Consequently, the cytosolic constriction for Cl− passage is widened in CLC-K such that the kinetic barrier previously postulated for Cl−/H+ transporter function would be reduced. Thus, reduction of a kinetic barrier in CLC channels enables fast flow of Cl− down its electrochemical gradient. PMID:28002411

  20. Structure of a CLC chloride ion channel by cryo-electron microscopy.

    PubMed

    Park, Eunyong; Campbell, Ernest B; MacKinnon, Roderick

    2017-01-26

    CLC proteins transport chloride (Cl(-)) ions across cellular membranes to regulate muscle excitability, electrolyte movement across epithelia, and acidification of intracellular organelles. Some CLC proteins are channels that conduct Cl(-) ions passively, whereas others are secondary active transporters that exchange two Cl(-) ions for one H(+). The structural basis underlying these distinctive transport mechanisms is puzzling because CLC channels and transporters are expected to share the same architecture on the basis of sequence homology. Here we determined the structure of a bovine CLC channel (CLC-K) using cryo-electron microscopy. A conserved loop in the Cl(-) transport pathway shows a structure markedly different from that of CLC transporters. Consequently, the cytosolic constriction for Cl(-) passage is widened in CLC-K such that the kinetic barrier previously postulated for Cl(-)/H(+) transporter function would be reduced. Thus, reduction of a kinetic barrier in CLC channels enables fast flow of Cl(-) down its electrochemical gradient.

  1. Micro structure processing on plastics by accelerated hydrogen molecular ions

    NASA Astrophysics Data System (ADS)

    Hayashi, H.; Hayakawa, S.; Nishikawa, H.

    2017-08-01

    A proton has 1836 times the mass of an electron and is the lightest nucleus to be used for accelerator in material modification. We can setup accelerator with the lowest acceleration voltage. It is preferable characteristics of Proton Beam Writer (PBW) for industrial applications. On the contrary ;proton; has the lowest charge among all nuclei and the potential impact to material is lowest. The object of this research is to improve productivity of the PBW for industry application focusing on hydrogen molecular ions. These ions are generated in the same ion source by ionizing hydrogen molecule. There is no specific ion source requested and it is suitable for industrial use. We demonstrated three dimensional (3D) multilevel micro structures on polyester base FPC (Flexible Printed Circuits) using proton, H2+ and H3+. The reactivity of hydrogen molecular ions is much higher than that of proton and coincident with the level of expectation. We can apply this result to make micro devices of 3D multilevel structures on FPC.

  2. Freestanding single-crystalline magnetic structures fabricated by ion bombardment

    SciTech Connect

    Schoenherr, P.; Bischof, A.; Boehm, B.; Eib, P.; Grimm, S.; Gross, L.; Allenspach, R.; Alvarado, S. F.

    2015-01-19

    Starting from an ultrathin Fe film grown epitaxially on top of a GaAs(001) substrate, we show that freestanding structures can be created by ion-beam treatment. These structures are single-crystalline blisters and only a few nanometers thick. Anisotropic stress in the rim of a blister induces magnetic domain states magnetized in the direction normal to the blister edge. Experimental evidence is provided that the lateral size can be confined by starting from a nanostructured template.

  3. Ion Bombardment of Microprotrusions in High Gradient Accelerating Structures

    SciTech Connect

    Nusinovich, Gregory S.; Kashyn, Dmytro; Antonsen, Thomas Jr.; Haber, Irving

    2010-11-04

    This paper starts from a brief overview of theoretical studies of high-gradient accelerating structures at the University of Maryland. The rest of the paper is devoted to the analysis of ion bombardment of small protrusions in such structures. First, this problem is studied analytically. Then, some results of particle-in-cell simulations performed with the use of code WARP are presented and discussed.

  4. Direct atomic structure determination by the inspection of structural phase.

    PubMed

    Nakashima, Philip N H; Moodie, Alexander F; Etheridge, Joanne

    2013-08-27

    A century has passed since Bragg solved the first atomic structure using diffraction. As with this first structure, all atomic structures to date have been deduced from the measurement of many diffracted intensities using iterative and statistical methods. We show that centrosymmetric atomic structures can be determined without the need to measure or even record a diffracted intensity. Instead, atomic structures can be determined directly and quickly from the observation of crystallographic phases in electron diffraction patterns. Furthermore, only a few phases are required to achieve high resolution. This represents a paradigm shift in structure determination methods, which we demonstrate with the moderately complex α-Al2O3. We show that the observation of just nine phases enables the location of all atoms with a resolution of better than 0.1 Å. This level of certainty previously required the measurement of thousands of diffracted intensities.

  5. Direct atomic structure determination by the inspection of structural phase

    PubMed Central

    Nakashima, Philip N. H.; Moodie, Alexander F.; Etheridge, Joanne

    2013-01-01

    A century has passed since Bragg solved the first atomic structure using diffraction. As with this first structure, all atomic structures to date have been deduced from the measurement of many diffracted intensities using iterative and statistical methods. We show that centrosymmetric atomic structures can be determined without the need to measure or even record a diffracted intensity. Instead, atomic structures can be determined directly and quickly from the observation of crystallographic phases in electron diffraction patterns. Furthermore, only a few phases are required to achieve high resolution. This represents a paradigm shift in structure determination methods, which we demonstrate with the moderately complex α-Al2O3. We show that the observation of just nine phases enables the location of all atoms with a resolution of better than 0.1 Å. This level of certainty previously required the measurement of thousands of diffracted intensities. PMID:23940343

  6. Determinants of Long Bone Structural Properties

    NASA Technical Reports Server (NTRS)

    Cleek, T. M.; Katz, B.; Whalen, R. T.; Wade, Charles E. (Technical Monitor)

    1994-01-01

    The objective of our research is to determine whether a non-invasive determination of long bone cross-sectional areal properties using only the mineral component of bone accurately predicts the true structural properties. In this study section properties of a whole long bone were compared using two methods: (1) special analysis of bone densitometry data, and (2) experimental determination of flexural rigidities from bone surface strain measurements during controlled loading.

  7. AUTOMATED DETERMINATION OF PRECURSOR ION, PRODUCT ION, AND NEUTRAL LOSS COMPOSITIONS AND DECONVOLUTION OF COMPOSITE MASS SPECTRA USING ION CORRELATION BASED ON EXACT MASSES AND RELATIVE ISOTOPIC ABUNDANCES

    EPA Science Inventory

    After a dispersive event, rapid determination of elemental compositions of ions in mass spectra is essential for tentatively identifying compounds. A Direct Analysis in Real Time (DART)® ion source interfaced to a JEOL AccuTOF® mass spectrometer provided exact masses accurate to ...

  8. Method for determining trace quantities of chloride in polymeric materials using ion selective electrodes: Final report

    SciTech Connect

    Salary, J.

    1987-02-01

    A method for determining trace quantities of chloride in polymeric materials has been developed. Ion-selective electrodes and the standard addition method were used in all the analyses. The ion-selective electrode method was compared with neutron activation, ion chromatography and chloridometer titration. The ion-selective electrode technique results for chloride were similar to those of neutron activation, which is the acknowledged referee method. This ion-selective electrode method showed the highest standard recovery when compared with the ion chromatography and chloridometer titration methods.

  9. Protein structure determination from NMR chemical shifts.

    PubMed

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

    2007-06-05

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

  10. Ion aggregation in high salt solutions. V. Graph entropy analyses of ion aggregate structure and water hydrogen bonding network

    NASA Astrophysics Data System (ADS)

    Choi, Jun-Ho; Cho, Minhaeng

    2016-05-01

    Dissolved ions in water tend to form polydisperse ion aggregates such as ion pairs, relatively compact ion clusters, and even spatially extended ion networks with increasing salt concentration. Combining molecular dynamics simulation and graph theoretical analysis methods, we recently studied morphological structures of ion aggregates with distinctively different characteristics. They can be distinguished from each other by calculating various spectral graph theoretical properties such as eigenvalues and eigenvectors of adjacency matrices of ion aggregates and water hydrogen-bonding networks, minimum path lengths, clustering coefficients, and degree distributions. Here, we focus on percolation and graph entropic properties of ion aggregates and water hydrogen-bonding networks in high salt solutions. Ion network-forming K+ and SCN- ions at high concentrations show a percolating behavior in their aqueous solutions, but ion cluster-forming ions in NaCl solutions do not show such a transition from isolated ion aggregates to percolating ion-water mixture morphology. Despite that the ion aggregate structures are strikingly different for either cluster- or network-forming ions in high salt solutions, it is interesting that the water structures remain insensitive to the electrostatic properties, such as charge densities and polydentate properties, of dissolved ions, and morphological structures of water H-bonding networks appear to be highly robust regardless of the nature and concentration of salt. We anticipate that the present graph entropy analysis results would be of use in understanding a variety of anomalous behaviors of interfacial water around biomolecules as well as electric conductivities of high electrolyte solutions.

  11. Simple approach for ranking structure determining residues.

    PubMed

    Luna-Martínez, Oscar D; Vidal-Limón, Abraham; Villalba-Velázquez, Miryam I; Sánchez-Alcalá, Rosalba; Garduño-Juárez, Ramón; Uversky, Vladimir N; Becerril, Baltazar

    2016-01-01

    Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the stability of global structure, regardless of the protein topology. This method evaluates all of the residues in a 3D structure of a given globular protein by ranking them according to their connectivity and movement restrictions without topology constraints. Our results matched up with sequence-based predictors that look up for intrinsically disordered segments, suggesting that protein disorder can also be described with the proposed methodology.

  12. Simple approach for ranking structure determining residues

    PubMed Central

    Luna-Martínez, Oscar D.; Vidal-Limón, Abraham; Villalba-Velázquez, Miryam I.; Sánchez-Alcalá, Rosalba; Garduño-Juárez, Ramón; Uversky, Vladimir N.

    2016-01-01

    Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the stability of global structure, regardless of the protein topology. This method evaluates all of the residues in a 3D structure of a given globular protein by ranking them according to their connectivity and movement restrictions without topology constraints. Our results matched up with sequence-based predictors that look up for intrinsically disordered segments, suggesting that protein disorder can also be described with the proposed methodology. PMID:27366642

  13. Evaluation of dry ashing in conjunction with ion chromatographic determination of transition metal ions in pig feed samples.

    PubMed

    Van paemel, Marleen R; De Rycke, Herman; Millet, Sam; Hesta, Myriam; Janssens, Geert P J

    2005-03-23

    The contents of transition metal ions iron, copper, zinc, and manganese were simultaneously determined in pig feed using an ion chromatographic technique (IC) preceded by dry ashing. Employing ion exchange, the ions were separated on an IonPac CS5A column used in combination with a pyridine-2,6-dicarboxylic acid based eluent. The separation was followed by spectrophotometric detection after postcolumn reaction with 4-(2-pyridylazo)resorcinol. Dry ashing parameters were varied to assess their role in potential analyte loss. Quantitative recoveries (>95%) were obtained for all analytes with a dry ashing method that included a moderate temperature-time regime and ash leaching support in the form of sonication and heat treatment. The use of HCl as leaching acid and the presence of alkaline earths in the matrix solution did not interfere with the chromatographic separation.

  14. Enhancement of maximum attainable ion energy in the radiation pressure acceleration regime using a guiding structure

    DOE PAGES

    Bulanov, S. S.; Esarey, E.; Schroeder, C. B.; ...

    2015-03-13

    Radiation Pressure Acceleration is a highly efficient mechanism of laser driven ion acceleration, with the laser energy almost totally transferrable to the ions in the relativistic regime. There is a fundamental limit on the maximum attainable ion energy, which is determined by the group velocity of the laser. In the case of a tightly focused laser pulses, which are utilized to get the highest intensity, another factor limiting the maximum ion energy comes into play, the transverse expansion of the target. Transverse expansion makes the target transparent for radiation, thus reducing the effectiveness of acceleration. Utilization of an external guidingmore » structure for the accelerating laser pulse may provide a way of compensating for the group velocity and transverse expansion effects.« less

  15. Enhancement of maximum attainable ion energy in the radiation pressure acceleration regime using a guiding structure

    SciTech Connect

    Bulanov, S. S.; Esarey, E.; Schroeder, C. B.; Bulanov, S. V.; Esirkepov, T. Zh.; Kando, M.; Pegoraro, F.; Leemans, W. P.

    2015-03-13

    Radiation Pressure Acceleration is a highly efficient mechanism of laser driven ion acceleration, with the laser energy almost totally transferrable to the ions in the relativistic regime. There is a fundamental limit on the maximum attainable ion energy, which is determined by the group velocity of the laser. In the case of a tightly focused laser pulses, which are utilized to get the highest intensity, another factor limiting the maximum ion energy comes into play, the transverse expansion of the target. Transverse expansion makes the target transparent for radiation, thus reducing the effectiveness of acceleration. Utilization of an external guiding structure for the accelerating laser pulse may provide a way of compensating for the group velocity and transverse expansion effects.

  16. A hybrid structure gaseous detector for ion backflow suppression

    NASA Astrophysics Data System (ADS)

    Zhang, Yu-Lian; Qi, Hui-Rong; Hu, Bi-Tao; Wang, Hai-Yun; Ou-Yang, Qun; Chen, Yuan-Bo; Zhang, Jian; Wen, Zhi-Wen

    2017-05-01

    A new concept for a hybrid structure gaseous detector module with ion backflow suppression for the time projection chamber in a future circular collider is presented. It is a hybrid structure cascaded Gas Electron Multiplier (GEM) with a Micromegas detector. Both Micromegas and GEM have the capability to naturally reduce most of the ions produced in the amplification region. The GEM also acts as the preamplifer device and increases gas gain together with the Micromegas. Feasibility tests of the hybrid detector are performed using an 55Fe X-ray source. The energy resolution is better than 27% for 5.9 keV X-rays. It is demonstrated that a backflow ratio better than 0.2% can be reached in the hybrid readout structure at a gain of 5000. Supported by National Key Programme for S&T Research and Development (2016YFA0400400) and by National Natural Science Foundation of China (11275224)

  17. Metal ion influence on eumelanin fluorescence and structure

    NASA Astrophysics Data System (ADS)

    Sutter, Jens-Uwe; Birch, David J. S.

    2014-06-01

    Melanin has long been thought to have an unworkably weak and complex fluorescence, but here we study its intrinsic fluorescence in order to demonstrate how metal ions can be used to control the rate of formation, constituents and structure of eumelanin formed from the well-known laboratory auto-oxidation of 3,4-dihydroxy-L-phenylalanine (L-DOPA). The effect on eumelanin absorption and fluorescence of a range of solvated metal ions is reported including Cu, Zn, Ni, Na and K. Monovalent cations and Zn have little effect, but the effect of transition metal cations can be considerable. For example, at pH 10, copper ions are shown to accelerate the onset of eumelanin formation, but not the rate of formation once it commences, and simplify the usual complex structure and intrinsic fluorescence of eumelanin in a way that is consistent with an increased abundance of 5,5-dihydroxyindole-2-carboxylic acid (DHICA). The presence of a dominant 6 ns fluorescence decay time at 480 nm, when excited at 450 nm describes a distinct photophysical species, which we tentatively assign to small oligomers. Copper is well-known to normally quench fluorescence, but increasing amounts of copper surprisingly leads to an increase in the fluorescence decay time of eumelanin, while reducing the fluorescence intensity, suggesting copper modification of the excited state. Such results have bearing on diverse areas. The most accepted morphology for melanin is that of a graphite-like sheet structure, and one which readily binds metal ions, an interaction that is thought to have an important, though as yet unclear bearing on several areas of medicine including neurology. There is also increasing interest in bio-mimicry by preparing and labelling sheet structures with metal ions for new electronic and photonic materials.

  18. Atomic Data for Nebular Abundance Determinations: Photoionization and Recombination Properties of Xenon Ions

    NASA Astrophysics Data System (ADS)

    Sterling, Nicholas C.; Kerlin, Austin B.

    2016-01-01

    We present preliminary results of a study of the photoionization (PI) and recombination properties of low-charge Xe ions. The abundances of neutron(n)-capture elements (atomic number Z > 30) are of interest in planetary nebulae (PNe) since they can be enriched by slow n-capture nucleosynthesis (the ``s-process'') in the progenitor asymptotic giant branch (AGB) stars. Xe is particularly valuable, because it is the most widely-observed ``heavy-s'' species (Z > 40) in PNe. Its abundance relative to lighter n-capture elements can be used to determine s-process neutron exposures, and constrain s-process enrichment patterns as a function of progenitor metallicity. Using the atomic structure code AUTOSTRUCTURE (Badnell 2011, Comp. Phys. Comm., 182, 1528), we have computed multi-configuration Breit-Pauli distorted-wave PI cross sections and radiative recombination (RR) and dielectronic recombination (DR) rate coefficients for neutral through six-times ionized Xe, data which are critically needed for accurate Xe abundance determinations in ionized nebulae. We find good agreement between our computed direct PI cross sections and experimental measurements. Internal uncertainties are estimated for our calculations by using three different configuration interaction expansions for each ion, and by testing the sensitivity of our results to the radial orbital scaling parameters. As found for other n-capture elements (Sterling & Witthoeft 2011, A&A, 529, A147; Sterling 2011, A&A, 533, A62), DR is the dominant recombination mechanism for Xe ions at nebular temperatures (~104 K). Following Sterling et al. (2015, ApJS, 218, 25), these data will be added to nebular modeling codes to compute ionization correction factors for unobserved Xe ions in PNe, which will enable elemental Xe abundances to be determined with much higher accuracy than is currently possible. This work is supported by NSF award AST-1412928.

  19. Porous structure of ion exchange membranes investigated by various techniques.

    PubMed

    Kononenko, N; Nikonenko, V; Grande, D; Larchet, C; Dammak, L; Fomenko, M; Volfkovich, Yu

    2017-08-01

    A comparative review of various techniques is provided: mercury intrusion porosimetry, nitrogen sorption porosimetry, differential scanning calorimetry (DSC)-based thermoporosimetry, and standard contact porosimetry (SCP), which allows determining pore volume distribution versus pore radius/water binding energy in ion-exchange membranes (IEMs). IEMs in the swollen state have a labile structure involving micro-, meso- and macropores, whose size is a function of the external water vapor pressure. For such materials, the most appropriate methods for quantifying their porosity are DSC and SCP. Especially significant information is given by the SCP method allowing measuring porosimetric curves in a very large pore size range from 1 to 10(5)nm. Experimental results of water distribution in homogeneous and heterogeneous commercial and modified IEMs are presented. The effect of various factors on water distribution is reviewed, i.e. nature of polymeric matrix and functional groups, method for membrane preparation, membrane ageing. A special attention is given to the effect of membrane modification by embedding nanoparticles in their structure. The porosimetric curves are considered along with the results of electrochemical characterization involving the measurements of membrane conductivity, as well as diffusion and electroosmotic permeability. It is shown that addition of nanoparticles may lead to either increase or decrease of water content in IEMs, different ranges of pore size being affected. Hybrid membranes modified with hydrated zirconium dioxide exhibit much higher permselectivity in comparison with the pristine membranes. The diversity of the responses of membrane properties to their modification allows for formation of membranes suitable for fuel cells, electrodialysis or other applications. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Reduction and structural modification of zirconolite on He+ ion irradiation

    NASA Astrophysics Data System (ADS)

    Gupta, Merry; Kulriya, P. K.; Shukla, Rishabh; Dhaka, R. S.; Kumar, Raj; Ghumman, S. S.

    2016-07-01

    The immobilization of minor actinides and alkaline-earth metal is a major concern in nuclear industry due to their long-term radioactive contribution to the high level waste (HLW). Materials having zirconolite, pyrochlore, and perovskite structure are promising candidates for immobilization of HLW. The zirconolite which exhibits high radiation stability and corrosion resistance behavior is investigated for its radiation stability against alpha particles in the present study. CaZrTi2O7 pellets prepared using solid state reaction techniques, were irradiated with 30 keV He+ ions for the ion fluence varying from 1 × 1017 to 1 × 1021 ions/m2. Scanning electron microscopy (SEM) images of the un-irradiated sample exhibited well separated grains with average size of about 6.8 μm. On the ion irradiation, value of the average grains size was about 7.1 μm, and change in the microstructure was insignificant. The X-ray photoelectron spectroscopy (XPS) studies showed a shift in the core level peak position (of Ca 2p, Ti 2p and Zr 3d) towards lower binding energy with respect to pristine sample as well as loss of oxygen was also observed for sample irradiated with the ion fluence of 1 × 1020 ions/m2. These indicate a decrease in co-ordination number and the ionic character of Msbnd O bond. Moreover, core level XPS signal was not detected for sample irradiated with ion fluence of 1 × 1021 ions/m2, suggesting surface damage of the sample at this ion fluence. However, X-ray diffraction (XRD) studies showed that zirconolite was not amorphized even on irradiation up to a fluence order of 1 × 1021 ion/m2. But, significant decrease in peak intensity due to creation of defects and a marginal positive peak shift due to tensile strain induced by irradiation, were observed. Thus, XRD along with XPS investigation suggests that reduction, decrease in co-ordination number, and increase in covalency are responsible for the radiation damage in zirconolite.

  1. Structure of the alkali-metal-atom + strontium molecular ions: Towards photoassociation and formation of cold molecular ions

    SciTech Connect

    Aymar, M.; Dulieu, O.; Guerout, R.

    2011-08-14

    The potential energy curves, permanent and transition dipole moments, and the static dipolar polarizability, of molecular ions composed of one alkali-metal atom and a strontium ion are determined with a quantum chemistry approach. The molecular ions are treated as effective two-electron systems and are treated using effective core potentials including core polarization, large gaussian basis sets, and full configuration interaction. In the perspective of upcoming experiments aiming at merging cold atom and cold ion traps, possible paths for radiative charge exchange, photoassociation of a cold lithium or rubidium atom and a strontium ion are discussed, as well as the formation of stable molecular ions.

  2. Coherent structures in ion temperature gradient turbulence-zonal flow

    NASA Astrophysics Data System (ADS)

    Singh, Rameswar; Singh, R.; Kaw, P.; Gürcan, Ã.-. D.; Diamond, P. H.

    2014-10-01

    Nonlinear stationary structure formation in the coupled ion temperature gradient (ITG)-zonal flow system is investigated. The ITG turbulence is described by a wave-kinetic equation for the action density of the ITG mode, and the longer scale zonal mode is described by a dynamic equation for the m = n = 0 component of the potential. Two populations of trapped and untrapped drift wave trajectories are shown to exist in a moving frame of reference. This novel effect leads to the formation of nonlinear stationary structures. It is shown that the ITG turbulence can self-consistently sustain coherent, radially propagating modulation envelope structures such as solitons, shocks, and nonlinear wave trains.

  3. Membrane Protein Structure Determination in Membrana

    PubMed Central

    DING, YI; YAO, YONG; MARASSI, FRANCESCA M.

    2014-01-01

    CONSPECTUS The two principal components of biological membranes, the lipid bilayer and the proteins integrated within it, have coevolved for specific functions that mediate the interactions of cells with their environment. Molecular structures can provide very significant insights about protein function. In the case of membrane proteins, the physical and chemical properties of lipids and proteins are highly interdependent; therefore structure determination should include the membrane environment. Considering the membrane alongside the protein eliminates the possibility that crystal contacts or detergent molecules could distort protein structure, dynamics, and function and enables ligand binding studies to be performed in a natural setting. Solid-state NMR spectroscopy is compatible with three-dimensional structure determination of membrane proteins in phospholipid bilayer membranes under physiological conditions and has played an important role in elucidating the physical and chemical properties of biological membranes, providing key information about the structure and dynamics of the phospholipid components. Recently, developments in the recombinant expression of membrane proteins, sample preparation, pulse sequences for high-resolution spectroscopy, radio frequency probes, high-field magnets, and computational methods have enabled a number of membrane protein structures to be determined in lipid bilayer membranes. In this Account, we illustrate solid-state NMR methods with examples from two bacterial outer membrane proteins (OmpX and Ail) that form integral membrane β-barrels. The ability to measure orientation-dependent frequencies in the solid-state NMR spectra of membrane-embedded proteins provides the foundation for a powerful approach to structure determination based primarily on orientation restraints. Orientation restraints are particularly useful for NMR structural studies of membrane proteins because they provide information about both three

  4. Membrane protein structure determination in membrana.

    PubMed

    Ding, Yi; Yao, Yong; Marassi, Francesca M

    2013-09-17

    The two principal components of biological membranes, the lipid bilayer and the proteins integrated within it, have coevolved for specific functions that mediate the interactions of cells with their environment. Molecular structures can provide very significant insights about protein function. In the case of membrane proteins, the physical and chemical properties of lipids and proteins are highly interdependent; therefore structure determination should include the membrane environment. Considering the membrane alongside the protein eliminates the possibility that crystal contacts or detergent molecules could distort protein structure, dynamics, and function and enables ligand binding studies to be performed in a natural setting. Solid-state NMR spectroscopy is compatible with three-dimensional structure determination of membrane proteins in phospholipid bilayer membranes under physiological conditions and has played an important role in elucidating the physical and chemical properties of biological membranes, providing key information about the structure and dynamics of the phospholipid components. Recently, developments in the recombinant expression of membrane proteins, sample preparation, pulse sequences for high-resolution spectroscopy, radio frequency probes, high-field magnets, and computational methods have enabled a number of membrane protein structures to be determined in lipid bilayer membranes. In this Account, we illustrate solid-state NMR methods with examples from two bacterial outer membrane proteins (OmpX and Ail) that form integral membrane β-barrels. The ability to measure orientation-dependent frequencies in the solid-state NMR spectra of membrane-embedded proteins provides the foundation for a powerful approach to structure determination based primarily on orientation restraints. Orientation restraints are particularly useful for NMR structural studies of membrane proteins because they provide information about both three-dimensional structure

  5. Surface Structure and Lattice Dynamics of Alkali Halide Crystals Studied by High-Resolution Ion Scattering

    NASA Astrophysics Data System (ADS)

    Kido, Yoshiaki; Okazawa, Tetsuaki

    The rumpled surface structure and thermal lattice vibrations of KI(001) and RbI(001) were measured directly by high-resolution medium energy ion scattering (MEIS). The relaxation of interlayer distance between the top and second layer and the rumpling of the top and second layers were determined using the ion shadowing effect with an accuracy of 0.01 Å. From the displaced lattice positions determined above, we derived the dipole moments of the top- and second-layer ions self-consistently employing the polarizabilities estimated from the optical refractive index combined with the Clausius Mossotti relation. The balance between a short-range force and a long-range Coulombic one made it possible to judge the applicability of the short-range pair potentials proposed so far. We also determined the root-mean-square (rms) thermal vibration amplitudes of the bulk and the top-layer ions together with the correlations of the ions in the [001] and [101] strings by taking various kinds of scattering geometries. The results obtained were compared with those calculated from the molecular dynamics (MD) simulations based on a classical model using the dipole moments determined above and the Born Mayer type pair potential. The present MEIS results are in overall agreement with the MD simulations.

  6. Investigation of Semiconductor Surface Structure by Transmission Ion Channeling.

    NASA Astrophysics Data System (ADS)

    Lyman, Paul Francis

    The primary thrust of this dissertation is the investigation of the composition and structure of two important surface systems on Si, and the study of how this structure evolves under the influence of ion bombardment or film growth. I have studied the initial stages of oxidation of Si immediately following removal of a surface oxide by an HF etch. I have also studied the structure of Ge deposited on clean Si(100) at low temperatures. These systems are of considerable technological interest, but were chosen because they naturally pose fundamental questions regarding physical and chemical processes at surfaces. In the study of the oxidation of Si, I have focused on the influence of the bombarding ion beam in altering the structure and composition of the surface layer. Thus, the system then provides a natural vehicle to study ion-induced chemistry. In the study of low-temperature growth of Ge, I have focused on the structure of the Ge layer and the evolution of that structure upon further deposition or upon heating. This simple system is a model one for observing strained semiconductor heteroepitaxial growth. The primary probe for these studies was transmission channeling of MeV ions. The sensitivity of this technique to correlations between the substrate and an overlayer allowed us to make the following observations. The O, Si and H bound in the thin oxide formed after an HF etch and H_2O rinse occupy preferred positions with respect to the Si matrix. Upon ion bombardment, the O further reacts with the Si (the reaction proceeds linearly with the ion fluence) and the portion of the H that is uncorrelated to the substrate is preferentially desorbed. For the case of Ge growth on Si(100)-(2 x 1) at room temperature, a substantial fraction of the Ge films is strained to occupy sites having the lattice constant of the Si substrate (pseudomorphic growth). A model for film growth is proposed in which pseudomorphic domains constitute roughly half of the Ge films up to a

  7. A structural determinant required for RNA editing

    PubMed Central

    Tian, Nan; Yang, Yun; Sachsenmaier, Nora; Muggenhumer, Dominik; Bi, Jingpei; Waldsich, Christina; Jantsch, Michael F.; Jin, Yongfeng

    2011-01-01

    RNA editing by adenosine deaminases acting on RNAs (ADARs) can be both specific and non-specific, depending on the substrate. Specific editing of particular adenosines may depend on the overall sequence and structural context. However, the detailed mechanisms underlying these preferences are not fully understood. Here, we show that duplex structures mimicking an editing site in the Gabra3 pre-mRNA unexpectedly fail to support RNA editing at the Gabra3 I/M site, although phylogenetic analysis suggest an evolutionarily conserved duplex structure essential for efficient RNA editing. These unusual results led us to revisit the structural requirement for this editing by mutagenesis analysis. In vivo nuclear injection experiments of mutated editing substrates demonstrate that a non-conserved structure is a determinant for editing. This structure contains bulges either on the same or the strand opposing the edited adenosine. The position of these bulges and the distance to the edited base regulate editing. Moreover, elevated folding temperature can lead to a switch in RNA editing suggesting an RNA structural change. Our results indicate the importance of RNA tertiary structure in determining RNA editing. PMID:21427087

  8. Advances on surface structural determination by LEED.

    PubMed

    Soares, Edmar A; de Castilho, Caio M C; de Carvalho, Vagner E

    2011-08-03

    In the last 40 years, low energy electron diffraction (LEED) has proved to be the most reliable quantitative technique for surface structural determination. In this review, recent developments related to the theory that gives support to LEED structural determination are discussed under a critical analysis of the main theoretical approximation-the muffin-tin calculation. The search methodologies aimed at identifying the best matches between theoretical and experimental intensity versus voltage curves are also considered, with the most recent procedures being reviewed in detail.

  9. Correlation of ion dynamics and structure of superionic tellurite glasses

    SciTech Connect

    Dutta, D.; Ghosh, A.

    2008-01-28

    Ion dynamics and structure of a series of superionic AgI-doped silver tellurite glasses have been investigated in this paper. The composition dependence of the dc conductivity and the activation energy of these glasses has been compared with those of AgI-doped silver phosphate and borate glasses. We have observed that the conductivity increases and the activation energy decreases with increase of AgI content and that the tellurite glasses have higher conductivity than those for phosphate or borate glasses. We have analyzed the ac electrical data in the framework of the power law and the electric modulus formalisms. We have established a correlation between the crossover rate of the mobile silver ions and the rearrangement of the structural units in tellurite glasses. The scaling of the conductivity spectra has been used to interpret the temperature and composition dependence of the relaxation dynamics. Analysis of the dielectric relaxation in the framework of modulus formalism indicates an increase in the ion-ion cooperation in the glass compositions with increasing AgI content.

  10. Low energy electrons and swift ion track structure in PADC

    SciTech Connect

    Fromm, Michel; Quinto, Michele A.; Weck, Philippe F.; Champion, Christophe

    2015-05-27

    The current work aims at providing an accurate description of the ion track-structure in poly-allyl dyglycol carbonate (PADC) by using an up-to-date Monte-Carlo code-called TILDA-V (a French acronym for Transport d’Ions Lourds Dans l’Aqua & Vivo). In this simulation the ion track-structure in PADC is mainly described in terms of ejected electrons with a particular attention done to the Low Energy Electrons (LEEs). After a brief reminder of the most important channels through which LEEs are prone to break a chemical bond, we will report on the simulated energetic distributions of LEEs along an ion track in PADC for particular incident energies located on both sides of the Bragg-peak position. Lastly, based on the rare data dealing with LEEs interaction with polymers or organic molecules, we will emphasise the role played by the LEEs in the formation of a latent track in PADC, and more particularly the one played by the sub-ionization electrons.

  11. Low energy electrons and swift ion track structure in PADC

    DOE PAGES

    Fromm, Michel; Quinto, Michele A.; Weck, Philippe F.; ...

    2015-05-27

    The current work aims at providing an accurate description of the ion track-structure in poly-allyl dyglycol carbonate (PADC) by using an up-to-date Monte-Carlo code-called TILDA-V (a French acronym for Transport d’Ions Lourds Dans l’Aqua & Vivo). In this simulation the ion track-structure in PADC is mainly described in terms of ejected electrons with a particular attention done to the Low Energy Electrons (LEEs). After a brief reminder of the most important channels through which LEEs are prone to break a chemical bond, we will report on the simulated energetic distributions of LEEs along an ion track in PADC for particularmore » incident energies located on both sides of the Bragg-peak position. Lastly, based on the rare data dealing with LEEs interaction with polymers or organic molecules, we will emphasise the role played by the LEEs in the formation of a latent track in PADC, and more particularly the one played by the sub-ionization electrons.« less

  12. Low energy electrons and swift ion track structure in PADC

    NASA Astrophysics Data System (ADS)

    Fromm, Michel; Quinto, Michele A.; Weck, Philippe F.; Champion, Christophe

    2015-10-01

    The current work aims at providing an accurate description of the ion track-structure in poly-allyl dyglycol carbonate (PADC) by using an up-to-date Monte-Carlo code-called TILDA-V (a French acronym for Transport d'Ions Lourds Dans l'Aqua & Vivo). In this simulation the ion track-structure in PADC is mainly described in terms of ejected electrons with a particular attention done to the Low Energy Electrons (LEEs). After a brief reminder of the most important channels through which LEEs are prone to break a chemical bond, we will report on the simulated energetic distributions of LEEs along an ion track in PADC for particular incident energies located on both sides of the Bragg-peak position. Finally, based on the rare data dealing with LEEs interaction with polymers or organic molecules, we will emphasise the role played by the LEEs in the formation of a latent track in PADC, and more particularly the one played by the sub-ionization electrons.

  13. Studying Radiation Damage in Structural Materials by Using Ion Accelerators

    NASA Astrophysics Data System (ADS)

    Hosemann, Peter

    2011-02-01

    Radiation damage in structural materials is of major concern and a limiting factor for a wide range of engineering and scientific applications, including nuclear power production, medical applications, or components for scientific radiation sources. The usefulness of these applications is largely limited by the damage a material can sustain in the extreme environments of radiation, temperature, stress, and fatigue, over long periods of time. Although a wide range of materials has been extensively studied in nuclear reactors and neutron spallation sources since the beginning of the nuclear age, ion beam irradiations using particle accelerators are a more cost-effective alternative to study radiation damage in materials in a rather short period of time, allowing researchers to gain fundamental insights into the damage processes and to estimate the property changes due to irradiation. However, the comparison of results gained from ion beam irradiation, large-scale neutron irradiation, and a variety of experimental setups is not straightforward, and several effects have to be taken into account. It is the intention of this article to introduce the reader to the basic phenomena taking place and to point out the differences between classic reactor irradiations and ion irradiations. It will also provide an assessment of how accelerator-based ion beam irradiation is used today to gain insight into the damage in structural materials for large-scale engineering applications.

  14. Automated identification of elemental ions in macromolecular crystal structures

    SciTech Connect

    Echols, Nathaniel Morshed, Nader; Afonine, Pavel V.; McCoy, Airlie J.; Read, Randy J.; Terwilliger, Thomas C.; Adams, Paul D.

    2014-04-01

    The solvent-picking procedure in phenix.refine has been extended and combined with Phaser anomalous substructure completion and analysis of coordination geometry to identify and place elemental ions. Many macromolecular model-building and refinement programs can automatically place solvent atoms in electron density at moderate-to-high resolution. This process frequently builds water molecules in place of elemental ions, the identification of which must be performed manually. The solvent-picking algorithms in phenix.refine have been extended to build common ions based on an analysis of the chemical environment as well as physical properties such as occupancy, B factor and anomalous scattering. The method is most effective for heavier elements such as calcium and zinc, for which a majority of sites can be placed with few false positives in a diverse test set of structures. At atomic resolution, it is observed that it can also be possible to identify tightly bound sodium and magnesium ions. A number of challenges that contribute to the difficulty of completely automating the process of structure completion are discussed.

  15. A Floating Potential Method for Determining Ion Density

    NASA Astrophysics Data System (ADS)

    Evans, John D.; Chen, Francis F.

    2001-10-01

    The density n in partially ionized discharges is often found from the saturation ion current Ii of a cylindrical Langmuir probe. Collisionless probe theories, however, disagree with measured I - V curves probably because of collisions^1. We use a heuristic method that yields n from probe data agreeing with microwave interferometry. Probe current I is raised to the 4/3 power and fitted to a straight line on an I^4/3-V plot. The line is extrapolated to the floating potential V_f, thus approximating I_i(V_f). The sheath thickness d_sh for V = Vf is calculated from the Child-Langmuir (CL) law, and applying the Bohm sheath criterion to the surface at r_sh = Rp + d_sh yields n when Ii = I_i(V_f). This method works, but it cannot be justified by theory. Neglected are (a) cylindrical convergence of the ion charge, (b) finite ion energy at r = r_sh, (c) ions orbiting the probe, and (d) escape of ions axially. The Allen-Boyd-Reynolds theory, which treats (a) and (b) and neglects (c) and (d), gives too low n's. Apparently the errors self-cancel, and the simple Vf method gives the right result. ^1 F.F. Chen, Phys. Plasmas 8, 3029 (2001).

  16. Sensor-actuator system for dynamic chloride ion determination.

    PubMed

    de Graaf, Derk Balthazar; Abbas, Yawar; Gerrit Bomer, Johan; Olthuis, Wouter; van den Berg, Albert

    2015-08-12

    Chloride is a crucial anion for various analytical applications from biological to environmental applications. In order to measure the chloride ion concentration, a measurement system is needed which can detect this concentration for prolonged times reliably. Chronopotentiometry is a technique which does not need a long term stable reference electrode and is therefore very suitable for prolonged ion concentration measurements. As the used electrode might be fouled by reaction products, this work focuses on a chronopotentiometric approach with a separated sensing electrode (sensor) and actuating electrode (actuator). Both actuation and sensor electrode are made of Ag/AgCl. A constant current is applied to the actuator and will start the reaction between Ag and Cl-, while the resulting Cl- ion concentration change is observed through the sensor, which is placed close to the actuator. The time it takes to locally deplete the Cl- ions is called transition time. Experiments were performed to verify the feasibility of this approach. The performed experiments show that the sensor detects the local concentration changes resulting from the current applied to the actuator. A linear relation between the Cl- ion concentration and the square root of the transition time was observed, just as was predicted by theory. The calibration curves for different chips showed that both a larger sensor and a larger distance between sensor and actuator resulted in a larger time delay between the transition time detected at the actuator and the sensor.

  17. Filamented ion tail structures at Titan: A hybrid simulation study

    NASA Astrophysics Data System (ADS)

    Feyerabend, Moritz; Simon, Sven; Motschmann, Uwe; Liuzzo, Lucas

    2015-11-01

    This study investigates the processes that lead to the detection of split signatures in ion density during several crossings of the Cassini spacecraft through Titan's mid-range plasma tail (T9, T63, and T75). During each of these flybys, the Cassini Plasma Spectrometer detected Titan's ionospheric ion population twice; i.e., the spacecraft passed through two spatially separated regions where cold ions were detected, with the regions also being dominated by ions of different masses in the case of T9. Whether this filamented tail structure is an omnipresent feature of Titan's plasma interaction or a result of non-stationary upstream conditions during specific flybys is still unclear. To explain these features, we apply the hybrid simulation code AIKEF (kinetic ions and fluid electrons). Our model includes chemical reactions as well as a realistic photoionization model for a sophisticated description of the ionospheric composition of Titan. Our simulations show that the filamentation of Titan's tail is indeed a common feature of the moon's plasma interaction. Light ionospheric species escape along draped magnetic field lines to form a parabolically shaped filament structure, which is mainly seen in planes that contain the upstream magnetospheric magnetic field and the upstream flow direction. In addition, transport of ions of all species from the ramside towards downstream produces a cone structure behind Titan, with a region of decreased density inside and filaments of 1-2 RT (RT=2575 km) thickness and enhanced density at the surface of the cone. Spacecraft trajectories that penetrate these structures allow for the detection of split signatures in the tail. The orientation of the upstream magnetic field and plasma flow as well as local time effects (i.e., Titan's orbital position) influence the location of the filaments in the tail and can also cause asymmetries in their sizes and densities. The detection of the split signatures along a spacecraft trajectory may

  18. Photoprotein Aequorin Structure Determination by NMR Spectroscopy

    DTIC Science & Technology

    1993-07-09

    AD-A267 066 July 9, 1993 Final Rept. 15 Apr. 1992-31 Dec. 1992 Photoprotein Aequorin Structure Determination by NMR Spectroscopy Grant # N00014-92-J...specific assignments of proteins using homo- and heteronuclear 2D-NMR. Assignments were made for approximately 95% of the 1H and 15N atoms of Bacillus... structure of r-aequorin is included. 028 93-1584993 7 . -,I m!,,•slil Aequorin, bioluminescence, nuclear magnetic reburndie, 3D structure . Unclassified

  19. Performance optimized, small structurally integrated ion thruster system

    NASA Technical Reports Server (NTRS)

    Hyman, J., Jr.

    1973-01-01

    A 5-cm structurally integrated ion thruster has been developed for attitude control and stationkeeping of synchronous satellites. As optimized with a conventional ion extraction system, the system demonstrates a thrust T = 0.47 mlb at a beam voltage of 1600 V, total mass efficiency of 76%, and electrical efficiency of 56%. Under the subject contract effort, no significant performance change was noted for operation with two dimensional electrostatic thrust-vectoring grids. Structural integrity with the vectoring grids was demonstrated for shock (+ or - 30 G), sinusoidal (9 G), and random (19.9 G rms) accelerations. System envelope is 31.2 cm long by 13.4 cm flange bolt circle, with a mass of 9.0 Kg, including 6.8 Kg mercury propellant.

  20. Examining the Influence of Phosphorylation on Peptide Ion Structure by Ion Mobility Spectrometry-Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Glover, Matthew S.; Dilger, Jonathan M.; Acton, Matthew D.; Arnold, Randy J.; Radivojac, Predrag; Clemmer, David E.

    2016-05-01

    Ion mobility spectrometry-mass spectrometry (IMS-MS) techniques are used to study the general effects of phosphorylation on peptide structure. Cross sections for a library of 66 singly phosphorylated peptide ions from 33 pairs of positional isomers, and unmodified analogues were measured. Intrinsic size parameters (ISPs) derived from these measurements yield calculated collision cross sections for 85% of these phosphopeptide sequences that are within ±2.5% of experimental values. The average ISP for the phosphoryl group (0.64 ± 0.05) suggests that in general this moiety forms intramolecular interactions with the neighboring residues and peptide backbone, resulting in relatively compact structures. We assess the capability of ion mobility to separate positional isomers (i.e., peptide sequences that differ only in the location of the modification) and find that more than half of the isomeric pairs have >1% difference in collision cross section. Phosphorylation is also found to influence populations of structures that differ in the cis/ trans orientation of Xaa-Pro peptide bonds. Several sequences with phosphorylated Ser or Thr residues located N-terminally adjacent to Pro residues show fewer conformations compared to the unmodified sequences.

  1. Determination of ammonia in ethylene using ion mobility spectrometry

    NASA Technical Reports Server (NTRS)

    Cross, J. H.; Limero, T. F.; Lane, J. L.; Wang, F.

    1997-01-01

    A simple procedure to analyze ammonia in ethylene by ion mobility spectrometry is described. The spectrometer is operated with a silane polymer membrane., 63Ni ion source, H+ (H2O)n reactant ion, and nitrogen drift and source gas. Ethylene containing parts per billion (ppb) (v/v) concentrations of ammonia is pulled across the membrane and diffuses into the spectrometer. Preconcentration or preseparation is unnecessary, because the ethylene in the spectrometer has no noticeable effect on the analytical results. Ethylene does not polymerize in the radioactive source. Ethylene's flammability is negated by the nitrogen inside the spectrometer. Response to ammonia concentrations between 200 ppb and 1.5 ppm is near linear, and a detection limit of 25 ppb is calculated.

  2. Determination of ammonia in ethylene using ion mobility spectrometry

    NASA Technical Reports Server (NTRS)

    Cross, J. H.; Limero, T. F.; Lane, J. L.; Wang, F.

    1997-01-01

    A simple procedure to analyze ammonia in ethylene by ion mobility spectrometry is described. The spectrometer is operated with a silane polymer membrane., 63Ni ion source, H+ (H2O)n reactant ion, and nitrogen drift and source gas. Ethylene containing parts per billion (ppb) (v/v) concentrations of ammonia is pulled across the membrane and diffuses into the spectrometer. Preconcentration or preseparation is unnecessary, because the ethylene in the spectrometer has no noticeable effect on the analytical results. Ethylene does not polymerize in the radioactive source. Ethylene's flammability is negated by the nitrogen inside the spectrometer. Response to ammonia concentrations between 200 ppb and 1.5 ppm is near linear, and a detection limit of 25 ppb is calculated.

  3. Ion aggregation in high salt solutions. IV. Graph-theoretical analyses of ion aggregate structure and water hydrogen bonding network

    NASA Astrophysics Data System (ADS)

    Choi, Jun-Ho; Cho, Minhaeng

    2015-09-01

    Ions in high salt solutions form a variety of ion aggregates, from ion pairs to clusters and networks. Their influences on water hydrogen bonding (H-bonding) network structures have long been of great interest. Recently, we have shown that the morphological structures of ion aggregates can be analyzed by using a spectral graph analysis theory, where each ion cluster or ion network is represented by a properly defined graph with edges and vertices. Here, to further examine the network properties of ion aggregates and water H-bonding networks in high salt solutions, we consider a few representative graph-theoretical descriptors: clustering coefficient, minimum path length, global efficiency, and degree distribution of ion aggregates. From the molecular dynamics trajectories, these graph theoretical properties of ion aggregates and water structures in NaCl and kosmotropic solutions are calculated and shown to be strongly dependent on the two types of ion aggregate structures, i.e., ion cluster and ion network. Ion clusters in high NaCl solutions exhibit typical behaviors of scale free network. The corresponding graph theoretical properties of ion networks in high KSCN solutions are notably different from those of NaCl ion clusters and furthermore they are very similar to those of water hydrogen-bonding network. The present graph-theoretical analysis results indicate that the high solubility limits of KSCN and other ion-network-forming salts might originate from their ability to form a large scale morphological network that can be intertwined with co-existing water H-bonding network. Furthermore, it is shown that the graph-theoretical properties of water H-bonding network structures do not strongly depend on the nature of dissolved ions nor on the morphological structures of ion aggregates, indicating that water's H-bonding interaction and network-forming capability are highly robust. We anticipate that the present graph-theoretical analysis results of high salt

  4. Ion aggregation in high salt solutions. IV. Graph-theoretical analyses of ion aggregate structure and water hydrogen bonding network.

    PubMed

    Choi, Jun-Ho; Cho, Minhaeng

    2015-09-14

    Ions in high salt solutions form a variety of ion aggregates, from ion pairs to clusters and networks. Their influences on water hydrogen bonding (H-bonding) network structures have long been of great interest. Recently, we have shown that the morphological structures of ion aggregates can be analyzed by using a spectral graph analysis theory, where each ion cluster or ion network is represented by a properly defined graph with edges and vertices. Here, to further examine the network properties of ion aggregates and water H-bonding networks in high salt solutions, we consider a few representative graph-theoretical descriptors: clustering coefficient, minimum path length, global efficiency, and degree distribution of ion aggregates. From the molecular dynamics trajectories, these graph theoretical properties of ion aggregates and water structures in NaCl and kosmotropic solutions are calculated and shown to be strongly dependent on the two types of ion aggregate structures, i.e., ion cluster and ion network. Ion clusters in high NaCl solutions exhibit typical behaviors of scale free network. The corresponding graph theoretical properties of ion networks in high KSCN solutions are notably different from those of NaCl ion clusters and furthermore they are very similar to those of water hydrogen-bonding network. The present graph-theoretical analysis results indicate that the high solubility limits of KSCN and other ion-network-forming salts might originate from their ability to form a large scale morphological network that can be intertwined with co-existing water H-bonding network. Furthermore, it is shown that the graph-theoretical properties of water H-bonding network structures do not strongly depend on the nature of dissolved ions nor on the morphological structures of ion aggregates, indicating that water's H-bonding interaction and network-forming capability are highly robust. We anticipate that the present graph-theoretical analysis results of high salt

  5. Neutral Exosphere Densities and Structures at Titan Inferred from Pickup Ions Observed by CAPS

    NASA Astrophysics Data System (ADS)

    Hartle, R. E.; Sittler, E. C.; Neubauer, F. M.; Johnson, R. E.; Crary, F.; McComas, D. J.; Young, D. T.; Coates, A. J.; Simpson, D. J.; Bolton, S.; Reisenfeld, D.; Szego, K.; Berthelier, J.

    2005-12-01

    Measurements of pickup ions, born from neutral exospheres imbedded in moving plasmas, can be used to determine the composition and structure of the parent neutral exosphere constituents [1]. Pickup ions have been observed in Saturn's rotating magnetosphere near Titan by the Cassini Plasma Spectrometer (CAPS) instrument during the Cassini orbiter's recent flybys of the moon. Pickup ions observed by CAPS include H+, H2+, N+/CH2+, CH4+, and N2+. These ions slow down Saturn's magnetospheric plasma beyond Titan's ionosphere through mass loading. Because of its relatively high mass and high concentration, CH4+ is the dominant mass loading ion. The other ions make negligible contributions to the mass loading process except for N2+ just above the ionopause, where its concentration becomes important. The phase space densities of pickup ions are sensitive functions of the spatial variations of the parent exosphere gasses of the pickup ions [2]. Accounting for such variations, model phase space densities [2], derived from the Vlasov equation, are used in an algorithm to obtain ion density and velocity moments from CAPS measurements. The model implicitly maps an ions trajectory from its observation point to its source point. The analysis shows that because the gyroradius of CH4+ is much greater than the scale height of the source gas, CH4, the ion fluxes are beamlike with velocities distributed over a narrow range. The observed pickup ion velocities are found to be in ring distributions, with the light ion H+ occupying all of its allowed velocities and CH4+ only a small portion of its ring velocities. Applying the algorithm, exosphere densities are inferred. Using CAPS time-of-flight data and empirical cracking patterns, we show that the 14 amu ion is more likely N+. We compare ratios of the inferred N and CH4 exosphere densities with existing exosphere models. 1. Hartle, R. E., K. W. Ogilvie and C. S. Wu, Planet Space Sci., 21, 2181, 1973. 2. Hartle, R. E. and E. C. Sittler

  6. Hydrodynamic theory for ion structure and stopping power in quantum plasmas.

    PubMed

    Shukla, P K; Akbari-Moghanjoughi, M

    2013-04-01

    We present a theory for the dynamical ion structure factor (DISF) and ion stopping power in an unmagnetized collisional quantum plasma with degenerate electron fluids and nondegenerate strongly correlated ion fluids. Our theory is based on the fluctuation dissipation theorem and the quantum plasma dielectric constant that is deduced from a linearized viscoelastic quantum hydrodynamical (LVQHD) model. The latter incorporates the essential physics of quantum forces, which are associated with the quantum statistical pressure, electron-exchange, and electron-correlation effects, the quantum electron recoil effect caused by the dispersion of overlapping electron wave functions that control the dynamics of degenerate electron fluids, and the viscoelastic properties of strongly correlated ion fluids. Both degenerate electrons and nondegenerate strongly correlated ions are coupled with each other via the space charge electric force. Thus, our LVQHD theory is valid for a collisional quantum plasma at atomic scales with a wide range of the ion coupling parameter, the plasma composition, and plasma number densities that are relevant for compressed plasmas in laboratories (inertial confinement fusion schemes) and in astrophysical environments (e.g., warm dense matter and the cores of white dwarf stars). It is found that quantum electron effects and viscoelastic properties of strongly correlated ions significantly affect the features of the DISF and the ion stopping power (ISP). Unlike previous theories, which have studied ion correlations in terms of the ion coupling parameter, by neglecting the essential physics of collective effects that are competing among each other, we have here developed a method to evaluate the dependence of the plasma static and dynamical features in terms of individual parameters, like the Wigner-Seitz radius, the ion atomic number, and the ion temperature. It is found that due to the complex nature of charge screening in quantum plasmas, the ion

  7. Representing Personal Determinants in Causal Structures.

    ERIC Educational Resources Information Center

    Bandura, Albert

    1984-01-01

    Responds to Staddon's critique of the author's earlier article and addresses issues raised by Staddon's (1984) alternative models of causality. The author argues that it is not the formalizability of causal processes that is the issue but whether cognitive determinants of behavior are reducible to past stimulus inputs in causal structures.…

  8. Applying ion-molecule reactions to studies of gas-phase protein structure

    SciTech Connect

    Ogorzalek Loo, R.R.; Loo, J.A.; Smith, R.D.

    1992-06-01

    Whether solution phase differences in protein higher order structure persist in the gas phase, is examined by means of proton transfer reactions on ions generated by electrospray ionization of different solution conformations. Ion-molecule reactions were carried out in the atmosphere-vacuum interface of a quadrupole mass spectrometer with a Y-shaped capillary inlet-reactor. An amine (dimethyl-, trimethyl-, or diethyl-) were delivered to one inlet arm. Reactivities of bovine cytochrome c ions sprayed from denatured and native solutions were determined; the ions generated shifted to about the same charge states. Addition of equal amounts of amine to ions generated from different solution conformations of bovine ubiquitin also yielded similar final charge states; however, the average charge state increased with temperature. Myoglobin and apomyoglobin also yielded similar final charge states. The results suggest that for the non-disulfide linked proteins, either there are not significant differences in gas phase higher order structure, or proton transfer reactions are not sensitive enough to detect higher order structural differences arising from noncovalent interactions. 2 refs, 2 figs. (DLC)

  9. Ion transport in a model gramicidin channel. Structure and thermodynamics.

    PubMed Central

    Roux, B; Karplus, M

    1991-01-01

    The potential of mean force for Na+ and K+ ions as a function of position in the interior of a periodic poly(L,D)-alanine model for the gramicidin beta-helix is calculated with a detailed atomic model and realistic interactions. The calculated free energy barriers are 4.5 kcal/mol for Na+ and 1.0 kcal/mol for K+. A decomposition of the free energy demonstrates that the water molecules make a significant contribution to the free energy of activation. There is an increase in entropy at the transition state associated with greater fluctuations. Analysis reveals that the free energy profile of ions in the periodic channel is controlled not by the large interaction energy involving the ion but rather by the weaker water-water, water-peptide and peptide-peptide hydrogen bond interactions. The interior of the channel retains much of the solvation properties of a liquid in its interactions with the cations. Of particular importance is the flexibility of the helix, which permits it to respond to the presence of an ion in a fluidlike manner. The distortion of the helix is local (limited to a few carbonyls) because the structure is too flexible to transmit a perturbation to large distances. The plasticity of the structure (i.e., the property to deform without generating a large energy stress) appears to be an essential factor in the transport of ions, suggesting that a rigid helix model would be inappropriate. Images FIGURE 1 FIGURE 10 PMID:1714305

  10. Imaging and structural studies of DNA-protein complexes and membrane ion channels.

    PubMed

    Marini, M; Limongi, T; Falqui, A; Genovese, A; Allione, M; Moretti, M; Lopatin, S; Tirinato, L; Das, G; Torre, B; Giugni, A; Cesca, F; Benfenati, F; Di Fabrizio, E

    2017-02-23

    In bio-imaging by electron microscopy, damage of the sample and limited contrast are the two main hurdles for reaching high image quality. We extend a new preparation method based on nanofabrication and super-hydrophobicity to the imaging and structural studies of nucleic acids, nucleic acid-protein complexes (DNA/Rad51 repair protein complex) and neuronal ion channels (gap-junction, K(+) and GABAA channels) as paradigms of biological significance and increasing complexity. The preparation method is based on the liquid phase and is compatible with physiological conditions. Only in the very last stage, samples are dried for TEM analysis. Conventional TEM and high-resolution TEM (HRTEM) were used to achieve a resolution of 3.3 and 1.5 Å, respectively. The EM dataset quality allows the determination of relevant structural and metrological information on the DNA structure, DNA-protein interactions and ion channels, allowing the identification of specific macromolecules and their structure.

  11. Method of fan sound mode structure determination

    NASA Technical Reports Server (NTRS)

    Pickett, G. F.; Sofrin, T. G.; Wells, R. W.

    1977-01-01

    A method for the determination of fan sound mode structure in the Inlet of turbofan engines using in-duct acoustic pressure measurements is presented. The method is based on the simultaneous solution of a set of equations whose unknowns are modal amplitude and phase. A computer program for the solution of the equation set was developed. An additional computer program was developed which calculates microphone locations the use of which results in an equation set that does not give rise to numerical instabilities. In addition to the development of a method for determination of coherent modal structure, experimental and analytical approaches are developed for the determination of the amplitude frequency spectrum of randomly generated sound models for use in narrow annulus ducts. Two approaches are defined: one based on the use of cross-spectral techniques and the other based on the use of an array of microphones.

  12. Combining the Power of Irmpd with Ion-Molecule Reactions: the Structure and Reactivity of Radical Ions of Cysteine and its Derivatives

    NASA Astrophysics Data System (ADS)

    Lesslie, Michael; Osburn, Sandra; Berden, Giel; Oomens, J.; Ryzhov, Victor

    2015-06-01

    Most of the work on peptide radical cations has involved protons as the source of charge. Nonetheless, using metal ions as charge sources often offers advantages like stabilization of the structure via multidentate coordination and the elimination of the "mobile proton". Moreover, characterization of metal-bound amino acids is of general interest as the interaction of peptide side chains with metal ions in biological systems is known to occur extensively. In the current study, we generate thiyl radicals of cysteine and homocysteine in the gas phase complexed to alkali metal ions. Subsequently, we utilize infrared multiple-photon dissociation (IRMPD) and ion-molecule reactions (IMR) to characterize the structure and reactivity of these radical ions. Our group has worked extensively with the cysteine-based radical cations and anions, characterizing the gas-phase reactivity and rearrangement of the amino acid and several of its derivatives. In a continuation of this work, we are perusing the effects of metal ions as the charge bearing species on the reactivity of the sulfur radical. Our S-nitroso chemistry can easily be used in conjunction with metal ion coordination to produce initial S-based radicals in peptide radical-metal ion complexes. In all cases we have been able to achieve radical formation with significant yield to study reactivity. Ion-molecule reactions of metallated radicals with allyl iodide, dimethyl disulfide, and allyl bromide have all shown decreasing reactivity going down group 1A. Recently, we determined the experimental IR spectra for the homocysteine radical cation with Li+, Na+, and K+ as the charge bearing species at the FELIX facility. For comparison, the protonated IR spectrum of homocysteine has previously been obtained by our group. A preliminary match of the IR spectra has been confirmed. Finally, calculations are underway to determine the bond distances of all the metal adduct structures.

  13. Structure, dynamics, and ion conductance of the phospholamban pentamer.

    PubMed

    Maffeo, Christopher; Aksimentiev, Aleksei

    2009-06-17

    A 52-residue membrane protein, phospholamban (PLN) is an inhibitor of an adenosine-5'-triphosphate-driven calcium pump, the Ca2+-ATPase. Although the inhibition of Ca2+-ATPase involves PLN monomers, in a lipid bilayer membrane, PLN monomers form stable pentamers of unknown biological function. The recent NMR structure of a PLN pentamer depicts cytoplasmic helices extending normal to the bilayer in what is known as the bellflower conformation. The structure shows transmembrane helices forming a hydrophobic pore 4 A in diameter, which is reminiscent of earlier reports of possible ion conductance through PLN pentamers. However, recent FRET measurements suggested an alternative structure for the PLN pentamer, known as the pinwheel model, which features a narrower transmembrane pore and cytoplasmic helices that lie against the bilayer. Here, we report on structural dynamics and conductance properties of the PLN pentamers from all-atom (AA) and coarse-grained (CG) molecular dynamics simulations. Our AA simulations of the bellflower model demonstrate that in a lipid bilayer membrane or a detergent micelle, the cytoplasmic helices undergo large structural fluctuations, whereas the transmembrane pore shrinks and becomes asymmetric. Similar asymmetry of the transmembrane region was observed in the AA simulations of the pinwheel model; the cytoplasmic helices remained in contact with the bilayer. Using the CG approach, structural dynamics of both models were investigated on a microsecond timescale. The cytoplasmic helices of the CG bellflower model were observed to fall against the bilayer, whereas in the CG pinwheel model the conformation of the cytoplasmic helices remained stable. Using steered molecular dynamics simulations, we investigated the feasibility of ion conductance through the pore of the bellflower model. The resulting approximate potentials of mean force indicate that the PLN pentamer is unlikely to function as an ion channel.

  14. The Determination of Atmospheric Fluoride with a Specific Ion Electrode

    NASA Technical Reports Server (NTRS)

    Feldstein, M.; Levaggi, D. A.

    1971-01-01

    Atmospheric fluoride is collected on lime-coated filter paper exposed to the ambient atmosphere for 30-day periods. The fluoride is eluted from the paper and analyzed with the use of a fluoride specific ion electrode. The technique permits evaluation of potential fluoride sources in terms of downwind concentrations and provides a simple, rapid procedure for the analysis of large numbers of samples.

  15. Dynamics of lithium ions in borotellurite mixed former glasses: Correlation between the characteristic length scales of mobile ions and glass network structural units

    SciTech Connect

    Shaw, A.; Ghosh, A.

    2014-10-28

    We have studied the mixed network former effect on the dynamics of lithium ions in borotellurite glasses in wide composition and temperature ranges. The length scales of ion dynamics, such as characteristic mean square displacement and spatial extent of sub-diffusive motion of lithium ions have been determined from the ac conductivity and dielectric spectra, respectively, in the framework of linear response theory. The relative concentrations of different network structural units have been determined from the deconvolution of the FTIR spectra. A direct correlation between the ion dynamics and the characteristic length scales and the relative concentration of BO{sub 4} units has been established for different compositions of the borotellurite glasses.

  16. Determination of rheogenic ion transport in rat proximal colon in vivo.

    PubMed

    Haag, K; Lübcke, R; Knauf, H; Berger, E; Gerok, W

    1985-01-01

    A direct clamping technique is demonstrated, which allows monitoring of rapid changes of the short-circuit current (Isc) and the specific transepithelial resistance (Rm) as well as measurement of ion fluxes under short-circuit conditions in vivo. Due to the cylindrical symmetry of the colon the intraluminal electrode was devised as a centrally fixed silver rod, by which radial current injection was achieved. The geometrical arrangement of the electrodes guaranteed zero potential difference (PD) along the whole axis of the colon segment. The Isc was determined to 3.3 +/- 0.7 mueq h-1 cm-2 and Rm equal to 121 +/- 5 omega cm2. These data obtained by direct short-circuiting agree well with our earlier Rm and Isc data based on cable analysis, where the Isc was calculated from the open-circuit PD and Rm. This is considered as evidence for the reliability of the two independent in vivo techniques. Their validity was confirmed by the expected effects of drugs acting on rheogenic ion transport. Both the indirect (via Rm) as well as the direct Isc determination may be used alternatively as required; one may serve to match the other. For larger tubular structures like the rat colon the direct clamping should be preferred as the standard procedure for the Isc determination in vivo.

  17. Crystal structure of meteoritic schreibersites: determination of absolute structure

    NASA Astrophysics Data System (ADS)

    Skála, Roman; Císařová, Ivana

    Minerals of the schreibersite nickelphosphide series (Fe,Ni)3P crystallize in the non-centrosymmetric space group Ibar 4. As a consequence, they can possess two different spatial arrangements of the constituting atoms within the unit cell, related by the inversion symmetry operation. Here, we present the crystal structure refinements from single crystal X-ray diffraction data for schreibersite grains from iron meteorites Acuña, Carlton, Hex River Mts. (three different crystals), Odessa (two different crystals), Sikhote Alin, and Toluca aiming for the determination of the absolute structure of the examined crystals. The crystals studied cover the composition range from 58 mol% to 80 mol% Fe3P end-member. Unit-cell parameter a and volume of the unit cell V, as well as certain topological structural parameters tightly correlate with Fe3P content. Unit-cell parameter c, on the other hand, does not show such strong correlation. Eight of the nine crystal structure refinements allowed unambiguous absolute structure assignment. The single crystal extracted from Toluca is, however, of poor quality and consequently the structure refinement did not provide as good results as the rest of the materials. Also, this crystal has only weak inversion distinguishing power to provide unequivocal absolute structure determination. Six of the eight unambiguous absolute structure determinations indicated inverted atomic arrangement compared to that reported in earlier structure refinements (here called standard). Only two grains, one taken from Odessa iron and the other from the Hex River Mts. meteorite, reveal the dominance of standard crystal structure setting.

  18. Structural evolution of zirconium carbide under ion irradiation

    NASA Astrophysics Data System (ADS)

    Gosset, D.; Dollé, M.; Simeone, D.; Baldinozzi, G.; Thomé, L.

    2008-02-01

    Zirconium carbide is one of the candidate materials to be used for some fuel components of the high temperature nuclear reactors planned in the frame of the Gen-IV project. Few data exist regarding its behaviour under irradiation. We have irradiated ZrC samples at room temperature with slow heavy ions (4 MeV Au, fluence from 10 11 to 5 × 10 15 cm -2) in order to simulate neutron irradiations. Grazing incidence X-Ray diffraction (GIXRD) and transmission electron microscopy (TEM) analysis have been performed in order to study the microstructural evolution of the material versus ion fluence. A high sensitivity to oxidation is observed with the formation of zirconia precipitates during the ion irradiations. Three damage stages are observed. At low fluence (<10 12 cm -2), low modifications are observed. At intermediate fluence, high micro-strains appear together with small faulted dislocation loops. At the highest fluence (>10 14 cm -2), the micro-strains saturate and the loops coalesce to form a dense dislocation network. No other structural modification is observed. The material shows a moderate cell parameter increase, corresponding to a 0.6 vol.% swelling, which saturates around 10 14 ions/cm 2, i.e., a few Zr dpa. As a result, in spite of a strong covalent bonding component, ZrC seems to have a behaviour under irradiation close to cubic metals.

  19. Determination of the force transmitted by an ion thruster plasma plume to an orbital object

    NASA Astrophysics Data System (ADS)

    Alpatov, A.; Cichocki, F.; Fokov, A.; Khoroshylov, S.; Merino, M.; Zakrzhevskii, A.

    2016-02-01

    An approach to determine the force transmitted by the plasma plume of an ion thruster to an orbital object immersed in it using its central projection on a selected plane is proposed. A photo camera is used to obtain the image of the object central projection. The algorithms for the calculation of the transmission of momentum by the impacting ion beam are developed including the determination of the object contour and the correction of the error due to a camera offset from the ion beam axis, and the computation of the fraction of the ion beam that impinges on the object surface.

  20. Structure determination of molecules of biochemical interest

    NASA Astrophysics Data System (ADS)

    Honzatko, R. B.

    1985-10-01

    In the past year we have established a new laboratory for the determination of macromolecular structure. Currently, facilities are in place for data collection, data processing, molecular modeling and X-ray refinement of structures of up to 100,000 molecular weight in their crystallographic asymmetric unit. In parallel with establishing a new laboratory, we have pursued structure investigations of hemoglobin from the sea lamprey, aspartate carbamoyltransferase from Escherichia coli and p-nitrobenzylidine aminoguanidine, a small molecule which is an acceptor of the adenosine diphosphate ribosyl group in an enzyme mediated reaction. In addition to the structural studies above we have made a theoretical study by techniques of energy minimization of possible modes of aggregation of lamprey hemoglobin and the relationship between aggregate formation and cooperativity expressed in solutions by lamprey hemoglobin.

  1. Determination of metal ions by fluorescence anisotropy exhibits a broad dynamic range

    NASA Astrophysics Data System (ADS)

    Thompson, Richard B.; Maliwal, Badri P.; Fierke, Carol A.

    1998-05-01

    Recently, we have shown that metal ions free in solution may be determined at low levels by fluorescence anisotropy (polarization) measurements. Anisotropy measurements enjoy the advantages of wavelength ratiometric techniques for determining metal ions such as calcium, because anisotropy measurements are ratiometric as well. Furthermore, fluorescence anisotropy may be imaged in the microscope. An advantage of anisotropy not demonstrated for wavelength ratiometric approaches using indicators such as Fura-2 and Indo-1 is that under favorable circumstances anisotropy-based determinations exhibit a much broader dynamic range in metal ion concentration. Determinations of free Zn(II) in the picomolar range are demonstrated.

  2. Ion-Beam-Induced Atomic Mixing in Ge, Si, and SiGe, Studied by Means of Isotope Multilayer Structures

    PubMed Central

    Radek, Manuel; Liedke, Bartosz; Schmidt, Bernd; Voelskow, Matthias; Bischoff, Lothar; Lundsgaard Hansen, John; Nylandsted Larsen, Arne; Bougeard, Dominique; Böttger, Roman; Prucnal, Slawomir; Posselt, Matthias; Bracht, Hartmut

    2017-01-01

    Crystalline and preamorphized isotope multilayers are utilized to investigate the dependence of ion beam mixing in silicon (Si), germanium (Ge), and silicon germanium (SiGe) on the atomic structure of the sample, temperature, ion flux, and electrical doping by the implanted ions. The magnitude of mixing is determined by secondary ion mass spectrometry. Rutherford backscattering spectrometry in channeling geometry, Raman spectroscopy, and transmission electron microscopy provide information about the structural state after ion irradiation. Different temperature regimes with characteristic mixing properties are identified. A disparity in atomic mixing of Si and Ge becomes evident while SiGe shows an intermediate behavior. Overall, atomic mixing increases with temperature, and it is stronger in the amorphous than in the crystalline state. Ion-beam-induced mixing in Ge shows no dependence on doping by the implanted ions. In contrast, a doping effect is found in Si at higher temperature. Molecular dynamics simulations clearly show that ion beam mixing in Ge is mainly determined by the thermal spike mechanism. In the case of Si thermal spike, mixing prevails at low temperature whereas ion beam-induced enhanced self-diffusion dominates the atomic mixing at high temperature. The latter process is attributed to highly mobile Si di-interstitials formed under irradiation and during damage annealing. PMID:28773172

  3. Defect engineering in the MOSLED structure by ion implantation

    NASA Astrophysics Data System (ADS)

    Prucnal, S.; Wójtowicz, A.; Pyszniak, K.; Drozdziel, A.; Zuk, J.; Turek, M.; Rebohle, L.; Skorupa, W.

    2009-05-01

    When amorphous SiO2 films are bombarded with energetic ions, various types of defects are created as a consequence of ion-solid interaction (peroxy radicals POR, oxygen deficient centres (ODC), non-bridging oxygen hole centres (NBOHC), E‧ centres, etc.). The intensity of the electroluminescence (EL) from oxygen deficiency centres at 2.7 eV, non-bridging oxygen hole centres at 1.9 eV and defect centres with emission at 2.07 eV can be easily modified by the ion implantation of the different elements (H, N, O) into the completely processed MOSLED structure. Nitrogen implanted into the SiO2:Gd layer reduces the concentration of the ODC and NBOHC while the doping of the oxygen increases the EL intensity observed from POR defect and NBOHC. Moreover, after oxygen or hydrogen implantation into the SiO2:Ge structure fourfold or fifth fold increase of the germanium related EL intensity was observed.

  4. DNA Nanotubes for NMR Structure Determination of Membrane Proteins

    PubMed Central

    Bellot, Gaëtan; McClintock, Mark A.; Chou, James J; Shih, William M.

    2013-01-01

    Structure determination of integral membrane proteins by solution NMR represents one of the most important challenges of structural biology. A Residual-Dipolar-Coupling-based refinement approach can be used to solve the structure of membrane proteins up to 40 kDa in size, however, a weak-alignment medium that is detergent-resistant is required. Previously, availability of media suitable for weak alignment of membrane proteins was severely limited. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400nm-long six-helix bundles each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, towards collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes via counter ions and small DNA binding molecules. This detergent-resistant liquid-crystal media offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility, and structural programmability. Production of sufficient nanotubes for 4–5 NMR experiments can be completed in one week by a single individual. PMID:23518667

  5. Ion-selective electrodes for determination of organic ammonium ions: Ways for selectivity control.

    PubMed

    Egorov, Vladimir V; Bolotin, Alexander A

    2006-12-15

    The influence of the ISE membrane composition on the selectivity for primary, secondary, tertiary, and quaternary alkylammonium cations, as well as for cations of physiologically active amines, has been investigated. Factors studied include the effect of plasticizer (2-nitrophenyl octyl ether, o-NPOE; dibutyl phthalate, DBP; dinonyl adipate, DNA; tris(2-ethylhexyl) phosphate, TEHP) and ion exchanger (potassium tetrakis(4-chlorophenyl)borate, K(TpClPB); potassium tris(nonyloxy)benzenesulfonate, K(TNOBS)), as well as that of the lipophilic cationic additive (tetradecylammonium nitrate, (TDA)NO(3)) and neutral carrier (dibenzo-18-crown-6) presence in membrane. It has been established that plasticizer nature affects K(i,j)(pot) values both when the target and/or foreign ions have non-ionic polar groups capable of specific interaction with plasticizer, and when the only difference consists in the substitution degree of their ionic groups. K(i,j)(pot) values for quaternary alkylammonium cations over primary-tertiary ones change in the following order: TEHP>DBP approximately DNA>o-NPOE. The highest K(i,j)(pot) value change is achieved for the primary-quaternary alkylammonium cation pair, amounting to 3 and 4.7 orders for membranes containing K(TNOBS) and K(TpClPB) as ion exchangers, respectively. In its turn, the ion exchanger influence on the selectivity depends on plasticizer nature, it being maximal for o-NPOE (about 2 orders) and practically non-existent for TEHP. On the whole, as compared to K(TpClPB)-based ISEs, those based on K(TNOBS) show higher selectivity for primary-tertiary alkylammonium cations over quaternary ones. Incorporation of (TDA)NO(3) into membrane causes further improvement of selectivity for primary-tertiary alkylammonium cations in the case of K(TNOBS) only. The maximal total effect of the ion exchanger and lipophilic ionic additive is observed for ISEs with DNA-plasticized membranes and is over 3 orders. The influence of crown ether on the

  6. Temperature dependence of ion-beam mixing in crystalline and amorphous germanium isotope multilayer structures

    SciTech Connect

    Radek, M.; Bracht, H.; Posselt, M.; Liedke, B.; Schmidt, B.; Bougeard, D.

    2014-01-14

    Self-atom mixing induced by 310 keV gallium (Ga) ion implantation in crystalline and preamorphized germanium (Ge) at temperatures between 164 K and 623 K and a dose of 1 × 10{sup 15} cm{sup −2} is investigated using isotopic multilayer structures of alternating {sup 70}Ge and {sup nat}Ge layers grown by molecular beam epitaxy. The distribution of the implanted Ga atoms and the ion-beam induced depth-dependent self-atom mixing was determined by means of secondary ion mass spectrometry. Three different temperature regimes of self-atom mixing, i.e., low-, intermediate-, and high-temperature regimes are observed. At temperatures up to 423 K, the mixing is independent of the initial structure, whereas at 523 K, the intermixing of the preamorphized Ge structure is about twice as high as that of crystalline Ge. At 623 K, the intermixing of the initially amorphous Ge structure is strongly reduced and approaches the mixing of the crystalline material. The temperature dependence of ion-beam mixing is described by competitive amorphization and recrystallization processes.

  7. Ion chromatography for the separation of heparin and structurally related glycoaminoglycans: A review.

    PubMed

    Fasciano, Jennifer M; Danielson, Neil D

    2016-03-01

    The global crisis resulting from adulterated heparin in late 2007 and early 2008 revived the importance of analytical techniques for the purity analysis of heparin products. The utilization of ion chromatography techniques for the separation, detection, and structural determination of heparin and structurally related glycoaminoglycans, including their corresponding oligosaccharides, has become increasingly important. This review summarizes the primary HPLC approaches, particularly strong anion exchange, weak ion exchange, and reversed-phase ion-pair, used for heparin purity analysis as well as structural characterization. Strong anion exchange HPLC has been studied most extensively and currently offers the best separation of crude heparin and heparin-like compounds. Weak anion exchange HPLC has been shown to provide shorter analysis times with lower salt concentrations in the mobile phase but is not as widely developed for the separation of all glycoaminoglycans of interest. Reversed-phase ion-pair HPLC offers fast and effective separations of oligosaccharides derived from glycoaminoglycans that can be coupled to mass spectrometry for structural analysis. However, this method generally does not provide sufficient retention of intact glycoaminoglycans.

  8. Ion selective electrode for determination of chloride ion in biological materials, food products, soils and waste water.

    PubMed

    Sekerka, I; Lechner, J F

    1978-11-01

    The chloride ion selective electrode is used for a rapid, simple, and reliable determination of chloride ion in biological materials (blood serum, urine, fish, and plant tissues), food products (milk, beef extract, nutrient broth and orange, tomato, and grapefruit juices), soils, and waste water (industrial and municipal). The method consists of treating the samples with perchloric acid (pH 1) and potassium peroxydisulfate and determining the chloride content either by a calibration curve or by known addition or analyte addition, using the chloride ion selective electrode. Such sample treatment eliminates most of the interferences occurring in the samples, including iodide, complexing and reducing compounds, and macromolecular and surface-active species. The method is suitable for a wide range of chloride concentration, e.g., 5010 ppm Cl- in nutrient broth and 4890 ppm in beef extract and as low as 12 and 80 ppm in soil extracts.

  9. Requirements for structure determination of aperiodic crystals

    SciTech Connect

    Li, X.; Stern, E.A.; Ma, Y. )

    1991-01-15

    Using computer simulation, we compared the Patterson functions of one-dimensional (1D) randomly packed and quasiperiodic Fibonacci lattices with or without disorder, and a 2D Penrose lattice and random packing of pentagons (icosahedral glass model). Based on these comparisons, we derived some empirical guidelines for distinguishing ideal quasicrystals from aperiodic crystals with disorder using diffraction data. In contrast to periodic crystals, it is essential to include the background to obtain correct Patterson functions of the average structure since the background contains unresolved peaks. In particular, a Bragg peak scattering measurement {ital cannot}, in general, determine the structure of aperiodic crystals. Instead, a diffuse scattering measurement is required, which determines the absolute value of the diffraction background, in addition to the Bragg peaks. We further estimate that, dependent upon the disorder present, it is necessary to include up to 75% of the total diffracted intensity in any analysis.

  10. Solution structure of copper ion-induced molecular aggregates of tyrosine melanin.

    PubMed

    Gallas, J M; Littrell, K C; Seifert, S; Zajac, G W; Thiyagarajan, P

    1999-08-01

    Melanin, the ubiquitous biological pigment, provides photoprotection by efficient filtration of light and also by its antioxidant behavior. In solutions of synthetic melanin, both optical and antioxidant behavior are affected by the aggregation states of melanin. We have utilized small-angle x-ray and neutron scattering to determine the molecular dimensions of synthetic tyrosine melanin in its unaggregated state in D(2)O and H(2)O to study the structure of melanin aggregates formed in the presence of copper ions at various copper-to-melanin molar ratios. In the absence of copper ions, or at low copper ion concentrations, tyrosine melanin is present in solution as a sheet-like particle with a mean thickness of 12.5 A and a lateral extent of approximately 54 A. At a copper-to-melanin molar ratio of 0.6, melanin aggregates to form long, rod-like structures with a radius of 32 A. At a higher copper ion concentration, with a copper-to-melanin ratio of 1.0, these rod-like structures further aggregate, forming sheet-like structures with a mean thickness of 51 A. A change in the charge of the ionizable groups induced by the addition of copper ions is proposed to account for part of the aggregation. The data also support a model for the copper-induced aggregation of melanin driven by pi stacking assisted by peripheral Cu(2+) complexation. The relationship between our results and a previous hypothesis for reduced cellular damage from bound-to-melanin redox metal ions is also discussed.

  11. Solution structure of copper ion-induced molecular aggregates of tyrosine melanin.

    PubMed Central

    Gallas, J M; Littrell, K C; Seifert, S; Zajac, G W; Thiyagarajan, P

    1999-01-01

    Melanin, the ubiquitous biological pigment, provides photoprotection by efficient filtration of light and also by its antioxidant behavior. In solutions of synthetic melanin, both optical and antioxidant behavior are affected by the aggregation states of melanin. We have utilized small-angle x-ray and neutron scattering to determine the molecular dimensions of synthetic tyrosine melanin in its unaggregated state in D(2)O and H(2)O to study the structure of melanin aggregates formed in the presence of copper ions at various copper-to-melanin molar ratios. In the absence of copper ions, or at low copper ion concentrations, tyrosine melanin is present in solution as a sheet-like particle with a mean thickness of 12.5 A and a lateral extent of approximately 54 A. At a copper-to-melanin molar ratio of 0.6, melanin aggregates to form long, rod-like structures with a radius of 32 A. At a higher copper ion concentration, with a copper-to-melanin ratio of 1.0, these rod-like structures further aggregate, forming sheet-like structures with a mean thickness of 51 A. A change in the charge of the ionizable groups induced by the addition of copper ions is proposed to account for part of the aggregation. The data also support a model for the copper-induced aggregation of melanin driven by pi stacking assisted by peripheral Cu(2+) complexation. The relationship between our results and a previous hypothesis for reduced cellular damage from bound-to-melanin redox metal ions is also discussed. PMID:10423458

  12. Structure and thermodynamic properties of positive and negative cluster ions in saturated vapour over barium dichloride

    NASA Astrophysics Data System (ADS)

    Pogrebnoi, Alexander M.; Pogrebnaya, Tatiana P.; Kudin, Lev S.; Tuyizere, Sarathiel

    2013-11-01

    Geometrical structure, vibration spectra, and enthalpies of dissociation have been investigated for the ions BaCl3-, Ba2Cl3+, Ba3Cl5+, and Ba4Cl7+ which were detected earlier in the saturated vapour over BaCl2. Quantum chemical methods of density functional theory, the second and the fourth order Møller-Plesset perturbation theory have been applied. The effective core potential with cc-pVTZ basis set for barium atom and two full-electron basis sets including the diffuse and polarised basis functions for chlorine atom were used. The effect of the basis set size and the computation method on the results was analysed. According to the results, all the ions possess the compact shaped structure. The equilibrium geometrical structures were found as follows: the planar D3h for BaCl3-, triple bridged bipyramidal D3h for Ba2Cl3+, hexabridged D3h for Ba3Cl5+, and septuple bridged C2v for Ba4Cl7+. For positive ions, the different isomeric structures were considered, but no isomers for these ions have been found. The geometrical parameters and vibration frequencies were utilised for computing of thermodynamic functions of the ions, and then the thermodynamic functions were used for the treatment of the experimental mass spectrometric data. The enthalpies of formation ΔfH°(0 K) of the ions were determined (in kJ/mol): -994 ± 6 (BaCl3-), -481 ± 10 (Ba2Cl3+), -1276 ± 14 (Ba3Cl5+), -2048 ± 35 (Ba4Cl7+).

  13. Distributed structure determination at the JCSG

    PubMed Central

    van den Bedem, Henry; Wolf, Guenter; Xu, Qingping; Deacon, Ashley M.

    2011-01-01

    The Joint Center for Structural Genomics (JCSG), one of four large-scale structure-determination centers funded by the US Protein Structure Initiative (PSI) through the National Institute for General Medical Sciences, has been operating an automated distributed structure-solution pipeline, Xsolve, for well over half a decade. During PSI-2, Xsolve solved, traced and partially refined 90% of the JCSG’s nearly 770 MAD/SAD structures at an average resolution of about 2 Å without human intervention. Xsolve executes many well established publicly available crystallography software programs in parallel on a commodity Linux cluster, resulting in multiple traces for any given target. Additional software programs have been developed and integrated into Xsolve to further minimize human effort in structure refinement. ConsensusModeler exploits complementarities in traces from Xsolve to compute a single optimal model for manual refinement. Xpleo is a powerful robotics-inspired algorithm to build missing fragments and qFit automatically identifies and fits alternate conformations. PMID:21460455

  14. Spontaneous nucleation of structural defects in inhomogeneous ion chains

    NASA Astrophysics Data System (ADS)

    De Chiara, Gabriele; del Campo, Adolfo; Morigi, Giovanna; Plenio, Martin B.; Retzker, Alex

    2010-11-01

    Structural defects in ion crystals can be formed during a linear quench of the transverse trapping frequency across the mechanical instability from a linear chain to a zigzag structure. The density of defects after the sweep can be conveniently described by the Kibble-Zurek mechanism (KZM). In particular, the number of kinks in the zigzag ordering can be derived from a time-dependent Ginzburg-Landau equation for the order parameter, here the zigzag transverse size, under the assumption that the ions are continuously laser cooled. In a linear Paul trap, the transition becomes inhomogeneous, since the charge density is larger in the center and more rarefied at the edges. During the linear quench, the mechanical instability is first crossed in the center of the chain, and a front, at which the mechanical instability is crossed during the quench, is identified that propagates along the chain from the center to the edges. If the velocity of this front is smaller than the sound velocity, the dynamics become adiabatic even in the thermodynamic limit and no defect is produced. Otherwise, the nucleation of kinks is reduced with respect to the case in which the charges are homogeneously distributed, leading to a new scaling of the density of kinks with the quenching rate. The analytical predictions are verified numerically by integrating the Langevin equations of motion of the ions, in the presence of a time-dependent transverse confinement. We argue that the non-equilibrium dynamics of an ion chain in a Paul trap constitutes an ideal scenario to test the inhomogeneous extension of the KZM, which lacks experimental evidence to date.

  15. Structural determinants of sigma receptor affinity

    SciTech Connect

    Largent, B.L.; Wikstroem, H.G.; Gundlach, A.L.; Snyder, S.H.

    1987-12-01

    The structural determinants of sigma receptor affinity have been evaluated by examining a wide range of compounds related to opioids, neuroleptics, and phenylpiperidine dopaminergic structures for affinity at sigma receptor-binding sites labeled with (+)-(/sup 3/H)3-PPP. Among opioid compounds, requirements for sigma receptor affinity differ strikingly from the determinants of affinity for conventional opiate receptors. Sigma sites display reverse stereoselectivity to classical opiate receptors. Multi-ringed opiate-related compounds such as morphine and naloxone have negligible affinity for sigma sites, with the highest sigma receptor affinity apparent for benzomorphans which lack the C ring of opioids. Highest affinity among opioids and other compounds occurs with more lipophilic N-substituents. This feature is particularly striking among the 3-PPP derivatives as well as the opioids. The butyrophenone haloperidol is the most potent drug at sigma receptors we have detected. Among the series of butyrophenones, receptor affinity is primarily associated with the 4-phenylpiperidine moiety. Conformational calculations for various compounds indicate a fairly wide range of tolerance for distances between the aromatic ring and the amine nitrogen, which may account for the potency at sigma receptors of structures of considerable diversity. Among the wide range of structures that bind to sigma receptor-binding sites, the common pharmacophore associated with high receptor affinity is a phenylpiperidine with a lipophilic N-substituent.

  16. Kinetic Studies with Ion Selective Electrodes: Determination of Creatinine in Urine with a Picrate Ion Selective Electrode: A Laboratory Experiment.

    ERIC Educational Resources Information Center

    Diamandis, E. P.; And Others

    1983-01-01

    The kinetic of the Jaffe reaction with picrate ion selective electrode (ISE) and a kinetic method for determining creatinine in urine is presented. The experiment could be used to familarize students with the application of ISE in kinetic studies and chemical analysis. (Author/JN)

  17. Greatly Increasing Trapped Ion Populations for Mobility Separations Using Traveling Waves in Structures for Lossless Ion Manipulations

    SciTech Connect

    Deng, Liulin; Ibrahim, Yehia M.; Garimella, Sandilya V. B.; Webb, Ian K.; Hamid, Ahmed M.; Norheim, Randolph V.; Prost, Spencer A.; Sandoval, Jeremy A.; Baker, Erin S.; Smith, Richard D.

    2016-10-18

    The initial use of traveling waves (TW) for ion mobility (IM) separations using a structures for lossless ion manipulations (SLIM) employed an ion funnel trap (IFT) to accumulate ions from a continuous electrospray ionization source, and limited to injected ion populations of ~106 charges due to the onset of space charge effects in the trapping region. Additional limitations arise due to the loss of resolution for the injection of ions over longer periods (e.g. in extended pulses). In this work a new SLIM ‘flat funnel’ (FF) module has been developed and demonstrated to enable the accumulation of much larger ion populations and their injection for IM separations. Ion current measurements indicate a capacity of ~3.2×108 charges for the extended trapping volume, over an order of magnitude greater than the IFT. The orthogonal ion injection into a funnel shaped separation region can greatly reduce space charge effects during the initial IM separation stage, and the gradually reduced width of the path allows the ion packet to be increasingly compressed in the lateral dimension as the separation progresses, allowing e.g. efficient transmission through conductance limits or compatibility with subsequent ion manipulations. This work examined the TW, RF, and DC confining field SLIM parameters involved in ion accumulation, injection, transmission and separation in the FF IM module using both direct ion current and MS measurements. Wide m/z range ion transmission is demonstrated, along with significant increases in signal to noise (S/N) ratios due to the larger ion populations injected. Additionally, we observed a reduction in the chemical background, which was attributed to more efficient desolvation of solvent related clusters over the extended ion accumulation periods. The TW SLIM FF IM module is anticipated to be especially effective as a front end for long path SLIM IM separation modules.

  18. Greatly Increasing Trapped Ion Populations for Mobility Separations Using Traveling Waves in Structures for Lossless Ion Manipulations.

    PubMed

    Deng, Liulin; Ibrahim, Yehia M; Garimella, Sandilya V B; Webb, Ian K; Hamid, Ahmed M; Norheim, Randolph V; Prost, Spencer A; Sandoval, Jeremy A; Baker, Erin S; Smith, Richard D

    2016-10-07

    The initial use of traveling waves (TW) for ion mobility (IM) separations using structures for lossless ion manipulations (SLIM) employed an ion funnel trap (IFT) to accumulate ions from a continuous electrospray ionization source and was limited to injected ion populations of ∼10(6) charges due to the onset of space charge effects in the trapping region. Additional limitations arise due to the loss of resolution for the injection of ions over longer periods, such as in extended pulses. In this work a new SLIM "flat funnel" (FF) module has been developed and demonstrated to enable the accumulation of much larger ion populations and their injection for IM separations. Ion current measurements indicate a capacity of ∼3.2 × 10(8) charges for the extended trapping volume, over an order of magnitude greater than that of the IFT. The orthogonal ion injection into a funnel shaped separation region can greatly reduce space charge effects during the initial IM separation stage, and the gradually reduced width of the path allows the ion packet to be increasingly compressed in the lateral dimension as the separation progresses, allowing efficient transmission through conductance limits or compatibility with subsequent ion manipulations. This work examined the TW, rf, and dc confining field SLIM parameters involved in ion accumulation, injection, transmission, and IM separation in the FF module using both direct ion current and MS measurements. Wide m/z range ion transmission is demonstrated, along with significant increases in the signal-to-noise ratios (S/N) due to the larger ion populations injected. Additionally, we observed a reduction in the chemical background, which was attributed to more efficient desolvation of solvent related clusters over the extended ion accumulation periods. The TW SLIM FF IM module is anticipated to be especially effective as a front end for long path SLIM IM separation modules.

  19. Determination of water-soluble forms of oxalic and formic acids in soils by ion chromatography

    NASA Astrophysics Data System (ADS)

    Karicheva, E.; Guseva, N.; Kambalina, M.

    2016-03-01

    Carboxylic acids (CA) play an important role in the chemical composition origin of soils and migration of elements. The content of these acids and their salts is one of the important characteristics for agrochemical, ecological, ameliorative and hygienic assessment of soils. The aim of the article is to determine water-soluble forms of same carboxylic acids — (oxalic and formic acids) in soils by ion chromatography with gradient elution. For the separation and determination of water-soluble carboxylic acids we used reagent-free gradient elution ion-exchange chromatography ICS-2000 (Dionex, USA), the model solutions of oxalate and formate ions, and leachates from soils of the Kola Peninsula. The optimal gradient program was established for separation and detection of oxalate and formate ions in water solutions by ion chromatography. A stability indicating method was developed for the simultaneous determination of water-soluble organic acids in soils. The method has shown high detection limits such as 0.03 mg/L for oxalate ion and 0.02 mg/L for formate ion. High signal reproducibility was achieved in wide range of intensities which correspond to the following ion concentrations: from 0.04 mg/g to 10 mg/L (formate), from 0.1 mg/g to 25 mg/L (oxalate). The concentration of formate and oxalate ions in soil samples is from 0.04 to 0.9 mg/L and 0.45 to 17 mg/L respectively.

  20. Synthesis, characterization and crystal structure determination of Mn (II) ion based 1D polymer constructed from 2, 2′ bipyridyl and azide group, its thermal stability, magnetic properties and Hirshfeld surface analysis

    SciTech Connect

    Mudsainiyan, R.K. Jassal, Amanpreet Kaur; Chawla, S.K.

    2015-05-15

    The 1-D polymeric complex (I) is having formula [Mn(2,2′-BP).(N{sub 3}){sub 2}]{sub n}, which has been crystallized in distilled water and characterized by elemental analyses, FT-IR spectrum, powder X-ray diffraction analyses and single-crystal diffraction analysis. This polymer possesses 1D helical chains or coils where Mn–azide–Mn forms the base of the coil which is alternatively garlanded by rigid bi-pyridine rings, where coordinates are in anti-fashion. The Mn (II) ions in the repeating units are linked by two end-on azide groups which extend through the two end-to-end azide ligands to the next unit forming a 1-D polymeric chain. The present study suggests that the use of this rigid and neutral building block leads to give better arrangement of the polymeric motif with [010] chains in 2-c uninodal net. During investigation of strong or weak intermolecular interactions, X-ray diffraction analysis and Hirshfeld surface analysis give rise to comparable results but in Hirshfeld surface analysis, two-third times more results of close contacts are obtained. The fingerprint plots demonstrate that these weak non-bonding interactions are important for stabilizing the crystal packing. Magnetic properties of the complex (I) were analyzed on the basis of an alternating ferro- and antiferromagnetic Heisenberg chain of Mn (II) ions. The J-exchange parameters found are J{sub 1}=64.3 K (45.3 cm{sup −1}), and J{sub 2}=−75.7 K (−53.3 cm{sup −1}). Magnetic properties are discussed in comparison with those of other similar molecular magnets of [Mn(L–L)(N{sub 3}){sub 2}]{sub n} type. - - Highlights: • Synthesized 1-D polymeric complex of Mn (II) ions with 2, 2′ bipyridyl and azide group. • X-ray data of complex (I) is in a good agreement with TGA and other spectroscopic techniques. • DFT calculations were done and compared with the parameter of experimental and theoretical data. • Intermolecular interactions calculated by Hirshfeld surface analysis

  1. Ion manipulations in structures for lossless ion manipulations (SLIM): computational evaluation of a 90° turn and a switch

    SciTech Connect

    Garimella, Sandilya V. B.; Ibrahim, Yehia. M.; Webb, Ian K.; Ipsen, Andreas B.; Chen, Tsung-Chi; Tolmachev, Aleksey V.; Baker, Erin S.; Anderson, Gordon A.; Smith, Richard D.

    2015-08-19

    The process of redirecting ions through 90° turns and ‘tee’ switches utilizing Structures for Lossless Ion Manipulations (SLIM) was evaluated using theoretical and simulation methods at 4 Torr pressure. SIMION simulations were used to optimize and evaluate conditions for performing turns without loss of signal intensity or ion mobility resolving power. Fundamental considerations indicated that the “race track” effect during ion turns may incur only small losses to the ion mobility resolving power at 4 Torr pressure for the typical plume widths predicted in an optimized SLIM ‘tee’ switch design. The dynamic switching of ions into orthogonal channels was also evaluated using SIMION ion trajectory simulations, and achieved similar performance. Simulation results were in close agreement with experimental results and were used to refine SLIM designs and applied potentials for their use.

  2. Ion manipulations in structures for lossless ion manipulations (SLIM): computational evaluation of a 90° turn and a switch

    DOE PAGES

    Garimella, Sandilya V. B.; Ibrahim, Yehia. M.; Webb, Ian K.; ...

    2015-08-19

    The process of redirecting ions through 90° turns and ‘tee’ switches utilizing Structures for Lossless Ion Manipulations (SLIM) was evaluated using theoretical and simulation methods at 4 Torr pressure. SIMION simulations were used to optimize and evaluate conditions for performing turns without loss of signal intensity or ion mobility resolving power. Fundamental considerations indicated that the “race track” effect during ion turns may incur only small losses to the ion mobility resolving power at 4 Torr pressure for the typical plume widths predicted in an optimized SLIM ‘tee’ switch design. The dynamic switching of ions into orthogonal channels was alsomore » evaluated using SIMION ion trajectory simulations, and achieved similar performance. Simulation results were in close agreement with experimental results and were used to refine SLIM designs and applied potentials for their use.« less

  3. Frictional and structural characterization of ion-nitrided low and high chromium steels

    NASA Technical Reports Server (NTRS)

    Spalvins, T.

    1985-01-01

    Low Cr steels AISI 41410, AISI 4340, and high Cr austenitic stainless steels AISI 304, AISI 316 were ion nitrided in a dc glow discharge plasma consisting of a 75 percent H2 - 25 percent N2 mixture. Surface compound layer phases were identified, and compound layer microhardness and diffusion zone microhardness profiles were established. Distinct differences in surface compound layer hardness and diffusion zone profiles were determined between the low and high Cr alloy steels. The high Cr stainless steels after ion nitriding displayed a hard compound layer and an abrupt diffusion zone. The compound layers of the high Cr stainless steels had a columnar structure which accounts for brittleness when layers are exposed to contact stresses. The ion nitrided surfaces of high and low Cr steels displayed a low coefficient of friction with respect to the untreated surfaces when examined in a pin and disk tribotester.

  4. Frictional and structural characterization of ion-nitrided low and high chromium steels

    NASA Technical Reports Server (NTRS)

    Spalvins, T.

    1985-01-01

    Low Cr steels AISI 41410, AISI 4340, and high Cr austenitic stainless steels AISI 304, AISI 316 were ion nitrided in a dc glow discharge plasma consisting of a 75 percent H2 - 25 percent N2 mixture. Surface compound layer phases were identified, and compound layer microhardness and diffusion zone microhardness profiles were established. Distinct differences in surface compound layer hardness and diffusion zone profiles were determined between the low and high Cr alloy steels. The high Cr stainless steels after ion nitriding displayed a hard compound layer and an abrupt diffusion zone. The compound layers of the high Cr stainless steels had a columnar structure which accounts for brittleness when layers are exposed to contact stresses. The ion nitrided surfaces of high and low Cr steels displayed a low coefficient of friction with respect to the untreated surfaces when examined in a pin and disk tribotester.

  5. Sodium Cation Affinities of Commonly Used MALDI Matrices Determined by Guided Ion Beam Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Chinthaka, S. D. M.; Rodgers, M. T.

    2012-04-01

    The sodium cation affinities of six commonly used MALDI matrices are determined here using guided ion beam tandem mass spectrometry techniques. The collision-induced dissociation behavior of six sodium cationized MALDI matrices, Na+(MALDI), with Xe is studied as a function of kinetic energy. The MALDI matrices examined here include: nicotinic acid, quinoline, 3-aminoquinoline, 4-nitroaniline, picolinic acid, and 3-hydroxypicolinic acid. In all cases, the primary dissociation pathway corresponds to endothermic loss of the intact MALDI matrix. The cross section thresholds are interpreted to yield zero and 298 K Na+-MALDI bond dissociation energies (BDEs), or sodium cation affinities, after accounting for the effects of multiple ion-neutral collisions, the kinetic and internal energy distributions of the reactants, and dissociation lifetimes. Density functional theory calculations at the B3LYP/6-311+G(2d,2p)//B3LYP/6-31G* and MP2(full)/6-311+G(2d,2p)//B3LYP/6-31G* levels of theory are used to characterized the structures and energetics for these systems. The calculated BDEs exhibit very good agreement with the measured values for most systems. The experimental and theoretical Na+-MALDI BDEs determined here are compared with those previously measured by cation transfer equilibrium methods.

  6. Plastic membrane ion-selective electrode for the determination of denatonium benzoate (Bitrex).

    PubMed

    Nambiar, O G; Gosavi, K; Ravindranathan, T

    1991-10-01

    A poly(vinyl chloride) matrix membrane ion-selective electrode for the determination of the denatonium ion based on the denatonium salt of tetraphenylborate is described. The response characteristics of the electrode for the denatonium ion and for several quaternary ammonium compounds were studied. The potentiometric determination of denatonium benzoate in rapeseed oil in the range 1-10 ppm agreed to within +/-5% of the spiked amounts. The application of the electrode to the titrimetric determination of several quaternary ammonium compounds using sodium tetraphenylborate as the titrant is also described.

  7. Synthesis, characterization and crystal structure determination of Mn (II) ion based 1D polymer constructed from 2, 2‧ bipyridyl and azide group, its thermal stability, magnetic properties and Hirshfeld surface analysis

    NASA Astrophysics Data System (ADS)

    Mudsainiyan, R. K.; Jassal, Amanpreet Kaur; Chawla, S. K.

    2015-05-01

    The 1-D polymeric complex (I) is having formula [Mn(2,2‧-BP).(N3)2]n, which has been crystallized in distilled water and characterized by elemental analyses, FT-IR spectrum, powder X-ray diffraction analyses and single-crystal diffraction analysis. This polymer possesses 1D helical chains or coils where Mn-azide-Mn forms the base of the coil which is alternatively garlanded by rigid bi-pyridine rings, where coordinates are in anti-fashion. The Mn (II) ions in the repeating units are linked by two end-on azide groups which extend through the two end-to-end azide ligands to the next unit forming a 1-D polymeric chain. The present study suggests that the use of this rigid and neutral building block leads to give better arrangement of the polymeric motif with [010] chains in 2-c uninodal net. During investigation of strong or weak intermolecular interactions, X-ray diffraction analysis and Hirshfeld surface analysis give rise to comparable results but in Hirshfeld surface analysis, two-third times more results of close contacts are obtained. The fingerprint plots demonstrate that these weak non-bonding interactions are important for stabilizing the crystal packing. Magnetic properties of the complex (I) were analyzed on the basis of an alternating ferro- and antiferromagnetic Heisenberg chain of Mn (II) ions. The J-exchange parameters found are J1=64.3 K (45.3 cm-1), and J2=-75.7 K (-53.3 cm-1). Magnetic properties are discussed in comparison with those of other similar molecular magnets of [Mn(L-L)(N3)2]n type.

  8. ION CHROMATOGRAPHIC DETERMINATION OF PERCHLORATE ION: ANALYSIS OF FERTILIZERS AND RELATED MATERIALS

    EPA Science Inventory

    A solid fertilizer sample is dissolved or leached to solutilize the perchlorate as the aqueous anion. If needed, the liquid is filtered or centrifuged. The rsulting solution is subjected to ion chromatography using an adaptation of EPA Method 314.0. Preliminary screenng is requir...

  9. Source Determination for Substorm-Related Ion Injections

    NASA Technical Reports Server (NTRS)

    Strangeway, Robert J.; Evans, David (Technical Monitor)

    2001-01-01

    The grant supported an effort to restore and analyze data from the Spacecraft Charging at High Altitude (SCATHA) spacecraft. This spacecraft, which was originally an Air Force mission, was launched into a near geo-synchronous orbit in early 1979 to, investigate the inner magnetosphere at altitudes where it was known that spacecraft can undergo significant charging events. SCATHA included an ion composition experiment (designated SC8) and in many ways was a precursor to other missions, such as the AMPTE Charge Composition Explorer.

  10. Coherent structures in ion temperature gradient turbulence-zonal flow

    SciTech Connect

    Singh, Rameswar; Singh, R.; Kaw, P.; Gürcan, Ö. D.; Diamond, P. H.

    2014-10-15

    Nonlinear stationary structure formation in the coupled ion temperature gradient (ITG)-zonal flow system is investigated. The ITG turbulence is described by a wave-kinetic equation for the action density of the ITG mode, and the longer scale zonal mode is described by a dynamic equation for the m = n = 0 component of the potential. Two populations of trapped and untrapped drift wave trajectories are shown to exist in a moving frame of reference. This novel effect leads to the formation of nonlinear stationary structures. It is shown that the ITG turbulence can self-consistently sustain coherent, radially propagating modulation envelope structures such as solitons, shocks, and nonlinear wave trains.

  11. Effect of the surface on the secondary structure of soft landed peptide ions

    SciTech Connect

    Hu, Qichi; Wang, Peng; Laskin, Julia

    2010-10-01

    Ion soft landing (SL) enables highly selective modification of substrates for applications in materials science, nanotechnology and biology. Our previous study showed that SL can be used for preparation of conformation-selected peptide arrays. Here we present a first study of the effect of the surface on the secondary structures of peptides soft-landed onto self-assembled monolayer surfaces (SAMs). Conformations of soft-landed peptide ions were examined using the newly constructed instrument that enables in situ infrared reflection absorption spectroscopy (IRRAS) characterization of surfaces during and after ion deposition. Polyalanine peptides, Ac-AnK and Ac-KAn (n=7, 15), that have been extensively studied both in solution and in the gas phase were used as model systems in this study. We demonstrate that physical and chemical properties of SAM surfaces have a strong effect on the conformations of soft-landed peptides ions. For example, deposition of the α-helical [Ac-A15K+H]+ ion on the CH3-terminated (HSAM) surface results in immobilization of both the α- and 310-helical conformations. In contrast, a significant fraction of Ac-A15K molecules are present in the β-sheet conformation on the CF3- (FSAM) and COOH-terminated (COOH-SAM) surfaces. We show that the kinetic energy of the polyalanine ion, the charge, and the initial conformation have only a minor effect on the conformation of deposited species suggesting that the interaction between the molecule and the surface plays a major role in determining the secondary structures of immobilized polyalanines. This study demonstrates that SL of mass-selected ions can be utilized for obtaining fundamental understanding of the intrinsic properties of biomolecules and surfaces responsible for conformational changes upon adsorption.

  12. DETERMINING ION COMPOSITIONS USING AN ACCURATE MASS, TRIPLE QUADRUPOLE MASS SPECTROMETER

    EPA Science Inventory

    For the past decade, we have used double focusing mass spectrometers to determine
    compositions of ions observed in mass spectra produced from compounds introduced by GC
    based on measured exact masses of the ions and their +1 and +2 isotopic profiles arising from atoms of ...

  13. DETERMINING ION COMPOSITIONS USING AN ACCURATE MASS, TRIPLE QUADRUPOLE MASS SPECTROMETER

    EPA Science Inventory

    For the past decade, we have used double focusing mass spectrometers to determine
    compositions of ions observed in mass spectra produced from compounds introduced by GC
    based on measured exact masses of the ions and their +1 and +2 isotopic profiles arising from atoms of ...

  14. Cationic Net Charge and Counter Ion Type as Antimicrobial Activity Determinant Factors of Short Lipopeptides.

    PubMed

    Greber, Katarzyna E; Dawgul, Malgorzata; Kamysz, Wojciech; Sawicki, Wieslaw

    2017-01-01

    To get a better insight into the antimicrobial potency of short cationic lipopeptides, 35 new entities were synthesized using solid phase peptide strategy. All newly obtained lipopeptides were designed to be positively charged from +1 to +4. This was achieved by introducing basic amino acid - lysine - into the lipopeptide structure and had a hydrophobic fatty acid chain attached. Lipopeptides were subjected to microbiological tests using reference strains of Gram-negative bacteria: Escherichia coli, Klebsiella pneumoniae, Proteus vulgaris, Pseudomonas aeruginosa, Gram-positive bacteria: Staphylococcus aureus, Staphylococcus epidermidis, Bacillus subtilis, Enterococcus faecalis, and fungi: Candida albicans, Candida tropicalis, Aspergillus brasiliensis. The minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC) and minimal fungicidal concentration (MFC) were established for each strain. The toxicity toward human cells was determined by hemolysis tests via minimum hemolytic concentration (MHC) determination. The effect of the trifluoroacetic acid (TFA) counter ion on the antimicrobial activity of lipopeptides was also examined by its removing and performing the antimicrobial tests using counter ion-free compounds. The study shows that lipopeptides are more potent against Gram-positive than Gram-negative strains. It was revealed that positive charge equals at least +2 is a necessary condition to observe significant antimicrobial activity, but only when it is balanced with a proper length of hydrophobic fatty acid chain. The hemolytic activity of lipopeptides strongly depends on amino acid composition of the hydrophilic portion of the molecule as well as fatty acid chain length. Compounds endowed with a greater positive charge were more toxic to human erythrocytes. This should be considered during new lipopeptide molecules design. Our studies also revealed the TFA counter ion has no significant effect on the antimicrobial behavior of cationic

  15. Cationic Net Charge and Counter Ion Type as Antimicrobial Activity Determinant Factors of Short Lipopeptides

    PubMed Central

    Greber, Katarzyna E.; Dawgul, Malgorzata; Kamysz, Wojciech; Sawicki, Wieslaw

    2017-01-01

    To get a better insight into the antimicrobial potency of short cationic lipopeptides, 35 new entities were synthesized using solid phase peptide strategy. All newly obtained lipopeptides were designed to be positively charged from +1 to +4. This was achieved by introducing basic amino acid - lysine - into the lipopeptide structure and had a hydrophobic fatty acid chain attached. Lipopeptides were subjected to microbiological tests using reference strains of Gram-negative bacteria: Escherichia coli, Klebsiella pneumoniae, Proteus vulgaris, Pseudomonas aeruginosa, Gram-positive bacteria: Staphylococcus aureus, Staphylococcus epidermidis, Bacillus subtilis, Enterococcus faecalis, and fungi: Candida albicans, Candida tropicalis, Aspergillus brasiliensis. The minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC) and minimal fungicidal concentration (MFC) were established for each strain. The toxicity toward human cells was determined by hemolysis tests via minimum hemolytic concentration (MHC) determination. The effect of the trifluoroacetic acid (TFA) counter ion on the antimicrobial activity of lipopeptides was also examined by its removing and performing the antimicrobial tests using counter ion-free compounds. The study shows that lipopeptides are more potent against Gram-positive than Gram-negative strains. It was revealed that positive charge equals at least +2 is a necessary condition to observe significant antimicrobial activity, but only when it is balanced with a proper length of hydrophobic fatty acid chain. The hemolytic activity of lipopeptides strongly depends on amino acid composition of the hydrophilic portion of the molecule as well as fatty acid chain length. Compounds endowed with a greater positive charge were more toxic to human erythrocytes. This should be considered during new lipopeptide molecules design. Our studies also revealed the TFA counter ion has no significant effect on the antimicrobial behavior of cationic

  16. Emerging models of glutamate receptor ion channel structure and function.

    PubMed

    Mayer, Mark L

    2011-10-12

    Excitatory synaptic transmission in the brain is mediated by ligand-gated ion channels (iGluRs) activated by glutamate. Distinct from other neurotransmitter receptors, the extracellular domains of iGluRs are loosely packed assemblies with two clearly distinct layers, each of which has both local and global 2-fold axes of symmetry. By contrast, the iGluR transmembrane segments have 4-fold symmetry and share a conserved pore loop architecture found in tetrameric voltage-gated ion channels. The striking layered architecture of iGluRs revealed by the 3.6 Å resolution structure of an AMPA receptor homotetramer likely arose from gene fusion events that occurred early in evolution. Although this modular design has greatly facilitated biophysical and structural studies on individual iGluR domains, and suggested conserved mechanisms for iGluR gating, recent work is beginning to reveal unanticipated diversity in the structure, allosteric regulation, and assembly of iGluR subtypes.

  17. Group Additivity Determination for Enthalpies of Formation of Carbenium Ions

    SciTech Connect

    Bjorkman, Kathryn R.; Sung, Chun-Yi; Mondor, Eric; Cheng, Janine C.; Jan, Deng-Yang; Broadbelt, Linda J.

    2014-12-05

    Modeling of acid-catalyzed hydrocarbon conversion processes at the mechanistic level requires rate coefficients for a large number of reactions. The computational demand of finding activation energy barriers for each reaction is substantially reduced by employing structure–reactivity correlations such as the Evans–Polanyi relationship that correlates activation energy with the enthalpy of reaction. However, there are many species for which the enthalpies of formation are unknown. Therefore, group additivity methods to specify enthalpies of formation for each species involved in the reaction network are valuable. Quantum mechanical (QM) calculations and isodesmic reactions were used to calculate enthalpies of formation for a number of acyclic and cyclic carbenium ions, including allylic carbenium ions. These values compare favorably with experimental values, establishing Gaussian-4 as an accurate QM method for these calculations. Using these values, Benson-type group additivity values for enthalpies of formation were then derived through multiple linear regression. Enthalpies of formation values calculated from the group additivity scheme capture experimental and QM enthalpies of formation well and enhance the range of species that can be described by the group additivity approach.

  18. Hydrated Ions: From Individual Ions to Ion Pairs to Ion Clusters.

    PubMed

    Chen, Houyang; Ruckenstein, Eli

    2015-10-01

    The structure of hydrated ions plays a central role in chemical and biological sciences. In the present paper, five ions, namely, Na(+), K(+), Mg(2+), Ca(2+) and Cl(-), are examined using molecular dynamics simulations. In addition to hydrated individual ions and ion pairs identified previously, hydrated ion clusters containing 3, 4, 5, or more ions are identified in the present paper. The dependence of hydration numbers and mole fractions of individual ions, ion pairs, and larger ion clusters on the electrolyte concentration is determined. As the electrolyte concentration increases, the mole fraction of hydrated individual ions decreases, and the mole fraction of hydrated larger ion clusters increases. The results also reveal that the hydrogen bonding numbers of the H2O molecules of the first hydration shells of individual ions, ion pairs, and larger ion clusters are insensitive to the electrolyte concentration, but sensitive to the nature and conformation of ions.

  19. Ion structure in dense plasmas: MSA versus HNC

    NASA Astrophysics Data System (ADS)

    Wünsch, K.; Vorberger, J.; Gregori, G.; Gericke, D. O.

    2009-05-01

    We present results for the ionic structure in dense, moderately to strongly coupled plasmas using two models: the mean spherical approximation (MSA) and the hypernetted chain (HNC) approach. While the first method allows for an analytical solution, the latter has to be solved iteratively. Independent of the coupling strength, the results show only small differences when the ions are considered to form an unscreened one-component plasma (OCP) system. If the electrons are treated as a polarizable background, the different ways to incorporate the screening yield, however, large discrepancies between the models, particularly for more strongly coupled plasmas.

  20. High Resolution Powder Diffraction and Structure Determination

    SciTech Connect

    Cox, D. E.

    1999-04-23

    It is clear that high-resolution synchrotrons X-ray powder diffraction is a very powerful and convenient tool for material characterization and structure determination. Most investigations to date have been carried out under ambient conditions and have focused on structure solution and refinement. The application of high-resolution techniques to increasingly complex structures will certainly represent an important part of future studies, and it has been seen how ab initio solution of structures with perhaps 100 atoms in the asymmetric unit is within the realms of possibility. However, the ease with which temperature-dependence measurements can be made combined with improvements in the technology of position-sensitive detectors will undoubtedly stimulate precise in situ structural studies of phase transitions and related phenomena. One challenge in this area will be to develop high-resolution techniques for ultra-high pressure investigations in diamond anvil cells. This will require highly focused beams and very precise collimation in front of the cell down to dimensions of 50 {micro}m or less. Anomalous scattering offers many interesting possibilities as well. As a means of enhancing scattering contrast it has applications not only to the determination of cation distribution in mixed systems such as the superconducting oxides discussed in Section 9.5.3, but also to the location of specific cations in partially occupied sites, such as the extra-framework positions in zeolites, for example. Another possible application is to provide phasing information for ab initio structure solution. Finally, the precise determination of f as a function of energy through an absorption edge can provide useful information about cation oxidation states, particularly in conjunction with XANES data. In contrast to many experiments at a synchrotron facility, powder diffraction is a relatively simple and user-friendly technique, and most of the procedures and software for data analysis

  1. Instability-Enhanced Collisional Friction Determines the Bohm Criterion in Multiple-Ion-Species Plasmas

    NASA Astrophysics Data System (ADS)

    Baalrud, S. D.; Hegna, C. C.; Callen, J. D.

    2009-11-01

    Ion-ion streaming instabilities are excited in the presheath region of plasmas with multiple ion species if the ions are much colder than the electrons. Streaming instabilities onset when the relative fluid flow between ion species exceeds a critical speed, δVc, of order the ion thermal speeds. Using a generalized Lenard-Balescu theory that accounts for instability-enhanced collective responses [1], one is able to show the instabilities rapidly enhance the collisional friction between ion species far beyond the contribution from Coulomb collisions alone. This strong frictional force determines the relative fluid speed between species. When this condition is combined with the Bohm criterion generalized for multiple ion species, the fluid speed of each ion species is determined at the sheath edge. For each species, this speed differs from the common ``system'' sound speed by a factor that depends on the species concentrations, masses and δVc.[4pt] [1] S.D. Baalrud, J.D. Callen, and C.C. Hegna, Phys. Plasmas 15, 092111 (2008).

  2. DUAL HEATED ION SOURCE STRUCTURE HAVING ARC SHIFTING MEANS

    DOEpatents

    Lawrence, E.O.

    1959-04-14

    An ion source is presented for calutrons, particularly an electrode arrangement for the ion generator of a calutron ion source. The ion source arc chamber is heated and an exit opening with thermally conductive plates defines the margins of the opening. These plates are electrically insulated from the body of the ion source and are connected to a suitable source of voltage to serve as electrodes for shaping the ion beam egressing from the arc chamber.

  3. Determination of new Cu+, Cu2+, and Zn2+ Lennard-Jones ion parameters in acetonitrile.

    PubMed

    Torras, Juan; Alemán, Carlos

    2013-09-12

    We present new Lennard-Jones (LJ) parameters for Cu(+), Cu(2+), and Zn(2+) ion-acetonitrile interactions. The adjustment of ion parameters is made to reproduce simultaneously experimental solvation free energy and structural properties, namely ion-N distance and coordination numbers. Initially, the methodology has been validated deriving parameters for well-studied Na(+) and Cl(-) ions in acetonitrile being compared with experimental and theoretical data. The transferability of parameters is checked by the calculation of thermodynamic and structural properties with three different acetonitrile models. The results obtained for transition metal ions show an overall agreement with reference values. The solvation free energy calculated with new LJ trained parameters using a six-site acetonitrile model, and two older three- and six-site acetonitrile models presents, respectively, percent differences of 0.4, 4.8, and 7.3% when compared with experimental values.

  4. On the significance of including the thermal motion of ions in determining the ion distribution behind a satellite

    NASA Technical Reports Server (NTRS)

    Samir, U.; Widjaja, D.

    1981-01-01

    A comparative investigation concerning the spatial distribution of ions in the wake of small bodies was conducted using the theoretical wake models of Call (1969) and Parker (1976). Results for bodies with radius/ambient Debye length ratios of 2 and 5, with an electron temperature equal to the ambient electron temperature, and for the ionic Mach numbers S = 2, 4, 6, 8 are presented. Since the main physical difference between the models is in the consideration of the thermal motion of ions (Parker) versus ignoring this component (Call), a comparison between the models yields the quantitative significance of this component in determining the distribution of ions in the wake of artificial satellites. The application of this result to future experiments to be conducted on board the Spacelab and for any other large space platform in the area of space plasma physics is mentioned.

  5. On the significance of including the thermal motion of ions in determining the ion distribution behind a satellite

    NASA Technical Reports Server (NTRS)

    Samir, U.; Widjaja, D.

    1981-01-01

    A comparative investigation concerning the spatial distribution of ions in the wake of small bodies was conducted using the theoretical wake models of Call (1969) and Parker (1976). Results for bodies with radius/ambient Debye length ratios of 2 and 5, with an electron temperature equal to the ambient electron temperature, and for the ionic Mach numbers S = 2, 4, 6, 8 are presented. Since the main physical difference between the models is in the consideration of the thermal motion of ions (Parker) versus ignoring this component (Call), a comparison between the models yields the quantitative significance of this component in determining the distribution of ions in the wake of artificial satellites. The application of this result to future experiments to be conducted on board the Spacelab and for any other large space platform in the area of space plasma physics is mentioned.

  6. The molecular structure of the isopoly complex ion, decavanadate (V10O286-)

    USGS Publications Warehouse

    Evans, H.T.

    1966-01-01

    The structure of the decavanadate ion V10O286- has been found by a determination of the crystal structure of K2Zn2V10O28?? 16H2O. The soluble, orange crystals are triclinic with space group P1 and have a unit cell with a = 10.778 A, b = 11.146 A, c = 8.774 A, ?? = 104?? 57???, ?? = 109?? 3???', and ?? = 65?? 0??? (Z = 1). The structure was solved from a three-dimensional Patterson map based on 5143 Weissenberg-film data. The full-matrix, least-squares refinement gave R = 0.094 and ?? for V-O bond lengths of 0.008 A. The unit cell contains one V10O286- unit, two Zn(H2O)62+ groups, two K+ ions, and four additional water molecules. The decavanadate ion is an isolated group of ten condensed VO6 octahedra, six in a rectangular 2 x 3 array sharing edges, and four more, two fitted in above and two below by sharing sloping edges. The structure, which is based on a sodium-chloride-like arrangement of V and O atoms, has a close relationship to other isopoly complex molybdates, niobates, and tantalates. Strong distortions in the VO6 octahedra are analogous to square-pyramid and other special coordination features known in other vanadate structures.

  7. Photoelectron holography applied to surface structural determination

    SciTech Connect

    Petersen, Barry Lee

    1995-05-01

    Photoemitted electron waves are used as coherent source waves for angstrom-scale holographic imaging of local atomic geometry at surfaces. Electron angular distribution patterns are collected above a sample surface and serve as a record of the interference between source wave and waves scattered from surrounding ion cores. Using a mathematical imaging integral transformation, the three-dimensional structural information is obtained directly from these collected patterns. Patterns measured with different electron kinetic energies are phase-summed for image improvement. Pt (111) surface is used as a model system. A pattern 9.6Å-1 (351 eV) is used to generate a full 3-D image of atom locations around an emitter with nearest neighbors within 0.lÅ of the expected bulk positions. Atoms several layers beyond the nearest neighbors are also apparent. Twin-image reduction and artifact suppression is obtained by phase-summing eight patterns measured from 8.8 to 10.2Å-1 (295 to 396 eV). 32 were measured in 0.2Å-1 steps from 6.0 to 12.2Å-1 (137 to 567 eV) are presented here. Simple models of two-slit interference are compared with electron scattering to illuminate understanding of holographic recording of the structural information. This also shows why it sometimes fails due to destructive interferences. Simple theoretical models of electron scattering are compared to experiment to show the origin of the structural information and the differences that result from atomic scattering and from the source wave. Experimental parameters and their relation to imaging is discussed. Comparison is made to the Pt pattern measured at 351 eV using the simple theoretical model. The remaining data set is also modeled, and the eight appropriate theoretical patterns are used to regenerate the multiple-wavenumber experimental result. A clean Cu (001) surface is also measured and imaged.

  8. DEVELOPMENT AND VALIDATION OF AN ION CHROMATOGRAPHIC METHOD FOR DETERMINING PERCHLORATE IN FERTILIZERS

    EPA Science Inventory

    A method has been developed for the determination of perchlorate in fertilizers. Materials are leached with deionized water to dissolve any soluble perchlorate compounds. Ion chromatographic separation is followed by suppressed conductivity for detection. Perchlorate is retained ...

  9. DEVELOPMENT AND VALIDATION OF AN ION CHROMATOGRAPHIC METHOD FOR DETERMINING PERCHLORATE IN FERTILIZERS

    EPA Science Inventory

    A method has been developed for the determination of perchlorate in fertilizers. Materials are leached with deionized water to dissolve any soluble perchlorate compounds. Ion chromatographic separation is followed by suppressed conductivity for detection. Perchlorate is retained ...

  10. Structure Determination of Novel Polydiacetylene Materials.

    NASA Astrophysics Data System (ADS)

    Thakur, Mrinal Kanti

    The major objective of this work has been to synthesize and characterize some novel diacetylene polymers. Monomers of the general type HC(TBOND)C-(CH(,2))(,n)-C(TBOND)CH were oxidatively coupled (Glaser coupling) to synthesize polymers of the form ( (CH(,2))(,n)-C(TBOND)C-C(TBOND)C )(,x). These polymers (n = 5, 6, 8), termed macromonomers, were subsequently exposed to CO('60)-(gamma) radiation to effect the diacetylene polymerization. The resulting materials, called crosspolymerized macromonomers, were composed of regular two-dimensional networks of polydiacetylene and hydrocarbon chains. Crystal structures of macromonomers before and after crosspolymerization were determined essentially by electron diffraction analysis, with supporting information from x-ray fiber diffraction. A detailed investigation of the crosspolymerization reaction was made by C-13 NMR in solid state. A very special type of diacetylene monomer was synthesized by dimerizing 1,11-dodecadiyne through a controlled oxidative coupling. Preliminary characterization of these dimers was accomplished by using GPC, DSC and electron diffraction. Macroscopic single crystals of polymerized dimer were obtained by radiation ((gamma)-radiation) induced polymerization and simultaneous crystallization from solution. X -ray diffraction analysis was employed for the crystal structure determination of this material. The structure was found to be composed of sheets of alternating polydiacetylene and polyacetylene chains. The nearest neighbor distance between a polydiacetylene and a polyacetylene chain was approximately 4(ANGSTROM). The electrical conductivity of this undoped material was measured and found to be reasonably high ((TURN)10('-2) (OMEGA)('-1)cm('-1)). A (pi)-electron band structure calculation indicated that such high conductivity resulted because of significant interchain interaction within the unit cell. A detailed investigation of the consequences of anharmonic interaction on diffraction intensities

  11. Sugar-metal ion interactions: the complicated coordination structures of cesium ion with D-ribose and myo-inositol.

    PubMed

    Hu, Haijian; Xue, Junhui; Wen, Xiaodong; Li, Weihong; Zhang, Chao; Yang, Limin; Xu, Yizhuang; Zhao, Guozhong; Bu, Xiaoxia; Liu, Kexin; Chen, Jia'er; Wu, Jinguang

    2013-11-18

    The novel cesium chloride-D-ribose complex (CsCl·C5H10O5; Cs-R) and cesium chloride-myo-inositol complex (CsCl·C6H12O6; Cs-I) have been synthesized and characterized using X-ray diffraction and FTIR, FIR, THz, and Raman spectroscopy. Cs(+) is eight-coordinated to three chloride ions, O1 and O2 from one D-ribose molecule, O1 from another D-ribose molecule, and O4 and O5 from the third D-ribose molecule in Cs-R. For one D-ribose molecule, the oxygen atom O1 in the ring is coordinated to two cesium ions as an oxygen bridge, O2 is cocoordinated with O1 to one of the two cesium ions, and O4 and O5 are coordinated to the third cesium ion, respectively. O3 does not coordinate to metal ions and only takes part in forming hydrogen bonds. One chloride ion is connected to three cesium ions. Thus, a complicated structure of Cs-D-ribose forms. For Cs-I, Cs(+) is 10-coordinated to three chloride ions, O1 and O2 from one myo-inositol molecule, O3 and O4 from another myo-inositol molecule, O5 and O6 from the third myo-inositol molecule, and O6 from the fourth myo-inositol molecule. One metal ion is connected to four ligands, and one myo-inositol is coordinated to four Cs(+) ions, which is also a complicated coordination structure. Crystal structure results, FTIR, FIR, THz, and Raman spectra provide detailed information on the structure and coordination of hydroxyl groups to metal ions in the cesium chloride-D-ribose and cesium chloride-myo-inositol complexes.

  12. Compositional, structural, and optical changes of polyimide implanted by 1.0 MeV Ni+ ions

    NASA Astrophysics Data System (ADS)

    Mikšová, R.; Macková, A.; Pupikova, H.; Malinský, P.; Slepička, P.; Švorčík, V.

    2017-09-01

    The ion irradiation leads to deep structural and compositional changes in the irradiated polymers. Ni+ ions implanted polymers were investigated from the structural and compositional changes point of view and their optical properties were investigated. Polyimide (PI) foils were implanted with 1.0 MeV Ni+ ions at room temperature with fluencies of 1.0 × 1013-1.0 × 1015 cm-2 and two different ion implantation currents densities (3.5 and 7.2 nA/cm2). Rutherford Back-Scattering (RBS) and Elastic Recoil Detection Analysis (ERDA) were used for determination of oxygen and hydrogen escape in implanted PI. Atomic Force Microscopy (AFM) was used to follow surface roughness modification after the ion implantation and UV-Vis spectroscopy was employed to check the optical properties of the implanted PI. The implanted PI structural changes were analysed using Attenuated Total Reflection Fourier Transform Infrared Spectroscopy (ATR-FTIR). High energy Ni-ion implantation causes only a minor release of hydrogen and oxygen close to the polymer sub-surface region in about 60 nm thick layer penetrated by the ion beam; especially at ion fluencies below 1.0 × 1014 cm-2. The mostly pronounced structural changes of the Ni implanted PI were found for the samples implanted above ion fluence 1.0 × 1015 cm-2 and at the ion current density 7.2 nA/cm2, where the optical band gap significantly decreases and the reduction of more complex structural unit of PI monomer was observed.

  13. Two active site divalent ions in the crystal structure of the hammerhead ribozyme bound to a transition state analogue

    DOE PAGES

    Mir, Aamir; Golden, Barbara L.

    2015-11-09

    The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositioning a divalent metal ion such that it could, ultimately, interact directly with the scissile phosphate. This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second divalent ion is observed coordinated to O6 of G12. This metal ion is well-placed to help tune the pKA of G12. Finally, on the basis of this crystalmore » structure as well as a wealth of biochemical studies, in this paper we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid.« less

  14. Two active site divalent ions in the crystal structure of the hammerhead ribozyme bound to a transition state analogue

    SciTech Connect

    Mir, Aamir; Golden, Barbara L.

    2015-11-09

    The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositioning a divalent metal ion such that it could, ultimately, interact directly with the scissile phosphate. This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second divalent ion is observed coordinated to O6 of G12. This metal ion is well-placed to help tune the pKA of G12. Finally, on the basis of this crystal structure as well as a wealth of biochemical studies, in this paper we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid.

  15. Crystal structures of a double-barrelled fluoride ion channel

    PubMed Central

    Stockbridge, Randy B.; Kolmakova-Partensky, Ludmila; Shane, Tania; Koide, Akiko; Koide, Shohei; Miller, Christopher; Newstead, Simon

    2016-01-01

    To contend with hazards posed by environmental fluoride, microorganisms export this anion through F--specific ion channels of the Fluc family1–4. Since the recent discovery of Fluc channels, numerous idiosyncratic features of these proteins have been unearthed, including extreme selectivity for F- over Cl- and dual-topology dimeric assembly5–6. To understand the chemical basis for F- permeation and how the antiparallel subunits convene to form a F--selective pore, we solved crystal structures of two bacterial Fluc homologues in complex with three different monobody inhibitors, with and without F- present, to a maximum resolution of 2.1 Å. The structures reveal a surprising “double-barrelled” channel architecture in which two F- ion pathways span the membrane and the dual-topology arrangement includes a centrally coordinated cation, most likely Na+. F- selectivity is proposed to arise from the very narrow pores and an unusual anion coordination that exploits the quadrupolar edges of conserved phenylalanine rings. PMID:26344196

  16. Glutamate Receptor Ion Channels: Structure, Regulation, and Function

    PubMed Central

    Wollmuth, Lonnie P.; McBain, Chris J.; Menniti, Frank S.; Vance, Katie M.; Ogden, Kevin K.; Hansen, Kasper B.; Yuan, Hongjie; Myers, Scott J.; Dingledine, Ray

    2010-01-01

    The mammalian ionotropic glutamate receptor family encodes 18 gene products that coassemble to form ligand-gated ion channels containing an agonist recognition site, a transmembrane ion permeation pathway, and gating elements that couple agonist-induced conformational changes to the opening or closing of the permeation pore. Glutamate receptors mediate fast excitatory synaptic transmission in the central nervous system and are localized on neuronal and non-neuronal cells. These receptors regulate a broad spectrum of processes in the brain, spinal cord, retina, and peripheral nervous system. Glutamate receptors are postulated to play important roles in numerous neurological diseases and have attracted intense scrutiny. The description of glutamate receptor structure, including its transmembrane elements, reveals a complex assembly of multiple semiautonomous extracellular domains linked to a pore-forming element with striking resemblance to an inverted potassium channel. In this review we discuss International Union of Basic and Clinical Pharmacology glutamate receptor nomenclature, structure, assembly, accessory subunits, interacting proteins, gene expression and translation, post-translational modifications, agonist and antagonist pharmacology, allosteric modulation, mechanisms of gating and permeation, roles in normal physiological function, as well as the potential therapeutic use of pharmacological agents acting at glutamate receptors. PMID:20716669

  17. UV spectroscopy determination of aqueous lead and copper ions in water

    NASA Astrophysics Data System (ADS)

    Tan, C. H.; Moo, Y. C.; Mat Jafri, M. Z.; Lim, H. S.

    2014-05-01

    Lead (Pb2+) and copper (Cu2+) ions are very common pollutants in water which have dangerous potential causing serious disease and health problems to human. The aim of this paper is to determine lead and copper ions in aqueous solution using direct UV detection without chemical reagent waste. This technique allow the determination of lead and copper ions from range 0.2 mg/L to 10 mg/L using UV wavelength from 205 nm to 225 nm. The method was successfully applied to synthetic sample with high performance.

  18. Syntheses and Structure Determinations of Calcium Thiolates.

    PubMed

    Chadwick, Scott; Englich, Ulrich; Noll, Bruce; Ruhlandt-Senge, Karin

    1998-09-07

    The exploration of synthetic methodologies toward heavy alkaline-earth chalcogenolates resulted in the preparation and structural characterization of a family of calcium thiolates, including [Ca(SC(6)F(5))(2)(py)(4)], 1 (py = pyridine), the separated ion-triple [Ca(18-crown-6)(NH(3))(3))][SMes](2).2THF, 2 (Mes = 2,4,6-tBu(3)C(6)H(2)), and the contact triple [Ca(18-crown-6)(SMes)(2)].THF, 3. Compound 1 was prepared by treating [Ca(N(SiMe(3))(2))(2)](2) with 4 equiv of HSC(6)F(5) under addition of pyridine. The thiolates 2 and 3 were synthesized by treatment of calcium metal dissolved in dry, liquid NH(3) under addition of 2 equiv of HSMes and crown ether or, alternatively, by the reduction of MesSSMes with calcium metal in dry, liquid ammonia. We also report two reaction products isolated during attempted calcium thiolate syntheses: [CaBr(4)(THF)(2)(&mgr;(2)-Li)(2)(THF)(4)], 4, isolated as the product of a salt elimination reaction between CaBr(2) and 2 equiv of [Li(THF)(n)()S-2,4,6-(i)()Pr(3)C(6)H(2)](m)(). [(NH(4))(py)(SC(6)F(5))], 5, was obtained as the sole product in the reaction of metallic calcium with HSC(6)F(5) in liquid ammonia under addition of pyridine. All compounds were characterized by single-crystal X-ray crystallography in addition to IR and NMR spectroscopy.

  19. Determination of thiocyanate (biomarkers of ETS) and other inorganic ions in human nasal discharge samples using ion chromatography.

    PubMed

    Narkowicz, Sylwia; Polkowska, Żaneta; Marć, Mariusz; Simeonov, Vasil; Namieśnik, Jacek

    2013-10-01

    Environmental tobacco smoke (ETS) is a mixture of air and tobacco smoke containing more than 4000 chemical substances. In view of the health risks of many of these substances, studies are needed to determine biomarkers of exposure to ETS constituents in people who actively or passively are exposed to the toxic compounds. The methodologies for determining most biomarkers from saliva, urine and blood samples are known, but methods for analyzing these compounds in nasal discharges are not available. The objective of this work was to develop an analytical procedure for the determination of thiocyanate and other biomarker compounds in samples of nasal discharge using ion chromatography.

  20. Structure and electronic properties features of amorphous chalhogenide semiconductor films prepared by ion-plasma spraying

    SciTech Connect

    Korobova, N. Timoshenkov, S.; Almasov, N.; Prikhodko, O.; Tsendin, K.

    2014-10-21

    Structure of amorphous chalcogenide semiconductor glassy As-S-Se films, obtained by high-frequency (HF) ion-plasma sputtering has been investigated. It was shown that the length of the atomic structure medium order and local structure were different from the films obtained by thermal vacuum evaporation. Temperature dependence of dark conductivity, as well as the dependence of the spectral transmittance has been studied. Conductivity value was determined at room temperature. Energy activation conductivity and films optical band gap have been calculated. Temperature and field dependence of the drift mobility of charge carriers in the HF As-S-Se films have been shown. Bipolarity of charge carriers drift mobility has been confirmed. Absence of deep traps for electrons in the As{sub 40}Se{sub 30}S{sub 30} spectrum of localized states for films obtained by HF plasma ion sputtering was determined. Bipolar drift of charge carriers was found in amorphous As{sub 40}Se{sub 30}S{sub 30} films obtained by ion-plasma sputtering of high-frequency, unlike the films of these materials obtained by thermal evaporation.

  1. Track Structure in DNA Irradiated with Heavy Ions

    SciTech Connect

    Bowman, Michael K.; Becker, David; Sevilla, Michael D.; Zimbrick, John D.

    2005-04-01

    The spatial properties of trapped radicals produced in heavy ion-irradiated solid DNA at 77 K have been probed using pulsed Electron Paramagnetic Double Resonance (PELDOR or DEER) techniques. Salmon testes DNA hydrated to twelve water molecules per nucleotide was irradiated with 40Ar ions of energy 100 MeV/nucleon and LET ranging from 300 to 400 keV/?. Irradiated samples were maintained at cryogenic temperature at all times. PELDOR measurements were made using a refocused echo detection sequence that allows dipolar interaction between trapped radicals to be observed. The EPR spectrum is attributed to electron loss/gain DNA base radicals and neutral carbon-centered radicals that likely arise from sugar damage. We find a radical concentration of 13.5*1018 cm-3 in the tracks and a track radius of 6.79 nm. The cross section of these tracks is 144 nm2 yielding a lineal radical density of 2.6 radicals/nm. Based upon the yields previously determined for particles having calculated LET values of 300-400 keV/mm and our measured lineal density, we obtain an LET of 270 keV/mm, which is in good agreement with the calculated range of values. These measurements of radical density and spatial extent provide the first direct experimental determination of track characteristics in irradiated DNA.

  2. Ion Acceleration in Solar Flares Determined by Solar Neutron Observations

    NASA Astrophysics Data System (ADS)

    Watanabe, K.; Solar Neutron Observation Group

    2013-05-01

    Large amounts of particles can be accelerated to relativistic energy in association with solar flares and/or accompanying phenomena (e.g., CME-driven shocks), and they sometimes reach very near the Earth and penetrate the Earth's atmosphere. These particles are observed by ground-based detectors (e.g., neutron monitors) as Ground Level Enhancements (GLEs). Some of the GLEs originate from high energy solar neutrons which are produced in association with solar flares. These neutrons are also observed by ground-based neutron monitors and solar neutron telescopes. Recently, some of the solar neutron detectors have also been operating in space. By observing these solar neutrons, we can obtain information about ion acceleration in solar flares. Such neutrons were observed in association with some X-class flares in solar cycle 23, and sometimes they were observed by two different types of detectors. For example, on 2005 September 7, large solar neutron signals were observed by the neutron monitor at Mt. Chacaltaya in Bolivia and Mexico City, and by the solar neutron telescopes at Chacaltaya and Mt. Sierra Negra in Mexico in association with an X17.0 flare. The neutron signal continued for more than 20 minutes with high statistical significance. Intense gamma-ray emission was also registered by INTEGRAL, and by RHESSI during the decay phase. We analyzed these data using the solar-flare magnetic-loop transport and interaction model of Hua et al. (2002), and found that the model could successfully fit the data with intermediate values of loop magnetic convergence and pitch angle scattering parameters. These results indicate that solar neutrons were produced at the same time as the gamma-ray line emission and that ions were continuously accelerated at the emission site. In this paper, we introduce some of the solar neutron observations in solar cycle 23, and discuss the tendencies of the physical parameters of solar neutron GLEs, and the energy spectrum and population of the

  3. Formation of the dendrite structure at ion beam synthesis in the external magnetic field

    NASA Astrophysics Data System (ADS)

    Gumarov, G. G.; Petukhov, V. Yu.; Bukharaev, A. A.; Biziaev, D. A.; Nuzhdin, V. I.; Khaibullin, R. I.

    2009-05-01

    For the first time the dendrite structure on the surface of single-crystal silicon wafers implanted with Fe+ at high fluences in the applied magnetic field was revealed by atomic-force microscopy. The nucleation and growth of dendrites were simulated using the modified model of the diffusion limited aggregation at ion implantation. The magnetic dipole-dipole interaction between diffusing implanted atoms and forming ferromagnetic clusters was also considered. In the frame of this model the form of the dendrite structure is mainly determined by the effective magnetic moment and the diffusion coefficient.

  4. Modelling of ion permeation in K+ channels by nonequilibrium molecular dynamics simulations: I. Permeation energetics and structure stability.

    PubMed

    Neamţu, A; Suciu, Daniela

    2004-01-01

    Because of the great importance of physiological and pathophysiological processes in which ion channels are involved and because their operation is described by physicochemical laws, there have been many attempts to develop physical models able to describe the membrane permeability and also the structural and functional properties of the channel protein structures. In this study (in two parts) we present a series of simulations on a K+ channel model (KcsA) using Nonequilibrium Molecular Dynamics simulations (NEMD), in order to follow structure stability, permeation energetics and the possibility of obtaining quantitative information about the permeation process using the Linear Response Theory (LRT). On K+ ions were applied external forces to determine them to pass through the channel in a relatively small amount of time, accessible computationally. We ascertained a high resistance of the protein to deformation even in conditions when great forces were applied on ions (the system was far from equilibrium). The estimation of energy profiles in the course of ions passage through the channel demonstrates that these proteins create a conductivity pathway with no energetic barriers for ions movement across the channel (which could be present due to ions dehydration). The dynamic model used demonstrates (as proposed before in the literature after the examination of the static KcsA structure obtained by X-Ray crystallography) that this is due to the interaction of ions with the negatively charged carbonyl oxygens of the main polypeptide chain in the selectivity filter region.

  5. Seeking structural specificity: direct modulation of pentameric ligand-gated ion channels by alcohols and general anesthetics.

    PubMed

    Howard, Rebecca J; Trudell, James R; Harris, R Adron

    2014-01-01

    Alcohols and other anesthetic agents dramatically alter neurologic function in a wide range of organisms, yet their molecular sites of action remain poorly characterized. Pentameric ligand-gated ion channels, long implicated in important direct effects of alcohol and anesthetic binding, have recently been illuminated in renewed detail thanks to the determination of atomic-resolution structures of several family members from lower organisms. These structures provide valuable models for understanding and developing anesthetic agents and for allosteric modulation in general. This review surveys progress in this field from function to structure and back again, outlining early evidence for relevant modulation of pentameric ligand-gated ion channels and the development of early structural models for ion channel function and modulation. We highlight insights and challenges provided by recent crystal structures and resulting simulations, as well as opportunities for translation of these newly detailed models back to behavior and therapy.

  6. Seeking Structural Specificity: Direct Modulation of Pentameric Ligand-Gated Ion Channels by Alcohols and General Anesthetics

    PubMed Central

    Trudell, James R.; Harris, R. Adron

    2014-01-01

    Alcohols and other anesthetic agents dramatically alter neurologic function in a wide range of organisms, yet their molecular sites of action remain poorly characterized. Pentameric ligand-gated ion channels, long implicated in important direct effects of alcohol and anesthetic binding, have recently been illuminated in renewed detail thanks to the determination of atomic-resolution structures of several family members from lower organisms. These structures provide valuable models for understanding and developing anesthetic agents and for allosteric modulation in general. This review surveys progress in this field from function to structure and back again, outlining early evidence for relevant modulation of pentameric ligand-gated ion channels and the development of early structural models for ion channel function and modulation. We highlight insights and challenges provided by recent crystal structures and resulting simulations, as well as opportunities for translation of these newly detailed models back to behavior and therapy. PMID:24515646

  7. Determination of Cyanogenic Compounds in Edible Plants by Ion Chromatography

    PubMed Central

    Cho, Hye-Jeon; Do, Byung-Kyung; Shim, Soon-Mi; Lee, Dong-Ha; Nah, Ahn-Hee; Choi, Youn-Ju; Lee, Sook-Yeon

    2013-01-01

    Cyanogenic glycosides are HCN-producing phytotoxins; HCN is a powerful and a rapidly acting poison. It is not difficult to find plants containing these compounds in the food supply and/or in medicinal herb collections. The objective of this study was to investigate the distribution of total cyanide in nine genera (Dolichos, Ginkgo, Hordeum, Linum, Phaseolus, Prunus, Phyllostachys, Phytolacca, and Portulaca) of edible plants and the effect of the processing on cyanide concentration. Total cyanide content was measured by ion chromatography following acid hydrolysis and distillation. Kernels of Prunus genus are used medicinally, but they possess the highest level of total cyanide of up to 2259.81 CN−/g dry weight. Trace amounts of cyanogenic compounds were detected in foodstuffs such as mungbeans and bamboo shoots. Currently, except for the WHO guideline for cassava, there is no global standard for the allowed amount of cyanogenic compounds in foodstuffs. However, our data emphasize the need for the guidelines if plants containing cyanogenic glycosidesare to be developed as dietary supplements. PMID:24278641

  8. Angle-resolved x-ray spectroscopic scheme to determine overlapping hyperfine splittings in highly charged heliumlike ions

    NASA Astrophysics Data System (ADS)

    Wu, Z. W.; Volotka, A. V.; Surzhykov, A.; Fritzsche, S.

    2017-07-01

    An angle-resolved x-ray spectroscopic scheme is presented for determining the hyperfine splitting of highly charged ions. For heliumlike ions, in particular, we propose to measure either the angular distribution or polarization of the 1 s 2 p P31,F →1 s2 S10,Ff emission following the stimulated decay of the initial 1 s 2 s S10,Fi level. It is found that both the angular and polarization characteristics of the emitted x-ray photons strongly depend on the (relative) splitting of the partially overlapping hyperfine 1 s 2 p P31,F resonances and may thus help resolve their hyperfine structure. The proposed scheme is feasible with present-day photon detectors and allows a measurement of the hyperfine splitting of heliumlike ions with a relative accuracy of about 10-4.

  9. Selective and sensitive spectrophotometric method for determination of sub-micro-molar amounts of aluminium ion.

    PubMed

    Shokrollahi, A; Ghaedi, M; Niband, M S; Rajabi, H R

    2008-03-01

    A simple and accurate spectrophotometric method for determination of trace and ultra-trace amounts of Al3+ ion in tap and wastewater sample has been described. Using the eriochrome cyanine R (ECR) in the presence of N,N-dodecyltrimethylammonium bromide (DTAB) as cationic surfactant spectrophotometric determination of Al3+ ion has been carried out. The Beer's law is obeyed over the concentration range of 4-400 ng mL(-1) of Al3+ ion with the detection limits of 0.14 ng mL(-1), while the molar absorptivity of complexes is 1.19x10(5) L mol(-1) cm(-1). The influence of type and amount of surfactant, pH, and amount of ligand on sensitivity of spectrophotometric method were optimized. The method has been successfully applied for Al3+ ion determination in real sample.

  10. Computer simulation of field ion images of nanoporous structure in the irradiated materials

    NASA Astrophysics Data System (ADS)

    Medvedeva, E. V.; Alexandrova, S. S.; Belykh, T. A.

    2012-02-01

    Computer simulation and interpretation of field ion microscopy images of ion irradiated platinum are discussed. Field ion microscopy technique provides direct precise atomic scale investigation of crystal lattice defects of atomically pure surface of material; at the same time it allows to analyze the structural defects in volume by controlled and sequential removal of surface atoms by electric field. Defects identification includes the following steps: at the first stage the type of crystalline structure and spatial orientation of crystallographic directions were determined. Thus, we obtain the data about exact position of all atoms of the given volume, i.e. the model image of an ideal crystal. At the second stage, the ion image was processed used the program to obtain the data about real arrangement of atoms of the investigated sample. At the third stage the program compares these two data sets, with a split-hair accuracy revealing a site of all defects in a material. Results of the quantitative analysis show that shape of nanopores are spherical or cylindrical, diameter on nanopores was varied from 1 to 5 run, their depth was fond to be from 1 to 9 nm. It was observed that nearly 40% of nanopores are concentrated in the subsurface layer 10 nm thick, the concentration of nanopores decreased linearly with the distance from the irradiated surface.

  11. Capillary electrophoresis/mass spectrometry determination of inorganic ions using an ion spray-sheath flow interface.

    PubMed

    Huggins, T G; Henion, J D

    1993-01-01

    The determination of inorganic cations and anions by capillary electrophoresis/mass spectrometry (CE/MS) is reported using an ion spray-sheath flow interface coupling. A twelve-component synthetic mixture of cations which included the positive ions of K, Ba, Ca, Mn, Cd, Co, Pb, Cr, Ni, Zn, Ag, and Cu was loaded into the capillary column at levels ranging from 30 to 300 pg, separated by CE, and detected by indirect UV and in the full-scan (m/z 35-450) positive ion CE/MS mode using an aqueous buffer containing 30 mM creatinine and 8 mM alpha-hydroxyisobutyric acid, pH 4.8. Creatinine forms adducts with the cations which are observed in the gas phase and requires rather high (120 electron volts) declustering energy to dissociate. This produces a reduction in charge state to form the free, singly charged, inorganic cations which are observed in the mass spectra. CE/MS analysis of an aqueous acidic extract of used aircraft engine oil revealed high levels of lead as well as lower levels of chromium and nickel. CE-indirect UV analysis of a synthetic mixture containing 300 pg each of 11 inorganic ions, which included the anions of Br, Cl, NO2, NO3, S2O3, N3, SCN, SO4, SeO4, oxalate, and MoO4, is shown. The running buffer which affected this separation contained 5 mM ammonium dichromate, 10 mM ammonium acetate, and 20 mM diethylenetriamine at pH 9.3. Although indirect UV detection revealed good separation of these anions, CE/MS analysis of this mixture was complicated by interfering ion current signals from the cluster ions formed by the interaction between the additives and the analytes.(ABSTRACT TRUNCATED AT 250 WORDS)

  12. A novel flow injection potentiometric graphite coated ion-selective electrode for the low level determination of uranyl ion.

    PubMed

    Shamsipur, Mojtaba; Mizani, Farhang; Mousavi, Mir Fazlollah; Alizadeh, Naader; Alizadeh, Kamal; Eshghi, Hossein; Karami, Hassan

    2007-04-18

    Solution studies on the binding properties of uranyl ion toward four different recently synthesized benzo-substituted macrocyclic diamides L1-L4 revealed the occurrence of a 1:1 complexation of the ligands with UO(2)(2+) ion, with a stability order of L2>L1>L4>L3. Consequently, L2 was used as a suitable neutral ionophore for the preparation of novel polymeric membrane (PME) and coated graphite (CGE) UO(2)(2+)-selective electrodes. The electrodes exhibit a Nernstian behavior for UO(2)(2+) ions over wide concentration ranges (1.0 x 10(-6) - 1.0 x 10(-1) M for PME and 1.0 x 10(-7) - 1.0 x 10(-1) M for CGE) and very low limits of detection (8.0 x 10(-7) M for PME and 7.3 x 10(-8) M for CGE). The proposed potentiometric sensors manifest advantages of fast response and, most importantly, good selectivity with respect to many alkali, alkaline earth, transition, and heavy metal ions. The potentiometric responses of the electrodes are independent of the pH of the test solution in the pH range 2.9-3.7. The CGE was used in flow injection potentiometry and resulted in well defined peaks for uranyl ions with stable baseline, excellent reproducibility and very high sampling rate of 170 injections per hour. The proposed FIP system was used for the determination of trace uranyl ions in real and synthetic samples.

  13. Structural Determinants of Misfolding in Multidomain Proteins.

    PubMed

    Tian, Pengfei; Best, Robert B

    2016-05-01

    Recent single molecule experiments, using either atomic force microscopy (AFM) or Förster resonance energy transfer (FRET) have shown that multidomain proteins containing tandem repeats may form stable misfolded structures. Topology-based simulation models have been used successfully to generate models for these structures with domain-swapped features, fully consistent with the available data. However, it is also known that some multidomain protein folds exhibit no evidence for misfolding, even when adjacent domains have identical sequences. Here we pose the question: what factors influence the propensity of a given fold to undergo domain-swapped misfolding? Using a coarse-grained simulation model, we can reproduce the known propensities of multidomain proteins to form domain-swapped misfolds, where data is available. Contrary to what might be naively expected based on the previously described misfolding mechanism, we find that the extent of misfolding is not determined by the relative folding rates or barrier heights for forming the domains present in the initial intermediates leading to folded or misfolded structures. Instead, it appears that the propensity is more closely related to the relative stability of the domains present in folded and misfolded intermediates. We show that these findings can be rationalized if the folded and misfolded domains are part of the same folding funnel, with commitment to one structure or the other occurring only at a relatively late stage of folding. Nonetheless, the results are still fully consistent with the kinetic models previously proposed to explain misfolding, with a specific interpretation of the observed rate coefficients. Finally, we investigate the relation between interdomain linker length and misfolding, and propose a simple alchemical model to predict the propensity for domain-swapped misfolding of multidomain proteins.

  14. Structural Determinants of Misfolding in Multidomain Proteins

    PubMed Central

    Tian, Pengfei; Best, Robert B.

    2016-01-01

    Recent single molecule experiments, using either atomic force microscopy (AFM) or Förster resonance energy transfer (FRET) have shown that multidomain proteins containing tandem repeats may form stable misfolded structures. Topology-based simulation models have been used successfully to generate models for these structures with domain-swapped features, fully consistent with the available data. However, it is also known that some multidomain protein folds exhibit no evidence for misfolding, even when adjacent domains have identical sequences. Here we pose the question: what factors influence the propensity of a given fold to undergo domain-swapped misfolding? Using a coarse-grained simulation model, we can reproduce the known propensities of multidomain proteins to form domain-swapped misfolds, where data is available. Contrary to what might be naively expected based on the previously described misfolding mechanism, we find that the extent of misfolding is not determined by the relative folding rates or barrier heights for forming the domains present in the initial intermediates leading to folded or misfolded structures. Instead, it appears that the propensity is more closely related to the relative stability of the domains present in folded and misfolded intermediates. We show that these findings can be rationalized if the folded and misfolded domains are part of the same folding funnel, with commitment to one structure or the other occurring only at a relatively late stage of folding. Nonetheless, the results are still fully consistent with the kinetic models previously proposed to explain misfolding, with a specific interpretation of the observed rate coefficients. Finally, we investigate the relation between interdomain linker length and misfolding, and propose a simple alchemical model to predict the propensity for domain-swapped misfolding of multidomain proteins. PMID:27163669

  15. Quantum quenches of ion Coulomb crystals across structural instabilities. II. Thermal effects

    NASA Astrophysics Data System (ADS)

    Baltrusch, Jens D.; Cormick, Cecilia; Morigi, Giovanna

    2013-03-01

    We theoretically analyze the efficiency of a protocol for creating mesoscopic superpositions of ion chains, described in Baltrusch [Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.84.063821 84, 063821 (2011)], as a function of the temperature of the crystal. The protocol makes use of state-dependent forces, so that a coherent superposition of the electronic states of one ion evolves into an entangled state between the chain's internal and external degrees of freedom. Ion Coulomb crystals are well isolated from the external environment and should therefore experience a coherent, unitary evolution, which follows the quench and generates structural Schrödinger-cat-like states. The temperature of the chain, however, introduces a statistical uncertainty in the final state. We characterize the quantum state of the crystal by means of the visibility of Ramsey interferometry performed on one ion of the chain and determine its decay as a function of the crystal's initial temperature. This analysis allows one to determine the conditions on the chain's initial state in order to efficiently perform the protocol.

  16. DETERMINATION OF ELEMENTAL COMPOSITIONS FROM MASS PEAK PROFILES OF THE MOLECULAR ION (M) AND THE M + 1 AND M + 2 IONS

    EPA Science Inventory

    The relative abundances of M + 1 and M + 2 ions help to identify the elemental composition of the molecular ion (M). But scan speed, snesitiity, and resolution limitations of mass spectrometers have impeded determination of these abundances. Mass peak profiling from selected ion ...

  17. Determination of amines used in the oil and gas industry (upstream section) by ion chromatography.

    PubMed

    Kadnar, R

    1999-07-30

    During production and purification of crude oil and natural gas several different amines are used as chemicals or operating materials, e.g. film forming long chain amines as corrosion inhibitors, steam volatile amines for pH correction and corrosion protection, alkanolamines as absorbents in sour gas treatment plants, etc. For analytical checks, e.g. determination of corrosion inhibitor concentration in produced media, classical chemical methods are used predominantly, because most of them can be performed in small field laboratories. Some amines, especially the small molecular aliphatic and heterocyclic amines can also be determined by ion chromatography. In our laboratory two types of separation columns (IonPac CS10 and CS12A) were available for ion chromatographic separation. The analysis of the amines in low-salt-containing water, soft water or steam condensate can be performed without problems. The presence of alkali and/or alkaline earth ions in the sample can lead to coelution with these ions, to poor peak resolution or enhanced analysis times, depending on the chromatographic conditions. This work shows some examples of ion chromatography applications for the determination of low-molecular-mass ethanolamines, morpholine and piperazine and discusses the possible interferences and troubles caused by alkali and alkaline earth ions in the matrix.

  18. Time-dependent cylindrical and spherical ion-acoustic solitary structures in relativistic degenerate multi-ion plasmas with positively-charged heavy ions

    NASA Astrophysics Data System (ADS)

    Hossen, M. R.; Nahar, L.; Mamun, A. A.

    2014-12-01

    The properties of time-dependent cylindrical and spherical, modified ion-acoustic (mIA) solitary structures in relativistic degenerate multi-ion plasmas (containing degenerate electron fluids, inertial positively-, as well as negatively-, charged light ions, and positively-charged static heavy ions) have been investigated theoretically. This investigation is valid for both non-relativistic and ultra-relativistic limits. The well-known reductive perturbation method has been used to derive the Korteweg-de Vries (K-dV) and the mK-dV equations for studying the basic features of solitary waves. The fundamental characteristics of mIA solitary waves are found to be significantly modified by the effects of the degenerate pressures of the electron and the ion fluids, their number densities, and the various charge states of heavy ions. The relevance of our results in astrophysical compact objects like white dwarfs and neutron stars, which are of scientific interest, is briefly discussed.

  19. Ion exchange membranes as novel passive sampling material for organic ions: application for the determination of freely dissolved concentrations.

    PubMed

    Oemisch, Luise; Goss, Kai-Uwe; Endo, Satoshi

    2014-11-28

    Many studies in pharmacology, toxicology and environmental science require a method for determining the freely dissolved concentration of a target substance. A recently developed tool for this purpose is equilibrium passive sampling with polymeric materials. However, this method has rarely been applied to ionic organic substances, primarily due to limited availability of convenient sorption materials. This study introduces ion exchange membranes (IEMs) as a novel passive sampling material for organic ions. The partitioning of 4-ethylbenzene-1-sulfonate, 2,4-dichlorophenoxyacetic acid and pentachlorophenol to one anion exchange membrane (FAS) and of difenzoquat, nicotine and verapamil to one cation exchange membrane (FKS) was investigated. All test substances exhibited a sufficiently high affinity for the respective IEM with logarithmic IEM-water partition coefficients >2.3. Sorption equilibrium was established quickly, within several hours for the FAS membrane and within 1-3 days for the FKS membrane. For permanently charged substances the partitioning to the IEMs was independent of pH, but was influenced by the salt composition of the test solution. For all test substances sorption to IEM was dependent on the substance concentration. Bovine serum albumin-water partition coefficients determined by passive sampling with IEMs agree well with those determined by the conventional dialysis method. The results of this study indicate that IEMs exhibit the potential to measure freely dissolved concentrations of organic ions in a simple and time-saving manner. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Structural Changes in Polymer Films by Fast Ion Implantation

    NASA Astrophysics Data System (ADS)

    Parada, M. A.; Minamisawa, R. A.; Muntele, C.; Muntele, I.; De Almeida, A.; Ila, D.

    2006-11-01

    In applications from food wrapping to solar sails, polymers films can be subjected to intense charged panicle bombardment and implantation. ETFE (ethylenetetrafluoroethylene) with high impact resistance is used for pumps, valves, tie wraps, and electrical components. PFA (tetrafluoroethylene-per-fluoromethoxyethylene) and FEP (tetrafluoroethylene-hexa-fluoropropylene) are sufficiently biocompatible to be used as transcutaneous implants since they resist damage from the ionizing space radiation, they can be used in aerospace engineering applications. PVDC (polyvinyllidene-chloride) is used for food packaging, and combined with others plastics, improves the oxygen barrier responsible for the food preservation. Fluoropolymers are also known for their radiation dosimetry applications, dependent on the type and energy of the radiation, as well as of the beam intensity. In this work ETFE, PFA, FEP and PVDC were irradiated with ions of keV and MeV energies at several fluences and were analyzed through techniques as RGA, OAP, FTIR, ATR and Raman spectrophotometry. CF3 is the main specie emitted from PFA and FEP when irradiated with MeV protons. H and HF are released from ETFE due to the broken C-F and C-H bonds when the polymer is irradiated with keV Nitrogen ions and protons. At high fluence, especially for keV Si and N, damage due to carbonization is observed with the formation of hydroperoxide and polymer dehydroflorination. The main broken bonds in PVDC are C-O and C-Cl, with the release of Cl and the formation of double carbon bonds. The ion fluence that causes damage, which could compromise fluoropolymer film applications, has been determined.

  1. Crystallization of ultrathin W-Si multilayer structures by high-energy heavy ion irradiations

    SciTech Connect

    Marfaing, J.; Marine, W. ); Vidal, B. ); Toulemonde, M. ); Hage Ali, M.; Stoquert, J.P. )

    1990-10-22

    Ultrathin amorphous multilayers structures (1.55 nm bilayer period) were irradiated by high-energy heavy ion ({sup 127}I and {sup 238}U ions). Transmission electron microscopy study shows that the ion-material interaction in such a configuration leads to an irreversible transformation of the initial amorphous structures. In this letter, we report the first observation of the crystallization of the multilayers induced by the heavy ion irradiations with a subsequent formation of a new WSi structure. The crucial role of the electronic effects in the crystallization process is discussed relatively to the other phenomena induced under the ion irradiation.

  2. Insight toward epithelial Na+ channel mechanism revealed by the acid-sensing ion channel 1 structure.

    PubMed

    Stockand, James D; Staruschenko, Alexander; Pochynyuk, Oleh; Booth, Rachell E; Silverthorn, Dee U

    2008-09-01

    The epithelial Na(+) channel/degenerin (ENaC/DEG) protein family includes a diverse group of ion channels, including nonvoltage-gated Na(+) channels of epithelia and neurons, and the acid-sensing ion channel 1 (ASIC1). In mammalian epithelia, ENaC helps regulate Na(+) and associated water transport, making it a critical determinant of systemic blood pressure and pulmonary mucosal fluidity. In the nervous system, ENaC/DEG proteins are related to sensory transduction. While the importance and physiological function of these ion channels are established, less is known about their structure. One hallmark of the ENaC/DEG channel family is that each channel subunit has only two transmembrane domains connected by an exceedingly large extracellular loop. This subunit structure was recently confirmed when Jasti and colleagues determined the crystal structure of chicken ASIC1, a neuronal acid-sensing ENaC/DEG channel. By mapping ENaC to the structural coordinates of cASIC1, as we do here, we hope to provide insight toward ENaC structure. ENaC, like ASIC1, appears to be a trimeric channel containing 1alpha, 1beta, and 1gamma subunit. Heterotrimeric ENaC and monomeric ENaC subunits within the trimer possibly contain many of the major secondary, tertiary, and quaternary features identified in cASIC1 with a few subtle but critical differences. These differences are expected to have profound effects on channel behavior. In particular, they may contribute to ENaC insensitivity to acid and to its constitutive activity in the absence of time- and ligand-dependent inactivation. Experiments resulting from this comparison of cASIC1 and ENaC may help clarify unresolved issues related to ENaC architecture, and may help identify secondary structures and residues critical to ENaC function.

  3. Image-Based Chemical Structure Determination.

    PubMed

    Ofner, Johannes; Brenner, Florian; Wieland, Karin; Eitenberger, Elisabeth; Kirschner, Johannes; Eisenmenger-Sittner, Christoph; Török, Szilvia; Döme, Balazs; Konegger, Thomas; Kasper-Giebl, Anne; Hutter, Herbert; Friedbacher, Gernot; Lendl, Bernhard; Lohninger, Hans

    2017-07-28

    Chemical imaging is a powerful tool for understanding the chemical composition and nature of heterogeneous samples. Recent developments in elemental, vibrational, and mass-spectrometric chemical imaging with high spatial resolution (50-200 nm) and reasonable timescale (a few hours) are capable of providing complementary chemical information about various samples. However, a single technique is insufficient to provide a comprehensive understanding of chemically complex materials. For bulk samples, the combination of different analytical methods and the application of statistical methods for extracting correlated information across different techniques is a well-established and powerful concept. However, combined multivariate analytics of chemical images obtained via different imaging techniques is still in its infancy, hampered by a lack of analytical methodologies for data fusion and analysis. This study demonstrates the application of multivariate statistics to chemical images taken from the same sample via various methods to assist in chemical structure determination.

  4. Granular structure determined by terahertz scattering

    NASA Astrophysics Data System (ADS)

    Born, Philip; Rothbart, Nick; Sperl, Matthias; Hübers, Heinz-Wilhelm

    2014-05-01

    Light scattering from particles reveals static and dynamical information about the particles and their correlations. Such methods are particularly powerful when the wavelength of the light is chosen similar to the sizes and distances of the particles. To apply scattering to investigate granular matter in particular —or other objects of similar submillimeter size— light of suitable wavelength in the terahertz regime needs to be chosen. By using a quantum cascade laser in a benchtop setup we determine the angle-dependent scattering of spherical particles as well as coffee powder and sugar grains. The scattering from single particles can be interpreted by form factors derived within the Mie theory. In addition, collective correlations can be extracted as static structure factors and compared to recent computer simulations.

  5. Some electronic and magnetic properties of Fluoride ion in Fluoride structure nanocrystals

    NASA Astrophysics Data System (ADS)

    Imtani, Ali Nasir

    2012-01-01

    We have investigated the effects of the environment potential around Fluoride ion on some important electronic and magnetic properties such as dipole polarisability, moment of oscillator strengths S(k) and magnetic susceptibility. The theoretical procedure is based on the variational-perturbation theory with two parameter trial functions incorporated in an ionic model. We estimate these properties in four cases for Fluoride ion; free ion, ion under different potentials, ion in the crystals and ion in nanocrystal, CdF2, CaF2, PbF2, SrF2 and BaF2. Our results indicate that these properties vary with ion environments and the free state of Fluoride ion has higher values and there is linearity behaviour of these properties with lattice constant. For Fluoride ion in nanocrystal, we have found that there is an extra parameter that can also affect the dipole polarisability, the number of ions in the structure.

  6. Vibrational stark effects to identify ion pairing and determine reduction potentials in electrolyte-free environments

    SciTech Connect

    Mani, Tomoyasu; Grills, David C.; Miller, John R.

    2015-01-02

    A recently-developed instrument for time-resolved infrared detection following pulse radiolysis has been used to measure the ν(C≡N) IR band of the radical anion of a CN-substituted fluorene in tetrahydrofuran. Specific vibrational frequencies can exhibit distinct frequency shifts due to ion-pairing, which can be explained in the framework of the vibrational Stark effect. Measurements of the ratio of free ions and ion-pairs in different electrolyte concentrations allowed us to obtain an association constant and free energy change for ion-pairing. As a result, this new method has the potential to probe the geometry of ion-pairing and allows the reduction potentials of molecules to be determined in the absence of electrolyte in an environment of low dielectric constant.

  7. Vibrational stark effects to identify ion pairing and determine reduction potentials in electrolyte-free environments

    DOE PAGES

    Mani, Tomoyasu; Grills, David C.; Miller, John R.

    2015-01-02

    A recently-developed instrument for time-resolved infrared detection following pulse radiolysis has been used to measure the ν(C≡N) IR band of the radical anion of a CN-substituted fluorene in tetrahydrofuran. Specific vibrational frequencies can exhibit distinct frequency shifts due to ion-pairing, which can be explained in the framework of the vibrational Stark effect. Measurements of the ratio of free ions and ion-pairs in different electrolyte concentrations allowed us to obtain an association constant and free energy change for ion-pairing. As a result, this new method has the potential to probe the geometry of ion-pairing and allows the reduction potentials of moleculesmore » to be determined in the absence of electrolyte in an environment of low dielectric constant.« less

  8. Ion induced changes in the structure of bordered pit membranes.

    PubMed

    Lee, Jinkee; Holbrook, N Michele; Zwieniecki, Maciej A

    2012-01-01

    Ion-mediated changes in xylem hydraulic resistance are hypothesized to result from hydrogel like properties of pectins located in the bordered pit membranes separating adjacent xylem vessels. Although the kinetics of the ion-mediated changes in hydraulic resistance are consistent with the swelling/deswelling behavior of pectins, there is no direct evidence of this activity. In this report we use atomic force microscopy (AFM) to investigate structural changes in bordered pit membranes associated with changes in the ionic concentration of the surrounding solution. When submerged in de-ionized water, AFM revealed bordered pit membranes as relatively smooth, soft, and lacking any sharp edges surface, in contrast to pictures from scanning electron microscope (SEM) or AFM performed on air-dry material. Exposure of the bordered pit membranes to 50 mM KCl solution resulted in significant changes in both surface physical properties and elevation features. Specifically, bordered pit membranes became harder and the fiber edges were clearly visible. In addition, the membrane contracted and appeared much rougher due to exposed microfibers. In neither solution was there any evidence of discrete pores through the membrane whose dimensions were altered in response to the ionic composition of the surrounding solution. Instead the variable hydraulic resistance appears to involve changes in the both the permeability and the thickness of the pit membrane.

  9. Experimentally Determined Plasma Parameters in a 30 cm Ion Engine

    NASA Technical Reports Server (NTRS)

    Sengupta, Anita; Goebel, Dan; Fitzgerald, Dennis; Owens, Al; Tynan, George; Dorner, Russ

    2004-01-01

    Single planar Langmuir probes and fiber optic probes are used to concurrently measure the plasma properties and neutral density variation in a 30cm diameter ion engine discharge chamber, from the immediate vicinity of the keeper to the near grid plasma region. The fiber optic probe consists of a collimated optical fiber recessed into a double bore ceramic tube fitted with a stainless steel light-limiting window. The optical fiber probe is used to measure the emission intensity of excited neutral xenon for a small volume of plasma, at various radial and axial locations. The single Langmuir probes, are used to generate current-voltage characteristics at a total of 140 spatial locations inside the discharge chamber. Assuming a maxwellian distribution for the electron population, the Langmuir probe traces provide spatially resolved measurements of plasma potential, electron temperature, and plasma density. Data reduction for the NSTAR TH8 and TH15 throttle points indicates an electron temperature range of 1 to 7.9 eV and an electron density range of 4e10 to le13 cm(sup -3), throughout the discharge chamber, consistent with the results in the literature. Plasma potential estimates, computed from the first derivative of the probe characteristic, indicate potential from 0.5V to 11V above the discharge voltage along the thruster centerline. These values are believed to be excessively high due to the sampling of the primary electron population along the thruster centerline. Relative neutral density profiles are also obtained with a fiber optic probe sampling photon flux from the 823.1 nm excited to ground state transition. Plasma parameter measurements and neutral density profiles will be presented as a function of probe location and engine discharge conditions. A discussion of the measured electron energy distribution function will also be presented, with regards to variation from pure maxwellian. It has been found that there is a distinct primary population found along

  10. Experimentally Determined Plasma Parameters in a 30 cm Ion Engine

    NASA Technical Reports Server (NTRS)

    Sengupta, Anita; Goebel, Dan; Fitzgerald, Dennis; Owens, Al; Tynan, George; Dorner, Russ

    2004-01-01

    Single planar Langmuir probes and fiber optic probes are used to concurrently measure the plasma properties and neutral density variation in a 30cm diameter ion engine discharge chamber, from the immediate vicinity of the keeper to the near grid plasma region. The fiber optic probe consists of a collimated optical fiber recessed into a double bore ceramic tube fitted with a stainless steel light-limiting window. The optical fiber probe is used to measure the emission intensity of excited neutral xenon for a small volume of plasma, at various radial and axial locations. The single Langmuir probes, are used to generate current-voltage characteristics at a total of 140 spatial locations inside the discharge chamber. Assuming a maxwellian distribution for the electron population, the Langmuir probe traces provide spatially resolved measurements of plasma potential, electron temperature, and plasma density. Data reduction for the NSTAR TH8 and TH15 throttle points indicates an electron temperature range of 1 to 7.9 eV and an electron density range of 4e10 to le13 cm(sup -3), throughout the discharge chamber, consistent with the results in the literature. Plasma potential estimates, computed from the first derivative of the probe characteristic, indicate potential from 0.5V to 11V above the discharge voltage along the thruster centerline. These values are believed to be excessively high due to the sampling of the primary electron population along the thruster centerline. Relative neutral density profiles are also obtained with a fiber optic probe sampling photon flux from the 823.1 nm excited to ground state transition. Plasma parameter measurements and neutral density profiles will be presented as a function of probe location and engine discharge conditions. A discussion of the measured electron energy distribution function will also be presented, with regards to variation from pure maxwellian. It has been found that there is a distinct primary population found along

  11. ION MANIPULATIONS IN STRUCTURES FOR LOSSLESS ION MANIPULATIONS (SLIM): COMPUTATIONAL EVALUATION OF A 90° TURN AND A SWITCH

    PubMed Central

    Garimella, Sandilya V.B.; Ibrahim, Yehia. M; Webb, Ian K.; Ipsen, Andreas B.; Chen, Tsung-Chi; Tolmachev, Aleksey V.; Baker, Erin S.; Anderson, Gordon A.; Smith, Richard D.

    2015-01-01

    The process of redirecting ions through 90° turns and ‘tee’ switches utilizing Structures for Lossless Ion Manipulations (SLIM) was evaluated at 4 Torr pressure using SIMION simulations and theoretical methods. The nature of pseudo-potential in SLIM-tee structures has also been explored. Simulations show that 100% transmission efficiency in SLIM devices can be achieved with guard electrode voltages lower than ~10 V. The ion plume width in these conditions is ~1.6 mm while at lower guard voltages lead to greater plume widths. Theoretical calculations show marginal loss of ion mobility resolving power (<5%) during ion turn due to the finite plume widths (i.e. race track effect). More robust SLIM designs that reduce the race track effect while maximizing ion transmission are also reported. In addition to static turns, the dynamic switching of ions into orthogonal channels was also evaluated both using SIMION ion trajectory simulations and experimentally. Simulations and theoretical calculations were in close agreement with experimental results and were used to develop more refined SLIM designs. PMID:26289106

  12. Ion manipulations in structures for lossless ion manipulations (SLIM): computational evaluation of a 90° turn and a switch.

    PubMed

    Garimella, Sandilya V B; Ibrahim, Yehia M; Webb, Ian K; Ipsen, Andreas B; Chen, Tsung-Chi; Tolmachev, Aleksey V; Baker, Erin S; Anderson, Gordon A; Smith, Richard D

    2015-10-21

    The process of redirecting ions through 90° turns and 'tee' switches utilizing Structures for Lossless Ion Manipulations (SLIM) was evaluated at 4 Torr pressure using SIMION simulations and theoretical methods. The nature of pseudo-potential in SLIM-tee structures has also been explored. Simulations show that 100% transmission efficiency in SLIM devices can be achieved with guard electrode voltages lower than ∼10 V. The ion plume width in these conditions is ∼1.6 mm while at lower guard voltages lead to greater plume widths. Theoretical calculations show marginal loss of ion mobility resolving power (<5%) during ion turn due to the finite plume widths (i.e. race track effect). More robust SLIM designs that reduce the race track effect while maximizing ion transmission are also reported. In addition to static turns, the dynamic switching of ions into orthogonal channels was also evaluated both using SIMION ion trajectory simulations and experimentally. Simulations and theoretical calculations were in close agreement with experimental results and were used to develop more refined SLIM designs.

  13. Achieving High Resolution Ion Mobility Separations Using Traveling Waves in Compact Multiturn Structures for Lossless Ion Manipulations

    SciTech Connect

    Hamid, Ahmed M.; Garimella, Sandilya V. B.; Ibrahim, Yehia M.; Deng, Liulin; Zheng, Xueyun; Webb, Ian K.; Anderson, Gordon A.; Prost, Spencer A.; Norheim, Randolph V.; Tolmachev, Aleksey V.; Baker, Erin S.; Smith, Richard D.

    2016-09-20

    We report on ion mobility separations (IMS) achievable using traveling waves in a Structures for Lossless Ion Manipulations (TW-SLIM) module having a 44-cm path length and sixteen 90º turns. The performance of the TW-SLIM module was evaluated for ion transmission, and ion mobility separations with different RF, TW parameters and SLIM surface gaps in conjunction with mass spectrometry. In this work TWs were created by the transient and dynamic application of DC potentials. The TW-SLIM module demonstrated highly robust performance and the ion mobility resolution achieved even with sixteen close spaced turns was comparable to a similar straight path TW-SLIM module. We found an ion mobility peak capacity of ~ 31 and peak generation rate of 780 s-1 for TW speeds of <210 m/s using the current multi-turn TW-SLIM module. The separations achieved for isomers of peptides and tetrasaccharides were found to be comparable to those from a ~ 0.9-m drift tube-based IMS-MS platform operated at the same pressure (4 torr). The combined attributes of flexible design, low voltage requirements and lossless ion transmission through multiple turns for the present TW-SLIM module provides a basis for SLIM devices capable of achieving much greater ion mobility resolutions via greatly extended ion path lengths and compact serpentine designs that do not significantly impact the instrumentation profile, a direction described in a companion manuscript.

  14. Status of structural analysis of 30 cm diameter ion optics

    NASA Technical Reports Server (NTRS)

    Macrae, Gregory S.; Hering, Gary T.

    1990-01-01

    Three structural finite element programs are compared with theory, experimental data, and each other to evaluate their usefulness for modeling the thermomechanical deflection of ion engine electrodes. Two programs, NASTRAN and MARC, used a Cray XMP and the third, Algor, used an IBM compatible personal computer. The shape of the applied temperature gradient greatly affects off-axis displacement, implying that an accurate temperature distribution is required to analyze new designs. The use of bulk material constants to model the perforated electrodes was investigated. The stress and displacement predictions are shown to be sensitive to the temperature gradient and the Young's modulus, and insensitive to number of nodes, above some minimum value, and the Poisson ratio used. The models are shown to be useful tools for evaluating designs. Experimental measurements of temperatures and displacements was identified as the most critical area.

  15. Ion Channel Function and Cross-Species Determinants in Viral Assembly of Nonprimate Hepacivirus p7

    PubMed Central

    Walter, Stephanie; Bollenbach, Alexander; Doerrbecker, Juliane; Pfaender, Stephanie; Brown, Richard J. P.; Vieyres, Gabrielle; Scott, Claire; Foster, Richard; Kumar, Abhinav; Zitzmann, Nicole; Griffin, Stephen; Penin, François; Pietschmann, Thomas

    2016-01-01

    ABSTRACT Nonprimate hepacivirus (NPHV), the closest homolog of hepatitis C virus (HCV) described to date, has recently been discovered in horses. Even though the two viruses share a similar genomic organization, conservation of the encoded hepaciviral proteins remains undetermined. The HCV p7 protein is localized within endoplasmic reticulum (ER) membranes and is important for the production of infectious particles. In this study, we analyzed the structural and functional features of NPHV p7 in addition to its role during virus assembly. Three-dimensional homology models for NPHV p7 using various nuclear magnetic resonance spectroscopy (NMR) structures were generated, highlighting the conserved residues important for ion channel function. By applying a liposome permeability assay, we observed that NPHV p7 exhibited liposome permeability features similar to those of HCV p7, indicative of similar ion channel activity. Next, we characterized the viral protein using a p7-based trans-complementation approach. A similar subcellular localization pattern at the ER membrane was observed, although production of infectious particles was likely hindered by genetic incompatibilities with HCV proteins. To further characterize these cross-species constraints, chimeric viruses were constructed by substituting different regions of HCV p7 with NPHV p7. The N terminus and transmembrane domains were nonexchangeable and therefore constitute a cross-species barrier in hepaciviral assembly. In contrast, the basic loop and the C terminus of NPHV p7 were readily exchangeable, allowing production of infectious trans-complemented viral particles. In conclusion, comparison of NPHV and HCV p7 revealed structural and functional homology of these proteins, including liposome permeability, and broadly acting determinants that modulate hepaciviral virion assembly and contribute to the host-species barrier were identified. IMPORTANCE The recent discovery of new relatives of hepatitis C virus (HCV

  16. Surface diffusion activation energy determination using ion beam microtexturing

    NASA Technical Reports Server (NTRS)

    Rossnagel, S. M.; Robinson, R. S.

    1982-01-01

    The activation energy for impurity atom (adatom) surface diffusion can be determined from the temperature dependence of the spacing of sputter cones. These cones are formed on the surface during sputtering while simultaneously adding impurities. The impurities form clusters by means of surface diffusion, and these clusters in turn initiate cone formation. Values are given for the surface diffusion activation energies for various materials on polycrystalline Cu, Al, Pb, Au, and Ni. The values for different impurity species on each of these substrates are approximately independent of impurity species within the experimental uncertainty, suggesting the absence of strong chemical bonding effects on the diffusion.

  17. Determination of optimum voltages of ion focusing devices using computer techniques

    NASA Technical Reports Server (NTRS)

    Eckstein, B. A.

    1980-01-01

    Electric potentials for two dimensional cross sections of ion focusing devices used in a mass spectrometer are calculated via a series of computer programs designed to compute potentials between areas of fixed voltages. Ion trajectories within these devices may be determined by computer and a histogram obtained which plots ion density against ion position along a plate of the focusing device. For each lens system, a plate voltage may be changed, the electric potentials recalculated, and a new histogram calculated in order to determine if the new voltage configuration has increased the device's efficiency. This process may be repeated until the optimum voltage values have been found for maximum particle transmission in each focusing device.

  18. Determination of plasma density from data on the ion current to cylindrical and planar probes

    SciTech Connect

    Voloshin, D. G. Vasil’eva, A. N.; Kovalev, A. S.; Mankelevich, Yu. A.; Rakhimova, T. V.

    2016-12-15

    To improve probe methods of plasma diagnostics, special probe measurements were performed and numerical models describing ion transport to a probe with allowance for collisions were developed. The current–voltage characteristics of cylindrical and planar probes were measured in an RF capacitive discharge in argon at a frequency of 81 MHz and plasma densities of 10{sup 10}–10{sup 11} cm{sup –3}, typical of modern RF reactors. 1D and 2D numerical models based on the particle-in-cell method with Monte Carlo collisions for simulating ion motion and the Boltzmann equilibrium for electrons are developed to describe current collection by a probe. The models were used to find the plasma density from the ion part of the current–voltage characteristic, study the effect of ion collisions, and verify simplified approaches to determining the plasma density. A 1D hydrodynamic model of the ion current to a cylindrical probe with allowance for ion collisions is proposed. For a planar probe, a method to determine the plasma density from the averaged numerical results is developed. A comparative analysis of different approaches to calculating the plasma density from the ion current to a probe is performed.

  19. A new buffer system for the potentiometric determination of fluoride ion

    SciTech Connect

    Zhobinskii, E.Y.; Askochenskaya, R.M.; Novikova, L.B; Wl' Figarov, O.S.

    1985-05-01

    This paper attempts to eliminate the lengthy stage of hydrolytic separation of the elements during the potentiometric determination of fluoride ions and also to develop a universal method for the determination of flouride ions. During the development of a procedure for the determination of fluoride ions it is necessary to eliminate the interfering effects of elements which form stable fluoride complexes such as A1 (III), Fe (III), Si (III), Ti (IV), V (IV), Mo (V), and W (V). By the addition of diethylenetriaminepentaacetate to the buffer solution and preliminary extraction of the benzoylphenylhydroxylaminates of the interfering elements with chloroform it was possible to develop a method for the determination of fluoride with a detection limit of 1.10/sup -5/ M.

  20. Structure and substrate ion binding in the sodium/proton antiporter PaNhaP

    PubMed Central

    Wöhlert, David; Kühlbrandt, Werner; Yildiz, Özkan

    2014-01-01

    Sodium/proton antiporters maintain intracellular pH and sodium levels. Detailed structures of antiporters with bound substrate ions are essential for understanding how they work. We have resolved the substrate ion in the dimeric, electroneutral sodium/proton antiporter PaNhaP from Pyrococcus abyssi at 3.2 Å, and have determined its structure in two different conformations at pH 8 and pH 4. The ion is coordinated by three acidic sidechains, a water molecule, a serine and a main-chain carbonyl in the unwound stretch of trans-membrane helix 5 at the deepest point of a negatively charged cytoplasmic funnel. A second narrow polar channel may facilitate proton uptake from the cytoplasm. Transport activity of PaNhaP is cooperative at pH 6 but not at pH 5. Cooperativity is due to pH-dependent allosteric coupling of protomers through two histidines at the dimer interface. Combined with comprehensive transport studies, the structures of PaNhaP offer unique new insights into the transport mechanism of sodium/proton antiporters. DOI: http://dx.doi.org/10.7554/eLife.03579.001 PMID:25426802

  1. Structural and optical study on antimony-silicate glasses doped with thulium ions.

    PubMed

    Dorosz, D; Zmojda, J; Kochanowicz, M; Miluski, P; Jelen, P; Sitarz, M

    2015-01-05

    Structural, spectroscopic and thermal properties of SiO₂-Al₂O₃-Sb₂O₃-Na₂O glass system doped with 0.2 mol% Tm₂O₃ have been presented. Synthesis of antimony-silicate glasses with relatively low phonon energy (600 cm(-1), which implicates a small non-radiative decay rate) was performed by conventional high-temperature melt-quenching methods. The effect of SiO₂/Sb₂O₃ ratio in fabricated Tm(3+) doped glass on thermal, structural and luminescence properties was investigated. On the basis of structural investigations decomposition of absorption bands in the infrared FTIR region was performed, thus determining that antimony ions are the only glass-forming ions, setting up the lattice of fabricated glasses. Luminescence band at the wavelength of 1.8 μm corresponding to (3)F₄→(3)H₆ transition in thulium ions was obtained under 795 nm laser pumping. It was observed that combination of relatively low phonon energy and greater separation of optically active centers in the fabricated glasses influenced in decreasing the luminescence intensity at 1800 nm.

  2. Lutetium(iii) aqua ion: On the dynamical structure of the heaviest lanthanoid hydration complex

    NASA Astrophysics Data System (ADS)

    Sessa, Francesco; Spezia, Riccardo; D'Angelo, Paola

    2016-05-01

    The structure and dynamics of the lutetium(iii) ion in aqueous solution have been investigated by means of a polarizable force field molecular dynamics (MD). An 8-fold square antiprism (SAP) geometry has been found to be the dominant configuration of the lutetium(iii) aqua ion. Nevertheless, a low percentage of 9-fold complexes arranged in a tricapped trigonal prism (TTP) geometry has been also detected. Dynamic properties have been explored by carrying out six independent MD simulations for each of four different temperatures: 277 K, 298 K, 423 K, 632 K. The mean residence time of water molecules in the first hydration shell at room temperature has been found to increase as compared to the central elements of the lanthanoid series in agreement with previous experimental findings. Water exchange kinetic rate constants at each temperature and activation parameters of the process have been determined from the MD simulations. The obtained structural and dynamical results suggest that the water exchange process for the lutetium(iii) aqua ion proceeds with an associative mechanism, in which the SAP hydration complex undergoes temporary structural changes passing through a 9-fold TTP intermediate. Such results are consistent with the water exchange mechanism proposed for heavy lanthanoid atoms.

  3. Development of a single ion detector for radiation track structure studies

    NASA Astrophysics Data System (ADS)

    Vasi, F.; Casiraghi, M.; Bashkirov, V.; Giesen, U.; Schulte, R. W.

    2016-09-01

    The track structure of ionizing radiation predominantly determines the biological effects after irradiation. A new detector to register 3D track structure segments in low pressure gas was proposed in a previous work. The device combines the operational principle of thick gas electron multipliers (THGEM), working in reverse polarity, and resistive plate chambers. In this work, the detector was further developed. Optimization of THGEM thickness, hole pitch and cathode resistivity were studied. A new detector prototype was built and tested with a microbeam providing different radiation qualities. The detector rate capability and ion collection efficiency were also investigated. Results show that the detector efficiency increases with increasing THGEM thickness and decreasing cathode resistivity. Preliminary results show that the ion collection efficiency is low and that the detector performance is limited by a long dead time. The detector is able to register single ions with a low dark rate. However, further development is needed in order to obtain the efficiency necessary to reconstruct 3D track structure.

  4. Lutetium(iii) aqua ion: On the dynamical structure of the heaviest lanthanoid hydration complex.

    PubMed

    Sessa, Francesco; Spezia, Riccardo; D'Angelo, Paola

    2016-05-28

    The structure and dynamics of the lutetium(iii) ion in aqueous solution have been investigated by means of a polarizable force field molecular dynamics (MD). An 8-fold square antiprism (SAP) geometry has been found to be the dominant configuration of the lutetium(iii) aqua ion. Nevertheless, a low percentage of 9-fold complexes arranged in a tricapped trigonal prism (TTP) geometry has been also detected. Dynamic properties have been explored by carrying out six independent MD simulations for each of four different temperatures: 277 K, 298 K, 423 K, 632 K. The mean residence time of water molecules in the first hydration shell at room temperature has been found to increase as compared to the central elements of the lanthanoid series in agreement with previous experimental findings. Water exchange kinetic rate constants at each temperature and activation parameters of the process have been determined from the MD simulations. The obtained structural and dynamical results suggest that the water exchange process for the lutetium(iii) aqua ion proceeds with an associative mechanism, in which the SAP hydration complex undergoes temporary structural changes passing through a 9-fold TTP intermediate. Such results are consistent with the water exchange mechanism proposed for heavy lanthanoid atoms.

  5. Crystal structure of a SLC11 (NRAMP) transporter reveals the basis for transition-metal ion transport.

    PubMed

    Ehrnstorfer, Ines A; Geertsma, Eric R; Pardon, Els; Steyaert, Jan; Dutzler, Raimund

    2014-11-01

    Members of the SLC11 (NRAMP) family transport iron and other transition-metal ions across cellular membranes. These membrane proteins are present in all kingdoms of life with a high degree of sequence conservation. To gain insight into the determinants of ion selectivity, we have determined the crystal structure of Staphylococcus capitis DMT (ScaDMT), a close prokaryotic homolog of the family. ScaDMT shows a familiar architecture that was previously identified in the amino acid permease LeuT. The protein adopts an inward-facing conformation with a substrate-binding site located in the center of the transporter. This site is composed of conserved residues, which coordinate Mn2+, Fe2+ and Cd2+ but not Ca2+. Mutations of interacting residues affect ion binding and transport in both ScaDMT and human DMT1. Our study thus reveals a conserved mechanism for transition-metal ion selectivity within the SLC11 family.

  6. Neutron activation analysis for reference determination of the implantation dose of cobalt ions

    SciTech Connect

    Garten, R.P.H.; Bubert, H.; Palmetshofer, L.

    1992-05-15

    The authors prepared depth profilling reference materials by cobalt ion implantation at an ion energy of 300 keV into n-type silicon. The implanted Co dose was then determined by instrumental neutron activation analysis (INAA) giving an analytical dynamic range of almost 5 decades and uncertainty of 1.5%. This form of analysis allows sources of error (beam spreading, misalignment) to be corrected. 70 refs., 3 tabs.

  7. Determining the Amount of Copper(II) Ions in a Solution Using a Smartphone

    ERIC Educational Resources Information Center

    Montangero, Marc

    2015-01-01

    When dissolving copper in nitric acid, copper(II) ions produce a blue-colored solution. It is possible to determine the concentration of copper(II) ions, focusing on the hue of the color, using a smartphone camera. A free app can be used to measure the hue of the solution, and with the help of standard copper(II) solutions, one can graph a…

  8. Determining the Amount of Copper(II) Ions in a Solution Using a Smartphone

    ERIC Educational Resources Information Center

    Montangero, Marc

    2015-01-01

    When dissolving copper in nitric acid, copper(II) ions produce a blue-colored solution. It is possible to determine the concentration of copper(II) ions, focusing on the hue of the color, using a smartphone camera. A free app can be used to measure the hue of the solution, and with the help of standard copper(II) solutions, one can graph a…

  9. Fast ion conductivity in strained defect-fluorite structure created by ion tracks in Gd2Ti2O7

    PubMed Central

    Aidhy, Dilpuneet S.; Sachan, Ritesh; Zarkadoula, Eva; Pakarinen, Olli; Chisholm, Matthew F.; Zhang, Yanwen; Weber, William J.

    2015-01-01

    The structure and ion-conducting properties of the defect-fluorite ring structure formed around amorphous ion-tracks by swift heavy ion irradiation of Gd2Ti2O7 pyrochlore are investigated. High angle annular dark field imaging complemented with ion-track molecular dynamics simulations show that the atoms in the ring structure are disordered, and have relatively larger cation-cation interspacing than in the bulk pyrochlore, illustrating the presence of tensile strain in the ring region. Density functional theory calculations show that the non-equilibrium defect-fluorite structure can be stabilized by tensile strain. The pyrochlore to defect-fluorite structure transformation in the ring region is predicted to be induced by recrystallization during a melt-quench process and stabilized by tensile strain. Static pair-potential calculations show that planar tensile strain lowers oxygen vacancy migration barriers in pyrochlores, in agreement with recent studies on fluorite and perovskite materials. In view of these results, it is suggested that strain engineering could be simultaneously used to stabilize the defect-fluorite structure and gain control over its high ion-conducting properties. PMID:26555848

  10. Fast ion conductivity in strained defect-fluorite structure created by ion tracks in Gd2Ti2O7

    DOE PAGES

    Aidhy, Dilpuneet S.; Sachan, Ritesh; Zarkadoula, Eva; ...

    2015-11-10

    The structure and ion-conducting properties of the defect-fluorite ring structure formed around amorphous ion-tracks by swift heavy ion irradiation of Gd2Ti2O7 pyrochlore are investigated. High angle annular dark field imaging complemented with ion-track molecular dynamics simulations show that the atoms in the ring structure are disordered, and have relatively larger cation-cation interspacing than in the bulk pyrochlore, illustrating the presence of tensile strain in the ring region. Density functional theory calculations show that the non-equilibrium defect-fluorite structure can be stabilized by tensile strain. The pyrochlore to defect-fluorite structure transformation in the ring region is predicted to be induced by recrystallizationmore » during a melt-quench process and stabilized by tensile strain. Static pair-potential calculations show that planar tensile strain lowers oxygen vacancy migration barriers in pyrochlores, in agreement with recent studies on fluorite and perovskite materials. Lastly, in view of these results, it is suggested that strain engineering could be simultaneously used to stabilize the defect-fluorite structure and gain control over its high ion-conducting properties.« less

  11. Fast ion conductivity in strained defect-fluorite structure created by ion tracks in Gd2Ti2O7.

    PubMed

    Aidhy, Dilpuneet S; Sachan, Ritesh; Zarkadoula, Eva; Pakarinen, Olli; Chisholm, Matthew F; Zhang, Yanwen; Weber, William J

    2015-11-10

    The structure and ion-conducting properties of the defect-fluorite ring structure formed around amorphous ion-tracks by swift heavy ion irradiation of Gd2Ti2O7 pyrochlore are investigated. High angle annular dark field imaging complemented with ion-track molecular dynamics simulations show that the atoms in the ring structure are disordered, and have relatively larger cation-cation interspacing than in the bulk pyrochlore, illustrating the presence of tensile strain in the ring region. Density functional theory calculations show that the non-equilibrium defect-fluorite structure can be stabilized by tensile strain. The pyrochlore to defect-fluorite structure transformation in the ring region is predicted to be induced by recrystallization during a melt-quench process and stabilized by tensile strain. Static pair-potential calculations show that planar tensile strain lowers oxygen vacancy migration barriers in pyrochlores, in agreement with recent studies on fluorite and perovskite materials. In view of these results, it is suggested that strain engineering could be simultaneously used to stabilize the defect-fluorite structure and gain control over its high ion-conducting properties.

  12. Mobility-Resolved Ion Selection in Uniform Drift Field Ion Mobility Spectrometry/Mass Spectrometry: Dynamic Switching in Structures for Lossless Ion Manipulations

    DOE PAGES

    Webb, Ian K.; Garimella, Sandilya V. B.; Tolmachev, Aleksey V.; ...

    2014-09-15

    A Structures for Lossless Ion Manipulations (SLIM) module that allows ion mobility separations and the switching of ions between alternative drift paths is described. The SLIM switch component has a “Tee” configuration and allows switching of ions between a linear path and a 90-degree bend. By controlling switching times, ions can be deflected to an alternative channel as a function of their mobilities. In the initial evaluation the switch is used in a static mode and shown compatible with high performance ion mobility separations at 4 torr. In the “dynamic mode” we show that mobility-selected ions can be switched intomore » the alternative channel, and that various ion species can be independently selected based on their mobilities for time-of-flight mass spectrometer (TOF MS) IMS detection and mass analysis. Ultimately, this development also provides the basis for e.g. the selection of specific mobilities for storage and accumulation, and key modules for the assembly of SLIM devices enabling much more complex sequences of ion manipulations.« less

  13. Mobility-resolved ion selection in uniform drift field ion mobility spectrometry/mass spectrometry: dynamic switching in structures for lossless ion manipulations.

    PubMed

    Webb, Ian K; Garimella, Sandilya V B; Tolmachev, Aleksey V; Chen, Tsung-Chi; Zhang, Xinyu; Cox, Jonathan T; Norheim, Randolph V; Prost, Spencer A; LaMarche, Brian; Anderson, Gordon A; Ibrahim, Yehia M; Smith, Richard D

    2014-10-07

    A Structures for Lossless Ion Manipulations (SLIM) module that allows ion mobility separations and the switching of ions between alternative drift paths is described. The SLIM switch component has a "Tee" configuration and allows the efficient switching of ions between a linear path and a 90-degree bend. By controlling switching times, ions can be efficiently directed to an alternative channel as a function of their mobilities. In the initial evaluation the switch is used in a static mode and shown compatible with high performance ion mobility separations at 4 Torr. In the dynamic mode, we show that mobility-selected ions can be switched into the alternative channel, and that various ion species can be independently selected based on their mobilities for time-of-flight mass spectrometer (TOF MS) IMS detection and mass analysis. This development also provides the basis of, for example, the selection of specific mobilities for storage and accumulation, and the key component of modules for the assembly of SLIM devices enabling much more complex sequences of ion manipulations.

  14. A novel Schiff base: Synthesis, structural characterisation and comparative sensor studies for metal ion detections

    NASA Astrophysics Data System (ADS)

    Köse, Muhammet; Purtas, Savas; Güngör, Seyit Ali; Ceyhan, Gökhan; Akgün, Eyup; McKee, Vickie

    2015-02-01

    A novel Schiff base ligand was synthesized by the condensation reaction of 2,6-diformylpyridine and 4-aminoantipyrine in MeOH and characterised by its melting point, elemental analysis, FT-IR, 1H, 13C NMR and mass spectroscopic studies. Molecular structure of the ligand was determined by single crystal X-ray diffraction technique. The electrochemical properties of the Schiff base ligand were studied in different solvents at various scan rates. Sensor ability of the Schiff base ligand was investigated by colorimetric and fluorometric methods. Visual colour change of the ligand was investigated in MeOH solvent in presence of various metal ions Na+, Mg2+, Al3+, K+, Cr3+, Mn2+, Fe3+, Co2+, Ni2+, Cu2+, Zn2+, Cd2+, Hg2+ and Pb2+. Upon addition of Al3+ ion into a MeOH solution of the ligand, an orange colour developed which is detectable by naked eye. Fluorescence emission studies showed that the ligand showed single emission band at 630-665 nm upon excitation at 560 nm. Addition of metal ions Na+, Mg2+, K+, Cr3+, Mn2+, Fe3+, Co2+, Ni2+, Cu2+, Zn2+, Cd2+, Hg2+ and Pb2+ (1:1 M ratio) cause fluorescence quenching, however addition of Al+3 resulted in an increase in fluorescence intensity. No significant variation was observed in the fluorescence intensity caused by Al3+ in presence of other metal ions. Therefore, the Schiff base ligand can be used for selective detection of Al3+ ions in the presence of the other metal ions studied.

  15. Structural transitions in ion coordination driven by changes in competition for ligand binding.

    PubMed

    Varma, Sameer; Rempe, Susan B

    2008-11-19

    Transferring Na(+) and K(+) ions from their preferred coordination states in water to states having different coordination numbers incurs a free energy cost. In several examples in nature, however, these ions readily partition from aqueous-phase coordination states into spatial regions having much higher coordination numbers. Here we utilize statistical theory of solutions, quantum chemical simulations, classical mechanics simulations, and structural informatics to understand this aspect of ion partitioning. Our studies lead to the identification of a specific role of the solvation environment in driving transitions in ion coordination structures. Although ion solvation in liquid media is an exergonic reaction overall, we find it is also associated with considerable free energy penalties for extracting ligands from their solvation environments to form coordinated ion complexes. Reducing these penalties increases the stabilities of higher-order coordinations and brings down the energetic cost to partition ions from water into overcoordinated binding sites in biomolecules. These penalties can be lowered via a reduction in direct favorable interactions of the coordinating ligands with all atoms other than the ions themselves. A significant reduction in these penalties can, in fact, also drive up ion coordination preferences. Similarly, an increase in these penalties can lower ion coordination preferences, akin to a Hofmeister effect. Since such structural transitions are effected by the properties of the solvation phase, we anticipate that they will also occur for other ions. The influence of other factors, including ligand density, ligand chemistry, and temperature, on the stabilities of ion coordination structures are also explored.

  16. Structural and Thermodynamic Properties of Selective Ion Binding in a K+ Channel

    PubMed Central

    Lockless, Steve W; Zhou, Ming; MacKinnon, Roderick

    2007-01-01

    Thermodynamic measurements of ion binding to the Streptomyces lividans K+ channel were carried out using isothermal titration calorimetry, whereas atomic structures of ion-bound and ion-free conformations of the channel were characterized by x-ray crystallography. Here we use these assays to show that the ion radius dependence of selectivity stems from the channel's recognition of ion size (i.e., volume) rather than charge density. Ion size recognition is a function of the channel's ability to adopt a very specific conductive structure with larger ions (K+, Rb+, Cs+, and Ba2+) bound and not with smaller ions (Na+, Mg2+, and Ca2+). The formation of the conductive structure involves selectivity filter atoms that are in direct contact with bound ions as well as protein atoms surrounding the selectivity filter up to a distance of 15 Å from the ions. We conclude that ion selectivity in a K+ channel is a property of size-matched ion binding sites created by the protein structure. PMID:17472437

  17. Structural aspects of rubidium ion selectivity by tribenzo-21-crown-7

    SciTech Connect

    Bryan, J.C.; Sachleben, R.A.; Lavis, J.M.; Davis, M.C.; Burns, J.H.; Hay, B.P.

    1998-06-01

    The structural origins of the selectivity of rubidium ion over other alkali metal ions (Cs, Rb, Na, Re) by tribenzo-21-crown-7 is investigated from single-crystal X-ray diffraction. The structures reported here are the first reported for a tribenzo-21-crown-7, and the alkali metal ion complexes are the first reported structures of these ions with any 21-crown-7 ether. Different crown conformations are observed for each structure. Molecular mechanics calculations were performed on all conformers, and the results are related to the observed extraction selectivity for rubidium.

  18. Compositions and Structures of Vanadium Oxide Cluster Ions VmOn(±) (m = 2-20) Investigated by Ion Mobility Mass Spectrometry.

    PubMed

    Wu, Jenna W J; Moriyama, Ryoichi; Tahara, Hiroshi; Ohshimo, Keijiro; Misaizu, Fuminori

    2016-06-02

    Stable compositions and geometrical structures of vanadium oxide cluster ions, VmOn(±), were investigated by ion mobility mass spectrometry (IM-MS). The most stable compositions of vanadium oxide cluster cations were (V2O4)(V2O5)(m-2)/2(+) and (VO2)(V2O5)(m-1)/2(+), depending on the clusters with even and odd numbers of vanadium atoms. Compositions one-oxygen richer than the cations, such as (V2O5)m/2(-) and (VO3)(V2O5)(m-1)/2(-), were predominantly observed for cluster anions. Assignments of these stable cluster ion compositions, which were determined as a result of collision-induced dissociations in IM-MS, can partly be explained with consideration of spin density distribution. By comparing the experimental collision cross sections (CCSs) obtained from ion mobility measurement with CCSs of the theoretically calculated structures, we confirmed the patterned growth of geometrical structures partially discussed in previous theoretical and spectroscopic studies. We showed that even sized (V2O5)m/2(±) where m = 6-12 had right polygonal prism structures except for the anionic V12O30(-), and for the clusters of odd numbers of vanadium m, cations and anions can either have bridged or pyramid structures. Both of the odd sized structures proposed were derivatives from the even sized right polygonal prism structures. The exception, V12O30(-), which had a CCS almost equal to that of the neighboring smaller V11O28(-), should have a structure of higher density than the right hexagonal prism, in which it was proposed to be a captured pyramid structure, derived from V11O28(-).

  19. Charge-state shifting of individual multiply-charged ions of bovine albumin dimer and molecular weight determination using an individual-ion approach

    SciTech Connect

    Cheng, X.; Bakhtiar, R.; Van Orden, S.; Smith, R.D. )

    1994-07-01

    Ion-molecule reactions of individual multiply-protonated ions of bovine albumin dimer, formed from electrospray ionization, have been studied using a Fourier transform ion cyclotron resonance mass spectrometer. Upon reaction of ammonia with a group of individual ions, charge-state shifting was observed due to proton transfer. Repeated additions of ammonia during remeasurements of the same ion population were observed to induce multiple-step charge-state shifts. Charge-state-dependent reactivity, as well as nonstatistical behavior in reactivity, was observed due to the small ion population. The molecular weights of individual ions whose charge state shifted during reaction were determined with an accuracy of 67 ppm, the first example of using an individual-ion approach to the determination of molecular weight for a large biopolymer. The molecular weight distribution of a group of ions can be determined with a precision related to the number of ions examined and the weight heterogeneity of the sample. We obtained the molecular weight for eight individual ions from which a molecular weight of 133 320 [+-] 210 Da was calculated for bovine albumin dimer. 17 refs., 3 figs., 1 tab.

  20. 3D lattice distortions and defect structures in ion-implanted nano-crystals

    PubMed Central

    Hofmann, Felix; Tarleton, Edmund; Harder, Ross J.; Phillips, Nicholas W.; Ma, Pui-Wai; Clark, Jesse N.; Robinson, Ian K.; Abbey, Brian; Liu, Wenjun; Beck, Christian E.

    2017-01-01

    Focussed Ion Beam (FIB) milling is a mainstay of nano-scale machining. By manipulating a tightly focussed beam of energetic ions, often gallium (Ga+), FIB can sculpt nanostructures via localised sputtering. This ability to cut solid matter on the nano-scale revolutionised sample preparation across the life, earth and materials sciences. Despite its widespread usage, detailed understanding of the FIB-induced structural damage, intrinsic to the technique, remains elusive. Here we examine the defects caused by FIB in initially pristine objects. Using Bragg Coherent X-ray Diffraction Imaging (BCDI), we are able to spatially-resolve the full lattice strain tensor in FIB-milled gold nano-crystals. We find that every use of FIB causes large lattice distortions. Even very low ion doses, typical of FIB imaging and previously thought negligible, have a dramatic effect. Our results are consistent with a damage microstructure dominated by vacancies, highlighting the importance of free-surfaces in determining which defects are retained. At larger ion fluences, used during FIB-milling, we observe an extended dislocation network that causes stresses far beyond the bulk tensile strength of gold. These observations provide new fundamental insight into the nature of the damage created and the defects that lead to a surprisingly inhomogeneous morphology. PMID:28383028

  1. High Mobility SiGe/Si Transistor Structures on Sapphire Substrates Using Ion Implantation

    NASA Technical Reports Server (NTRS)

    Alterovitz, S. A.; Mueller, C. H.; Croke, E. T.

    2003-01-01

    High mobility n-type SiGe/Si transistor structures have been fabricated on sapphire substrates by ion implanting phosphorus ions into strained 100 Angstrom thick silicon channels for the first time. The strained Si channels were sandwiched between Si(sub 0.7)Ge(sub 0.3) layers, which, in turn, were deposited on Si(sub 0.7)Ge(sub 0.3) virtual substrates and graded SiGe buffer layers. After the molecular beam epitaxy (MBE) film growth process was completed, ion thick silicon channels implantation and post-annealing were used to introduce donors. The phosphorous ions were preferentially located in the Si channel at a peak concentration of approximately 1x10(exp 18)/cu cm. Room temperature electron mobilities exceeding 750 sq cm/V-sec at carrier densities of 1x10(exp 12)/sq cm were measured. Electron concentration appears to be the key factor that determines mobility, with the highest mobility observed for electron densities in the 1 - 2x10(exp 12)/sq cm range.

  2. 3D lattice distortions and defect structures in ion-implanted nano-crystals

    NASA Astrophysics Data System (ADS)

    Hofmann, Felix; Tarleton, Edmund; Harder, Ross J.; Phillips, Nicholas W.; Ma, Pui-Wai; Clark, Jesse N.; Robinson, Ian K.; Abbey, Brian; Liu, Wenjun; Beck, Christian E.

    2017-04-01

    Focussed Ion Beam (FIB) milling is a mainstay of nano-scale machining. By manipulating a tightly focussed beam of energetic ions, often gallium (Ga+), FIB can sculpt nanostructures via localised sputtering. This ability to cut solid matter on the nano-scale revolutionised sample preparation across the life, earth and materials sciences. Despite its widespread usage, detailed understanding of the FIB-induced structural damage, intrinsic to the technique, remains elusive. Here we examine the defects caused by FIB in initially pristine objects. Using Bragg Coherent X-ray Diffraction Imaging (BCDI), we are able to spatially-resolve the full lattice strain tensor in FIB-milled gold nano-crystals. We find that every use of FIB causes large lattice distortions. Even very low ion doses, typical of FIB imaging and previously thought negligible, have a dramatic effect. Our results are consistent with a damage microstructure dominated by vacancies, highlighting the importance of free-surfaces in determining which defects are retained. At larger ion fluences, used during FIB-milling, we observe an extended dislocation network that causes stresses far beyond the bulk tensile strength of gold. These observations provide new fundamental insight into the nature of the damage created and the defects that lead to a surprisingly inhomogeneous morphology.

  3. Magnetic and structural properties of manganese ion implanted silicon

    NASA Astrophysics Data System (ADS)

    Awo-Affouda, Chaffra A.

    2007-12-01

    This thesis focuses on semiconductor based spin electronics. The integration of ferromagnetic regions into semiconductor "spintronic" devices to produce spin polarized current is a dynamic research area. One avenue is to make conventional semiconductors ferromagnetic by doping with a transition metal impurity such as Mn. For this, we first investigated the magnetic properties of Mn-implanted Si. We were able to measure above room temperature ferromagnetic hysteresis loops. The high Curie temperature obtained (>400 K), indicated that the synthesis of a technologically useful Si-based magnetic semiconductor is possible. We then focused on studying the structure of the implanted samples in order to establish a correlation between the magnetic and structural properties. The structural investigation involved secondary ion mass spectrometry, Rutherford backscattering, and transmission electron microscopy (TEM) as the main characterization techniques. The combination of the structural and magnetic studies allowed us to isolate an "active" region from which the ferromagnetism originates. We then found that the magnetic properties of the samples are strongly dependant on the interaction of the Mn atoms with the residual implant damage. The evolution of the Mn concentration profiles was also found to be closely related to the distribution of the Si lattice defects. We also observed the formation of Mn rich secondary phases at high enough annealing temperatures >800°C. However, we argued that theses crystallites cannot account for all the observed magnetic properties due to the low Curie temperature of these compounds in bulk form. We concluded that achieving a room temperature Si-based DMS has great potential but careful synthesis of this material system is needed to prevent secondary phase formation.

  4. Highly charged ions for atomic clocks and search for variation of the fine structure constant

    NASA Astrophysics Data System (ADS)

    Dzuba, V. A.; Flambaum, V. V.

    2015-11-01

    We review a number of highly charged ions which have optical transitions suitable for building extremely accurate atomic clocks. This includes ions from Hf 12+ to U 34+, which have the 4 f 12 configuration of valence electrons, the Ir 17+ ion, which has a hole in almost filled 4 f subshell, the Ho 14+, Cf 15+, Es 17+ and Es 16+ ions. Clock transitions in most of these ions are sensitive to variation of the fine structure constant, α (α = e2/hbar c). E.g., californium and einsteinium ions have largest known sensitivity to α-variation while holmium ion looks as the most suitable ion for experimental study. We study the spectra of the ions and their features relevant to the use as frequency standards.

  5. Three-scale structure of diffusion region in the presence of cold ions

    NASA Astrophysics Data System (ADS)

    Divin, A.; Khotyaintsev, Yu. V.; Vaivads, A.; André, M.; Toledo-Redondo, S.; Markidis, S.; Lapenta, G.

    2016-12-01

    Kinetic simulations and spacecraft observations typically display the two-scale structure of collisionless diffusion region (DR), with electron and ion demagnetization scales governing the spatial extent of the DR. Recent in situ observations of the nightside magnetosphere, as well as investigation of magnetic reconnection events at the Earth's magnetopause, discovered the presence of a population of cold (tens of eV) ions of ionospheric origin. We present two-dimensional particle-in-cell simulations of collisionless magnetic reconnection in multicomponent plasma with ions consisting of hot and cold populations. We show that a new cold ion diffusion region scale is introduced in between that of hot ions and electrons. Demagnetization scale of cold ion population is several times (˜4-8) larger than the initial cold ion gyroradius. Cold ions are accelerated and thermalized during magnetic reconnection and form ion beams moving with velocities close to the Alfvén velocity.

  6. Structural disorder in hard amorphous carbon films implanted with nitrogen ions

    SciTech Connect

    Freire, F.L. Jr.; Franceschini, D.F.; Achete, C.A.; Brusa, R.S.; Mariotto, G.; Karwasz, G.P.; Canteri, R.

    1996-12-31

    Hard amorphous hydrogenated carbon films deposited by self-bias glow discharge were implanted at room temperature with 70 keV-nitrogen ions at fluences between 2.0 and 9.0 {times} 10{sup 16} N/cm{sup 2}. The implanted samples were analyzed by Raman spectroscopy, SIMS and positron annihilation spectroscopy (Doppler broadening technique with the determination of the parameter S). For samples implanted with 2.0 {times} 10{sup 16} N/cm{sup 2} the S parameter follows the vacancies depth profile predicted by Monte Carlo simulation. For higher fluences the authors observed a reduction in the measured value of S. This result is discussed in terms of both hydrogen loss and structural modifications (increase of disorder at local scale and of the number of graphitic domains) induced in the carbon film by ion implantation.

  7. Theoretical study of the alkaline-earth (LiBe)+ ion: structure, spectroscopy and dipole moments

    NASA Astrophysics Data System (ADS)

    Ghanmi, C.; Farjallah, M.; Berriche, H.

    2017-03-01

    We study theoretically the structure and spectroscopic properties of the alkali alkaline-earth (LiBe)+ ion. The potential energy curves and their spectroscopic parameters, permanent and transition dipole moments are determined with a quantum chemistry approach. The (LiBe)+ ion is modelled as two valence electron system moving in the field of Be2+ and Li+ cores, which are described by pseudopotentials. In addition, effective core-polarization potentials are included to correct the energy. The molecular calculations are performed using a standard quantum chemistry approach based on the pseudopotential model, Gaussian basis sets, effective core polarization potentials, and full configuration interaction (CI) calculations. The precision of our spectroscopic parameters are discussed by comparison with currently available theoretical results. A rather good agreement is observed for the ground and first excited states. The permanent dipole moments reveal many abrupt changes, which are localized at particular distances corresponding to the positions of the avoided crossings.

  8. Reef structure determined from vertical seismic profiling

    SciTech Connect

    Blackway, C.V.; Keho, T.; Turpening, R.M.; Omnes, G.

    1986-08-01

    MIT has access to a test borehole near a producing (Silurian) reef in Manistee County, Michigan. Data from a multi-offset vertical seismic profiling (VSP) experiment were analyzed and compared to a three-dimensional seismic survey. With the strong reflection at the B-salt/A-2 carbonate interface, they are able to image the reef. The salt and evaporite layers in the A-1 and A-2 formations off the reef give a double reflection that is also used for imaging. The offset VSPs cover three azimuths, two in the direction of the reef and one off the reef, which allow us to compare results on and off the reef. First, a one-dimensional velocity structure was determined from the zero offset VSP data using a waveform inversion. These velocity results compared favorably with the full waveform sonic data. Using these velocities, a model was constructed for VSP migration. The migration algorithm is a Kirchoff migration based on paraxial ray tracing. The reef image from this migration is in good agreement with the three-dimensional seismic survey.

  9. Determination of the structure of HBr DBr

    SciTech Connect

    Chen, Wei; Novick, S.E.; Walker, A.R.H.

    1995-12-31

    The authors have investigated the structure and dynamics of the weakly bound complex of the four bromine isotopomers of HBr DBr using pulsed-jet Fourier transform microwave spectroscopy. In the hydrogen halide dimers, allowed transitions are across the inversion doublet caused by the geared interchange of the donor and acceptor of the hydrogen bond. While in the classic study of (HF){sub 2}{sup 1}, it was observed that this splitting results in an inversion frequency in the microwave region of the spectrum, in (HCl){sub 2} and (HBr){sub 2} the lower inversion barrier results in an inversion frequency in the infrared. In order to investigate the hydrogen bromide dimer with the high precision allowed by an FT microwave experiment, the authors have {open_quotes}quenched{close_quotes} the inversion motion by substituting a deuterium for one of the hydrogens. The Br-Br distance in the complex is 4.136 {Angstrom}. Using measurements of the nuclear quadrupole coupling constants of the bromine nuclei, the wide amplitude bending motions of the hydrogen-bonded deuterium can be determined as can the wide amplitude bending angle of the non-bonding hydrogen atom. Preliminary analysis suggests that the Br---Br-D angle undergoes excursions of 29{degrees} about zero, and that the H-Br--Br angle oscillates 36{degrees} about its 90{degrees} equilibrium angle.

  10. Phosphate Ions Affect the Water Structure at Functionalized Membrane Surfaces.

    PubMed

    Barrett, Aliyah; Imbrogno, Joseph; Belfort, Georges; Petersen, Poul B

    2016-09-06

    Antifouling surfaces improve function, efficiency, and safety in products such as water filtration membranes, marine vehicle coatings, and medical implants by resisting protein and biofilm adhesion. Understanding the role of water structure at these materials in preventing protein adhesion and biofilm formation is critical to designing more effective coatings. Such fouling experiments are typically performed under biological conditions using isotonic aqueous buffers. Previous studies have explored the structure of pure water at a few different antifouling surfaces, but the effect of electrolytes and ionic strength (I) on the water structure at antifouling surfaces is not well studied. Here sum frequency generation (SFG) spectroscopy is used to characterize the interfacial water structure at poly(ether sulfone) (PES) and two surface-modified PES films in contact with 0.01 M phosphate buffer with high and low salt (Ionic strength, I= 0.166 and 0.025 M, respectively). Unmodified PES, commonly used as a filtration membrane, and modified PES with a hydrophobic alkane (C18) and with a poly(ethylene glycol) (PEG) were used. In the low ionic strength phosphate buffer, water was strongly ordered near the surface of the PEG-modified PES film due to exclusion of phosphate ions and the creation of a surface potential resulting from charge separation between phosphate anions and sodium cations. However, in the high ionic strength phosphate buffer, the sodium and potassium chloride (138 and 3 mM, respectively) in the phosphate buffered saline screened this charge and substantially reduced water ordering. A much smaller water ordering and subsequent reduction upon salt addition was observed for the C18-modified PES, and little water structure change was seen for the unmodified PES. The large difference in water structuring with increasing ionic strength between widely used phosphate buffer and phosphate buffered saline at the PEG interface demonstrates the importance of studying

  11. Determination of ion mobility collision cross sections for unresolved isomeric mixtures using tandem mass spectrometry and chemometric deconvolution.

    PubMed

    Harper, Brett; Neumann, Elizabeth K; Stow, Sarah M; May, Jody C; McLean, John A; Solouki, Touradj

    2016-10-05

    Ion mobility (IM) is an important analytical technique for determining ion collision cross section (CCS) values in the gas-phase and gaining insight into molecular structures and conformations. However, limited instrument resolving powers for IM may restrict adequate characterization of conformationally similar ions, such as structural isomers, and reduce the accuracy of IM-based CCS calculations. Recently, we introduced an automated technique for extracting "pure" IM and collision-induced dissociation (CID) mass spectra of IM overlapping species using chemometric deconvolution of post-IM/CID mass spectrometry (MS) data [J. Am. Soc. Mass Spectrom., 2014, 25, 1810-1819]. Here we extend those capabilities to demonstrate how extracted IM profiles can be used to calculate accurate CCS values of peptide isomer ions which are not fully resolved by IM. We show that CCS values obtained from deconvoluted IM spectra match with CCS values measured from the individually analyzed corresponding peptides on uniform field IM instrumentation. We introduce an approach that utilizes experimentally determined IM arrival time (AT) "shift factors" to compensate for ion acceleration variations during post-IM/CID and significantly improve the accuracy of the calculated CCS values. Also, we discuss details of this IM deconvolution approach and compare empirical CCS values from traveling wave (TW)IM-MS and drift tube (DT)IM-MS with theoretically calculated CCS values using the projected superposition approximation (PSA). For example, experimentally measured deconvoluted TWIM-MS mean CCS values for doubly-protonated RYGGFM, RMFGYG, MFRYGG, and FRMYGG peptide isomers were 288.8 Å(2), 295.1 Å(2), 296.8 Å(2), and 300.1 Å(2); all four of these CCS values were within 1.5% of independently measured DTIM-MS values.

  12. Biochemical and Structural Properties of a Thermostable Mercuric Ion Reductase from Metallosphaera sedula

    PubMed Central

    Artz, Jacob H.; White, Spencer N.; Zadvornyy, Oleg A.; Fugate, Corey J.; Hicks, Danny; Gauss, George H.; Posewitz, Matthew C.; Boyd, Eric S.; Peters, John W.

    2015-01-01

    Mercuric ion reductase (MerA), a mercury detoxification enzyme, has been tuned by evolution to have high specificity for mercuric ions (Hg2+) and to catalyze their reduction to a more volatile, less toxic elemental form. Here, we present a biochemical and structural characterization of MerA from the thermophilic crenarchaeon Metallosphaera sedula. MerA from M. sedula is a thermostable enzyme, and remains active after extended incubation at 97°C. At 37°C, the NADPH oxidation-linked Hg2+ reduction specific activity was found to be 1.9 μmol/min⋅mg, increasing to 3.1 μmol/min⋅mg at 70°C. M. sedula MerA crystals were obtained and the structure was solved to 1.6 Å, representing the first solved crystal structure of a thermophilic MerA. Comparison of both the crystal structure and amino acid sequence of MerA from M. sedula to mesophillic counterparts provides new insights into the structural determinants that underpin the thermal stability of the enzyme. PMID:26217660

  13. Ion-Scale Structure in Mercury's Magnetopause Reconnection Diffusion Region

    NASA Technical Reports Server (NTRS)

    Gershman, Daniel J.; Dorelli, John C.; DiBraccio, Gina A.; Raines, Jim M.; Slavin, James A.; Poh, Gangkai; Zurbuchen, Thomas H.

    2016-01-01

    The strength and time dependence of the electric field in a magnetopause diffusion region relate to the rate of magnetic reconnection between the solar wind and a planetary magnetic field. Here we use approximately 150 milliseconds measurements of energetic electrons from the Mercury Surface, Space Environment, GEochemistry, and Ranging (MESSENGER) spacecraft observed over Mercury's dayside polar cap boundary (PCB) to infer such small-scale changes in magnetic topology and reconnection rates. We provide the first direct measurement of open magnetic topology in flux transfer events at Mercury, structures thought to account for a significant portion of the open magnetic flux transport throughout the magnetosphere. In addition, variations in PCB latitude likely correspond to intermittent bursts of approximately 0.3 to 3 millivolts per meter reconnection electric fields separated by approximately 5 to10 seconds, resulting in average and peak normalized dayside reconnection rates of approximately 0.02 and approximately 0.2, respectively. These data demonstrate that structure in the magnetopause diffusion region at Mercury occurs at the smallest ion scales relevant to reconnection physics.

  14. Ion etching of human adenovirus 2: structure of the core

    SciTech Connect

    Newcomb, W.W.; Boring, J.W.; Brown, J.C.

    1984-07-01

    The surface of human adenovirus 2 was etched by irradiating intact virions with low-energy (1-keV) Ar/sup +/ ions in a Technics Hummer V sputter coater. Viral structures exposed by the etching process were shadowed and then examined in the electron microscope. Periods of etching that were sufficient to reduce the viral diameter by 20 to 30 nm revealed distinct substructural elements in the virion core. Cores were found to consist of a cluster of 12 large, uniformly sized spheres which abutted one another in the intact virion. The spheres, for which we suggest the name adenosomes, had a diameter of 23.0 +/- 2.3 nm, and they were related to each other by two-, three-, and fivefold axes of rotational symmetry. The results support the view, originally suggested by Brown et al. that the adenovirus 2 core is composed of 12 large spheres packed tightly together in such a way that each is directed toward the vertex of an icosahedron. Such a structure, constructed of 23.0-nm-diameter spheres, would have an outside diameter (vertex-to-vertex distance) of 67.0 nm and a face-to-face distance of 58.2 nm. It could be accommodated inside the icosahedral adenovirus capsid if each large sphere were located beneath a capsid vertex.

  15. Ion-Scale Structure in Mercury's Magnetopause Reconnection Diffusion Region

    NASA Technical Reports Server (NTRS)

    Gershman, Daniel J.; Dorelli, John C.; DiBraccio, Gina A.; Raines, Jim M.; Slavin, James A.; Poh, Gangkai; Zurbuchen, Thomas H.

    2016-01-01

    The strength and time dependence of the electric field in a magnetopause diffusion region relate to the rate of magnetic reconnection between the solar wind and a planetary magnetic field. Here we use approximately 150 milliseconds measurements of energetic electrons from the Mercury Surface, Space Environment, GEochemistry, and Ranging (MESSENGER) spacecraft observed over Mercury's dayside polar cap boundary (PCB) to infer such small-scale changes in magnetic topology and reconnection rates. We provide the first direct measurement of open magnetic topology in flux transfer events at Mercury, structures thought to account for a significant portion of the open magnetic flux transport throughout the magnetosphere. In addition, variations in PCB latitude likely correspond to intermittent bursts of approximately 0.3 to 3 millivolts per meter reconnection electric fields separated by approximately 5 to10 seconds, resulting in average and peak normalized dayside reconnection rates of approximately 0.02 and approximately 0.2, respectively. These data demonstrate that structure in the magnetopause diffusion region at Mercury occurs at the smallest ion scales relevant to reconnection physics.

  16. Structural and luminescence properties of Eu3+, Dy3+ and Tb3+ ions in lead germanate glasses obtained by conventional high-temperature melt-quenching technique

    NASA Astrophysics Data System (ADS)

    Żur, Lidia

    2013-06-01

    The subject of this paper is the structural and luminescence properties of selected rare earth ions in lead germanate glasses. Glasses were obtained by conventional high-temperature melt-quenching technique. Europium, dysprosium and terbium ions were chosen as active dopants. The spectroscopic parameters for Eu3+, Dy3+ and Tb3+ ions were determined based on excitation and emission measurements as well as luminescence decay analysis. Especially, the luminescence intensity ratios R/O (Eu3+), Y/B (Dy3+) and G/B (Tb3+) were calculated. Luminescence lifetimes for 5D0 state of Eu3+ ions, 4F9/2 state of Dy3+ ions and 5D4 state of Tb3+ ions were also determined. The amorphous nature and local structure of the studied lead germanate glass systems was confirmed by X-ray diffraction (XRD) and infrared (FT-IR) spectroscopy.

  17. Ion-chromatographic determination of carbocisteine in pharmaceuticals based on non-suppressed conductimetric detection.

    PubMed

    Megoulas, Nikolaos C; Koupparis, Michael A

    2004-02-13

    A novel method for the determination of carbocisteine (S-CMC), a mucolytic and expectorant drug with an acidic amino acid structure, was developed and validated, using non-suppressed ion-chromatographic system with conductimetric detection, and anion or cation exchange columns. Among the various combinations of column type and eluent composition tested, a cation exchange column with a 0.25 mM tri-fluoroacetic acid (TFA) as eluent in isocratic mode at 1.2 ml/min gave the best results. S-CMC was very well separated from all common amino acids (resolution > 2.6). The retention time was 3.5 min and the asymmetry factor 1.1. A linear calibration curve from 17 to 400 microg/ml (r = 0.99994), with a detection limit of 0.14 microg (5.6 microg/ml-25 microl injection volume) and a precision of 1.5% R.S.D. (100 microg/ml, n = 3) was achieved. The proposed method was applied for the determination of S-CMC content in intensely colored commercial formulations (syrups). No interference from excipients was found and the only pretreatment step was the appropriate dilution with the mobile phase. Recovery from standard additions was ranged from 96.0 to 104.9% and precision (R.S.D., n = 3) 1.8-3.6%.

  18. HPLC method for the determination of phytochelatin synthase activity specific for soft metal ion chelators.

    PubMed

    Ogawa, Shinya; Yoshidomi, Takahiro; Shirabe, Tomoo; Yoshimura, Etsuro

    2010-04-01

    Phytochelatins (PCs) are nonprotein peptides with the general structure (gamma-Glu-Cys)(n)-Gly (PC(n)), where n is greater than or equal to 2. They are synthesized through a reaction catalyzed by phytochelatin synthase (PCS) in the presence of metal cations and using the tripeptide glutathione (gamma-Glu-Cys-Gly) and/or previously synthesized PC(n) as the substrate. Here, a highly sensitive assay for PCS activity was devised, in which the dequenching of Cu(I)-bathocuproinedisulfonate complexes was used in the detection system of a reversed-phase high-performance liquid chromatograph. Using recombinant PCS from the higher plant Arabidopsis thaliana (rAtPCS1), this assay system was capable of determining PCS activity based on an amount of the enzyme preparation that was 100-fold less than that required for the 5,5'-dithiobis(2-nitrobenzoic acid) assay method. Although adsorption of the enzyme onto the reaction vessel hindered accurate activity determination, the inclusion of bovine serum albumin successfully resolved this issue. This method is a powerful tool for investigating PCS enzyme mechanisms with respect to the roles of metal ions. Copyright 2009 Elsevier Inc. All rights reserved.

  19. [Simultaneous determination of alendronate, pamidronate, ibandronate and risedronate using ion chromatography with integrated pulsed amperometric detection].

    PubMed

    Chen, Yu; Liu, Yuxiu; Chen, Zhidong; Chen, Meilan; Zhu, Yan

    2012-04-01

    A method for the simultaneous determination of alendronate, pamidronate, ibandronate and risedronate using ion chromatography with integrated pulsed amperometric detection (IPAD) has been developed. The electrochemical behavior showed the catalytic currents of these bisphosphonates are based on the oxidation of amines in their structures. Because the bisphosphonates are polar compounds and present as anions under alkaline condition, therefore, they can be separated by anion exchange chromatography. A Dionex AS18 column (250 mm x 2 mm) and an AG18 column (50 mm x 2 mm) and 24 mmol/L NaOH solution were used for the separation. Multi-step potential waveform parameters were optimized to maximize the signal-to-noise ratio (S/N), which exhibited adsorption/desorption catalytic features at the gold electrode surface in alkaline solution. Utilizing the optimized waveform, the method showed good linearity (r2 = 0.9972 - 0.9995), satisfactory repeatability (relative standard deviations (RSDs) of the peak areas in the range of 0.84% - 1.37%) and sufficient sensitivity (limits of detection of 0.061 - 0.18 microg/mL) for the identification of the four bisphosphonates. The recoveries were 80.81% - 97.32% with the RSDs of 1.46% - 3.02%. It is demonstrated that this method is a rapid and simple one for the determination of the four bisphosphonates in human plasma.

  20. Indirect determination of cyanide compounds by ion chromatography with conductivity measurement

    SciTech Connect

    Nonomura, M.

    1987-09-01

    Ion chromatography (IC) is a suitable analytical technique for the determination of anions. The cyanide is not detected by the conductivity detector of the ion chromatograph due to its low dissolution constant (pK = 9.2). This paper describes an IC procedure for the determination of free cyanide and metal cyanide complexes that uses a conductivity detector. It is based on the oxidation of cyanide ion by sodium hypochlorite to cyanate ion (pK = 3.66). Therefore, cyanide ion can now be measured indirectly by the conductivity detector. In this procedure, optimum operating conditions were examined. In addition, the interferences from anions and reducing agents were investigated. The method was applied to the determination of metal cyanide complexes. The coefficients of variation (%) for CN/sup -/ (1.05 mg/L), Zn(CN)/sub 4//sup 2 -/ (CN/sup -/, 0.80 mg/L), and Ni(CN)/sub 4//sup 2 -/ (CN/sup -/, 0.96 mg/L) were 1.1%, 1.5%, and 0.5%, respectively. The proposed method proved to be useful for the determination of cyanide compounds in natural water and waste water.

  1. Simultaneous determination of cationic surfactants and nonionic surfactants by ion-association titration.

    PubMed

    Sakai, Tadao; Teshima, Norio; Takatori, Yasufumi

    2003-09-01

    A simultaneous determination of cationic and nonionic surfactants has been developed using ion-association titration. Tetrabromophenolphthalein ethyl ester (TBPE) was used as an indicator. Benzalkonium reacted with TBPE to form a blue ion-associate in the organic phase. When tetrakis(4-fluorophenyl)borate was added dropwise to the solution, the color of the organic phase turned to yellow at the equivalence point. In addition, when a large amount of potassium ion was added to a solution including Triton X-100, Triton X-100 could be determined by the same technique as described above because of formation of the K+-Triton X-100 cation. The proposed method is available for the stepwise determination of cationic and nonionic surfactants in mixtures.

  2. MCTBI: a web server for predicting metal ion effects in RNA structures.

    PubMed

    Sun, Li-Zhen; Zhang, Jing-Xiang; Chen, Shi-Jie

    2017-08-01

    Metal ions play critical roles in RNA structure and function. However, web servers and software packages for predicting ion effects in RNA structures are notably scarce. Furthermore, the existing web servers and software packages mainly neglect ion correlation and fluctuation effects, which are potentially important for RNAs. We here report a new web server, the MCTBI server (http://rna.physics.missouri.edu/MCTBI), for the prediction of ion effects for RNA structures. This server is based on the recently developed MCTBI, a model that can account for ion correlation and fluctuation effects for nucleic acid structures and can provide improved predictions for the effects of metal ions, especially for multivalent ions such as Mg(2+) effects, as shown by extensive theory-experiment test results. The MCTBI web server predicts metal ion binding fractions, the most probable bound ion distribution, the electrostatic free energy of the system, and the free energy components. The results provide mechanistic insights into the role of metal ions in RNA structure formation and folding stability, which is important for understanding RNA functions and the rational design of RNA structures. © 2017 Sun et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  3. Determining spatial structures of ion crystals by simulated annealing method

    NASA Astrophysics Data System (ADS)

    Wu, Wen-Bo; Wu, Chun-Wang; Li, Jian; Ou, Bao-Quan; Xie, Yi; Wu, Wei; Chen, Ping-Xing

    2017-08-01

    Not Available Project supported by the National Basic Research Program of China (Grant No. 2016YFA0301903), the National Natural Science Foundation of China (Grant Nos. 11304387, 11174370, 61632021, 61205108, and 11305262), and the Research Plan Project of National University of Defense Technology (Grant No. ZK16-03-04).

  4. Determination of calcium ion in sap using carbon nanotube-based ion-selective electrodes.

    PubMed

    Hernández, Rafael; Riu, Jordi; Rius, F Xavier

    2010-08-01

    A new reduced-size solid-state electrode using carbon nanotubes as the transducing layer has been developed for the direct determination of Ca(2+) in sap, overcoming problems encountered by commercial ISEs analysing real complex samples. We show that this solid-contact ISE, which can be easily miniaturized, can be used directly in diluted real samples without any other pretreatment. The performance parameters of the new ISE include a Nernstian slope and excellent stability, good coefficients of selectivity, range of linearity (10(-5) to 10(-2.5) M) and limit of detection (10(-6.2) M), thus making it an excellent tool for determining Ca(2+) in a wide range of plant species.

  5. Ion Spectral Structures Observed by the Van Allen Probes and Cluster

    NASA Astrophysics Data System (ADS)

    Ferradas, C.; Zhang, J.; Luo, H.; Kistler, L. M.; Spence, H. E.; Larsen, B.; Skoug, R. M.; Funsten, H. O.; Reeves, G. D.

    2014-12-01

    During the last decades several missions have recorded the presence of dynamic spectral features of energetic ions in the inner magnetosphere. Previous studies have revealed single "nose-like" structures occurring alone and simultaneous nose-like structures (up to three). In this study we also include signatures of new types of ion structure, namely "trunk-like" and "tusk-like" structures. All the ion structures are named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. They constitute the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. Multi-spacecraft analysis of these structures is important to understand their spatial distribution and temporal evolution. Mass spectrometers onboard Cluster (in a polar orbit) and the Van Allen Probes (in an equatorial orbit) measure energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet, where these ion structures are observed. We present a statistical study of the ion structures, using >1-year measurements from the two missions during the Van Allen Probes era. The results provide important details about the spatial distribution (dependence on geocentric distance and magnetic local time), spectral features of the structures (e.g., characteristic energy and differences among species), and geomagnetic and solar wind conditions under which these structures occur.

  6. Determination of bromate ion in drinking water by capillary zone electrophoresis with direct photometric detection.

    PubMed

    Takayanagi, Toshio; Ishida, Makoto; Mbuna, Julius; Driouich, Rim; Motomizu, Shoji

    2006-09-22

    Bromate ion in drinking water was determined by capillary zone electrophoresis (CZE) with direct photometric detection. Bromate ion in the sample solution was introduced and concentrated into the capillary by electrokinetic injection for 50s at -10 kV. Electrophoretic separation was made at an applied voltage of -25 kV and bromate ion was detected at wavelength 193 nm, at which the baseline was stabilized with less UV-absorbing acidic phosphate buffer. Bromate ion was detected within 5 min in the electropherogram. By increasing the electric conductivity in the migrating solution with 10 mM Na2SO4, a limit of detection (LOD) of 9 x 10(-10)M (0.1 microg/L BrO3-) was achieved. The proposed method was applied to the analysis of tap water and river water samples, but bromate ion was not detected. Because the practical samples contain relatively large amount of foreign ionic substances, the tap water sample was diluted to avoid the matrix ions. Bromate ion added in a tap water at the concentration of 8 x 10(-8)M was quantitatively recovered by diluting it 1/10.

  7. Peptide structural analysis using continuous Ar cluster and C60 ion beams.

    PubMed

    Aoyagi, Satoka; Fletcher, John S; Sheraz Rabbani, Sadia; Kawashima, Tomoko; Berrueta Razo, Irma; Henderson, Alex; Lockyer, Nicholas P; Vickerman, John C

    2013-08-01

    A novel application of time-of-flight secondary ion mass spectrometry (ToF-SIMS) with continuous Ar cluster beams to peptide analysis was investigated. In order to evaluate peptide structures, it is necessary to detect fragment ions related to multiple neighbouring amino acid residues. It is, however, difficult to detect these using conventional ToF-SIMS primary ion beams such as Bi cluster beams. Recently, C60 and Ar cluster ion beams have been introduced to ToF-SIMS as primary ion beams and are expected to generate larger secondary ions than conventional ones. In this study, two sets of model peptides have been studied: (des-Tyr)-Leu-enkephalin and (des-Tyr)-Met-enkephalin (molecular weights are approximately 400 Da), and [Asn(1) Val(5)]-angiotensin II and [Val(5)]-angiotensin I (molecular weights are approximately 1,000 Da) in order to evaluate the usefulness of the large cluster ion beams for peptide structural analysis. As a result, by using the Ar cluster beams, peptide molecular ions and large fragment ions, which are not easily detected using conventional ToF-SIMS primary ion beams such as Bi3 (+), are clearly detected. Since the large fragment ions indicating amino acid sequences of the peptides are detected by the large cluster beams, it is suggested that the Ar cluster and C60 ion beams are useful for peptide structural analysis.

  8. Predicted Structure, Thermo-Mechanical Properties and Li Ion Transport in LiAlF4 Glass

    SciTech Connect

    Stechert, T. R.; Rushton, M. J. D.; Grimes, R. W.; Dillon, A. C.

    2012-08-15

    Materials with the LiAlF{sub 4} composition are of interest as protective electrode coatings in Li ion battery applications due to their high cationic conductivity. Here classical molecular dynamics calculations are used to produce amorphous model structures by simulating a quench from the molten state. These are analysed in terms of their individual pair correlation functions and atomic coordination environments. This indicates that amorphous LiAlF{sub 4} is formed of a network of corner sharing AlF{sub 6} octahedra. Li ions are distributed within this network, primarily associated with non-bridging fluorine atoms. The nature of the octahedral network is further analysed through intra- and interpolyhedral bond angle distributions and the relative populations of bridging and non-bridging fluorine ions are calculated. Network topology is considered through the use of ring statistics, which indicates that, although topologically well connected, LiAlF{sub 4} contains an appreciable number of corner-linked branch-like AlF{sub 6} chains. Thermal expansion values are determined above and below the predicted glass transition temperature of 1340 K. Finally, movement of Li ions within the network is examined with predictions of the mean squared displacements, diffusion coefficients and Li ion activation energy. Different regimes for lithium ion movement are identified, with both diffusive and sessile Li ions observed. For migrating ions, a typical trajectory is illustrated and discussed in terms of a hopping mechanism for Li transport.

  9. Determination of epichlorohydrin by sulfite derivatization and ion chromatography: characterization of the sulfite derivatives by ion chromatography-mass spectrometry.

    PubMed

    Bruzzoniti, Maria Concetta; Andrensek, Samo; Novic, Milko; Perrachon, Daniela; Sarzanini, Corrado

    2004-04-23

    This work is an upgrade of a previously developed method (J. Chromatogr. A 884 (2000) 251] for epichlorohydrin determination by ion chromatography (IC) and conductivity detection. Here, an ion chromatography-mass spectrometry (IC-MS) coupling has been employed for the separation and the identification of products of epichlorohydrin when reacted with the nucleophilic agent SO3(2-). The high capacity column (IonPac AS11-HC) used for separation provided good resolution. This allowed evaluation of the IC behavior and mass spectrometric identification of epichlorohydrin sulfite derivatives. By using atmospheric pressure interfaces (ESI and APCI) the following species were tentatively identified: 2,3-dihydroxy-1-propanesulfonic, 2,3-epoxy-1-propanesulfonic,1,3-dihydroxy-2-propanesulfonic and 3-oxetanesulfonic acids and 2-hydroxy-1,3-propanedisulfonic acid (or its isomer 3-hydroxy-1,2-propanedisulfonic acid). The study showed that chlorine atoms are displaced from epichlorohydrin during the reaction, while mass spectrometry confirmed that none of the products formed contains chlorine atoms.

  10. Use of accelerated helium-3 ions for determining oxygen and carbon impurities in some pure materials

    NASA Technical Reports Server (NTRS)

    Aleksandrova, G. I.; Borisov, G. I.; Demidov, A. M.; Zakharov, Y. A.; Sukhov, G. V.; Shmanenkova, G. I.; Shchelkova, V. P.

    1978-01-01

    Methods are developed for the determination of O impurity in Be and Si carbide and concurrent determination of C and O impurities in Si and W by irradiation with accelerated He-3 ions and subsequent activity measurements of C-11 and F-18 formed from C and O with the aid of a gamma-gamma coincidence spectrometer. Techniques for determining O in Ge and Ga arsenide with radiochemical separation of F-18 are also described.

  11. Determination of effective capacities of ion-exchangeable materials by measuring the equilibrium conductivity.

    PubMed

    Okabe, Toshiaki; Yokoyama, Yukio

    2010-01-01

    The effective ion-exchange capacities of ion-exchange materials were determined by measuring the change in the equilibrium conductivity of a column packed with analyte. The developed instrumental method can provide effective ion-exchange capacities for both cation and anion exchangers with simple operations. The cation-exchange capacity of a weak-acid cation-exchange resin (TSKgel SuperIC-Cation column) depended on the conditioning pH and the molar concentration of the conditioning agent. Plots of effective cation-exchange capacities over the conditioning pH exhibited three inflection points, suggesting the presence of two carboxy groups and one phenolic OH group in the resin, probably due to the inherent base polymer. This method was applied to several commercial analytical columns for ion chromatography, and could provide scientifically useful results for characterizing the resin properties.

  12. Determination of metal ions by high-performance liquid chromatographic separation of their hydroxamic acid chelates

    SciTech Connect

    Palmieri, M.D.; Fritz, J.S.

    1987-09-15

    Metal ions are determined by adding N-methylfurohydroxamic acid to an aqueous sample and then separating the metal chelates by direct injection onto a liquid chromatographic column. Separations on a C/sub 8/ silica column and a polystyrene-divinylbenzene column are compared, with better separations seen on the polymeric column. The complexes formed at low pH values are cationic and are separated by an ion pairing mechanism. Retention times and selectivity of the metal complexes can be varied by changing the pH. Several metal ions can be separated and quantified; separation conditions, linear calibration curve ranges, and detection limits are presented for Zr(IV), Hf(IV), Fe(III), Nb(V), Al(III), and Sb(III). Interferences due to the presence of other ions in solution are investigated. Finally, an antiperspirant sample is analyzed for zirconium by high-performance liquid chromatography.

  13. X-ray and neutron scattering studies of the hydration structure of alkali ions in concentrated aqueous solutions.

    PubMed

    Ansell, S; Barnes, A C; Mason, P E; Neilson, G W; Ramos, S

    2006-12-01

    The presence of ions in water provides a rich and varied environment in which many natural processes occur with important consequences in biology, geology and chemistry. This article will focus on the structural properties of ions in water and it will be shown how the 'difference' methods of neutron diffraction with isotopic substitution (NDIS) and anomalous X-ray diffraction (AXD) can be used to obtain direct information regarding the radial pair distribution functions of many cations and anions in solution. This information can subsequently be used to calculate coordination numbers and to determine ion-water conformation in great detail. As well as enabling comparisons to be made amongst ions in particular groups in the periodic table, such information can also be contrasted with results provided by molecular dynamics (MD) simulation techniques. To illustrate the power of these 'difference' methods, reference will be made to the alkali group of ions, all of which have been successfully investigated by the above methods, with the exception of the radioactive element francium. Additional comments will be made on how NDIS measurements are currently being combined with MD simulations to determine the structure around complex ions and molecules, many of which are common in biological systems.

  14. Spectroscopic and structural study of proton and halide ion cooperative binding to gfp.

    PubMed

    Arosio, Daniele; Garau, Gianpiero; Ricci, Fernanda; Marchetti, Laura; Bizzarri, Ranieri; Nifosì, Riccardo; Beltram, Fabio

    2007-07-01

    This study reports the influence of halogens on fluorescence properties of the Aequorea victoria Green Fluorescent Protein variant S65T/T203Y (E(2)GFP). Halide binding forms a specific nonfluorescent complex generating a substantial drop of the fluorescence via static quenching. Spectroscopic analysis under different solution conditions reveals high halogen affinity, which is strongly dependent on the pH. This evidences the presence in E(2)GFP of interacting binding sites for halide ions and for protons. Thermodynamic link and cooperative interaction are assessed demonstrating that binding of one halide ion is associated with the binding of one proton in a cooperative fashion with the formation, in the pH range 4.5-10, of a single fully protonated E(2)GFP.halogen complex. To resolve the structural determinants of E(2)GFP sensitivity to halogens, high-resolution crystallographic structures were obtained for the halide-free and I(-), Br(-), and Cl(-) bound E(2)GFP. Remarkably the first high-resolution (1.4 A) crystallographic structure of a chloride-bound GFP is reported. The chloride ion occupies a specific and unique binding pocket in direct contact (3.4 A) with the chromophore imidazolidinone aromatic ring. Unanticipated flexibility, strongly modulated by halide ion interactions, is observed in the region surrounding the chromophore. Furthermore molecular dynamics simulations identified E222 residue (along with the chromophore Y66 residue) being in the protonated state when E(2)GFP.halogen complex is formed. The impact of these results on high-sensitivity biosensor design will be discussed.

  15. Spectroscopic and Structural Study of Proton and Halide Ion Cooperative Binding to GFP

    PubMed Central

    Arosio, Daniele; Garau, Gianpiero; Ricci, Fernanda; Marchetti, Laura; Bizzarri, Ranieri; Nifosì, Riccardo; Beltram, Fabio

    2007-01-01

    This study reports the influence of halogens on fluorescence properties of the Aequorea victoria Green Fluorescent Protein variant S65T/T203Y (E2GFP). Halide binding forms a specific nonfluorescent complex generating a substantial drop of the fluorescence via static quenching. Spectroscopic analysis under different solution conditions reveals high halogen affinity, which is strongly dependent on the pH. This evidences the presence in E2GFP of interacting binding sites for halide ions and for protons. Thermodynamic link and cooperative interaction are assessed demonstrating that binding of one halide ion is associated with the binding of one proton in a cooperative fashion with the formation, in the pH range 4.5–10, of a single fully protonated E2GFP·halogen complex. To resolve the structural determinants of E2GFP sensitivity to halogens, high-resolution crystallographic structures were obtained for the halide-free and I−, Br−, and Cl− bound E2GFP. Remarkably the first high-resolution (1.4 Å) crystallographic structure of a chloride-bound GFP is reported. The chloride ion occupies a specific and unique binding pocket in direct contact (3.4 Å) with the chromophore imidazolidinone aromatic ring. Unanticipated flexibility, strongly modulated by halide ion interactions, is observed in the region surrounding the chromophore. Furthermore molecular dynamics simulations identified E222 residue (along with the chromophore Y66 residue) being in the protonated state when E2GFP·halogen complex is formed. The impact of these results on high-sensitivity biosensor design will be discussed. PMID:17434942

  16. Characterization of Cross-Linked Cellulosic Ion-Exchange Adsorbents: 1. Structural Properties

    PubMed Central

    Angelo, James M.; Cvetkovic, Aleksandar; Gantier, Rene; Lenhoff, Abraham M.

    2014-01-01

    The structural characteristics of the HyperCel family of cellulosic ion-exchange materials (Pall Corporation) were assessed using methods to gauge the pore dimensions and the effect of ionic strength on intraparticle architecture. Inverse size exclusion chromatography (ISEC) was applied to the S and STAR AX HyperCel derivatives. The theoretical analysis yielded an average pore radius for each material of about 5 nm, with a particularly narrow pore-size distribution. Electron microscopy techniques were used to visualize the particle structure and relate it to macroscopic experimental data. Microscopy of Q and STAR AX HyperCel anion exchangers presented some qualitative differences in pore structure that can be attributed to the derivatization using conventional quaternary ammonium and salt-tolerant ligands, respectively. Finally, the effect of ionic strength was studied through the use of salt breakthrough experiments to determine to what extent Donnan exclusion plays a role in restricting the accessible pore volume for small ions. It was determined that Donnan effects were prevalent at total ionic strengths (TIS) less than 150 mM, suggesting the presence of a ligand-containing partitioning volume within the pore space. PMID:24188996

  17. New frontiers for mass spectrometry based upon structures for lossless ion manipulations.

    PubMed

    Ibrahim, Yehia M; Hamid, Ahmed M; Deng, Liulin; Garimella, Sandilya V B; Webb, Ian K; Baker, Erin S; Smith, Richard D

    2017-03-06

    Structures for lossless ion manipulations (SLIM) provide a new paradigm for efficient, complex and extended gas phase ion manipulations. SLIM are created from electric fields generated by the application of DC and RF potentials to arrays of electrodes patterned on two parallel surfaces. The electric fields provide lossless ion manipulations, including effective ion transport and storage. SLIM modules have been developed using both constant and oscillatory electric fields (e.g. traveling waves) to affect the ion motion. Ion manipulations demonstrated to date with SLIM include: extended trapping, ion selection, ion dissociation, and ion mobility spectrometry (IMS) separations achieving unprecedented ultra high resolution. SLIM thus provide the basis for previously impractical manipulations, such as very long path length ion mobility separations where ions traverse a serpentine path multiple times, as well as new capabilities that extend the utility of these developments based on temporal and spatial compression of ion mobility separations and other ion distributions. The evolution of SLIM devices developed over the last three years is reviewed and we provide examples of various ion manipulations performed, and briefly discuss potential applications and new directions.

  18. The importance of dehydration in determining ion transport in narrow pores.

    PubMed

    Richards, Laura A; Schäfer, Andrea I; Richards, Bryce S; Corry, Ben

    2012-06-11

    The transport of hydrated ions through narrow pores is important for a number of processes such as the desalination and filtration of water and the conductance of ions through biological channels. Here, molecular dynamics simulations are used to systematically examine the transport of anionic drinking water contaminants (fluoride, chloride, nitrate, and nitrite) through pores ranging in effective radius from 2.8 to 6.5 Å to elucidate the role of hydration in excluding these species during nanofiltration. Bulk hydration properties (hydrated size and coordination number) are determined for comparison with the situations inside the pores. Free energy profiles for ion transport through the pores show energy barriers depend on pore size, ion type, and membrane surface charge and that the selectivity sequence can change depending on the pore size. Ion coordination numbers along the trajectory showed that partial dehydration of the transported ion is the main contribution to the energy barriers. Ion transport is greatly hindered when the effective pore radius is smaller than the hydrated radius, as the ion has to lose some associated water molecules to enter the pore. Small energy barriers are still observed when pore sizes are larger than the hydrated radius due to re-orientation of the hydration shell or the loss of more distant water. These results demonstrate the importance of ion dehydration in transport through narrow pores, which increases the current level of mechanistic understanding of membrane-based desalination and transport in biological channels. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

    PubMed Central

    2008-01-01

    Alkali (Li+, Na+, K+, Rb+, and Cs+) and halide (F−, Cl−, Br−, and I−) ions play an important role in many biological phenomena, roles that range from stabilization of biomolecular structure, to influence on biomolecular dynamics, to key physiological influence on homeostasis and signaling. To properly model ionic interaction and stability in atomistic simulations of biomolecular structure, dynamics, folding, catalysis, and function, an accurate model or representation of the monovalent ions is critically necessary. A good model needs to simultaneously reproduce many properties of ions, including their structure, dynamics, solvation, and moreover both the interactions of these ions with each other in the crystal and in solution and the interactions of ions with other molecules. At present, the best force fields for biomolecules employ a simple additive, nonpolarizable, and pairwise potential for atomic interaction. In this work, we describe our efforts to build better models of the monovalent ions within the pairwise Coulombic and 6-12 Lennard-Jones framework, where the models are tuned to balance crystal and solution properties in Ewald simulations with specific choices of well-known water models. Although it has been clearly demonstrated that truly accurate treatments of ions will require inclusion of nonadditivity and polarizability (particularly with the anions) and ultimately even a quantum mechanical treatment, our goal was to simply push the limits of the additive treatments to see if a balanced model could be created. The applied methodology is general and can be extended to other ions and to polarizable force-field models. Our starting point centered on observations from long simulations of biomolecules in salt solution with the AMBER force fields where salt crystals formed well below their solubility limit. The likely cause of the artifact in the AMBER parameters relates to the naive mixing of the Smith and Dang chloride parameters with AMBER

  20. Polyphosphate ions encapsulated in oxothiomolybdate rings: synthesis, structure, and behavior in solution.

    PubMed

    Cadot, Emmanuel; Pouet, Marie-José; Robert-Labarre, Chantal; du Peloux, Charlotte; Marrot, Jérôme; Sécheresse, Francis

    2004-07-28

    Cyclic oxothiomolybdates containing polyphosphate ions were prepared by simple reactions in aqueous medium of the corresponding polyphosphate ions and the cyclic precursor K(2)I(2)Mo(10)S(10)O(10)(OH)(10)(OH(2))(5).15H(2)O. K(5)[Cl(P(2)O(7)]Mo(12)S(12)O(12)(OH)(12)(H(2)O)(4)].22H(2)O (1) was isolated from concentrated chloride solution (2.5 mol.L(-1)). 1 reveals a remarkable complex containing two different substrates encapsulated in a dodecanuclear ring, a H-bonded Cl(-) ion, and a covalently bonded [P(2)O(7)] group. The chloride ion in 1 can be selectively removed for a monohydrogenophosphate group yielding K(6)[(HPO(4))(P(2)O(7))Mo(12)S(12)O(12)(OH)(12)(H(2)O)(2)].19H(2)O (2), a mixed species containing a [P(2)O(7)] and a [HPO(4)] group. The substitution is accompanied by a significant change of the ring, which adopts a "pear-shape" conformation. In the presence of triphosphate ion, the "heart-shaped" decanuclear ring Rb(3)[(H(2)P(3)O(10))Mo(10)S(10)O(10)(OH)(10)].17.5H(2)O (3) is formed containing a linear [P(3)O(10)] group intimately embedded in the inorganic cyclic host. The three compounds were structurally characterized by single-crystal X-ray diffraction. The behaviors of 1, 2, and 3 in solution were studied by (31)P NMR. Variable temperature experiments, supported by a two-dimensional COSY (31)P experiment, revealed that the supramolecular interaction existing between the chloride ion and the ring in solid 1 is maintained in solution. Nevertheless, 1 remains labile, and successive equilibria were evidenced and interpreted as an ion-pair association involving a halide ion (Cl, Br, or I), responsible for the conformational change of the [P(2)O(7)] group within the cavity. The influence of the nature of the halide guest (Cl(-), Br(-), and I(-)) on the successive equilibria was studied, and the thermodynamic constant related to the postulated equilibrium was determined. The stability of the supramolecular association decreases in the order Cl > Br > I. In

  1. Protein structure determination using metagenome sequence data.

    PubMed

    Ovchinnikov, Sergey; Park, Hahnbeom; Varghese, Neha; Huang, Po-Ssu; Pavlopoulos, Georgios A; Kim, David E; Kamisetty, Hetunandan; Kyrpides, Nikos C; Baker, David

    2017-01-20

    Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families and that metagenome sequence data more than triple the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact-based structure matching, and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the Protein Data Bank. This approach provides the representative models for large protein families originally envisioned as the goal of the Protein Structure Initiative at a fraction of the cost. Copyright © 2017, American Association for the Advancement of Science.

  2. Protein Structure Determination using Metagenome sequence data

    PubMed Central

    Ovchinnikov, Sergey; Park, Hahnbeom; Varghese, Neha; Huang, Po-Ssu; Pavlopoulos, Georgios A.; Kim, David E.; Kamisetty, Hetunandan; Kyrpides, Nikos C.; Baker, David

    2017-01-01

    Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families, and that metagenome sequence data more than triples the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact based structure matching and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the PDB. This approach provides the representative models for large protein families originally envisioned as the goal of the protein structure initiative at a fraction of the cost. PMID:28104891

  3. Mass determination of megadalton-DNA Electrospray Ions usingCharge Detection Mass Spectrometry

    SciTech Connect

    Schultz, Jocelyn C.; Hack, Christopher; Benner, Henry W.

    1997-10-01

    Charge detection mass spectrometry (CD-MS) has been used to determine the mass of double-stranded, circular DNA and single-stranded, circular DNA in the range of 2500 to 8000 base pairs (1.5-5.0 MDa). Simultaneous measurement of the charge and velocity of an electrostatically accelerated ion allows a mass determination of the ion, with instrument calibration determined independently of samples. Positive ion mass spectra of electrosprayed commercial DNA samples supplied in tris(hydroxymethyl)ethylenediamine tetraacetic acid buffer, diluted in 50 vol. percent acetonitrile, were obtained without cleanup of the sample. ACD mass spectrum constructed from 3000 ion measurements takes 10 min to acquire and yields the DNA molecular mass directly (mass resolution = 6). The data collected represent progress toward a more automatable alternative to sizing of DNA by gel electrophoresis. In addition to the mass spectra, CD-MS generates charge versus mass plots, which provide another means to investigate the creation and fate of large electrospray ions.

  4. Swift heavy ion irradiation of Pt nanocrystals: II. Structural changes and H desorption

    SciTech Connect

    Giulian, R.; Araujo, L.L.; Kluth, P.; Sprouster, D.J.; Schnohr, C.S.; Byrne, A.P.; Ridgway, M.C.

    2014-09-24

    The structural properties and H desorption from embedded Pt nanocrystals (NCs) following irradiation with swift heavy ions were investigated as a function of energy and fluence. From x-ray absorption near-edge spectroscopy analysis, Pt-H bonding was identified in NCs annealed in a forming gas (95% N{sub 2} + 5% H{sub 2}) ambient. The H content decreased upon irradiation and the desorption process was NC-size dependent such that larger NCs required a higher fluence to achieve a H-free state. Pt-H bonding and NC dissolution both perturbed the NC structural parameters (coordination number, bond-length and mean-square relative displacement) as determined with extended x-ray absorption fine structure measurements.

  5. Modifying the Target Normal Sheath Accelerated Ion Spectrum Using Structured Targets

    NASA Astrophysics Data System (ADS)

    George, Kevin Mitchell

    In the interaction of high intensity (> 1018 W/cm2), ultrashort (< 1 ps) laser pulses with solid targets, the laser couples energy into the target through a population of energetic electrons. An electrostatic sheath field is formed along the target surface due to the induced charge separation between the expanding energetic electron cloud and relatively heavy, slow ions. This electrostatic field is capable of accelerating ions to energies greater than 10 MeV/nucleon through the physical mechanism known as target normal sheath acceleration (TNSA). Since its discovery in 2000, TNSA has been widely studied throughout the High Energy Density Physics community in order to understand and enhance this process for its potential applications ranging from cancer therapy to radiography. However, much of this work has been conducted on thin (1s to 10s of microns thick) metal foils exploring optimization only through critical laser parameters such as intensity, energy, and prepulse. This thesis addresses the development of novel micro-structured targets for the enhancement of TNSA ions. These targets were developed through the use of optical lithography techniques to pattern micron-scale structures onto thin substrates at the OSU Nanosystem Laboratory (NSL) user facility. These targets permit on-demand patterning of designs with 1 mum lateral resolution, heights varying between 0.5-2 mum, on substrates ranging from 0.5-2 mum thick with high throughput. An experiment was conducted at the Scarlet laser facility to characterize the effect of structuring the laser-target interface on the energy spectrum of TNSA protons. A comparison of the proton dose from structured versus at photoresist on silicon nitride substrates was performed. Results obtained using radiochromic film demonstrate an increase in proton dose by a factor of 2.3 through the use of structured photoresist as compared to unstructured photoresist of the same thickness. Two dimensional absorption simulations were

  6. Ion probe determinations of the rare earth concentrations of individual meteoritic phosphate grains

    NASA Technical Reports Server (NTRS)

    Crozaz, G.; Zinner, E.

    1985-01-01

    A new ion probe method for quantitative measurements of the concentrations of all the REE down to the ppm level in 5-20 micron spots is presented. The first application of the method is the determination of REE abundances in meteoritic phosphates. Results are shown to be in good agreement with previous INAA and ion probe determinations. The merrillites in the St. Severin amphoterite are richer in REE than the apatites (the enrichment factors, for various REE, range from 2.3 to 14.2) in contradiction with the results of Ebihara and Honda (1983). Provided good standards for other mineral phases are found or implanted marker ion techniques are used, the method should find a wide range of applications for the study of both terrestrial and extraterrestrial crystals at the microscopic level.

  7. Ion probe determinations of the rare earth concentrations of individual meteoritic phosphate grains

    NASA Technical Reports Server (NTRS)

    Crozaz, G.; Zinner, E.

    1985-01-01

    A new ion probe method for quantitative measurements of the concentrations of all the REE down to the ppm level in 5-20 micron spots is presented. The first application of the method is the determination of REE abundances in meteoritic phosphates. Results are shown to be in good agreement with previous INAA and ion probe determinations. The merrillites in the St. Severin amphoterite are richer in REE than the apatites (the enrichment factors, for various REE, range from 2.3 to 14.2) in contradiction with the results of Ebihara and Honda (1983). Provided good standards for other mineral phases are found or implanted marker ion techniques are used, the method should find a wide range of applications for the study of both terrestrial and extraterrestrial crystals at the microscopic level.

  8. Ion chromatographic determination of inositol in infant formulae and clinical products for enteral feeding.

    PubMed

    Tagliaferri, E G; Bonetti, G; Blake, C J

    2000-05-26

    An ion chromatographic method is described for the determination of inositol in infant formula and products for enteral feeding. A two-step procedure for hydrolysis and extraction of total inositol has been developed, involving alkaline hydrolysis with 3 M potassium hydroxide and enzymatic dephosphorylation. Substances having a long chromatographic retention time were removed with an ion-exchange resin. Inositol was separated on a high-resolution ion-exchange column and detected by pulsed amperometric detection. Phytic acid interferes only slightly in the analysis. This method can be used for determination of total inositol in infant formulae, and enteral feeding products. The analytical method gave an average recovery of 94% from infant formula samples spiked with inositol and a recovery of 86+/-3% from products spiked with lecithin.

  9. Determination of Ion Content and Ion Fluxes in the Halotolerant Alga Dunaliella salina

    PubMed Central

    Pick, Uri; Karni, Leah; Avron, Mordhay

    1986-01-01

    A method to determine intracellular cation contents in Dunaliella by separation on cation-exchange minicolumns is described. The separation efficiency of cells from extracellular cations is over 99.9%; the procedure causes no apparent perturbation to the cells and can be applied to measure both fluxes and internal content of any desired cation. Using this technique it is demonstrated that the intracellular averaged Na+, K+, and Ca2+ concentrations in Dunaliella salina cultured at 1 to 4 molar NaCl, 5 millimolar K+, and 0.3 millimolar Ca2+ are 20 to 100 millimolar, 150 to 250 millimolar, and 1 to 3 millimolar, respectively. The intracellular K+ concentration is maintained constant over a wide range of media K+ concentrations (0.5-10 millimolar), leading to a ratio of K+ in the cells to K+ in the medium of 10 to 1,000. Severe limitation of external K+, induces loss of K+ and increase in Na+ inside the cells. The results suggest that Dunaliella cells possess efficient mechanisms to eliminate Na+ and accumulate K+ and that intracellular Na+ and K+ concentrations are carefully regulated. The contribution of the intracellular Na+ and K+ salts to the total osmotic pressure of cells grown at 1 to 4 molar NaCl, is 5 to 20%. PMID:16664814

  10. Determining the topology of virus assembly intermediates using ion mobility spectrometry-mass spectrometry.

    PubMed

    Knapman, Tom W; Morton, Victoria L; Stonehouse, Nicola J; Stockley, Peter G; Ashcroft, Alison E

    2010-10-30

    We have combined ion mobility spectrometry-mass spectrometry with tandem mass spectrometry to characterise large, non-covalently bound macromolecular complexes in terms of mass, shape (cross-sectional area) and stability (dissociation) in a single experiment. The results indicate that the quaternary architecture of a complex influences its residual shape following removal of a single subunit by collision-induced dissociation tandem mass spectrometry. Complexes whose subunits are bound to several neighbouring subunits to create a ring-like three-dimensional (3D) architecture undergo significant collapse upon dissociation. In contrast, subunits which have only a single neighbouring subunit within a complex retain much of their original shape upon complex dissociation. Specifically, we have determined the architecture of two transient, on-pathway intermediates observed during in vitro viral capsid assembly. Knowledge of the mass, stoichiometry and cross-sectional area of each viral assembly intermediate allowed us to model a range of potential structures based on the known X-ray structure of the coat protein building blocks. Comparing the cross-sectional areas of these potential architectures before and after dissociation provided tangible evidence for the assignment of the topologies of the complexes, which have been found to encompass both the 3-fold and the 5-fold symmetry axes of the final icosahedral viral shell. Such insights provide unique information about virus assembly pathways that could allow the design of anti-viral therapeutics directed at the assembly step. This methodology can be readily applied to the structural characterisation of many other non-covalently bound macromolecular complexes and their assembly pathways. Copyright © 2010 John Wiley & Sons, Ltd.

  11. Piezoelectric sensor for sensitive determination of metal ions based on the phosphate-modified dendrimer

    NASA Astrophysics Data System (ADS)

    Wang, S. H.; Shen, C. Y.; Lin, Y. M.; Du, J. C.

    2016-08-01

    Heavy metal ions arising from human activities are retained strongly in water; therefore public water supplies must be monitored regularly to ensure the timely detection of potential problems. A phosphate-modified dendrimer film was investigated on a quartz crystal microbalance (QCM) for sensing metal ions in water at room temperature in this study. The chemical structures and sensing properties were characterized by Fourier transform infrared spectroscopy and QCM measurement, respectively. This phosphate-modified dendrimer sensor can directly detect metal ions in aqueous solutions. This novel sensor was evaluated for its capacity to sense various metal ions. The sensor exhibited a higher sensitivity level and shorter response time to copper(II) ions than other sensors. The linear detection range of the prepared QCM based on the phosphate-modified dendrimer was 0.0001 ∼ 1 μM Cu(II) ions (R2 = 0.98). The detection properties, including sensitivity, response time, selectivity, reusability, maximum adsorption capacity, and adsorption equilibrium constants, were also investigated.

  12. Spectrophotometric determination of lithium ion using a water-soluble octabromoporphyrin in aqueous solution.

    PubMed

    Tabata, M; Nishimoto, J; Kusano, T

    1998-08-01

    A water-soluble porphyrin, (2,3,7,8,12,13,17,18-octabromo-5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin; H(2)obtpps(4-)) was synthesized and developed for the determination of lithium ion in aqueous solution. The octabromo groups lower the basicity of the porphyrin by their electron-withdrawing effect, and enable the porphyrin to react with the lithium ion in alkaline solution to form the lithium complex along with a shift of absorption maximum: lambda max/nm (logepsilon/mol(-1) dm(3) cm(-1)) of the lithium porphyrin are 490.5 nm (5.31) and 734 nm (4.36). Sodium and potassium ions did not react with the porphyrin. The equilibrium constant for the reaction Li(+)+Hobtpps(5-)right harpoon over left harpoon[Li(obtpps)](5-)+H(+) was found to be 10(-8.80) and the conditional formation constant of the [Li(obtpps)](5-) at pH 13 is 10(4.21). The above results were applied to the determination of lithium ion in aqueous solution. The interference from transition and heavy metal ions was masked by using N,N'-1,2-ethanediylbis[N(carboxylmethy)glycinato]magnesium(II) ([Mg(edta)](2-)) solution. Absorbance at 490 nm was measured against a blank solution. A calibration graph was linear over the range of 0.007-0.7 mug cm(-3) (1x10(-6)-1x10(-4) mol dm(-3)) of lithium(I) with a correlation factor of 0.967. Lithium ion less than ppm level was determined spectrophtometrically in aqueous solution. The proposed method was applied to the determination of lithium in human serum and sea water samples.

  13. Ion Binding Energies Determining Functional Transport of ClC Proteins

    NASA Astrophysics Data System (ADS)

    Yu, Tao; Guo, Xu; Zou, Xian-Wu; Sang, Jian-Ping

    2014-06-01

    The ClC-type proteins, a large family of chloride transport proteins ubiquitously expressed in biological organisms, have been extensively studied for decades. Biological function of ClC proteins can be reflected by analyzing the binding situation of Cl- ions. We investigate ion binding properties of ClC-ec1 protein with the atomic molecular dynamics simulation approach. The calculated electrostatic binding energy results indicate that Cl- at the central binding site Scen has more binding stability than the internal binding site Sint. Quantitative comparison between the latest experimental heat release data isothermal titration calorimetry (ITC) and our calculated results demonstrates that chloride ions prefer to bind at Scen than Sint in the wild-type ClC-ec1 structure and prefer to bind at Sext and Scen than Sint in mutant E148A/E148Q structures. Even though the chloride ions make less contribution to heat release when binding to Sint and are relatively unstable in the Cl- pathway, they are still part contributors for the Cl- functional transport. This work provides a guide rule to estimate the importance of Cl- at the binding sites and how chloride ions have influences on the function of ClC proteins.

  14. Determining the Locations of Ions and Water around DNA from X-Ray Scattering Measurements

    PubMed Central

    Meisburger, Steve P.; Pabit, Suzette A.; Pollack, Lois

    2015-01-01

    Nucleic acids carry a negative charge, attracting salt ions and water. Interactions with these components of the solvent drive DNA to condense, RNA to fold, and proteins to bind. To understand these biological processes, knowledge of solvent structure around the nucleic acids is critical. Yet, because they are often disordered, ions and water evade detection by x-ray crystallography and other high-resolution methods. Small-angle x-ray scattering (SAXS) is uniquely sensitive to the spatial correlations between solutes and the surrounding solvent. Thus, SAXS provides an experimental constraint to guide or test emerging solvation theories. However, the interpretation of SAXS profiles is nontrivial because of the difficulty in separating the scattering signals of each component: the macromolecule, ions, and hydration water. Here, we demonstrate methods for robustly deconvoluting these signals, facilitating a more straightforward comparison with theory. Using SAXS data collected on an absolute intensity scale for short DNA duplexes in solution with Na+, K+, Rb+, or Cs+ counterions, we mathematically decompose the scattering profiles into components (DNA, water, and ions) and validate the decomposition using anomalous scattering measurements. In addition, we generate a library of physically motivated ion atmosphere models and rank them by agreement with the scattering data. The best-fit models have relatively compact ion atmospheres when compared to predictions from the mean-field Poisson-Boltzmann theory of electrostatics. Thus, the x-ray scattering methods presented here provide a valuable measurement of the global structure of the ion atmosphere that can be used to test electrostatics theories that go beyond the mean-field approximation. PMID:26083928

  15. Determining the Locations of Ions and Water around DNA from X-Ray Scattering Measurements.

    PubMed

    Meisburger, Steve P; Pabit, Suzette A; Pollack, Lois

    2015-06-16

    Nucleic acids carry a negative charge, attracting salt ions and water. Interactions with these components of the solvent drive DNA to condense, RNA to fold, and proteins to bind. To understand these biological processes, knowledge of solvent structure around the nucleic acids is critical. Yet, because they are often disordered, ions and water evade detection by x-ray crystallography and other high-resolution methods. Small-angle x-ray scattering (SAXS) is uniquely sensitive to the spatial correlations between solutes and the surrounding solvent. Thus, SAXS provides an experimental constraint to guide or test emerging solvation theories. However, the interpretation of SAXS profiles is nontrivial because of the difficulty in separating the scattering signals of each component: the macromolecule, ions, and hydration water. Here, we demonstrate methods for robustly deconvoluting these signals, facilitating a more straightforward comparison with theory. Using SAXS data collected on an absolute intensity scale for short DNA duplexes in solution with Na(+), K(+), Rb(+), or Cs(+) counterions, we mathematically decompose the scattering profiles into components (DNA, water, and ions) and validate the decomposition using anomalous scattering measurements. In addition, we generate a library of physically motivated ion atmosphere models and rank them by agreement with the scattering data. The best-fit models have relatively compact ion atmospheres when compared to predictions from the mean-field Poisson-Boltzmann theory of electrostatics. Thus, the x-ray scattering methods presented here provide a valuable measurement of the global structure of the ion atmosphere that can be used to test electrostatics theories that go beyond the mean-field approximation.

  16. Determination of Benzene, Toluene, and Xylene by means of an ion mobility spectrometer device using photoionization

    NASA Technical Reports Server (NTRS)

    Leonhardt, J. W.; Bensch, H.; Berger, D.; Nolting, M.; Baumbach, J. I.

    1995-01-01

    The continuous monitoring of changes on the quality of ambient air is a field of advantage of ion mobility spectrometry. Benzene, Toluene, and Xylene are substances of special interest because of their toxicity. We present an optimized drift tube for ion mobility spectrometers, which uses photo-ionization tubes to produce the ions to be analyzed. The actual version of this drift tube has a length of 45 mm, an electric field strength established within the drift tube of about 180 V/cm and a shutter-opening-time of 400 mus. With the hydrogen tube used for ionisation a mean flux of 10(exp 12) photons/sq cm s was established for the experiments described. We discuss the results of investigations on Benzene, Toluene, and Xylene in normal used gasoline SUPER. The detection limits obtained with the ion mobility spectrometer developed in co-operation are in the range of 10 ppbv in this case. Normally, charge transfer from Benzene ions to Toluene takes place. Nevertheless the simultaneous determination in mixtures is possible by a data evaluation procedure developed for this case. The interferences found between Xylene and others are rather weak. The ion mobility spectra of different concentrations of gasoline SUPER are attached as an example for the resolution and the detection limit of the instrument developed. Resolution and sensitivity of the system are well demonstrated. A hand-held portable device produced just now is to be tested for special environmental analytical problems in some industrial and scientific laboratories in Germany.

  17. Determination of ion mobility in EHD flow zone of plasma generator

    NASA Astrophysics Data System (ADS)

    Sumariyah, Kusminarto, Hermanto, Arief; Nuswantoro, Pekik

    2015-12-01

    Determination has been carried out for ion mobility in EHD flow zone generated using a pin-concentric multiple ring electrodes and a pin-single ring electrode used as a comparator. The pin needle was made from stainless steel with a tip diameter of 0.18 mm. The concentris multiple ring electrode in form three/two concentric ring electrodes which made of metal material connected to each other. Each ring of three concentric ring electrode has a diameter of 24 mm, 16 mm and 8 mm. And each ring of two concentric ring electrode has a diameter of 24 mm and 16 mm. Single ring electrode has a diameter24 mm. The all ring has same of width and thickness were 2 mm and 3 mm. EHD was generated by using a DC high voltage of 10 kV. Pin functional as an active electrode of corona discharge while the all ring electrodes acted as ions collector and passive electrodes. The experimental results show that the ion current is proportional to V2 according to calculations by Chouelo for hyperbolic-field approach. Ion mobility obtained from the quadratic polynomial fitting of experimental data were current and voltage as well as Choelo formulation. The results showed that the mobility of ions in the EHD flow zones utilizing pin-consentric multiple ring electrode larger than utilizing pin-single ring electrode. Pin-three Consentic ring electrode has the largest of ion mobility

  18. STRUCTURE AS A DETERMINANT OF DEMOCRATIC ADMINISTRATION.

    ERIC Educational Resources Information Center

    COLLINS, CHARLES C.

    THE DEGREE OF OPERATIONAL DEMOCRACY WITHIN A JUNIOR COLLEGE AND, BY EXTENSION, WITHIN ANY SCHOOL OR COLLEGE IS LARGELY DEPENDENT UPON THE KIND OF ORGANIZATIONAL STRUCTURE WHICH IS ESTABLISHED. THE STRUCTURE AND MECHANICS MOST SUPPORTIVE TO THE DEMOCRATIC DEVELOPMENT OF THE COLLEGE AND ITS INSTRUCTIONAL PROGRAM SHOULD HAVE MAXIMAL OPPORTUNITY FOR…

  19. Determining the isomeric heterogeneity of neutral oligosaccharide-alditols of bovine submaxillary mucin using negative ion traveling wave ion mobility mass spectrometry.

    PubMed

    Li, Hongli; Bendiak, Brad; Siems, William F; Gang, David R; Hill, Herbert H

    2015-02-17

    Negative ions produced by electrospray ionization were used to evaluate the isomeric heterogeneity of neutral oligosaccharide-alditols isolated from bovine submaxillary mucin (BSM). The oligosaccharide-alditol mixture was preseparated on an off-line high-performance liquid chromatography (HPLC) column, and the structural homogeneity of individual LC fractions was investigated using a Synapt G2 traveling wave ion mobility spectrometer coupled between quadupole and time-of-flight mass spectrometers. Mixtures of isomers separated by both chromatography and ion mobility spectrometry were studied. Tandem mass spectrometry (MS/MS) of multiple mobility peaks having the same mass-to-charge ratio (m/z) demonstrated the presence of different structural isomers and not differences in ion conformations due to charge site location. Although the oligosaccharide-alditol mixture was originally separated by HPLC, multiple ion mobility peaks due to structural isomers were observed for a number of oligosaccharide-alditols from single LC fractions. The collision-induced dissociation cells located in front of and after the ion mobility separation device enabled oligosaccharide precursor or product ions to be separated by ion mobility and independent fragmentation spectra to be acquired for isomeric carbohydrate precursor or product ions. MS/MS spectra so obtained for independent mobility peaks at a single m/z demonstrated the presence of structural variants or stereochemical isomers having the same molecular formula. This was observed both for oligosaccharide precursor and product ions. In addition, mobilities of both [M - H](-) and [M + Cl](-) ions, formed by adding NH4OH or NH4Cl to the electrospray solvent, were examined and compared for selected oligosaccharide-alditols. Better separation among structural isomers appeared to be achieved for some [M + Cl](-) anions.

  20. Structural performance of a multifunctional spacecraft structure based on plastic lithium-ion batteries

    NASA Astrophysics Data System (ADS)

    Roberts, Samuel C.; Aglietti, Guglielmo S.

    2010-08-01

    A multifunctional structure reduces the mass and volume of a spacecraft through the removal of parasitic components of a functional structure, such as the purely structural "packaging" of the battery. Commercially available cells, of the plastic lithium-ion type, may be incorporated into structural sandwich panels, eliminating the need for a secondary structure in the battery subsystem. Locating the cells in the structure also removes them from the bus, which reduces the volume of the craft and, consequently, reduces the mass of the primary structure. Although the batteries studied in this work exhibited low mechanical properties, this paper will show that, by placing the cells carefully within the sandwich panel, structural performance is not compromised. Finite element models show a reduction in peak stress and deformation in multifunctional panels, compared to a conventional design, when a favourable layout is selected. Less conclusive results for peak acceleration, however, suggest that this type of multifunctional structure may not be appropriate for all applications. Comparison of the finite element modelling technique with a real panel's behaviour shows that the deformation and stress predicted by the model is consistent with reality, whilst the acceleration is reliable for low frequencies.

  1. Determining Ion-Aerosol Nucleation Rates in the Lower Atmosphere: Thermodynamic and Kinetic Modeling and Data Requirements

    NASA Astrophysics Data System (ADS)

    D'Auria, R.; Turco, R. P.

    2005-12-01

    In situ measurements in the free troposphere [Eichkorn et al., 2002] have detected massive positively charged clusters (up to 2500 amu) that appear to be composed of water, acetone and sulfuric acid. Previous modeling studies have suggested that such ionic clusters participate in a number of atmospheric processes, including aerosol formation [Yu and Turco, 1999] and phase transitions in polar stratospheric clouds [D'Auria and Turco, 2001a]. Other work [Lee et al., 2003] indicates that ultrafine particle bursts detected in the upper troposphere can be explained by negative ion clustering mechanisms constrained by laboratory thermodynamic data [Lovejoy et al., 2004], offering further evidence for ion-mediated nucleation. In the lower troposphere, where charged clusters containing hydrated acids, ammonia and a variety of organic compounds are seen, ion-based modeling can often explain nucleation events observed in this region [Yu and Turco, 2001]. We discuss the thermodynamic and kinetic aspects of ion growth and activation in the atmosphere, and describe a "hybrid" representation for common ion families that integrates laboratory measurements with quantum mechanical simulations of charged cluster structure and energetics [D'Auria and Turco, 2001b]. We show that a kinetic model of ion cluster evolution applicable to atmospheric phenomena, including particle nucleation, can be constructed using a hybrid data approach. We present recent results--based on high-level quantum mechanical geometry optimization and thermochemical calculations--for positive ion clusters composed of water, sulfuric acid and acetone [D'Auria, 2005]. It is argued that ions with ternary compositions provide a high degree of cluster stabilization, and are therefore likely to generate pre-condensation nuclei throughout the lower atmosphere. We also discuss errors in the determination of cluster free energies and entropies under atmospheric conditions, and identify the types and precision of data

  2. Polarographic Determination of Composition and Thermodynamic Stability Constant of a Complex Metal Ion.

    ERIC Educational Resources Information Center

    Marin, Dolores; Mendicuti, Francisco

    1988-01-01

    Describes a laboratory experiment designed to encourage laboratory cooperation among individual undergraduate students or groups. Notes each student contributes results individually and the exchange of data is essential to obtain final results. Uses the polarographic method for determining complex metal ions. (MVL)

  3. Rapid determination of quinine in soft drinks by reversed phase ion pair chromatography.

    PubMed

    Jeuring, H J; van den Hoeven, W; van Doorninck, P; ten Broeke, R

    1979-10-01

    Quinine can easily be determined in soft drinks by means of reversed-phase ion-pair chromatography. Sample preparation is not necessary. Quinine is detected by fluorescence and UV spectrophotometry by continuous monitoring of the column effluent. A rectilinear response is obtained in the concentration range of 20--100 mg/l. The complete assay procedure takes about 8 min.

  4. Analytical Determination of Fluoride Ion Using Gran's Semi-Antilog Plot.

    ERIC Educational Resources Information Center

    Barnhard, Ralph J.

    1983-01-01

    A quantitative determination for fluoride ion using a commercially available fluoride electrode is described. The procedure referred to as known-addition is employed with the data processed on Gran's Plot Paper. Background information, experimental procedures, and advantages/disadvantages of the method are discussed. (JN)

  5. Polarographic Determination of Composition and Thermodynamic Stability Constant of a Complex Metal Ion.

    ERIC Educational Resources Information Center

    Marin, Dolores; Mendicuti, Francisco

    1988-01-01

    Describes a laboratory experiment designed to encourage laboratory cooperation among individual undergraduate students or groups. Notes each student contributes results individually and the exchange of data is essential to obtain final results. Uses the polarographic method for determining complex metal ions. (MVL)

  6. Improvement of iron determination by use of ferroin-organic dye ion-association complexes.

    PubMed

    Knízek, M; Musilová, M

    1968-05-01

    Extraction of ion-associates of tris(1,10-phenanthroline)-iron(II) cation with monosulphonated azo dye anion into 1,2-dichloroethane is described. The method increases the sensitivity of the colorimetric determination of bivalent iron with 1,10-phenanthro-line.

  7. Analytical Determination of Fluoride Ion Using Gran's Semi-Antilog Plot.

    ERIC Educational Resources Information Center

    Barnhard, Ralph J.

    1983-01-01

    A quantitative determination for fluoride ion using a commercially available fluoride electrode is described. The procedure referred to as known-addition is employed with the data processed on Gran's Plot Paper. Background information, experimental procedures, and advantages/disadvantages of the method are discussed. (JN)

  8. Determination of Collision Cross Sections Using a Fourier Transform Electrostatic Linear Ion Trap Mass Spectrometer.

    PubMed

    Dziekonski, Eric T; Johnson, Joshua T; Lee, Kenneth W; McLuckey, Scott A

    2017-07-11

    Collision cross sections (CCSs) were determined from the frequency-domain linewidths in a Fourier transform electrostatic linear ion trap. With use of an ultrahigh-vacuum precision leak valve and nitrogen gas, transients were recorded as the background pressure in the mass analyzer chamber was varied between 4× 10(-8) and 7 × 10(-7) Torr. The energetic hard-sphere ion-neutral collision model, described by Xu and coworkers, was used to relate the recorded image charge to the CCS of the molecule. In lieu of our monoisotopically isolating the mass of interest, the known relative isotopic abundances were programmed into the Lorentzian fitting algorithm such that the linewidth was extracted from a sum of Lorentzians. Although this works only if the isotopic distribution is known a priori, it prevents ion loss, preserves the high signal-to-noise ratio, and minimizes the experimental error on our homebuilt instrument. Six tetraalkylammonium cations were used to correlate the CCS measured in the electrostatic linear ion trap with that measured by drift-tube ion mobility spectrometry, for which there was an excellent correlation (R (2) ≈ 0.9999). Although the absolute CCSs derived with our method differ from those reported, the extracted linear correlation can be used to correct the raw CCS. With use of [angiotensin II](2+) and reserpine, the corrected CCSs (334.9 ± 2.1 and 250.1 ± 0.5, respectively) were in good agreement with the reported ion mobility spectrometry CCSs (335 and 254.3, respectively). With sufficient signal-to-noise ratio, the CCSs determined are reproducible to within a fraction of a percent, comparable to the uncertainties reported on dedicated ion mobility instruments. Graphical Abstract ᅟ.

  9. Determination of Collision Cross Sections Using a Fourier Transform Electrostatic Linear Ion Trap Mass Spectrometer

    NASA Astrophysics Data System (ADS)

    Dziekonski, Eric T.; Johnson, Joshua T.; Lee, Kenneth W.; McLuckey, Scott A.

    2017-07-01

    Collision cross sections (CCSs) were determined from the frequency-domain linewidths in a Fourier transform electrostatic linear ion trap. With use of an ultrahigh-vacuum precision leak valve and nitrogen gas, transients were recorded as the background pressure in the mass analyzer chamber was varied between 4× 10-8 and 7 × 10-7 Torr. The energetic hard-sphere ion-neutral collision model, described by Xu and coworkers, was used to relate the recorded image charge to the CCS of the molecule. In lieu of our monoisotopically isolating the mass of interest, the known relative isotopic abundances were programmed into the Lorentzian fitting algorithm such that the linewidth was extracted from a sum of Lorentzians. Although this works only if the isotopic distribution is known a priori, it prevents ion loss, preserves the high signal-to-noise ratio, and minimizes the experimental error on our homebuilt instrument. Six tetraalkylammonium cations were used to correlate the CCS measured in the electrostatic linear ion trap with that measured by drift-tube ion mobility spectrometry, for which there was an excellent correlation (R 2 ≈ 0.9999). Although the absolute CCSs derived with our method differ from those reported, the extracted linear correlation can be used to correct the raw CCS. With use of [angiotensin II]2+ and reserpine, the corrected CCSs (334.9 ± 2.1 and 250.1 ± 0.5, respectively) were in good agreement with the reported ion mobility spectrometry CCSs (335 and 254.3, respectively). With sufficient signal-to-noise ratio, the CCSs determined are reproducible to within a fraction of a percent, comparable to the uncertainties reported on dedicated ion mobility instruments.

  10. Structural and dynamical properties of ionic liquids: the influence of ion size disparity.

    PubMed

    Spohr, H V; Patey, G N

    2008-08-14

    The influence of ion size disparity on structural and dynamical properties of ionic liquids is systematically investigated employing molecular dynamics simulations. Ion size ratios are varied over a realistic range (from 1:1 to 5:1) while holding other important molecular and system parameters fixed. In this way we isolate and identify effects that stem from size disparity alone. In strongly size disparate systems the larger species (cations in our model) tend to dominate the structure; the anion-anion distribution is largely determined by anion-cation correlations. The diffusion coefficients of both species increase, and the shear viscosity decreases with increasing size disparity. The influence of size disparity is strongest up to a size ratio of 3:1, then decreases, and by 5:1 both the diffusion coefficients and viscosity appear to be approaching limiting values. The conventional Stokes-Einstein expression for diffusion coefficients holds reasonably well for the cations but fails for the smaller anions as size disparity increases likely due to the neglect of strong anion-cation correlations. The electrical conductivity is not a simple monotonic function of size disparity; it first increases up to size ratios of 2:1, remains nearly constant until 3:1, then decreases such that the conductivities of the 1:1 and 5:1 systems are similar. This behavior is traced to the competing influences of ion diffusion (enhancing) and ion densities (reducing) on conductivities at constant packing fraction. The temperature dependence of the transport properties is examined for the 1:1 and 3:1 systems. In accord with experiment, the temperature dependence of all transport properties is well represented by the Vogel-Fulcher-Tammann equation. The dependence of the diffusion coefficients on the temperature/viscosity ratio is well described by the fractional Stokes-Einstein relation D proportional to (T/eta)(beta) with beta approximately = 0.8, consistent with the exponent observed for

  11. Determination of trace uranyl ion by thermoresponsive porphyrin-terminated polymeric sensor.

    PubMed

    Shu, Xiaowen; Wang, Yingjie; Zhang, Shuang; Huang, Li; Wang, Shuao; Hua, Daoben

    2015-01-01

    Uranyl ion exists at trace levels in the environment and can cause severe adverse effects to human health. Therefore, it is desirable to develop analytical methods that can determine the trace uranyl ion in aqueous medium. We report here a new method using a thermo-responsive polymeric fluorescent sensor. Specifically, 5,10,15,20-tetrakis(4-carboxyphenyl)-porphyrin terminated poly(N-isopropylacrylamide) (TCPP-PNIPAM) was synthesized by controlled free radical polymerization for the detection of uranyl ion. The maximum fluorescence intensity at ~ 658 nm of TCPP-PNIPAM increases with molecular weights and is also closely related to the temperature. The polymeric sensor is sensitive to pH (1.0 ~ 5.0) with a fast responsive time (~ 3 min). Under optimized experimental conditions, the sensor exhibits a stable response for uranyl ion with high selectivity over a concentration range from 1.0 × 10(-3) to 1.0 × 10(-7)mol/L. For the trace uranyl ion (such as 1.0 × 10(-8) or 10(-9)mol/L), the determination could be successfully achieved after concentrating 100 times by centrifugation above 32°C. The properties enable the polymeric sensor to have great potential for environmental application.

  12. Synthesis, structural characterization, and performance evaluation of resorcinol-formaldehyde (R-F) ion-exchange resin

    SciTech Connect

    Hubler, T.L.; Franz, J.A.; Shaw, W.J.; Bryan, S.A.; Hallen, R.T.; Brown, G.N.; Bray, L.A.; Linehan, J.C.

    1995-08-01

    The 177 underground storage tanks at the DOE`s Hanford Site contain an estimated 180 million tons of high-level radioactive wastes. It is desirable to remove and concentrate the highly radioactive fraction of the tank wastes for vitrification. Resorcinol-formaldehyde (R-F) resin, an organic ion-exchange resin with high selectivity and capacity for the cesium ion, which is a candidate ion-exchange material for use in remediation of tank wastes. The report includes information on the structure/function analysis of R-F resin and the synthetic factors that affect performance of the resin. CS-100, a commercially available phenol-formaldehyde (P-F) resin, and currently the baseline ion-exchanger for removal of cesium ion at Hanford, is compared with the R-F resin. The primary structural unit of the R-F resin was determined to consist of a 1,2,3,4-tetrasubstituted resorcinol ring unit while CS-100, was composed mainly of a 1,2,4-trisubstituted ring. CS-100 shows the presence of phenoxy-ether groups, and this may account for the much lower decontamination factor of CS-100 for cesium ion. Curing temperatures for the R-F resin were found to be optimal at 105--130C. At lower temperatures, insufficient curing, hence crosslinking, of the polymer resin occurs and selectivity for cesium drops. Curing at elevated temperatures leads to chemical degradation. Optimal particle size for R-F resin is in the range of 20--50 mesh-sized particles. R-F resin undergoes chemical degradation or oxidation which destroys ion-exchange sites. The ion-exchange sites (hydroxyl groups) are converted to quinones and ketones. CS-100, though it has much lower performance for cesium ion-exchange, is significantly more chemically stable than R-F resin. To gamma radiation, CS-100 is more radiolytically stable than R-F resin.

  13. Determining crystal structures through crowdsourcing and coursework.

    PubMed

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A; Cooper, Seth; Flatten, Jeff; Rogawski, David S; Koropatkin, Nicole M; Hailu, Tsinatkeab T; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S; Chapman, Matthew R; Sikkema, Andrew P; Skiba, Meredith A; Maloney, Finn P; Beinlich, Felix R M; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C A

    2016-09-16

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

  14. Determining crystal structures through crowdsourcing and coursework

    NASA Astrophysics Data System (ADS)

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Silveira Belo Nascimento Roque, Paulo Sergio; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K.; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

    2016-09-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

  15. Determining crystal structures through crowdsourcing and coursework

    PubMed Central

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Roque, Paulo Sergio Silveira Belo Nascimento; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

    2016-01-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality. PMID:27633552

  16. A protocol for the refinement of NMR structures using simultaneously pseudocontact shift restraints from multiple lanthanide ions.

    PubMed

    Sala, Davide; Giachetti, Andrea; Luchinat, Claudio; Rosato, Antonio

    2016-11-01

    The binding of paramagnetic metal ions to proteins produces a number of different effects on the NMR spectra of the system. In particular, when the magnetic susceptibility of the metal ion is anisotropic, pseudocontact shifts (PCSs) arise and can be easily measured. They constitute very useful restraints for the solution structure determination of metal-binding proteins. In this context, there has been great interest in the use of lanthanide(III) ions to induce PCSs in diamagnetic proteins, e.g. through the replacement native calcium(II) ions. By preparing multiple samples in each of which a different ion of the lanthanide series is introduced, it is possible to obtain multiple independent PCS datasets that can be used synergistically to generate protein structure ensembles (typically called bundles). For typical NMR-based determination of protein structure, it is necessary to perform an energetic refinement of such initial bundles to obtain final structures whose geometric quality is suitable for deposition in the PDB. This can be conveniently done by using restrained molecular dynamics simulations (rMD) in explicit solvent. However, there are no available protocols for rMD using multiple PCS datasets as part of the restraints. In this work, we extended the PCS module of the AMBER MD package to handle multiple datasets and tuned a previously developed protocol for NMR structure refinement to achieve consistent convergence with PCS restraints. Test calculations with real experimental data show that this new implementation delivers the expected improvement of protein geometry, resulting in final structures that are of suitable quality for deposition. Furthermore, we observe that also initial structures generated only with traditional restraints can be successfully refined using traditional and PCS restraints simultaneously.

  17. Determination of Ammonium Ion Using a Reagentless Amperometric Biosensor Based on Immobilized Alanine Dehydrogenase

    PubMed Central

    Tan, Ling Ling; Musa, Ahmad; Lee, Yook Heng

    2011-01-01

    The use of the enzyme alanine dehydrogenase (AlaDH) for the determination of ammonium ion (NH4+) usually requires the addition of pyruvate substrate and reduced nicotinamide adenine dinucleotide (NADH) simultaneously to effect the reaction. This addition of reagents is inconvenient when an enzyme biosensor based on AlaDH is used. To resolve the problem, a novel reagentless amperometric biosensor using a stacked methacrylic membrane system coated onto a screen-printed carbon paste electrode (SPE) for NH4+ ion determination is described. A mixture of pyruvate and NADH was immobilized in low molecular weight poly(2-hydroxyethyl methacrylate) (pHEMA) membrane, which was then deposited over a photocured pHEMA membrane (photoHEMA) containing alanine dehydrogenase (AlaDH) enzyme. Due to the enzymatic reaction of AlaDH and the pyruvate substrate, NH4+ was consumed in the process and thus the signal from the electrocatalytic oxidation of NADH at an applied potential of +0.55 V was proportional to the NH4+ ion concentration under optimal conditions. The stacked methacrylate membranes responded rapidly and linearly to changes in NH4+ ion concentrations between 10–100 mM, with a detection limit of 0.18 mM NH4+ ion. The reproducibility of the amperometrical NH4+ biosensor yielded low relative standard deviations between 1.4–4.9%. The stacked membrane biosensor has been successfully applied to the determination of NH4+ ion in spiked river water samples without pretreatment. A good correlation was found between the analytical results for NH4+ obtained from the biosensor and the Nessler spectrophotometric method. PMID:22163699

  18. Determination of ammonium ion using a reagentless amperometric biosensor based on immobilized alanine dehydrogenase.

    PubMed

    Tan, Ling Ling; Musa, Ahmad; Lee, Yook Heng

    2011-01-01

    The use of the enzyme alanine dehydrogenase (AlaDH) for the determination of ammonium ion (NH(4)(+)) usually requires the addition of pyruvate substrate and reduced nicotinamide adenine dinucleotide (NADH) simultaneously to effect the reaction. This addition of reagents is inconvenient when an enzyme biosensor based on AlaDH is used. To resolve the problem, a novel reagentless amperometric biosensor using a stacked methacrylic membrane system coated onto a screen-printed carbon paste electrode (SPE) for NH(4)(+) ion determination is described. A mixture of pyruvate and NADH was immobilized in low molecular weight poly(2-hydroxyethyl methacrylate) (pHEMA) membrane, which was then deposited over a photocured pHEMA membrane (photoHEMA) containing alanine dehydrogenase (AlaDH) enzyme. Due to the enzymatic reaction of AlaDH and the pyruvate substrate, NH(4)(+) was consumed in the process and thus the signal from the electrocatalytic oxidation of NADH at an applied potential of +0.55 V was proportional to the NH(4)(+) ion concentration under optimal conditions. The stacked methacrylate membranes responded rapidly and linearly to changes in NH(4)(+) ion concentrations between 10-100 mM, with a detection limit of 0.18 mM NH(4)(+) ion. The reproducibility of the amperometrical NH(4)(+) biosensor yielded low relative standard deviations between 1.4-4.9%. The stacked membrane biosensor has been successfully applied to the determination of NH(4)(+) ion in spiked river water samples without pretreatment. A good correlation was found between the analytical results for NH(4)(+) obtained from the biosensor and the Nessler spectrophotometric method.

  19. Centrality determination in heavy-ion collisions with the CBM experiment

    NASA Astrophysics Data System (ADS)

    Klochkov; Selyuzhenkov, I.; CBM collaboration

    2017-01-01

    The size and evolution of the medium created in a heavy-ion collision depends on collision geometry. Experimentally collisions can be characterized by the measured particle multiplicities around midrapidity or by the energy measured in the forward rapidity region, which is sensitive to the spectator fragments. In the Compressed Baryonic Matter (CBM) experiment at the future Facility for Antiproton and Ion Research (FAIR) the multiplicity of produced particles is measured with the silicon tracking system (STS). The projectile spectator detector (PSD) measures the energy of spectator fragments. We present the procedure of collision centrality determination in CBM and its performance using the PSD and the STS information.

  20. Determination of Cr(III) in chromic acid. Comparison of spectrophotometric and ion chromatographic methods

    SciTech Connect

    Smith, R.E.; Smith, C.H.

    1986-04-01

    Two methods have been developed for determining Cr(III) in chromic acid solutions. Both methods are based on the formation of a Cr-EDTA complex. The ion chromatographic method detects the Cr-EDTA as an anion using chemically suppressed conductivity. The spectrophotometric method detects the Cr-EDTA as a colored complex by measuring the absorbance at 540 nm. The conditions necessary for forming the Cr-EDTA complex are described. The results obtained by the spectrophotometric and ion chromatographic methods are compared. 15 refs., 5 figs., 1 tab.

  1. Stable compositions and geometrical structures of titanium oxide cluster cations and anions studied by ion mobility mass spectrometry

    NASA Astrophysics Data System (ADS)

    Ohshimo, Keijiro; Norimasa, Naoya; Moriyama, Ryoichi; Misaizu, Fuminori

    2016-05-01

    Geometrical structures of titanium oxide cluster cations and anions have been investigated by ion mobility mass spectrometry and quantum chemical calculations based on density functional theory. Stable cluster compositions with respect to collision induced dissociation were also determined by changing ion injection energy to an ion drift cell for mobility measurements. The TinO2n-1+ cations and TinO2n- anions were predominantly observed at high injection energies, in addition to TinO2n+ for cations and TinO2n+1- for anions. Collision cross sections of TinO2n+ and TinO2n+1- for n = 1-7, determined by ion mobility mass spectrometry, were compared with those obtained theoretically as orientation-averaged cross sections for the optimized structures by quantum chemical calculations. All of the geometrical structures thus assigned have three-dimensional structures, which are in marked contrast with other oxides of late transition metals. One-oxygen atom dissociation processes from TinO2n+ and TinO2n+1- by collisions were also explained by analysis of spin density distributions.

  2. Stable compositions and geometrical structures of titanium oxide cluster cations and anions studied by ion mobility mass spectrometry.

    PubMed

    Ohshimo, Keijiro; Norimasa, Naoya; Moriyama, Ryoichi; Misaizu, Fuminori

    2016-05-21

    Geometrical structures of titanium oxide cluster cations and anions have been investigated by ion mobility mass spectrometry and quantum chemical calculations based on density functional theory. Stable cluster compositions with respect to collision induced dissociation were also determined by changing ion injection energy to an ion drift cell for mobility measurements. The TinO2n-1 (+) cations and TinO2n (-) anions were predominantly observed at high injection energies, in addition to TinO2n (+) for cations and TinO2n+1 (-) for anions. Collision cross sections of TinO2n (+) and TinO2n+1 (-) for n = 1-7, determined by ion mobility mass spectrometry, were compared with those obtained theoretically as orientation-averaged cross sections for the optimized structures by quantum chemical calculations. All of the geometrical structures thus assigned have three-dimensional structures, which are in marked contrast with other oxides of late transition metals. One-oxygen atom dissociation processes from TinO2n (+) and TinO2n+1 (-) by collisions were also explained by analysis of spin density distributions.

  3. Structure and mechanism of formation of an important ion in doping control

    NASA Astrophysics Data System (ADS)

    Borges, Chad R.; Taccogno, James; Crouch, Dennis J.; Le, Ly; Truong, Thanh N.

    2005-12-01

    An ion with m/z 143 serves as a biomarker that is often continuously monitored in urine samples undergoing screening by electron ionization gas chromatography/mass spectrometry (EI GC/MS) for banned anabolic agents. The