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. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. Determination of gas phase protein ion densities via ion mobility analysis with charge reduction.

    PubMed

    Maisser, Anne; Premnath, Vinay; Ghosh, Abhimanyu; Nguyen, Tuan Anh; Attoui, Michel; Hogan, Christopher J

    2011-12-28

    We use a charge reduction electrospray (ESI) source and subsequent ion mobility analysis with a differential mobility analyzer (DMA, with detection via both a Faraday cage electrometer and a condensation particle counter) to infer the densities of single and multiprotein ions of cytochrome C, lysozyme, myoglobin, ovalbumin, and bovine serum albumin produced from non-denaturing (20 mM aqueous ammonium acetate) and denaturing (1 : 49.5 : 49.5, formic acid : methanol : water) ESI. Charge reduction is achieved through use of a Po-210 radioactive source, which generates roughly equal concentrations of positive and negative ions. Ions produced by the source collide with and reduce the charge on ESI generated drops, preventing Coulombic fissions, and unlike typical protein ESI, leading to gas-phase protein ions with +1 to +3 excess charges. Therefore, charge reduction serves to effectively mitigate any role that Coulombic stretching may play on the structure of the gas phase ions. Density inference is made via determination of the mobility diameter, and correspondingly the spherical equivalent protein volume. Through this approach it is found that for both non-denaturing and denaturing ESI-generated ions, gas-phase protein ions are relatively compact, with average densities of 0.97 g cm(-3) and 0.86 g cm(-3), respectively. Ions from non-denaturing ESI are found to be slightly more compact than predicted from the protein crystal structures, suggesting that low charge state protein ions in the gas phase are slightly denser than their solution conformations. While a slight difference is detected between the ions produced with non-denaturing and denaturing ESI, the denatured ions are found to be much more dense than those examined previously by drift tube mobility analysis, in which charge reduction was not employed. This indicates that Coulombic stretching is typically what leads to non-compact ions in the gas-phase, and suggests that for gas phase

  3. 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)

  4. 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.

  5. 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.

  6. 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).

  7. 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.

  8. 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

  9. Structural determination of zinc dithiophosphates in lubricating oils by gas chromatography-mass spectrometry with electron impact and electron-capture negative ion chemical ionization.

    PubMed

    Becchi, M; Perret, F; Carraze, B; Beziau, J F; Michel, J P

    2001-01-05

    Pentafluorobenzyl ester derivatives were used to identify zinc dialkyldithiophosphates and diaryldithiophosphates antiwear engine oil additives by GC-electron impact ionization (EI) MS and GC-electron-capture negative ion chemical ionization (ECNCI) MS analysis. GC-EI-MS of the dialkyldithiophosphate-pentafluorobenzyl derivatives afforded characteristic fragment ions corresponding to the cleavage of one and two alkyl radicals. In most cases, information was only obtained on one alkyl chain. Additional and complete information was obtained with retention time indices using synthetic derivatives and with GC-ECNCI-MS analysis. ECNCI afforded characteristic dithiophosphate anions which allowed the determination of the total number of carbon atoms in the alkyl radicals. The diastereoisomer mixtures of 2-hydroxy-sec.-alkyl radicals were completely separated on GC analysis.

  10. 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.

  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. 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.

  13. 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

  14. 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.

  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. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. [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%.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

    2017-03-17

    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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  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. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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

  11. 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

  12. 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.

  13. 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.

  14. 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.

  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. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  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. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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 ...

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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.…

  7. 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.

  8. 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.

  9. 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.

  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

    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.

  12. 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

  13. 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.

  14. 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).

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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

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

    NASA Astrophysics Data System (ADS)

    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

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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.

  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. 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.

  11. 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.

  12. 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.

  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. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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+).

  5. 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)

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  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. 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

  17. 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...

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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).

  6. 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.

  7. 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 ...

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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

  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. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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)

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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.

  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. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  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. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  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. 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

  16. 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.

  17. 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

  18. 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.

  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. 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%.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  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. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. 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…

  7. 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.

  8. 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.

  9. 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.

  10. 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)

  11. 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)

  12. 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.

  13. 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

  14. 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.

  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. 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

  17. 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

  18. 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.

  19. Determination of molybdenum (VI) in sea water with preliminary concentration by the method of ion flotation

    SciTech Connect

    Andreeva, I. Yu.; Drapchinskaya, O.L.; Lebedeva, L.I.

    1985-10-01

    The purpose of this paper is to assess the feasibility of using the method of ion flotation for the concentration of microamounts of molybdenum (VI) during determination in sea water. The ion flotation method is used for the purification of industrial sewage from the ions of nonferrous metals, including molybdenum (VI) with its content of up to 50 mg/liter. A 1.10/sup -4/M solution of sodium molybdate in 0.1M NaOH was used. The effect of different factors on the ion flotation process of molybdenum (VI) was investigated: pH of the solution, flotation times, concentrations of surface-active substances (SAS), molybdenum (IV), extraneous salts. Data presented show that the ion flotation method in conjunction with the photometric method of determining molybdenum with brompyrogallol red (BPR) and cetylpridinium chloride (CP) (limit of detection 0.02 micrograms/liter) allows the content of molybdenum (VI) in sea water to be established with sufficient reliability and reproducibility.

  20. 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

  1. 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.

  2. Structural Determination of Biomolecules in Microfluidic Systems

    NASA Astrophysics Data System (ADS)

    Butler, John C.; Menard, Etienne; Rogers, John A.; Wong, Gerard C. L.

    2004-03-01

    Supramolecular biological complexes are often too large to be crystallized for structural studies. Here, we explore the use of microfluidic arrays to order a model self-assembled cytoskeletal system. Filamentous actin (F-actin) is a negatively charged protein rod and is a key structural component in the eukaryotic cytoskeleton. In this context, F-actin can self-assemble with actin binding proteins (ABP) in a highly regulated manner to dynamically form structures for a wide range of biomechanical functions. In this work, we will systematically study the action of 3 types of actin binding proteins (a-actinin, fimbrin, cofilin) on the self-assembled structures of F-actin that have been aligned in microfluidic arrays.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Structural determinants of TRIM protein function.

    PubMed

    Esposito, Diego; Koliopoulos, Marios G; Rittinger, Katrin

    2017-02-08

    Tripartite motif (TRIM) proteins constitute one of the largest subfamilies of Really Interesting New Gene (RING) E3 ubiquitin ligases and contribute to the regulation of numerous cellular activities, including innate immune responses. The conserved TRIM harbours a RING domain that imparts E3 ligase activity to TRIM family proteins, whilst a variable C-terminal region can mediate recognition of substrate proteins. The knowledge of the structure of these multidomain proteins and the functional interplay between their constituent domains is paramount to understanding their cellular roles. To date, available structural information on TRIM proteins is still largely restricted to subdomains of many TRIMs in isolation. Nevertheless, applying a combination of structural, biophysical and biochemical approaches has recently allowed important progress to be made towards providing a better understanding of the molecular features that underlie the function of TRIM family proteins and has uncovered an unexpected diversity in the link between self-association and catalytic activity.

  9. Depth distribution of boron determined by slow neutron induced lithium ion emission

    NASA Astrophysics Data System (ADS)

    Chen-Mayer, Huaiyu H.; Lamaze, George P.

    1998-02-01

    Neutron Depth Profiling (NDP) has been established as a non-destructive technique to determine the near surface distribution of light elements, particularly boron. By analyzing the residual energy spectrum of the emitted particles of known initial energy as a result of nuclear capture within the target material, information about the site and amount of the reactions can be deduced. In the event of 10B neutron capture, an alpha particle (1473 keV) and an excited 7Li ion (840 keV) are emitted, both conveying the same information. However, because the Li ion has a greater charge, the stopping power in a given matrix is higher than that for the alpha particle. Consequently, for boron near the surface, the location of the origin of the emission can be determined with better depth resolution. At the NIST NDP facility, routine analysis using the alpha particle has been established earlier. This paper reports the progress of using the 7Li ion stopping power to determine the boron depth distribution in the near surface of several matrices. This study has been performed on semiconductor device-related systems - boron in silicon glass, and carbon matrices. Various factors affecting the depth resolution are assessed when comparing the analysis of the alpha particle with that of the 7Li ion.

  10. Structural basis for potentiation by alcohols and anaesthetics in a ligand-gated ion channel

    PubMed Central

    Sauguet, Ludovic; Howard, Rebecca J.; Malherbe, Laurie; Lee, Ui S.; Corringer, Pierre-Jean; Harris, R. Adron; Delarue, Marc

    2014-01-01

    Ethanol alters nerve signalling by interacting with proteins in the central nervous system, particularly pentameric ligand-gated ion channels. A recent series of mutagenesis experiments on Gloeobacter violaceus ligand-gated ion channel, a prokaryotic member of this family, identified a single-site variant that is potentiated by pharmacologically relevant concentrations of ethanol. Here we determine crystal structures of the ethanol-sensitized variant in the absence and presence of ethanol and related modulators, which bind in a transmembrane cavity between channel subunits and may stabilize the open form of the channel. Structural and mutagenesis studies defined overlapping mechanisms of potentiation by alcohols and anaesthetics via the inter-subunit cavity. Furthermore, homology modelling show this cavity to be conserved in human ethanol-sensitive glycine and GABA(A) receptors, and to involve residues previously shown to influence alcohol and anaesthetic action on these proteins. These results suggest a common structural basis for ethanol potentiation of an important class of targets for neurological actions of ethanol. PMID:23591864

  11. Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules.

    PubMed

    Sun, Li-Zhen; Zhang, Dong; Chen, Shi-Jie

    2017-03-15

    In addition to continuous rapid progress in RNA structure determination, probing, and biophysical studies, the past decade has seen remarkable advances in the development of a new generation of RNA folding theories and models. In this article, we review RNA structure prediction models and models for ion-RNA and ligand-RNA interactions. These new models are becoming increasingly important for a mechanistic understanding of RNA function and quantitative design of RNA nanotechnology. We focus on new methods for physics-based, knowledge-based, and experimental data-directed modeling for RNA structures and explore the new theories for the predictions of metal ion and ligand binding sites and metal iondependent RNA stabilities. The integration of these new methods with theories about the cellular environment effects in RNA folding, such as molecular crowding and cotranscriptional kinetic effects, may ultimately lead to an all-encompassing RNA folding model. Expected final online publication date for the Annual Review of Biophysics Volume 46 is May 20, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  12. Determinants of Protein Elution Rates from Preparative Ion-Exchange Adsorbents

    PubMed Central

    Angelo, James M.; Lenhoff, Abraham M.

    2016-01-01

    The rate processes involved in elution in preparative chromatography can affect both peak resolution and hence selectivity as well as practical factors such as facility fit. These processes depend on the physical structure of the adsorbent particles, the amount of bound solute, the solution conditions for operation or some combination of these factors. Ion-exchange adsorbents modified with covalently attached or grafted polymer layers have become widely used in preparative chromatography. Their often easily accessible microstructures offer substantial binding capacities for biomolecules, but elution has sometimes been observed to be undesirably slow. In order to determine which physicochemical phenomena control elution behavior, commercially available cellulosic, dextran-grafted and unmodified agarose materials were characterized here by their uptake and elution profiles at various conditions, including different degrees of loading. Elution data were analyzed under the assumption of purely diffusion-limited control, including the role of pore structure properties such as porosity and tortuosity. In general, effective elution rates decreased with the reduction of accessible pore volume, but differences among different proteins indicated the roles of additional factors. Additional measurements and analysis, including the use of confocal laser scanning microscopy to observe elution within single chromatographic particles, indicated the importance of protein association within the particle during elution. The use of protein stabilizing agents was explored in systems presenting atypical elution behavior, and L-arginine and disaccharide excipients were shown to alleviate the effects for one protein, lysozyme, in the presence of sodium chloride. Incorporation of these excipients into eluent buffer gave rise to faster elution and significantly lower pool volumes in elution from polymer-modified adsorbents. PMID:26948763

  13. Determinants of protein elution rates from preparative ion-exchange adsorbents.

    PubMed

    Angelo, James M; Lenhoff, Abraham M

    2016-04-01

    The rate processes involved in elution in preparative chromatography can affect both peak resolution and hence selectivity as well as practical factors such as facility fit. These processes depend on the physical structure of the adsorbent particles, the amount of bound solute, the solution conditions for operation or some combination of these factors. Ion-exchange adsorbents modified with covalently attached or grafted polymer layers have become widely used in preparative chromatography. Their often easily accessible microstructures offer substantial binding capacities for biomolecules, but elution has sometimes been observed to be undesirably slow. In order to determine which physicochemical phenomena control elution behavior, commercially available cellulosic, dextran-grafted and unmodified agarose materials were characterized here by their elution profiles at various conditions, including different degrees of loading. Elution data were analyzed under the assumption of purely diffusion-limited control, including the role of pore structure properties such as porosity and tortuosity. In general, effective elution rates decreased with the reduction of accessible pore volume, but differences among different proteins indicated the roles of additional factors. Additional measurements and analysis, including the use of confocal laser scanning microscopy to observe elution within single chromatographic particles, indicated the importance of protein association within the particle during elution. The use of protein stabilizing agents was explored in systems presenting atypical elution behavior, and l-arginine and disaccharide excipients were shown to alleviate the effects for one protein, lysozyme, in the presence of sodium chloride. Incorporation of these excipients into eluent buffer gave rise to faster elution and significantly lower pool volumes in elution from polymer-modified adsorbents.

  14. Determination of relative sensitivity factors during secondary ion sputtering of silicate glasses by Au+, Au2+ and Au3+ ions.

    PubMed

    King, Ashley; Henkel, Torsten; Rost, Detlef; Lyon, Ian C

    2010-01-01

    In recent years, Au-cluster ions have been successfully used for organic analysis in secondary ion mass spectrometry. Cluster ions, such as Au(2)(+) and Au(3)(+), can produce secondary ion yield enhancements of up to a factor of 300 for high mass organic molecules with minimal sample damage. In this study, the potential for using Au(+), Au(2)(+) and Au(3)(+) primary ions for the analysis of inorganic samples is investigated by analyzing a range of silicate glass standards. Practical secondary ion yields for both Au(2)(+) and Au(3)(+) ions are enhanced relative to those for Au(+), consistent with their increased sputter rates. No elevation in ionization efficiency was found for the cluster primary ions. Relative sensitivity factors for major and trace elements in the standards showed no improvement in quantification with Au(2)(+) and Au(3)(+) ions over the use of Au(+) ions. Higher achievable primary ion currents for Au(+) ions than for Au(2)(+) and Au(3)(+) allow for more precise analyses of elemental abundances within inorganic samples, making them the preferred choice, in contrast to the choice of Au(2)(+) and Au(3)(+) for the analysis of organic samples. The use of delayed secondary ion extraction can also boost secondary ion signals, although there is a loss of overall sensitivity.

  15. Contemporary Methodology for Protein Structure Determination.

    ERIC Educational Resources Information Center

    Hunkapiller, Michael W.; And Others

    1984-01-01

    Describes the nature and capabilities of methods used to characterize protein and peptide structure, indicating that they have undergone changes which have improved the speed, reliability, and applicability of the process. Also indicates that high-performance liquid chromatography and gel electrophoresis have made purifying proteins and peptides a…

  16. Electron Diffraction Determination of Nanoscale Structures

    SciTech Connect

    Parks, Joel H

    2013-03-01

    Dominant research results on adsorption on gold clusters are reviewed, including adsorption of H{sub 2}O and O{sub 2} on gold cluster cations and anions, kinetics of CO adsorption to middle sized gold cluster cations, adsorption of CO on Au{sub n}{sup +} with induced changes in structure, and H{sub 2}O enhancement of CO adsorption.

  17. Determination of ammonium in a buddingtonite sample by ion-chromatography

    USGS Publications Warehouse

    Klock, P.R.; Lamothe, P.J.

    1986-01-01

    An ion-chromatographic method for the direct determination of ammonium, potassium, and sodium in geologic materials is described. Samples are decomposed with a mixture of hydrofluoric and hydrochloric acids in a sealed polycarbonate bottle heated in a microwave oven. The ion-chromatograph separates the cations and determines them by conductivity measurement. The ammonium concentrations thus determined have been verified by use of an ammonia-specific electrode. A total of 32 analyses of ammonium salts by both techniques showed an average error of -4%, with a relative standard deviation (RSD) of 6%. The ammonium concentrations found in a buddingtonite sample had an RSD of 2.2% and their mean agreed with that obtained by the Kjeldahl method. By use of the prescribed dilution of the sample, detection limits of 0.1% can be achieved for all three cations. ?? 1986.

  18. Potentiometric Determination of Phytic Acid and Investigations of Phytate Interactions with Some Metal Ions.

    PubMed

    Marolt, Gregor; Pihlar, Boris

    2015-01-01

    Determination of correct amount (concentration) of phytic acid is of vital importance when dealing with protonation and/or metal complexation equilibria. A novel approach for precise and reliable assay of phytic acid, based on the difference between end points by potentiometric titration, has been presented. Twelve phytic acid protons are classified into three groups of acidity, which enables detection of 2 to 3 distinct equivalent points (EPs) depending on experimental conditions, e.g. counter-ion concentration. Using the differences between individual EPs enables correct phytate determination as well as identification of potential contamination and/or determination of initial protonation degree. Impact of uncertainty of phytate amount on the calculation of protonation constants has been evaluated using computer simulation program (Hyperquad2013). With the analysis of titration curves different binding sites on phytate ligand have been proposed for complexation of Ca2+ and Fe3+ ions.

  19. 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 ion is known to arise from trimethylsilyl (TMS)-derivatized synthetic 17-hydroxy, 17-methyl steroids. The purpose of this work was to characterize, in detail, the origin(s), structure(s), and mechanism(s) of formation of such ions with m/z 143. High resolution mass spectrometry (HRMS) data revealed the elemental composition of the D-ring derived m/z 143 ion to be C7H15OSi. Analysis of dihydrotestosterone (DHT) and its 2-methyl substituted analog dromostanolone by HRMS revealed that an elementally equivalent ion of m/z 143 could be derived from the A-ring of TMS-derivatized 3-keto-enol steroids demonstrating that an abnormally intense peak in the m/z 143 extracted ion chromatogram of urine samples undergoing screening for banned anabolic agents does not necessarily indicate the presence of a 17-hydroxy, 17-methyl steroid. To gain information on ion structure, breakdown curves for the most abundant product ions of the m/z 143 ion were generated using both native and perdeutero-TMS derivatives, providing structures for second, third, and fourth generation product ions. An EI-mass spectrum of [16,16,17-2H3]-DHT (DHT-d3) demonstrated that one of the C-16 hydrogen atoms is removed prior to the formation of an ion that is highly analogous to the ion with m/z 143 strongly suggesting, in accord with all other evidence, one particular fragmentation pathway and resulting product: a resonance stabilized 3-(O-trimethylsilyl)but-1-ene ion.

  20. Vascular structure determines pulmonary blood flow distribution

    NASA Technical Reports Server (NTRS)

    Hlastala, M. P.; Glenny, R. W.

    1999-01-01

    Scientific knowledge develops through the evolution of new concepts. This process is usually driven by new methodologies that provide observations not previously available. Understanding of pulmonary blood flow determinants advanced significantly in the 1960s and is now changing rapidly again, because of increased spatial resolution of regional pulmonary blood flow measurements.

  1. Effect of GeO2 content on structural and spectroscopic properties of antimony glasses doped with Sm3+ ions

    NASA Astrophysics Data System (ADS)

    Zmojda, J.; Kochanowicz, M.; Miluski, P.; Leśniak, M.; Sitarz, M.; Pisarski, W.; Pisarska, J.; Dorosz, D.

    2016-12-01

    Antimony-based glasses with different germanium oxide content doped with Sm3+ ions have been developed. On the basis of decomposition of absorption bands (FTIR) in the mid infrared region, was determined that antimony and germanium ions are the glass-forming ions, setting up the lattice of fabricated glasses. The effect of GeO2/Sb2O3 ratio in fabricated glass doped with samarium ions on thermal, structural and luminescent properties was also investigated. Characteristic bright reddish-orange luminescence from the 4G5/2 state to the lower lying levels 6HJ with J = 5/2, 7/2, 9/2 and 11/2 with maximum intensity at the wavelength of 603 nm originating from 4G5/2 → 6H7/2 transition was observed. The asymmetry nature of molecular structure around samarium ion have been determined from intensity ratio between 4G5/2 → 6H9/2 (ED) and 4G5/2 → 6H5/2 (MD) transitions. An introduction of GeO2 to the antimony glass results in the increasing of 4G5/2 lifetime and decreasing of the orange-to-red intensity ratio, which is are related to reduction of non-briding oxygens.

  2. [Determination of choline chloride and trimethylamine in feedstuff by ion chromatography].

    PubMed

    Ding, Yongsheng; Mou, Shifen

    2004-03-01

    A method was developed for the determination of choline chloride (CC) and trimethylamine (TMA) in feedstuff by ion chromatography. The separation of eight ions including Li+, Na+, NH4+, K+, TMA, choline, Mg2+ and Ca2+ was achieved by using an IonPac CS12 column (250 mm x 4 mm i.d.) and 8.5 mmol/L H2SO4 as eluent. Cations were detected by suppressed conductivity detection. The limits of detection of CC and TMA were 0.1 mg/L and 0.05 mg/L, respectively. The method recoveries were between 99.25% and 102.5%. The method was sensitive, selective, and simple. The results of sample analysis showed that the method was very useful for the authenticating of choline chloride in feedstuffs.

  3. Method of determining the x-ray limit of an ion gauge

    DOEpatents

    Edwards, Jr., David; Lanni, Christopher P.

    1981-01-01

    An ion gauge having a reduced "x-ray limit" and means for measuring that limit. The gauge comprises an ion gauge of the Bayard-Alpert type having a short collector and having means for varying the grid-collector voltage. The "x-ray limit" (i.e. the collector current resulting from x-rays striking the collector) may then be determined by the formula: ##EQU1## where: I.sub.x ="x-ray limit", I.sub.l and I.sub.h =the collector current at the lower and higher grid voltage respectively; and, .alpha.=the ratio of the collector current due to positive ions at the higher voltage to that at the lower voltage.

  4. Achieving High Resolution Ion Mobility Separations Using Traveling Waves in Compact Multiturn Structures for Lossless Ion Manipulations

    PubMed Central

    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.

    2017-01-01

    We report on ion mobility (IM) separations achievable using traveling waves (TW) in a Structures for Lossless Ion Manipulations (SLIM) module having a 44 cm path length and 16 90° turns. The performance of the TW-SLIM module was evaluated for ion transmission and IM 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 module demonstrated highly robust performance and, even with 16 closely spaced turns, achieving IM resolution performance and ion transmission comparable to a similar straight path module. We found an IM peak capacity of ~31 and peak generation rate of 780 s−1 for TW speeds of ~80 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 IM-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 IM resolution via greatly extended ion path lengths and using compact serpentine designs. PMID:27479234

  5. Nanocomposites with embedded structures for lithium-ion batteries

    NASA Astrophysics Data System (ADS)

    Yang, Zichao

    Lithium-ion batteries (LIBs) have been widely employed in portable electronics and are rapidly expanding into emerging markets such as hybrid and electric vehicles and potentially electric grid storage. These new opportunities create new challenges for LIBs and further improvement of specific energy, cycling performance and rate capability are required. A major strategy in performance enhancement for the electrode materials involves the creation of carbon composites to provide mechanical buffering of active material and to improve electrical conductivity. In the current work, a platform is developed for creating functional hybrid materials by copolymerization of organic molecules and inorganic compounds followed by thermal pyrolysis, and the approach yields nanostructured composites in which nanoparticles are uniformly embedded in a porous, partially graphitic carbon matrix. Depending upon the chemistry of the starting materials, nanocomposites with embedded structures created using the approach are attractive as anode or cathode materials for next-generation rechargeable lithium battery systems. The platform is very versatile and through ex situ conversion or utilization of multiple precursors, can be applied to various classes of materials including metal oxides (single or mixed), metals, metal sulfides, alloys, metalloids, phosphates, etc. The approach also lends itself to the development of scalable processes for production of nanostructured battery materials. Mechanistic analysis was performed and reveals that the performance enhancement of the embedded nanocomposite configuration is mainly brought about by the mechanical buffering effect offered by the carbon matrix. The active material loading was shown to be an important factor in the design of the composites as electrode materials. In addition to the polymerization-based approach, other in situ methods such as one based on spray pyrolysis are also explored and demonstrate the versatility of the in situ

  6. Anode-electrolyte double-layer of Li-ion batteries: Structure and Li-ion intercalation

    NASA Astrophysics Data System (ADS)

    Wipf, David O.; Abou Hamad, Ibrahim; Rikvold, Per Arne; Novotny, Mark A.

    2011-03-01

    The electrochemical double-layer structure plays an important role in Li-ion intercalation during charging of Li-ion batteries with a graphite anode. In our recent Molecular Dynamics studies of a proposed accelerated charging method [I. Abou Hamad~et al., Phys. Chem. Chem. Phys. 12, 2740-2743 (2010)], we notice that ethylene carbonate and propylene carbonate molecules of the electrolyte assemble themselves in a preferred orientation at the electrode-electrolyte interface. On the other hand, they are randomly oriented in the bulk electrolyte. We show that the structure of the double layer is affected by the intercalating Li-ion: while the dipole moments of double-layer molecules far from the intercalating Li-ion point toward the graphite sheets of the anode, they point away from the intercalation site close to the intercalating Li-ion. This observation should contribute to a better understanding of the intercalation process. This work was supported in part by NSF Grant No. DMR-0802288.

  7. Simultaneous spectrophotometric determination of phosphate and silicate ions in river water by using ion-exclusion chromatographic separation and post-column derivatization.

    PubMed

    Nakatani, Nobutake; Kozaki, Daisuke; Masuda, Wakako; Nakagoshi, Nobukazu; Hasebe, Kiyoshi; Mori, Masanobu; Tanaka, Kazuhiko

    2008-06-30

    The simultaneous spectrophotometric determination of phosphate and silicate ions in river water was examined by using ion-exclusion chromatography and post-column derivatization. Phosphate and silicate ions were separated by the ion-exclusion column packed with a polymethacrylate-based weakly acidic cation-exchange resin in the H(+)-form (TSKgel Super IC-A/C) by using ultra pure water as an eluent. After the post-column derivatization with molybdate and ascorbic acid, so-called molybdenum-blue, both ions were determined simultaneously by spectrophotometry. The effects of sulfuric acid, sodium molybdate and ascorbic acid concentrations and reaction coil length, which have relation to form the reduced complexes of molybdate and ions, on the detector response for phosphate and silicate ions were investigated. Under the optimized conditions (color-forming reactant, 50 mM sulfuric acid-10 mM sodium molybdate; reducing agent, 50 mM ascorbic acid; reaction coil length, 6 m), the calibration curves of phosphate and silicate ions were linear in the range of 50-2000 microg L(-1) as P and 250-10,000 microg L(-1) as Si. This method was successfully applied to water quality monitoring of Kurose-river watershed and it suggested that the effluent from a biological sewage treatment plant was significant source of phosphate ion in Kurose-river water.

  8. Absolute infrared vibrational band intensities of molecular ions determined by direct laser absorption spectroscopy in fast ion beams

    SciTech Connect

    Keim, E.R.; Polak, M.L.; Owrutsky, J.C.; Coe, J.V.; Saykally, R.J. )

    1990-09-01

    The technique of direct laser absorption spectroscopy in fast ion beams has been employed for the determination of absolute integrated band intensities ({ital S}{sup 0}{sub {ital v}}) for the {nu}{sub 3} fundamental bands of H{sub 3}O{sup +} and NH{sup +}{sub 4}. In addition, the absolute band intensities for the {nu}{sub 1} fundamental bands of HN{sup +}{sub 2} and HCO{sup +} have been remeasured. The values obtained in units of cm{sup {minus}2} atm{sup {minus}1} at STP are 1880(290) and 580(90) for the {nu}{sub 1} fundamentals of HN{sup +}{sub 2} and HCO{sup +}, respectively; and 4000(800) and 1220(190) for the {nu}{sub 3} fundamentals of H{sub 3}O{sup +} and NH{sup +}{sub 4}, respectively. Comparisons with {ital ab} {ital initio} results are presented.

  9. Effect of ion irradiation on the surface, structural and mechanical properties of brass

    NASA Astrophysics Data System (ADS)

    Ahmad, Shahbaz; Bashir, Shazia; Ali, Nisar; Umm-i-Kalsoom; Yousaf, Daniel; Faizan-ul-Haq; Naeem, Athar; Ahmad, Riaz; Khlaeeq-ur-Rahman, M.

    2014-04-01

    Modifications to the surface, structural and mechanical properties of brass after ion irradiation have been investigated. Brass targets were bombarded by carbon ions of 2 MeV energy from a Pelletron linear accelerator for various fluences ranging from 56 × 1012 to 26 × 1013 ions/cm2. A scanning electron microscope and X-ray diffractometer were utilized to analyze the surface morphology and crystallographic structure respectively. To explore the mechanical properties e.g., yield stress, ultimate tensile strength and microhardness of irradiated brass, an universal tensile testing machine and Vickers microhardness tester were used. Scanning electron microscopy results revealed an irregular and randomly distributed sputter morphology for a lower ion fluence. With increasing ion fluence, the incoherently shaped structures were transformed into dendritic structures. Nano/micro sized craters and voids, along with the appearance of pits, were observed at the maximum ion fluence. From X-ray diffraction results, no new phases were observed to be formed in the brass upon irradiation. However, a change in the peak intensity and higher and lower angle shifting were observed, which represents the generation of ion-induced defects and stresses. Analyses confirmed modifications in the mechanical properties of irradiated brass. The yield stress, ultimate tensile strength and hardness initially decreased and then increased with increasing ion fluence. The changes in the mechanical properties of irradiated brass are well correlated with surface and crystallographic modifications and are attributed to the generation, augmentation, recombination and annihilation of the ion-induced defects.

  10. Structurally colored biopolymer thin films for detection of dissolved metal ions in aqueous solution

    NASA Astrophysics Data System (ADS)

    Cathell, Matthew David

    Natural polymers, such as the polysaccharides alginate and chitosan, are noted sorbents of heavy metals. Their polymer backbone structures are rich in ligands that can interact with metal ions through chelation, electrostatics, ion exchange and nonspecific mechanisms. These water-soluble biopolymer materials can be processed into hydrogel thin films, creating high surface area interfaces ideal for binding and sequestering metal ions from solution. By virtue of their uniform nanoscale dimensions (with thicknesses smaller than wavelengths of visible light) polymer thin films exhibit structure-based coloration. This phenomenon, frequently observed in nature, causes the transparent and essentially colorless films to reflect light in a wide array of colors. The lamellar film structures act as one-dimensional photonic crystals, allowing selective reflection of certain wavelengths of light while minimizing other wavelengths by out-of-phase interference. The combination of metal-binding and reflective properties make alginate and chitosan thin films attractive candidates for analyte sensing. Interactions with metal ions can induce changes in film thicknesses and refractive indices, thus altering the path of light reflected through the film. Small changes in dimensional or optical properties can lead to shifts in film color that are perceivable by the unaided eye. These thin films offer the potential for optical sensing of toxic dissolved materials without the need for instrumentation, external power or scientific expertise. With the use of a spectroscopic ellipsometer and a fiber optic reflectance spectrometer, the physical and optical characteristics of biopolymer thin films have been characterized in response to 50 ppm metal ion solutions. It has been determined that metal interactions can lead to measurable changes in both film thicknesses and effective refractive indices. The intrinsic response behaviors of alginate and chitosan, as well as the responses of modified

  11. Rapid determination of nicotine in urine by direct thermal desorption ion trap mass spectrometry

    SciTech Connect

    Wise, M.B.; Ilgner, R.H.; Guerin, M.R.

    1990-01-01

    The measurement of nicotine and cotinine in physiological fluids (urine, blood serum, and saliva) is widely used as a means of assessing human exposure to environmental tobacco smoke (ETS). Although numerous analytical methods exist for these measurements, they generally involve extensive sample preparation which increases cost and decreases sample throughput. We report the use of thermal desorption directly into an ion trap mass spectrometer (ITMS) for the rapid determination of nicotine and cotinine in urine. A 1{mu}L aliquot of urine is injected into a specially designed inlet and flash vaporized directly into an ITMS through an open-split capillary restrictor interface. Isobutane chemical ionization is used to generate (M+H){sup +} ions of the analytes and collision induced dissociation is used to generate characteristic fragment ions which are used to confirm their identity. Quantification is achieved by integrating the ion current for the characteristic ions and comparing with an external working curve. Detection limits are approximately 50 pg per analyte and the sample turnaround time is approximately 3 minutes without the need for extensive sample preparation. 12 refs., 5 figs.

  12. Determination of optimum structure of backpropagation networks

    NASA Astrophysics Data System (ADS)

    Phien, Huynh N.; Sureerattanan, Songyot

    2000-10-01

    The paper proposes the use of the Baysian Information Criterion (BIC), along with an algorithm to systematically select the appropriate structure of the backpropagation (BP) network for a given set of data. Simulation results with hydrological and economic data show that the algorithm performs very satisfactorily. Moreover, it compares with the method of Daqi and Shouyi for one hidden layer network and it is also used for the networks with more than one hidden layer.

  13. Solid Electrolytes: Alkali-Ion Transport in Skeleton Structures

    DTIC Science & Technology

    1976-06-30

    side if necessary and identify by block number) solid electrolytes alkali -ion transport sodium -sulfur batteries fast -ion transport O ABSTRACT...molten Na 2 S4 for 10 days at 400’C indicated chemical stability, similar testing i-1 molten sodium was initiated, and it has been established that...tests under dynamic conditions are necessary before long-term stability of tile material can be established. Tests for stability in molten sodium have

  14. Structural Modification of Nanocrystalline Ceria by Ion Beams

    SciTech Connect

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

    2011-05-25

    Using energetic ions, we have demonstrated effective modification of grain size in nanocrystalline ceria in the critical region for controlling exceptional size-dependent electronicionic conductivity. The grain size increases and follows an exponential law as a function of ion fluence that increases with temperature, while the cubic phase is stable under the irradiation. The unique self-healing response of radiation damage at grain boundaries is utilized to control the grain size at the nanoscale.

  15. Structure and properties of solid polymer electrolyte based on chitosan and ZrO2 nanoparticle for lithium ion battery

    NASA Astrophysics Data System (ADS)

    Sudaryanto, Yulianti, Evi; Patimatuzzohrah

    2016-02-01

    In order to develop all solid lithium ion battery, study on the structure and properties of solid polymer electrolytes (SPE) based on chitosan has been done. The SPE were prepared by adding Zirconia (ZrO2) nanoparticle and LiClO4 as lithium salt into the chitosan solution followed by casting method. Effect of the ZrO2 and salt concentration to the structure and properties of SPE were elaborated using several methods. The structure of the SPE cast film, were characterized mainly by using X-ray diffractometer (XRD). While the electrical properties of SPE were studied by electrochemical impedance spectrometer (EIS) and ion transference number measurement. XRD profiles show that the addition of ZrO2 and LiClO4 disrupts the crystality of chitosan. The decrease in sample crytalinity with the nanoparticle and salt addition may increase the molecular mobility result in the increasing sample conductivity and cathionic transference number as determined by EIS and ion transference number measurement, respectively. The highest ionic conductivity (3.58×10-4 S cm-1) was obtained when 4 wt% of ZrO2 nanoparticle and 40 wt% of LiClO4 salt were added to the chitosan. The ion transference number with that composition was 0.55. It is high enough to be used as SPE for lithium ion battery.

  16. Spectrophotometric sequential injection determination of D-penicillamine based on a complexation reaction with nickel ion.

    PubMed

    Martinović-Bevanda, Anita; Radić, Njegomir

    2013-01-01

    A simple and sensitive spectrophotometric method, based on reaction between Ni(II) ion and D-penicillamine (PEN), was developed. The proposed SIA system enhanced the analytical applicability of the reaction of complexation, and allowed the determination of PEN in the concentration range of 3.0 × 10(-6) - 2.0 × 10(-4) mol L(-1) with a sampling rate of 200 h(-1). With the proposed SIA system, PEN could be accurately determinated up to 0.9 nmol quantity. The method was successfully applied to the determination of PEN in laboratory samples and pharmaceuticals.

  17. The Effect of Thermal Annealing on Structural-phase Changes in the Ni-Ti Alloy Implanted with Krypton Ions

    NASA Astrophysics Data System (ADS)

    Poltavtseva, V. P.; Kislitsin, S. B.; Ghyngazov, S. A.

    2016-06-01

    The influence of thermal annealing within the temperature range 100-300°C on the structural-phase state of a Ni-Ti alloy with shape memory effect (SME) implanted with 84Kr ions at the energies E = 280 keV and 1.75 MeV/nucl and the fluences within 5·1012-1·1020 ion/m2 is investigated. For the samples modified by 84Kr ions at E = 1.75 MeV/nucl up to the fluences 1·1020 and 5·1012 ion/m2, the formation of a martensitic NiTi phase with the B19 ' structure, responsible for the SME, is revealed at the annealing temperatures 100 and 300°C, respectively, in the near-surface region corresponding to the outrange area. This is accompanied by the formation of nanosized NiTi particles in the R-phase. As the implantation fluence increases, the probability of their formation decreases. It is shown that annealing of the implanted structures can increase the strength of the Ni-Ti alloy. The degree of hardening is determined by the value of annealing temperature, and an increase in strength is primarily due to ordering of the radiation-induced defect structures (phases). A correlation between the onset temperature of a forward martensitic transition and the structural-phase state of the thermally annealed Ni-Ti alloy is established.

  18. Ion flow and sheath structure near positively biased electrodes

    NASA Astrophysics Data System (ADS)

    Hood, Ryan; Scheiner, Brett; Baalrud, Scott; Hopkins, Matthew; Barnat, Ed; Yee, Benjamin; Merlino, Robert; Skiff, Fred

    2016-10-01

    Measurements of the ion velocity distribution function (IVDF) and plasma potential were made near small positively biased electrodes using laser-induced fluorescence (LIF) and an emissive probe. The effect of dielectric around the electrode was tested and compared with a 2D particle-in-cell (PIC) simulation. Both measurements and simulation reveal that if the electrode is embedded within a surrounding dielectric, ions are accelerated toward the electrode to approximately 0.5 times the ion sound speed before being deflected radially by the electron sheath potential barrier. The axial potential profile in this case contains a virtual cathode. In comparison, when the surrounding dielectric is removed, both the ion flow and virtual cathode depth are dramatically reduced. These measurements suggest that the ion presheath from the dielectric may enclose the electron sheath of the electrode resulting in a virtual cathode that substantially influences the local ion flow profile. This research was supported by the Office of Fusion Energy Sciences at the U.S. Department of Energy under contract DE-AC04-94SL85000.

  19. Surface structure and lattice dynamics of KI(001) studied by high-resolution ion scattering combined with molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

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

    2002-09-01

    The rumpled surface structure and thermal lattice vibrations of KI(001) were studied by high-resolution medium-energy ion scattering (MEIS) and molecular dynamics (MD) simulation. The relaxation of the interlayer distance between the top and second layer and the rumpling of the top and second layers were measured directly by MEIS 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 K+ and I- ions self-consistently using the polalizabilities 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 thermal vibration amplitudes of the bulk and top-layer ions together with the correlations between the top- and second-layer ions by means of the ion shadowing effect applied to various kinds of scattering geometries. The results obtained were compared with those calculated from the MD simulations based on a semiclassical model using the dipole moments determined above and a Born-Mayer- or Hellmann-type pair potential. The present results are in overall agreement with the MD simulations employing the pair potential proposed by Catlow et al. [J. Phys. C 10, 1395 (1977)].

  20. Semi empirical formula for electronic stopping power determination of 24Mg, 27Al and 28Si ions crossing Formvar foil in the ion energy domain of LSS theory

    NASA Astrophysics Data System (ADS)

    Guesmia, A.; Ammi, H.; Mammeri, S.; Dib, A.; Pineda-Vargas, C. A.; Msimanga, M.; Hedibel, M.

    2014-03-01

    We have determined continuous stopping power of heavy ions in thin Formvar foil for 28Si, 27Al and 24Mg ions over an energy range of (0.1-0.5) MeV/nucleon. Heavy Ions Elastic Recoil Detection Analysis (HI-ERDA) technique coupled with time of flight (ToF) spectrometer has been used to measure energy loss of charged particles in this thin absorber. Lindhard, Scharff and Schiott (LSS) theory compared with the corresponding determined stopping values in Formvar, shows significantly large deviations. However, a novel semi empirical expression has been proposed here and tested for better stopping power calculations at low velocity in the ion energy domain of LSS theory for 28Si, 27Al and 24Mg ions crossing thin Formvar foil. The results were compared to the obtained experimental stopping power data, predictions of LSS theory and also to those generated by SRIM-2010 computer code. The obtained results exhibit good agreement with experimental data.

  1. Using support vector machines to improve elemental ion identification in macromolecular crystal structures

    SciTech Connect

    Morshed, Nader; Echols, Nathaniel; Adams, Paul D.

    2015-05-01

    A method to automatically identify possible elemental ions in X-ray crystal structures has been extended to use support vector machine (SVM) classifiers trained on selected structures in the PDB, with significantly improved sensitivity over manually encoded heuristics. In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.

  2. A spectrophotometric method for the determination of zinc, copper, and cobalt ions in metalloproteins using Zincon.

    PubMed

    Säbel, Crystal E; Neureuther, Joseph M; Siemann, Stefan

    2010-02-15

    Zincon (2-carboxy-2'-hydroxy-5'-sulfoformazylbenzene) has long been known as an excellent colorimetric reagent for the detection of zinc and copper ions in aqueous solution. To extend the chelator's versatility to the quantification of metal ions in metalloproteins, the spectral properties of Zincon and its complexes with Zn(2+), Cu(2+), and Co(2+) were investigated in the presence of guanidine hydrochloride and urea, two common denaturants used to labilize metal ions in proteins. These studies revealed the detection of metals to be generally more sensitive with urea. In addition, pH profiles recorded for these metals indicated the optimal pH for complex formation and stability to be 9.0. As a consequence, an optimized method that allows the facile determination of Zn(2+), Cu(2+), and Co(2+) with detection limits in the high nanomolar range is presented. Furthermore, a simple two-step procedure for the quantification of both Zn(2+) and Cu(2+) within the same sample is described. Using the prototypical Cu(2+)/Zn(2+)-protein superoxide dismutase as an example, the effectiveness of this method of dual metal quantification in metalloproteins is demonstrated. Thus, the spectrophotometric determination of metal ions with Zincon can be exploited as a rapid and inexpensive means of assessing the metal contents of zinc-, copper-, cobalt-, and zinc/copper-containing proteins.

  3. Stepwise determination of quaternary ammonium salts and aromatic amines in pharmaceuticals by ion association titration.

    PubMed

    Sakai, T

    2001-12-01

    A stepwise titrimetric method has been developed for the simultaneous determination of pharmaceutical quaternary ammonium salts (R4N+) and aromatic amines (R3N). The method is based on the solvent extraction of R4N+ and R3NH+ with an ion association reagent. Sodium tetrakis(4-fluorophenyl)borate and sodium tetraphenylborate were used as titrants and potassium tetrabromophenolphthalein ethyl ester (TBPE) was used as an indicator. The ion associate which formed between R4N+ ion and TBPE made a blue color in 1,2-dichloroethane, while the ion associate formed between R3NH+ and TBPE showed a red-violet one. Sample solutions containing quaternary ammonium and/or amine compounds were titrated with sodium tetrakis(4-fluorophenyl)borate or sodium tetraphenylborate. When one drop of excess titrant was added, the color of the organic phase turned from blue or red-violet to yellow at the equivalence point. On the other hand, in the mixture of R4N+ and R3N, the color changed from blue to red-violet at the first equivalence point, and then its color turned to yellow at the second equivalence point. The quaternary ammonium compound and aromatic amine in pharmaceuticals could be simultaneously and successfully determined by the proposed titration method.

  4. Zinc ion availability--the determinant of efficacy in zinc lozenge treatment of common colds.

    PubMed

    Eby, G A

    1997-10-01

    This is a re-analysis of reports from 1984 to 1992 of double-blind, placebo-controlled, clinical trials of zinc lozenges in the treatment of common colds. This re-analysis was performed to test the hypothesis that major variations in daily zinc ion availability (ZIA) between chemically different lozenge formulations caused differing results in these clinical trials. Solution chemistry computations determined the bioavailability of Zn2+ ions at physiological pH from the lozenges used in these clinical trails. ZIA was derived from Fick's laws of diffusion in a bio-electric field. Lozenges that released Zn2+ ions at physiological pH (positive ZIAs) shortened colds. Lozenges that released negatively charged zinc species at physiological pH (negative ZIAs) lengthened colds. Lozenges having a zero ZIA had no effect on common colds. Lozenges with ZIA = 100 shortened colds by 7 days while ZIA = -55 lozenges lengthened colds by 4.4 days. A linear dose-response relationship exists between ZIAs of zinc lozenges and changes in duration of common colds. It is concluded that: prospective efficacy of zinc lozenges can be predicted based upon readily determined ZIA factors and ZIAs; chemically different zinc lozenge formulations having greatly different ZIAs resulted in greatly differing results in clinical trials; mast cell granule-derived Zn2+ ions are the foundation of the primary immune system; and high ZIA zinc acetate lozenges are beneficial for common colds.

  5. Pure zinc sulfide quantum dot as highly selective luminescent probe for determination of hazardous cyanide ion.

    PubMed

    Shamsipur, Mojtaba; Rajabi, Hamid Reza

    2014-03-01

    A rapid and simple fluorescence method is presented for selective and sensitive determination of hazardous cyanide ion in aqueous solution based on functionalized zinc sulfide (ZnS) quantum dot (QD) as luminescent prob. The ultra-small ZnS QDs were synthesized using a chemical co-precipitation method in the presence of 2-mercaptoethanol (ME) as an efficient capping agent. The prepared pure ZnS QDs was applied as an optical sensor for determination of cyanide ions in aqueous solutions. ZnS nanoparticles have exhibited a strong fluorescent emission at about 424 nm. The fluorescence intensity of QDs is linearly proportional to the cyanide ion concentration in the range 2.44×10(-6) to 2.59×10(-5)M with a detection limit of 1.70×10(-7)M at pH11. The designed fluorescent sensor possesses remarkable selectivity for cyanide ion over other anions such as Cl(-), Br(-), F(-), I(-), IO3(-), ClO4(-), BrO3(-), CO3(2-), NO2(-), NO3(-), SO4(2-), S2O4(2-), C2O4(2-), SCN(-), N3(-), citrate and tartarate with negligible influences on the cyanide detection by fluorescence spectroscopy.

  6. Precise Determination of the Lyman-1 Transition Energy in Hydrogen-like Gold Ions with Microcalorimeters

    NASA Astrophysics Data System (ADS)

    Kraft-Bermuth, S.; Andrianov, V.; Bleile, A.; Echler, A.; Egelhof, P.; Grabitz, P.; Kilbourne, C.; Kiselev, O.; McCammon, D.; Scholz, P.

    2014-09-01

    The precise determination of the transition energy of the Lyman-1 line in hydrogen-like heavy ions provides a sensitive test of quantum electrodynamics in very strong Coulomb fields. We report the determination of the Lyman-1 transition energy of gold ions (Au) with microcalorimeters at the experimental storage ring at GSI. X-rays produced by the interaction of 125 MeV/u Au ions with an internal argon gas-jet target were detected. The detector array consisted of 14 pixels with silicon thermistors and Sn absorbers, for which an energy resolution of 50 eV for an X-ray energy of 59.5 keV was obtained in the laboratory. The Lyman-1 transition energy was determined for each pixel in the laboratory frame, then transformed into the emitter frame and averaged. A Dy-159 source was used for energy calibration. The absolute positions of the detector pixels, which are needed for an accurate correction of the Doppler shift, were determined by topographic measurements and by scanning a collimated Am-241 source across the cryostat window. The energy of the Lyman-1 line in the emitter frame is eV, in good agreement with theoretical predictions. The systematic error is dominated by the uncertainty in the position of the cryostat relative to the interaction region of beam and target.

  7. Structural transitions in ion coordination driven by changes in competition for ligand binding

    PubMed Central

    Varma, Sameer; Rempe, Susan B.

    2009-01-01

    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 over-coordinated 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. PMID:18954053

  8. ION-EXCLUSION CHROMATOGRAPHIC DETERMINATION OF CARBOXYLIC ACIDS USED TO SUPPORT THE MICROBIALLY MEDIATED REDUCTIVE DECHLORINATION OF TETRACHLOROETHENE

    EPA Science Inventory

    An analytical method was developed for the determination of lactic acid, formic acid, acetic acid, propionic acid, and butyric acid in environmental microcosm samples using ion-exclusion chromatography. The chromatographic behavior of various eluents was studied to determine the ...

  9. Structural determinants of MALT1 protease activity.

    PubMed

    Wiesmann, Christian; Leder, Lukas; Blank, Jutta; Bernardi, Anna; Melkko, Samu; Decock, Arnaud; D'Arcy, Allan; Villard, Frederic; Erbel, Paulus; Hughes, Nicola; Freuler, Felix; Nikolay, Rainer; Alves, Juliano; Bornancin, Frederic; Renatus, Martin

    2012-05-25

    The formation of the CBM (CARD11-BCL10-MALT1) complex is pivotal for antigen-receptor-mediated activation of the transcription factor NF-κB. Signaling is dependent on MALT1 (mucosa-associated lymphoid tissue lymphoma translocation protein 1), which not only acts as a scaffolding protein but also possesses proteolytic activity mediated by its caspase-like domain. It remained unclear how the CBM activates MALT1. Here, we provide biochemical and structural evidence that MALT1 activation is dependent on its dimerization and show that mutations at the dimer interface abrogate activity in cells. The unliganded protease presents itself in a dimeric yet inactive state and undergoes substantial conformational changes upon substrate binding. These structural changes also affect the conformation of the C-terminal Ig-like domain, a domain that is required for MALT1 activity. Binding to the active site is coupled to a relative movement of caspase and Ig-like domains. MALT1 binding partners thus may have the potential of tuning MALT1 protease activity without binding directly to the caspase domain.

  10. Numerical and experimental evaluation of the relationship between porous electrode structure and effective conductivity of ions and electrons in lithium-ion batteries

    NASA Astrophysics Data System (ADS)

    Inoue, Gen; Kawase, Motoaki

    2017-02-01

    This study aims to develop a correlation equation between a porous electrode structure and the effective conductivity so as to design an optimal structure for a thick electrode layer of a high-capacity battery. We carried out a three-dimensional reconstruction of a lithium cobalt oxide and graphite electrode based on the cross-sectional images obtained via focused ion beam-scanning electron microscopy (FIB-SEM). The Li ion and electron conductivities are evaluated based on the effective conductive path determined from simulation and these values are compared with the experimental results obtained by electrochemical impedance spectroscopy carries out with a symmetric cell and the direct conductivity measurement under compression. Moreover, the amount of binder and the diameter of the active material particles are increased and decreased numerically using an actual reconstructed electrode structure, and the effect of those structures on the effective conductivity is examined. The most dominant factors that degrade ionic conductivity are the binder distribution and the particle morphology, respectively, in the cathode and anode, and a correlation equation with the function of porosity is obtained. These values are compared with those obtained by theoretical model equations, and the difference between the current effective ionic conductivity and the physical limiting value is determined.

  11. Three Dimensional Structure of the Electron and Ion Scales of Reconnection

    NASA Astrophysics Data System (ADS)

    Ashour-Abdalla, M.; Lapenta, G.; Walker, R. J.; El-Alaoui, M.; Liang, H.; Zhou, M.; Goldstein, M. L.

    2015-12-01

    We have investigated the location and extent of magnetic reconnection in a realistic magnetotail configuration by using a combination of the UCLA global MHD simulation of the solar wind, magnetosphere and ionosphere system and the iPIC3D large scale particle in cell simulation. In this approach we first run a global MHD simulation driven by upstream solar wind observations. Then we use the results from the MHD simulation to set the initial and boundary conditions for the large scale 3D PIC simulation. The evolution of the system is constrained by the initial MHD state but evolves fully kinetically. The electrons and ions are followed in fields determined by using Maxwell's equations. This approach combines both macro-MHD and small-kinetic scales in a single numerical simulation. For many studies the magnetotail can be thought of as invariant in the dawn dusk or Y direction. However, in many other situations the tail is kinked and/or flaps in time and one cannot assume invariance in the Y direction. We report an investigation of a case where the structure of the tail varies significantly in the Y-direction and a PIC simulation in a realistic configuration is necessary. We have found that the reconnection electric field and the ion outflow jet regions expand in Y. But the reconnection region remains localized and is accompanied by a narrow electron jet with a Y-extent comparable to an ion skin depth. This narrow jet does not show any sign of expanding in Y, but remains narrow despite the wider ion scale. Implications for the MMS mission will be discussed.

  12. N+ ion-target interactions in PPO polymer: A structural characterization

    NASA Astrophysics Data System (ADS)

    Das, A.; Dhara, S.; Patnaik, A.

    1999-01-01

    N + ion beam induced effects on the spin coated amorphous poly(2,6-dimethyl phenylene oxide) (PPO) films in terms of chemical structure and electronic and vibrational properties were investigated using Fourier Transform Infrared spectroscopy (FTIR) and Ultraviolet-Visible (UV-VIS) spectroscopy. Both techniques revealed that the stability of PPO was very weak towards 100 keV N + ions revealing the threshold fluence to be 10 14 ions/cm 2 for fragmentation of the polymer. FTIR analysis showed disappearance of all characteristic IR bands at a total fluence of 10 14 ions/cm 2 except for the band CC at 1608 cm -1 which was found to shift to a lower wave number along with an enhancement in the full width half maximum (FWHM) value with increasing fluence. A new bond appeared due to oxidation as a shoulder at 1680 cm -1 in FTIR spectra indicating the presence of CO type bond as a result of N + implantation on PPO films. The optical band gap ( Eg) deduced from absorption spectra, was observed to decrease from 4.4 to 0.5 eV with fluence. The implantation induced carbonaceous clusters, determined using Robertson's formula for the optical band gap, were found to consist of ˜160 fused hexagonal aromatic rings at the maximum energy fluence. An enhanced absorption coefficient as a function of fluence indicated incorporation of either much larger concentration of charge carriers or their mobility than that of the pristine sample. Calculated band tail width from Urbach band tail region for the implanted samples pointed the band edge sharpness to be strongly dependent on fluence indicating an increased disorder with increasing fluence.

  13. Surface ion trap structures with excellent optical access for quantum information processing

    NASA Astrophysics Data System (ADS)

    Maunz, P.; Blain, M.; Benito, F.; Chou, C.; Clark, C.; Descour, M.; Ellis, R.; Haltli, R.; Heller, E.; Kemme, S.; Sterk, J.; Tabakov, B.; Tigges, C.; Stick, D.

    2013-05-01

    Microfabricated surface electrode ion traps are necessary for the advancement of trapped ion quantum information processing as it offers a scalable way for realizing complex trap structures capable of storing and controlling many ions. The most promising way of performing two-qubit quantum gates in a chain of trapped ions is to focus laser beams on individual ions of the chain to drive gates. However, in surface ion traps the close proximity of the ions to the surface and the size of the chips usually cannot accommodate the tightly focused laser beams necessary to address individual ions parallel to the chip surface. Here we present a surface electrode ion trap monolithically fabricated in standard silicon technology that implements a linear quadrupole trap on a bowtie shaped chip with a narrow section that is only 1.2 mm wide. Laser beams parallel to the surface can be focused down to a waist of 4 μm with enough separation from the trap chip to prevent light scattering. The trap structure incorporates two Y-junctions for reordering ions and is optimized for quantum information processing. This work was supported by the Intelligence Advanced Research Projects Activity (IARPA). Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the US Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  14. “Trunk-like” heavy ion structures observed by the Van Allen Probes

    DOE PAGES

    Zhang, J. -C.; Kistler, L. M.; Spence, H. E.; ...

    2015-10-27

    Dynamic ion spectral features in the inner magnetosphere are the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. Here, we report “trunk-like” ion structures observed by the Van Allen Probes on 2 November 2012. This new type of ion structure looks like an elephant's trunk on an energy-time spectrogram, with the energy of the peak flux decreasing Earthward. The trunks are present in He+ and O+ ions but not in H+. During the event, ion energies in the He+ trunk, located at L=3.6–2.6, magnetic local time (MLT)=9.1–10.5, and magnetic latitude (MLAT) =-2.4–0.09°, vary monotonically from 3.5more » to 0.04 keV. Values at the two end points of the O+ trunk are energy=4.5–0.7keV, L=3.6–2.5, MLT=9.1–10.7, and MLAT=-2.4–0.4°. Our results from backward ion drift path tracings indicate that the trunks are likely due to (1) a gap in the nightside ion source or (2) greatly enhanced impulsive electric fields associated with elevated geomagnetic activity. Different ion loss lifetimes cause the trunks to differ among ion species.« less

  15. "Trunk-like" heavy ion structures observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Zhang, J.-C.; Kistler, L. M.; Spence, H. E.; Wolf, R. A.; Reeves, G.; Skoug, R.; Funsten, H.; Larsen, B. A.; Niehof, J. T.; MacDonald, E. A.; Friedel, R.; Ferradas, C. P.; Luo, H.

    2015-10-01

    Dynamic ion spectral features in the inner magnetosphere are the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. We report "trunk-like" ion structures observed by the Van Allen Probes on 2 November 2012. This new type of ion structure looks like an elephant's trunk on an energy-time spectrogram, with the energy of the peak flux decreasing Earthward. The trunks are present in He+ and O+ ions but not in H+. During the event, ion energies in the He+ trunk, located at L = 3.6-2.6, magnetic local time (MLT) = 9.1-10.5, and magnetic latitude (MLAT) = -2.4-0.09°, vary monotonically from 3.5 to 0.04 keV. The values at the two end points of the O+ trunk are energy = 4.5-0.7 keV, L = 3.6-2.5, MLT = 9.1-10.7, and MLAT = -2.4-0.4°. Results from backward ion drift path tracings indicate that the trunks are likely due to (1) a gap in the nightside ion source or (2) greatly enhanced impulsive electric fields associated with elevated geomagnetic activity. Different ion loss lifetimes cause the trunks to differ among ion species.

  16. “Trunk-like” heavy ion structures observed by the Van Allen Probes

    SciTech Connect

    Zhang, J. -C.; Kistler, L. M.; Spence, H. E.; Wolf, R. A.; Reeves, G.; Skoug, R.; Funsten, H.; Larsen, B. A.; Niehof, J. T.; MacDonald, E. A.; Friedel, R.; Ferradas, C. P.; Luo, H.

    2015-10-27

    Dynamic ion spectral features in the inner magnetosphere are the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. Here, we report “trunk-like” ion structures observed by the Van Allen Probes on 2 November 2012. This new type of ion structure looks like an elephant's trunk on an energy-time spectrogram, with the energy of the peak flux decreasing Earthward. The trunks are present in He+ and O+ ions but not in H+. During the event, ion energies in the He+ trunk, located at L=3.6–2.6, magnetic local time (MLT)=9.1–10.5, and magnetic latitude (MLAT) =-2.4–0.09°, vary monotonically from 3.5 to 0.04 keV. Values at the two end points of the O+ trunk are energy=4.5–0.7keV, L=3.6–2.5, MLT=9.1–10.7, and MLAT=-2.4–0.4°. Our results from backward ion drift path tracings indicate that the trunks are likely due to (1) a gap in the nightside ion source or (2) greatly enhanced impulsive electric fields associated with elevated geomagnetic activity. Different ion loss lifetimes cause the trunks to differ among ion species.

  17. Impact of ion irradiation on the thermal, structural, and mechanical properties of metallic glasses

    SciTech Connect

    Mayr, S.G.

    2005-04-01

    The impact of ion-beam irradiation on the thermal, structural, and mechanical properties of metallic glasses is investigated using the model glass, CuTi, in molecular dynamics computer simulations. It is found that ion-beam bombardment successively modifies the compositional and structural order toward a universal steady state, which proves to be independent of the initial relaxation state and thermal history of the unirradiated sample. This is reflected by key materials properties, including enthalpy, structural and compositional short-range order, as well as Young's modulus and fracture behavior. The results are interpreted within the framework of competing dynamics, where radiation-induced plastic relaxation counteracts ion-beam disordering.

  18. Probing ion-molecule structure and dynamics in isolated molecular clusters and proteins

    NASA Astrophysics Data System (ADS)

    Abate, Yohannes

    identify several distinct isomers in the (MgC2O2H4)+ cluster that can dissociate directly following internal conversion to the major observed daughter ions, Mg+, MgOH+, and Mg(H2O) +. We have discovered new structural determinants that significantly improve pKa predictions of His residues: Cation-pi and pi-pi interactions of histidine with aromatic residues (Tyr, Trp and Phe), N-H hydrogen bonds from backbone amide groups and coupled titration effects. Cation-pi and pi-pi interactions are key contributors to the prediction of Histidine pKa values in proteins.

  19. How Structure Determines Correlations in Neuronal Networks

    PubMed Central

    Pernice, Volker; Staude, Benjamin; Cardanobile, Stefano; Rotter, Stefan

    2011-01-01

    Networks are becoming a ubiquitous metaphor for the understanding of complex biological systems, spanning the range between molecular signalling pathways, neural networks in the brain, and interacting species in a food web. In many models, we face an intricate interplay between the topology of the network and the dynamics of the system, which is generally very hard to disentangle. A dynamical feature that has been subject of intense research in various fields are correlations between the noisy activity of nodes in a network. We consider a class of systems, where discrete signals are sent along the links of the network. Such systems are of particular relevance in neuroscience, because they provide models for networks of neurons that use action potentials for communication. We study correlations in dynamic networks with arbitrary topology, assuming linear pulse coupling. With our novel approach, we are able to understand in detail how specific structural motifs affect pairwise correlations. Based on a power series decomposition of the covariance matrix, we describe the conditions under which very indirect interactions will have a pronounced effect on correlations and population dynamics. In random networks, we find that indirect interactions may lead to a broad distribution of activation levels with low average but highly variable correlations. This phenomenon is even more pronounced in networks with distance dependent connectivity. In contrast, networks with highly connected hubs or patchy connections often exhibit strong average correlations. Our results are particularly relevant in view of new experimental techniques that enable the parallel recording of spiking activity from a large number of neurons, an appropriate interpretation of which is hampered by the currently limited understanding of structure-dynamics relations in complex networks. PMID:21625580

  20. Irradiation effects on secondary structure of protein induced by keV ions

    NASA Astrophysics Data System (ADS)

    Cui, F. Z.; Lin, Y. B.; Zhang, D. M.; Tian, M. B.

    2001-01-01

    Protein secondary structure changes by low-energy ion irradiation are reported for the first time. The selected system is 30 keV N + irradiation on bovine serum albumin (BSA). After irradiation at increasing fluences from 1.0×10 15 to 2.5×10 16 ion/cm 2, Fourier transform infrared spectra analysis was conducted. It was found that the secondary structures of BSA molecules were very sensitive to ion irradiation. Secondary conformations showed different trends of change during irradiation. With the increase of ion fluence from 0 to 2.5×10 16 ion/cm 2, the fraction of α-helix and β-turns decreased from 17 to 12%, and from 40 to 31%, respectively, while that of random coil and β-sheet structure increased from 18 to 27%, and from 25 to 30%, respectively. Possible explanations for the secondary conformational changes of protein are proposed.

  1. Carbohydrate Structure Characterization by Tandem Ion Mobility Mass Spectrometry (IMMS)2

    PubMed Central

    Li, Hongli; Bendiak, Brad; Siems, William F.; Gang, David R.; Hill, Herbert H.

    2013-01-01

    A high resolution ion mobility spectrometer was interfaced to a Synapt G2 high definition mass spectrometer (HDMS) to produce IMMS-IMMS analysis. The hybrid instrument contained an electro-spray ionization source, two ion gates, an ambient pressure linear ion mobility drift tube, a quadrupole mass filter, a traveling wave ion mobility spectrometer (TWIMS) and a time of flight mass spectrometer. The dual gate drift tube ion mobility spectrometer (DTIMS) could be used to acquire traditional IMS spectra, but also could selectively transfer specific mobility selected precursor ions to the Synapt G2 HDMS for mass filtration (quadrupole). The mobility and mass selected ions could then be introduced into a collision cell for fragmentation followed by mobility separation of the fragment ions with the traveling wave ion mobility spectrometer. These mobility separated fragment ions are finally mass analyzed using a time-of-flight mass spectrometer. This results in an IMMS-IMMS analysis and provides a method to evaluate the isomeric heterogeneity of precursor ions by both DTIMS and TWIMS, to acquire a mobility-selected and mass-filtered fragmentation pattern and to additionally obtain traveling wave ion mobility spectra of the corresponding product ions. This new IMMS2 instrument enables the structural diversity of carbohydrates to be studied in greater detail. The physical separation of isomeric oligosaccharide mixtures was achieved by both DTIMS and TWIMS, with DTIMS demonstrating higher resolving power (70~80) than TWIMS (30~40). Mobility selected MS/MS spectra were obtained, and TWIMS evaluation of product ions showed that isomeric forms of fragment ions existed for identical m/z values. PMID:23330948

  2. Carbohydrate structure characterization by tandem ion mobility mass spectrometry (IMMS)2.

    PubMed

    Li, Hongli; Bendiak, Brad; Siems, William F; Gang, David R; Hill, Herbert H

    2013-03-05

    A high resolution ion mobility spectrometer was interfaced to a Synapt G2 high definition mass spectrometer (HDMS) to produce IMMS-IMMS analysis. The hybrid instrument contained an electrospray ionization source, two ion gates, an ambient pressure linear ion mobility drift tube, a quadrupole mass filter, a traveling wave ion mobility spectrometer (TWIMS), and a time-of-flight mass spectrometer. The dual gate drift tube ion mobility spectrometer (DTIMS) could be used to acquire traditional IMS spectra but also could selectively transfer specific mobility selected precursor ions to the Synapt G2 HDMS for mass filtration (quadrupole). The mobility and mass selected ions could then be introduced into a collision cell for fragmentation followed by mobility separation of the fragment ions with the traveling wave ion mobility spectrometer. These mobility separated fragment ions are finally mass analyzed using a time-of-flight mass spectrometer. This results in an IMMS-IMMS analysis and provides a method to evaluate the isomeric heterogeneity of precursor ions by both DTIMS and TWIMS to acquire a mobility-selected and mass-filtered fragmentation pattern and to additionally obtain traveling wave ion mobility spectra of the corresponding product ions. This new IMMS(2) instrument enables the structural diversity of carbohydrates to be studied in greater detail. The physical separation of isomeric oligosaccharide mixtures was achieved by both DTIMS and TWIMS, with DTIMS demonstrating higher resolving power (70-80) than TWIMS (30-40). Mobility selected MS/MS spectra were obtained, and TWIMS evaluation of product ions showed that isomeric forms of fragment ions existed for identical m/z values.

  3. Ion Mobility Separations of Isomers based upon Long Path Length Structures for Lossless Ion Manipulations Combined with Mass Spectrometry

    SciTech Connect

    Deng, Liulin; Ibrahim, Yehia M.; Baker, Erin S.; Aly, Noor A.; Hamid, Ahmed M.; Zhang, Xing; Zheng, Xueyun; Garimella, Sandilya V. B.; Webb, Ian K.; Prost, Spencer A.; Sandoval, Jeremy A.; Norheim, Randolph V.; Anderson, Gordon A.; Tolmachev, Aleksey V.; Smith, Richard D.

    2016-07-01

    Mass spectrometry (MS)-based multi-omic measurements, including proteomics, metabolomics, lipidomics, and glycomics, are increasingly transforming our ability to characterize and understand biological systems, but, presently have limitations due to the chemical diversity and range of abundances of biomolecules in complex samples. Advances addressing these challenges increasingly are based upon the ability to quickly separate, react and otherwise manipulate sample components for analysis by MS. Here we report on a new approach using Structures for Lossless Ion Manipulations (SLIM) to enable long serpentine path ion mobility spectrometry (IMS) separations followed by MS analyses. This approach provides previously unachieved mobility biomolecule isomer separations for biomolecular species, in conjunction with more effective ion utilization, and producing a basis for the improved characterization of very small samples.

  4. Conduction Mechanisms and Structure of Ionomeric Single-Ion Conductors

    SciTech Connect

    Colby, Ralph H.; Maranas, Janna K.; Mueller, Karl T.; Runt, James; Winey, Karen I.

    2015-03-01

    Our team has designed using DFT (Gaussian) and synthesized low glass transition temperature single-ion conductors that are either polyanions that conduct small cations Li+, Na+, Cs+ or polycations that conduct small anions F-, OH-, Br-. We utilize a wide range of complimentary experimental materials characterization tools to understand ion transport; differential scanning calorimetry, dielectric relaxation spectroscopy, infrared spectroscopy, nuclear magnetic resonance spectroscopy, linear viscoelasticity, X-ray scattering and molecular dynamics simulations. The glass transition temperature Tg needs to be as low as possible to facilitate ion transport, so the nonionic parts of the polymer need to be polar, flexible and have strong solvation interactions with the ions. The lowest Tg we have managed for polyanions conducting Li+ is -60 °C. In contrast, polysiloxanes with PEO side chains and tetrabutylphosphonium cationic side groups have Tg ≈ -75 °C that barely increases with ion content, as anticipated by DFT. A survey of all polyanions in the literature suggests that Tg < -80 °C is needed to achieve the 10-4 S/cm conductivity needed for battery separators.

  5. Synthesis and structure of novel lithium-ion conductor Li7Ge3PS12

    NASA Astrophysics Data System (ADS)

    Inoue, Yuki; Suzuki, Kota; Matsui, Naoki; Hirayama, Masaaki; Kanno, Ryoji

    2017-02-01

    The novel lithium-ion conductor Li7Ge3PS12 was synthesized by slow cooling from the ternary Li2S-GeS2-P2S5 system, and was shown to exhibit a cubic argyrodite-type structure. The phase composition was determined by varying the ratio of starting materials; the observed monophasic properties were close to those for the Li7Ge3PS12 composition. The lattice parameter (a =9.80192(3) Å) of Li7Ge3PS12 was slightly smaller than that of Li7PS6 (a =9.993 Å), indicating that substitution of a Li cation by the smaller Ge cation contracted the cubic lattice. In addition, the novel structure consisted of a framework composed of four isolated (Ge/P)S4 tetrahedra. Li+ ions occupied tetrahedral sites within the framework, forming a three-dimensional conduction pathway. Finally, Li7Ge3PS12 exhibited a high ionic conductivity of 1.1×10-4 S cm-1 at 25 °C and an activation energy of 25 kJ mol-1.

  6. Computer simulation of structural modifications induced by highly energetic ions in uranium dioxide

    NASA Astrophysics Data System (ADS)

    Sasajima, Y.; Osada, T.; Ishikawa, N.; Iwase, A.

    2013-11-01

    The structural modification caused by the high-energy-ion irradiation of single-crystalline uranium dioxide was simulated by the molecular dynamics method. As the initial condition, high kinetic energy was supplied to the individual atoms within a cylindrical region of nanometer-order radius located in the center of the specimen. The potential proposed by Basak et al. [C.B. Basak, A.K. Sengupta, H.S. Kamath, J. Alloys Compd. 360 (2003) 210-216] was utilized to calculate interaction between atoms. The supplied kinetic energy was first spent to change the crystal structure into an amorphous one within a short period of about 0.3 ps, then it dissipated in the specimen. The amorphous track radius Ra was determined as a function of the effective stopping power gSe, i.e., the kinetic energy of atoms per unit length created by ion irradiation (Se: electronic stopping power, g: energy transfer ratio from stopping power to lattice vibration energy). It was found that the relationship between Ra and gSe follows the relation Ra2=aln(gS)+b. Compared to the case of Si and β-cristobalite single crystals, it was harder to produce amorphous track because of the long range interaction between U atoms.

  7. Types and concentrations of metal ions affect local structure and dynamics of RNA

    NASA Astrophysics Data System (ADS)

    Wang, Jun; Xiao, Yi

    2016-10-01

    The roles that metal ions play in the structure and dynamics of RNA molecules are long-standing problems that have been studied extensively but are still not well understood. Here we show that metal ions have distributions around RNA molecules that strongly depend on the types and concentrations of the metal ions and also the electrostatic surface of the molecule. In particular, the ion distributions may not balance all the local electronegativity of the molecule. These ion distributions do not only greatly affect local structures but also lead to different local dynamics of RNA. We studied the effects of different ion solutions on the structure and dynamics of RNA by taking the pre Q1 riboswitch aptamer domain as an illustrative example and using molecular dynamics simulations. Since the local structures and dynamics of RNAs are important to their functions, our results also indicate that the selection of proper ion conditions is necessary to model them correctly, in contrast to the use of diverse ion solutions in current molecular dynamics simulations.

  8. Structural phase transitions and topological defects in ion Coulomb crystals

    SciTech Connect

    Partner, Heather L.; Nigmatullin, Ramil; Burgermeister, Tobias; Keller, Jonas; Pyka, Karsten; Plenio, Martin B.; Retzker, Alex; Zurek, Wojciech Hubert; del Campo, Adolfo; Mehlstaubler, Tanja E.

    2014-11-19

    We use laser-cooled ion Coulomb crystals in the well-controlled environment of a harmonic radiofrequency ion trap to investigate phase transitions and defect formation. Topological defects in ion Coulomb crystals (kinks) have been recently proposed for studies of nonlinear physics with solitons and as carriers of quantum information. Defects form when a symmetry breaking phase transition is crossed non-adiabatically. For a second order phase transition, the Kibble-Zurek mechanism predicts that the formation of these defects follows a power law scaling in the rate of the transition. We demonstrate a scaling of defect density and describe kink dynamics and stability. We further discuss the implementation of mass defects and electric fields as first steps toward controlled kink preparation and manipulation.

  9. Ion streaming instabilities with application to collisionless shock wave structure

    NASA Technical Reports Server (NTRS)

    Golden, K. I.; Linson, L. M.; Mani, S. A.

    1973-01-01

    The electromagnetic dispersion relation for two counterstreaming ion beams of arbitrary relative strength flowing parallel to a dc magnetic field is derived. The beams flow through a stationary electron background and the dispersion relation in the fluid approximation is unaffected by the electron thermal pressure. The dispersion relation is solved with a zero net current condition applied and the regions of instability in the k-U space (U is the relative velocity between the two ion beams) are presented. The parameters are then chosen to be applicable for parallel shocks. It was found that unstable waves with zero group velocity in the shock frame can exist near the leading edge of the shock for upstream Alfven Mach numbers greater than 5.5. It is suggested that this mechanism could generate sufficient turbulence within the shock layer to scatter the incoming ions and create the required dissipation for intermediate strength shocks.

  10. Ion streaming instabilities with application to collisionless shock wave structure

    NASA Technical Reports Server (NTRS)

    Golden, K. I.; Linson, L. M.; Mani, S. A.

    1973-01-01

    The electromagnetic dispersion relation for two counterstreaming ion beams of arbitrary relative strength flowing parallel to a dc magnetic field is derived. The beams flow through a stationary electron background and the dispersion relation in the fluid approximation is unaffected by the electron thermal pressure. Magnetic effects on the ion beams are included, but the electrons are treated as a magnetized fluid. The dispersion relation is solved with a zero net current condition applied and the regions of instability in the k-U space (U is the relative velocity between the two ion beams) are presented. These results are extensions of Kovner's analysis for weak beams. The parameters are then chosen to be applicable for parallel shocks. It is found that unstable waves with zero group velocity in the shock frame can exist near the leading edge of the shock for upstream Alfven Mach numbers greater than 5.5.

  11. Structural determinants of criticality in biological networks

    PubMed Central

    Valverde, Sergi; Ohse, Sebastian; Turalska, Malgorzata; West, Bruce J.; Garcia-Ojalvo, Jordi

    2015-01-01

    Many adaptive evolutionary systems display spatial and temporal features, such as long-range correlations, typically associated with the critical point of a phase transition in statistical physics. Empirical and theoretical studies suggest that operating near criticality enhances the functionality of biological networks, such as brain and gene networks, in terms for instance of information processing, robustness, and evolvability. While previous studies have explained criticality with specific system features, we still lack a general theory of critical behavior in biological systems. Here we look at this problem from the complex systems perspective, since in principle all critical biological circuits have in common the fact that their internal organization can be described as a complex network. An important question is how self-similar structure influences self-similar dynamics. Modularity and heterogeneity, for instance, affect the location of critical points and can be used to tune the system toward criticality. We review and discuss recent studies on the criticality of neuronal and genetic networks, and discuss the implications of network theory when assessing the evolutionary features of criticality. PMID:26005422

  12. Atmospheric structure determined from satellite data

    NASA Technical Reports Server (NTRS)

    Knight, K. S.; Scoggins, J. R.

    1981-01-01

    The capabilities of the Nimbus 6 satellite sounding data for use in synoptic analysis were considered and interpreted. An evaluation of the ability of the satellite sounding data to detect and depict structural features of the atmosphere was made on the basis of vertical profiles of average difference and standard deviation of differences between satellite and rawinsonde data at nine pressure levels from 850 to 100 mb; and constant pressure charts and cross sections of satellite, rawinsonde and difference values. Results indicate that satellite measurements of temperature as well as the vertical lapse rate and horizontal gradient of temperature are accurate enough to show large scale patterns but not to precisely define fronts or tropopauses; satellite measurements of dew point temperature are smoothed enough to severely reduce contrasts between air masses across fronts; the magnitude of the standard deviation of differences between rawinsonde and satellite data for most variables increases with the synoptic activity in the region; and the most reliable variables to examine from satellite data for depiction of synoptic features are the temperature equivalent potential temperature and mixing ratio.

  13. A molecular-gap device for specific determination of mercury ions

    PubMed Central

    Guo, Zheng; Liu, Zhong-Gang; Yao, Xian-Zhi; Zhang, Kai-Sheng; Chen, Xing; Liu, Jin-Huai; Huang, Xing-Jiu

    2013-01-01

    Specific determination/monitoring of trace mercury ions (Hg2+) in environmental water is of significant importance for drinking safety. Complementarily to conventional inductively coupled plasma mass spectrometry and atomic emission/absorption spectroscopy, several methods, i.e., electrochemical, fluorescent, colorimetric, and surface enhanced Raman scattering approaches, have been developed recently. Despite great success, many inevitably encounter the interferences from other metal ions besides the complicated procedures and sophisticated equipments. Here we present a molecular-gap device for specific determination of trace Hg2+ in both standardized solutions and environmental samples based on conductivity-modulated glutathione dimer. Through a self-assembling technique, a thin film of glutathione monolayer capped Au nanoparticles is introduced into 2.5 μm-gap-electrodes, forming numerous double molecular layer gaps. Notably, the fabricated molecular-gap device shows a specific response toward Hg2+ with a low detection limit actually measured down to 1 nM. Theoretical calculations demonstrate that the specific sensing mechanism greatly depends on the electron transport ability of glutathione dimer bridged by heavy metal ions, which is determined by its frontier molecular orbital, not the binding energy. PMID:24178058

  14. [Determination of residual aluminium Ion in Huoxiang Zhengqi pellets by GFAAS with EDTA complexation extraction].

    PubMed

    Wang, Xue-Na; Ran, Cong-Cong; Li, Qing-Lian; Du, Chao-Hui; Jiang, Ye

    2015-06-01

    To establish an EDTA complexation extraction pretreatment combining with GFAAS method for the determination of residual aluminium ion in Huoxiang zhengqi pellets without digestive treatment, systematical investigation was made on sample preparation, and EDTA was used for the complexation extraction of residual aluminium ion in samples. The pH, concentration and volume of extraction solution, the temperature and time of microwave extraction, and graphite furnace temperature program were investigated. The results were compared with the microwave digestion. It was showed that, 0.1 g of sample weight was added in 20 mL 0.05 mol x L(-1) EDTA solution (pH 3.5), followed by heating at 150 degrees C for 10 min in the microwave extraction device. The determination of GFAAS was performed at optimized detection wavelength (257.4 nm) as well as graphite furnace temperature program, the detection limits and quantification limits were 2.37 μg x L(-1) and 7.89 μg x L(-1), respectively. The precision (RSD) was less than 2.3%. The average recovery was 96.9% -101%. The present method is easy, rapid and accurate for the determination of residual aluminium ion in Huoxiang zhengqi pellets.

  15. A molecular-gap device for specific determination of mercury ions

    NASA Astrophysics Data System (ADS)

    Guo, Zheng; Liu, Zhong-Gang; Yao, Xian-Zhi; Zhang, Kai-Sheng; Chen, Xing; Liu, Jin-Huai; Huang, Xing-Jiu

    2013-11-01

    Specific determination/monitoring of trace mercury ions (Hg2+) in environmental water is of significant importance for drinking safety. Complementarily to conventional inductively coupled plasma mass spectrometry and atomic emission/absorption spectroscopy, several methods, i.e., electrochemical, fluorescent, colorimetric, and surface enhanced Raman scattering approaches, have been developed recently. Despite great success, many inevitably encounter the interferences from other metal ions besides the complicated procedures and sophisticated equipments. Here we present a molecular-gap device for specific determination of trace Hg2+ in both standardized solutions and environmental samples based on conductivity-modulated glutathione dimer. Through a self-assembling technique, a thin film of glutathione monolayer capped Au nanoparticles is introduced into 2.5 μm-gap-electrodes, forming numerous double molecular layer gaps. Notably, the fabricated molecular-gap device shows a specific response toward Hg2+ with a low detection limit actually measured down to 1 nM. Theoretical calculations demonstrate that the specific sensing mechanism greatly depends on the electron transport ability of glutathione dimer bridged by heavy metal ions, which is determined by its frontier molecular orbital, not the binding energy.

  16. Fine structures and ion images on fresh frozen dried ultrathin sections by transmission electron and scanning ion microscopy

    NASA Astrophysics Data System (ADS)

    Takaya, K.; Okabe, M.; Sawataishi, M.; Takashima, H.; Yoshida, T.

    2003-01-01

    Ion microscopy (IM) of air-dried or freeze-dried cryostat and semi-thin cryosections has provided ion images of elements and organic substances in wide areas of the tissue. For reproducible ion images by a shorter time of exposure to the primary ion beam, fresh frozen dried ultrathin sections were prepared by freezing the tissue in propane chilled with liquid nitrogen, cryocut at 60 nm, mounted on grids and silicon wafer pieces, and freeze-dried. Rat Cowper gland and sciatic nerve, bone marrow of the rat administered of lithium carbonate, tree frog and African toad spleen and buffy coat of atopic dermatitis patients were examined. Fine structures and ion images of the corresponding areas in the same or neighboring sections were observed by transmission electron microscopy (TEM) followed by sector type and time-of-flight type IM. Cells in the buffy coat contained larger amounts of potassium and magnesium while plasma had larger amounts of sodium and calcium. However, in the tissues, lithium, sodium, magnesium, calcium and potassium were distributed in the cell and calcium showed a granular appearance. A granular cell of the tree frog spleen contained sodium and potassium over the cell and magnesium and calcium were confined to granules.

  17. Structural Determinants of Sleeping Beauty Transposase Activity.

    PubMed

    Abrusán, György; Yant, Stephen R; Szilágyi, András; Marsh, Joseph A; Mátés, Lajos; Izsvák, Zsuzsanna; Barabás, Orsolya; Ivics, Zoltán

    2016-08-01

    Transposases are important tools in genome engineering, and there is considerable interest in engineering more efficient ones. Here, we seek to understand the factors determining their activity using the Sleeping Beauty transposase. Recent work suggests that protein coevolutionary information can be used to classify groups of physically connected, coevolving residues into elements called "sectors", which have proven useful for understanding the folding, allosteric interactions, and enzymatic activity of proteins. Using extensive mutagenesis data, protein modeling and analysis of folding energies, we show that (i) The Sleeping Beauty transposase contains two sectors, which span across conserved domains, and are enriched in DNA-binding residues, indicating that the DNA binding and endonuclease functions of the transposase coevolve; (ii) Sector residues are highly sensitive to mutations, and most mutations of these residues strongly reduce transposition rate; (iii) Mutations with a strong effect on free energy of folding in the DDE domain of the transposase significantly reduce transposition rate. (iv) Mutations that influence DNA and protein-protein interactions generally reduce transposition rate, although most hyperactive mutants are also located on the protein surface, including residues with protein-protein interactions. This suggests that hyperactivity results from the modification of protein interactions, rather than the stabilization of protein fold.

  18. Structural determinants of Sleeping Beauty transposase activity

    PubMed Central

    Abrusán, György; Yant, Stephen R.; Szilágyi, András; Marsh, Joseph A.; Mátés, Lajos; Izsvák, Zsuzsanna; Barabás, Orsolya; Ivics, Zoltán

    2016-01-01

    Transposases are important tools in genome engineering, and there is considerable interest in engineering more efficient ones. Here we seek to understand the factors determining their activity using the Sleeping Beauty transposase. Recent work suggests that protein co-evolutionary information can be used to classify groups of physically connected, co-evolving residues into elements called ‘sectors’, which have proven useful for understanding the folding, allosteric interactions, and enzymatic activity of proteins. Using extensive mutagenesis data, protein modeling and analysis of folding energies, we show that 1) The Sleeping Beauty transposase contains two sectors, which span across conserved domains, and are enriched in DNA-binding residues, indicating that the DNA binding and endonuclease functions of the transposase coevolve; 2) Sector residues are highly sensitive to mutations, and most mutations of these residues strongly reduce transposition rate; 3) Mutations with a strong effect on free energy of folding in the DDE domain of the transposase significantly reduce transposition rate. 4) Mutations that influence DNA and protein-protein interactions generally reduce transposition rate, although most hyperactive mutants are also located on the protein surface, including residues with protein-protein interactions. This suggests that hyperactivity results from the modification of protein interactions, rather than the stabilization of protein fold. PMID:27401040

  19. Effects of ion dynamics on kinetic structures of the diffusion region during magnetic reconnection

    NASA Astrophysics Data System (ADS)

    Chen, L. J.; Shuster, J. R.; Bessho, N.; Li, G.; Torbert, R. B.; Daughton, W. S.

    2014-12-01

    Based on results from Particle-in-cell (PIC) simulations, we report how ion dynamics influencethe Hall electric field and electron velocity distributions in the diffusion region of magnetic reconnection.The Hall electric field is due to charge imbalance in the diffusion region. At early times, within a few ion cyclotron oscillations from the peak reconnection,electron orbit dynamics dominate, and the Hall electric field layer assumes the width of the electron current layer.As the pre-existing current sheet ions are accelerated and jetted away, inflowing ions form an ion phase space hole structure.The ion hole structure is self-consistently supported by the Hall electric field. The ion meandering orbit width increasesover the course of about 10 ion cyclotron oscillations from several to approximately 40 electron skin depths (two ion skin depths,where the skin depth is based on the initial current sheet density), and theHall electric field layer widens in the same manner to become much broader than the electron diffusion region.The electron velocity distributions upstream of the electron diffusion region and within the regionof counter streaming ions become fragmented as the ion hole establishes itself.The fragmentation is carried into the electron diffusion region, and through the electron outflow jet, leading to a multitude of arcs in the electron distributions at the end of the jet. The broadening of the Hall electric field layer resolves a longstanding discrepancy concerning whether the narrowest width of the layer is of the electron [Chen et al., 2008] or ion [Mozer et al., 2002] scale. The fragmentation of the electron distributions may be due to an electron-ion instability, and is underinvestigation.

  20. A micro-structured ion-implanted magnonic crystal

    SciTech Connect

    Obry, Bjoern; Pirro, Philipp; Chumak, Andrii V.; Ciubotaru, Florin; Serga, Alexander A.; Hillebrands, Burkard; Braecher, Thomas; Osten, Julia; Fassbender, Juergen

    2013-05-20

    We investigate spin-wave propagation in a microstructured magnonic-crystal waveguide fabricated by localized ion implantation. The irradiation caused a periodic variation in the saturation magnetization along the waveguide. As a consequence, the spin-wave transmission spectrum exhibits a set of frequency bands, where spin-wave propagation is suppressed. A weak modification of the saturation magnetization by 7% is sufficient to decrease the spin-wave transmission in the band gaps by a factor of 10. These results evidence the applicability of localized ion implantation for the fabrication of efficient micron- and nano-sized magnonic crystals for magnon spintronic applications.

  1. Nanoscale surface structuring during ion bombardment of elemental semiconductors

    NASA Astrophysics Data System (ADS)

    Anzenberg, Eitan

    2013-01-01

    Nano-patterning of surfaces with uniform ion bombardment yields a rich phase-space of topographic patterns. Particle irradiation can cause surface ultra-smoothing or self-organized nanoscale pattern formation in surface topography. Topographic pattern formation has previously been attributed to the effects of the removal of target atoms by sputter erosion. In this thesis, the surface morphology evolution of Si(100) and Ge(100) during low energy ion bombardment of Ar+ and Kr+ ions, respectively, is studied. Our facilities for studies of surface processes at the National Synchrotron Light Source (NSLS) allow in-situ characterization of surface morphology evolution during ion bombardment using grazing incidence small angle x-ray scattering (GISAXS). This technique is used to measure in reciprocal space the kinetics of formation or decay of correlated nanostructures on the surface, effectively measuring the height-height correlations. A linear model is used to characterize the early time kinetic behavior during ion bombardment as a function of ion beam incidence angle. The curvature coefficients predicted by the widely used erosive model of Bradley and Harper are quantitatively negligible and of the wrong sign when compared to the observed effect in both Si and Ge. A mass-redistribution model explains the observed ultra-smoothing at low angles, exhibits an instability at higher angles, and predicts the observed 45° critical angle separating these two regimes in Si. The Ge surface evolution during Kr+ irradiation is qualitatively similar to that observed for Ar+ irradiation of Si at the same ion energy. However, the critical angle for Ge cannot be quantitatively reproduced by the simple mass redistribution model. Crater function theory, as developed by Norris et al., incorporates both mass redistributive and erosive effects, and predicts constraining relationships between curvature coefficients. These constraints are compared to experimental data of both Si and Ge

  2. Influence of calcium ions on the structural and magnetic properties of Cd-Mg ferrites nanoparticles.

    PubMed

    Zaki, H M; Al-Heniti, S

    2012-09-01

    Cadmium magnesium ferrites doped with calcium having the chemical formula Cd0.5Mg0.5-x Ca(x)Fe2O4 (0.0 < or = x < or = 0.3) were prepared by the Co-precipitation method. X-ray diffraction analysis confirmed the formation of a single phase with spinel crystal structure for the samples. The lattice parameter is determined for each composition and has been found to increase from 8.505 angstroms to 8.626 angstroms with increasing calcium concentration. Cation distribution for the studied ferrite system is proposed in terms of the structural and magnetic properties by means of X-ray diffraction (XRD), infrared spectroscopy (IR), vibrating sample magnetometer (VSM) and is found to be reliable. The experimental and theoretical lattice constants show the same trend with increasing calcium concentration indicating the validity of the proposed cation distribution. The analysis of infrared spectra indicates the presence of splitting in the absorption band which may be attributed to the presence of small amounts of Fe2+ ions in the ferrite system. The appearance of a shoulder around 700 cm(-1) suggests the presence of calcium ions in the tetrahedral site. The addition of non magnetic calcium ions in the ferrites suppressed the A-interaction and developed a B-B interaction, which is reflected in reducing the saturation magnetization in the present samples. The coercive field (H(c)) is also found to increase by increasing of Ca2+ concentration and has been explained on the bases of direct relationship with anisotropy constant.

  3. Determination of Ice Characteristics for Marine Hydroengineering Structures

    SciTech Connect

    Kantarzhi, I. G.; Maderich, V. S. Koshebutskii, V. I.

    2016-01-15

    Problems and potential approaches to determining ice characteristics for sea hydroengineering structures design are considered. A system for numerical modeling of ice dynamics is presented. The system may be used to define ice characteristics on approaches to structures with due regard for local hydrometeorological conditions and ice loads on structures. System application examples are presented for determining computational scenarios for ice loads at structures of the Pevek floating nuclear power plant (FNPP), as well as for the breakwater pier under reconstruction in Vanino. A scenario approach is used to determined ice loads.

  4. Structure of alcohol cluster ions in the gas phase, according to spectrometry and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Krisilov, A. V.; Lantsuzskaya, E. V.; Levina, A. M.

    2017-01-01

    Reduced ion mobility and scattering cross sections are calculated from experimentally obtained spectra of the ion mobility of linear aliphatic alcohols with carbon atom numbers from 2 to 9. A linear increase in the scattering cross sections as the molecular weight grows is found. According to the results from experiments and quantum chemical calculations, alcohol cluster ions do not form a compact structure. Neither are dipole moments compensated for during dimerization, in contrast to the aldehydes and ketones described earlier. It was concluded from ab initio calculations that charge delocalization in monomeric and dimeric ions of alcohols increases the dipole moment many times over.

  5. Analysis of ion-implanted surface and interface structures by computer-simulated backscattering spectra

    NASA Astrophysics Data System (ADS)

    Kido, Y.; Kakeno, M.; Yamada, K.; Kawamoto, J.; Ohsawa, H.

    1985-10-01

    Computer codes for synthesizing random and channeling backscattering spectra have been elaborated to characterize the surface and interface structures formed or modified by ion implantation. Both effects of isotopes and energy fluctuation are taken into account in the spectrum simulation. This backscattering measurement combined with the simulation method is applied to characterization of the N(+)-implanted Al films and to quantitative analysis of chemical reaction and interdiffusion induced by ion-beam mixing. An ion-beam-induced damage profile and its epitaxial recovery of crystallinity are analyzed by the simulation of channeling spectra from ion-implanted Al2O3 substrates.

  6. Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase

    SciTech Connect

    Xia, Shuangluo; Wang, Mina; Blaha, Gregor; Konigsberg, William H.; Wang, Jimin

    2011-10-20

    We have captured a preinsertion ternary complex of RB69 DNA polymerase (RB69pol) containing the 3' hydroxyl group at the terminus of an extendable primer (ptO3') and a nonhydrolyzable 2'-deoxyuridine 5'-{alpha},{beta}-substituted triphosphate, dUpXpp, where X is either NH or CH{sub 2}, opposite a complementary templating dA nucleotide residue. Here we report four structures of these complexes formed by three different RB69pol variants with catalytically inert Ca{sup 2+} and four other structures with catalytically competent Mn{sup 2+} or Mg{sup 2+}. These structures provide new insights into why the complete divalent metal-ion coordination complexes at the A and B sites are required for nucleotidyl transfer. They show that the metal ion in the A site brings ptO3' close to the {alpha}-phosphorus atom (P{alpha}) of the incoming dNTP to enable phosphodiester bond formation through simultaneous coordination of both ptO3' and the nonbridging Sp oxygen of the dNTP's {alpha}-phosphate. The coordination bond length of metal ion A as well as its ionic radius determines how close ptO3' can approach P{alpha}. These variables are expected to affect the rate of bond formation. The metal ion in the B site brings the pyrophosphate product close enough to P{alpha} to enable pyrophosphorolysis and assist in the departure of the pyrophosphate. In these dUpXpp-containing complexes, ptO3' occupies the vertex of a distorted metal ion A coordination octahedron. When ptO3' is placed at the vertex of an undistorted, idealized metal ion A octahedron, it is within bond formation distance to P{alpha}. This geometric relationship appears to be conserved among DNA polymerases of known structure.

  7. Comparison of Several Methods for Determining the Internal Resistance of Lithium Ion Cells

    PubMed Central

    Schweiger, Hans-Georg; Obeidi, Ossama; Komesker, Oliver; Raschke, André; Schiemann, Michael; Zehner, Christian; Gehnen, Markus; Keller, Michael; Birke, Peter

    2010-01-01

    The internal resistance is the key parameter for determining power, energy efficiency and lost heat of a lithium ion cell. Precise knowledge of this value is vital for designing battery systems for automotive applications. Internal resistance of a cell was determined by current step methods, AC (alternating current) methods, electrochemical impedance spectroscopy and thermal loss methods. The outcomes of these measurements have been compared with each other. If charge or discharge of the cell is limited, current step methods provide the same results as energy loss methods. PMID:22219678

  8. Language Structure Is Partly Determined by Social Structure

    PubMed Central

    Lupyan, Gary; Dale, Rick

    2010-01-01

    Background Languages differ greatly both in their syntactic and morphological systems and in the social environments in which they exist. We challenge the view that language grammars are unrelated to social environments in which they are learned and used. Methodology/Principal Findings We conducted a statistical analysis of >2,000 languages using a combination of demographic sources and the World Atlas of Language Structures— a database of structural language properties. We found strong relationships between linguistic factors related to morphological complexity, and demographic/socio-historical factors such as the number of language users, geographic spread, and degree of language contact. The analyses suggest that languages spoken by large groups have simpler inflectional morphology than languages spoken by smaller groups as measured on a variety of factors such as case systems and complexity of conjugations. Additionally, languages spoken by large groups are much more likely to use lexical strategies in place of inflectional morphology to encode evidentiality, negation, aspect, and possession. Our findings indicate that just as biological organisms are shaped by ecological niches, language structures appear to adapt to the environment (niche) in which they are being learned and used. As adults learn a language, features that are difficult for them to acquire, are less likely to be passed on to subsequent learners. Languages used for communication in large groups that include adult learners appear to have been subjected to such selection. Conversely, the morphological complexity common to languages used in small groups increases redundancy which may facilitate language learning by infants. Conclusions/Significance We hypothesize that language structures are subjected to different evolutionary pressures in different social environments. Just as biological organisms are shaped by ecological niches, language structures appear to adapt to the environment (niche) in

  9. Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3.

    PubMed

    Hosaka, Toshiaki; Yoshizawa, Susumu; Nakajima, Yu; Ohsawa, Noboru; Hato, Masakatsu; DeLong, Edward F; Kogure, Kazuhiro; Yokoyama, Shigeyuki; Kimura-Someya, Tomomi; Iwasaki, Wataru; Shirouzu, Mikako

    2016-08-19

    The light-driven inward chloride ion-pumping rhodopsin Nonlabens marinus rhodopsin-3 (NM-R3), from a marine flavobacterium, belongs to a phylogenetic lineage distinct from the halorhodopsins known as archaeal inward chloride ion-pumping rhodopsins. NM-R3 and halorhodopsin have distinct motif sequences that are important for chloride ion binding and transport. In this study, we present the crystal structure of a new type of light-driven chloride ion pump, NM-R3, at 1.58 Å resolution. The structure revealed the chloride ion translocation pathway and showed that a single chloride ion resides near the Schiff base. The overall structure, chloride ion-binding site, and translocation pathway of NM-R3 are different from those of halorhodopsin. Unexpectedly, this NM-R3 structure is similar to the crystal structure of the light-driven outward sodium ion pump, Krokinobacter eikastus rhodopsin 2. Structural and mutational analyses of NM-R3 revealed that most of the important amino acid residues for chloride ion pumping exist in the ion influx region, located on the extracellular side of NM-R3. In contrast, on the opposite side, the cytoplasmic regions of K. eikastus rhodopsin 2 were reportedly important for sodium ion pumping. These results provide new insight into ion selection mechanisms in ion pumping rhodopsins, in which the ion influx regions of both the inward and outward pumps are important for their ion selectivities.

  10. Probing the nuclear structure with heavy-ion reactions

    SciTech Connect

    Broglia, R.A.

    1982-01-01

    Nuclei display distortions in both ordinary space and in gauge space. It is suggested that it is possible to learn about the spatial distribution of the Nilsson orbitals and about the change of the pairing gap with the rotational frequency through the analysis of one- and two-nucleon transfer reactions induced in heavy-ion collisions.

  11. Folding of RNA tertiary structure: Linkages between backbone phosphates, ions, and water.

    PubMed

    Draper, David E

    2013-12-01

    The functional forms of many RNAs have compact architectures. The placement of phosphates within such structures must be influenced not only by the strong electrostatic repulsion between phosphates, but also by networks of interactions between phosphates, water, and mobile ions. This review first explores what has been learned of the basic thermodynamic constraints on these arrangements from studies of hydration and ions in simple DNA molecules, and then gives an overview of what is known about ion and water interactions with RNA structures. A brief survey of RNA crystal structures identifies several interesting architectures in which closely spaced phosphates share hydration shells or phosphates are buried in environments that provide intramolecular hydrogen bonds or site-bound cations. Formation of these structures must require strong coupling between the uptake of ions and release of water.

  12. Relativistic Calculating the Spectral Lines Hyperfine Structure Parameters for Heavy Ions

    SciTech Connect

    Khetselius, O. Yu.

    2008-10-22

    The energies and constants of the hyperfine structure, derivatives of the one-electron characteristics on nuclear radius, nuclear electric quadrupole, magnetic dipole moments for some Li-like multicharged ions are calculated.

  13. 'Trunk-like' ion structures observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Zhang, J.; Kistler, L. M.; Spence, H.; Wolf, R.; Reeves, G. D.; Skoug, R. M.; Funsten, H. O.; Larsen, B.; Niehof, J. T.; MacDonald, E.; Friedel, R. H.

    2013-12-01

    Dynamic ion spectral features in the inner magnetosphere are the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. In this study, we report 'trunk-like' ion structures observed in situ by the Van Allen Probes on 2 November 2012. The trunk structures are present in heavy ions but not in H+. For the particular event, ion energies in the He+ trunks, located at L = 3.7-2.6, MLT = 8.8-10.3, and MLAT = -2.0-0.03°, vary monotonically from 3.5 to 0.04 keV. It is suggested that the trunk phenomenon is due to a combination of 1) deeper ion injections from storm activity, 2) the longer charge exchange lifetimes of heavy ions than H+, 3) the separation of a narrow layer of ions around the Alfvén layer from other convecting ions, and 4) the trajectory of the Van Allen Probes (i.e., an orbital effect). Both observation analysis and numerical modeling are utilized in the study.

  14. Critical issues in the formation of quantum computer test structures by ion implantation

    SciTech Connect

    Schenkel, T.; Lo, C. C.; Weis, C. D.; Schuh, A.; Persaud, A.; Bokor, J.

    2009-04-06

    The formation of quantum computer test structures in silicon by ion implantation enables the characterization of spin readout mechanisms with ensembles of dopant atoms and the development of single atom devices. We briefly review recent results in the characterization of spin dependent transport and single ion doping and then discuss the diffusion and segregation behaviour of phosphorus, antimony and bismuth ions from low fluence, low energy implantations as characterized through depth profiling by secondary ion mass spectrometry (SIMS). Both phosphorus and bismuth are found to segregate to the SiO2/Si interface during activation anneals, while antimony diffusion is found to be minimal. An effect of the ion charge state on the range of antimony ions, 121Sb25+, in SiO2/Si is also discussed.

  15. Monte-Carlo Simulations of Heavy Ions Track Structures and Applications

    NASA Technical Reports Server (NTRS)

    Plante, Ianik; Cucinotta, Francia A.

    2013-01-01

    In space, astronauts are exposed to protons, high ]energy heavy (HZE) ions that have a high charge (Z) and energy (E), and secondary radiation, including neutrons and recoil nuclei produced by nuclear reactions in spacecraft walls or in tissue. The astronauts can only be partly shielded from these particles. Therefore, on travelling to Mars, it is estimated that every cell nucleus in an astronaut fs body would be hit by a proton or secondary electron (e.g., electrons of the target atoms ionized by the HZE ion) every few days and by an HZE ion about once a month. The risks related to these heavy ions are not well known and of concern for long duration space exploration missions. Medical ion therapy is another situation where human beings can be irradiated by heavy ions, usually to treat cancer. Heavy ions have a peculiar track structure characterized by high levels of energy ]deposition clustering, especially in near the track ends in the so ]called eBragg peak f region. In radiotherapy, these features of heavy ions can provide an improved dose conformation with respect to photons, also considering that the relative biological effectiveness (RBE) of therapeutic ions in the plateau region before the peak is sufficiently low. Therefore, several proton and carbon ion therapy facilities are under construction at this moment

  16. Influence of electronic energy deposition on the structural modification of swift heavy-ion-irradiated amorphous germanium layers

    SciTech Connect

    Steinbach, T.; Schnohr, C. S.; Wesch, W.; Kluth, P.; Giulian, R.; Araujo, L. L.; Sprouster, D. J.; Ridgway, M. C.

    2011-02-01

    Swift heavy-ion (SHI) irradiation of amorphous germanium (a-Ge) layers leads to a strong volume expansion accompanied by a nonsaturating irreversible plastic deformation (ion hammering), which are consequences of the high local electronic energy deposition within the region of the a-Ge layer. We present a detailed study of the influence of SHI irradiation parameters on the effect of plastic deformation and structural modification. Specially prepared a-Ge layers were irradiated using two SHI energies and different angles of incidence, thus resulting in a variation of the electronic energy deposition per depth {epsilon}{sub e} between 14.0 and 38.6 keV nm{sup -1}. For all irradiation parameters used a strong swelling of the irradiated material was observed, which is caused by the formation and growth of randomly distributed voids, leading to a gradual transformation of the amorphous layer into a sponge-like porous structure as established by cross-section scanning electron microscopy investigations. The swelling depends linearly on the ion fluence and on the value of {epsilon}{sub e}, thus clearly demonstrating that the structural changes are determined solely by the electronic energy deposited within the amorphous layer. Plastic deformation shows a superlinear dependence on the ion fluence due to the simultaneous volume expansion. This influence of structural modification on plastic deformation is described by a simple approach, thus allowing estimation of the deformation yield. With these results the threshold values of the electronic energy deposition for the onset of both structural modification and plastic deformation due to SHI irradiation are determined. Furthermore, based on these results, the longstanding question concerning the reason for the structural modification observed in SHI-irradiated crystalline Ge is answered.

  17. Experimental test of instability enhanced collisional friction for determining ion loss in two ion species plasmas a)

    NASA Astrophysics Data System (ADS)

    Hershkowitz, N.; Yip, C.-S.; Severn, G. D.

    2011-05-01

    Recent experiments have shown that ions in weakly collisional plasmas containing two ion species of comparable densities approximately reach a common velocity at the sheath edge equal to the bulk plasma ion sound velocity. A recent theory [S. D. Baalrud, C. C. Hegna, and J. D. Callen, Phys. Rev. Lett. 103, 205002 (2009)] suggests that this is a consequence of collisional friction between the two ion species enhanced by the two stream instability. The theory finds that the difference in velocities at the sheath edge depends on the relative concentrations of the two ions. The difference in velocities is small, with both species approaching to the bulk sound velocity, when the concentrations are comparable, and is large, with each species reaching its own Bohm velocity, when the relative concentration differences are large. To test these findings, drift velocities of Ar and Xe ions were measured with laser-induced fluorescence in Ar-Xe and He-Xe plasmas and combined with ion acoustic wave and plasma potential data. In addition, electron temperature was varied by a Maxwell demon [K. R. MacKenzie et al., App. Phys. Lett. 18, 529 (1971)]. The predictions were found to be in excellent agreement with the experimental data. The generalized Bohm criterion in two ion species plasmas is also verified in a wider variety of relative ion concentrations.

  18. Ab initio Determination of Formation Energies and Charge Transfer Levels of Charged Ions in Water

    NASA Astrophysics Data System (ADS)

    Vatti, Anoop Kishore; Todorova, Mira; Neugebauer, Joerg

    The ability to describe the complex atomic and electronic structure of liquid water and hydrated ions on a microscopic level is a key requirement to understand and simulate electro-chemical and biological processes. Identifying theoretical concepts which enable us to achieve an accurate description in a computationally efficient way is thereby of central importance. Aiming to unravel the importance and influence of different contributions on the hydration energy of ions we perform extensive ab-initio molecular dynamics simulations for charged and neutral cations (Zn, Mg) and anions (Cl, Br, I) in water. The structural correlations and electronic properties of the studied ions are analysed and compared to experimental observations. Following an approach inspired by the defect chemistry in semiconductors and aligning the water band edges on an absolute scale allows us to benchmark the calculated formation energies, identify transition states and compare the results to experiment. Based on these results we discuss the performance of various DFT xc-functionals to predict charge transfer levels and photo-emission experiments.

  19. Coupled ion Binding and Structural Transitions Along the Transport Cycle of Glutamate Transporters

    SciTech Connect

    Verdon, Gregory; Oh, SeCheol; Serio, Ryan N.; Boudker, Olga

    2014-05-19

    Membrane transporters that clear the neurotransmitter glutamate from synapses are driven by symport of sodium ions and counter-transport of a potassium ion. Previous crystal structures of a homologous archaeal sodium and aspartate symporter showed that a dedicated transport domain carries the substrate and ions across the membrane. We report new crystal structures of this homologue in ligand-free and ions-only bound outward- and inward-facing conformations. We then show that after ligand release, the apo transport domain adopts a compact and occluded conformation that can traverse the membrane, completing the transport cycle. Sodium binding primes the transport domain to accept its substrate and triggers extracellular gate opening, which prevents inward domain translocation until substrate binding takes place. Moreover, we describe a new cation-binding site ideally suited to bind a counter-transported ion. We suggest that potassium binding at this site stabilizes the translocation-competent conformation of the unloaded transport domain in mammalian homologues.

  20. Structural and electronic transitions in G e2S b2T e5 induced by ion irradiation damage

    NASA Astrophysics Data System (ADS)

    Privitera, S. M. S.; Mio, A. M.; Smecca, E.; Alberti, A.; Zhang, W.; Mazzarello, R.; Benke, J.; Persch, C.; La Via, F.; Rimini, E.

    2016-09-01

    G e2S b2T e5 polycrystalline films either in the trigonal stable phase or in the metastable rock-salt structure have been irradiated with 150 keV Ar+ ions. The effects of disorder are studied by electrical, optical, and structural measurements and density functional theory (DFT) simulations. In the metastable structure, the main effect of ion irradiation is a progressive amorphization, with an optical threshold at a fluence of 3 ×1013c m-2 . For the trigonal structure, a metal-insulator transition and a crystalline transition to rock-salt structure occur prior to amorphization, which requires a fluence of 8 ×1013c m-2 . The bonds of Te atoms close to the van der Waals gaps, present in the trigonal phase and identified by Raman spectroscopy, change as a function of the disorder induced by the irradiation. Comparison with DFT simulations shows that ion irradiation leads to the gradual filling of the van der Waals gaps with displaced Ge and Sb lattice atoms, giving rise first to a metal-insulator transition (9 % of displaced atoms) correlated to the modification of the Te bonds and then induces a structural transition to the metastable rock-salt phase (15 % of displaced atoms). The data presented here not only show the possibility to tune the degree of order, and therefore the electrical properties and the structure of phase change materials by ion irradiation, but also underline the importance of the van der Waals gaps in determining the transport mechanisms and the stability of the crystalline structure.

  1. Determination of lanthanide(III) ions by using a flotation-spectrophotometric method

    SciTech Connect

    Kang Jingwan; Zhang Xiaoling; Yang Huiling; Gao Jingzhang; Bai Guangbi )

    1990-01-01

    This paper reports the authors' attempt at determining Ln(III) ions by using a flotation-spectrophotometric method and their findings. When a ternary ion-association complex of Ln(III) coordinated by thiocyanate (SCN{sup {minus}}) and diantipyryl methane (DAM) is separated by a mixed solvent containing benzene and chloroform at pH 3.1 - 4.2, a third phase is observed between the aqueous and organic phases. The solid ternary complex can be dissolved in acetone that contains thenoyltrifluoroacetone (TTA). The individual Ln(III) ion can be determined by using the 4th derivative spectra directly. The equilibrium constant of the ternary composition ratio of Ln(III) to ligand is estimated by the equilibrium shift method. The mole ratio of Ln(III) to DAM and to SCN{sup {minus}} is 1:3 each. The composition of the ternary complex seems to be Ln(III):DAM:SCN{sup {minus}} = 1:3:3.

  2. Application of DV-SIA manifold for determination of thiocyanate ions in human saliva samples.

    PubMed

    Acebal, Carolina Cecilia; Sklenářová, Hana; Skrlíková, Jana; Srámková, Ivana; Andruch, Vasil; Balogh, Ioseph S; Solich, Petr

    2012-07-15

    An automated, simple and inexpensive double-valve sequential injection analysis (DV-SIA) spectrophotometic method with online liquid-liquid extraction, for the determination of thiocyanate has been developed. The method has been based on the formation of an ion associate between thiocyanate and Astra Phloxine in acidic medium, and the subsequent extraction with amylacetate. The absorbance of the extracted ion associate was measured at 550nm. The calibration function was linear in the range 0.05-0.50mmolL(-1) and the regression equation was A=(1.887±0.053) [SCN(-)mmolL(-1)]+(0.037±0.014) with a correlation coefficient of 0.995. The precision of the proposed method was evaluated by the relative standard deviation (RSD) values at two concentration levels: 0.20 and 0.50mmolL(-1). The obtained results were 1.0 and 2.8%, respectively, for the intra-day precision, and 4.2 and 3.8%, respectively for the inter-day precision. The calculated detection limit was 0.02mmolL(-1). The developed method has been successfully applied for determining thiocyanate ions in human saliva samples.

  3. Electrochemical determination of copper ions in spirit drinks using carbon paste electrode modified with biochar.

    PubMed

    Oliveira, Paulo Roberto; Lamy-Mendes, Alyne C; Rezende, Edivaltrys Inayve Pissinati; Mangrich, Antonio Sálvio; Marcolino, Luiz Humberto; Bergamini, Márcio F

    2015-03-15

    This work describes for first time the use of biochar as electrode modifier in combination with differential pulse adsorptive stripping voltammetric (DPAdSV) techniques for preconcentration and determination of copper (II) ions in spirit drinks samples (Cachaça, Vodka, Gin and Tequila). Using the best set of the experimental conditions a linear response for copper ions in the concentration range of 1.5 × 10(-6) to 3.1 × 10(-5) mol L(-1) with a Limit of Detection (LOD) of 4.0 × 10(-7) mol L(-1). The repeatability of the proposed sensor using the same electrode surface was measured as 3.6% and 6.6% using different electrodes. The effect of foreign species on the voltammetric response was also evaluated. Determination of copper ions content in different samples of spirit drinks samples was also realized adopting inductively coupled plasma optical emission spectroscopy (ICP-OES) and the results achieved are in agreement at a 95% of confidence level.

  4. Forging Fast Ion Conducting Nanochannels with Swift Heavy Ions: The Correlated Role of Local Electronic and Atomic Structure

    DOE PAGES

    Sachan, Ritesh; Cooper, Valentino R.; Liu, Bin; ...

    2016-12-19

    Atomically disordered oxides have attracted significant attention in recent years due to the possibility of enhanced ionic conductivity. However, the correlation between atomic disorder, corresponding electronic structure, and the resulting oxygen diffusivity is not well understood. The disordered variants of the ordered pyrochlore structure in gadolinium titanate (Gd2Ti2O7) are seen as a particularly interesting prospect due to intrinsic presence of a vacant oxygen site in the unit atomic structure, which could provide a channel for fast oxygen conduction. In this paper, we provide insights into the subangstrom scale on the disordering-induced variations in the local atomic environment and its effectmore » on the electronic structure in high-energy ion irradiation-induced disordered nanochannels, which can be utilized as pathways for fast oxygen ion transport. With the help of an atomic plane-by-plane-resolved analyses, the work shows how the presence of various types of TiOx polyhedral that exist in the amorphous and disordered crystalline phase modify the electronic structures relative to the ordered pyrochlore phase in Gd2Ti2O7. Finally, the correlated molecular dynamics simulations on the disordered structures show a remarkable enhancement in oxygen diffusivity as compared with ordered pyrochlore lattice and make that a suitable candidate for applications requiring fast oxygen conduction.« less

  5. Forging Fast Ion Conducting Nanochannels with Swift Heavy Ions: The Correlated Role of Local Electronic and Atomic Structure

    SciTech Connect

    Sachan, Ritesh; Cooper, Valentino R.; Liu, Bin; Aidhy, Dilpuneet S.; Voas, Brian K.; Lang, Maik; Ou, Xin; Trautmann, Christina; Zhang, Yanwen; Chisholm, Matthew F.; Weber, William J.

    2016-12-19

    Atomically disordered oxides have attracted significant attention in recent years due to the possibility of enhanced ionic conductivity. However, the correlation between atomic disorder, corresponding electronic structure, and the resulting oxygen diffusivity is not well understood. The disordered variants of the ordered pyrochlore structure in gadolinium titanate (Gd2Ti2O7) are seen as a particularly interesting prospect due to intrinsic presence of a vacant oxygen site in the unit atomic structure, which could provide a channel for fast oxygen conduction. In this paper, we provide insights into the subangstrom scale on the disordering-induced variations in the local atomic environment and its effect on the electronic structure in high-energy ion irradiation-induced disordered nanochannels, which can be utilized as pathways for fast oxygen ion transport. With the help of an atomic plane-by-plane-resolved analyses, the work shows how the presence of various types of TiOx polyhedral that exist in the amorphous and disordered crystalline phase modify the electronic structures relative to the ordered pyrochlore phase in Gd2Ti2O7. Finally, the correlated molecular dynamics simulations on the disordered structures show a remarkable enhancement in oxygen diffusivity as compared with ordered pyrochlore lattice and make that a suitable candidate for applications requiring fast oxygen conduction.

  6. Goadsporin, a chemical substance which promotes secondary metabolism and Morphogenesis in streptomycetes. II. Structure determination.

    PubMed

    Igarashi, Y; Kan, Y; Fujii, K; Fujita, T; Harada, K; Naoki, H; Tabata, H; Onaka, H; Furumai, T

    2001-12-01

    The structure of goadsporin was determined by using spectroscopic techniques. NMR analysis revealed that goadsporin consists of 19 amino acids, two of which are dehydroalanines (Deala), and six of which are cyclized to oxazoles (Oxz) and thiazoles (Thz) by dehydrative cyclization and dehydrogenation from serine, threonine and cysteine. NMR analysis established seven partial structures, and their sequence was determined by CID-MS/MS. Negative mode FAB-MS/MS gave product ions arising from charge-remote fragmentation that allowed determination of the sequence of the amino acid components as AcNH-Ala-MeOxz-Val-Deala-MeOxz-Ile-Leu-Thz-Ser-Gly-Gly-MeOxz-Leu-Deala-Oxz-Ala-Gly-Thz-Val-OH. The chiral amino acids were determined by the advanced Marfey's method to have L-configurations.

  7. Stripline fast faraday cup for measuring GHz structure of ion beams

    DOEpatents

    Bogaty, John M.

    1992-01-01

    The Stripline Fast Faraday Cup is a device which is used to quantitatively and qualitatively measure gigahertz time structure characteristics of ion beams with energies up to at least 30 Mev per nucleon. A stripline geometry is employed in conjunction with an electrostatic screen and a Faraday cup to provide for analysis of the structural characteristics of an ion beam. The stripline geometry allows for a large reduction in the size of the instrument while the electrostatic screen permits measurements of the properties associated with low speed ion beams.

  8. Shallow nitrogen ion implantation: Evolution of chemical state and defect structure in titanium

    NASA Astrophysics Data System (ADS)

    Manojkumar, P. A.; Chirayath, V. A.; Balamurugan, A. K.; Krishna, Nanda Gopala; Ilango, S.; Kamruddin, M.; Amarendra, G.; Tyagi, A. K.; Raj, Baldev

    2016-09-01

    Evolution of chemical states and defect structure in titanium during low energy nitrogen ion implantation by Plasma Immersion Ion Implantation (PIII) process is studied. The underlying process of chemical state evolution is investigated using secondary ion mass spectrometry and X-ray photoelectron spectroscopy. The implantation induced defect structure evolution as a function of dose is elucidated using variable energy positron annihilation Doppler broadening spectroscopy (PAS) and the results were corroborated with chemical state. Formation of 3 layers of defect state was modeled to fit PAS results.

  9. Ion-beam induced domain structure in piezoelectric PMN-PT single crystal

    SciTech Connect

    Kim, Kyou-Hyun; Payne, David A.; Zuo Jianmin

    2010-12-27

    We report an investigation of the domain structure in Pb(Mg{sub 1/3}Nb{sub 2/3})O{sub 3}-30%PbTiO{sub 3} single crystals after ion milling. We show that ion milling induces microdomains, typically 0.1-1 {mu}m in size. The induced microdomains disappear after temperature annealing or electric poling, leaving behind nanodomains of a few nanometers in size. We attribute the microdomains to surface stress induced by ion milling. The results demonstrate the general importance of separating sample preparation artifacts from the true domain structure in the study of ferroic materials.

  10. Electronic structure ‘engineering’ in the development of materials for Li-ion and Na-ion batteries

    NASA Astrophysics Data System (ADS)

    Molenda, Janina

    2017-03-01

    Transition metal oxides with a general formula A x M a O b (A  =  Li, Na, M  =  transition metal) constitute a group of potential electrode materials for a new generation of alkaline batteries. This application is related to the fact that these compounds can reversibly intercalate high amounts of alkaline ions (1 or more moles per mole of M a O b ) already at room temperature, without significant changes in their crystallographic structure. The author of this work basing on her own investigations of A x M a O b (A  =  Li, Na; M  =  3d, 4d, 5d) has demonstrated that the electronic structure of these materials plays an important role in the intercalation process. Electronic model of intercalation process is presented. Author’s studies show that electronic structure ‘engineering’ is an excellent method of controlling properties of the cathode materials for Li-ion and Na-ion batteries, changing their unfavorable character of the discharge curve, from step-like to monotonic, through modification and control density of states function of a cathode material. Keynote talk at 8th International Workshop on Advanced Materials Science and Nanotechnology (IWAMSN2016), 8–12 November 2016, Ha Long City, Vietnam.

  11. Magnetosheath Filamentary Structures Formed by Ion Acceleration at the Quasi-Parallel Bow Shock

    NASA Technical Reports Server (NTRS)

    Omidi, N.; Sibeck, D.; Gutynska, O.; Trattner, K. J.

    2014-01-01

    Results from 2.5-D electromagnetic hybrid simulations show the formation of field-aligned, filamentary plasma structures in the magnetosheath. They begin at the quasi-parallel bow shock and extend far into the magnetosheath. These structures exhibit anticorrelated, spatial oscillations in plasma density and ion temperature. Closer to the bow shock, magnetic field variations associated with density and temperature oscillations may also be present. Magnetosheath filamentary structures (MFS) form primarily in the quasi-parallel sheath; however, they may extend to the quasi-perpendicular magnetosheath. They occur over a wide range of solar wind Alfvénic Mach numbers and interplanetary magnetic field directions. At lower Mach numbers with lower levels of magnetosheath turbulence, MFS remain highly coherent over large distances. At higher Mach numbers, magnetosheath turbulence decreases the level of coherence. Magnetosheath filamentary structures result from localized ion acceleration at the quasi-parallel bow shock and the injection of energetic ions into the magnetosheath. The localized nature of ion acceleration is tied to the generation of fast magnetosonic waves at and upstream of the quasi-parallel shock. The increased pressure in flux tubes containing the shock accelerated ions results in the depletion of the thermal plasma in these flux tubes and the enhancement of density in flux tubes void of energetic ions. This results in the observed anticorrelation between ion temperature and plasma density.

  12. Void structure of O+ ions in the inner magnetosphere observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Nakayama, Y.; Ebihara, Y.; Ohtani, S.; Gkioulidou, M.; Takahashi, K.; Kistler, L. M.; Tanaka, T.

    2016-12-01

    The Van Allen Probes Helium Oxygen Proton Electron instrument observed a new type of enhancement of O+ ions in the inner magnetosphere during substorms. As the satellite moved outward in the premidnight sector, the flux of the O+ ions with energy 10 keV appeared first in the energy-time spectrograms. Then, the enhancement of the flux spread toward high and low energies. The enhanced flux of the O+ ions with the highest energy remained, whereas the flux of the ions with lower energy vanished near apogee, forming what we call the void structure. The structure cannot be found in the H+ spectrogram. We studied the generation mechanism of this structure by using numerical simulation. We traced the trajectories of O+ ions in the electric and magnetic fields from the global magnetohydrodynamics simulation and calculated the flux of O+ ions in the inner magnetosphere in accordance with the Liouville theorem. The simulated spectrograms are well consistent with the ones observed by Van Allen Probes. We suggest the following processes. (1) When magnetic reconnection starts, an intensive equatorward and tailward plasma flow appears in the plasma lobe. (2) The flow transports plasma from the lobe to the plasma sheet where the radius of curvature of the magnetic field line is small. (3) The intensive dawn-dusk electric field transports the O+ ions earthward and accelerates them nonadiabatically to an energy threshold; (4) the void structure appears at energies below the threshold.

  13. Magnetosheath filamentary structures formed by ion acceleration at the quasi-parallel bow shock

    NASA Astrophysics Data System (ADS)

    Omidi, N.; Sibeck, D.; Gutynska, O.; Trattner, K. J.

    2014-04-01

    Results from 2.5-D electromagnetic hybrid simulations show the formation of field-aligned, filamentary plasma structures in the magnetosheath. They begin at the quasi-parallel bow shock and extend far into the magnetosheath. These structures exhibit anticorrelated, spatial oscillations in plasma density and ion temperature. Closer to the bow shock, magnetic field variations associated with density and temperature oscillations may also be present. Magnetosheath filamentary structures (MFS) form primarily in the quasi-parallel sheath; however, they may extend to the quasi-perpendicular magnetosheath. They occur over a wide range of solar wind Alfvénic Mach numbers and interplanetary magnetic field directions. At lower Mach numbers with lower levels of magnetosheath turbulence, MFS remain highly coherent over large distances. At higher Mach numbers, magnetosheath turbulence decreases the level of coherence. Magnetosheath filamentary structures result from localized ion acceleration at the quasi-parallel bow shock and the injection of energetic ions into the magnetosheath. The localized nature of ion acceleration is tied to the generation of fast magnetosonic waves at and upstream of the quasi-parallel shock. The increased pressure in flux tubes containing the shock accelerated ions results in the depletion of the thermal plasma in these flux tubes and the enhancement of density in flux tubes void of energetic ions. This results in the observed anticorrelation between ion temperature and plasma density.

  14. The Structure and Transport of Water and Hydrated Ions Within Hydrophobic, Nanoscale Channels

    SciTech Connect

    Holt, J K; Herberg, J L; Wu, Y; Schwegler, E; Mehta, A

    2009-06-15

    The purpose of this project includes an experimental and modeling investigation into water and hydrated ion structure and transport at nanomaterials interfaces. This is a topic relevant to understanding the function of many biological systems such as aquaporins that efficiently shuttle water and ion channels that permit selective transport of specific ions across cell membranes. Carbon nanotubes (CNT) are model nanoscale, hydrophobic channels that can be functionalized, making them artificial analogs for these biological channels. This project investigates the microscopic properties of water such as water density distributions and dynamics within CNTs using Nuclear Magnetic Resonance (NMR) and the structure of hydrated ions at CNT interfaces via X-ray Absorption Spectroscopy (XAS). Another component of this work is molecular simulation, which can predict experimental measurables such as the proton relaxation times, chemical shifts, and can compute the electronic structure of CNTs. Some of the fundamental questions this work is addressing are: (1) what is the length scale below which nanoscale effects such as molecular ordering become important, (2) is there a relationship between molecular ordering and transport?, and (3) how do ions interact with CNT interfaces? These are questions of interest to the scientific community, but they also impact the future generation of sensors, filters, and other devices that operate on the nanometer length scale. To enable some of the proposed applications of CNTs as ion filtration media and electrolytic supercapacitors, a detailed knowledge of water and ion structure at CNT interfaces is critical.

  15. Gas phase studies of the Pesci decarboxylation reaction: synthesis, structure, and unimolecular and bimolecular reactivity of organometallic ions.

    PubMed

    O'Hair, Richard A J; Rijs, Nicole J

    2015-02-17

    promoting the formation of the organometallic ion. Where isomeric organometallic ions are generated and normal MS approaches cannot distinguish them, we describe approaches to elucidate the decarboxylation mechanism via determination of their structure. These "unmasked" organometallic ions, [RM(L)n](x), can also be structurally interrogated spectroscopically or via CID. We have thus compared the gas-phase structures and decomposition of several highly reactive and synthetically important organometallic ions for the first time. Perhaps the most significant aspect of this work is the study of bimolecular reactions, which provides experimental information on mechanistically obscure bond-formation and cross-coupling steps and the intrinsic reactivity of ions. We have sought to understand transformations of substrates including acid-base and hydrolysis reactions, along with reactions resulting in C-C bond formation. Our studies also allow a direct comparison of the performance of different metal catalysts in the individual elementary steps associated with protodecarboxylation and decarboxylative alkylation cycles. Electronic structure (DFT and ab initio) and dynamics (RRKM) calculations provide further mechanistic insights into these reactions. The broad implications of this research are that new reactions can be discovered and that the performance of metal catalysts can be evaluated in terms of each of their elementary steps. This has been particularly useful for the study of metal-mediated decarboxylation reactions.

  16. Automating the determination of 3D protein structure

    SciTech Connect

    Rayl, K.D.

    1993-12-31

    The creation of an automated method for determining 3D protein structure would be invaluable to the field of biology and presents an interesting challenge to computer science. Unfortunately, given the current level of protein knowledge, a completely automated solution method is not yet feasible, therefore, our group has decided to integrate existing databases and theories to create a software system that assists X-ray crystallographers in specifying a particular protein structure. By breaking the problem of determining overall protein structure into small subproblems, we hope to come closer to solving a novel structure by solving each component. By generating necessary information for structure determination, this method provides the first step toward designing a program to determine protein conformation automatically.

  17. Corrosion of Carbon Steel and Corrosion-Resistant Rebars in Concrete Structures Under Chloride Ion Attack

    NASA Astrophysics Data System (ADS)

    Mohamed, Nedal; Boulfiza, Mohamed; Evitts, Richard

    2013-03-01

    Corrosion of reinforced concrete is the most challenging durability problem that threatens reinforced concrete structures, especially structures that are subject to severe environmental conditions (i.e., highway bridges, marine structures, etc.). Corrosion of reinforcing steel leads to cracking and spalling of the concrete cover and billions of dollars are spent every year on repairing such damaged structures. New types of reinforcements have been developed to avoid these high-cost repairs. Thus, it is important to study the corrosion behavior of these new types of reinforcements and compare them to the traditional carbon steel reinforcements. This study aimed at characterizing the corrosion behavior of three competing reinforcing steels; conventional carbon steel, micro-composite steel (MMFX-2) and 316LN stainless steel, through experiments in carbonated and non-carbonated concrete exposed to chloride-laden environments. Synthetic pore water solutions have been used to simulate both cases of sound and carbonated concrete under chloride ions attack. A three-electrode corrosion cell is used for determining the corrosion characteristics and rates. Multiple electrochemical techniques were applied using a Gamry PC4™ potentiostat manufactured by Gamry Instruments (Warminster, PA). DC corrosion measurements were applied on samples subjected to fixed chloride concentration in the solution.

  18. Ion chromatographic separation and determination of phosphate and arsenate in water and hair.

    PubMed

    Antony, P J; Karthikeyan, S; Iyer, C S P

    2002-02-15

    A simple and sensitive method for the sequential determination of phosphate and arsenate was developed based on initial ion chromatographic separation followed by detection as the ion-association complex formed by heteropolymolybdophosphate and arsenate with bismuth. With 200 microl sample injection and separation on a AS4A-SC column using an eluent of 3.5 mM sodium hydrogen carbonate-10.0 mM sodium hydroxide, the detection limits which are calculated as the concentration equivalent to twice the baseline noise, were found to be 0.8 microg/l and 4.2 microg/l for P and As, respectively. Spiked samples were analyzed and recoveries were found to be satisfactory in the range of 95-105% for phosphate and 90-105% for arsenate. Samples of water and hair were analyzed by the proposed method.

  19. Qualitative and quantitative determination of nitrite and nitrate with ion chromatography.

    PubMed

    Kissner, Reinhard; Koppenol, Willem H

    2005-01-01

    Reactions of nitrogen monoxide and peroxynitrite often yield nitrite and nitrate as stable end products. The simultaneous detection of these two ions by anion chromatography with conductivity detection is described. The chromatographic system used is similar to conventional isocratic or gradient high-performance liquid chromatography equipment. The columns are packed with ion-exchanging resins instead of silica-derived adsorbents. Conductivity, though inherently nonspecific, has the advantage of covering a linear dynamic signal range of five orders of magnitude, which is far better than spectroscopic techniques; these are generally limited to two orders of magnitude. Typical run times per chromatogram are 15-30 min, and sample and standard concentrations can be between 100 nM and 10 mM. Injection volumes vary from 5 to 200 microl. Unlike with the Griess method, which determines only nitrite, a true mass balance from independent signals can be obtained if nitrate and nitrite are the only products.

  20. Ion Uptake Determination of Dendrochronologically-Dated Trees Using Neutron Activation Analysis

    SciTech Connect

    Kenan Unlu; P.I. Kuniholm; D.K.H. Schwarz; N.O. Cetiner; J.J. Chiment

    2009-03-30

    Uptake of metal ions by plan roots is a function of the type and concentration of metal in the soil, the nutrient biochemistry of the plant, and the immediate environment of the root. Uptake of gold (Au) is known to be sensitive to soil pH for many species. Soil acidification due to acid precipitation following volcanic eruptions can dramatically increase Au uptake by trees. Identification of high Au content in tree rings in dendrochronologically-dated, overlapping sequences of trees allows the identification of temporally-conscribed, volcanically-influenced periods of environmental change. Ion uptake, specifically determination of trace amounts of gold, was performed for dendrochronologically-dated tree samples utilizing Neutron Activation Analysis (NAA) technique. The concentration of gold was correlated with known enviironmental changes, e.g. volcanic activities, during historic periods.

  1. Quantitative determination of Mg in Al-alloys by ion-exchange TLC

    SciTech Connect

    Petrovic, M.; Kastelan-Macan, M. . Lab. for Analytical Chemistry); Turina, S.; Ivankovic, V. . Faculty of Mechanical Engineering and Naval Architecture)

    1993-01-01

    Analytical procedure for the quantitative determination of Mg in Al-alloys using ion-exchange thin layer chromatography is described. Chromatographic plates were coated with Amberlite IRP-69 (strong-acid cation exchanger in H[sup +]-form) mixed in different ratios with microcrystalline cellulose. Solutions of HCl and HNO[sub 3] respectively, in the concentration range from 0.5-2.0 mol dm[sup [minus]3] were used as developers. Chromatograms were visualized by spraying with ethanolic solution of 8-hydroxyquinoline and spots were scanned using Camag Turner Fluorometer 111. The optical separation was obtained on TLC plates containing 23% of ion-exchanger (particle size < 60 [mu]m) and by eluting with 1.25 M HCl. R[sub F] (Al) = 0.12, R[sub F](Mg) = 0.41.

  2. Determination of the deposition order of overlapping latent fingerprints and inks using secondary ion mass spectrometry.

    PubMed

    Bright, Nicholas J; Webb, Roger P; Bleay, Stephen; Hinder, Steven; Ward, Neil I; Watts, John F; Kirkby, Karen J; Bailey, Melanie J

    2012-05-01

    A new protocol using time-of-flight secondary ion mass spectrometry (ToF-SIMS) has been developed to identify the deposition order of a fingerprint overlapping an ink line on paper. By taking line scans of fragment ions characteristic of the ink molecules (m/z 358.2 and 372.2) where the fingerprint and ink overlap and by calculating the normalized standard deviation of the intensity variation across the line scan, it is possible to determine whether or not a fingerprint is above ink on a paper substrate. The protocol adopted works for a selection of fingerprints from four donors tested here and for a fingerprint that was aged for six months; for one donor, the very faint fingerprints could not be visualized using either standard procedures (ninhydrin development) or SIMS, and therefore the protocol correctly gives an inconclusive result.

  3. Algorithms for Determining Physical Responses of Structures Under Load

    NASA Technical Reports Server (NTRS)

    Richards, W. Lance; Ko, William L.

    2012-01-01

    Ultra-efficient real-time structural monitoring algorithms have been developed to provide extensive information about the physical response of structures under load. These algorithms are driven by actual strain data to measure accurately local strains at multiple locations on the surface of a structure. Through a single point load calibration test, these structural strains are then used to calculate key physical properties of the structure at each measurement location. Such properties include the structure s flexural rigidity (the product of the structure's modulus of elasticity, and its moment of inertia) and the section modulus (the moment of inertia divided by the structure s half-depth). The resulting structural properties at each location can be used to determine the structure s bending moment, shear, and structural loads in real time while the structure is in service. The amount of structural information can be maximized through the use of highly multiplexed fiber Bragg grating technology using optical time domain reflectometry and optical frequency domain reflectometry, which can provide a local strain measurement every 10 mm on a single hair-sized optical fiber. Since local strain is used as input to the algorithms, this system serves multiple purposes of measuring strains and displacements, as well as determining structural bending moment, shear, and loads for assessing real-time structural health. The first step is to install a series of strain sensors on the structure s surface in such a way as to measure bending strains at desired locations. The next step is to perform a simple ground test calibration. For a beam of length l (see example), discretized into n sections and subjected to a tip load of P that places the beam in bending, the flexural rigidity of the beam can be experimentally determined at each measurement location x. The bending moment at each station can then be determined for any general set of loads applied during operation.

  4. Electrostatic Propulsion Beam Divergence Effects on Spacecraft Surfaces. Volume 2, Addendum 1: 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

    The analysis of ion exhaust beam current flow for multiply charged ion species and the application to propellant utilization for the thruster are discussed. The ion engine in use in the experiments is a twenty centimeter diameter electromagnet electron bombardment engine. The experimental technique to determine the multiply charged ion abundance ratios using ion time of flight is described. An analytical treatment of the discharge action in producing various ion species has been carried out.

  5. Target selection and determination of function in structural genomics.

    PubMed

    Watson, James D; Todd, Annabel E; Bray, James; Laskowski, Roman A; Edwards, Aled; Joachimiak, Andrzej; Orengo, Christine A; Thornton, Janet M

    2003-01-01

    The first crucial step in any structural genomics project is the selection and prioritization of target proteins for structure determination. There may be a number of selection criteria to be satisfied, including that the proteins have novel folds, that they be representatives of large families for which no structure is known, and so on. The better the selection at this stage, the greater is the value of the structures obtained at the end of the experimental process. This value can be further enhanced once the protein structures have been solved if the functions of the given proteins can also be determined. Here we describe the methods used at either end of the experimental process: firstly, sensitive sequence comparison techniques for selecting a high-quality list of target proteins, and secondly the various computational methods that can be applied to the eventual 3D structures to determine the most likely biochemical function of the proteins in question.

  6. Laser-heating thermal modulation voltammetric determination of phosphate ion using a graphite-reinforced carbon electrode.

    PubMed

    Shariar, Shovon Mohammad; Suga, Mizuki; Nishikawa, Yumiko; Hinoue, Teruo

    2009-04-01

    Thermal modulation (TM) voltammetry was successfully applied to the determination of phosphate ion in natural water, by using a He-Cd dual laser as a heating source and a graphite-reinforced carbon (GRC) electrode. A heteropoly ion, i.e., 12-molybdophosphate ion ([PMo(VI)(12)O(40)](3-)), was formed through a reaction between a phosphate ion and molybdate ions in an acidic solution, and its electroreduction was examined in a flow electrolytic cell by TM voltammetry. Measured TM voltammograms showed two peaks corresponding to two successive two-electron reductions of the 12-molybdophosphate ion, and the peak intensities were proportional to the concentration of the phosphate ion. Because of the strong adsorption of 12-molybdophosphate ion onto the GRC electrode, a detection limit as low as 0.8 nmol dm(-3) (S/N = 3) was achieved. The determination of phosphate ion in real samples (river water) was carried out by spectrophotometry (the molybdenum-blue method) and TM voltammetry, and the determination values obtained by both methods were in a good agreement with each other. These results prove the possibility of TM voltammetry as an electroanalytical method.

  7. Discovery and Structure Determination of the Orphan Enzyme Isoxanthopterin Deaminase

    SciTech Connect

    Hall, R.S.; Swaminathan, S.; Agarwal, R.; Hitchcock, D.; Sauder, J. M.; Burley, S. K.; Raushel, F. M.

    2010-05-25

    Two previously uncharacterized proteins have been identified that efficiently catalyze the deamination of isoxanthopterin and pterin 6-carboxylate. The genes encoding these two enzymes, NYSGXRC-9339a (gi|44585104) and NYSGXRC-9236b (gi|44611670), were first identified from DNA isolated from the Sargasso Sea as part of the Global Ocean Sampling Project. The genes were synthesized, and the proteins were subsequently expressed and purified. The X-ray structure of Sgx9339a was determined at 2.7 {angstrom} resolution (Protein Data Bank entry 2PAJ). This protein folds as a distorted ({beta}/{alpha}){sub 8} barrel and contains a single zinc ion in the active site. These enzymes are members of the amidohydrolase superfamily and belong to cog0402 within the clusters of orthologous groups (COG). Enzymes in cog0402 have previously been shown to catalyze the deamination of guanine, cytosine, S-adenosylhomocysteine, and 8-oxoguanine. A small compound library of pteridines, purines, and pyrimidines was used to probe catalytic activity. The only substrates identified in this search were isoxanthopterin and pterin 6-carboxylate. The kinetic constants for the deamination of isoxanthopterin with Sgx9339a were determined to be 1.0 s{sup -1}, 8.0 {micro}M, and 1.3 x 10{sup 5} M{sup -1} s{sup -1} (k{sub cat}, K{sub m}, and k{sub cat}/K{sub m}, respectively). The active site of Sgx9339a most closely resembles the active site for 8-oxoguanine deaminase (Protein Data Bank entry 2UZ9). A model for substrate recognition of isoxanthopterin by Sgx9339a was proposed on the basis of the binding of guanine and xanthine in the active site of guanine deaminase. Residues critical for substrate binding appear to be conserved glutamine and tyrosine residues that form hydrogen bonds with the carbonyl oxygen at C4, a conserved threonine residue that forms hydrogen bonds with N5, and another conserved threonine residue that forms hydrogen bonds with the carbonyl group at C7. These conserved active site

  8. Ion trap mass spectrometry in the structural analysis of haemoglobin peptides modified by epichlorohydrin and diepoxybutane.

    PubMed

    Miraglia, Nadia; Basile, Adriana; Pieri, Maria; Acampora, Antonio; Malorni, Livia; De Giulio, Beatrice; Sannolo, Nicola

    2002-01-01

    Ion trap mass spectrometry has been shown to be particularly suitable for the structural analysis of high molecular weight peptides directly fragmented in the mass analyser without needing further sub-digestion reactions. Here we report the advantages of using multi-stage ion trap mass spectrometry in the structural characterisation of haemoglobin alkylated with epichlorohydrin and diepoxybutane. Alkylated globins were digested with trypsin and the peptide mixtures were analysed by MS(3). This technique allows the sequential fragmentation of peptides under analysis, giving rise to MS(3) product ion spectra with additional information with respect to MS(2) mass spectra. The results obtained complete the previously reported structural characterisation of alkylated haemoglobin, demonstrating the potential of ion trap mass spectrometry.

  9. On the influence of ion exchange on the local structure of the titanosilicate ETS-10.

    PubMed

    Pavel, Claudiu C; Zibrowius, Bodo; Löffler, Elke; Schmidt, Wolfgang

    2007-07-14

    The effect of ion exchange with different monovalent cations (NH(4)(+), K(+), Na(+) and Cs(+)) on the local structure of the titanosilicate ETS-10 has been studied by (29)Si MAS NMR and Raman spectroscopy. Although X-ray diffraction shows no significant influence of ion exchange on the long range order, ammonium exchange is found to result in substantial damage to the local structure. Ion exchange experiments with alkali cations under significantly more acidic conditions clearly show that the structural damage brought about by ammonium exchange is not caused by the low pH of the exchange solution. The exchange with potassium and caesium ions also leads to significant changes in the (29)Si NMR and Raman spectra. However, these changes can largely be reversed by sodium back-exchange.

  10. Magnesium behavior and structural defects in Mg+ ion implanted silicon carbide

    NASA Astrophysics Data System (ADS)

    Jiang, Weilin; Jung, Hee Joon; Kovarik, Libor; Wang, Zhaoying; Roosendaal, Timothy J.; Zhu, Zihua; Edwards, Danny J.; Hu, Shenyang; Henager, Charles H.; Kurtz, Richard J.; Wang, Yongqiang

    2015-03-01

    As a candidate material for fusion reactor applications, silicon carbide (SiC) undergoes transmutation reactions under high-energy neutron irradiation with magnesium as the major metallic transmutant; the others include aluminum, beryllium and phosphorus in addition to helium and hydrogen gaseous species. The impact of these transmutants on SiC structural stability is currently unknown. This study uses ion implantation to introduce Mg into SiC. Multiaxial ion-channeling analysis of the as-produced damage state indicates a lower dechanneling yield observed along the <1 0 0> axis. The microstructure of the annealed sample was examined using high-resolution scanning transmission electron microscopy. The results show a high concentration of likely non-faulted tetrahedral voids and possible stacking fault tetrahedra near the damage peak. In addition to lattice distortion, dislocations and intrinsic and extrinsic stacking faults are also observed. Magnesium in 3C-SiC prefers to substitute for Si and it forms precipitates of cubic Mg2Si and tetragonal MgC2. The diffusion coefficient of Mg in 3C-SiC single crystal at 1573 K has been determined to be 3.8 ± 0.4 × 10-19 m2/s.

  11. Size-to-charge dispersion of collision-induced dissociation product ions for enhancement of structural information and product ion identification.

    PubMed

    Zinnel, Nathanael F; Russell, David H

    2014-05-20

    Ion mobility is used to disperse product ions formed by collision-induced dissociation (CID) on the basis of charge state and size-to-charge ratio. We previously described an approach for combining CID with ion mobility mass spectrometry (IM-MS) for dispersing fragment ions along charge state specific trend lines (Zinnel, N. F.; Pai, P. J.; Russell, D. H. Anal. Chem. 2012, 84, 3390; Sowell, R. A.; Koeniger, S. L.; Valentine, S. J.; Moon, M. H.; Clemmer, D. E. J. Am. Soc. Mass Spectrom. 2004, 15, 1341; McLean, J. A.; Ruotolo, B. T.; Gillig, K. J.; Russell, D. H. Int. J. Mass Spectrom. 2005, 240, 301), and this approach was used to assign metal ion binding sites for human metallothionein protein MT-2a (Chen, S. H.; Russell, W. K.; Russell, D. H. Anal. Chem. 2013, 85, 3229). Here, we use this approach to distinguish b-type N-terminal fragment ions from both internal fragment ions and y-type C-terminal fragment ions. We also show that in some cases specific secondary structural elements, viz., extended coils or helices, can be obtained for the y-type fragment ions series. The advantage of this approach is that product ion identity can be correlated to gas-phase ion structure, which provides rapid identification of the onset and termination of extended coil structure in peptides.

  12. Using support vector machines to improve elemental ion identification in macromolecular crystal structures

    DOE PAGES

    Morshed, Nader; Echols, Nathaniel; Adams, Paul D.

    2015-04-25

    In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalousmore » diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.« less

  13. Using support vector machines to improve elemental ion identification in macromolecular crystal structures

    SciTech Connect

    Morshed, Nader; Echols, Nathaniel; Adams, Paul D.

    2015-04-25

    In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.

  14. Using support vector machines to improve elemental ion identification in macromolecular crystal structures.

    PubMed

    Morshed, Nader; Echols, Nathaniel; Adams, Paul D

    2015-05-01

    In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.

  15. Lanthanide ion probes of structure in biology. Environmentally sensitive fine structure in laser-induced terbium(III) luminescence.

    PubMed

    Sudnick, D R; Horrocks, W D

    1979-05-23

    The 488 nm line of the CW argon ion laser provides a convenient visible source for the direct excitation of the emissive 5D4 state of the Tb(III) ion. Room temperature emission spectra of Tb(III) in a variety of environments have been examined under relatively high resolution. The samples studied include structurally well-characterized crystalline solids, model chelate complexes in solution and Tb(III) bound to the enzyme thermolysin and the protein parvalbumin. The fine structure in the emissions is caused by ligand field splittings of both ground and excited state J manifolds. These spectra provide signatures sensitive to the immediate coordination environment of the Tb(III) ion. Solid state/solution state structural comparisons are made. The emission fine structure reveal differences between the EF side calcium-binding sites of parvalbumin and the calcium site 1 of thermolysin.

  16. Identification of Ion-Pair Structures in Solution by Vibrational Stark Effects.

    PubMed

    Hack, John; Grills, David C; Miller, John R; Mani, Tomoyasu

    2016-02-18

    Ion pairing is a fundamental consideration in many areas of chemistry and has implications in a wide range of sciences and technologies that include batteries and organic photovoltaics. Ions in solution are known to inhabit multiple possible states, including free ions (FI), contact ion pairs (CIP), and solvent-separated ion pairs (SSIP). However, in solutions of organic radicals and nonmetal electrolytes, it is often difficult to distinguish between these states. In the first part of this work, we report evidence for the formation of SSIPs in low-polarity solvents and distinct measurements of CIP, SSIP, and FI, by using the ν(C≡N) infrared (IR) band of a nitrile-substituted fluorene radical anion. Use of time-resolved IR detection following pulse radiolysis allowed us to unambiguously assign the peak of the FI. In the presence of nonmetal electrolytes, two distinct red-shifted peaks were observed and assigned to the CIP and SSIP. The assignments are interpreted in the framework of the vibrational Stark effect (VSE) and are supported by (1) the solvent dependence of ion-pair populations, (2) the observation of a cryptand-separated sodium ion pair that mimics the formation of SSIPs, and (3) electronic structure calculations. In the second part of this work, we show that a blue-shift of the ν(C≡N) IR band due to the VSE can be induced in a nitrile-substituted fluorene radical anion by covalently tethering it to a metal-chelating ligand that forms an intramolecular ion pair upon reduction and complexation with sodium ion. This adds support to the conclusion that the shift in IR absorptions by ion pairing originates from the VSE. These results combined show that we can identify ion-pair structures by using the VSE, including the existence of SSIPs in a low-polarity solvent.

  17. Identification of ion-pair structures in solution by vibrational stark effects

    DOE PAGES

    Hack, John; Mani, Tomoyasu; Grills, David C.; ...

    2016-01-25

    Here, ion pairing is a fundamental consideration in many areas of chemistry and has implications in a wide range of sciences and technologies that include batteries and organic photovoltaics. Ions in solution are known to inhabit multiple possible states, including free ions (FI), contact ion pairs (CIP), and solvent-separated ion pairs (SSIP). However, in solutions of organic radicals and nonmetal electrolytes, it is often difficult to distinguish between these states. In the first part of this work, we report evidence for the formation of SSIPs in low-polarity solvents and distinct measurements of CIP, SSIP, and FI, by using the ν(C≡N)more » infrared (IR) band of a nitrile-substituted fluorene radical anion. Use of time-resolved IR detection following pulse radiolysis allowed us to unambiguously assign the peak of the FI. In the presence of nonmetal electrolytes, two distinct red-shifted peaks were observed and assigned to the CIP and SSIP. The assignments are interpreted in the framework of the vibrational Stark effect (VSE) and are supported by (1) the solvent dependence of ion-pair populations, (2) the observation of a cryptand-separated sodium ion pair that mimics the formation of SSIPs, and (3) electronic structure calculations. In the second part of this work, we show that a blue-shift of the ν(C≡N) IR band due to the VSE can be induced in a nitrile-substituted fluorene radical anion by covalently tethering it to a metal-chelating ligand that forms an intramolecular ion pair upon reduction and complexation with sodium ion. This adds support to the conclusion that the shift in IR absorptions by ion pairing originates from the VSE. These results combined show that we can identify ion-pair structures by using the VSE, including the existence of SSIPs in a low-polarity solvent.« less

  18. Identification of ion-pair structures in solution by vibrational stark effects

    SciTech Connect

    Hack, John; Mani, Tomoyasu; Grills, David C.; Miller, John R.

    2016-01-25

    Here, ion pairing is a fundamental consideration in many areas of chemistry and has implications in a wide range of sciences and technologies that include batteries and organic photovoltaics. Ions in solution are known to inhabit multiple possible states, including free ions (FI), contact ion pairs (CIP), and solvent-separated ion pairs (SSIP). However, in solutions of organic radicals and nonmetal electrolytes, it is often difficult to distinguish between these states. In the first part of this work, we report evidence for the formation of SSIPs in low-polarity solvents and distinct measurements of CIP, SSIP, and FI, by using the ν(C≡N) infrared (IR) band of a nitrile-substituted fluorene radical anion. Use of time-resolved IR detection following pulse radiolysis allowed us to unambiguously assign the peak of the FI. In the presence of nonmetal electrolytes, two distinct red-shifted peaks were observed and assigned to the CIP and SSIP. The assignments are interpreted in the framework of the vibrational Stark effect (VSE) and are supported by (1) the solvent dependence of ion-pair populations, (2) the observation of a cryptand-separated sodium ion pair that mimics the formation of SSIPs, and (3) electronic structure calculations. In the second part of this work, we show that a blue-shift of the ν(C≡N) IR band due to the VSE can be induced in a nitrile-substituted fluorene radical anion by covalently tethering it to a metal-chelating ligand that forms an intramolecular ion pair upon reduction and complexation with sodium ion. This adds support to the conclusion that the shift in IR absorptions by ion pairing originates from the VSE. These results combined show that we can identify ion-pair structures by using the VSE, including the existence of SSIPs in a low-polarity solvent.

  19. The Gellyfish: an in-situ equilibrium-based sampler for determining multiple free metal ion concentrations in marine ecosystems

    EPA Science Inventory

    Free metal ions are usually the most bioavailable and toxic metal species to aquatic organisms, but they are difficult to measure because of their extremely low concentrations in the marine environment. Many of the current methods for determining free metal ions are complicated a...

  20. Determination of Cu Concentrations in CdTe/CdS Devices by High Mass Resolution Secondary Ion Mass Spectrometry

    SciTech Connect

    Asher, S. E.; Reedy, R. C.; Dhere, R.; Gessert, t. A.; Young, M. R.

    2000-01-01

    We have used secondary ion mass spectrometry (SIMS) to quantitatively determine the concentration of Cu in CdTe/CdS devices. Empirical standards were fabricated by ion implantation of Cu into single-crystal and polycrystalline CdTe and single-crystal CdS.

  1. Hydrolysis Studies and Quantitative Determination of Aluminum Ions Using [superscript 27]Al NMR: An Undergraduate Analytical Chemistry Experiment

    ERIC Educational Resources Information Center

    Curtin, Maria A.; Ingalls, Laura R.; Campbell, Andrew; James-Pederson, Magdalena

    2008-01-01

    This article describes a novel experiment focused on metal ion hydrolysis and the equilibria related to metal ions in aqueous systems. Using [superscript 27]Al NMR, the students become familiar with NMR spectroscopy as a quantitative analytical tool for the determination of aluminum by preparing a standard calibration curve using standard aluminum…

  2. Li-Ion Localization and Energetics as a Function of Anode Structure.

    PubMed

    McNutt, Nicholas W; McDonnell, Marshall; Rios, Orlando; Keffer, David J

    2017-03-01

    In this work, we study the effect of carbon composite anode structure on the localization and energetics of Li-ions. A computational molecular dynamics study is combined with experimental results from neutron scattering experiments to understand the effect of composite density, crystallite size, volume fraction of crystalline carbon, and ion loading on the nature of ion storage in novel, lignin-derived composite materials. In a recent work, we demonstrated that these carbon composites display a fundamentally different mechanism for Li-ion storage than traditional graphitic anodes. The edges of the crystalline and amorphous fragments of aromatic carbon that exist in these composites are terminated by hydrogen atoms, which play a crucial role in adsorption. In this work, we demonstrate how differences in composite structure due to changes in the processing conditions alter the type and extent of the interface between the amorphous and crystalline domains, thus impacting the nature of Li-ion storage. The effects of structural properties are evaluated using a suite of pair distribution functions as well as an original technique to extract archetypal structures, in the form of three-dimensional atomic density distributions, from highly disordered systems. The energetics of Li-ion binding are understood by relating changes in the energy and charge distributions to changes in structural properties. The distribution of Li-ion energies reveals that some structures lead to greater chemisorption, while others have greater physisorption. Carbon composites with a high volume fraction of small crystallites demonstrate the highest ion storage capacity because of the high interfacial area between the crystalline and amorphous domains. At these interfaces, stable H atoms, terminating the graphitic crystallites, provide favorable sites for reversible Li adsorption.

  3. Sheath structure in plasmas with nonextensively distributed electrons and thermal ions

    SciTech Connect

    Hatami, M. M.

    2015-02-15

    Sheath region of an electropositive plasma consisting of q-nonextensive electrons and singly charged positive ions with finite temperature is modeled. Using Sagdeev's pseudo potential technique to derive the modified sheath formation criterion, it is shown that the velocity of ions at the sheath edge is directly proportional to the ion temperatures and inversely proportional to the degree of nonextensivity of electrons (q-parameter). Using the modified Bohm criterion, effect of degree of nonextensivity of electrons and temperature of positive ions on the characteristics of the sheath region are investigated numerically. It is shown that an increase in the ion temperature gives rise to an increase in the electrostatic potential and the velocity of ions in the sheath regardless of the value of q. Furthermore, it is seen that the sheath width and the density distribution of the charged particles decrease by increasing the temperature of positive ions. In addition, it is found that the positive ion temperature is less effective on the sheath structure for higher values of the q-parameter. Finally, the results obtained for a thermal plasma with nonextensively distributed electrons are compared with the results of a cold plasma with nonextensive electrons and an extensive (Maxwellian) plasma with thermal ions.

  4. Determination of chloroacetic acids in drinking water using suppressed ion chromatography with solid-phase extraction.

    PubMed

    Yoshikawa, Kenji; Soda, Yuko; Sakuragawa, Akio

    2009-12-01

    Suppressed ion chromatography with a conductivity detector was developed for the determination of trace amounts of underivatized chloroacetic acids (CAAs). When sodium carbonate and methanol were used as a mobile phase, the simultaneous determination of each CAA took approximately 25 min. The linearity, reproducibility and detection limits were determined for the proposed method. For the solid-phase extraction step, the effects of the pH of the sample solution, sample volume and the eluting agent were tested. Under the optimized extracting conditions, the average recoveries for CAAs spiked in tap water were 83-107%, with an optimal preconcentration factor of 20. The reproducibility of recovery rate for CAAs was 1.2-3.8%, based upon 6 repetitions of the recovery experiments.

  5. Calculation of Heavy Ion Inactivation and Mutation Rates in Radial Dose Model of Track Structure

    NASA Technical Reports Server (NTRS)

    Cucinotta, Francis A.; Wilson, John W.; Shavers, Mark R.; Katz, Robert

    1997-01-01

    In the track structure model, the inactivation cross section is found by summing an inactivation probability over all impact parameters from the ion to the sensitive sites within the cell nucleus. The inactivation probability is evaluated by using the dose response of the system to gamma rays and the radial dose of the ions and may be equal to unity at small impact parameters. We apply the track structure model to recent data with heavy ion beams irradiating biological samples of E. Coli, B. Subtilis spores, and Chinese hamster (V79) cells. Heavy ions have observed cross sections for inactivation that approach and sometimes exceed the geometric size of the cell nucleus. We show how the effects of inactivation may be taken into account in the evaluation of the mutation cross sections in the track structure model through correlation of sites for gene mutation and cell inactivation. The model is fit to available data for HPRT (hypoxanthine guanine phosphoribosyl transferase) mutations in V79 cells, and good agreement is found. Calculations show the high probability for mutation by relativistic ions due to the radial extension of ions track from delta rays. The effects of inactivation on mutation rates make it very unlikely that a single parameter such as LET (linear energy transfer) can be used to specify radiation quality for heavy ion bombardment.

  6. Effect of calcium/sodium ion exchange on the osmotic properties and structure of polyelectrolyte gels.

    PubMed

    Horkay, Ferenc; Basser, Peter J; Hecht, Anne-Marie; Geissler, Erik

    2015-12-01

    We discuss the main findings of a long-term research program exploring the consequences of sodium/calcium ion exchange on the macroscopic osmotic and elastic properties, and the microscopic structure of representative synthetic polyelectrolyte (sodium polyacrylate, (polyacrylic acid)) and biopolymer gels (DNA). A common feature of these gels is that above a threshold calcium ion concentration, they exhibit a reversible volume phase transition. At the macroscopic level, the concentration dependence of the osmotic pressure shows that calcium ions influence primarily the third-order interaction term in the Flory-Huggins model of polymer solutions. Mechanical tests reveal that the elastic modulus is practically unaffected by the presence of calcium ions, indicating that ion bridging does not create permanent cross-links. At the microscopic level, small-angle neutron scattering shows that polyacrylic acid and DNA gels exhibit qualitatively similar structural features in spite of important differences (e.g. chain flexibility and chemical composition) between the two polymers. The main effect of calcium ions is that the neutron scattering intensity increases due to the decrease in the osmotic modulus. At the level of the counterion cloud around dissolved macroions, anomalous small-angle X-ray scattering measurements made on DNA indicate that divalent ions form a cylindrical sheath enveloping the chain, but they are not localized. Small-angle neutron scattering and small-angle X-ray scattering provide complementary information on the structure and interactions in polymer solutions and gels.

  7. Protein Structure Determination Using Protein Threading and Sparse NMR Data

    SciTech Connect

    Crawford, O.H.; Einstein, J.R.; Xu, D.; Xu, Y.

    1999-11-14

    It is well known that the NMR method for protein structure determination applies to small proteins and that its effectiveness decreases very rapidly as the molecular weight increases beyond about 30 kD. We have recently developed a method for protein structure determination that can fully utilize partial NMR data as calculation constraints. The core of the method is a threading algorithm that guarantees to find a globally optimal alignment between a query sequence and a template structure, under distance constraints specified by NMR/NOE data. Our preliminary tests have demonstrated that a small number of NMR/NOE distance restraints can significantly improve threading performance in both fold recognition and threading-alignment accuracy, and can possibly extend threading's scope of applicability from structural homologs to structural analogs. An accurate backbone structure generated by NMR-constrained threading can then provide a significant amount of structural information, equivalent to that provided by the NMR method with many NMR/NOE restraints; and hence can greatly reduce the amount of NMR data typically required for accurate structure determination. Our preliminary study suggests that a small number of NMR/NOE restraints may suffice to determine adequately the all-atom structure when those restraints are incorporated in a procedure combining threading, modeling of loops and sidechains, and molecular dynamics simulation. Potentially, this new technique can expand NMR's capability to larger proteins.

  8. Determining the surface and interface structure of nanomaterials

    SciTech Connect

    Van Hove, Michel A.

    2004-06-14

    This paper informally speculates on the challenges of determining the atomic-scale surface and interface structure of nanomaterials. The relative capabilities of different techniques are compared. This includes discussion of theoretical methods needed to interpret experimental techniques.

  9. Determination of Inorganic Cations and Anions in Chitooligosaccharides by Ion Chromatography with Conductivity Detection.

    PubMed

    Cao, Lidong; Li, Xiuhuan; Fan, Li; Zheng, Li; Wu, Miaomiao; Zhang, Shanxue; Huang, Qiliang

    2017-02-22

    Chitooligosaccharides (COSs) are a promising drug candidate and food ingredient because they are innately biocompatible, non-toxic, and non-allergenic to living tissues. Therefore, the impurities in COSs must be clearly elucidated and precisely determined. As for COSs, most analytical methods focus on the determination of the average degrees of polymerization (DPs) and deacetylation (DD), as well as separation and analysis of the single COSs with different DPs. However, little is known about the concentrations of inorganic cations and anions in COSs. In the present study, an efficient and sensitive ion chromatography coupled with conductivity detection (IC-CD) for the determination of inorganic cations Na⁺, NH₄⁺, K⁺, Mg(2+), Ca(2+), and chloride, acetate and lactate anions was developed. Detection limits were 0.01-0.05 μM for cations and 0.5-0.6 μM for anions. The linear range was 0.001-0.8 mM. The optimized analysis was carried out on IonPac CS12A and IonPac AS12A analytical column for cations and anions, respectively, using isocratic elution with 20 mM methanesulfonic acid and 4 mM sodium hydroxide aqueous solution as the mobile phase at a 1.0 mL/min flow rate. Quality parameters, including precision and accuracy, were fully validated and found to be satisfactory. The fully validated IC-CD method was readily applied for the quantification of various cations and anions in commercial COS technical concentrate.

  10. Determination of Inorganic Cations and Anions in Chitooligosaccharides by Ion Chromatography with Conductivity Detection

    PubMed Central

    Cao, Lidong; Li, Xiuhuan; Fan, Li; Zheng, Li; Wu, Miaomiao; Zhang, Shanxue; Huang, Qiliang

    2017-01-01

    Chitooligosaccharides (COSs) are a promising drug candidate and food ingredient because they are innately biocompatible, non-toxic, and non-allergenic to living tissues. Therefore, the impurities in COSs must be clearly elucidated and precisely determined. As for COSs, most analytical methods focus on the determination of the average degrees of polymerization (DPs) and deacetylation (DD), as well as separation and analysis of the single COSs with different DPs. However, little is known about the concentrations of inorganic cations and anions in COSs. In the present study, an efficient and sensitive ion chromatography coupled with conductivity detection (IC-CD) for the determination of inorganic cations Na+, NH4+, K+, Mg2+, Ca2+, and chloride, acetate and lactate anions was developed. Detection limits were 0.01–0.05 μM for cations and 0.5–0.6 μM for anions. The linear range was 0.001–0.8 mM. The optimized analysis was carried out on IonPac CS12A and IonPac AS12A analytical column for cations and anions, respectively, using isocratic elution with 20 mM methanesulfonic acid and 4 mM sodium hydroxide aqueous solution as the mobile phase at a 1.0 mL/min flow rate. Quality parameters, including precision and accuracy, were fully validated and found to be satisfactory. The fully validated IC-CD method was readily applied for the quantification of various cations and anions in commercial COS technical concentrate. PMID:28241416

  11. Orientation and electronic structure of ion exchanged dye molecules on mica: An X-ray absorption study

    SciTech Connect

    Fischer, D.; Caseri, W.R.; Haehner, G.

    1998-02-15

    Dye molecules are frequently used to determine the specific surface area and the ion exchange capacity of high-surface-area materials such as mica. The organic molecules are often considered to be planar and to adsorb in a flat orientation. In the present study the authors have investigated the orientation and electronic structure of crystal violet (CV) and malachite green (MG) on muscovite mica, prepared by immersing the substrates for extended periods into aqueous solutions of the dyes of various concentrations. The K{sup +} ions of the mica surface are replaced by the organic cations via ion exchange. X-ray photoelectron spectroscopy reveals that only one amino group is involved in the interaction of CV and MG with the muscovite surface, i.e., certain resonance structures are abolished upon adsorption. With near edge X-ray absorption fine structure spectroscopy a significant tilt angle with respect to the surface was found for all investigated species. A flat orientation, as has often been proposed before, can effectively be ruled out. Hence, results are in marked contrast to the often quoted orientation and suggest that the specific surface areas determined with dyes may, in general, be overestimated.

  12. A novel polymer inclusion membranes based optode for sensitive determination of Al3+ ions

    NASA Astrophysics Data System (ADS)

    Suah, Faiz Bukhari Mohd; Ahmad, Musa; Heng, Lee Yook

    2015-06-01

    A novel approach for the determination of Al3+ from aqueous samples was developed using an optode membrane produced by physical inclusion of Al3+ selective reagent, which is morin into a plasticized poly(vinyl chloride). The inclusion of Triton X-100 was found to be valuable and useful for enhancing the sorption of Al3+ ions from liquid phase into the membrane phase, thus increasing the intensity of optode's absorption. The optode showed a linear increase in the absorbance at λmax = 425 nm over the concentration range of 1.85 × 10-6-1.1 × 10-4 mol L-1 (0.05-3 μg mL-1) of Al3+ ions in aqueous solution after 5 min. The limit of detection was determined to be 1.04 × 10-6 mol L-1 (0.028 μg mL-1). The optode developed in the present work was easily prepared and found to be stable, has good mechanical strength, sensitive and reusable. In addition, the optode was tested for Al3+ determination in lake water, river water and pharmaceutical samples, which the result was satisfactory.

  13. [Determination of nucleotides in infant formula milk powder by ion chromatography].

    PubMed

    Ye, Mingli; Pan, Guangwen; Hu, Zhongyang; Wang, Qiong

    2010-09-01

    A method was developed for the determination of nucleotides in infant formula milk powder by ion chromatography (IC). The separation was performed on an IonPac AS16 column with KOH solution as the mobile phase at a flow rate of 1.0 mL/min and 25 degrees C. The detection wavelength was set at 260 nm and the sample injection volume was 25 microL. There were good linear relationships between the mass concentrations and the peak areas of cytidine monophosphate (CMP), adenosine monophosphate (AMP), uridine monophosphate (UMP), inosine monophosphate (IMP) and guanosine monophosphate (GMP) in the ranges of 0.09-50, 0.06-50, 0.06-50, 0.09-50, 0.06-50 mg/L, respectively. The limits of detection (S/N = 3) of CMP, AMP, UMP, IMP and GMP were 0.03, 0.02, 0.02, 0.03 and 0.02 mg/L, respectively. The method has been applied for the determination of the five nucleotides in infant formula milk powder with the recoveries of 92.5%-102.4%. This method is rapid, simple and suitable for the determination of real samples.

  14. Ambiguity of structure determination from a minimum of diffraction intensities.

    PubMed

    Al-Asadi, Ahmed; Leggas, Dimitri; Tsodikov, Oleg V

    2014-07-01

    Although the ambiguity of the crystal structures determined directly from diffraction intensities has been historically recognized, it is not well understood in quantitative terms. Bernstein's theorem has recently been used to obtain the number of one-dimensional crystal structures of equal point atoms, given a minimum set of diffraction intensities. By a similar approach, the number of two- and three-dimensional crystal structures that can be determined from a minimum intensity data set is estimated herein. The ambiguity of structure determination from the algebraic minimum of data increases at least exponentially fast with the increasing structure size. Substituting lower-resolution intensities by higher-resolution ones in the minimum data set has little or no effect on this ambiguity if the number of such substitutions is relatively small.

  15. Selective colorimetric and fluorescent quenching determination of uranyl ion via its complexation with curcumin

    NASA Astrophysics Data System (ADS)

    Zhu, Jing-Hui; Zhao, Xin; Yang, Jidong; Tan, Yu-Ting; Zhang, Lei; Liu, Shao-Pu; Liu, Zhong-Fang; Hu, Xiao-Li

    2016-04-01

    Under pH 4.0 HAc-NaAc buffer medium, curcumin alone possesses extraordinary weak fluorescence emission. Nevertheless, the introduction of Triton X-100 micelles can largely enhance the fluorescence intensity of curcumin. Uranyl ions can complex with micelles-capped curcumin, along with the slight red shift of curcumin fluorescence (about 1-7 nm), a clear decrement of absorbance (424 nm) and fluorescence (507 nm) intensities, and a distinct color change from bright yellow to orange. The fluorescence decrements (ΔF, 507 nm) are positively correlated to the amount of uranyl ions in the concentration range of 3.7 × 10- 6-1.4 × 10- 5 mol L- 1. The detection limit of this fluorescence quenching methods is 3.7 × 10- 6 mol L- 1, which is nearly 9000 times lower than the maximum allowable level in drinking water proposed by World Health Organization. Good selectivity is achieved because of a majority of co-existing substances (such as Ce4 +, La3 +, and Th4 +) do not affect the detection. The content of uranyl ions in tap water samples was determined by the proposed method with satisfactory results.

  16. Selective colorimetric and fluorescent quenching determination of uranyl ion via its complexation with curcumin.

    PubMed

    Zhu, Jing-Hui; Zhao, Xin; Yang, Jidong; Tan, Yu-Ting; Zhang, Lei; Liu, Shao-Pu; Liu, Zhong-Fang; Hu, Xiao-Li

    2016-04-15

    Under pH4.0 HAc-NaAc buffer medium, curcumin alone possesses extraordinary weak fluorescence emission. Nevertheless, the introduction of Triton X-100 micelles can largely enhance the fluorescence intensity of curcumin. Uranyl ions can complex with micelles-capped curcumin, along with the slight red shift of curcumin fluorescence (about 1-7 nm), a clear decrement of absorbance (424 nm) and fluorescence (507 nm) intensities, and a distinct color change from bright yellow to orange. The fluorescence decrements (ΔF, 507 nm) are positively correlated to the amount of uranyl ions in the concentration range of 3.7×10(-6)-1.4×10(-5) mol L(-1). The detection limit of this fluorescence quenching methods is 3.7×10(-6) mol L(-1), which is nearly 9000 times lower than the maximum allowable level in drinking water proposed by World Health Organization. Good selectivity is achieved because of a majority of co-existing substances (such as Ce(4+), La(3+), and Th(4+)) do not affect the detection. The content of uranyl ions in tap water samples was determined by the proposed method with satisfactory results.

  17. Validation of a sensitive ion chromatography method for determination of monoethylsulfate in Indinavir sulfate drug substance.

    PubMed

    Prasanna, S John; Sharma, Hemant Kumar; Mukkanti, K; Sivakumaran, M; Pavan Kumar, K S R; Kumar, V Jagadeesh

    2009-12-05

    The present study relates to the optimization of an ion chromatography method to determine the content of monoethylsulfate at very low levels in Indinavir sulfate drug substance, and subsequent validation of the method to prove its suitability, reliability and sensitivity. Monoethylsulfate is a potential impurity of Indinavir sulfate, and may forms during the preparation as well as during storage. The ion chromatography method was developed in such a way that to enhance the detection level by introducing suppressor, and minimizing acquisition time by using suitable buffer of 3.2 mmole of sodium carbonate and 1 mmole of sodium hydrogen carbonate in water as eluent. The retention time of monoethylsulfate was about 9.5 min and the total acquisition time was 25 min. The optimized method was validated to prove its performance characteristics by demonstrating selectivity, sensitivity (limit of detection and quantification), linearity, precision and accuracy. The established limit of detection and quantification of monoethylsulfate in Indinavir sulfate by this method was found to be 24 ng/ml and 74 ng/ml respectively, and the overall percent accuracy (recovery) of samples evaluated at different concentration levels was found to be 97.1, indicating the sensitivity and accuracy of this optimized ion chromatography method.

  18. Determination of trace sulfides in turbid waters by gas dialysis/ion chromatography

    SciTech Connect

    Goodwin, L.R.; Francom, D.; Urso, A.; Dieken, F.P.

    1988-02-01

    The accuracy of the methylene blue colorimetric procedure for the determination of sulfide in environmental waters and waste waters is influenced by turbidity interferences even after application of recommended pretreatment techniques. The direct analysis of sulfide by ion chromatography (IC), without sample pretreatment, is complicated by field preservation of samples with zinc ion (or equivalent). A continuous-flow procedure has been developed that converts the acid-extractable sulfide to H/sub 2/S, which is separated from the sample matrix by a gas dialysis membrane and then trapped in a dilute sodium hydroxide solution. A 200-..mu..L portion of this solution is injected into the ion chromatograph for analysis with an electrochemical detector. Detection limits as low as 1.9 ng/mL have been obtained. Good agreement was found between the gas dialysis/IC and methylene blue methods for nonturbid standards. The addition of ascorbic acid as an antioxidant is required to obtain adequate recoveries from spiked tap and well waters.

  19. Determination of water-soluble ions in soils from the dry valleys of Antarctica

    NASA Astrophysics Data System (ADS)

    Bustin, R.

    1981-08-01

    The soil chemistry of the dry valleys of Antarctica was studied. These valleys furnish a terrestrial analog for the surface of Mars. The abundance of the water-soluble ions magnesium, calcium, potassium, sodium chloride, and nitrate in soil samples was determined. All samples examined contained water-soluble salts reflecting the aridity of the area. Movement of salts to low-lying areas was verified. Upward ionic migration was evident in all core samples. Of all cations observed, sodium showed the greatest degree of migration.

  20. Determination of Energy-Transfer Distributions in Ionizing Ion-Molecule Collisions.

    PubMed

    Maclot, S; Delaunay, R; Piekarski, D G; Domaracka, A; Huber, B A; Adoui, L; Martín, F; Alcamí, M; Avaldi, L; Bolognesi, P; Díaz-Tendero, S; Rousseau, P

    2016-08-12

    The ionization and fragmentation of the nucleoside thymidine in the gas phase has been investigated by combining ion collision with state-selected photoionization experiments and quantum chemistry calculations. The comparison between the mass spectra measured in both types of experiments allows us to accurately determine the distribution of the energy deposited in the ionized molecule as a result of the collision. The relation of two experimental techniques and theory shows a strong correlation between the excited states of the ionized molecule with the computed dissociation pathways, as well as with charge localization or delocalization.

  1. EnFET for urea determination in biological fluids using ammonium ion detection

    NASA Astrophysics Data System (ADS)

    Dawgul, Marek; Trybun, Tomasz; Pijanowska, Dorota G.; Torbicz, Wladyslaw

    2003-09-01

    In this paper a method of urease immobilization on the surface of the Siloprene membrane of the ammonium ion sensitive ChemFET is presented. The usability of the sensor for determination of urea in solutions at pH typical for biological fluids (pH 6 to pH 7.5) has been investigated. Due to the fact that the sensor exhibits high sensitivity to samples of low buffer capacity, the method of preliminary sample treatment, consisting in addition of buffers at adequate buffer capacity was developed. The sensors were tested in dialysate and blood plasma.

  2. Determination of water-soluble ions in soils from the dry valleys of Antarctica

    NASA Technical Reports Server (NTRS)

    Bustin, R.

    1981-01-01

    The soil chemistry of the dry valleys of Antarctica was studied. These valleys furnish a terrestrial analog for the surface of Mars. The abundance of the water-soluble ions magnesium, calcium, potassium, sodium chloride, and nitrate in soil samples was determined. All samples examined contained water-soluble salts reflecting the aridity of the area. Movement of salts to low-lying areas was verified. Upward ionic migration was evident in all core samples. Of all cations observed, sodium showed the greatest degree of migration.

  3. Study of structural and spectroscopic behavior of Sm3+ ions in lead-zinc borate glasses containing alkali metal ions

    NASA Astrophysics Data System (ADS)

    Sasi Kumar, M. V.; Babu, S.; Rajeswara Reddy, B.; Ratnakaram, Y. C.

    2017-02-01

    High luminescence behavior of rare earth inorganic glasses have a variety of uses in the industry. In the past few decades, rare earth ions with characteristic photonics applications are being hosted by heavy metal oxide glasses. Among the rare earth ions Sm3+ ion has features which make it apt for high density optical storage. The authors of the paper have experimented to synthesize Sm3+ doped glasses. In this regard a new series of borate glasses doped with 1 mol% Sm3+ ion are developed by using melt-quenching technique. XRD, FTIR, optical absorption, luminescence techniques are used to study the various characteristics of Sm3+ ion in the present glass matrices. The XRD spectra confirms the amorphous nature of glasses. Further, the researchers have used differential thermal analysis to study the glass transition temperature. The structural groups in the prepared glasses are studied using Fourier transform infrared spectra. From the measurement of its optical absorption, three phenomenological Judd-Ofelt intensity parameters (Ω2, Ω4 and Ω6) have been computed. Based on these Judd-Ofelt intensity parameters, radiative properties such as radiative probabilities (Arad), branching ratios (β), and radiative life time (τR) are calculated. The excitation spectra of Sm3+ doped lithium heavy metal borate glass matrix is recorded under the emission wavelength of 600 nm. The emission spectra are recorded under 404 nm excitation wavelength. From various emission transitions, 4G5/2 → 6H7/2 and 4G5/2 → 6H9/2 bands could be of interest for various applications. The decay profiles of 4G5/2 level exhibit single exponential nature in all the prepared glass matrices. The potassium glass matrix exhibits higher quantum efficiency than the other glass matrices. Finally, by going through these several spectroscopic characterizations, it is concluded that the prepared Sm3+ doped lead-zinc borate glasses might be useful for visible light applications.

  4. Surface Structure and Electron Density Dependence of Scattered Ne^+ Ion Fractions From the Si(100)-(2x1) Surface

    NASA Astrophysics Data System (ADS)

    Wolfgang, John; Nordlander, Peter; Vaquilla, Isadora; Lui, K. M.; Rabalais, J. W.

    2000-03-01

    Experimental measurements of ion neutralization rates scattered from semiconductor surfaces have shown strong dependence on local surface structure and charge density. Recent scattering experiments utilizing 4 KeV Ne^+ scattered from a Si(100)-(2x1)surface exhibit strong azmuthal anisotropy, and can be shown to directly correlate to the reconstructed silicon surface geometry. Using a simple rate equation approach, a model based on the local charge density of the silicon surface has been used to determine the final neutral ion fraction from this scattering experiment. This rate equation approach has also been applied to scattering events between 4 KeV Ne^+ and a n- or p-type Si(100)-(2x1) surface. In the case of an n-doped Si surface, little or no change in the final ion neutralization is observed, while p-doping of the Si surface presents a significant decrease in the final neutral ion fractions compared to the undoped case. This effect will be discussed using a rate equation analysis, examining contributions from modification of the valence and conduction bands as a result of Si doping upon the overall charge transfer and ion neutralization.

  5. Toward a Rational Design of Highly Folded Peptide Cation Conformations. 3D Gas-Phase Ion Structures and Ion Mobility Characterization.

    PubMed

    Pepin, Robert; Laszlo, Kenneth J; Marek, Aleš; Peng, Bo; Bush, Matthew F; Lavanant, Helène; Afonso, Carlos; Tureček, František

    2016-10-01

    Heptapeptide ions containing combinations of polar Lys, Arg, and Asp residues with non-polar Leu, Pro, Ala, and Gly residues were designed to study polar effects on gas-phase ion conformations. Doubly and triply charged ions were studied by ion mobility mass spectrometry and electron structure theory using correlated ab initio and density functional theory methods and found to exhibit tightly folded 3D structures in the gas phase. Manipulation of the basic residue positions in LKGPADR, LRGPADK, KLGPADR, and RLGPADK resulted in only minor changes in the ion collision cross sections in helium. Replacement of the Pro residue with Leu resulted in only marginally larger collision cross sections for the doubly and triply charged ions. Disruption of zwitterionic interactions in doubly charged ions was performed by converting the C-terminal and Asp carboxyl groups to methyl esters. This resulted in very minor changes in the collision cross sections of doubly charged ions and even slightly diminished collision cross sections in most triply charged ions. The experimental collision cross sections were related to those calculated for structures of lowest free energy ion conformers that were obtained by extensive search of the conformational space and fully optimized by density functional theory calculations. The predominant factors that affected ion structures and collision cross sections were due to attractive hydrogen bonding interactions and internal solvation of the charged groups that overcompensated their Coulomb repulsion. Structure features typically assigned to the Pro residue and zwitterionic COO-charged group interactions were only secondary in affecting the structures and collision cross sections of these gas-phase peptide ions. Graphical Abstract ᅟ.

  6. Toward a Rational Design of Highly Folded Peptide Cation Conformations. 3D Gas-Phase Ion Structures and Ion Mobility Characterization

    NASA Astrophysics Data System (ADS)

    Pepin, Robert; Laszlo, Kenneth J.; Marek, Aleš; Peng, Bo; Bush, Matthew F.; Lavanant, Helène; Afonso, Carlos; Tureček, František

    2016-10-01

    Heptapeptide ions containing combinations of polar Lys, Arg, and Asp residues with non-polar Leu, Pro, Ala, and Gly residues were designed to study polar effects on gas-phase ion conformations. Doubly and triply charged ions were studied by ion mobility mass spectrometry and electron structure theory using correlated ab initio and density functional theory methods and found to exhibit tightly folded 3D structures in the gas phase. Manipulation of the basic residue positions in LKGPADR, LRGPADK, KLGPADR, and RLGPADK resulted in only minor changes in the ion collision cross sections in helium. Replacement of the Pro residue with Leu resulted in only marginally larger collision cross sections for the doubly and triply charged ions. Disruption of zwitterionic interactions in doubly charged ions was performed by converting the C-terminal and Asp carboxyl groups to methyl esters. This resulted in very minor changes in the collision cross sections of doubly charged ions and even slightly diminished collision cross sections in most triply charged ions. The experimental collision cross sections were related to those calculated for structures of lowest free energy ion conformers that were obtained by extensive search of the conformational space and fully optimized by density functional theory calculations. The predominant factors that affected ion structures and collision cross sections were due to attractive hydrogen bonding interactions and internal solvation of the charged groups that overcompensated their Coulomb repulsion. Structure features typically assigned to the Pro residue and zwitterionic COO-charged group interactions were only secondary in affecting the structures and collision cross sections of these gas-phase peptide ions.

  7. Structural basis for alcohol modulation of a pentameric ligand-gated ion channel.

    PubMed

    Howard, Rebecca J; Murail, Samuel; Ondricek, Kathryn E; Corringer, Pierre-Jean; Lindahl, Erik; Trudell, James R; Harris, R Adron

    2011-07-19

    Despite its long history of use and abuse in human culture, the molecular basis for alcohol action in the brain is poorly understood. The recent determination of the atomic-scale structure of GLIC, a prokaryotic member of the pentameric ligand-gated ion channel (pLGIC) family, provides a unique opportunity to characterize the structural basis for modulation of these channels, many of which are alcohol targets in brain. We observed that GLIC recapitulates bimodal modulation by n-alcohols, similar to some eukaryotic pLGICs: methanol and ethanol weakly potentiated proton-activated currents in GLIC, whereas n-alcohols larger than ethanol inhibited them. Mapping of residues important to alcohol modulation of ionotropic receptors for glycine, γ-aminobutyric acid, and acetylcholine onto GLIC revealed their proximity to transmembrane cavities that may accommodate one or more alcohol molecules. Site-directed mutations in the pore-lining M2 helix allowed the identification of four residues that influence alcohol potentiation, with the direction of their effects reflecting α-helical structure. At one of the potentiation-enhancing residues, decreased side chain volume converted GLIC into a highly ethanol-sensitive channel, comparable to its eukaryotic relatives. Covalent labeling of M2 positions with an alcohol analog, a methanethiosulfonate reagent, further implicated residues at the extracellular end of the helix in alcohol binding. Molecular dynamics simulations elucidated the structural consequences of a potentiation-enhancing mutation and suggested a structural mechanism for alcohol potentiation via interaction with a transmembrane cavity previously termed the "linking tunnel." These results provide a unique structural model for independent potentiating and inhibitory interactions of n-alcohols with a pLGIC family member.

  8. Collisonal Friction Enhanced by Two-Stream Instabilities Determines the Bohm Criterion in Plasmas With Multiple Ion Species

    NASA Astrophysics Data System (ADS)

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

    2009-10-01

    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 (within a few Debye lengths) 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 concentration and δVc.[4pt] [1] S.D. Baalrud, J.D. Callen, and C.C. Hegna, Phys. Plasmas 15, 092111 (2008).

  9. Controlled deposition of sulphur-containing semiconductor and dielectric nano-structured films on metals in SF{sub 6} ion-ion plasma

    SciTech Connect

    Rafalskyi, Dmytro; Bredin, Jérôme; Aanesland, Ane

    2013-12-07

    In the present paper, the deposition processes and formation of films in SF{sub 6} ion-ion plasma, with positive and negative ion flows accelerated to the surface, are investigated. The PEGASES (acronym for Plasma Propulsion with Electronegative GASES) source is used as an ion-ion plasma source capable of generating almost ideal ion-ion plasma with negative ion to electron density ratio more than 2500. It is shown that film deposition in SF{sub 6} ion-ion plasma is very sensitive to the polarity of the incoming ions. The effect is observed for Cu, W, and Pt materials. The films formed on Cu electrodes during negative and positive ion assisted deposition were analyzed. Scanning electron microscope analysis has shown that both positive and negative ion fluxes influence the copper surface and leads to film formation, but with different structures of the surface: the low-energy positive ion bombardment causes the formation of a nano-pored film transparent for ions, while the negative ion bombardment leads to a continuous smooth insulating film. The transversal size of the pores in the porous film varies in the range 50–500 nm, and further analysis of the film has shown that the film forms a diode together with the substrate preventing positive charge drain, and positive ions are neutralized by passing through the nano-pores. The film obtained with the negative ion bombardment has an insulating surface, but probably with a multi-layer structure: destroying the top surface layer allows to measure similar “diode” IV-characteristics as for the nano-pored film case. Basing on results, practical conclusions for the probes and electrodes cleaning in ion-ion SF{sub 6} plasmas have been made. Different applications are proposed for the discovered features of the controlled deposition from ion-ion plasmas, from Li-sulphur rechargeable batteries manufacturing and nanofluidics issues to the applications for microelectronics, including low-k materials formation.

  10. Structural Elucidation of cis/trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry.

    PubMed

    Zheng, Xueyun; Renslow, Ryan S; Makola, Mpho M; Webb, Ian K; Deng, Liulin; Thomas, Dennis G; Govind, Niranjan; Ibrahim, Yehia M; Kabanda, Mwadham M; Dubery, Ian A; Heyman, Heino M; Smith, Richard D; Madala, Ntakadzeni E; Baker, Erin S

    2017-04-06

    Due to the recently uncovered health benefits and anti-HIV activities of dicaffeoylquinic acids (diCQAs), understanding their structures and functions is of great interest for drug discovery efforts. DiCQAs are analytically challenging to identify and quantify since they commonly exist as a diverse mixture of positional and geometric (cis/trans) isomers. In this work, we utilized ion mobility spectrometry coupled with mass spectrometry to separate the various isomers before and after UV irradiation. The experimental collision cross sections were then compared with theoretical structures to differentiate and identify the diCQA isomers. Our analyses found that naturally the diCQAs existed predominantly as trans/trans isomers, but after 3 h of UV irradiation, cis/cis, cis/trans, trans/cis, and trans/trans isomers were all present in the mixture. This is the first report of successful differentiation of cis/trans diCQA isomers individually, which shows the great promise of IMS coupled with theoretical calculations for determining the structure and activity relationships of different isomers in drug discovery studies.

  11. Near-complete structural characterization of phosphatidylcholines using electron impact excitation of ions from organics.

    PubMed

    Campbell, J Larry; Baba, Takashi

    2015-06-02

    Although lipids are critical components of many cellular assemblies and biological pathways, accurate descriptions of their molecular structures remain difficult to obtain. Many benchtop characterization methods require arduous and time-consuming procedures, and multiple assays are required whenever a new structural feature is probed. Here, we describe a new mass-spectrometry-based workflow for enhanced structural lipidomics that, in a single experiment, can yield almost complete structural information for a given glycerophospholipid (GPL) species. This includes the lipid's sum (Brutto) composition from the accurate mass measured for the intact lipid ion and the characteristic headgroup fragment, the regioisomer composition from fragment ions unique to the sn-1 and sn-2 positions, and the positions of carbon-carbon double bonds in the lipid acyl chains. Here, lipid ions are fragmented using electron impact excitation of ions from organics (EIEIO)--a technique where the singly charged lipid ions are irradiated by an electron beam, producing diagnostic product ions. We have evaluated this methodology on various lipid standards, as well as on a biological extract, to demonstrate this new method's utility.

  12. Structure and dynamics of hydrated ion pairs in a hydrophobic environment.

    PubMed

    Benjamin, Ilan

    2010-10-28

    The structure, energetics, and dynamics of different alkali halide ion pairs hydrated in a hydrophobic medium are studied using molecular dynamics computer simulations. One or two water molecules hydrating NaCl, NaI, KCl, KI, and KF in bulk carbon tetrachloride are considered. The ion pairs remain in contact throughout the simulations, so the structure of the hydration complex is well characterized. The ions' interaction energy and hydration structure are examined and correlated with the ion sizes and charges. For the first four salts, the stronger interaction of the water molecules with the cation than with the anion of the ion pair is in agreement with recent experiments. However, when the anion is significantly smaller than the cation (as in the case of KF, which was not studied experimentally), the opposite behavior is found. The asymmetry of interaction with the cation and the anion are further elucidated by examining hypothetical ion pairs made from equal-sized cations and anions and by defining an asymmetry hydration parameter, which is found to correlate well with the structural characteristics, as well as with the water molecules' reorientation dynamics.

  13. Computational Methods for Structural and Functional Studies of Alzheimer's Amyloid Ion Channels.

    PubMed

    Jang, Hyunbum; Arce, Fernando Teran; Lee, Joon; Gillman, Alan L; Ramachandran, Srinivasan; Kagan, Bruce L; Lal, Ratnesh; Nussinov, Ruth

    2016-01-01

    Aggregation can be studied by a range of methods, experimental and computational. Aggregates form in solution, across solid surfaces, and on and in the membrane, where they may assemble into unregulated leaking ion channels. Experimental probes of ion channel conformations and dynamics are challenging. Atomistic molecular dynamics (MD) simulations are capable of providing insight into structural details of amyloid ion channels in the membrane at a resolution not achievable experimentally. Since data suggest that late stage Alzheimer's disease involves formation of toxic ion channels, MD simulations have been used aiming to gain insight into the channel shapes, morphologies, pore dimensions, conformational heterogeneity, and activity. These can be exploited for drug discovery. Here we describe computational methods to model amyloid ion channels containing the β-sheet motif at atomic scale and to calculate toxic pore activity in the membrane.

  14. Simultaneous voltammetric determination of nitrate and nitrite ions using a copper electrode pretreated by dissolution/redeposition.

    PubMed

    Shariar, Shovon Mohammad; Hinoue, Teruo

    2010-01-01

    Nitrate and nitrite ions were found to be successfully electroreduced at an in situ electrochemically pretreated copper electrode in acidic media, and their reduction peaks of a cyclic voltammogram were found at two distinct electrode potentials. Cyclic voltammetric experiments revealed a highly sensitive behavior of the pretreated copper electrode upon the electroreduction of nitrate and nitrite ions, and showed that a simultaneous voltammetric determination of the ions was achievable. Differential pulse voltammetry (DPV) was applied to the simultaneous determination. As a result, the detection limits were 0.26 and 0.17 µmol dm(-3) for nitrate and nitrite ions, respectively. Simultaneous determinations for real samples (river water) were carried out by DPV at the pretreated copper electrode and spectrophotometry (the Griess method). The determination values obtained by both methods were in a good agreement with each other.

  15. Superconducting accelerating structures for very low velocity ion beams

    SciTech Connect

    Xu, J.; Shepard, K.W.; Ostroumov, P.N.; Fuerst, J.D.; Waldschmidt, G.; Gonin, I.V.; /Fermilab

    2008-01-01

    This paper presents designs for four types of very-low-velocity superconducting accelerating cavity capable of providing several MV of accelerating potential per cavity, and suitable for particle velocities in the range 0.006 < v/c < 0.06. Superconducting TEM-class cavities have been widely applied to CW acceleration of ion beams. SC linacs can be formed as an array of independently-phased cavities, enabling a variable velocity profile to maximize the output energy for each of a number of different ion species. Several laboratories in the US and Europe are planning exotic beam facilities based on SC linacs. The cavity designs presented here are intended for the front-end of such linacs, particularly for the post-acceleration of rare isotopes of low charge state. Several types of SC cavities have been developed recently to cover particle velocities above 0.06c. Superconducting four-gap quarter-wave resonators for velocities 0.008 < {beta} = v/c < 0.05 were developed about two decades ago and have been successfully operated at the ATLAS SC linac at Argonne National Laboratory. Since that time, progress in simulation tools, cavity fabrication and processing have increased SC cavity gradients by a factor of 3-4. This paper applies these tools to optimize the design of a four-gap quarter-wave resonator for exotic beam facilities and other low-velocity applications.

  16. High-spin nuclear structure studies with radioactive ion beams

    SciTech Connect

    Baktash, C.

    1992-12-31

    Two important developments in the sixties, namely the advent of heavy-ion accelerators and fabrication of Ge detectors, opened the way for the experimental studies of nuclear properties at high angular momentum. Addition of a new degree of freedom, namely spin, made it possible to observe such fascinating phenomena as occurrences and coexistence of a variety of novel shapes, rise, fall and occasionally rebirth of nuclear collectivity, and disappearance of pairing correlations. Today, with the promise of development of radioactive ion beams (RIB) and construction of the third-generation Ge-detection systems (GAMMASPHERE and EUROBALL), the authors are poised to explore new and equally fascinating phenomena that have been hitherto inaccessible. With the addition of yet another dimension, namely the isospin, they will be able to observe and verify predictions for exotic shapes as varied as rigid triaxiality, hyperdeformation and triaxial octupole shapes, or to investigate the T = 0 pairing correlations. In this paper, they shall review, separately for neutron-deficient and neutron-rich nuclei, these and a few other new high-spin physics opportunities that may be realized with RIB. Following this discussion, they shall present a list of the beam species, intensities and energies that are needed to fulfill these goals. The paper will conclude with a description of the experimental techniques and instrumentations that are required for these studies.

  17. Fine Structural Detection of Calcium Ions by Photoconversion

    PubMed Central

    Poletto, V.; Galimberti, V.; Guerra, G.; Rosti, V.; Moccia, F.; Biggiogera, M.

    2016-01-01

    We propose a tool for a rapid high-resolution detection of calcium ions which can be used in parallel with other techniques. We have applied a new approach by photo-oxidation of diaminobenzidine in presence of the emission of an excited fluorochrome specific for calcium detection. This method combines the selectivity of available fluorophores to the high spatial resolution offered by transmission electron microscopy to detect fluorescing molecules even when present in low amounts in membrane-bounded organelles. We show in this paper that Mag-Fura 2 photoconversion via diaminobenzidine oxidation is an efficient way for localizing Ca2+ ions at electron microscopy level, is easily carried out and reproducible, and can be obtained on a good amount of cells, since the exposure in our conditions is not limited to the direct irradiation of the sample via an objective but obtained with a germicide lamp. The end product is sufficiently electron dense to be detected clearly when present in sufficient amount within a membrane boundary. PMID:27734989

  18. Enhancing Target Normal Sheath Accelerated Ions with Micro-structured Targets

    NASA Astrophysics Data System (ADS)

    George, Kevin; Snyder, Joseph; Ji, Liangliang; Rubin, Trevor; Handler, Abraham; Poole, Patrick; Willis, Christopher; Daskalova, Rebecca; Cochran, Ginevra; Schumacher, Douglass

    2016-10-01

    Laser driven target normal sheath acceleration (TNSA) of ions has been widely studied due to its fundamental importance, use as a probe, and for possible applications such as cancer therapy and neutron generation. Much of this work has been conducted on thin foils with peak ion energy and yield optimized using laser parameters such as energy and spot size. Micro-structured targets, however, have demonstrated increased peak ion energy and yield by controlling and enhancing mechanisms preferential to TNSA. Novel micro-structured targets were developed using optical lithography techniques on thin substrates at the OSU NanoSystem Laboratory. Variable structure height (0.5-2 micron) and transverse patterning (up to 1 micron resolution) permit the survey of a range of structured target variables in the study of ion acceleration. We describe the development of these targets and an experiment investigating the enhancement of TNSA ions from lithography produced micro-structured targets conducted at the Scarlet Laser Facility. Experimental results show increased proton and Carbon yield >2 MeV and higher peak Carbon energy from structured targets. This work was supported by the Air Force Office of Scientific Research.

  19. Formalism for the determination of structural isotope effects with neutrons

    SciTech Connect

    Neuefeind, Joerg C; Benmore, Chris J

    2009-01-01

    In general the analysis of neutron isotopic substitution experiments in terms of partial structure factors and partial pair distribution functions is based on the assumption that the structure of isotopic variants of a molecule is identical. This assumption is clearly only an approximation especially in the case of hydrogen bonding molecular liquids like liquid water and structural isotope effects have been measured with X-rays for more than 20 years. A analysis method of neutron isotope data is presented that avoids the necessity to assume structural equality and allows the determination of the isotope effect in the hydrogen-hydrogen partial structure factor of liquid water from neutron data. It is shown that a combination of X-ray and neutron scattering measurements allows in principle the determination of the isotope effects on all all partials structure factors of liquid water.

  20. Introducing Chemists to X-Ray Structure Determination.

    ERIC Educational Resources Information Center

    Enemark, John H.

    1988-01-01

    Presents the organization of a one-semester graduate course in structural chemistry including lectures and problems. Discusses the coverage of diffraction from real crystals and structure determination. Summarizes experiments on real crystals conducted by students in the X-ray laboratory. (CW)