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Sample records for ion structure determination

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

    PubMed

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

    2016-01-26

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2013-08-01

    Travelling wave ion mobility was investigated for its ability to separate N-glycans from other compounds and for resolution of isomers. Charged glycans, exemplified by sialylated complex N-glycans released from bovine fetuin and ionised by electrospray, could be separated from residual glycopeptides allowing the minor, more highly sialylated compounds to be detected where their ions were obscured by ions from other compounds in different charge states. This technique was also found to be excellent for extracting the N-glycan profiles from contaminated samples. Structural identification of the glycans was performed by negative ion CID fragmentation, a method that provides a wealth of structurally diagnostic ions. However, fragment ions can also appear in the glycan profiles where they can be mistaken for glycan molecular ions. Fragments and molecular ions were frequently shown to have different drift time profiles, allowing them to be differentiated. Some separation of isomers was found but only for the smallest compounds. Differentiation from conformers was achieved by plotting drift time profiles of the fragments; these profiles matched those of the precursor ions where conformers were present. The techniques were applied to investigations of N-glycans released from the fungus Piptoporus betulinus where the technique was used to separate different carbohydrate types present in biological extracts. PMID:23712623

  4. Structure Determination of Noble Metal Clusters by Trapped Ion Electron Diffraction

    NASA Astrophysics Data System (ADS)

    Schooss, Detlef

    2006-03-01

    The structures of noble metal cluster ions have been studied by the recently developed technique of trapped ion electron diffraction (TIED)^1. In brief, cluster ions are generated by a magnetron sputter source and injected into a cooled (95 K) quadrupole ion trap. After mass selection and thermalization, the trapped ions are irradiated with a 40 keV electron beam. The resulting diffraction pattern is integrated with a CCD detector. The assignment of the structural motif is done via a comparison of the experimental and simulated scattering function, calculated from density functional theory structure calculations. The structures of mass selected silver cluster cations Ag19^+, Ag38^+, Ag55^+, Ag59^+, Ag75^+ and Ag79^+ have been investigated^2. The resulting experimental data are best described by structures based on the icosahedral motif, while closed packed structures could be ruled out. Additionally, we present a comparison of the structures of Cu20^+/-, Ag20^+/- and Au20^+/-. Our findings show unambiguously that the structure of Au20^- is predominantly given by a tetrahedron in agreement with the results of L.S. Wang et al.^3 In contrast, structures of Ag20^- and Cu20^- based on the icosahedral motif agree best with the experimental data. Small structural differences between the charge states are observed. The possibilities and limitations of the TIED method are discussed. (1) M. Maier-Borst, D. B. Cameron, M. Rokni, and J. H. Parks, Physical Review A 59 (5), R3162 (1999); S. Krückeberg, D. Schooss, M. Maier-Borst, and J. H. Parks, Physical Review Letters 85 (21), 4494 (2000). (2) D. Schooss, M.N. Blom, B. v. Issendorff, J. H. Parks, and M.M. Kappes, Nano Letters 5 (10), 1972 (2005). (3) J. Li, X. Li, H. J. Zhai, and L. S. Wang, Science 299, 864 (2003)

  5. 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.

  6. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

  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. Ionoluminescence as Sensor of Structural Disorder in Crystalline SiO2: Determination of Amorphization Threshold by Swift Heavy Ions

    NASA Astrophysics Data System (ADS)

    Peña-Rodríguez, Ovidio; Jiménez-Rey, David; Manzano-Santamaría, Javier; Olivares, José; Muñoz, Angel; Rivera, Antonio; Agulló-López, Fernando

    2012-01-01

    Ionoluminescence (IL) has been used in this work as a sensitive tool to probe the microscopic electronic processes and structural changes produced on quartz by the irradiation with swift heavy ions. The IL yields have been measured as a function of irradiation fluence and electronic stopping power. The results are consistent with the assignment of the 2.7 eV (460 nm) band to the recombination of self-trapped excitons at the damaged regions in the irradiated material. Moreover, it was possible to determine the threshold for amorphization by a single ion impact, as ˜1.7 keV/nm, which agrees well with the results of previous studies.

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

    PubMed

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

    2015-06-01

    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. PMID:26172810

  11. 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.

  12. Reaction of positronium with doped ions in silica-based glasses in the size determination of subnanometer structural open spaces

    NASA Astrophysics Data System (ADS)

    Inoue, K.; Kataoka, H.; Nagai, Y.; Hasegawa, M.; Kobayashi, Y.

    2013-10-01

    Positron annihilation spectroscopy is employed to estimate the size of subnanometer-scale open spaces in insulating materials. In most cases, the size is estimated from the lifetime of long-lived ortho-positronium (o-Ps) by pickoff annihilation using a simplified model. However, reactions of Ps with surrounding electrons other than the pickoff reaction, such as spin conversion or chemical reaction, could give a substantially underestimated size using the simplified model. In the present paper, we report that the size of the open spaces can be evaluated correctly by the angular correlation of positron annihilation radiation (ACAR) with a magnetic field using the spin-polarization effect on Ps formation, even if such reactions of Ps occur in the material. This method is applied to the subnanometer-scale structural open spaces of silica-based glass doped with Fe. We demonstrate the influence of the Ps reaction on size-estimation of the open spaces from the o-Ps lifetime. Furthermore, the type of reaction, whether spin conversion or chemical, is distinguished from the magnetic field dependence of the Ps self-annihilation component intensity in the ACAR spectra. The Ps reaction in silica-based glass doped with Fe is a chemical reaction (most likely oxidation) rather than spin conversion, with Fe ions. The chemical quenching rate with Fe ions is determined from the dependence of the o-Ps lifetime on the Fe content.

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

    DOE PAGESBeta

    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-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

  14. 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.

  15. 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.

  16. 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

    2015-09-01

    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. PMID:26287361

  17. 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.

  18. Structure determination of the CoSi2(111) surface using medium-energy ion scattering

    NASA Astrophysics Data System (ADS)

    Vrijmoeth, J.; Schins, A. G.; van der Veen, J. F.

    1989-08-01

    The surface structure of epitaxially grown CoSi2 crystals on Si(111) has been investigated with use of medium-energy ion scattering. A Co- or a Si-rich surface composition is obtained, depending on the preparation conditions. The structure of the Co-rich surface is shown to be bulklike, i.e., the crystal is terminated by a Si-Co-Si triple layer. The Si-rich surface is found to have, on top of the last Si-Co-Si triple layer, a Si double layer of the same orientation as the CoSi2 bulk lattice. This accounts for the difficulty to grow a 180°-rotated Si film on top of CoSi2(111) by normal molecular-beam-epitaxy techniques. The topmost Co atoms of the Si-rich surface are eightfold coordinated.

  19. 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.

  20. Ion chromatographic determination of sulfur in fuels

    NASA Technical Reports Server (NTRS)

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

    1978-01-01

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

  1. 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). PMID:16099170

  2. 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.

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

    SciTech Connect

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

    2014-08-23

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

  4. 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

  5. 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.

  6. 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.

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

    NASA Technical Reports Server (NTRS)

    Omidi, N.; Winske, D.

    1992-01-01

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

  8. 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

  9. Ab initio simulations for the ion-ion structure factor of warm dense aluminum.

    PubMed

    Rüter, Hannes R; Redmer, Ronald

    2014-04-11

    We perform ab initio simulations based on finite-temperature density functional theory in order to determine the static and dynamic ion-ion structure factor in aluminum. We calculate the dynamic structure factor via the intermediate scattering function and extract the dispersion relation for the collective excitations. The results are compared with available experimental x-ray scattering data. Very good agreement is obtained for the liquid metal domain. In addition we perform simulations for warm dense aluminum in order to obtain the ion dynamics in this strongly correlated quantum regime. We determine the sound velocity for both liquid and warm dense aluminum which can be checked experimentally using narrow-bandwidth free electron laser radiation. PMID:24765982

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

    SciTech Connect

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

    2015-01-06

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

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

    PubMed Central

    2015-01-01

    Structures for lossless ion manipulations (SLIM) have recently demonstrated the ability for near lossless ion focusing, transfer, and trapping in subatmospheric pressure regions. While lossless ion manipulations are advantageously applied to the applications of ion mobility separations and gas phase reactions, ion introduction through ring electrode ion funnels or more conventional ion optics to SLIM can involve discontinuities in electric fields or other perturbations that result in ion losses. In this work, we developed and investigated a new funnel design that aims to seamlessly couple to SLIM at the funnel exit. This rectangular ion funnel (RIF) was initially evaluated by ion simulations, fabricated utilizing printed circuit board technology, and tested experimentally. The RIF was integrated to a SLIM-time of flight (TOF) MS system, and the operating parameters, including RF, DC bias of the RIF electrodes, and electric fields for effectively interfacing with a SLIM, were characterized. The RIF provided a 2-fold sensitivity increase without significant discrimination over a wide m/z range and well matched to that of SLIM, along with greatly improved SLIM operational stability. PMID:25409343

  12. 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.

  13. Crystal structure determination of Efavirenz

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    Needle-shaped single crystals of the title compound, C14H9ClF3NO2, 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.

  14. Determinants and Polynomial Root Structure

    ERIC Educational Resources Information Center

    De Pillis, L. G.

    2005-01-01

    A little known property of determinants is developed in a manner accessible to beginning undergraduates in linear algebra. Using the language of matrix theory, a classical result by Sylvester that describes when two polynomials have a common root is recaptured. Among results concerning the structure of polynomial roots, polynomials with pairs of…

  15. Structural determinants of limited proteolysis.

    PubMed

    Kazanov, Marat D; Igarashi, Yoshinobu; Eroshkin, Alexey M; Cieplak, Piotr; Ratnikov, Boris; Zhang, Ying; Li, Zhanwen; Godzik, Adam; Osterman, Andrei L; Smith, Jeffrey W

    2011-08-01

    Limited or regulatory proteolysis plays a critical role in many important biological pathways like blood coagulation, cell proliferation, and apoptosis. A better understanding of mechanisms that control this process is required for discovering new proteolytic events and for developing inhibitors with potential therapeutic value. Two features that determine the susceptibility of peptide bonds to proteolysis are the sequence in the vicinity of the scissile bond and the structural context in which the bond is displayed. In this study, we assessed statistical significance and predictive power of individual structural descriptors and combination thereof for the identification of cleavage sites. The analysis was performed on a data set of >200 proteolytic events documented in CutDB for a variety of mammalian regulatory proteases and their physiological substrates with known 3D structures. The results confirmed the significance and provided a ranking within three main categories of structural features: exposure > flexibility > local interactions. Among secondary structure elements, the largest frequency of proteolytic cleavage was confirmed for loops and lower but significant frequency for helices. Limited proteolysis has lower albeit appreciable frequency of occurrence in certain types of β-strands, which is in contrast with some previous reports. Descriptors deduced directly from the amino acid sequence displayed only marginal predictive capabilities. Homology-based structural models showed a predictive performance comparable to protein substrates with experimentally established structures. Overall, this study provided a foundation for accurate automated prediction of segments of protein structure susceptible to proteolytic processing and, potentially, other post-translational modifications. PMID:21682278

  16. Structural determinants of limited proteolysis

    PubMed Central

    Kazanov, Marat D.; Igarashi, Yoshinobu; Eroshkin, Alexey M.; Cieplak, Piotr; Ratnikov, Boris; Zhang, Ying; Li, Zhanwen; Godzik, Adam; Osterman, Andrei L.; Smith1, Jeffrey W.

    2011-01-01

    Limited or regulatory proteolysis plays a critical role in many important biological pathways like blood coagulation, cell proliferation, and apoptosis. A better understanding of mechanisms that control this process is required for discovering new proteolytic events and for developing inhibitors with potential therapeutic value. Two features that determine the susceptibility of peptide bonds to proteolysis are the sequence in the vicinity of the scissile bond and the structural context in which the bond is displayed. In this study we assessed statistical significance and predictive power of individual structural descriptors and combination thereof for the identification of cleavage sites. The analysis was performed on a dataset of >200 proteolytic events documented in CutDB for a variety of mammalian regulatory proteases and their physiological substrates with known 3D structures. The results confirmed the significance and provided a ranking within three main categories of structural features: exposure > flexibility > local interactions. Among secondary structure elements, the largest frequency of proteolytic cleavage was confirmed for loops and lower but significant frequency for helices. Limited proteolysis has lower albeit appreciable frequency of occurrence in certain types of β-strands, which is in contrast with some previous reports. Descriptors deduced directly from the amino acid sequence displayed only marginal predictive capabilities. Homology-based structural models showed a predictive performance comparable to protein substrates with experimentally established structures. Overall, this study provided a foundation for accurate automated prediction of segments of protein structure susceptible to proteolytic processing and, potentially, other post-translational modifications. PMID:21682278

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  18. Stabilizing effects of large counter ion: Synthesis, characterization and single crystal X-ray structure determination of [Co(NH 3) 6][HgI 4]I·H 2O

    NASA Astrophysics Data System (ADS)

    Sharma, Raj Pal; Singh, Ajnesh; Venugopalan, Paloth; Smolentsev, Anton I.; Gubanov, Alexander I.

    2010-06-01

    In an attempt to synthesize [Co(NH 3) 6][Hg 2I 7], a new cobalt(III) complex salt, [Co(NH 3) 6][HgI 4]I·H 2O ( 1) was crystallized from a solution of hexaamminecobalt(III) bromide and potassium heptaiodatodimercurate(II) in aqueous medium in 1:1 M ratio. It has been characterized by elemental analyses, spectroscopic techniques (e.g. UV/visible, IR), solubility product and conductance measurements. The complex salt crystallizes in trigonal crystal system with space group R3c. Single crystal X-ray structure determination revealed the presence of discrete ions: [Co(NH 3) 6] 3+ cation, one [HgI 4] 2-, one I - anions and one lattice water molecule. The crystal structure of complex salt, consist of a bilayered structure demonstrating "rosette structure" arrangements involving N sbnd H…I and N sbnd H…O hydrogen-bond interactions through second sphere coordination. The crystal lattice is stabilized by these non-covalent interactions besides electrostatic interaction.

  19. On the structure of etched ion tracks in polymers

    NASA Astrophysics Data System (ADS)

    Hnatowicz, V.; Vacik, J.; Apel, P. Y.

    2016-04-01

    A simple model describing the radial structure of latent tracks produced by energetic ions in polymers is presented and used for examination of the process of preferential track etching and determination of the shape of the etched pores. The model is based on the assumption that the local composition of the latent track results from chemical reactions of transient degradation products created by ion passage, but it does not take into account details of the whole process. In accordance with the established idea the model calculations lead to the latent track structure with an easily etchable core surrounded by a relatively thin layer of cross-linked structures and a far reaching halo with a progressively decreasing concentration of the degradation products. The etching of the latent track with such a structure leads to funnel-type pores which have been observed in recent conductometric experiments.

  20. 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.

  1. 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.

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

    SciTech Connect

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

    2011-02-15

    A model that uniquely determines the flow speed of each ion species at the sheath edge of two ion species plasmas is developed. In this analysis, ion-ion two-stream instabilities can play an important role because they significantly enhance the friction between ion species. Two-stream instabilities arise when the difference in flow speeds between the ion species exceeds a critical value: V{sub 1}-V{sub 2}{identical_to}{Delta}V{>=}{Delta}V{sub c}. The resultant instability-enhanced friction rapidly becomes so strong that {Delta}V cannot significantly exceed {Delta}V{sub c}. Using the condition provided by {Delta}V={Delta}V{sub c} and the generalized Bohm criterion, the speed of each ion species is uniquely determined as it leaves a quasineutral plasma and enters a sheath. Previous work [S. D. Baalrud et al., Phys. Rev. Lett. 103, 205002 (2009)] considered the cold ion limit (T{sub i}{yields}0), in which case {Delta}V{sub c}{yields}0 and each ion species obtains a common ''system'' sound speed at the sheath edge. Finite ion temperatures are accounted for in this work. The result is that {Delta}V{sub c} depends on the density and thermal speed of each ion species; {Delta}V{sub c} has a minimum when the density ratio of the two ion species is near one, and becomes larger as the density ratio deviates from unity. As {Delta}V{sub c} increases, the speed of each ion species approaches its individual sound speed at the sheath edge.

  3. 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.

  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. PMID:15250415

  5. The structure of the dithionite ion

    NASA Astrophysics Data System (ADS)

    Peter, L.; Meyer, B.

    The Raman spectra of aqueous and solid sodium dithionite have been recorded. Differences in the location, intensity, and number of observed bands are attributed to conformational changes in the dithionite ion. The structure of the aqueous ion is non-planar with a C2h symmetry with an SS bond distance estimated to be 0.220-0.226 nm, as opposed to the dithionite structure in the Na2S2O4·2H2O salt which is known to have C2ν structure with a bond distance of 0.2389 nm. The Raman spectra of aqueous dithionite are assigned to Ag (SO) = 997 cm-1; Bg (SO) at 912 cm-1, Bg SO2 twist at 324 cm-1. The remaining bands are a strong Ag, the SO2 wag, the SO2 scissor, and the SS stretch at 584, 461, and 232 cm-1, respectively, but due to coupling all three motions are expected to exhibit substantial SS character. The variation of the spectra of the solid and aqueous sodium dithionite indicate strong environmental effect on the structure of the anion.

  6. The structure of the dithionite ion

    NASA Astrophysics Data System (ADS)

    Peter, L.; Meyer, B.

    1982-11-01

    The Raman spectra of aqueous and solid sodium dithionite have been recorded. Differences in the location, intensity, and number of observed bands are attributed to conformational changes in the dithionite ion. The structure of the aqueous ion is non-planar with a C2h symmetry with an SS bond distance estimated to be 0.220-0.226 nm, as opposed to the dithionite structure in the Na 2S 2O 4·2H 2O salt which is known to have C2 ν structure with a bond distance of 0.2389 nm. The Raman spectra of aqueous dithionite are assigned to Ag (SO) = 997 cm -1; Bg (SO) at 912 cm -1, Bg SO 2 twist at 324 cm -1. The remaining bands are a strong Ag, the SO 2 wag, the SO 2 scissor, and the SS stretch at 584, 461, and 232 cm -1, respectively, but due to coupling all three motions are expected to exhibit substantial SS character. The variation of the spectra of the solid and aqueous sodium dithionite indicate strong environmental effect on the structure of the anion.

  7. 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.

  8. Jet Structure in Heavy Ion Collisions

    NASA Astrophysics Data System (ADS)

    Blaizot, J.-P.; Mehtar-Tani, Y.

    We review recent theoretical developments in the study of the structure of jets that are produced in ultra relativistic heavy ion collisions. The core of the review focusses on the dynamics of the parton cascade that is induced by the interactions of a fast parton crossing a quark-gluon plasma. We recall the basic mechanisms responsible for medium induced radiation, underline the rapid disappearance of coherence effects, and the ensuing probabilistic nature of the medium induced cascade. We discuss how large radiative corrections modify the classical picture of the gluon cascade, and how these can be absorbed in a renormalization of the jet quenching parameter hat q. Then, we analyze the (wave)-turbulent transport of energy along the medium induced cascade, and point out the main characteristics of the angular structure of such a cascade. Finally, color decoherence of the incone jet structure is discussed. Modest contact with phenomenology is presented towards the end of the review.

  9. Ion channel voltage sensors: structure, function, and pathophysiology.

    PubMed

    Catterall, William A

    2010-09-23

    Voltage-gated ion channels generate electrical signals in species from bacteria to man. Their voltage-sensing modules are responsible for initiation of action potentials and graded membrane potential changes in response to synaptic input and other physiological stimuli. Extensive structure-function studies, structure determination, and molecular modeling are now converging on a sliding-helix mechanism for electromechanical coupling in which outward movement of gating charges in the S4 transmembrane segments catalyzed by sequential formation of ion pairs pulls the S4-S5 linker, bends the S6 segment, and opens the pore. Impairment of voltage-sensor function by mutations in Na+ channels contributes to several ion channelopathies, and gating pore current conducted by mutant voltage sensors in Na(V)1.4 channels is the primary pathophysiological mechanism in hypokalemic periodic paralysis. The emerging structural model for voltage sensor function opens the way to development of a new generation of ion-channel drugs that act on voltage sensors rather than blocking the pore. PMID:20869590

  10. Structural Determinants of Arrestin Functions

    PubMed Central

    Gurevich, Vsevolod V.; Gurevich, Eugenia V.

    2015-01-01

    Arrestins are a small protein family with only four members in mammals. Arrestins demonstrate an amazing versatility, interacting with hundreds of different G protein-coupled receptor (GPCR) subtypes, numerous nonreceptor signaling proteins, and components of the internalization machinery, as well as cytoskeletal elements, including regular microtubules and centrosomes. Here, we focus on the structural determinants that mediate various arrestin functions. The receptor-binding elements in arrestins were mapped fairly comprehensively, which set the stage for the construction of mutants targeting particular GPCRs. The elements engaged by other binding partners are only now being elucidated and in most cases we have more questions than answers. Interestingly, even very limited and imprecise identification of structural requirements for the interaction with very few other proteins has enabled the development of signaling-biased arrestin mutants. More comprehensive understanding of the structural underpinning of different arrestin functions will pave the way for the construction of arrestins that can link the receptor we want to the signaling pathway of our choosing. PMID:23764050

  11. Structure and selectivity in bestrophin ion channels

    DOE PAGESBeta

    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 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

  12. 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.

  13. Nanoscale ion sequestration to determine the polarity selectivity of ion conductance in carriers and channels.

    PubMed

    Cranfield, Charles G; Bettler, Taren; Cornell, Bruce

    2015-01-01

    The nanoscale spacing between a tethered lipid bilayer membrane (tBLM) and its supporting gold electrode can be utilized to determine the polarity selectivity of the conduction of ion channels and ion carriers embedded in a membrane. The technique relies upon a bias voltage sequestering or eliminating ions, of a particular polarity, into or out of the aqueous electrolyte region between the gold electrode and the tethered membrane. A demonstration is given, using ac swept frequency impedance spectrometry, of the bias polarity dependence of the ionophore conductance of gramicidin A, a cationic selective channel, and valinomycin, a potassium ion selective carrier. We further use pulsed amperometry to show that the intrinsic voltage dependence of the ion conduction is actually selective of the polarity of the transported ion and not simply of the direction of the ionic current flow. PMID:25474616

  14. Free ion yields in liquids: Molecular structure and track effects

    SciTech Connect

    Holroyd, R.

    1992-05-01

    The signal generated in a liquid-filled ionization chamber is proporational to the ions that escape, the free ion yield or, G{sub fi}. Recent results show how molecular structure, rate of energy loss (dE/dx) and pressure affect G{sub fi} and give further insight into the ionization process in liquids. As a consequence of the passage of high energy charged particles through a liquid, molecules are ionized and excited. The electrons have kinetic energy initially which allow them to travel some distance away from their geminate cations. The electrons may lose energy to vibrational modes but a significant fraction of the separation occurs while the electrons have subvibrational (near thermal) energy. When the electron finally thermalizes it is within the coulombic field of its parent cation and the two ions constitute a geminate pair. The free ion yield is determined by the fraction of geminate pairs which separate to form free ions as against those that recombine to form excited states.

  15. Free ion yields in liquids: Molecular structure and track effects

    SciTech Connect

    Holroyd, R.

    1992-01-01

    The signal generated in a liquid-filled ionization chamber is proporational to the ions that escape, the free ion yield or, G{sub fi}. Recent results show how molecular structure, rate of energy loss (dE/dx) and pressure affect G{sub fi} and give further insight into the ionization process in liquids. As a consequence of the passage of high energy charged particles through a liquid, molecules are ionized and excited. The electrons have kinetic energy initially which allow them to travel some distance away from their geminate cations. The electrons may lose energy to vibrational modes but a significant fraction of the separation occurs while the electrons have subvibrational (near thermal) energy. When the electron finally thermalizes it is within the coulombic field of its parent cation and the two ions constitute a geminate pair. The free ion yield is determined by the fraction of geminate pairs which separate to form free ions as against those that recombine to form excited states.

  16. 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.

  17. Study of coal structure using secondary ion mass spectrometry

    SciTech Connect

    Tingey, G.L.; Lytle, J.M.; Baer, D.R.; Thomas, M.T.

    1980-12-01

    Secondary-ion Mass Spectrometry (SIMS) is examined as a tool for studying the chemical structure of coal. SIMS has potential for analysis of coal because of the following characteristics: sensitivity to chemical structure; high sensitivity to all masses; application to solids; excellent depth resolution; and reasonable spatial resolution. SIMS spectra of solid coals show differences with respect to coal rank, the spectra of high rank coal being similar to that of graphite, and the spectra of low rank coal being similar to that of wood. Some functional group analysis is also possible using SIMS. Low rank coals show a larger peak at 15 amu indicating more methyl groups than found in the higher rank coals. Fragments with two and three carbon atoms have also been examined; much larger fragments are undoubtedly present but were not evaluated in this study. Examination of these groups, which are expected to contain valuable information on coal structure, is planned for future work. It has been observed that mineral atoms present in the coal have large secondary ion yields which complicate the interpretation of the spectra. Studies on mineral-free coals and model compounds are therefore recommended to facilitate determination of organic coal structure. In addition, mass spectrometry with much greater mass resolution will aid in distinguishing between various ion species.

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

    PubMed

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

    2008-09-01

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

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

    PubMed Central

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

    2010-01-01

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

  20. 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.

  1. Computational and ESR studies of electron attachment to decafluorocyclopentane, octafluorocyclobutane, and hexafluorocyclopropane: electron affinities of the molecules and the structures of their stable negative ions as determined from 13C and 19F hyperfine coupling constants.

    PubMed

    ElSohly, Adel M; Tschumper, Gregory S; Crocombe, Richard A; Wang, Jih Tzong; Williams, Ffrancon

    2005-08-01

    High-resolution ESR spectra of the ground-state negative ions of hexafluorocyclopropane (c-C3F6*-), octafluorocyclobutane (c-C4F8*-), and decafluorocyclopentane (c-C5F10*-) are reported and their isotropic 19F hyperfine coupling constants (hfcc) of 198.6 +/- 0.4 G, 147.6 +/- 0.4 G, and 117.9 +/- 0.4 G, respectively, are in inverse ratio to the total number of fluorine atoms per anion. Together with the small value of 5.2 +/- 0.4 G determined for the isotropic 13C hfcc of c-C4F8*-, these results indicate that in each case the singly occupied molecular orbital (SOMO) is delocalized over the equivalent fluorines and possesses a nodal plane through the carbon atoms of a time-averaged D(nh) structure. A series of quantum chemical computations were carried out to further characterize these anions and their neutral counterparts. Both the B3LYP density functional and second-order Møller-Plesset perturbation theory (MP2) indicate that c-C3F6*- adopts a D(3h) geometry and a (2)A2'' ground electronic state, that c-C4F8*- adopts a D(4h) geometry and a (2)A2u ground electronic state, and that c-C5F10*- adopts a C(s) structure and a (2)A' electronic state. Moreover, the 19F hyperfine coupling constants computed with the MP2 method and a high quality triple-zeta basis set are within 1% of the experimental values. Also, the values computed for the 13C hfcc of c-C4F8*- are consistent with the experimental value of 5.2 G. Therefore, in keeping with the ESR results, these negative ions derived from first-row elements can be characterized as pi* species. In addition, the hypervalency of these perfluorocycloalkane radical anions has been clarified. PMID:16045345

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

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

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

  3. Ion Channel Voltage Sensors: Structure, Function, and Pathophysiology

    PubMed Central

    Catterall, William A.

    2010-01-01

    Voltage-gated ion channels generate electrical signals in species from bacteria to man. Their voltage-sensing modules are responsible for initiation of action potentials and graded membrane potential changes in response to synaptic input and other physiological stimuli. Extensive structure-function studies, structure determination, and molecular modeling are now converging on a sliding-helix mechanism for electromechanical coupling in which outward movement of gating charges in the S4 transmembrane segments catalyzed by sequential formation of ion pairs pulls the S4-S5 linker, bends the S6 segment, and opens the pore. Impairment of voltage-sensor function by mutations in Na+ channels contributes to several ion channelopathies, and gating pore current conducted by mutant voltage sensors in NaV1.4 channels is the primary pathophysiological mechanism in Hypokalemic Periodic Paralysis. The emerging structural model for voltage sensor function opens the way to development of a new generation of ionchannel drugs that act on voltage sensors rather than blocking the pore. PMID:20869590

  4. Electronic Structure Calculations of Highly Charged Ions

    NASA Astrophysics Data System (ADS)

    Bromley, Steve; Ziolkowski, Marcin; Marler, Joan

    2016-05-01

    Exotic systems like Highly Charged Ions (HCIs) are attracting more attention based on their properties and possible interactions. Abundance of HCIs in the solar wind and their interaction with the upper atmosphere puts them in the attention of astro- and atmospheric physicists. Also, their unique properties originating in the high charge make them an excellent candidate for precision measurements and the next generation of atomic clocks. For a better understanding of the dynamics of processes involving HCIs a combined theoretical and experimental effort is needed to study their basic properties and interactions. Both theory and experiment need to be combined due to the extreme nature of these systems. We present preliminary insight into electronic structure of light HCIs, their interactions with neutral atoms and dynamics of charge transfer processes.

  5. State-of-the-art ion chromatographic determination of inorganic ions in food.

    PubMed

    Buldini, P L; Cavalli, S; Trifirò, A

    1997-11-21

    A review of the applications of ion chromatography (IC) to the determination of inorganic ions in food is presented. The most promising sample preparation techniques, such as accelerated solvent extraction, supercritical fluid extraction, solid-phase extraction, UV photolysis, microwave-oven digestion and pyrohydrolysis are discussed. Among the various inorganic anions, nitrogen, sulphur and phosphorus species and halides are widely determined in foods and to a lesser extent only, cyanide, carbonate, arsenic and selenium species are considered. IC determination of inorganic cations deals with ammonium ion, alkali, alkaline-earth, heavy and transition metals particularly and only a small amount of literature is found on the other ones, like aluminium and plantinum. A particular advantage of IC over traditional techniques is the simultaneous determination of several species. PMID:9440294

  6. Structure determination of transient transcription complexes.

    PubMed

    Cramer, Patrick

    2016-08-15

    The determination of detailed 3D structures of large and transient multicomponent complexes remains challenging. Here I describe the approaches that were used and developed by our laboratory to achieve structure solution of eukaryotic transcription complexes. I hope this collection serves as a resource for structural biologists seeking solutions for difficult structure determination projects. PMID:27528766

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

    NASA Astrophysics Data System (ADS)

    Konda, Chiharu; Bendiak, Brad; Xia, Yu

    2013-12-01

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

  8. Determination of sulphite in wines using suppressed ion chromatography.

    PubMed

    Yoshikawa, Kenji; Uekusa, Yuki; Sakuragawa, Akio

    2015-05-01

    Suppressed ion chromatography with the use of a conductivity detector was developed for the determination of sulphite ions in wine samples. When a mixed solution of sodium carbonate, sodium bicarbonate, and acetone was used as the mobile phase, simultaneous determination of eight inorganic anions (i.e., fluoride, chloride, nitrite, nitrate, sulphite, phosphate, sulphate, and thiosulphate) was completed in approximately 25 min. Linearity, reproducibility, and detection limits were determined for the proposed method. In the case of sulphite detection, a linear calibration curve with a good correlation coefficient of 0.9992 was obtained from the peak height of sulphite with a relative standard deviation (n = 6) 1.48%. In addition, the detection limit of sulphite was 0.27 mg/L at a signal-to-noise ratio of 3. Further, the developed method was applied for the determination of sulphite contained in several wine samples. PMID:25529696

  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. Dissociative recombination of interstellar ions: electronic structure calculations for HCO/sup +/

    SciTech Connect

    Kraemer, W.P.; Hazi, A.U.

    1985-07-02

    The present study of the interstellar formyl ion HCO/sup +/ is the first attempt to investigate dissociative recombination for a triatomic molecular ion using an entirely theoretical approach. We describe a number of fairly extensive electronic structure calculations that were performed to determine the reaction mechanism of the e-HCO/sup +/ process. Similar calculations for the isoelectronic ions HOC/sup +/ and HN/sub 2//sup +/ are in progress. 60 refs.

  11. Structural aspects of host molecules acting as ionophores in ion-selective electrodes

    NASA Astrophysics Data System (ADS)

    Bocheńska, Maria

    1998-09-01

    Structural aspects of ligand molecules acting as neutral ionophores in ion-selective membrane electrodes are discussed and examples of Li-selective ionophores are presented. The relationship between the structure of ionophore and its complex determined by X-ray and NMR study and the selectivity of ISE was determined.

  12. Track structure of carbon ions: measurements and simulations.

    PubMed

    Conte, V; Colautti, P; Moro, D; Grosswendt, B

    2014-10-01

    The likelihood of radiation to produce clustered damages in irradiated biological tissue and the reparability of such damages are closely related to the stochastics of localised ionising interactions within small volumes of nanometre sizes, determined by the particle track structure. Track structure investigations in nanometre-sized volumes have been subject of research for several decades, mainly by means of Monte Carlo simulations. Today, the 'track-nanodosimeter', installed at the TANDEM-ALPI accelerator complex of LNL, is a measuring device able to count the electrons produced in a 20-nm equivalent sensitive site (De Nardo et al. A detector for track-nanodosimetry. Nucl. Instrum. Methods. Phys. Res. A 484: , 312-326 (2002)). It allows studying track structure properties both in the near neighbourhood of a primary particle trajectory and separately in the penumbra region. An extended study for different ionising particles of medical interest has been recently performed with the track-nanodosimeter (Conte et al. Track structure of light ions: experiments and simulations. New J. Phys. 14: , 093010, (2012)). Here, new experimental data and results of Monte Carlo simulations for 240- and 96-MeV (12)C-ions are presented and discussed. PMID:24249779

  13. Determination of Alkali Ions in Biological and Environmental Samples.

    PubMed

    Hauser, Peter C

    2016-01-01

    An overview of the common methods for the determination of the alkali metals is given. These are drawn from all of the three principle branches of quantitative analysis and consist mainly of optical atomic spectrometric methods, ion-selective electrodes, and the separation methods of ion-chromatography and capillary electrophoresis. Their main characteristics and performance parameters are discussed. Important specific applications are also examined, namely clinical analysis, single cell analysis, the analysis of soil samples and hydroponic nutrient solutions, as well as the detection of the radioactive (137)Cs isotope. PMID:26860298

  14. Disposable sensor for electrochemical determination of chloride ions.

    PubMed

    Bujes-Garrido, Julia; Arcos-Martínez, M Julia

    2016-08-01

    This work describes the development of a new, simple and inexpensive method for the determination of chloride ions, by using voltammetric disposable sensors. The sensor includes three screen printed electrodes: a working, an auxiliary (both carbon based paste electrodes), and a pseudo-reference Ag/AgCl paste based electrode. Since the presence of chloride ions in the solution modifies the equilibrium potential of Ag/AgCl electrode, the concentration of this analyte has been determined through the systematic shift of the voltammetric peak potential of a control species such as potassium ferricyanide, potassium ferrocyanide or ferrocenemethanol. These control species can be used in solution or mixed into the carbon paste of the working screen printed electrode. In order to characterize the developed methods, reproducibility, repeatability and detection limit of the sensors were calculated in each case. Reproducibility values below 3% (n=5) were obtained. When ferrocenemethanol was used as control species, the lowest quantity of chloride ions detected was 10.0mM. A comprehensive study of interfering ions was also carried out. These sensors were successfully applied to determine the chloride content in sea water and in a commercial saline solution sample. PMID:27216668

  15. Cryogenic Ion Mobility-Mass Spectrometry: Tracking Ion Structure from Solution to the Gas Phase.

    PubMed

    Servage, Kelly A; Silveira, Joshua A; Fort, Kyle L; Russell, David H

    2016-07-19

    Electrospray ionization (ESI) combined with ion mobility-mass spectrometry (IM-MS) is adding new dimensions, that is, structure and dynamics, to the field of biological mass spectrometry. There is increasing evidence that gas-phase ions produced by ESI can closely resemble their solution-phase structures, but correlating these structures can be complicated owing to the number of competing effects contributing to structural preferences, including both inter- and intramolecular interactions. Ions encounter unique hydration environments during the transition from solution to the gas phase that will likely affect their structure(s), but many of these structural changes will go undetected because ESI-IM-MS analysis is typically performed on solvent-free ions. Cryogenic ion mobility-mass spectrometry (cryo-IM-MS) takes advantage of the freeze-drying capabilities of ESI and a cryogenically cooled IM drift cell (80 K) to preserve extensively solvated ions of the type [M + xH](x+)(H2O)n, where n can vary from zero to several hundred. This affords an experimental approach for tracking the structural evolution of hydrated biomolecules en route to forming solvent-free gas-phase ions. The studies highlighted in this Account illustrate the varying extent to which dehydration can alter ion structure and the overall impact of cryo-IM-MS on structural studies of hydrated biomolecules. Studies of small ions, including protonated water clusters and alkyl diammonium cations, reveal structural transitions associated with the development of the H-bond network of water molecules surrounding the charge carrier(s). For peptide ions, results show that water networks are highly dependent on the charge-carrying species within the cluster. Specifically, hydrated peptide ions containing lysine display specific hydration behavior around the ammonium ion, that is, magic number clusters with enhanced stability, whereas peptides containing arginine do not display specific hydration around the

  16. Determining structure and function in nanomaterial biocomposites

    NASA Astrophysics Data System (ADS)

    Griffin, David M.

    Polymeric biomaterials represent the leading technologies available today for the repair of tissue damage and for targeted drug delivery. Perhaps the most valuable aspect of polymer-based systems is the extent to which their physical properties (e.g. elasticity, porosity, etc.) can be controlled and tuned by regulating experimental parameters during their synthesis. Biomaterial performance can be improved further still by including supplementary components resulting in a composite material. Synergetic interactions between the constituents of composite materials often results in bulk physical properties that are substantially more than the sum of individual parts. Through understanding and exploiting these sympathetic relationships, novel biocomposites can be developed which exhibit improved efficacy and biocompatibility. Here we report on the synthesis strategies and characterization of novel biocomposites from our laboratory. We look specifically at hydrogel composites containing a physically-associated network of PluronicRTM block copolymer along with a calcium-phosphate mineral component. Rheological results show that composites containing an in situ deposited mineral exhibit a significantly higher elastic modulus than composites of similar composition formed by conventional means. Moreover, analysis of the calcium-phosphate phase of in situ composites revealed that system parameters such as acidity play an integral role in determining the size and stability of the resultant mineral and subsequently the materials' expected in vivo performance. Changes to the structure in PluronicRTM/calcium-phosphate composite hydrogels during dehydration was investigated to provide a look into the mechanisms involved in composite formation. Small angle X-ray scattering analysis of these systems shows that hydrogen bonding interactions between phosphate ions and the polyethylene oxide (PEO) polymer block significantly impact the nanoscale structure and long-range order contained

  17. Fluorometric determination of ammonium ion by ion chromatography using postcolumn derivatization with o-phthaldialdehyde.

    PubMed

    Kuo, Chun-Ting; Wang, Po-Yen; Wu, Chien-Hou

    2005-08-26

    A postcolumn fluorometric derivatization method for the determination of trace amounts of ammonium ion (microg/L level) under matrices with high concentrations of sodium and amino acids has been developed. In this method, ammonium ion was determined by ion chromatography combined with fluorometric detection (IC-FL) in less than 16 min. IC was performed in a high-capacity cation-exchange Dionex IonPac CS16 analytical column (250 mm x 5 mm) under isocratic conditions with 30 mM methanesulfonic acid (MSA) as mobile phase at flow-rate 1.0 mL/min. To remove amino acid interference, the postcolumn derivatization based on the reaction of ammonia with o-phthaldialdehyde (OPA) and sulfite was applied. The excitation and emission wavelengths were 364 and 425 nm, respectively. The effects of pH, reaction temperature and time, OPA-reagent composition and concentration, and sample matrix were studied. The linear range and detection limit of this method were similar to the standard method. The IC-FL method with a postcolumn fluorometric derivatization allows the routine determination of ammonium ion in extreme matrices where the ratios of sodium and amino acids to ammonium are up to 2,800,000:1 and 28,000:1, respectively. PMID:16106853

  18. Determination of selected anions in water by ion chromatography

    USGS Publications Warehouse

    Fishman, Marvin J.; Pyen, Grace

    1979-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

    Preparation of Zn2+ 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 Zn2+ 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 Zn2+ 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 Zn2+ 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.

  20. Determination of chloride in geological samples by ion chromatography

    USGS Publications Warehouse

    Wilson, S.A.; Gent, C.A.

    1983-01-01

    Samples of silicate rocks are prepared by sodium carbonate fusion and then treated by ion chromatography. The method was tested for geological standards with chloride concentration between 0.003 and 3%. Observed chloride concentrations comparedd favorably with literature values. The relative standard deviation and detection limit for the method were 8% and 7 ppm, respectively. Up to 30 determination per 24-hour period were possible. ?? 1983.

  1. 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.

  2. Structure Determination of Natural Products by Mass Spectrometry.

    PubMed

    Biemann, Klaus

    2015-01-01

    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. PMID:26161970

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

    PubMed

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

    2015-06-16

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

  4. 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

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

    PubMed

    Hughes-Currie, Rosa B; Ivanovskikh, Konstantin V; R Wells, Jon-Paul; 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. PMID:26941175

  6. 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.

  7. 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.

  8. 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

    2015-04-01

    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. PMID:25645232

  9. Modeling the multi-ion structure of the solar corona

    NASA Astrophysics Data System (ADS)

    Ofman, Leon; Provornikova, Elena; Wang, Tongjiang

    2014-06-01

    The solar corona is typically observed in EUV by SDO/AIA and other instruments using the heavy ion emission lines such as Fe IX, Fe XII, and other ion emission lines. However, the relative (to protons) abundance of the emitting ions is very low and the collisional coupling between the Fe ions and electrons decreases rapidly with height in the low corona, while gravitational settling may become significant in quiescent long-lived magnetic structures, such as streamers. Thus, the structure of the weakly collisional solar corona imaged in Fe IX (and other heavy ions) may differ significantly from the structure of the main electron-proton constituents of the corona. The electron structure is observed by white light coronagraphs, and during solar eclipses in the low corona. I present the results of multi-fluid modeling of coronal streamers and other magnetic structures that demonstrate the effects of weak coupling between the heavy ions and the coronal electron-proton components, and show that the multi-ion coronal structure must be taken into account in interpretation of EUV observations.

  10. Determination of SrSO 04 ion pair formation using conductimetric and ion exchange techniques

    NASA Astrophysics Data System (ADS)

    Reardon, E. J.

    1983-11-01

    The dissociation constant for SrSO 04 ion pair was determined at 25°C using conductance and ion-exchange techniques. Both approaches yield values for pK of SrSO 04 at zero ionic strength in the range 2.28-2.31. Previously reported values range from 2.1 to 3.0. The refinement in the dissociation constant should allow more reliable appraisals of the extent of strontium mineral solubility controls on strontium concentrations in natural water systems. The Lee and Wheaton conductance model was used to interpret the results of the conductivity measurements in strontium sulphate solutions at 25°C. Because of the limitations imposed by the solubility of celestite, a sufficiently-wide concentration range to enable determination of all three of the parameters - dissociation constant, Λ0, and the distance parameter could not be made. Instead, values are reported for the dissociation constant and Λ0 using reasonable limiting values for the distance parameter. Dowex-50 was used in the ion-exchange technique to determine the dissociation constant for SrSO 04. This method was used to determine values at other temperatures as well. Although there is considerable scatter in the temperature data, a standard enthalpy for the dissociation reaction: SrSO04→ Sr2+ + SO2-4 is computed to be 8.7 ± 2 kJmole-1 at 25°C.

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

    SciTech Connect

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

    2007-01-01

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

  12. 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.

  13. Determination of heparin on intraocular lens surfaces by ion chromatography.

    PubMed

    Ander, B; Karlsson, A; Ohrlund, A

    2001-05-11

    A sensitive and selective method has been developed for the determination of heparin on heparin coated PMMA, poly(methyl methacrylate), intraocular lenses. Heparin was hydrolysed to glucosamine and glucuronic acid, and the content of glucosamine was determined using ion chromatography with pulsed amperometric detection. In order to verify that a complete hydrolysis was obtained for the heparin on the coated intraocular lenses, electron spectroscopy for chemical analysis (ESCA) was used for analysing traces of sulphur on the lens surfaces. The sensitivity of the method allows quantitative determination of 150 ng of heparin on one individual lens. The new method was compared to a standard spectrophotometric method, measuring the colour intensity of a heparin toluidine blue complex. Correlation between the methods was shown for samples prepared from PMMA lenses coated with different amounts of heparin. PMID:11403462

  14. Structural insights into protein-metal ion partnerships.

    PubMed

    Barondeau, David P; Getzoff, Elizabeth D

    2004-12-01

    New metalloprotein structures continue to provide discoveries regarding protein-metal ion partnerships. Many recent structures reveal metal ion sites that control or are controlled by protein conformational change, including modulation by alternative splice variants and striking conformational changes. Only a few novel catalytic metal centers have been revealed recently, such as the surprising Ni-hook superoxide dismutase catalytic site and the cubane-like Mn(3)CaO(4) photosynthetic oxygen-evolving center. However, important new variations on old heme themes, breakthroughs in the fields of metal ion regulation and metallochaperones, and captivating insights into partnerships between proteins and minerals have also been described. Very high resolution metal site structures and metalloprotein design will be increasingly important in order to leverage the wealth of native metalloprotein structures into a deep understanding of metal ion site specificity and activity. PMID:15582401

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

    PubMed

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

    2015-06-01

    Facet-dependent stripping behavior in the determination of Pb(II): Well-defined Cu2O microcrystals with different structures show facet-dependent electrochemical behaviors toward heavy metal ions. This provides an important insight into the understanding the efficiency of facet-dependent properties of microcrystals on electroanalytical performance for the rational design of electrochemical analytical techniques for efficient detection of heavy metal ions. PMID:25630388

  16. 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.

  17. A comparative study of the structure and cytotoxicity of polytetrafluoroethylene after ion etching and ion implantation

    NASA Astrophysics Data System (ADS)

    Shtansky, D. V.; Glushankova, N. A.; Kiryukhantsev-Korneev, F. V.; Sheveiko, A. N.; Sigarev, A. A.

    2011-03-01

    The ion-plasma treatment has been widely used for modifying the surface structure of polymers in order to improve their properties, but it can lead to destruction of the surface and, as a consequence, to an increase in their toxicity. A comparative study of the structure and cytotoxicity of polytetrafluoroethylene (PTFE) after the ion etching (IE) and ion implantation (II) for 10 min with energy densities of 363 and 226 J/cm2, respectively, has been performed. It has been shown that, unlike the ion implantation, the ion etching results in the destruction of the polymer and in the appearance of the cytotoxicity. The factors responsible for this effect, which are associated with the bulk and surface treatment, as well as with the influence of the temperature, have been discussed.

  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. 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. PMID:26510005

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

    DOE PAGESBeta

    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.; et al

    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

  1. Ion mixing of III-V compound semiconductor layered structures

    SciTech Connect

    Xia, W.; Pappert, S.A.; Zhu, B.; Clawson, A.R.; Yu, P.K.L.; Lau, S.S. ); Poker, D.B.; White, C.W. ); Schwarz, S.A. )

    1992-03-15

    Compositional disordering of III-V compound superlattice structures has received considerable attention recently due to its potential application for photonic devices. The conventional method to induce compositional disorder in a layered structure is to implant a moderate dose of impurity ions ({similar to}10{sup 15}/cm{sup 2}) into the structure at room temperature, followed by a high-temperature annealing step (this process is referred to as IA here). Ion irradiation at room temperature alone does not cause any significant intermixing of layers. The subsequent high-temperature annealing step tends to restrict device processing flexibility. Ion mixing (IM) is capable of enhancing compositional disordering of layers at a rate which increases exponentially with the ion irradiation temperature. As a processing technique to planarize devices, ion mixing appears to be an attractive technology. In this work, we investigate compositional disordering in the AlGaAs/GaAs and the InGaAs/InP systems using ion mixing. We found that the ion mixing behavior of these two systems shows a thermally activated regime as well as an athermal regime, similar to that observed for metal-metal and metal-semiconductor systems. Ion mixing is observed to induce compositional disordering at significantly lower temperatures than that for the IA process. We have compared the two processes in terms of five parameters: (1) irradiation temperature, (2) dose dependence, (3) dose rate dependence, (4) annealing, and (5) ion dependence (including electrical effects and mass dependence). We found that the IM process is more efficient in utilizing the defects generated by ion irradiation to cause disordering. Both the physical mechanism of ion mixing and possible device implications will be discussed.

  2. Cryo-focused-ion-beam applications in structural biology.

    PubMed

    Rigort, Alexander; Plitzko, Jürgen M

    2015-09-01

    The ability to precisely control the preparation of biological samples for investigations by electron cryo-microscopy is becoming increasingly important for ultrastructural imaging in biology. Precision machining instruments such as the focused ion beam microscope (FIB) were originally developed for applications in materials science. However, today we witness a growing use of these tools in the life sciences mainly due to their versatility, since they can be used both as manipulation and as imaging devices, when complemented with a scanning electron microscope (SEM). The advent of cryo-preparation equipment and accessories made it possible to pursue work on frozen-hydrated biological specimens with these two beam (FIB/SEM) instruments. In structural biology, the cryo-FIB can be used to site-specifically thin vitrified specimens for transmission electron microscopy (TEM) and tomography. Having control over the specimen thickness is a decisive factor for TEM imaging, as the thickness of the object under scrutiny determines the attainable resolution. Besides its use for TEM preparation, the FIB/SEM microscope can be additionally used to obtain three-dimensional volumetric data from biological specimens. The unique combination of an imaging and precision manipulation tool allows sequentially removing material with the ion beam and imaging the milled block faces by scanning with the electron beam, an approach known as FIB/SEM tomography. This review covers both fields of cryo-FIB applications: specimen preparation for TEM cryo-tomography and volume imaging by cryo-FIB/SEM tomography. PMID:25703192

  3. Functional Insights from Glutamate Receptor Ion Channel Structures

    PubMed Central

    Kumar, Janesh; Mayer, Mark L.

    2014-01-01

    X-ray crystal structures for the soluble amino terminal and ligand binding domains of glutamate receptor ion channels, combined with a 3.6 Å resolution structure of the full length AMPA receptor GluA2 homotetramer, provide unique insights into the mechanisms of iGluR assembly and function. Increasingly sophisticated biochemical, computational and electrophysiological experiments are beginning to reveal the mechanism of action of partial agonists, and yield new models for the mechanism of action of allosteric modulators. Newly identified NMDA receptor ligands acting at novel sites offer hope for development of subtype selective modulators. Many issues remain unsolved, including the role of the ATD in AMPA receptor signaling, and the mechanisms by which auxiliary proteins regulate receptor activity. The structural basis for ion permeation and ion channel block also remain areas of uncertainty, and despite substantial progress, molecular dynamics simulations have yet to reveal how binding of glutamate opens the ion channel pore. PMID:22974439

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

    PubMed

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

    2015-06-01

    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. PMID:26002212

  5. Scaling behavior and local structure of ion aggregates in single-ion conductors.

    PubMed

    Lu, Keran; Rudzinski, Joseph F; Noid, W G; Milner, Scott T; Maranas, Janna K

    2014-02-21

    Single-ion conductors are attractive electrolyte materials because of their inherent safety and ease of processing. Most ions in a sodium-neutralized PEO sulfonated-isophthalate ionomer electrolyte exist as one dimensional chains, restricted in dimensionality by the steric hindrance of the attached polymer. Because the ions are slow to reconfigure, atomistic MD simulations of this material are unable to adequately sample equilibrium ion structures. We apply a novel coarse-graining scheme using a generalized-YBG procedure in which the polymer backbone is completely removed and implicitly represented by the effective potentials of the remaining ions. The ion-only coarse-grained simulation allows for substantial sampling of equilibrium aggregate configurations. We extend the wormlike micelle theory to model ion chain equilibrium. Our aggregates are random walks which become more positively charged with increasing size. Defects occur on the string-like structure in the form of “dust” and “knots,” which form due to cation coordination with open sites along the string. The presence of these defects suggest that cation hopping along open third-coordination sites could be an important mechanism of charge transport using ion aggregates. PMID:24983107

  6. 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.

  7. Global structural changes of an ion channel during its gating are followed by ion mobility mass spectrometry

    PubMed Central

    Konijnenberg, Albert; Yilmaz, Duygu; Ingólfsson, Helgi I.; Dimitrova, Anna; Marrink, Siewert J.; Li, Zhuolun; Vénien-Bryan, Catherine; Sobott, Frank; Koçer, Armağan

    2014-01-01

    Mechanosensitive ion channels are sensors probing membrane tension in all species; despite their importance and vital role in many cell functions, their gating mechanism remains to be elucidated. Here, we determined the conditions for releasing intact mechanosensitive channel of large conductance (MscL) proteins from their detergents in the gas phase using native ion mobility–mass spectrometry (IM-MS). By using IM-MS, we could detect the native mass of MscL from Escherichia coli, determine various global structural changes during its gating by measuring the rotationally averaged collision cross-sections, and show that it can function in the absence of a lipid bilayer. We could detect global conformational changes during MscL gating as small as 3%. Our findings will allow studying native structure of many other membrane proteins. PMID:25404294

  8. 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.

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

    DOE PAGESBeta

    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.; et al

    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

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

    SciTech Connect

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

    2014-11-01

    We report a conceptual study and computational evaluation of novel planar electrode Structures for Lossless Ion Manipulations (SLIM). Planar electrode SLIM 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 90o and dynamically switching selected ion species into orthogonal channels, are also 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 agree closely with experimental and theoretical IMS performance for a conventional drift tube design.

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

    DOE PAGESBeta

    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.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

  12. 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

  13. Microwave Spectrum of the SD+3 Ion: Molecular Structure.

    PubMed

    Araki; Ozeki; Saito

    1998-11-01

    The J = 1-0 to 4-3 spectral lines of SD+3 were measured in the 152-610 GHz region using a source-modulated microwave spectrometer. The SD+3 ion was generated in a free space absorption cell by a hollow-cathode discharge in a gas mixture of D2S and D2. The rotational constant B0 and the centrifugal distortion constants DJ and DJK were determined from the measured frequencies. A vibration-rotation analysis was carried out and the rz structures of SH+3 and SD+3 were derived from their zero point averaged rotational constants, expressed as SH+3: rz = 1.36512(22) Å and thetaz = 94.098(26) degrees, and SD+3: rz = 1.36086(16) Å and thetaz = 94.1211(195) degrees, where the difference between thetaz(HSH) and thetaz(DSD) was assumed to be the same as that between thetaz(HPH) of PH3 and thetaz(DPD) of PD3. From the shift between the rz structures of SH+3 and SD+3, the re structure of SH+3 was estimated to be re = 1.35001(113) Å, thetae = 94.181(135) degrees. Copyright 1998 Academic Press. PMID:9770407

  14. Structure of the TRPA1 ion channel suggests regulatory mechanisms

    PubMed Central

    Paulsen, Candice E.; Armache, Jean-Paul; Gao, Yuan; Cheng, Yifan; Julius, David

    2015-01-01

    The TRPA1 ion channel (a.k.a the ‘wasabi receptor’) is a detector of noxious chemical agents encountered in our environment or produced endogenously during tissue injury or drug metabolism. These include a broad class of electrophiles that activate the channel through covalent protein modification. TRPA1 antagonists hold potential for treating neurogenic inflammatory conditions provoked or exacerbated by irritant exposure. Despite compelling reasons to understand TRPA1 function, structural mechanisms underlying channel regulation remain obscure. Here, we use single-particle electron cryo-microscopy to determine the structure of full-length human TRPA1 to ~4Å resolution in the presence of pharmacophores, including a potent antagonist. A number of unexpected features are revealed, including an extensive coiled-coil assembly domain stabilized by polyphosphate co-factors and a highly integrated nexus that converges on an unpredicted TRP-like allosteric domain. These findings provide novel insights into mechanisms of TRPA1 regulation, and establish a blueprint for structure-based design of analgesic and anti-inflammatory agents. PMID:25855297

  15. 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.

  16. Potentiometric determination of free acidity in presence of hydrolysable ions and a sequential determination of hydrazine.

    PubMed

    Ganesh, S; Khan, Fahmida; Ahmed, M K; Pandey, S K

    2011-08-15

    A simple potentiometric method for the determination of free acidity in presence of hydrolysable ions and sequential determination of hydrazine is developed and described. Both free acid and hydrazine are estimated from the same aliquot. In this method, free acid is titrated with standard sodium carbonate solution after the metal ions in solutions are masked with EDTA. Once the end point for the free acid is determined at pH 3.0, an aliquot of formaldehyde is added to liberate the acid equivalent to hydrazine which is then titrated with the same standard sodium carbonate solution using an automatic titration system. The described method is simple, accurate and reproducible. This method is especially applicable to all ranges of nitric acid and heavy metal ion concentration relevant to Purex process used for nuclear fuel reprocessing. The overall recovery of nitric acid is 98.9% with 1.2% relative standard deviation. Hydrazine content has also been determined in the same aliquot with a recovery of nitric acid is 99% with 2% relative standard deviation. The major advantage of the method is that generation of corrosive analytical wastes containing oxalate or sulphate is avoided. Valuable metals like uranium and plutonium can easily be recovered from analytical waste before final disposal. PMID:21726724

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

    SciTech Connect

    Stacey, W. M.

    2014-04-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-02-01

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

  19. 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.

  20. Ions in solutions: Determining their polarizabilities from first-principles

    NASA Astrophysics Data System (ADS)

    Molina, John J.; Lectez, Sébastien; Tazi, Sami; Salanne, Mathieu; Dufrêche, Jean-François; Roques, Jérôme; Simoni, Eric; Madden, Paul A.; Turq, Pierre

    2011-01-01

    Dipole polarizabilities of a series of ions in aqueous solutions are computed from first-principles. The procedure is based on the study of the linear response of the maximally localized Wannier functions to an applied external field, within density functional theory. For most monoatomic cations (Li ^+, Na ^+, K ^+, Rb ^+, Mg ^{2+}, Ca ^{2+} and Sr ^{2+}) the computed polarizabilities are the same as in the gas phase. For Cs ^+ and a series of anions (F ^-, Cl ^-, Br ^- and I ^-), environmental effects are observed, which reduce the polarizabilities in aqueous solutions with respect to their gas phase values. The polarizabilities of H ^+_(aq), OH ^-_(aq) have also been determined along an ab initio molecular dynamics simulation. We observe that the polarizability of a molecule instantaneously switches upon proton transfer events. Finally, we also computed the polarizability tensor in the case of a strongly anisotropic molecular ion, UO _2^{2+}. The results of these calculations will be useful in building interaction potentials that include polarization effects.

  1. 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. PMID:27238484

  2. 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. PMID:21035599

  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. Observations on ion track structure in semiconductors : a phenomenological study

    NASA Technical Reports Server (NTRS)

    Selva, L. E.; Wallace, R. E.

    2001-01-01

    An ion track structure model at the nanometer scale is presented. The model is based on electrostatic principles and is supported by observed experimental results conducted on power MOSFETs. The model predicts the existence of a transient induced electric field following the passage of an energetic heavy ion. There are two segments to the field (a radial and an axial component). It is the interaction of this transient electric field with the local environment that can trigger a catastrophic failure.

  5. 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.

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

    PubMed Central

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

    2013-01-01

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

  7. 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

  8. 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. PMID:27366642

  9. Atomic structure of highly-charged ions. Final report

    SciTech Connect

    Livingston, A. Eugene

    2002-05-23

    Atomic properties of multiply charged ions have been investigated using excitation of energetic heavy ion beams. Spectroscopy of excited atomic transitions has been applied from the visible to the extreme ultraviolet wavelength regions to provide accurate atomic structure and transition rate data in selected highly ionized atoms. High-resolution position-sensitive photon detection has been introduced for measurements in the ultraviolet region. The detailed structures of Rydberg states in highly charged beryllium-like ions have been measured as a test of long-range electron-ion interactions. The measurements are supported by multiconfiguration Dirac-Fock calculations and by many-body perturbation theory. The high-angular-momentum Rydberg transitions may be used to establish reference wavelengths and improve the accuracy of ionization energies in highly charged systems. Precision wavelength measurements in highly charged few-electron ions have been performed to test the most accurate relativistic atomic structure calculations for prominent low-lying excited states. Lifetime measurements for allowed and forbidden transitions in highly charged few-electron ions have been made to test theoretical transition matrix elements for simple atomic systems. Precision lifetime measurements in laser-excited alkali atoms have been initiated to establish the accuracy of relativistic atomic many-body theory in many-electron systems.

  10. Effects of magnesium ions on the stabilization of RNA oligomers of defined structures.

    PubMed Central

    Serra, Martin J; Baird, John D; Dale, Taraka; Fey, Bridget L; Retatagos, Kimberly; Westhof, Eric

    2002-01-01

    Optical melting was used to determine the stabilities of 11 small RNA oligomers of defined secondary structure as a function of magnesium ion concentration. The oligomers included helices composed of Watson-Crick base pairs, GA tandem base pairs, GU tandem base pairs, and loop E motifs (both eubacterial and eukaryotic). The effect of magnesium ion concentration on stability was interpreted in terms of two simple models. The first assumes an uptake of metal ion upon duplex formation. The second assumes nonspecific electrostatic attraction of metal ions to the RNA oligomer. For all oligomers, except the eubacterial loop E, the data could best be interpreted as nonspecific binding of metal ions to the RNAs. The effect of magnesium ions on the stability of the eubacterial loop E was distinct from that seen with the other oligomers in two ways. First, the extent of stabilization by magnesium ions (as measured by either change in melting temperature or free energy) was three times greater than that observed for the other helical oligomers. Second, the presence of magnesium ions produces a doubling of the enthalpy for the melting transition. These results indicate that magnesium ion stabilizes the eubacterial loop E sequence by chelating the RNA specifically. Further, these results on a rather small system shed light on the large enthalpy changes observed upon thermal unfolding of large RNAs like group I introns. It is suggested that parts of those large enthalpy changes observed in the folding of RNAs may be assigned to variations in the hydration states and types of coordinating atoms in some specifically bound magnesium ions and to an increase in the observed cooperativity of the folding transition due to the binding of those magnesium ions coupling the two stems together. Brownian dynamic simulations, carried out to visualize the metal ion binding sites, reveal rather delocalized ionic densities in all oligomers, except for the eubacterial loop E, in which precisely

  11. Determination of sulfite ion by using microbial sensor

    SciTech Connect

    Suzuki, Masayasu; Lee, Soomi; Karube, Isao ); Fujii, Keiko; Arikawa, Yoshiko ); Kubo, Izumi ); Kanagawa, Takahiro; Mikami, Eiichi )

    1992-06-01

    Chemoautotrophic and aerobic bacterium Thiobacillus thioparus TK-m, which has sulfite oxidation pathways, was used for the development of sulfite ion sensor. The sensor consists of an oxygen electrode and T.thioparus immobilized between two nitrocellulose membranes. Since T.thioparus could not be cultivated in the medium containing sulfite as sulfur source, T.thiparus grown in the thiosulfate containing medium was used for the experiment. The selectivity for sulfite was gradually increased during the use as sulfite sensor. After 6 days, the response to thiosulfate became approximately 10% of that of sulfite. When the sensor was applied to the sulfite determination in batch system, calibration curve showed the linearity in the concentration range between 4 {mu}M and 280 {mu}M.

  12. Distributed structure determination at the JCSG

    SciTech Connect

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

    2011-04-01

    The software suite Xsolve semi-exhaustively explores key parameters of the X-ray structure-determination process to compute multiple three-dimensional protein structures independently and in parallel from a set of diffraction images. An optimal consensus model for subsequent manual refinement is computed from these structures. 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.

  13. 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.

  14. 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

  15. Ion implantation of B ions into CdHgTe/CdZnTe substrate and determination of optimum optical characteristics for making diode p-n structures in narrow(-band)-gap semiconductor material CdHgTe/CdZnTe

    NASA Astrophysics Data System (ADS)

    Udovitska, Ruslana S.; Kalisty, Genadiy V.; Fedulov, Vladimir V.

    2008-02-01

    The samples were prepared from CdZnTe substrate with thickness of 600µm, on wich thin CdHgTe (KRT) thin films with thicknesses of 16µm, 18.75 µm and the same sample with KRT thin film with thickness 21.6µm was coated by diamond thin film with thickness of 30nm. B ion implantation into KRT film on CdZnTe substrate was made with purpose of investigation of volt-ampere characteristics and defects formation. Ion doping of B in KRT with doses of (D=3.4 mCl/cm2, D=6.8 mCl/cm2) and energies (50 keV, 100 keV, 150 keV). The calculations by SRIM-TRIM 2003 software for condition of maximum ion distribution on the interface "filmsubstrate" have shown that the optimal energy is 100 keV for all mentioned samples. The results also have shown that implantation at ions energy 100 keV is optimal for form diode p-n structures in narrow(-band)-gap semiconductor material CdHgTe/CdZnTe.

  16. A structural determinant required for RNA editing

    PubMed Central

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

    2011-01-01

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

  17. 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.

  18. 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

  19. 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

  20. Ion Streaming Instabilities in Pair Ion Plasma and Localized Structure with Non-Thermal Electrons

    NASA Astrophysics Data System (ADS)

    Nasir Khattak, M.; Mushtaq, A.; Qamar, A.

    2015-12-01

    Pair ion plasma with a fraction of non-thermal electrons is considered. We investigate the effects of the streaming motion of ions on linear and nonlinear properties of unmagnetized, collisionless plasma by using the fluid model. A dispersion relation is derived, and the growth rate of streaming instabilities with effect of streaming motion of ions and non-thermal electrons is calculated. A qausi-potential approach is adopted to study the characteristics of ion acoustic solitons. An energy integral equation involving Sagdeev potential is derived during this process. The presence of the streaming term in the energy integral equation affects the structure of the solitary waves significantly along with non-thermal electrons. Possible application of the work to the space and laboratory plasmas are highlighted.

  1. 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.

  2. 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.…

  3. 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.

  4. 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.

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

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

    SciTech Connect

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

    2015-01-19

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

  8. Structure of mutant human oncogene protein determined

    SciTech Connect

    Baum, R.

    1989-01-16

    The protein encoded by a mutant human oncogene differs only slightly in structure from the native protein that initiates normal cell division, a finding that may complicate efforts to develop inhibitors of the mutant protein. Previously, the x-ray structure of the protein encoded by the normal c-Ha-ras gene, a protein believed to signal cells to start or stop dividing through its interaction with guanosine triphosphate (GTP), was reported. The structure of the protein encoded by a transforming c-Ha-ras oncogene, in which a valine codon replaces the normal glycine codon at position 12 in the gene, has now been determined. The differences in the structures of the mutant and normal proteins are located primarily in a loop that interacts with the /beta/-phosphate of a bound guanosine diphosphate (GDP) molecule.

  9. 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.

  10. 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.

  11. 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.

  12. Mechanochemically synthesized fluorides: local structures and ion transport.

    PubMed

    Preishuber-Pflügl, Florian; Wilkening, Martin

    2016-06-01

    The performance of new sensors or advanced electrochemical energy storage devices strongly depends on the active materials chosen to realize such systems. In particular, their morphology may greatly influence their overall macroscopic properties. Frequently, limitations in classical ways of chemical preparation routes hamper the development of materials with tailored properties. Fortunately, such hurdles can be overcome by mechanochemical synthesis. The versatility of mechanosynthesis allows the provision of compounds that are not available through common synthesis routes. The mechanical treatment of two or three starting materials in high-energy ball mills enables the synthesis not only of new compounds but also of nanocrystalline materials with unusual properties such as enhanced ion dynamics. Fast ion transport is of crucial importance in electrochemical energy storage. It is worth noting that mechanosynthesis also provides access to metastable phases that cannot be synthesized by conventional solid state synthesis. Ceramic synthesis routes often yield the thermally, i.e., thermodynamically, stable products rather than metastable compounds. In this perspective we report the mechanochemical synthesis of nanocrystalline fluorine ion conductors that serve as model substances to understand the relationship between local structures and ion dynamics. While ion transport properties were complementarily probed via conductivity spectroscopy and nuclear magnetic relaxation, local structures of the phases prepared were investigated by high-resolution (19)F NMR spectroscopy carried out by fast magic angle spinning. The combination of nuclear and non-nuclear techniques also helped us to shed light on the mechanisms controlling mechanochemical reactions in general. PMID:27172256

  13. Comprehensive Spectroscopic Determination of the Crystal Field Splitting in an Erbium Single-Ion Magnet.

    PubMed

    Rechkemmer, Yvonne; Fischer, Julia E; Marx, Raphael; Dörfel, María; Neugebauer, Petr; Horvath, Sebastian; Gysler, Maren; Brock-Nannestad, Theis; Frey, Wolfgang; Reid, Michael F; van Slageren, Joris

    2015-10-14

    The electronic structure of a novel lanthanide-based single-ion magnet, {C(NH2)3}5[Er(CO3)4]·11H2O, was comprehensively studied by means of a large number of different spectroscopic techniques, including far-infrared, optical, and magnetic resonance spectroscopies. A thorough analysis, based on crystal field theory, allowed an unambiguous determination of all relevant free ion and crystal field parameters. We show that inclusion of methods sensitive to the nature of the lowest-energy states is essential to arrive at a correct description of the states that are most relevant for the static and dynamic magnetic properties. The spectroscopic investigations also allowed for a full understanding of the magnetic relaxation processes occurring in this system. Thus, the importance of spectroscopic studies for the improvement of single-molecule magnets is underlined. PMID:26394012

  14. Crystal structure of methane oxidation enzyme determined

    SciTech Connect

    Baum, R.

    1994-01-10

    A team of chemists has determined to 2.2-[angstrom] resolution the crystal structure of the hydroxylase protein of methane monooxygenase, the enzyme system responsible for the biological oxidation of methane. The hydroxylase, at a molecular weight of 251,000 daltons, if by far the largest component of methane monooxygenase. Although the crystal structure of the hydroxylase did not reveal any startling surprises about the enzyme-many features of the hydroxylase had been inferred previously from modeling and spectroscopic studies -- obtaining it is a significant achievement. For one thing, the crystal structure unambiguously confirms aspects of the enzyme structure that been at least somewhat speculative. The three-dimensional structure of the enzyme, the chemist say, also provides important insight into biological methane oxidation, including how methane, a relatively inert gas, might diffuse to and bind near the active site of the enzyme. The structure points to particular amino acid residues that are likely to participate in catalysis, and clarifies the structure of the dinuclear iron core of the enzyme.

  15. Quantitative determination of residual active pharmaceutical ingredients and intermediates on equipment surfaces by ion mobility spectrometry.

    PubMed

    Qin, C; Granger, A; Papov, V; McCaffrey, J; Norwood, D L

    2010-01-01

    Ion mobility spectrometry (IMS) is an analytical technique that separates ions based on their gas phase mobility at atmospheric pressure. Since gas phase ion mobility is a function of the shape and structure of the ion, this technique has the potential to provide unique specificity and selectivity. Furthermore, IMS is very sensitive (subnanogram detection limits for many small molecules), and a single analysis is typically completed within 1 min. In principle, these features of IMS should make it an ideal choice for use in cleaning verification analysis of pharmaceutical manufacturing equipment. This report describes the successful development and validation of three different equipment cleaning verification methods using IMS. The methods were developed for a specific intermediate (Compound A) in the synthetic route for a drug substance as well as for final drug substances (active pharmaceutical ingredients Compounds B and C). The cleaning verification methods were validated with respect to specificity, linearity, precision, accuracy, stability, and limit-of-quantitation. In all cases, the limits-of-quantitation were determined to be at the nanogram or sub-nanogram level. Both swab and rinse samples collected from the equipment surfaces were successfully analyzed and manufacturing equipment down-time was significantly minimized due to the reduction in cleaning verification analysis time (for example, the total analysis time for more than 30 samples using IMS was reduced to less than 2h). PMID:19758781

  16. Membrane protein structure determination by electron crystallography

    PubMed Central

    Ubarretxena-Belandia, Iban; Stokes, David L.

    2012-01-01

    During the past year, electron crystallography of membrane proteins has provided structural insights into the mechanism of several different transporters and into their interactions with lipid molecules within the bilayer. From a technical perspective there have been important advances in high-throughput screening of crystallization trials and in automated imaging of membrane crystals with the electron microscope. There have also been key developments in software, and in molecular replacement and phase extension methods designed to facilitate the process of structure determination. PMID:22572457

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

    DOE PAGESBeta

    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 guidingmore » structure for the accelerating laser pulse may provide a way of compensating for the group velocity and transverse expansion effects.« less

  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. 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 ...

  20. 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.

  1. 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.

  2. 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.

  3. Structural modification of nanocrystalline ceria by ion beams

    SciTech Connect

    Zhang, Yanwen; Edmondson, Philip D.; Varga, Tamas; Moll, Sandra; Namavar, Fereydoon; Lan, Chune; 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 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. Structural modification by energetic ions is proposed to achieve desirable electronic–ionic conductivity.

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

    PubMed

    Choi, Jun-Ho; Cho, Minhaeng

    2016-05-28

    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. PMID:27250298

  5. 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.

  6. Complexation of beryllium(II) ion by phosphinate ligands in aqueous solution. Synthesis and XRPD structure determination of Be[(PhPO2)2CH2](H2O)2.

    PubMed

    Cecconi, Franco; Dominguez, Sixto; Masciocchi, Norberto; Midollini, Stefano; Sironi, Angelo; Vacca, Alberto

    2003-04-01

    Two bifunctional ligands, phenyl(carboxymethyl)phosphinate (ccp(2-) and P,P'-diphenylmethylenediphosphinate (pcp(2-)), have been tested as chelating agents of beryllium(II). Both ligands have the same charge and a similar chelating structure, but whereas the 1:1 adduct of pcp(2-), Be(pcp)(H(2)O)(2), could be isolated as a white powder, no pure compound could be isolated from solutions containing beryllium(II) and ccp(2-). Instead, the solutions were examined by means of potentiometry and (9)Be NMR spectroscopy. Analysis of the potentiometric titration data with the program HYPERQUAD suggested the formation of the complex species BeL, [BeHL](+), [BeL(2)](2-), and [BeHL(2)](-) (L = ccp). The formation constants for these species were determined at 25 degrees C and I = 0.5 mol dm(-3) NaClO(4). The (9)Be NMR spectra are consistent with this model. The formation constants found for the ccp(2-) complexes are lower than those reported for related phosphonate ligands. However, the effective stability constant (which gives a better indication of the intrinsic coordinating capacity of the ligand at a particular pH) of the complex [Be(ccp)(2)](2-) at pH < 4 is greater than the effective constants of the corresponding phosphonoacetate and methylenediphosphonate complexes. The structure of Be(pcp)(H(2)O)(2) was determined by X-ray powder diffraction methods and consists of discrete molecules interconnected by an extended 2D network of hydrogen bonds, resulting in a stacking of doublelayers with a polar core and a lipophilic surface. Crystal data: C(13)H(16)BeO(6)P(2), fw 339.21, monoclinic P2(1)/c, a = 16.174(1) A, b = 8.979(1) A, c = 10.929(1) A, beta = 90.398(9) degrees, V = 1587.2(3) A(3), Z = 4. PMID:12665369

  7. Structural determinants of proton blockage in aquaporins.

    PubMed

    Chakrabarti, Nilmadhab; Roux, Benoît; Pomès, Régis

    2004-10-15

    Aquaporins are an important class of membrane channels selective for water and linear polyols but impermeable to ions, including protons. Recent computational studies have revealed that the relay of protons through the water-conduction pathway of aquaporin channels is opposed by a substantial free energy barrier peaking at the signature NPA motifs. Here, free-energy simulations and continuum electrostatic calculations are combined to examine the nature and the magnitude of the contribution of specific structural elements to proton blockage in the bacterial glycerol uptake facilitator, GlpF. Potential of mean-force profiles for both hop and turn steps of structural diffusion in the narrow pore are obtained for artificial variants of the GlpF channel in which coulombic interactions between the pore contents and conserved residues Asn68 and Asn203 at the NPA signature motifs, Arg206 at the selectivity filter, and the peptidic backbone of the two half-helices M3 and M7, which are arranged in head-to-head fashion around the NPA motifs, are turned off selectively. A comparison of these results with electrostatic energy profiles for the translocation of a probe cation throughout the water permeation pathway indicates that the free-energy profile for proton movement inside the narrow pore is dominated by static effects arising from the distribution of charged and polar groups of the channel, whereas dielectric effects contribute primarily to opposing the access of H+ to the pore mouths (desolvation penalty). The single most effective way to abolish the free-energy gradients opposing the movement of H+ around the NPA motif is to turn off the dipole moments of helices M3 and M7. Mutation of either of the two NPA Asn residues to Asp compensates for charge-dipole and dipole-dipole effects opposing the hop and turn steps of structural diffusion, respectively, and dramatically reduces the free energy barrier of proton translocation, suggesting that these single mutants could

  8. 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.

  9. 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

  10. Application of the laser ion source for isotope shift and hyperfine structure investigation

    NASA Astrophysics Data System (ADS)

    Seliverstov, M. D.; Barzakh, A. E.; Chubukov, I. Ya.; Fedorov, D. V.; Panteleev, V. N.; Volkov, Yu. M.

    2000-08-01

    The study of nuclei far from stability requires high sensitivity of the experimental technique. The method of Resonance Ionization Spectroscopy in a Laser Ion Source (RIS/LIS) allows one to carry out measurements of the isotope shifts and hyperfine splittings for isotopes at the production rate about 102 atoms per second. The sensitivity of this method is determined by the high efficiency of the laser ion source and the low background of the detection system afforded by characteristic α particle registration. The isotope shifts and hyperfine structures of 155Yb, 154Tm (I=9 and I=2) and 153Tm (I=11/2) have been measured and the isotopic changes in mean square charge radii and nuclear electromagnetic moments have been determined. The further development of this experimental method - enhanced Target Ion Source system aimed to suppress thermionic background - enables direct detection of the photoions and widens the range of the applicability of the RIS/LIS method.

  11. Structure property relationships of carbonaceous films grown under ion enhancement

    SciTech Connect

    Weissmantel, C.; Ackermann, E.; Bewilogua, K.; Hecht, G.; Kupfer, H.; Rau, B.

    1986-11-01

    Based on our own results and in comparison with data published by other groups the structure property relationships of carbon and carbon/metal films prepared by sputtering and deposition of partially ionized species are discussed. Films grown by ion beam sputtering are dark brownish and amorphous with a small fraction of microcrystals. However, a transition to transparent and insulating layers can be effected by ion bombardment. C/Me coatings, where Me stands for Ti or Sn, were obtained by magnetron sputtering of composite targets. The films proved to be amorphous up to metal concentrations of more than 10 at. %, but metal and carbide crystals grow upon annealing. Measurements of the hardness, the electrical conductivity, and the contact behavior in dependence on the composition provided interesting information. For carbon films prepared by deposition of partially ionized benzene species it has been found that the properties depend characteristically on the ion energy; typical ''diamondlike'' i-C films are obtained by applying a bias voltage from 1--3 keV. The thermal stability of the amorphous coatings is discussed in conjunction with their electrical conductivity. Summarizing extensive structure investigations, a structure model based on tetrahedrally interlinked carbon rings is proposed. Composites of the type i-C/Me (Me: Al, Ti, Cr), which were prepared by simultaneous metal evaporation, exhibit a wide range of structure property relations.

  12. 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.

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

    NASA Astrophysics Data System (ADS)

    Hosemann, Peter

    2011-02-01

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

  14. 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.

  15. 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.

  16. 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.

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

    DOE PAGESBeta

    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 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

  18. NMR Structure and Ion Channel Activity of the p7 Protein from Hepatitis C Virus*

    PubMed Central

    Montserret, Roland; Saint, Nathalie; Vanbelle, Christophe; Salvay, Andrés Gerardo; Simorre, Jean-Pierre; Ebel, Christine; Sapay, Nicolas; Renisio, Jean-Guillaume; Böckmann, Anja; Steinmann, Eike; Pietschmann, Thomas; Dubuisson, Jean; Chipot, Christophe; Penin, François

    2010-01-01

    The small membrane protein p7 of hepatitis C virus forms oligomers and exhibits ion channel activity essential for virus infectivity. These viroporin features render p7 an attractive target for antiviral drug development. In this study, p7 from strain HCV-J (genotype 1b) was chemically synthesized and purified for ion channel activity measurements and structure analyses. p7 forms cation-selective ion channels in planar lipid bilayers and at the single-channel level by the patch clamp technique. Ion channel activity was shown to be inhibited by hexamethylene amiloride but not by amantadine. Circular dichroism analyses revealed that the structure of p7 is mainly α-helical, irrespective of the membrane mimetic medium (e.g. lysolipids, detergents, or organic solvent/water mixtures). The secondary structure elements of the monomeric form of p7 were determined by 1H and 13C NMR in trifluoroethanol/water mixtures. Molecular dynamics simulations in a model membrane were combined synergistically with structural data obtained from NMR experiments. This approach allowed us to determine the secondary structure elements of p7, which significantly differ from predictions, and to propose a three-dimensional model of the monomeric form of p7 associated with the phospholipid bilayer. These studies revealed the presence of a turn connecting an unexpected N-terminal α-helix to the first transmembrane helix, TM1, and a long cytosolic loop bearing the dibasic motif and connecting TM1 to TM2. These results provide the first detailed experimental structural framework for a better understanding of p7 processing, oligomerization, and ion channel gating mechanism. PMID:20667830

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

    SciTech Connect

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

    2011-05-15

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  1. 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

  2. Application of the laser ion source for isotope shift and hyperfine structure investigations

    NASA Astrophysics Data System (ADS)

    Barzakh, A. E.; Chubukov, I. Ya.; Fedorov, D. V.; Panteleev, V. N.; Seliverstov, M. D.; Volkov, Yu. M.

    1998-12-01

    A high-efficient method for measuring isotope shifts and hyperfine structures in optical transitions of radioactive atoms is presented. The method is based on application of laser resonance ionization in the mass-separator ion source. The sensitivity of the method is determined by a high efficiency of the laser ion source and low background of the detection system, making use of counting α-particles following the decay of the isotope under investigation. The possibilities of this method are shown in the experiment with 155Yb and 154Tm (I=9). The isotope shifts and electromagnetic moments have been measured.

  3. Solvation structures of protons and hydroxide ions in water

    NASA Astrophysics Data System (ADS)

    Chen, Chen; Huang, Congcong; Waluyo, Iradwikanari; Nordlund, Dennis; Weng, Tsu-Chien; Sokaras, Dimosthenis; Weiss, Thomas; Bergmann, Uwe; Pettersson, Lars G. M.; Nilsson, Anders

    2013-04-01

    X-ray Raman spectroscopy (XRS) combined with small-angle x-ray scattering (SAXS) were used to study aqueous solutions of HCl and NaOH. Hydrated structures of H+ and OH- are not simple mirror images of each other. While both ions have been shown to strengthen local hydrogen bonds in the hydration shell as indicated by XRS, SAXS suggests that H+ and OH- have qualitatively different long-range effects. The SAXS structure factor of HCl (aq) closely resembles that of pure water, while NaOH (aq) behaves similar to NaF (aq). We propose that protons only locally enhance hydrogen bonds while hydroxide ions induce tetrahedrality in the overall hydrogen bond network of water.

  4. Atomic Data for Nebular Abundance Determinations: Photoionization, Recombination, and Collisional Excitation of Rubidium and Bromine Ions

    NASA Astrophysics Data System (ADS)

    Kerlin, Austin; Macaluso, David A.; Bautista, Manuel; Bilodeau, Rene C.; Aguilar, Alejandro; Kilcoyne, A. L. David; Dumitriu, Ileana; Sterling, Nicholas C.

    2016-01-01

    We present results of an investigation into the photoionization (PI), recombination, and electron-impact excitation properties of low-charge Br and Rb ions. Br and Rb are among the relatively few neutron(n)-capture elements (atomic number Z > 30) that have been detected in planetary nebulae (PNe). Their abundances can reveal unique information regarding nucleosynthesis in asymptotic giant branch (AGB) stars, including slow n-capture (s-process) neutron densities and the dominant neutron source in more massive AGB stars (4-8 solar masses). However, the requisite atomic data needed for accurate Rb and Rb nebular abundance determinations are unknown. Our work addresses this need, via a synthesis of theoretical and experimental methods. Using the AUTOSTRUCTURE atomic structure code (Badnell 2011, Comp. Phys. Comm., 182, 1528), we have computed multi-configuration Breit-Pauli distorted-wave PI cross sections, and rate coefficients for radiative recombination (RR) and dielectronic recombination (DR) for neutral through six-times ionized Br and Rb. To benchmark our calculations, we have measured absolute PI cross sections of Br+-Br4+ and Rb+-Rb5+ at the Advanced Light Source synchrotron radiation facility in Berkeley, CA. Breit-Pauli R-matrix calculations are in progress to facilitate analysis of the experimental data, including resonance identifications and determining the metastable populations of the primary ion beams. Finally, we are performing R-matrix calculations of effective collision strengths for electron-impact excitation of astrophysically detected Br and Rb ions. Our Rb3+ effective collision strength results have been applied to two PNe, with excellent agreement found for ionic abundances determined from different [Rb IV] lines. The combination of these atomic data will dramatically improve the accuracy of Br and Rb abundance determinations in astrophysical nebulae, providing new insight into heavy element nucleosynthesis in low- and intermediate-mass stars

  5. Biomolecular Structure Determination with Divide and Concur

    NASA Astrophysics Data System (ADS)

    Kallus, Yoav; Elser, Veit

    2009-03-01

    Divide and concur (D-C) is a general computational approach, designed for the solution of highly frustrated problems. Recently applied to the problems of disk packing, the kissing number problem, and 3-SAT, it was competitive or outperformed special-purpose methods.ootnotetextS. Gravel and V. Elser, Phys. Rev. E 78, 036706 (2008) We present a method for applying the D-C framework to the problem of biomolecular structure determination. From a list of geometric constraints on groups of atoms in the molecule, we construct a deterministic iterative map that efficiently searches for structures simultaneously satisfying all constraints. As our method eschews an energy function and its minimization to focus on geometric constraints, it can very naturally integrate with the geometric constraints due to chemistry and physics, experimental constraints due to NMR data or many other experimental or biological hints. We present some results of our method.

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

    PubMed

    Shukla, P K; Akbari-Moghanjoughi, M

    2013-04-01

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

  7. 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).

  8. 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. PMID:26320957

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

    PubMed

    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. Graphical Abstract ᅟ. PMID:26860087

  10. 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.

  11. 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.

    2016-02-01

    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.

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. Structural difference rule for amorphous alloy formation by ion mixing

    NASA Technical Reports Server (NTRS)

    Liu, B.-X.; Johnson, W. L.; Nicolet, M.A.; Lau, S. S.

    1983-01-01

    A rule is formulated which establishes a sufficient condition that an amorphous binary alloy will be formed by ion mixing of multilayered samples when the two constituent metals are of different crystalline structure, regardless of their atomic sizes and electronegativities. The rule is supported by the experimental results obtained on six selected binary metal systems, as well as by the previous data reported in the literature. The amorphization mechanism is discussed in terms of the competition between two different structures resulting in frustration of the crystallization process.

  18. Photoelectron holography applied to surface structural determination

    SciTech Connect

    Petersen, B.L.

    1995-05-01

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

  19. 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.

  20. Mapping the structure and conformational movements of proteins with transition metal ion FRET

    PubMed Central

    Taraska, Justin W.; Puljung, Michael C.; Olivier, Nelson B.; Flynn, Galen E.; Zagotta, William N.

    2009-01-01

    SUMMARY Visualizing conformational dynamics in proteins has been difficult, and the atomic-scale motions responsible for the behavior of most allosteric proteins are unknown. Here, we report that FRET between a small fluorescent dye and a nickel ion bound to a di-histidine motif can be used to monitor small structural rearrangements in proteins. This method provides several key advantages over classical FRET including the ability to measure the dynamics of close range interactions, the use of small probes with short linkers, a low orientation dependence, and the ability to add and remove unique tunable acceptors. We used this ‘transition metal ion FRET’ approach along with x-ray crystallography to determine the structural changes of the gating-ring of the mouse hyperpolarization-activated cyclic nucleotide-regulated ion channel HCN2. Binding of cAMP to the isolated carboxyl-terminal region of HCN2 caused a structural rearrangement involving a movement of the C-helix towards the β-roll of the cAMP-binding domain and a movement of the F′ helix of the C-linker, along with a stabilization of the secondary structure of the helices. Our results suggest a general model for the conformational switch in the cyclic nucleotide-binding site of cyclic nucleotide-regulated ion channels. PMID:19525958

  1. 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.

  2. 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.

  3. Exploiting Microbeams for Membrane Protein Structure Determination.

    PubMed

    Warren, Anna J; Axford, Danny; Paterson, Neil G; Owen, Robin L

    2016-01-01

    A reproducible, and sample independent means of predictably obtaining large, well-ordered crystals has proven elusive in macromolecular crystallography. In the structure determination pipeline, crystallisation often proves to be a rate-limiting step, and the process of obtaining even small or badly ordered crystals can prove time-consuming and laborious. This is particularly true in the field of membrane protein crystallography and this is reflected in the limited number of unique membrane protein structures deposited in the protein data bank (less than 650 by June 2016 - http://blanco.biomol.uci.edu/mpstruc ). Over recent years the requirement for, and time and cost associated with obtaining, large crystals has been partially alleviated through the development of beamline instrumentation allowing data collection, and structure solution, from ever-smaller crystals. Advances in several areas have led to a step change in what might be considered achievable during a synchrotron trip over the last decade. This chapter will briefly review the current status of the field, the tools available to ease data collection and processing, and give some examples of exploitation of these for membrane protein microfocus macromolecular crystallography. PMID:27553238

  4. Nanoscale SiC production by ballistic ion beam mixing of C/Si multilayer structures

    NASA Astrophysics Data System (ADS)

    Battistig, G.; Zolnai, Z.; Németh, A.; Panjan, P.; Menyhárd, M.

    2016-05-01

    The ion beam-induced mixing process using Ar+, Ga+, and Xe+ ion irradiation has been used to form SiC rich layers on the nanometer scale at the interfaces of C/Si/C/Si/C multilayer structures. The SiC depth distributions were determined by Auger electron spectroscopy (AES) depth profiling and were compared to the results of analytical models developed for ballistic ion mixing and local thermal spike induced mixing. In addition, the measured SiC depth distributions were correlated to the Si and C mixing profiles simulated by the TRIDYN code which can follow the ballistic ion mixing process as a function of ion fluence. Good agreement has been found between the distributions provided by AES depth profiling and TRIDYN on the assumption that the majority of the Si (C) atoms transported to the neighboring C (Si) layer form the SiC compound. The ion beam mixing process can be successfully described by ballistic atomic transport processes. The results show that SiC production as a function of depth can be predicted, and tailored compound formation on the nanoscale becomes feasible, thus leading to controlled synthesis of protective SiC coatings at room temperature.

  5. Three-dimensional structure of recombinant carboxypeptidase T from Thermoactinomyces vulgaris without calcium ions

    SciTech Connect

    Akparov, V. Kh.; Timofeev, V. I. Kuranova, I. P.

    2011-07-15

    Crystals of recombinant carboxypeptidase T (CPT) from Thermoactinomyces vulgaris were grown in a capillary by the counterdiffusion method in the absence of calcium ions. The three-dimensional structure of CPT was solved at 1.69- Angstrom-Sign resolution using the X-ray diffraction data collected from the crystals of the enzyme on the SPring-8 synchrotron radiation facility and was then refined to Rfact = 16.903% and Rfree = 18.165%. The coordinates of the refined model were deposited in the Protein Data Bank (PDB ID: 3QNV). A comparison of this structure with the structure of wild-type CPT containing bound calcium ions, which was determined earlier, revealed a number of conformational changes both in the calcium-binding sites and the enzyme active site. Based on the results of this comparison, the possible factors responsible for the difference in the catalytic activity of the two forms of the enzyme are considered.

  6. Ion-cage interpretation for the structural and dynamic changes of ionic liquids under an external electric field.

    PubMed

    Shi, Rui; Wang, Yanting

    2013-05-01

    In many applications, ionic liquids (ILs) work in a nonequilibrium steady state driven by an external electric field. However, how the electric field changes the structure and dynamics of ILs and its underlying mechanism still remain poorly understood. In this paper, coarse-grained molecular dynamics simulations were performed to investigate the structure and dynamics of 1-ethyl-3-methylimidazolium nitrate ([EMIm][NO3]) under a static electric field. The ion cage structure was found to play an essential role in determining the structural and dynamic properties of the IL system. With a weak or moderate electric field (0-10(7) V/m), the external electric field is too weak to modify the ion cage structure in an influential way and thus the changes of structural and dynamic properties are negligible. With a strong electric field (10(7)-10(9) V/m) applied, ion cages expand and deform apparently, leading to the increase of ion mobility and self-diffusion coefficient with electric field, and the self-diffusion of ions along the electric field becomes faster than the other two directions due to the anisotropic deformation of ion cages. In addition, the Einstein relation connecting diffusion and mobility breaks down at strong electric fields, and it also breaks down for a single ion species even at moderate electric fields (linear-response region). PMID:23557150

  7. 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. PMID:10423458

  8. Structural Determinants of Misfolding in Multidomain Proteins

    PubMed Central

    Tian, Pengfei; Best, Robert B.

    2016-01-01

    Recent single molecule experiments, using either atomic force microscopy (AFM) or Förster resonance energy transfer (FRET) have shown that multidomain proteins containing tandem repeats may form stable misfolded structures. Topology-based simulation models have been used successfully to generate models for these structures with domain-swapped features, fully consistent with the available data. However, it is also known that some multidomain protein folds exhibit no evidence for misfolding, even when adjacent domains have identical sequences. Here we pose the question: what factors influence the propensity of a given fold to undergo domain-swapped misfolding? Using a coarse-grained simulation model, we can reproduce the known propensities of multidomain proteins to form domain-swapped misfolds, where data is available. Contrary to what might be naively expected based on the previously described misfolding mechanism, we find that the extent of misfolding is not determined by the relative folding rates or barrier heights for forming the domains present in the initial intermediates leading to folded or misfolded structures. Instead, it appears that the propensity is more closely related to the relative stability of the domains present in folded and misfolded intermediates. We show that these findings can be rationalized if the folded and misfolded domains are part of the same folding funnel, with commitment to one structure or the other occurring only at a relatively late stage of folding. Nonetheless, the results are still fully consistent with the kinetic models previously proposed to explain misfolding, with a specific interpretation of the observed rate coefficients. Finally, we investigate the relation between interdomain linker length and misfolding, and propose a simple alchemical model to predict the propensity for domain-swapped misfolding of multidomain proteins. PMID:27163669

  9. Proton assisted recoupling and protein structure determination

    PubMed Central

    De Paëpe, Gaël; Lewandowski, Józef R.; Loquet, Antoine; Böckmann, Anja; Griffin, Robert G.

    2008-01-01

    We introduce a homonuclear version of third spin assisted recoupling, a second-order mechanism that can be used for polarization transfer between 13C or 15N spins in magic angle spinning (MAS) NMR experiments, particularly at high spinning frequencies employed in contemporary high field MAS experiments. The resulting sequence, which we refer to as proton assisted recoupling (PAR), relies on a cross-term between 1H–13C (or 1H–15N) couplings to mediate zero quantum 13C–13C (or 15N–15N recoupling). In particular, using average Hamiltonian theory we derive an effective Hamiltonian for PAR and show that the transfer is mediated by trilinear terms of the form C1±C2∓HZ for 13C–13C recoupling experiments (or N1±N2∓HZ for 15N–15N). We use analytical and numerical simulations to explain the structure of the PAR optimization maps and to delineate the PAR matching conditions. We also detail the PAR polarization transfer dependence with respect to the local molecular geometry and explain the observed reduction in dipolar truncation. Finally, we demonstrate the utility of PAR in structural studies of proteins with 13C–13C spectra of uniformly 13C, 15N labeled microcrystalline Crh, a 85 amino acid model protein that forms a domain swapped dimer (MW=2×10.4 kDa). The spectra, which were acquired at high MAS frequencies (ωr2π>20 kHz) and magnetic fields (750–900 MHz 1H frequencies) using moderate rf fields, exhibit numerous cross peaks corresponding to long (up to 6–7 Å) 13C–13C distances which are particularly useful in protein structure determination. Using results from PAR spectra we calculate the structure of the Crh protein. PMID:19123534

  10. Proton assisted recoupling and protein structure determination

    NASA Astrophysics Data System (ADS)

    de Paëpe, Gaël; Lewandowski, Józef R.; Loquet, Antoine; Böckmann, Anja; Griffin, Robert G.

    2008-12-01

    We introduce a homonuclear version of third spin assisted recoupling, a second-order mechanism that can be used for polarization transfer between 13C or 15N spins in magic angle spinning (MAS) NMR experiments, particularly at high spinning frequencies employed in contemporary high field MAS experiments. The resulting sequence, which we refer to as proton assisted recoupling (PAR), relies on a cross-term between 1H-13C (or 1H-15N) couplings to mediate zero quantum 13C-13C (or 15N-15N recoupling). In particular, using average Hamiltonian theory we derive an effective Hamiltonian for PAR and show that the transfer is mediated by trilinear terms of the form C1+/-C2-/+HZ for 13C-13C recoupling experiments (or N1+/-N2-/+HZ for 15N-15N). We use analytical and numerical simulations to explain the structure of the PAR optimization maps and to delineate the PAR matching conditions. We also detail the PAR polarization transfer dependence with respect to the local molecular geometry and explain the observed reduction in dipolar truncation. Finally, we demonstrate the utility of PAR in structural studies of proteins with 13C-13C spectra of uniformly 13C, 15N labeled microcrystalline Crh, a 85 amino acid model protein that forms a domain swapped dimer (MW=2×10.4 kDa). The spectra, which were acquired at high MAS frequencies (ωr2π>20 kHz) and magnetic fields (750-900 MHz 1H frequencies) using moderate rf fields, exhibit numerous cross peaks corresponding to long (up to 6-7 A˚) 13C-13C distances which are particularly useful in protein structure determination. Using results from PAR spectra we calculate the structure of the Crh protein.

  11. Structural Determinants of Misfolding in Multidomain Proteins.

    PubMed

    Tian, Pengfei; Best, Robert B

    2016-05-01

    Recent single molecule experiments, using either atomic force microscopy (AFM) or Förster resonance energy transfer (FRET) have shown that multidomain proteins containing tandem repeats may form stable misfolded structures. Topology-based simulation models have been used successfully to generate models for these structures with domain-swapped features, fully consistent with the available data. However, it is also known that some multidomain protein folds exhibit no evidence for misfolding, even when adjacent domains have identical sequences. Here we pose the question: what factors influence the propensity of a given fold to undergo domain-swapped misfolding? Using a coarse-grained simulation model, we can reproduce the known propensities of multidomain proteins to form domain-swapped misfolds, where data is available. Contrary to what might be naively expected based on the previously described misfolding mechanism, we find that the extent of misfolding is not determined by the relative folding rates or barrier heights for forming the domains present in the initial intermediates leading to folded or misfolded structures. Instead, it appears that the propensity is more closely related to the relative stability of the domains present in folded and misfolded intermediates. We show that these findings can be rationalized if the folded and misfolded domains are part of the same folding funnel, with commitment to one structure or the other occurring only at a relatively late stage of folding. Nonetheless, the results are still fully consistent with the kinetic models previously proposed to explain misfolding, with a specific interpretation of the observed rate coefficients. Finally, we investigate the relation between interdomain linker length and misfolding, and propose a simple alchemical model to predict the propensity for domain-swapped misfolding of multidomain proteins. PMID:27163669

  12. 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

  13. Crystal structure of a heterotetrameric NMDA receptor ion channel

    PubMed Central

    Karakas, Erkan; Furukawa, Hiro

    2014-01-01

    N -methyl-D-aspartate (NMDA) receptors belong to the family of ionotropic glutamate receptors, which mediate most excitatory synaptic transmission in mammalian brains. Calcium permeation triggered by activation of NMDA receptors is the pivotal event for initiation of neuronal plasticity. Here we show the crystal structure of the intact heterotetrameric GluN1/GluN2B NMDA receptor ion channel at 4 Å. The NMDA receptors are arranged as a dimer of GluN1-GluN2B heterodimers with the two-fold symmetry axis running through the entire molecule composed of an amino terminal domain (ATD), a ligand-binding domain (LBD), and a transmembrane domain (TMD). The ATD and LBD are much more highly packed in the NMDA receptors than non-NMDA receptors, which may explain why ATD regulates ion channel activity in NMDA receptors but not in non-NMDA receptors. PMID:24876489

  14. Determination of Effective Stability Constants of Ion-Carrier Complexes in Ion Selective Nanospheres with Charged Solvatochromic Dyes.

    PubMed

    Xie, Xiaojiang; Bakker, Eric

    2015-11-17

    Ionophores are widely used ion carriers in ion selective sensors. The effective stability constant (β) is a key physical parameter providing valuable guidelines to the design of ionophores and carrier-based ion selective sensors. The β value of ion-carrier complex in plasticized poly(vinyl chloride) (PVC) membranes and solutions have been determined in the past by various techniques, but most of them are difficult to implement at the nanoscale owing to the ultrasmall sample volume. A new methodology based on charged solvatochromic dyes is introduced here for the first time to determine β values directly within ion selective nanospheres. Four ionophores with different selectivities toward Na(+), K(+), Ca(2+), and H(+), respectively, are successfully characterized in nanospheres composed of triblock copolymer Pluronic F-127 and bis(2-ethylhexyl) sebacate. The values determined in the nanospheres are smaller compared with those in plasticized PVC membranes, indicating a more polar nanosphere microenvironment and possible uneven distribution of the sensing components in the interfacial region. PMID:26502342

  15. 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.

  16. Instability-Enhanced Collisional Friction Can Determine the Bohm Criterion in Multiple-Ion-Species Plasmas

    SciTech Connect

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

    2009-11-13

    A generalized Lenard-Balescu theory that accounts for instability-enhanced collective responses is used to calculate the collisional friction between ion species in the plasma-boundary transition region (presheath). Ion-ion streaming instabilities are shown to cause such a strong frictional force that the relative flow speed between ion species cannot significantly exceed the critical threshold value (DELTAV{sub c}) at which instability onset occurs. When combined with the Bohm criterion, this condition uniquely determines the flow speed of each ion species at the plasma-sheath boundary. For cold ions, DELTAV{sub c}->0 and each ion species leaves the plasma at a common system sound speed c{sub s}.

  17. Instability-enhanced collisional friction can determine the Bohm criterion in multiple-ion-species plasmas.

    PubMed

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

    2009-11-13

    A generalized Lenard-Balescu theory that accounts for instability-enhanced collective responses is used to calculate the collisional friction between ion species in the plasma-boundary transition region (presheath). Ion-ion streaming instabilities are shown to cause such a strong frictional force that the relative flow speed between ion species cannot significantly exceed the critical threshold value (DeltaV(c)) at which instability onset occurs. When combined with the Bohm criterion, this condition uniquely determines the flow speed of each ion species at the plasma-sheath boundary. For cold ions, DeltaV(c) --> 0 and each ion species leaves the plasma at a common system sound speed c(s). PMID:20365986

  18. Nuclear structure and heavy-ion fusion. [Lecture

    SciTech Connect

    Stokstad, R.G.

    1980-10-01

    A series of lectures is presented on experimental studies of heavy-ion fusion reactions with emphasis on the role of nuclear structure in the fusion mechanism. The experiments considered are of three types: the fusion of lighter heavy ions at subcoulomb energies is studied with in-beam ..gamma..-ray techniques; the subbarrier fusion of /sup 16/O and /sup 40/Ar with the isotopes of samarium is detected out of beam by x-radiation from delayed activity; and measurements at very high energies, again for the lighter ions, employ direct particle identification of evaporation residues. The experimental data are compared with predictions based on the fusion of two spheres with the only degree of freedom being the separation of the centers, and which interact via potentials that vary smoothly with changes in the mass and charge of the projectile and target. The data exhibit with the isotopes of samarium, a portion of these deviations can be understood in terms of the changing deformation of the target nucleus, but an additional degree of freedom such as neck formation appears necessary. The results on /sup 10/B + /sup 16/O and /sup 12/C + /sup 14/N ..-->.. /sup 26/Al at high bombarding energies indicate a maximum limiting angular momentum characteristic of the compound nucleus. At lower energies the nuclear structure of the colliding ion seems to affect strongly the cross section for fusion. Measurements made at subbarrier energies for a variety of projectile-target combinations in the 1p and 2s - 1d shell also indicate that the valence nucleons can affect the energy dependence for fusion. About half the systems studied so far have structureless excitation functions which follow a standard prediction. The other half exhibit large variations from this prediction. The possible importance of neutron transfer is discussed. The two-center shell model appears as a promising approach for gaining a qualitative understanding of these phenomena. 95 references, 52 figures, 1 table.

  19. 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.

  20. Granular structure determined by terahertz scattering

    NASA Astrophysics Data System (ADS)

    Born, Philip; Rothbart, Nick; Sperl, Matthias; Hübers, Heinz-Wilhelm

    2014-05-01

    Light scattering from particles reveals static and dynamical information about the particles and their correlations. Such methods are particularly powerful when the wavelength of the light is chosen similar to the sizes and distances of the particles. To apply scattering to investigate granular matter in particular —or other objects of similar submillimeter size— light of suitable wavelength in the terahertz regime needs to be chosen. By using a quantum cascade laser in a benchtop setup we determine the angle-dependent scattering of spherical particles as well as coffee powder and sugar grains. The scattering from single particles can be interpreted by form factors derived within the Mie theory. In addition, collective correlations can be extracted as static structure factors and compared to recent computer simulations.

  1. Radii of atomic ions determined from diatomic ion-He bond lengths.

    PubMed

    Wright, Timothy G; Breckenridge, W H

    2010-03-11

    We propose a new definition of the effective radius of an atomic ion: the bond distance (R(e)) of the ion/He diatomic complex minus the van der Waals radius of the helium atom. Our rationale is that He is the most chemically inert and least polarizable atom, so that its interaction with the outer portions of the electron cloud causes the smallest perturbation of it. We show that such radii, which we denote R(XHe), make good qualitative sense. We also compare our R(XHe) values to more traditional ionic radii from solid crystal X-ray measurements, as well as estimates of such radii from "ionic" gas-phase MF, MOM, MF(+), and MO molecules, where M is a metal atom. Such comparisons lead to interesting conclusions about bonding in ionic crystals and in simple gas-phase oxide and fluoride molecules. The definition is shown to be reasonable for -1, +1, and even for many of the larger +2 atomic ions. Another advantage of the R(XHe) definition is that it is also consistently valid for ground states and excited states of both neutral atoms and atomic ions, even for open-shell np and nd cases where the electron clouds of the ions are not spherically symmetric and R(XHe) thus depends on the "approach" direction of the He atom. Finally, we note that when there is a contribution from covalent bonding with the He atom, and/or in cases where the ion is small and has a very high charge, so that there is distortion even of the He 1s electrons, R(XHe) is not expected to be representative of the size of the ion. We then suggest that in these cases small, and sometimes unphysical, values of R(XHe) are diagnostic of the fact that simple "physical" interactions have been supplemented by a "chemical" component. PMID:20055395

  2. 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.

  3. 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.

  4. 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)

  5. Structure and activity of the acid-sensing ion channels

    PubMed Central

    Sherwood, Thomas W.; Frey, Erin N.

    2012-01-01

    The acid-sensing ion channels (ASICs) are a family of proton-sensing channels expressed throughout the nervous system. Their activity is linked to a variety of complex behaviors including fear, anxiety, pain, depression, learning, and memory. ASICs have also been implicated in neuronal degeneration accompanying ischemia and multiple sclerosis. As a whole, ASICs represent novel therapeutic targets for several clinically important disorders. An understanding of the correlation between ASIC structure and function will help to elucidate their mechanism of action and identify potential therapeutics that specifically target these ion channels. Despite the seemingly simple nature of proton binding, multiple studies have shown that proton-dependent gating of ASICs is quite complex, leading to activation and desensitization through distinct structural components. This review will focus on the structural aspects of ASIC gating in response to both protons and the newly discovered activators GMQ and MitTx. ASIC modulatory compounds and their action on proton-dependent gating will also be discussed. This review is dedicated to the memory of Dale Benos, who made a substantial contribution to our understanding of ASIC activity. PMID:22843794

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

    EPA Science Inventory

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

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

    USGS Publications Warehouse

    Evans, H.T., Jr.

    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.

  8. 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.

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

    DOE PAGESBeta

    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 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

  10. ION MANIPULATIONS IN STRUCTURES FOR LOSSLESS ION MANIPULATIONS (SLIM): COMPUTATIONAL EVALUATION OF A 90o TURN AND A SWITCH

    SciTech Connect

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

    2015-08-19

    The process of redirecting ions through 90o 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.

  11. Structural Determinants of Individual Behavior in Organizations

    ERIC Educational Resources Information Center

    Rice, Linda E.; Mitchell, Terence R.

    1973-01-01

    A new conceptual view of organizational structure is presented, which integrates the two implicit views of structure found in the literature. In addition, some unique measures of a person's position in the organizational structure are shown. (Author)

  12. Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue.

    PubMed

    Mir, Aamir; Golden, Barbara L

    2016-02-01

    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. On the basis of this crystal structure as well as a wealth of biochemical studies, we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid. PMID:26551631

  13. 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.

  14. Impact of track structure calculations on biological treatment planning in ion radiotherapy

    NASA Astrophysics Data System (ADS)

    Elsässer, Thilo; Cunrath, Richard; Krämer, Michael; Scholz, Michael

    2008-07-01

    Treatment planning for ion therapy requires precise knowledge about the biological effectiveness of particle beams, which is strongly determined by the microscopic radial energy deposition around individual ion tracks. We analyse different amorphous track structure models based on simple analytical formulae as well as on radial dose distributions derived by means of Monte Carlo simulations. Moreover, these track structure representations are used as input for the local effect model (LEM) in order to determine their impact on the relative biological effectiveness (RBE) of cell inactivation. It demonstrates the relevance of the inner part of the ion track with a radius of the order of a few nanometres. We show that simple analytical formulae for the radial dose distributions give good results for the prediction of cell inactivation. However, they strongly depend on the assumptions about the local dose in the track core. Additionally, we discuss the interdependence of track structure calculations with other model constituents such as target size and the choice of the biological input data for conventional photon irradiation.

  15. 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.

  16. 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 ...

  17. Statistical Determinants of Selective Ionic Complexation: Ions in Solvent, Transport Proteins, and Other “Hosts”

    PubMed Central

    Bostick, David L.; Brooks, Charles L.

    2009-01-01

    To provide utility in understanding the molecular evolution of ion-selective biomembrane channels/transporters, globular proteins, and ionophoric compounds, as well as in guiding their modification and design, we present a statistical mechanical basis for deconstructing the impact of the coordination structure and chemistry of selective multidentate ionic complexes. The deconstruction augments familiar ideas in liquid structure theory to realize the ionic complex as an open ion-ligated system acting under the influence of an “external field” provided by the host (or surrounding medium). Using considerations derived from this basis, we show that selective complexation arises from exploitation of a particular ion's coordination preferences. These preferences derive from a balance of interactions much like that which dictates the Hofmeister effect. By analyzing the coordination-state space of small family IA and VIIA ions in simulated fluid media, we derive domains of coordinated states that confer selectivity for a given ion upon isolating and constraining particular attributes (order parameters) of a complex comprised of a given type of ligand. We demonstrate that such domains may be used to rationalize the ion-coordinated environments provided by selective ionophores and biological ion channels/transporters of known structure, and that they can serve as a means toward deriving rational design principles for ion-selective hosts. PMID:19486671

  18. DETERMINATION OF MOLECULAR WEIGHT CITRUS PECTIN USING ION CHROMATOGRAPHY

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Objective was to investigate the use of ELS as a mass detector coupled with MALLS for determining the molecular weights of pectins and other polysaccharides under changing buffer concentrations using HPLC. This would permit the direct determination of the charge to size ratio of pectin which is imp...

  19. 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

  20. 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

  1. Crystal structures of a double-barrelled fluoride ion channel.

    PubMed

    Stockbridge, Randy B; Kolmakova-Partensky, Ludmila; Shane, Tania; Koide, Akiko; Koide, Shohei; Miller, Christopher; Newstead, Simon

    2015-09-24

    To contend with hazards posed by environmental fluoride, microorganisms export this anion through F(-)-specific ion channels of the Fluc family. Since the recent discovery of Fluc channels, numerous idiosyncratic features of these proteins have been unearthed, including strong selectivity for F(-) over Cl(-) and dual-topology dimeric assembly. To understand the chemical basis for F(-) permeation and how the antiparallel subunits convene to form a F(-)-selective pore, here we solve the 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. Crystallographic structure of ubiquitin in complex with cadmium ions

    PubMed Central

    2009-01-01

    Background Ubiquitination plays a critical role in regulating many cellular processes, from DNA repair and gene transcription to cell cycle and apoptosis. It is catalyzed by a specific enzymatic cascade ultimately leading to the conjugation of ubiquitin to lysine residues of the target protein that can be the ubiquitin molecule itself and to the formation of poly-ubiquitin chains. Findings We present the crystal structure at 3.0 Å resolution of bovine ubiquitin crystallized in presence of cadmium ions. Two molecules of ubiquitin are present in the asymmetric unit. Interestingly this non-covalent dimeric arrangement brings Lys-6 and Lys-63 of each crystallographically-independent monomer in close contact with the C-terminal ends of the other monomer. Residues Leu-8, Ile-44 and Val-70 that form a hydrophobic patch at the surface of the Ub monomer are trapped at the dimer interface. Conclusions The structural basis for signalling by poly-Ub chains relies on a visualization of conformations of alternatively linked poly-Ub chains. This arrangement of ubiquitin could illustrate how linkages involving Lys-6 or Lys-63 of ubiquitin are produced in the cell. It also details how ubiquitin molecules can specifically chelate cadmium ions. PMID:20003470

  3. Diamond structure recovery during ion irradiation at elevated temperatures

    NASA Astrophysics Data System (ADS)

    Deslandes, Alec; Guenette, Mathew C.; Belay, Kidane; Elliman, Robert G.; Karatchevtseva, Inna; Thomsen, Lars; Riley, Daniel P.; Lumpkin, Gregory R.

    2015-12-01

    CVD diamond is irradiated by 5 MeV carbon ions, with each sample held at a different temperature (300-873 K) during irradiations. The defect structures resulting from the irradiations are evident as vacancy, interstitial and amorphous carbon signals in Raman spectra. The observed variation of the full width at half maximum (FWHM) and peak position of the diamond peak suggests that disorder in the diamond lattice is reduced for high temperature irradiations. The dumbbell interstitial signal is reduced for irradiations at 873 K, which suggests this defect is unstable at these temperatures and that interstitials have migrated to crystal surfaces. Near edge X-ray absorption fine structure (NEXAFS) spectroscopy results indicate that damage to the diamond structure at the surface has occurred for room temperature irradiations, however, this structure is at least partially recovered for irradiations performed at 473 K and above. The results suggest that, in a high temperature irradiation environment such as a nuclear fusion device, in situ annealing of radiation-created defects can maintain the diamond structure and prolong the lifetime of diamond components.

  4. 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.

  5. Swift heavy-ion irradiation-induced shape and structural transformation in cobalt nanoparticles

    NASA Astrophysics Data System (ADS)

    Sprouster, D. J.; Giulian, R.; Araujo, L. L.; Kluth, P.; Johannessen, B.; Cookson, D. J.; Ridgway, M. C.

    2011-06-01

    The shape and structural evolution of Co nanoparticles embedded in SiO2 and subjected to swift heavy-ion irradiation have been investigated over a wide energy and fluence range. Modifications of the nanoparticle size and shape were characterized with transmission electron microscopy and small-angle x-ray scattering. Nanoparticles below a threshold diameter remained spherical in shape and progressively decreased in size under irradiation due to dissolution. Nanoparticles above the threshold diameter transformed into nanorods with their major dimension parallel to the incident ion direction. Modifications of the atomic-scale structure of the Co nanoparticles were identified with x-ray absorption spectroscopy. Analysis of the x-ray absorption near-edge spectra showed that prior to irradiation all Co atoms were in a metallic state, while after irradiation Co atoms were in both oxidized and metallic environments, the former consistent with dissolution. The evolution of the nanoparticle short-range order was determined from extended x-ray absorption fine structure spectroscopy. Structural changes in the Co nanoparticles as a function of ion fluence included an increase in disorder and asymmetric deviation from a Gaussian interatomic distance distribution coupled with a decrease in bondlength. Such changes resulted from the irradiation-induced decrease in nanoparticle size and subsequent dissolution.

  6. Secondary structure confirmation and localization of Mg2+ ions in the mammalian CPEB3 ribozyme.

    PubMed

    Skilandat, Miriam; Rowinska-Zyrek, Magdalena; Sigel, Roland K O

    2016-05-01

    Most of today's knowledge of the CPEB3 ribozyme, one of the few small self-cleaving ribozymes known to occur in humans, is based on comparative studies with the hepatitis delta virus (HDV) ribozyme, which is highly similar in cleavage mechanism and probably also in structure. Here we present detailed NMR studies of the CPEB3 ribozyme in order to verify the formation of the predicted nested double pseudoknot in solution. In particular, the influence of Mg(2+), the ribozyme's crucial cofactor, on the CPEB3 structure is investigated. NMR titrations, Tb(3+)-induced cleavage, as well as stoichiometry determination by hydroxyquinoline sulfonic acid fluorescence and equilibrium dialysis, are used to evaluate the number, location, and binding mode of Mg(2+)ions. Up to eight Mg(2+)ions interact site-specifically with the ribozyme, four of which are bound with high affinity. The global fold of the CPEB3 ribozyme, encompassing 80%-90% of the predicted base pairs, is formed in the presence of monovalent ions alone. Low millimolar concentrations of Mg(2+)promote a more compact fold and lead to the formation of additional structures in the core of the ribozyme, which contains the inner small pseudoknot and the active site. Several Mg(2+)binding sites, which are important for the functional fold, appear to be located in corresponding locations in the HDV and CPEB3 ribozyme, demonstrating the particular relevance of Mg(2+)for the nested double pseudoknot structure. PMID:26966151

  7. 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.

  8. Ion chromatographic determination of transition metals in irradiated nuclear reactor surveillance samples.

    PubMed

    Louw, I

    1996-02-01

    The determination of transition metal ions in radioactive (+/-25 microCi/g) low-alloy steels (nuclear reactor surveillance samples) by ion chromatography (IC) is described. The analysis has been done directly without prior separation of the iron matrix. The eluted metal ions have been detected with a UV-visible spectrophotometric detector after post-column complexation with 4-(2-pyridylazo)resorcinol. The results are in a good agreement with the certified values for the standard reference material used. The method was applied to nuclear reactor surveillance samples for the determination of Cu, Mn, Co and Ni. PMID:15048428

  9. 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. PMID:26358093

  10. Selective exchange of divalent transition metal ions in cryptomelane-type manganic acid with tunnel structure

    SciTech Connect

    Tsuji, M. ); Komarneni, S. )

    1993-03-01

    The ion-exchange selectivity of divalent transition metal ions on cryptomelane-type manganic acid (CMA) with tunnel structure has been studied using the distribution coefficients ([ital K][sub [ital d

  11. Azimuthal structures of produced particles in heavy-ion interactions

    SciTech Connect

    Vokal, S. Orlova, G. I.; Lehocka, S.

    2009-02-15

    The angular structures of particles produced in {sup 208}Pb at 158 A GeV/c and {sup 197}Au at 11.6 A GeV/c induced interactions with Ag(Br) nuclei in emulsion detector have been investigated. Nonstatistical well-ordered ring-like structures of produced particles in azimuthal plane of a collision have been found, and their parameters have been determined.

  12. 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. PMID:18459164

  13. Determination of equilibrium constants of alkaline earth metal ion chelates with Dowex A-1 chelating resin.

    PubMed

    Harju, L; Krook, T

    1995-03-01

    A complexation chemistry model is applied to chelating ion-exchange systems and a method is presented for the determination of equilibrium constants for metal ion chelates with these resins. Protonation constants for the iminodiacetic based chelating resin Dowex A-1 were determined from potentiometric pH-data. Equilibrium constants were determined for 1:1 beryllium, magnesium, calcium, strontium and barium chelates with the resin in a wide pH range by measuring the concentrations of respective metal ions in the aqueous phase with direct current plasma atomic emission spectrometry (DCP-AES). A batch technique was used for the equilibrium experiments. At pH below 7 protonated 1:1 species were also found to be formed with the resin. From the obtained equilibrium constants, theoretical distribution coefficients were calculated as function of pH for respective metal ion resin system. PMID:18966248

  14. On the structural denaturation of biological analytes in trapped ion mobility spectrometry - mass spectrometry.

    PubMed

    Liu, Fanny C; Kirk, Samuel R; Bleiholder, Christian

    2016-06-01

    Key to native ion mobility/mass spectrometry is to prevent the structural denaturation of biological molecules in the gas phase. Here, we systematically assess structural changes induced in the protein ubiquitin during a trapped ion mobility spectrometry (TIMS) experiment. Our analysis shows that the extent of structural denaturation induced in ubiquitin ions is largely proportional to the amount of translational kinetic energy an ion gains from the applied electric field between two collisions with buffer gas particles. We then minimize the efficiency of the structural denaturation of ubiquitin ions in the gas phase during a TIMS experiment. The resulting "soft" TIMS spectra of ubiquitin are found largely identical to those observed on "soft" elevated-pressure ion mobility drift tubes and the corresponding calibrated cross sections are consistent with structures reported from NMR experiments for the native and A-state of ubiquitin. Thus, our analysis reveals that TIMS is useful for native ion mobility/mass spectrometry analysis. PMID:26998732

  15. Fluorescent nanohybrid of gold nanoclusters and quantum dots for visual determination of lead ions.

    PubMed

    Zhu, Houjuan; Yu, Tao; Xu, Hongda; Zhang, Kui; Jiang, Hui; Zhang, Zhongping; Wang, Zhenyang; Wang, Suhua

    2014-12-10

    Highly green emissive gold nanoclusters (Au NCs) are synthesized using glutathione as a stabilizing agent and mercaptopropionic acid as a ligand, and the intensity of fluorescence is specifically sensitive to lead ions. We then fabricated a ratiometric fluorescence nanohybrid by covalently linking the green Au NCs to the surface of silica nanoparticles embedded with red quantum dots (QDs) for on-site visual determination of lead ions. The green fluorescence can be selectively quenched by lead ions, whereas the red fluorescence is inert to lead ions as internal reference. The different response of the two emissions results in a continuous fluorescence color change from green to yellow that can be clearly observed by the naked eyes. The nanohybrid sensor exhibits high sensitivity to lead ions with a detection limit of 3.5 nM and has been demonstrated for determination of lead ions in real water samples including tap water, mineral water, groundwater, and seawater. For practical application, we dope the Au NCs in poly(vinyl alcohol) (PVA) film and fabricate fluorescence test strips to directly detect lead ions in water. The PVA-film method has a visual detection limit of 0.1 μM, showing its promising application for on-site identification of lead ions without the need for elaborate equipment. PMID:25354513

  16. Determination of cyanogenic compounds in edible plants by ion chromatography.

    PubMed

    Cho, Hye-Jeon; Do, Byung-Kyung; Shim, Soon-Mi; Kwon, Hoonjeong; Lee, Dong-Ha; Nah, Ahn-Hee; Choi, Youn-Ju; Lee, Sook-Yeon

    2013-06-01

    Cyanogenic glycosides are HCN-producing phytotoxins; HCN is a powerful and a rapidly acting poison. It is not difficult to find plants containing these compounds in the food supply and/or in medicinal herb collections. The objective of this study was to investigate the distribution of total cyanide in nine genera (Dolichos, Ginkgo, Hordeum, Linum, Phaseolus, Prunus, Phyllostachys, Phytolacca, and Portulaca) of edible plants and the effect of the processing on cyanide concentration. Total cyanide content was measured by ion chromatography following acid hydrolysis and distillation. Kernels of Prunus genus are used medicinally, but they possess the highest level of total cyanide of up to 2259.81 CN(-)/g dry weight. Trace amounts of cyanogenic compounds were detected in foodstuffs such as mungbeans and bamboo shoots. Currently, except for the WHO guideline for cassava, there is no global standard for the allowed amount of cyanogenic compounds in foodstuffs. However, our data emphasize the need for the guidelines if plants containing cyanogenic glycosidesare to be developed as dietary supplements. PMID:24278641

  17. Crystal Structure of a Potassium Ion Transporter TrkH

    SciTech Connect

    Y Cao; X Jin; H Huang; M Getahun Derebe; E Levin; V Kabaleeswaran; Y Pan; M Punta; J Love; et al.

    2011-12-31

    The TrkH/TrkG/KtrB proteins mediate K{sup +} uptake in bacteria and probably evolved from simple K{sup +} channels by multiple gene duplications or fusions. Here we present the crystal structure of a TrkH from Vibrio parahaemolyticus. TrkH is a homodimer, and each protomer contains an ion permeation pathway. A selectivity filter, similar in architecture to those of K{sup +} channels but significantly shorter, is lined by backbone and side-chain oxygen atoms. Functional studies showed that TrkH is selective for permeation of K{sup +} and Rb{sup +} over smaller ions such as Na{sup +} or Li{sup +}. Immediately intracellular to the selectivity filter are an intramembrane loop and an arginine residue, both highly conserved, which constrict the permeation pathway. Substituting the arginine with an alanine significantly increases the rate of K{sup +} flux. These results reveal the molecular basis of K{sup +} selectivity and suggest a novel gating mechanism for this large and important family of membrane transport proteins.

  18. DETERMINATION OF ELEMENTAL COMPOSITIONS FROM MASS PEAK PROFILES OF THE MOLECULAR ION (M) AND THE M + 1 AND M + 2 IONS

    EPA Science Inventory

    The relative abundances of M + 1 and M + 2 ions help to identify the elemental composition of the molecular ion (M). But scan speed, snesitiity, and resolution limitations of mass spectrometers have impeded determination of these abundances. Mass peak profiling from selected ion ...

  19. Profiling of phospholipids and related lipid structures using multidimensional ion mobility spectrometry-mass spectrometry

    NASA Astrophysics Data System (ADS)

    Trimpin, Sarah; Tan, Bo; Bohrer, Brian C.; O'Dell, David K.; Merenbloom, Samuel I.; Pazos, Mauricio X.; Clemmer, David E.; Walker, J. Michael

    2009-10-01

    Increasingly comprehensive questions related to the biosynthesis of lipids relevant to understanding new signaling pathways have created daunting tasks for their chemical analysis. Here, ion mobility spectrometry (IMS) and mass spectrometry (MS) techniques combined with electrospray ionization have been used to examine mixtures of closely related lipid structures. The drift time distributions of sphingomyelins show baseline separations for ethylene chain length differences ([Delta] ~ 1.2 ms) and partial separations in single unsaturation differences ([Delta] ~ 0.3 ms) revealing that the most compact structures are observed with shorter chains and increasing unsaturation. Drift time distributions of different ionizations frequently fall into families with the same drift times (isodrifts) indicating that the ion attached to the lipid has little structural influence. The present data show that phospholipids, especially phosphatidylinositol, aggregate to form inverted micelles. Phospholipids (phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, sphingomyelin, and phosphatidylinositol) are effectively separated according to their polar head groups. This method also provides information about the mixture composition of the chemically different lipids N-palmitoyl glycine, N-arachidonoyl ethanolamide, and phosphatidylcholine existing over an array of charge states and sizes (inverted micelles) depending on mixture concentration. Multidimensional IMS3-MS introduces an additional dimension to fragmentation analysis by separating the fragmented ions into groups related to size, shape and charge and allows determination of sn-1 and sn-2 substitution as is shown for phosphatidylglycerols. This contribution provides evidence for extending the targeted approach to global lipidomics analysis using the high-efficiency gas-phase separation afforded by multidimensional IMS-MS.

  20. 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

    2015-01-01

    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. PMID:25049172

  1. 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.

  2. Structure and substrate ion binding in the sodium/proton antiporter PaNhaP

    PubMed Central

    Wöhlert, David; Kühlbrandt, Werner; Yildiz, Özkan

    2014-01-01

    Sodium/proton antiporters maintain intracellular pH and sodium levels. Detailed structures of antiporters with bound substrate ions are essential for understanding how they work. We have resolved the substrate ion in the dimeric, electroneutral sodium/proton antiporter PaNhaP from Pyrococcus abyssi at 3.2 Å, and have determined its structure in two different conformations at pH 8 and pH 4. The ion is coordinated by three acidic sidechains, a water molecule, a serine and a main-chain carbonyl in the unwound stretch of trans-membrane helix 5 at the deepest point of a negatively charged cytoplasmic funnel. A second narrow polar channel may facilitate proton uptake from the cytoplasm. Transport activity of PaNhaP is cooperative at pH 6 but not at pH 5. Cooperativity is due to pH-dependent allosteric coupling of protomers through two histidines at the dimer interface. Combined with comprehensive transport studies, the structures of PaNhaP offer unique new insights into the transport mechanism of sodium/proton antiporters. DOI: http://dx.doi.org/10.7554/eLife.03579.001 PMID:25426802

  3. 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. PMID:27250314

  4. 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.

  5. 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.

  6. 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 measurement of temperatures and displacements was identified as the most critical area for further work.

  7. Optical properties of structurally modified glasses doped with gold ions.

    PubMed

    Qiu, Jianrong; Jiang, Xiongwei; Zhu, Congshan; Inouye, Hideyuki; Si, Jinhai; Hirao, Kazuyuki

    2004-02-15

    We report on the optical properties of a structurally modified silicate glass doped with Au ions. The area in the vicinity of the focal point of an 800-nm femtosecond laser in a glass sample became gray as a result of the formation of color centers after laser irradiation and turned red because of precipitation of Au nanoparticles after further annealing at 550 degrees C for 30 min. When the glass was excited by UV light at 365 nm, yellowish-white and orange-yellow emissions were observed in the laser-irradiated and the Au-nanoparticle-precipitated area, respectively. An optical Kerr shutter experiment showed that the Au nanoparticle-precipitated glass had an ultrafast nonlinear optical response, and the third-order nonlinear susceptibility was estimated to be approximately 10(-11) esu. PMID:14971756

  8. Optical properties of structurally modified glasses doped with gold ions

    NASA Astrophysics Data System (ADS)

    Qiu, Jianrong; Jiang, Xiongwei; Zhu, Congshan; Inouye, Hideyuki; Si, Jinhai; Hirao, Kazuyuki

    2004-02-01

    We report on the optical properties of a structurally modified silicate glass doped with Au ions. The area in the vicinity of the focal point of an 800-nm femtosecond laser in a glass sample became gray as a result of the formation of color centers after laser irradiation and turned red because of precipitation of Au nanoparticles after further annealing at 550 °C for 30 min. When the glass was excited by UV light at 365 nm, yellowish-white and orange-yellow emissions were observed in the laser-irradiated and the Au-nanoparticle-precipitated area, respectively. An optical Kerr shutter experiment showed that the Au nanoparticle-precipitated glass had an ultrafast nonlinear optical response, and the third-order nonlinear susceptibility was estimated to be ~10-11 esu.

  9. Vibrational stark effects to identify ion pairing and determine reduction potentials in electrolyte-free environments

    DOE PAGESBeta

    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

  10. 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.

  11. Synthesis, properties and structure of ion exchanged hydrosodalite

    NASA Astrophysics Data System (ADS)

    Kendrick, Emma; Dann, Sandra

    2004-04-01

    Alkali metal and alkali-earth metal hydrosodalites with the formula M6[AlSiO 4] 6·8H 2O ( M=Li, Na, K, Mg, Ca, Sr) have been prepared by ion exchange of Na 6[AlSiO 4] 6·8H 2O using a solution of the appropriate metal nitrate solution under reflux for a period of 24 h. The starting materials and products were characterized using a combination of techniques including IR, DSC, TGA, ICP, AA, MASNMR and X-ray diffraction. The alkali metal and alkali-earth metal hydrosodalites crystallize with the primitive cubic sodalite unit cell and an ordered AlO 4/SiO 4 framework in the space group P 4¯3n with cell parameters lying between 8.8 and 9.2 Å. The structures of these materials have been refined using powder X-ray diffraction data in order to delineate structural changes as a function of the occluded cation. Temperature-dependent powder X-ray diffraction has been used to observe changes in the structure as a function of temperature. Results from the DSC and TGA analysis show that the temperature at which water is lost from the β cages is a two-stage process. In the second stage, the temperature rises as the size of occluded cation increases, implying that the presence of a larger cation in the six-ring window blocks the path of the exiting water molecules.

  12. Structural Determinants of Juvenile Offenses in School.

    ERIC Educational Resources Information Center

    Kowalski, Gregory S.; And Others

    1983-01-01

    Using multiple regression techniques, evaluates the relative contributions of community structure, school structure, and crime prevention efforts to delinquency in public schools. Finds that distance from central business district, school size, and region are of predictive value, when crimes against persons, property, and perceived crime are…

  13. ION MANIPULATIONS IN STRUCTURES FOR LOSSLESS ION MANIPULATIONS (SLIM): COMPUTATIONAL EVALUATION OF A 90° TURN AND A SWITCH

    PubMed Central

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

    2015-01-01

    The process of redirecting ions through 90° turns and ‘tee’ switches utilizing Structures for Lossless Ion Manipulations (SLIM) was evaluated at 4 Torr pressure using SIMION simulations and theoretical methods. The nature of pseudo-potential in SLIM-tee structures has also been explored. Simulations show that 100% transmission efficiency in SLIM devices can be achieved with guard electrode voltages lower than ~10 V. The ion plume width in these conditions is ~1.6 mm while at lower guard voltages lead to greater plume widths. Theoretical calculations show marginal loss of ion mobility resolving power (<5%) during ion turn due to the finite plume widths (i.e. race track effect). More robust SLIM designs that reduce the race track effect while maximizing ion transmission are also reported. In addition to static turns, the dynamic switching of ions into orthogonal channels was also evaluated both using SIMION ion trajectory simulations and experimentally. Simulations and theoretical calculations were in close agreement with experimental results and were used to develop more refined SLIM designs. PMID:26289106

  14. Structural and vibrational properties of Co nanoparticles formed by ion implantation

    NASA Astrophysics Data System (ADS)

    Sprouster, D. J.; Giulian, R.; Araujo, L. L.; Kluth, P.; Johannessen, B.; Cookson, D. J.; Foran, G. J.; Ridgway, M. C.

    2010-01-01

    We report on the structural and vibrational properties of Co nanoparticles formed by ion implantation and thermal annealing in amorphous silica. The evolution of the nanoparticle size, phase, and structural parameters were determined as a function of the formation conditions using transmission electron microscopy, small-angle x-ray scattering, and x-ray absorption spectroscopy. The implantation fluence and annealing temperature governed the spherical nanoparticle size and phase. To determine the latter, x-ray absorption near-edge structure analysis was used to quantify the hexagonal close packed, face-centered cubic and oxide fractions. The structural properties were characterized by extended x-ray absorption fine structure spectroscopy (EXAFS) and finite-size effects were readily apparent. With a decrease in nanoparticle size, an increase in structural disorder and a decrease in both coordination number and bondlength were observed as consistent with the non-negligible surface-area-to-volume ratio characteristic of nanoparticles. The surface tension of Co nanoparticles calculated using a liquid drop model was more than twice that of bulk material. The size-dependent vibrational properties were probed with temperature-dependent EXAFS measurements. Using a correlated anharmonic Einstein model and thermodynamic perturbation theory, Einstein temperatures for both nanoparticles and bulk material were determined. Compared to bulk Co, the mean vibrational frequency of the smallest nanoparticles was reduced as attributed to a greater influence of loosely bonded, undercoordinated surface atoms relative to the effect of capillary pressure generated by surface curvature.

  15. 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.

  16. 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.

  17. Ion chromatographic determination of halogens, nitrogen, phosphorus, and sulfur in coals

    SciTech Connect

    Rigin, V.I.

    1987-12-10

    A method is proposed for simultaneous determination of sulfur, nitrogen, phosphorus, and halogens in fossil coals. The method consists in autoclave combustion of the sample in oxygen, absorption of the combustion products by a mixture of potassium carbonate and hydrogen peroxide solutions, and ion chromatographic determination of the anions formed.

  18. A novel Schiff base: Synthesis, structural characterisation and comparative sensor studies for metal ion detections.

    PubMed

    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, (1)H, (13)C 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(+), Mg(2+), Al(3+), K(+), Cr(3+), Mn(2+), Fe(3+), Co(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+), Hg(2+) and Pb(2+). Upon addition of Al(3+) 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 630-665nm upon excitation at 560nm. Addition of metal ions Na(+), Mg(2+), K(+), Cr(3+), Mn(2+), Fe(3+), Co(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+), Hg(2+) and Pb(2+) (1:1M 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 Al(3+) in presence of other metal ions. Therefore, the Schiff base ligand can be used for selective detection of Al(3+) ions in the presence of the other metal ions studied. PMID:25459697

  19. Compositions and Structures of Vanadium Oxide Cluster Ions VmOn(±) (m = 2-20) Investigated by Ion Mobility Mass Spectrometry.

    PubMed

    Wu, Jenna W J; Moriyama, Ryoichi; Tahara, Hiroshi; Ohshimo, Keijiro; Misaizu, Fuminori

    2016-06-01

    Stable compositions and geometrical structures of vanadium oxide cluster ions, VmOn(±), were investigated by ion mobility mass spectrometry (IM-MS). The most stable compositions of vanadium oxide cluster cations were (V2O4)(V2O5)(m-2)/2(+) and (VO2)(V2O5)(m-1)/2(+), depending on the clusters with even and odd numbers of vanadium atoms. Compositions one-oxygen richer than the cations, such as (V2O5)m/2(-) and (VO3)(V2O5)(m-1)/2(-), were predominantly observed for cluster anions. Assignments of these stable cluster ion compositions, which were determined as a result of collision-induced dissociations in IM-MS, can partly be explained with consideration of spin density distribution. By comparing the experimental collision cross sections (CCSs) obtained from ion mobility measurement with CCSs of the theoretically calculated structures, we confirmed the patterned growth of geometrical structures partially discussed in previous theoretical and spectroscopic studies. We showed that even sized (V2O5)m/2(±) where m = 6-12 had right polygonal prism structures except for the anionic V12O30(-), and for the clusters of odd numbers of vanadium m, cations and anions can either have bridged or pyramid structures. Both of the odd sized structures proposed were derivatives from the even sized right polygonal prism structures. The exception, V12O30(-), which had a CCS almost equal to that of the neighboring smaller V11O28(-), should have a structure of higher density than the right hexagonal prism, in which it was proposed to be a captured pyramid structure, derived from V11O28(-). PMID:27172006

  20. Fragmentation cross-section of relativistic oxygen ions and determination of overlap parameter

    NASA Technical Reports Server (NTRS)

    Verma, S. D.

    1977-01-01

    Results are presented for measurements of total fragmentation cross sections of relativistic O-16 ions in CsI crystals, which were performed using a monochromatic bevatron ion beam at energies of 0.5 and 2.1 GeV/nucleon. The total fragmentation cross section at each energy is determined on the basis of detected changes in the charge of the incident ions, and the values obtained at both energies are found to be the same to within the experimental errors. Values of the O-16 nucleon radius and overlap parameter are derived simultaneously from the measured cross sections.

  1. Determination of busulfan in plasma by GC-MS with selected-ion monitoring.

    PubMed

    Ehrsson, H; Hassan, M

    1983-10-01

    A GC-MS technique with selected-ion monitoring is described for the determination of busulfan in plasma. Busulfan is extracted from plasma with methylene chloride and converted to 1,4-diiodobutane. Analysis by GC-MS with selected-ion monitoring (m/z 183) gave a relative standard deviation of +/- 4.3% (n = 5) at the 10-ng/ml level. PMID:6644573

  2. 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…

  3. Determination of electron affinity of carbonyl radicals by means of negative ion mass spectrometry.

    PubMed

    Muftakhov; Vasil'ev; Mazunov

    1999-06-01

    Appearance energies of [M-H](-) ions from carbonyl compounds R-CO-R' (R,R' = H, CH(3), NH(2), OH) have been measured by means of negative ion mass spectrometry in resonant electron capture mode. Values of electron affinity of the corresponding radicals, CH(2)&dbond;C(X)O, NH&dbond;C(X)O and O&dbond;C(X)O, have been determined. Copyright 1999 John Wiley & Sons, Ltd. PMID:10407285

  4. 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.

  5. Biochemical and Structural Properties of a Thermostable Mercuric Ion Reductase from Metallosphaera sedula

    PubMed Central

    Artz, Jacob H.; White, Spencer N.; Zadvornyy, Oleg A.; Fugate, Corey J.; Hicks, Danny; Gauss, George H.; Posewitz, Matthew C.; Boyd, Eric S.; Peters, John W.

    2015-01-01

    Mercuric ion reductase (MerA), a mercury detoxification enzyme, has been tuned by evolution to have high specificity for mercuric ions (Hg2+) and to catalyze their reduction to a more volatile, less toxic elemental form. Here, we present a biochemical and structural characterization of MerA from the thermophilic crenarchaeon Metallosphaera sedula. MerA from M. sedula is a thermostable enzyme, and remains active after extended incubation at 97°C. At 37°C, the NADPH oxidation-linked Hg2+ reduction specific activity was found to be 1.9 μmol/min⋅mg, increasing to 3.1 μmol/min⋅mg at 70°C. M. sedula MerA crystals were obtained and the structure was solved to 1.6 Å, representing the first solved crystal structure of a thermophilic MerA. Comparison of both the crystal structure and amino acid sequence of MerA from M. sedula to mesophillic counterparts provides new insights into the structural determinants that underpin the thermal stability of the enzyme. PMID:26217660

  6. Ion Scattering Studies of Silicon Surfaces and Interfaces: Structure and Neutralization.

    NASA Astrophysics Data System (ADS)

    Haight, Richard Alan

    This thesis chronicles three experiments which represent the major thrust of studies performed during my tenure as a graduate student at the State University of New York at Albany. Chapter 1 introduces the fundamental considerations of the physics of ion scattering and its applications to studies of surfaces, interfaces and ion neutralization. Basic formula are stated and the two atom model using the Coulomb interaction potential is developed as an approximate prediction of the surface peak intensity. The second chapter discusses a study of the neutralization of 75-180 KeV He ions scattered from clean and Cs covered Si (100); an experiment performed at Bell Laboratories. It is shown that ion neutralization occurs at the surface of the solid; the ion retains no memory of its journey within the bulk. It is also observed that the ion fraction exhibits no dependence upon takeoff angle, a result which differs markedly from the exponential angular dependence observed at lower velocities. Changes in the Si scattered ion fraction upon cesiation of the Si surface are correlated with the work function change observed by other workers. A model is proposed, and developed in mathematical detail, which includes resonant transitions to the motionally broadened He n=2 quantum level and is compared with the experimental data. The third chapter discusses an ion scattering study of the interfacial structure of the Si-SiO(,2) interface. It is shown that the oxide is stoichiometric to within (TURN)1 monolayer of the interface. Measurements to determine the magnitude and direction of the Si atomic displacements at the interface were compared with Monte Carlo computer simulations and show small lateral and larger vertical displacements in two layers. A model, consistent with the data, is proposed and the effects of these displacements are related qualitatively with theory. The fourth chapter describes a thin Si (111) crystal transmission channeling experiment. In this experiment, the use

  7. Shape Determination for Large Static Structures

    NASA Technical Reports Server (NTRS)

    Rodriguez, G.; Scheid, Robert E., Jr.

    1986-01-01

    Parameter and shape estimates updated from new measurements. Involves statistical structural analysis, statistical electromagneticfield analysis, filtering, measurement modeling, and iterative prediction/correction procedures. Estimating algorithms result from generalizations of Kalman statistical-filter theory.

  8. Determining Probabilities by Examining Underlying Structure.

    ERIC Educational Resources Information Center

    Norton, Robert M.

    2001-01-01

    Discusses how dice games pose fairness issues that appeal to students and examines a structure for three games involving two dice in a way that leads directly to the theoretical probabilities for all possible outcomes. (YDS)

  9. STRUCTURAL CHARACTERIZATION OF SULFONATED AZO DYES USING LIQUID SECONDARY ION MASS SPECTROMETRY/TANDEM MASS SPECTROMETRY

    EPA Science Inventory

    Eight monosulfonated and disulfonated azo dyes were analyzed using liquid secondary ion mass spectrometry/tandem mass spectrometry, in the negative ion mode, under low-energy conditions (110-150 eV). any structurally characteristic fragment ions were obtained, several of which ha...

  10. Structural and Thermodynamic Properties of Selective Ion Binding in a K+ Channel

    SciTech Connect

    Lockless,S.; Zhou, M.; MacKinnon, R.

    2007-01-01

    Thermodynamic measurements of ion binding to the Streptomyces lividans K+ channel were carried out using isothermal titration calorimetry, whereas atomic structures of ion-bound and ion-free conformations of the channel were characterized by x-ray crystallography. Here we use these assays to show that the ion radius dependence of selectivity stems from the channel's recognition of ion size (i.e., volume) rather than charge density. Ion size recognition is a function of the channel's ability to adopt a very specific conductive structure with larger ions (K+, Rb+, Cs+, and Ba2+) bound and not with smaller ions (Na+, Mg2+, and Ca2+). The formation of the conductive structure involves selectivity filter atoms that are in direct contact with bound ions as well as protein atoms surrounding the selectivity filter up to a distance of 15 Angstroms from the ions. We conclude that ion selectivity in a K+ channel is a property of size-matched ion binding sites created by the protein structure.

  11. Structural and Thermodynamic Properties of Selective Ion Binding in a K+ Channel

    PubMed Central

    Lockless, Steve W; Zhou, Ming; MacKinnon, Roderick

    2007-01-01

    Thermodynamic measurements of ion binding to the Streptomyces lividans K+ channel were carried out using isothermal titration calorimetry, whereas atomic structures of ion-bound and ion-free conformations of the channel were characterized by x-ray crystallography. Here we use these assays to show that the ion radius dependence of selectivity stems from the channel's recognition of ion size (i.e., volume) rather than charge density. Ion size recognition is a function of the channel's ability to adopt a very specific conductive structure with larger ions (K+, Rb+, Cs+, and Ba2+) bound and not with smaller ions (Na+, Mg2+, and Ca2+). The formation of the conductive structure involves selectivity filter atoms that are in direct contact with bound ions as well as protein atoms surrounding the selectivity filter up to a distance of 15 Å from the ions. We conclude that ion selectivity in a K+ channel is a property of size-matched ion binding sites created by the protein structure. PMID:17472437

  12. 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.

  13. 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

  14. Fast ion conductivity in strained defect-fluorite structure created by ion tracks in Gd2Ti2O7

    DOE PAGESBeta

    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 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

  15. Selective determination of ammonium ions by high-speed ion-exclusion chromatography on a weakly basic anion-exchange resin column.

    PubMed

    Mori, Masanobu; Tanaka, Kazuhiko; Helaleh, Murad I H; Xu, Qun; Ikedo, Mikaru; Ogura, Yutaka; Sato, Shinji; Hu, Wenzhi; Hasebe, Kiyoshi

    2003-05-16

    This paper describes an ion-exclusion chromatographic system for the rapid and selective determination of ammonium ion. The optimized ion-exclusion chromatographic system was established with a polymethacrylate-based weakly basic anion-exchange resin column (TSKgel DEAE-5PW) as the separation column, an aqueous solution containing 0.05 mM tetramethylammonium hydroxide (pH 9.10) as eluent with conductimetric detection for the analyte determination. Under the optimum chromatographic conditions, ammonium ion was determined within 2.3 min with a detection limit (S/N=3) better than 0.125 microM. Ammonium ion in rain and river waters was precisely determined using this ion-exclusion chromatographic system. PMID:12830892

  16. Phosphate Ions Affect the Water Structure at Functionalized Membrane Surfaces.

    PubMed

    Barrett, Aliyah; Imbrogno, Joseph; Belfort, Georges; Petersen, Poul B

    2016-09-01

    Antifouling surfaces improve function, efficiency, and safety in products such as water filtration membranes, marine vehicle coatings, and medical implants by resisting protein and biofilm adhesion. Understanding the role of water structure at these materials in preventing protein adhesion and biofilm formation is critical to designing more effective coatings. Such fouling experiments are typically performed under biological conditions using isotonic aqueous buffers. Previous studies have explored the structure of pure water at a few different antifouling surfaces, but the effect of electrolytes and ionic strength (I) on the water structure at antifouling surfaces is not well studied. Here sum frequency generation (SFG) spectroscopy is used to characterize the interfacial water structure at poly(ether sulfone) (PES) and two surface-modified PES films in contact with 0.01 M phosphate buffer with high and low salt (Ionic strength, I= 0.166 and 0.025 M, respectively). Unmodified PES, commonly used as a filtration membrane, and modified PES with a hydrophobic alkane (C18) and with a poly(ethylene glycol) (PEG) were used. In the low ionic strength phosphate buffer, water was strongly ordered near the surface of the PEG-modified PES film due to exclusion of phosphate ions and the creation of a surface potential resulting from charge separation between phosphate anions and sodium cations. However, in the high ionic strength phosphate buffer, the sodium and potassium chloride (138 and 3 mM, respectively) in the phosphate buffered saline screened this charge and substantially reduced water ordering. A much smaller water ordering and subsequent reduction upon salt addition was observed for the C18-modified PES, and little water structure change was seen for the unmodified PES. The large difference in water structuring with increasing ionic strength between widely used phosphate buffer and phosphate buffered saline at the PEG interface demonstrates the importance of studying

  17. Ion-scale structure in Mercury's magnetopause reconnection diffusion region

    NASA Astrophysics Data System (ADS)

    Gershman, Daniel J.; Dorelli, John C.; DiBraccio, Gina A.; Raines, Jim M.; Slavin, James A.; Poh, Gangkai; Zurbuchen, Thomas H.

    2016-06-01

    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 ~150 ms 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 ~0.3-3 mV/m reconnection electric fields separated by ~5-10 s, resulting in average and peak normalized dayside reconnection rates of ~0.02 and ~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.

  18. Studying nucleon structure using an Electron-Ion Collider

    NASA Astrophysics Data System (ADS)

    Burton, Thomas; EIC Team

    2011-04-01

    The detailed composition of the spin of the nucleon remains unknown. Numerous experiments over the past two decades have shown that the spin of quarks alone cannot account for more than a third of the nucleon's spin. Proton-proton collisions at RHIC suggest a small gluon polarisation, but uncertainties remain large. An Electron-Ion Collider is proposed as future machine for precision studies of nucleon and nuclear structure. It will allow the study of the spin contribution from gluons and quarks, including their flavour decomposition, in heretofore unprecedented precision, and will access a much wider kinematic space than ever before, in particular extending to the currently unmeasured low Bjorken-x sea. The formalism of generalised parton distributions (GPDs), accessible for example via deeply-virtual Compton scattering, promises to allow study of the role of orbital angular momentum in nucleon spin. Furthermore, GPDs will extend understanding of parton distributions beyond the well-known one-dimensional PDFs, accessing three-dimensional structure via the impact parameter distributions of partons.

  19. 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%. PMID:14763743

  20. HPLC method for the determination of phytochelatin synthase activity specific for soft metal ion chelators.

    PubMed

    Ogawa, Shinya; Yoshidomi, Takahiro; Shirabe, Tomoo; Yoshimura, Etsuro

    2010-04-01

    Phytochelatins (PCs) are nonprotein peptides with the general structure (gamma-Glu-Cys)(n)-Gly (PC(n)), where n is greater than or equal to 2. They are synthesized through a reaction catalyzed by phytochelatin synthase (PCS) in the presence of metal cations and using the tripeptide glutathione (gamma-Glu-Cys-Gly) and/or previously synthesized PC(n) as the substrate. Here, a highly sensitive assay for PCS activity was devised, in which the dequenching of Cu(I)-bathocuproinedisulfonate complexes was used in the detection system of a reversed-phase high-performance liquid chromatograph. Using recombinant PCS from the higher plant Arabidopsis thaliana (rAtPCS1), this assay system was capable of determining PCS activity based on an amount of the enzyme preparation that was 100-fold less than that required for the 5,5'-dithiobis(2-nitrobenzoic acid) assay method. Although adsorption of the enzyme onto the reaction vessel hindered accurate activity determination, the inclusion of bovine serum albumin successfully resolved this issue. This method is a powerful tool for investigating PCS enzyme mechanisms with respect to the roles of metal ions. PMID:20074807

  1. Compressible coherent structures at ion scales in the slow solar wind

    NASA Astrophysics Data System (ADS)

    Perrone, Denise; Alexandrova, Olga; Mangeney, Andre; Maksimovic, Milan; Lacombe, Catherine

    2016-04-01

    We present a study of magnetic field fluctuations close to the ion scales in a slow solar wind stream. The nature of these fluctuations is found to be characterized by coherent structures. Although previous studies have shown that coherent current sheets can be considered as the principal cause of intermittency at the solar wind ion scales, here we show for the first time that, in the case of the slow solar wind, a large variety of coherent structures participates to intermittency at proton scales, and current sheets are not the most common ones. Precisely, we find here compressible (δB∥ ≫ δB⊥), linearly polarized structures in form of magnetic holes, solitons and shock waves. Examples of Alfvénic structures (δB⊥ > δB∥) are identified as current sheets and vortex-like structures. Some of these vortices have δB⊥≫ δB∥, but the majority of them are characterized by δB⊥ ≳ δB∥. Thanks to multi-point measurements by Cluster spacecraft, we could determine the normal of the coherent structures and their propagation velocity and spatial scale along this normal. Independently of the nature of the structures, the normal is always perpendicular to the local magnetic field, meaning that k⊥ ≫ k∥. The spatial scales of the studied structures are found to be 2 to 5 times the proton gyroradius or proton inertial length. Most of them are simply convected by the wind, but 25% propagate in the plasma frame. Possible interpretations of the observed structures and the connection with the plasma heating are discussed.

  2. Compressive Coherent Structures at Ion Scales in the Slow Solar Wind

    NASA Astrophysics Data System (ADS)

    Perrone, D.; Alexandrova, O.; Mangeney, A.; Maksimovic, M.; Lacombe, C.; Rakoto, V.; Kasper, J. C.; Jovanovic, D.

    2016-08-01

    We present a study of magnetic field fluctuations in a slow solar wind stream, close to ion scales, where an increase of the level of magnetic compressibility is observed. Here, the nature of these compressive fluctuations is found to be characterized by coherent structures. Although previous studies have shown that current sheets can be considered the principal cause of intermittency at ion scales, here we show for the first time that, in the case of the slow solar wind, a large variety of coherent structures contributes to intermittency at proton scales, and current sheets are not the most common. Specifically, we find compressive (δ {b}\\parallel \\gg δ {b}\\perp ), linearly polarized structures in the form of magnetic holes, solitons, and shock waves. Examples of Alfvénic structures (δ {b}\\perp \\gt δ {b}\\parallel ) are identified as current sheets and vortex-like structures. Some of these vortices have δ {b}\\perp \\gg δ {b}\\parallel , as in the case of Alfvén vortices, but the majority of them are characterized by δ {b}\\perp ≳ δ {b}\\parallel . Thanks to multi-point measurements by the Cluster spacecraft, for about 100 structures we could determine the normal, the propagation velocity, and the spatial scale along this normal. Independently of the nature of the structures, the normal is always perpendicular to the local magnetic field, meaning that k ⊥ ≫ k ∥. The spatial scales of the studied structures are found to be between two and eight times the proton gyroradius. Most of them are simply convected by the wind, but 25% propagate in the plasma frame. Possible interpretations of the observed structures and the connection with plasma heating are discussed.

  3. Raman and infrared studies of the structure of the dithionite ion in aqueous solution and force-constants of S 2O x2- type ions

    NASA Astrophysics Data System (ADS)

    Takahashi, Hiroaki; Kaneko, Norio; Miwa, Kohtaro

    The structure of the dithionite ion S 2O 42- in aqueous solution has been studied by Raman and i.r. spectroscopy. The anion which has an eclipsed configuration (C 2ν symmetry) in Na 2S 2O 4 crystals is found to have a staggered configuration (C 2 h symmetry) in aqueous solution. The force constants of S 2O x2- type ions having SS bonds, namely S 2O 32-, S 2O 42-, S 2O 52- and S 2O 62- are determined assuming a modified Urey-Bradley force field. The assignments of the normal vibrations of S 2O 42- and S 2O 52- ions are also made.

  4. Highly charged ions for atomic clocks and search for variation of the fine structure constant

    NASA Astrophysics Data System (ADS)

    Dzuba, V. A.; Flambaum, V. V.

    2015-11-01

    We review a number of highly charged ions which have optical transitions suitable for building extremely accurate atomic clocks. This includes ions from Hf 12+ to U 34+, which have the 4 f 12 configuration of valence electrons, the Ir 17+ ion, which has a hole in almost filled 4 f subshell, the Ho 14+, Cf 15+, Es 17+ and Es 16+ ions. Clock transitions in most of these ions are sensitive to variation of the fine structure constant, α (α = e2/hbar c). E.g., californium and einsteinium ions have largest known sensitivity to α-variation while holmium ion looks as the most suitable ion for experimental study. We study the spectra of the ions and their features relevant to the use as frequency standards.

  5. Mobility-Resolved Ion Selection in Uniform Drift Field Ion Mobility Spectrometry/Mass Spectrometry; Dynamic Switching in Structures for Lossless Ion Manipulations

    SciTech Connect

    Webb, Ian K.; Garimella, Venkata BS; Tolmachev, Aleksey V.; Chen, Tsung-Chi; Zhang, Xinyu; Cox, Jonathan T.; Norheim, Randolph V.; Prost, Spencer A.; Lamarche, Brian L.; Anderson, Gordon A.; Ibrahim, Yehia M.; Smith, Richard D.

    2014-10-07

    A Structures for Lossless Ion Manipulations (SLIM) module that allows ion mobility separations and the switching of ions between alternative drift paths is described. The SLIM switch component has a “Tee” configuration and allows switching of ions between a linear path and a 90-degree bend. By controlling switching times, ions can be deflected to an alternative channel as a function of their mobilities. In the initial evaluation the switch is used in a static mode and shown compatible with high performance ion mobility separations at 4 torr. In the “dynamic mode” we show that mobility-selected ions can be switched into the alternative channel, and that various ion species can be independently selected based on their mobilities for time-of-flight mass spectrometer (TOF MS) IMS detection and mass analysis. This development also provides the basis for e.g. the selection of specific mobilities for storage and accumulation, and key modules for the assembly of SLIM devices enabling much more complex sequences of ion manipulations.

  6. 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. PMID:16815625

  7. Indirect determination of cyanide compounds by ion chromatography with conductivity measurement

    SciTech Connect

    Nonomura, M.

    1987-09-01

    Ion chromatography (IC) is a suitable analytical technique for the determination of anions. The cyanide is not detected by the conductivity detector of the ion chromatograph due to its low dissolution constant (pK = 9.2). This paper describes an IC procedure for the determination of free cyanide and metal cyanide complexes that uses a conductivity detector. It is based on the oxidation of cyanide ion by sodium hypochlorite to cyanate ion (pK = 3.66). Therefore, cyanide ion can now be measured indirectly by the conductivity detector. In this procedure, optimum operating conditions were examined. In addition, the interferences from anions and reducing agents were investigated. The method was applied to the determination of metal cyanide complexes. The coefficients of variation (%) for CN/sup -/ (1.05 mg/L), Zn(CN)/sub 4//sup 2 -/ (CN/sup -/, 0.80 mg/L), and Ni(CN)/sub 4//sup 2 -/ (CN/sup -/, 0.96 mg/L) were 1.1%, 1.5%, and 0.5%, respectively. The proposed method proved to be useful for the determination of cyanide compounds in natural water and waste water.

  8. Use of accelerated helium-3 ions for determining oxygen and carbon impurities in some pure materials

    NASA Technical Reports Server (NTRS)

    Aleksandrova, G. I.; Borisov, G. I.; Demidov, A. M.; Zakharov, Y. A.; Sukhov, G. V.; Shmanenkova, G. I.; Shchelkova, V. P.

    1978-01-01

    Methods are developed for the determination of O impurity in Be and Si carbide and concurrent determination of C and O impurities in Si and W by irradiation with accelerated He-3 ions and subsequent activity measurements of C-11 and F-18 formed from C and O with the aid of a gamma-gamma coincidence spectrometer. Techniques for determining O in Ge and Ga arsenide with radiochemical separation of F-18 are also described.

  9. Electrotunable Friction with Ionic Liquid Lubricants: How Important Is the Molecular Structure of the Ions?

    PubMed

    Fajardo, O Y; Bresme, Fernando; Kornyshev, Alexei A; Urbakh, Michael

    2015-10-15

    Using nonequilibrium molecular dynamics simulations and a coarse-grained model of ionic liquids, we have investigated the impact that the shape and the intramolecular charge distribution of the ions have on the electrotunable friction with ionic liquid nanoscale films. We show that the electric field induces significant structural changes in the film, leading to dramatic modifications of the friction force. Comparison of the present work with previous studies using different models of ionic liquids indicate that the phenomenology presented here applies to a wide range of ionic liquids. In particular, the electric-field-induced shift of the slippage plane from the solid-liquid interface to the interior of the film and the nonmonotonic variation of the friction force are common features of ionic lubricants under strong confinement. We also demonstrate that the molecular structure of the ions plays an important role in determining the electrostriction and electroswelling of the confined film, hence showing the importance of ion-specific effects in electrotunable friction. PMID:26722768

  10. A study of the structural and magnetic properties of ZnO implanted by Gd ions

    NASA Astrophysics Data System (ADS)

    Macková, A.; Malinský, P.; Sofer, Z.; Šimek, P.; Sedmidubský, D.; Mikulics, M.; Wilhelm, R. A.

    2014-08-01

    The structural and magnetic properties of ZnO (0 0 0 1) single crystals implanted with 200 keV Gd ions up to a fluence of 5 × 1015 cm-2 and subsequently annealed at 800 °C in various atmospheres were studied. The chemical composition and concentration depth profiles of ion-implanted layers were characterised by Rutherford Back-Scattering spectrometry (RBS) and compared to SRIM simulations. The as-implanted Gd depth profiles were found to be broader than those simulated by SRIM, but the projected range coincided well with that simulated. After annealing at 800 °C, the depth profiles became narrower. The structural changes in the layers modified by ion implantation and subsequent annealing were characterised by RBS channelling. The annealing led to partial recrystallisation and a decrease in the number of Gd atoms situated in substitutional positions. Raman spectroscopy showed that the point defects in Zn and O vacancies had been created by implantation and that these defects are most effectively cured after annealing in oxygen atmosphere. AFM analysis was used to determine the surface-morphology changes after the implantation and annealing procedures. The as-implanted samples exhibited ferromagnetism persisting up to room temperature. The annealing procedure led to paramagnetic behaviour, probably caused by the formation of gadolinium clusters.

  11. 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.

  12. 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.

  13. 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…

  14. Structural Determinants of Publicly Subsidized Adult Education.

    ERIC Educational Resources Information Center

    Nordhaug, Odd

    1990-01-01

    Data on the amount of adult education activity were collected from 454 Norwegian municipalities. Variables were geographic centrality, population density, commuting status, educational resources, municipal finances, and municipal subsidies for adult education. Material and population structures had more effect on activity level than did economic…

  15. 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.

  16. The Structure of the Metal Transporter Tp34 and its Affinity for Divalent Metal Ions

    NASA Astrophysics Data System (ADS)

    Knutsen, Gregory; Deka, Ranjit; Brautigam, Chad; Tomchick, Diana; Machius, Mischa; Norgard, Michael

    2007-10-01

    Tp34 is periplasmic membrane protein of the nonculitvatable spirochete Treponema pallidum, the pathogen of syphillis. It was proposed that Tp34 is a divalent metal transporter, but the identity of the preferred metal ion(s) was unclear. In this study we investigated the ability of divalent metal ions to induce rTp34 dimerization using hydrodynamic techniques and determine the crystal structure of metal bound forms. Using analytical ultracentrifugation sedimentation velocity experiments, we determined that cobalt is superior to nickel at inducing the dimerization of rTp34. rTp34 was crystallized and selected crystals were incubated at a pH 7.5 with CuSO4 and NiSO4. Diffraction experiments were conducted and the processed electron density maps showed that copper was bound to the major metal binding site as well as to three additional minor binding sites. By contrast nickel was only bound to the major metal binding site in one monomer and to three additional minor sites. These results along with previous findings support evidence of Tp34 being involved with metal transport and/or iron utilization.

  17. 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.

  18. Determining Factor Structure in a Multidimensional Inventory.

    ERIC Educational Resources Information Center

    Deeter, Thomas E.; Gill, Diane L.

    A two-step procedure is described and used to revise a multidimensional inventory in its developmental stages. First, the latent factors influencing the observed variables on the inventory are determined and justified using the following five methods: Kaiser's criterion, root staring, examination of difference values, examination of root mean…

  19. Ion trap array mass analyzer: structure and performance.

    PubMed

    Li, Xiaoxu; Jiang, Gongyu; Luo, Chan; Xu, Fuxing; Wang, Yuanyuan; Ding, Li; Ding, Chuan-Fan

    2009-06-15

    An ion trap array (ITA) mass analyzer--a novel ion trap mass analyzer with multiple ion trapping and analyzing channels--was designed and constructed. Its property and performance were investigated and reported in this paper. The ITA was built with several planar electrodes including two parallel printed circuit board (PCB) plates. Each PCB plate was fabricated to several identical rectangular electric strips based on normal PCB fabrication technology and was placed symmetrically to those on the opposite plate. There is no electrode between any two adjacent strips. Every strip was supplied with an rf voltage while the polarity of the voltage applied to the adjacent two strips was opposite. So the electric potential at the central plane between two adjacent strips is zero. Multiple identical electric field regions that contain the dominant quadrupole plus some other high-order fields were produced between the two PCB plates. The multiple identical electric field regions will have the property of ion trapping, ion storage, and mass analysis functions. So an ITA could work as multiple ion trap mass analyzers. It could perform multiple sample ion storage, mass-selected ion isolation, ion ejection, and mass analysis simultaneously. The ITA was operated at both "digital ion trap mode" and "conventional rf mode" experimentally. A preliminary mass spectrum has been carried out in one of the ion trap channels, and it shows a mass resolution of over 1000. Additional functions such as mass-selected ion isolation and mass-selected ion ejection have also been tested. Furthermore, the ITA has a small size and very low cost. An ITA with four channels is less than 30 cm(3) in total volume, and it shows a great promise for the miniaturization of the whole mass spectrometer instrument and high-throughput mass analysis. PMID:19441854

  20. Some structural determinants of melody recall.

    PubMed

    Boltz, M

    1991-05-01

    Sophisticated musicians were asked to recall, using musical notation, a set of unfamiliar folk tunes that varied in rhythmic structure and referents of tonality. The results showed that memory was facilitated by tonic triad members marking phrase endings, but only when their presence was highlighted by a corresponding pattern of temporal accents. Conversely, recall significantly declined when tonal information was either absent or obscured by rhythmic structure. Error analyses further revealed that the retention of overall pitch contour and information at phrase ending points varied as a function of these manipulations. The results are discussed in terms of a framework that links the acts of perceiving and remembering to a common attentional scheme. PMID:1861610

  1. Structural features determining thermal adaptation of esterases.

    PubMed

    Kovacic, Filip; Mandrysch, Agathe; Poojari, Chetan; Strodel, Birgit; Jaeger, Karl-Erich

    2016-02-01

    The adaptation of microorganisms to extreme living temperatures requires the evolution of enzymes with a high catalytic efficiency under these conditions. Such extremophilic enzymes represent valuable tools to study the relationship between protein stability, dynamics and function. Nevertheless, the multiple effects of temperature on the structure and function of enzymes are still poorly understood at the molecular level. Our analysis of four homologous esterases isolated from bacteria living at temperatures ranging from 10°C to 70°C suggested an adaptation route for the modulation of protein thermal properties through the optimization of local flexibility at the protein surface. While the biochemical properties of the recombinant esterases are conserved, their thermal properties have evolved to resemble those of the respective bacterial habitats. Molecular dynamics simulations at temperatures around the optimal temperatures for enzyme catalysis revealed temperature-dependent flexibility of four surface-exposed loops. While the flexibility of some loops increased with raising the temperature and decreased with lowering the temperature, as expected for those loops contributing to the protein stability, other loops showed an increment of flexibility upon lowering and raising the temperature. Preserved flexibility in these regions seems to be important for proper enzyme function. The structural differences of these four loops, distant from the active site, are substantially larger than for the overall protein structure, indicating that amino acid exchanges within these loops occurred more frequently thereby allowing the bacteria to tune atomic interactions for different temperature requirements without interfering with the overall enzyme function. PMID:26647400

  2. Thermal structure of ions and electrons in Saturn's inner magnetosphere

    NASA Astrophysics Data System (ADS)

    Barbosa, D. D.

    1993-06-01

    A theoretical model of thermal ion and electron temperatures in Saturn's inner magnetospheres is presented which is based on a fast model of radial diffusive plasma transport. It is shown that the ion and electron temperatures and the latitudinal behavior of temperatures are consistent with the fast diffusion hypothesis, assuming that O(+) is the dominant ion and that its source is the Dione-Tethys plasma torus. The present results reinforce the conclusions of Barbosa (1990).

  3. Mass determination of megadalton-DNA Electrospray Ions usingCharge Detection Mass Spectrometry

    SciTech Connect

    Schultz, Jocelyn C.; Hack, Christopher; Benner, Henry W.

    1997-10-01

    Charge detection mass spectrometry (CD-MS) has been used to determine the mass of double-stranded, circular DNA and single-stranded, circular DNA in the range of 2500 to 8000 base pairs (1.5-5.0 MDa). Simultaneous measurement of the charge and velocity of an electrostatically accelerated ion allows a mass determination of the ion, with instrument calibration determined independently of samples. Positive ion mass spectra of electrosprayed commercial DNA samples supplied in tris(hydroxymethyl)ethylenediamine tetraacetic acid buffer, diluted in 50 vol. percent acetonitrile, were obtained without cleanup of the sample. ACD mass spectrum constructed from 3000 ion measurements takes 10 min to acquire and yields the DNA molecular mass directly (mass resolution = 6). The data collected represent progress toward a more automatable alternative to sizing of DNA by gel electrophoresis. In addition to the mass spectra, CD-MS generates charge versus mass plots, which provide another means to investigate the creation and fate of large electrospray ions.

  4. Dust-ion-acoustic solitary structure with opposite polarity ions and non-thermal electrons

    NASA Astrophysics Data System (ADS)

    Haider, M. M.

    2016-02-01

    The propagation of dust-ion-acoustic solitary waves in magnetized plasmas containing opposite polarity ions, opposite polarity dusts and non-thermal electrons has been studied. The fluid equations in the system are reduced to a Korteweg-de Vries equation in the limit of small amplitude perturbation. The effect of non-thermal electrons and the opposite polarity of ions and dusts in the solitary waves are presented graphically and numerically.

  5. Altitude distributions of upward flowing ion beams and solitary wave structures in the Viking data

    SciTech Connect

    Maelkki, A.; Lundin, R.

    1994-10-01

    The authors present a study of correlations between accelerated ion beam structures in the auroral zones, and the appearance of solitary waves, or weak double layers. The data is studied as a function of altitude in the stratosphere. They observe a clear correlation between the wave structures and the accelerated ion beams. They discuss several possible interpretations of this correlation.

  6. Magnetic Structure Determinations at NBS/NIST

    PubMed Central

    Lynn, J. W.; Borchers, J. A.; Huang, Q.; Santoro, A.; Erwin, R. W.

    2001-01-01

    Magnetic neutron scattering plays a central role in determining and understanding the microscopic properties of a vast variety of magnetic systems, from the fundamental nature, symmetry, and dynamics of magnetically ordered materials to elucidating the magnetic characteristics essential in technological applications. From the early days of neutron scattering measurements at NBS/NIST, magnetic diffraction studies have been a central theme involving many universities, industrial and government labs from around the United States and worldwide. Such measurements have been used to determine the spatial arrangement and directions of the atomic magnetic moments, the atomic magnetization density of the individual atoms in the material, and the value of the ordered moments as a function of thermodynamic parameters such as temperature, pressure, and applied magnetic field. These types of measurements have been carried out on single crystals, powders, thin films, and artificially grown multilayers, and often the information collected can be obtained by no other experimental technique. This article presents, in an historical perspective, a few examples of work carried out at the NIST Center for Neutron Research (NCNR), and discusses the key role that the Center can expect to play in future magnetism research.

  7. Cross-section scaling for track structure simulations of low-energy ions in liquid water.

    PubMed

    Schmitt, E; Friedland, W; Kundrát, P; Dingfelder, M; Ottolenghi, A

    2015-09-01

    Radiation damage by low-energy ions significantly contributes to the high biological efficiency of ion beams in distal Bragg peak regions as well as to the energy-dependent efficiency of neutron irradiation. To enable assessing biological effects of ions at energies <1 MeV u(-1) with track-structure based models, a Barkas-like scaling procedure is developed that provides ion cross sections in liquid water based on those for hydrogen ions. The resulting stopping power and range for carbon ions agree with the ICRU 73 database and other low-energy stopping power data. The method represents the basis for extending PARTRAC simulations of light ion track structures and biological effects down to the keV u(-1) range. PMID:25969528

  8. 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.

  9. Non-destructive Inspection of Chloride Ion in Concrete Structures Using Attenuated Total Reflection of Millimeter Waves

    NASA Astrophysics Data System (ADS)

    Tripathi, Saroj R.; Inoue, Hiroo; Hasegawa, Tsuyoshi; Kawase, Kodo

    2013-02-01

    The chloride induced corrosion of reinforcing steel bar is one of the major causes of deterioration of concrete structures. Therefore, it is essential to periodically monitor the level of chloride ion (Cl-) concentration in concrete structures. In this work, we developed millimeter wave attenuated total reflection measurement setup in order to determine the Cl- concentration in concrete structures. We prepared concrete samples with different compositions and varying Cl- concentrations and we measured their attenuated total reflectance at 65 GHz. We observed that the reflectance decreases almost linearly with the increase in Cl- concentration indicating that this technique could be used to inspect the Cl- concentration in concrete structures nondestructively.

  10. 700 keV Ni+2 ions induced modification in structural, surface, magneto-optic and optical properties of ZnO thin films

    NASA Astrophysics Data System (ADS)

    Fiaz Khan, M.; Siraj, K.; Anwar, M. S.; Irshad, M.; Hussain, J.; Faiz, H.; Majeed, S.; Dosmailov, M.; Patek, J.; Pedarnig, J. D.; Rafique, M. S.; Naseem, S.

    2016-02-01

    We investigate the effect of 700 keV Ni+2 ions irradiation at different ion fluences (1 × 1013, 1 × 1014, 2 × 1014, 5 × 1014 ions/cm2) on the structural, surface, magneto-optic and optical properties of ZnO thin films. The X-ray diffraction (XRD) results show improved crystallinity when ion fluence is increased to 2 × 1014 ions/cm2, while deterioration is observed at the highest ion fluence of 5 × 1014 ions/cm2. Scanning electron micrographs (SEM) show the formation of small grains at ion fluence 1 × 1013 ions/cm2, micro-rods at fluences 1 × 1014 and 2 × 1014 ions/cm2 and ultimate fracturing of thin film surface at ion fluence 5 × 1014 ions/cm2. Faraday rotation measurements are also performed and show a decrease in Verdet constant from 53 to 31 rad/(T-m) when irradiated at 1 × 1013 ions/cm2, increasing up to 45 rad/(T-m) at 2 × 1014 ions/cm2, and then decreasing again to 36 rad/(T-m) at 5 × 1014 ions/cm2. The optical band gap energy of the films is determined using spectroscopic ellipsometry, which shows an increase in optical band gap energy (Eg) from 3.04 eV to 3.19 eV when the fluence increases to 2 × 1014 ions/cm2 and a decrease to 3 eV at fluence 5 × 1014 ions/cm2. We argue that these properties can be explained using ion heating effect of thin films.

  11. 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.

  12. Determining 3-D motion and structure from image sequences

    NASA Technical Reports Server (NTRS)

    Huang, T. S.

    1982-01-01

    A method of determining three-dimensional motion and structure from two image frames is presented. The method requires eight point correspondences between the two frames, from which motion and structure parameters are determined by solving a set of eight linear equations and a singular value decomposition of a 3x3 matrix. It is shown that the solution thus obtained is unique.

  13. 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. PMID:27208947

  14. Stable compositions and geometrical structures of titanium oxide cluster cations and anions studied by ion mobility mass spectrometry

    NASA Astrophysics Data System (ADS)

    Ohshimo, Keijiro; Norimasa, Naoya; Moriyama, Ryoichi; Misaizu, Fuminori

    2016-05-01

    Geometrical structures of titanium oxide cluster cations and anions have been investigated by ion mobility mass spectrometry and quantum chemical calculations based on density functional theory. Stable cluster compositions with respect to collision induced dissociation were also determined by changing ion injection energy to an ion drift cell for mobility measurements. The TinO2n-1+ cations and TinO2n- anions were predominantly observed at high injection energies, in addition to TinO2n+ for cations and TinO2n+1- for anions. Collision cross sections of TinO2n+ and TinO2n+1- for n = 1-7, determined by ion mobility mass spectrometry, were compared with those obtained theoretically as orientation-averaged cross sections for the optimized structures by quantum chemical calculations. All of the geometrical structures thus assigned have three-dimensional structures, which are in marked contrast with other oxides of late transition metals. One-oxygen atom dissociation processes from TinO2n+ and TinO2n+1- by collisions were also explained by analysis of spin density distributions.

  15. Method to Determine Oxalate in High-Level Sludge by Ion Chromatography

    SciTech Connect

    Coleman, C.J.

    2002-12-19

    The Sludge Batch 3 macrobatch feed to the DWPF is expected to contain a relatively high concentration of oxalate. A simple acid addition at room temperature has been shown to be in high-level sludge. This sample preparation requires only about five minutes and yields solutions suitable for oxalate determinations by ion chromatography.

  16. 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)

  17. 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)

  18. Novel determination of phytate by ion chromatography in wild rice and diet composites

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have developed an ion chromatography (IC) assay using ultraviolet (UV) detection following post-column derivatization with ferric nitrate to determine phytate [inositol hexakis phosphate (iP6)] (1) (2) in wild rice samples and other diet composites. Samples were ground to a fine homogeneous powd...

  19. 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.

  20. 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

  1. 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.

  2. High-resolution structural study of zinc ion incorporation at the calcite cleavage surface.

    SciTech Connect

    Cheng, L.; Sturchio, N. C.; Woicik, J. C.; Kemner, K. M.; Lyman, P. F.; Bedzyk, M. J.; Northwestern Univ.; NIST

    1998-09-30

    The atomic-scale structure of Zn{sup 2+} incorporated at the CaCO{sub 3} (10{ovr 1}4) surface by adsorption from solution was determined by X-ray standing wave triangulation and surface extended X-ray absorption fine structure spectroscopy. At low coverage (approximately 0.1 ML), Zn{sup 2+} substitutes for Ca{sup 2+} in the surface layer. Structural relaxation of the adjacent in-plane CO{sup 2-}{sub 3} ions in the host surface is shown by the reduced nearest-neighbor distance of Zn-O relative to Ca-O. Relaxation of the Zn{sup 2+} ion in the out-of-plane direction is shown by the displacement of its lattice position from the ideal Ca{sup 2+} position. These relaxations, resulting in a local lattice buckling feature at the Zn{sup 2+} adsorption site, can be fully explained as the combined effect of the electrostatic relaxation of the nearest-neighbor anions in response to the smaller size of Zn{sup 2+}, and the bonding asymmetry due to surface truncation.

  3. 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

  4. 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.

  5. 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. PMID:27401040

  6. 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. PMID:26083928

  7. 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

  8. Structure of catalase determined by MicroED.

    PubMed

    Nannenga, Brent L; Shi, Dan; Hattne, Johan; Reyes, Francis E; Gonen, Tamir

    2014-01-01

    MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination. PMID:25303172

  9. 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. PMID:25281093

  10. Structural Characterization of Unsaturated Phosphatidylcholines Using Traveling Wave Ion Mobility Spectrometry

    PubMed Central

    Kim, Hugh I.; Kim, Hyungjun; Pang, Eric S.; Ryu, Ernest K.; Beegle, Luther W.; Loo, Joseph A.; Goddard, William A.; Kanik, Isik

    2009-01-01

    A number of phosphatidylcholine (PC) cations spanning a mass range of 400 to 1000 Da are investigated using electrospray ionization mass spectrometry coupled with traveling wave ion mobility spectrometry (TWIMS). A high correlation between mass and mobility is demonstrated with saturated phosphatidylcholine cations in N2. A significant deviation from this mass-mobility correlation line is observed for the unsaturated PC cation. We found that the double bond in the acyl chain causes a 5% reduction in drift time. The drift time is reduced at a rate of ~1% for each additional double bond. Theoretical collision cross sections of PC cations exhibit good agreement with experimentally evaluated values. Collision cross sections are determined using the recently derived relationship between mobility and drift time in TWIMS stacked ring ion guide (SRIG) and compared to estimate collision cross-sections using empiric calibration method. Computational analysis was performed using the modified trajectory (TJ) method with nonspherical N2 molecules as the drift gas. The difference between estimated collision cross-sections and theoretical collision cross-sections of PC cations is related to the sensitivity of the PC cation collision cross-sections to the details of the ion-neutral interactions. The origin of the observed correlation and deviation between mass and mobility of PC cations is discussed in terms of the structural rigidity of these molecules using molecular dynamic simulations. PMID:19764704

  11. The measurement results of carbon ion beam structure extracted by bent crystal from U-70 accelerator

    NASA Astrophysics Data System (ADS)

    Afonin, A. G.; Barnov, E. V.; Britvich, G. I.; Chesnokov, Yu A.; Chirkov, P. N.; Durum, A. A.; Kostin, M. Yu; Maisheev, V. A.; Pitalev, V. I.; Reshetnikov, S. F.; Yanovich, A. A.; Nazhmudinov, R. M.; Kubankin, A. S.; Shchagin, A. V.

    2016-07-01

    The carbon ion +6C beam with energy 25 GeV/nucleon was extracted by bent crystal from the U-70 ring. The bent angle of silicon crystal was 85 mrad. About 2×105 particles for 109 circulated ions in the ring were observed in beam line 4a after bent crystal. Geometrical parameters, time structure and ion beam structure were measured. The ability of the bent monocrystal to extract and generate ion beam with necessary parameters for regular usage in physical experiments is shown in the first time.

  12. Controlled deposition of sulphur-containing semiconductor and dielectric nano-structured films on metals in SF6 ion-ion plasma

    NASA Astrophysics Data System (ADS)

    Rafalskyi, Dmytro; Bredin, Jérôme; Aanesland, Ane

    2013-12-01

    In the present paper, the deposition processes and formation of films in SF6 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 SF6 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 SF6 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.

  13. Determination of Ammonium Ion Using a Reagentless Amperometric Biosensor Based on Immobilized Alanine Dehydrogenase

    PubMed Central

    Tan, Ling Ling; Musa, Ahmad; Lee, Yook Heng

    2011-01-01

    The use of the enzyme alanine dehydrogenase (AlaDH) for the determination of ammonium ion (NH4+) usually requires the addition of pyruvate substrate and reduced nicotinamide adenine dinucleotide (NADH) simultaneously to effect the reaction. This addition of reagents is inconvenient when an enzyme biosensor based on AlaDH is used. To resolve the problem, a novel reagentless amperometric biosensor using a stacked methacrylic membrane system coated onto a screen-printed carbon paste electrode (SPE) for NH4+ ion determination is described. A mixture of pyruvate and NADH was immobilized in low molecular weight poly(2-hydroxyethyl methacrylate) (pHEMA) membrane, which was then deposited over a photocured pHEMA membrane (photoHEMA) containing alanine dehydrogenase (AlaDH) enzyme. Due to the enzymatic reaction of AlaDH and the pyruvate substrate, NH4+ was consumed in the process and thus the signal from the electrocatalytic oxidation of NADH at an applied potential of +0.55 V was proportional to the NH4+ ion concentration under optimal conditions. The stacked methacrylate membranes responded rapidly and linearly to changes in NH4+ ion concentrations between 10–100 mM, with a detection limit of 0.18 mM NH4+ ion. The reproducibility of the amperometrical NH4+ biosensor yielded low relative standard deviations between 1.4–4.9%. The stacked membrane biosensor has been successfully applied to the determination of NH4+ ion in spiked river water samples without pretreatment. A good correlation was found between the analytical results for NH4+ obtained from the biosensor and the Nessler spectrophotometric method. PMID:22163699

  14. Perveance and ion bunch structure from a 'compact, high-pressure' laser ion source

    SciTech Connect

    Yeates, P.; Costello, J. T.; Kennedy, E. T.

    2010-12-15

    The Dublin City University (DCU) laser ion source (LIS) is a 'compact high-pressure' laser ion source utilizing a table top Q-switched laser. The DCU-LIS combines high laser fluence (F>4 kJ cm{sup -2}), high laser intensity (I>10{sup 11} W cm{sup -2}) with a short field free region (L=48 mm) and high source potential (V{sub ext}>40 kV) in order to offset recombination losses within the plasma and maximize the proportion of highly charged ions which are extracted from the plasma plume. Such a configuration also provides high peak currents (I{sub p}>3 mA), high current densities (J>5 mA cm{sup -2}), and high charge states (Cu{sup 6+}) in the extracted ion-bunch train. However, to obtain and utilize these parameter values in a high pressure LIS requires characterization and control of a number of processes related to ion dynamics and space charge effects on the extracted ions at the plasma plume-anode-extraction gap interface. Relevant issues include electric field distortion, Debye shielding, beam divergence, overfocusing, and perveance (P) in addition to current density profiles for the extracted ion beam. In this paper we focus on these issues and their impact on charge particle extraction and acceleration with a view to elucidating the parameter regimes within which the DCU-LIS performance envelope is optimal.

  15. 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.

  16. Auroral ion acceleration from lower hybrid solitary structures: A summary of sounding rocket observations

    NASA Astrophysics Data System (ADS)

    Lynch, K. A.; Arnoldy, R. L.; Kintner, P. M.; Schuck, P.; Bonnell, J. W.; Coffey, V.

    In this paper we present a review of sounding rocket observations of the ion acceleration seen in nightside auroral zone lower hybrid solitary structures. Observations from Topaz3, Amicist, and Phaze2 are presented on various spatial scales, including the two-point measurements of the Amicist mission. From this collection of observations we will demonstrate the following characteristics of transverse acceleration of ions (TAI) in lower hybrid solitary structures (LHSS). The ion acceleration process is narrowly confined to 90° pitch angle, in spatially confined regions of up to a few hundred meters across B. The acceleration process does not affect the thermal core of the ambient distribution and does not directly create a measurable effect on the ambient ion population outside the LHSS themselves. This precludes observation with these data of any nonlinear feedback between the ion acceleration and the existence or evolution of the density irregularities on which these LHSS events grow. Within the LHSS region the acceleration process creates a high-energy tail beginning at a few times the thermal ion speed. The ion acceleration events are closely associated with localized wave events. Accelerated ions bursts are also seen without a concurrent observation of a localized wave event, for two possible reasons. In some cases, the pitch angles of the accelerated tail ions are elevated above perpendicular; that is, the acceleration occurred below the observer and the mirror force has begun to act upon the distribution, moving it upward from the source. In other cases, the accelerated ion structure is spatially larger than the wave event structure, and the observation catches only the ion event. The occurrence rate of these ion acceleration events is related to the ambient environment in two ways: its altitude dependence can be modeled with the parameter B2/ne, and it is highest in regions of intense VLF activity. The cumulative ion outflow from these LHSS TAI is

  17. 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

  18. 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

  19. 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. PMID:26948763

  20. 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.

  1. 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.

  2. MOTOR: model assisted software for NMR structure determination.

    PubMed

    Schieborr, Ulrich; Sreeramulu, Sridhar; Elshorst, Bettina; Maurer, Marcus; Saxena, Krishna; Stehle, Tanja; Kudlinzki, Denis; Gande, Santosh Lakshmi; Schwalbe, Harald

    2013-11-01

    Eukaryotic proteins with important biological function can be partially unstructured, conformational flexible, or heterogenic. Crystallization trials often fail for such proteins. In NMR spectroscopy, parts of the polypeptide chain undergoing dynamics in unfavorable time regimes cannot be observed. De novo NMR structure determination is seriously hampered when missing signals lead to an incomplete chemical shift assignment resulting in an information content of the NOE data insufficient to determine the structure ab initio. We developed a new protein structure determination strategy for such cases based on a novel NOE assignment strategy utilizing a number of model structures but no explicit reference structure as it is used for bootstrapping like algorithms. The software distinguishes in detail between consistent and mutually exclusive pairs of possible NOE assignments on the basis of different precision levels of measured chemical shifts searching for a set of maximum number of consistent NOE assignments in agreement with 3D space. Validation of the method using the structure of the low molecular-weight-protein tyrosine phosphatase A (MptpA) showed robust results utilizing protein structures with 30-45% sequence identity and 70% of the chemical shift assignments. About 60% of the resonance assignments are sufficient to identify those structural models with highest conformational similarity to the real structure. The software was benchmarked by de novo solution structures of fibroblast growth factor 21 (FGF21) and the extracellular fibroblast growth factor receptor domain FGFR4 D2, which both failed in crystallization trials and in classical NMR structure determination. PMID:23852655

  3. 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.

  4. 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. PMID:26085413

  5. Nonlinear structure of ion-acoustic waves in completely degenerate electron-positron and ion plasma

    SciTech Connect

    Rasheed, A.; Tsintsadze, N. L.; Murtaza, G.

    2010-07-15

    A rigorous theoretical investigation has been made of fully nonlinear ion-acoustic waves in nonrelativistic and ultrarelativistic, collisionless, unmagnetized plasma containing of degenerate electrons and positrons, and classical cold ions. In both (nonrelativistic and ultrarelativistic) regimes the electrons and positrons are assumed to follow the corresponding Fermi distribution while the ions are described by the hydrodynamic equations. An energy balancelike equation involving a Sagdeev-type pseudopotential is derived separately for both the regimes. In addition, stationary periodic and solitary waves are also investigated for the two cases. The present work would be helpful to understand the excitation of nonlinear ion-acoustic waves in a degenerate plasma such as in superdense white dwarfs.

  6. 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.

  7. 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.

  8. 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.

  9. Dynamics of High Energy Ions at a Structured Collisionless Shock Front

    NASA Astrophysics Data System (ADS)

    Gedalin, M.; Dröge, W.; Kartavykh, Y. Y.

    2016-07-01

    Ions undergoing first-order Fermi acceleration at a shock are scattered in the upstream and downstream regions by magnetic inhomogeneities. For high energy ions this scattering is efficient at spatial scales substantially larger than the gyroradius of the ions. The transition from one diffusive region to the other occurs via crossing the shock, and the ion dynamics during this crossing is mainly affected by the global magnetic field change between the upstream and downstream region. We study the effects of the fine structure of the shock front, such as the foot-ramp-overshoot profile and the phase-standing upstream and downstream magnetic oscillations. We also consider time dependent features, including reformation and large amplitude coherent waves. We show that the influence of the spatial and temporal structure of the shock front on the dependence of the transition and reflection on the pitch angle of the ions is already weak at ion speeds five times the speed of the upstream flow.

  10. Xenon-ion Induced Magnetic and Structural Modifications of Ferromagnetic Alloys

    NASA Astrophysics Data System (ADS)

    Gupta, Ratnesh; Lieb, K. P.; Müller, G. A.; Schaaf, P.; Zhang, K.

    2005-01-01

    Thin polycrystalline films of permalloy (Ni79Fe21) and permendur (Co50Fe50) have been irradiated with Xe-ions to fluences of 1014 1016 ions/cm2. Ion-induced structural and magnetic modifications have been measured by grazing angle X-ray diffraction, Rutherford backscattering and magneto-optical Kerr effect. In the case of permendur, the Xe-ion implantation first reduced the coercivity, because of stress relaxation, while higher ion fluences increased the coercivity due to pinning centers generated in the film. The ion irradiation aligned the in-plane easy axis of the magnetization along the direction of the external magnetic field during implantation. Phase shifts obtained from magnetic force microscopy confirmed these modifications. The effects of Xe-ion irradiation in permalloy films are much weaker and underline the importance of magnetostriction in the variation of the coercivity and anisotropy.

  11. 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.

  12. Determining the static dielectric permittivity of ion conducting materials when obscured by electrode polarization

    NASA Astrophysics Data System (ADS)

    Grâsjö, Johan; Welch, Ken; Strømme, Maria

    2008-09-01

    A method is derived for the determination of the static dielectric permittivity of ion conducting materials when this parameter is obscured by electrode polarization in as-recorded low frequency dielectric spectra. The method requires permittivity measurements at two different electrode separations, and is applicable when the electric fields created by charge separation near the electrode surfaces do not induce nonlinear effects in the frequency region where electrode polarization begins to affect the dielectric response. The performance of the method is illustrated by the analysis of an ion conducting cellulose gel biosynthesized by the Acetobacter. xylinum bacterium. The method opens up possibilities to obtain more detailed information about dynamic processes in ion conducting materials from dielectric spectroscopy.

  13. Target Selection and Determination of Function in Structural Genomics

    PubMed Central

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

    2011-01-01

    Summary 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. PMID:12880206

  14. Acceleration of ions to suprathermal energies by turbulence in the plasmoid-like magnetic structures

    NASA Astrophysics Data System (ADS)

    Grigorenko, E. E.; Malykhin, A. Yu.; Kronberg, E. A.; Malova, Kh. V.; Daly, P. W.

    2015-08-01

    We study energetic spectra of H+, He+, and O+ ion fluxes in the energy range ≥130 keV measured by Cluster/Research with Adaptive Particle Imaging Detectors (RAPID) instruments during 37 intervals of the tailward bulk flow propagation in the near-Earth tail (at X ≤ -19 RE). In all events from our database, the plasmoid-like magnetic structures with the superimposed low-frequency magnetic and electric field fluctuations were observed along with the tailward bulk flows. The plasmoid-like structures were associated with the enhancements of energetic ion fluxes and the hardening of energy spectra of H+ and He+ ion components in 80% of events and of O+ ion component in 64% of events. The hardening of energy spectra was more pronounced for heavy ions than for protons. The analysis of the magnetic structures and power spectral density (PSD) of the magnetic and electric field fluctuations from our database revealed the following factors favorable for the ion energization: (1) the spatial scale of a plasmoid should exceed the thermal gyroradius of a given ion component in the neutral plane inside the plasmoid; (2) the PSD of the magnetic fluctuations near the gyrofrequency of a particular ion component should exceed ~ 50.0 nT2/Hz for oxygen ions; while the energization of helium ions and protons takes place for much lower values of the PSD. The kinetic analysis of ion dynamics in the plasmoid-like magnetic configuration similar to the observed one with the superimposed turbulence confirms the importance of ion resonant interactions with the low-frequency electromagnetic fluctuations for ion energization inside plasmoids.

  15. The structure of ions and zwitterionic lipids regulates the charge of dipolar membranes.

    PubMed

    Szekely, Or; Steiner, Ariel; Szekely, Pablo; Amit, Einav; Asor, Roi; Tamburu, Carmen; Raviv, Uri

    2011-06-21

    In pure water, zwitterionic lipids form lamellar phases with an equilibrium water gap on the order of 2 to 3 nm as a result of the dominating van der Waals attraction between dipolar bilayers. Monovalent ions can swell those neutral lamellae by a small amount. Divalent ions can adsorb onto dipolar membranes and charge them. Using solution X-ray scattering, we studied how the structure of ions and zwitterionic lipids regulates the charge of dipolar membranes. We found that unlike monovalent ions that weakly interact with all of the examined dipolar membranes, divalent and trivalent ions adsorb onto membranes containing lipids with saturated tails, with an association constant on the order of ∼10 M(-1). One double bond in the lipid tail is sufficient to prevent divalent ion adsorption. We suggest that this behavior is due to the relatively loose packing of lipids with unsaturated tails that increases the area per lipid headgroup, enabling their free rotation. Divalent ion adsorption links two lipids and limits their free rotation. The ion-dipole interaction gained by the adsorption of the ions onto unsaturated membranes is insufficient to compensate for the loss of headgroup free-rotational entropy. The ion-dipole interaction is stronger for cations with a higher valence. Nevertheless, polyamines behave as monovalent ions near dipolar interfaces in the sense that they interact weakly with the membrane surface, whereas in the bulk their behavior is similar to that of multivalent cations. Advanced data analysis and comparison with theory provide insight into the structure and interactions between ion-induced regulated charged interfaces. This study models biologically relevant interactions between cell membranes and various ions and the manner in which the lipid structure governs those interactions. The ability to monitor these interactions creates a tool for probing systems that are more complex and forms the basis for controlling the interactions between dipolar

  16. Photonic guiding structures in lithium niobate crystals produced by energetic ion beams

    NASA Astrophysics Data System (ADS)

    Chen, Feng

    2009-10-01

    A range of ion beam techniques have been used to fabricate a variety of photonic guiding structures in the well-known lithium niobate (LiNbO3 or LN) crystals that are of great importance in integrated photonics/optics. This paper reviews the up-to-date research progress of ion-beam-processed LiNbO3 photonic structures and reports on their fabrication, characterization, and applications. Ion beams are being used with this material in a wide range of techniques, as exemplified by the following examples. Ion beam milling/etching can remove the selected surface regions of LiNbO3 crystals via the sputtering effects. Ion implantation and swift ion irradiation can form optical waveguide structures by modifying the surface refractive indices of the LiNbO3 wafers. Crystal ion slicing has been used to obtain bulk-quality LiNbO3 single-crystalline thin films or membranes by exfoliating the implanted layer from the original substrate. Focused ion beams can either generate small structures of micron or submicron dimensions, to realize photonic bandgap crystals in LiNbO3, or directly write surface waveguides or other guiding devices in the crystal. Ion beam-enhanced etching has been extensively applied for micro- or nanostructuring of LiNbO3 surfaces. Methods developed to fabricate a range of photonic guiding structures in LiNbO3 are introduced. Modifications of LiNbO3 through the use of various energetic ion beams, including changes in refractive index and properties related to the photonic guiding structures as well as to the materials (i.e., electro-optic, nonlinear optic, luminescent, and photorefractive features), are overviewed in detail. The application of these LiNbO3 photonic guiding structures in both micro- and nanophotonics are briefly summarized.

  17. Electrospray liquid chromatography quadrupole ion trap mass spectrometry determination of phenyl urea herbicides in water.

    PubMed

    Draper, W M

    2001-06-01

    Phenyl urea herbicides were determined in water by electrospray quadrupole ion trap liquid chromatography-mass spectrometry (ES-QIT-LC-MS). Over a wide concentration range [M - H](-) and MH(+) ions were prominent in ES spectra. At high concentrations dimer and trimer ions appeared, and sodium, potassium, and ammonium adducts also were observed. In the case of isopturon, source collision-induced dissociation (CID) fragmentation with low offset voltages increased the ion current associated with MH(+) and diminished dimer and trimer ion abundance. In the mass analyzer CID involved common pathways, for example, daughter ions of [M - H](-) resulted from loss of R(2)NH in N',N'-dialkyl ureas or loss of C(3)H(5)NO(2) (87 amu) in N'-methoxy ureas. A 2 mm (i.d.) x 15 cm C(18) reversed phase column was used for LC-MS with a linear methanol/water gradient and 0.5 mL/min flow rate. Between 1 and 100 pg/microg/L the response was highly linear with instrument detection limits ranging from <10 to 50 pg injected. Whereas the positive ES signal intensity was greater for each of the compounds except fluometuron, negative ion monitoring gave the highest signal-to-noise ratio. Analysis of spiked Colorado River water, a source high in total dissolved solids and total organic carbon, demonstrated that ES-QIT-LC-MS was routinely capable of quantitative analysis at low nanogram per liter concentrations in conjunction with a published C(18) SPE method. Under these conditions experimental method detection limits were between 8.0 and 36 ng/L, and accuracy for measurements in the 20-50 parts per trillion range was from 77 to 96%. Recoveries were slightly lower in surface water (e.g., 39-76%), possibly due to suppression of ionization. PMID:11409961

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. "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.

  3. Heavy-ion effects: from track structure to DNA and chromosome damage

    NASA Astrophysics Data System (ADS)

    Ballarini, F.; Alloni, D.; Facoetti, A.; Ottolenghi, A.

    2008-07-01

    The use of carbon ions for the treatment of certain tumour types, especially radioresistant tumours, is becoming more frequent due to the carbon-ion dose localization and high relative biological effectiveness (RBE) in the Bragg peak region. Human beings can also be exposed to heavy ions in space, since galactic cosmic rays are a mixed field consisting of not only high-energy protons and He ions, but also heavier ions including iron. Due to their high linear energy transfer (LET), heavy ions have peculiar track structures, characterized by a high level of energy deposition clustering. Furthermore, high-energy ions produce energetic secondary electrons ('delta rays') which can give rise to energy depositions several micrometres away from the core of the primary particle track. Also in view of hadron therapy and space radiation applications, it is therefore important to characterize heavy-ion tracks from a physical and biophysical point of view. In this framework, herein we will discuss the main physical features of heavy-ion track structure, as well as heavy-ion-induced DNA double-strand breaks, which are regarded as one of the most important initial radiobiological lesions and chromosome aberrations, which are correlated both with cell death and with cell conversion to malignancy.

  4. Cryo-EM Structure Determination Using Segmented Helical Image Reconstruction.

    PubMed

    Fromm, S A; Sachse, C

    2016-01-01

    Treating helices as single-particle-like segments followed by helical image reconstruction has become the method of choice for high-resolution structure determination of well-ordered helical viruses as well as flexible filaments. In this review, we will illustrate how the combination of latest hardware developments with optimized image processing routines have led to a series of near-atomic resolution structures of helical assemblies. Originally, the treatment of helices as a sequence of segments followed by Fourier-Bessel reconstruction revealed the potential to determine near-atomic resolution structures from helical specimens. In the meantime, real-space image processing of helices in a stack of single particles was developed and enabled the structure determination of specimens that resisted classical Fourier helical reconstruction and also facilitated high-resolution structure determination. Despite the progress in real-space analysis, the combination of Fourier and real-space processing is still commonly used to better estimate the symmetry parameters as the imposition of the correct helical symmetry is essential for high-resolution structure determination. Recent hardware advancement by the introduction of direct electron detectors has significantly enhanced the image quality and together with improved image processing procedures has made segmented helical reconstruction a very productive cryo-EM structure determination method. PMID:27572732

  5. [Determination of alditols in foods by ion chromatography-mass spectrometry].

    PubMed

    Zhou, Hongbin; Xiong, Zhiyu; Li, Ping; Li, Jing; Sun, Li; Zhao, Yunxia

    2013-11-01

    A method for the determination of alditols in foods by ion chromatography-mass spectrometry (IC-MS) has been developed. The samples were extracted and cleaned up with the solid phase extraction (SPE). Then, the ion chromatographic separation was performed on a CarboPar MA1 column. The alditols were determined by MS with the selected ion monitoring (SIM) mode and quantified by the external standard method. The calibration curves showed good linearity in the certain ranges with the correlation coefficients (R2) greater than 0.99. The limits of quantification (S/N = 10) of erythritol, xylitol, D-sorbitol, D-mannitol, lactitol, maltitol were 0.98, 1.99, 2.24, 5.92, 13.56, 13.21 mg/kg and the limits of detection (S/N = 3) were 0.28, 0.59, 0.71, 1.74, 4.14, 4.03 mg/kg, respectively. The spiked recoveries of the alditols in the foods at different levels were in the range of 82.5%-108.0% with the relative standard deviations (RSDs) of 1.5%-7.6%. The sensitivity, accuracy and precision of the method meet the technical standards of the determination. The method can be applied to the determination of alditols in foods. PMID:24558846

  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. 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 ...

  8. 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. PMID:9372416

  9. Solid phase extraction and determination of sub-ppb levels of hazardous Hg2+ ions.

    PubMed

    Shamsipur, Mojtaba; Shokrollahi, Ardeshir; Sharghi, Hashem; Eskandari, Mohammad Mehdi

    2005-01-31

    A simple, rapid and reliable method has been developed to selectively separate and concentrate ultra trace amounts of mercury(II) ions from aqueous samples for its highly sensitive measurement by cold vapor atomic absorption spectrometry (CV-AAS). The Hg(2+) ions were adsorbed selectively and quantitatively during the passage of aqueous samples through octadecyl silica membrane disks modified by isopropyl 2-[(isopropoxycarbothiolyl)disulfanyl]ethane thioate (IIDE). The retained Hg(2+) ions were then stripped from the disk with minimal amounts of 0.5 M hydrobromic acid (two 8 ml portions) as eluent, and determined by CV-AAS. The break-through volume of the method is greater than 3000 ml, which results in enrichment factors >150. Maximum capacity of the membrane disks modified with 10mg of the ligand was found to be 350+/-30 microg of mercury(II), and the limit of detection is 0.005 ng ml(-1). The effect of various cationic interferences on the recovery of mercury in binary mixtures was studied. The method was applied to the recovery of Hg(2+) ions from different synthetic and tap water samples, as well as the determination of mercury in human hair samples. PMID:15629571

  10. Trace element siting in iron sulfides from coal determined by secondary ion mass spectrometry

    SciTech Connect

    Wiese, R.G. Jr. ); Muir, I.J.; Fyfe, W.S. )

    1990-01-01

    Intact samples of coal have been analyzed by SIMS (secondary ion mass spectrometry) ion imaging and ion probe techniques for determination of the distribution of trace elements in pyrite and marcasite and in the associated clay minerals. Ion mapping of site-specific concentrations of trace elements is important as one considers the environmental consequences of not only the combustion of coal, but also the disposal of coal-washing plant refuse and the placement of mine spoils during reclamation. Iron sulfides and clays are both involved in the oxidation-hydration reactions that result in the formation of acid waters and the release of trace elements into the ecosystem. Iron sulfides from selected Ohio coals contain site-specific concentrations of Mn, Co, Ni, Cu, As, and Pb. Clay minerals found within and marginal to the sulfides contain V, Cr, and also As and Co. The distribution of trace elements in the sulfides and associated clays clearly is related to microenvironments that existed during the formation of successive parts of the sulfide grains. The sulfide-clay relationships determine the extent to which the sulfides break down in oxidation-hydration reactions.

  11. 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. PMID:24433896

  12. 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

  13. Discovery and structure determination of the orphan enzyme isoxanthopterin deaminase .

    PubMed

    Hall, Richard S; Agarwal, Rakhi; Hitchcock, Daniel; Sauder, J Michael; Burley, Stephen K; Swaminathan, Subramanyam; Raushel, Frank 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 A resolution (Protein Data Bank entry 2PAJ ). This protein folds as a distorted (beta/alpha)(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(-1), 8.0 muM, and 1.3 x 10(5) M(-1) s(-1) (k(cat), K(m), and k(cat)/K(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 residues were used to identify 24 other genes

  14. 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

    2015-03-05

    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 charactization 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 ~ -75C that barely increases with ion content, as anticipated by DFT. A survey of all polyanions in the literature suggests that Tg < -80C is needed to achieve the 10-4 S/cm conductivity needed for battery separators.

  15. Trace mercury ion determination based on the highly selective redox reaction between stannous ion and mercury ion enhanced by gold nanoparticles

    NASA Astrophysics Data System (ADS)

    Zhang, Pingping; Chen, Shu; Kang, Yangfang; Long, Yunfei

    2012-12-01

    A novel resonance light scattering (RLS) spectrometric method for mercury ions (Hg2+) determination has been established in this article. Mercury (Hg) nanoparticle formed from the highly selective redox reaction between citrate-stabilized stannous ions (Sn2+) and Hg2+. As a result, the RLS intensities of the system can be enhanced and it can be sensitized in the presence of very little amount of gold nanoparticles (AuNPs). According to this phenomenon, trace Hg2+ in real water sample has been determined directly by RLS spectrometry. It has been found that the enhanced RLS intensities (ΔIRLS) characterized at 395 nm are proportional to the concentration of Hg2+ in the range of 0.1-30 μmol L-1 with a detection limit (3σ) of 0.051 μmol L-1. The method described herein has good sensitivity, selectivity, and without complicated sample pretreatment. Moreover, the feasibility for the analysis of Hg2+ in a wastewater sample was identified with a good recovery (100.2-106.3%).

  16. 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

  17. 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

    2013-03-01

    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 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. PMID:23330948

  18. Stability and structure of cluster ions: Halide ions with CO2

    NASA Astrophysics Data System (ADS)

    Hiraoka, Kenzo; Mizuse, Susumu; Yamabe, Shinichi

    1987-09-01

    Thermodynamic data, ΔH0n-1,n and ΔS0n-1,n, for clustering reactions of halide ions with CO2 were measured with a pulsed electron-beam high-pressure mass spectrometer. The large value of -ΔH00,1 (32.3 kcal/mol) and a sudden decrease of -ΔH01,2 (7.3 kcal/mol) for reaction F-(CO2)n-1+CO2=F-(CO2)n indicate the formation of the core ion, not F-ṡCO2, but FCO-2, i.e., FCO-2 is the fluoroformate ion. The measured binding energies -ΔH0n-1,n for the clusters F-(CO2)n were reproduced satisfactorily by the ab initio MO calculations. The FCO-2 ion is attacked successively and electrostatically by five CO2 molecules to form the first solvation shell. The two oxygen atoms in the core ion FCO-2 are able to accept four CO2 molecules as ligands. The bonding of CI-, Br-, and I- to CO2 is found to be mainly electrostatic.

  19. Structure and Dynamics of NaCl Ion Pairing in Solutions of Water and Methanol.

    PubMed

    Kelley, Morgan; Donley, Amber; Clark, Sue; Clark, Aurora

    2015-12-24

    Ion pairing can have profound effects upon the ionic strength of electrolyte solutions but is poorly understood in solutions containing more than one solvent. Herein a combined density functional theory and molecular dynamics approach is used to examine the effect of both methanol concentration and interionic distance upon the structure and dynamics within successive solvation shells of Na(+) and Cl(-) in water/methanol binary solutions. The structure and dynamics of the first and second solvation shells were studied along a reaction coordinate associated with ion pair formation using potential of mean force simulations. The lifetimes of the solvent-solvent hydrogen bonds become perturbed when the second solvation shells of the ions begin to interact. In contrast, the structural properties within the first and second solvation shells of the ions were found to be largely independent of both methanol concentration and interionic distance until a contact ion pair is formed. Thus, as the ions are brought together, the effect of the opposing ion manifests itself in the solvation dynamics before any structural changes are observed. As anticipated based upon the decreased dielectric constant of the binary solution, ion pair formation becomes energetically more favorable as the concentration of methanol increases. PMID:26641882

  20. 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.

  1. 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.

  2. 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.

  3. Crystallization and Structure Determination of Superantigens and Immune Receptor Complexes.

    PubMed

    Rödström, Karin E J; Lindkvist-Petersson, Karin

    2016-01-01

    Structure determination of superantigens and the complexes they form with immune receptors have over the years provided insight in their modes of action. This technique requires growing large and highly ordered crystals of the superantigen or receptor-superantigen complex, followed by exposure to X-ray radiation and data collection. Here, we describe methods for crystallizing superantigens and superantigen-receptor complexes using the vapor diffusion technique, how the crystals may be optimized, and lastly data collection and structure determination. PMID:26676036

  4. 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

  5. Large ions: Their vaporization, detection and structural analysis

    SciTech Connect

    Baer, T.; Ng, C.Y.; Powis, I.

    1997-12-31

    This book focuses on some of the fundamental chemistry and physics associated with the behavior of large ions, with the contributors addressing the issues in a quantitative fashion, in order to elucidate clearly some of the key recent advances which have taken place. As such, Large Ions provides an excellent snapshot of current research in this fascinating and important area. The six chapters are written by some of the leading experts in the field, and together they will be of great interest to experts and newcomers, both of whom will benefit from the in-depth discussion of the latest methods and results.

  6. Determination of meso-scale magnetotail structure using Cluster Data and nonlinear dynamics modeling

    NASA Astrophysics Data System (ADS)

    Holland, D. L.; Martin, R. F.; Fioretto, M.; Brennan, C.

    2013-12-01

    A commonly used approximation for the quiet-time magnetotail structure is the modified Harris magnetic field, B =B0[tanh(z/δ)ex + bzez] where B0 is the magnetic field strength far from the sheet, δ is the scale length of the current sheet thickness and bz is the ratio of the magnitude of the field at the midplane to the asymptotic field. Theory and simulations using the modified Harris model have predicted the existence of a signature of nonlinear charged particle dynamics that manifests itself a series of peaks in the ion distribution function. The separation of the peaks has been shown to scale as the fourth root of the normalized ion energy which in turn depends on the combination of parameters σ= bz2 δ. By measuring the location of the peaks in the ion distribution function or differential particle flux we may obtain a measured value for σ, however, we still need an independent measurement of either bz or δ to determine the meso-scale current sheet structure. Using a single spacecraft, precise measurement of either parameter is difficult. The current sheet scale length is problematic since relative motion of the spacecraft and the current sheet cannot be decoupled. This difficulty may be overcome using multiple satellites such as the Cluster mission. Even with multiple spacecrafts, however, the value of the field ratio bz is still difficult to ascertain since it is a small quantity and even a small tilt to the current sheet can result in significant percentage errors. In this paper, we present a statistical analysis of the current sheet structure using Cluster FGM data to determine the current sheet thickness and pitch angle resolved ion distribution function data from the Cluster HIA instrument to determine the value of σ and hence bz. We show that the measurements are in good agreement with those using other techniques, but with a significantly lower uncertainty.

  7. Standard addition method for free acid determination in solutions with hydrolyzable ions

    SciTech Connect

    Baumann, E.W.

    1981-01-01

    The free acid content of solutions containing hydrolyzable ions has been determined potentiometrically by a standard addition method. Two increments of acid are added to the sample in a 1M potassium thiocyanate solution. The sample concentration is calculated by solution of three simultaneous Nernst equations. The method has been demonstrated for solutions containing Al/sup 3 +/, Cr/sup 3 +/, Fe/sup 3 +/, Ni/sup 2 +/, Th/sup 4 +/, or UO/sub 2//sup 2 +/ with a metal-to-acid ratio of < 2.5. The method is suitable for determination of 10 ..mu..moles acid in 10 mL total volume. The accuracy is verifiable by reasonable agreement of the Nerst slopes found in the presence and absence of hydrolyzable ions. The relative standard deviation is < 2.5 percent.

  8. [Content determination of dencichine in Panax Notoginseng by a reversed phase ion-pair chromatography].

    PubMed

    Li, Lin; Wang, Cheng-xiao; Qu, Yuan; Cui, Xiu-ming

    2015-10-01

    To build a reversed phase ion-pair chromatography to determination content of Dencichine from Panax notoginseng. Using Tetrabutyl ammonium hydroxide ions by the combination of reagent and HPLC method without derivatization to test the content of dencichine directly. The optimum conditions of supersonic extraction were solid-to-liquid ratio 1: 20, Continuous ultrasonic extraction: twice, each time 15 minutes; 3,500 r · min⁻¹, then centrifuging 15 minutes. Dencichine in different age, place, part and the different Processing mode were examined. The method is simple with sound separation degree and stability, which can facilitate the determination of dencichine content directly and provide the basis in quality standard of raw material. PMID:27062822

  9. NMRFAM-SDF: a protein structure determination framework.

    PubMed

    Dashti, Hesam; Lee, Woonghee; Tonelli, Marco; Cornilescu, Claudia C; Cornilescu, Gabriel; Assadi-Porter, Fariba M; Westler, William M; Eghbalnia, Hamid R; Markley, John L

    2015-08-01

    The computationally demanding nature of automated NMR structure determination necessitates a delicate balancing of factors that include the time complexity of data collection, the computational complexity of chemical shift assignments, and selection of proper optimization steps. During the past two decades the computational and algorithmic aspects of several discrete steps of the process have been addressed. Although no single comprehensive solution has emerged, the incorporation of a validation protocol has gained recognition as a necessary step for a robust automated approach. The need for validation becomes even more pronounced in cases of proteins with higher structural complexity, where potentially larger errors generated at each step can propagate and accumulate in the process of structure calculation, thereby significantly degrading the efficacy of any software framework. This paper introduces a complete framework for protein structure determination with NMR--from data acquisition to the structure determination. The aim is twofold: to simplify the structure determination process for non-NMR experts whenever feasible, while maintaining flexibility by providing a set of modules that validate each step, and to enable the assessment of error propagations. This framework, called NMRFAM-SDF (NMRFAM-Structure Determination Framework), and its various components are available for download from the NMRFAM website (http://nmrfam.wisc.edu/software.htm). PMID:25900069

  10. Determination of titanium atom and ion densities in sputter deposition plasmas by optical emission spectroscopy

    NASA Astrophysics Data System (ADS)

    Vašina, P.; Fekete, M.; Hnilica, J.; Klein, P.; Dosoudilová, L.; Dvořák, P.; Navrátil, Z.

    2015-12-01

    The thorough characterizations of deposition plasma lead to important achievements in the fundamental understanding of the deposition process, with a clear impact on the development of technology. Measurement of the spatial and, in the case of pulse excited plasma, also temporal evolution, of the concentrations of sputtered atoms and ions is a primary task in the diagnostics of any sputter deposition plasma. However, it is difficult to estimate absolute number densities of the sputtered species (atoms and ions) in ground states directly from optical emission spectroscopy, because the species in the ground levels do not produce any optical signal. A method using effective branching fractions enables us to determine the density of non-radiating species from the intensities of self-absorbed spectral lines. The branching fractions method described in the first part of this paper was applied to determine the ground state densities of the sputtered titanium atoms and ions. The method is based on fitting the theoretically calculated branching fractions to experimentally measured ratios of the relative intensities of carefully selected resonant titanium atomic and ionic lines. The sputtered species density is determined in our experimental setup with a relative uncertainty of less than 5% for the dc driven magnetron and typically 15% for time-resolved measurements of high-power impulse magnetron sputtering (HiPIMS) discharge. In the second part of the paper, the method was applied to determine the evolution of titanium atom and ion densities in three typical cases ranging from the dc driven sputter process to HiPIMS.

  11. An ion-selective electrode method for determination of chlorine in geological materials

    USGS Publications Warehouse

    Aruscavage, P. J.; Campbell, E.Y.

    1983-01-01

    A method is presented for the determination of chlorine in geological materials, in which a chloride-selective ion electrode is used after decomposition of the sample with hydrofluoric acid and separation of chlorine in a gas-diffusion cell. Data are presented for 30 geological standard materials. The relative standard deviation of the method is estimated to be better than 8% for amounts of chloride of 10 ??g and greater. ?? 1983.

  12. Ion-exchanger colorimetry-I Micro determination of chromium, iron, copper and cobalt in water.

    PubMed

    Yoshimura, K; Waki, H; Ohashi, S

    1976-06-01

    A new sensitive, colorimetric method based on the direct measurement of light-absorption by an ion-exchange resin phase, which has sorbed the sample complex species, has been developed. Determinations ofchromium(VI) with diphenylearbazide, iron(II) with 1,10-phenanthroline, copper with Zincon and cobalt with thiocyanate have more than ten times the sensitivity obtainable with conventional solution colorimetry. The present method can be applied to natural water samples containing very low levels of these metals. PMID:18961894

  13. 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.

  14. Dissociation Enthalpies of Chloride Adducts of Nitrate and Nitrite Explosives Determined by Ion Mobility Spectrometry.

    PubMed

    Rajapakse, Maneeshin Y; Fowler, Peter E; Eiceman, Gary A; Stone, John A

    2016-02-11

    The kinetics for thermal dissociations of the chloride adducts of the nitrate explosives 1,3-dinitroglycerin (1,3-NG), 1,2-dinitroglycerin (1,2-NG), the nitrite explosive 3,4-dinitrotoluene (3,4-DNT), and the explosive taggant 2,3-dimethyl-2,3-dinitrobutane (DMNB) have been studied by atmospheric pressure ion mobility spectrometry. Both 1,3-NG·Cl(-) and1,2-NG·Cl(-) decompose in a gas-phase SN2 reaction in which Cl(-) displaces NO3(-) while 3,4-DNT·Cl(-) and DMNB·Cl(-) decompose by loss of Cl(-). The determined activation energy (kJ mol(-1)) and pre-exponential factor (s(-1)) values for the dissociations respectively are 1,3-NG·Cl(-), 86 ± 2 and 2.2 × 10(12); 1,2-NG·Cl(-), 97 ± 2 and 3.5 × 10(12); 3,4-DNT·Cl(-), 81 ± 2 and 4.8 × 10(13); and DMNB·Cl(-), 68 ± 2 and 9.7 × 10(11). Calculations by density functional theory show the structures of the nitrate ester adducts involve three hydrogen bonds: one from the hydroxyl group and the other two from the two nitrated carbons. The relative Cl(-) dissociation energies of the nitrates together with the previously reported smaller value for glycerol trinitrate and the calculated highest value for glycerol 1-mononitrate are explicable in terms of the number of hydroxyl hydrogen bond participants. The theoretical enthalpy changes for the nitrate ester displacement reactions are in agreement with those derived from the experimental activation energies but considerably higher for the nitro compounds. PMID:26777731

  15. Structure and simulation of a Zundel ion stabilized by 8-hydroxyquinoline-5, 7 disulphonic acid

    NASA Astrophysics Data System (ADS)

    Venkatakrishnan, Hasthi Annapurna; Venkatakrishnan, Ramaseshan; Pennathur, Anuj Krishnasundar; Pennathur, Gautam

    2016-07-01

    8-hydroxyquinoline-5, 7 disulphonic was synthesized and recrystallized in methanol to strip away molecules of water. The structure of the molecule revealed that Zundel ion was stabilized in the crystal. Ab-initio molecular dynamics simulation was then carried out to understand the dynamics of proton hopping in this complex. During the course of simulation, the Zundel ion coordinates with a water molecule to form an open H7O3+ structure. This transition state structure de-solvated rapidly forming Zundel ion facilitating proton hopping in the first solvation shell. One of the sulphonic acid groups in the 5 or 7 position of the 8-hydroxyquinoline 5,7 disulphonic acid bonds with the Zundel ion favoring the proton to be transferred to the nearby water molecule through the formation of proton defects. The simulation results support the structural diffusion mechanism and that charged complex migrates through the hydrogen bond network.

  16. 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. PMID:27365396

  17. 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.

  18. 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.

  19. Labor Market Structure and Salary Determination among Professional Basketball Players.

    ERIC Educational Resources Information Center

    Wallace, Michael

    1988-01-01

    The author investigates the labor market structure and determinants of salaries for professional basketball players. An expanded version of the resource perspective is used. A three-tiered model of labor market segmentation is revealed for professional basketball players, but other variables also are important in salary determination. (Author/CH)

  20. 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.

  1. Selective pretreatment and determination of phenazopyridine using an imprinted polymer-electrospray ionization ion mobility spectrometry system.

    PubMed

    Rezaei, B; Jafari, M T; Rahmanian, O

    2011-01-15

    In this research, selective separation and determination of phenazopyridine (PAP) is demonstrated using molecular imprinted polymer (MIP) coupled with electrospray ionization ion mobility spectrometry (ESI-IMS). In the non-covalent approach, selective MIP produced using PAP and methacrylic acid (MAA) as a template molecule and monomer, respectively. The created polymer is utilized as a media for solid-phase extraction (SPE), revealing selective binding properties for the analyte from pharmaceutical and serum samples. A coupled MIP-IMS makes it possible to quantitize PAP in the range of 1-100 ng mL(-1) and with a 0.2 ng mL(-1) detection limit. Furthermore, the MIP selectivity is evaluated by application of some substances with analogous and different molecular structures to that of PAP. This method is successfully applied for the determination of PAP in pharmaceutical and serum samples. PMID:21147318

  2. '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.

  3. Cooperation of Hydrophobic Gating, Knock-on Effect, and Ion Binding Determines Ion Selectivity in the p7 Channel.

    PubMed

    Padhi, Siladitya; Priyakumar, U Deva

    2016-05-19

    Ion channels selectively allow certain ions to pass through at much higher rates than others, and thereby modulate ionic concentrations across cell membranes. The current molecular dynamics study elucidates the intricate mechanisms that render ion selectivity to the viral channel p7 by employing free energy calculations. Free energy barriers of 5.4 and 19.4 kcal mol(-1) for K(+) and Ca(2+), respectively, explain the selectivity of the channel reported in experiments. Initially, the permeating ions encounter a hydrophobic barrier followed by stabilization in an ion-binding site. Electrostatic repulsion between the permeating ions propels one of the ions out of the binding site to complete the process of permeation. K(+) and Ca(2+) are seen to exhibit different modes of binding toward a ring of asparagine residues, which serves as the binding site. The findings illustrate how the overall selectivity of a channel can be achieved by a combination of subtle differences. PMID:27111292

  4. 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.

  5. 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.

  6. Isolation, crystallization and crystal structure determination of bovine kidney Na(+),K(+)-ATPase.

    PubMed

    Gregersen, Jonas Lindholt; Mattle, Daniel; Fedosova, Natalya U; Nissen, Poul; Reinhard, Linda

    2016-04-01

    Na(+),K(+)-ATPase is responsible for the transport of Na(+) and K(+) across the plasma membrane in animal cells, thereby sustaining vital electrochemical gradients that energize channels and secondary transporters. The crystal structure of Na(+),K(+)-ATPase has previously been elucidated using the enzyme from native sources such as porcine kidney and shark rectal gland. Here, the isolation, crystallization and first structure determination of bovine kidney Na(+),K(+)-ATPase in a high-affinity E2-BeF3(-)-ouabain complex with bound magnesium are described. Crystals belonging to the orthorhombic space group C2221 with one molecule in the asymmetric unit exhibited anisotropic diffraction to a resolution of 3.7 Å with full completeness to a resolution of 4.2 Å. The structure was determined by molecular replacement, revealing unbiased electron-density features for bound BeF3(-), ouabain and Mg(2+) ions. PMID:27050261

  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. Modified--Hill-determinant method for the hydrogen molecular-ion problem

    SciTech Connect

    Bhattacharjee, R.S.; Saxena, R.P.; Srivastava, P.K.; Sane, K.V.

    1983-10-01

    The problem of the H/sub 2/ molecular ion is reinvestigated with the use of a method of truncated Hill determinants. Modified Hill determinants are found such that the truncations thereof form a convergent sequence. The wave functions obtained from the present formulation are expected to be more reliable than those reported earlier and in fact are shown to be orthonormal to one part in 10/sup 6/. Equilibrium bond lengths (R/sub e/), stiffness constants, and the wave functions at R/sub e/ for various states are presented.

  9. Experimental investigation of ionisation track structure of carbon ions at HIL Warsaw.

    PubMed

    Bantsar, A; Hilgers, G; Pszona, S; Rabus, H; Szeflinski, Z

    2015-09-01

    In view of the upcoming radiation therapy with carbon ions, the ionisation structure of the carbon ion track at the nanometre scale is of particular interest. Two different nanodosimeters capable of measuring track structure of ionising particles in a gas target equivalent to a nanometric site in condensed matter were involved in the presented experimental investigation, namely the NCBJ Jet Counter and the PTB Ion Counter. At the accelerator facility of the HIL in Warsaw, simulated nanometric volumes were irradiated with carbon ions of 45 and 76 MeV of kinetic energy, corresponding to a range in the tissue of ∼85 µm and ∼190 µm, respectively. The filling gas of both nanodosimeters' ionisation volume was molecular nitrogen N2, and the ionisation cluster size distributions, i.e. the statistical distribution of the number of ionizations produced by one single primary carbon ion in the filling gas, were measured for the two primary particle energies. PMID:25897141

  10. Advances in ion trap mass spectrometry: Photodissociation as a tool for structural elucidation

    SciTech Connect

    Stephenson, J.L. Jr.; Booth, M.M.; Eyler, J.R.; Yost, R.A.

    1995-12-01

    Photo-induced dissociation (PID) is the next most frequently used method (after collisional activation) for activation of Polyatomic ions in tandem mass spectrometry. The range of internal energies present after the photon absorption process are much narrower than those obtained with collisional energy transfer. Therefore, the usefulness of PID for the study of ion structures is greatly enhanced. The long storage times and instrumental configuration of the ion trap mass spectrometer are ideally suited for photodissociation experiments. This presentation will focus on both the fundamental and analytical applications of CO{sub 2} lasers in conjunction with ion trap mass spectrometry. The first portion of this talk will examine the fundamental issues of wavelength dependence, chemical kinetics, photoabsorption cross section, and collisional effects on photodissociation efficiency. The second half of this presentation will look at novel instrumentation for electrospray/ion trap mass spectrometry, with the concurrent development of photodissociation as a tool for structural elucidation of organic compounds and antibiotics.

  11. 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.

  12. Structure of ion acoustic solitons and shock waves in a two-component plasma.

    NASA Technical Reports Server (NTRS)

    White, R. B.; Fried, B. D.; Coroniti, F. V.

    1972-01-01

    Time-independent solitary waves and shocks are investigated in a two-component plasma using a fluid model and kinetic theory. It is found that very small concentrations of a light ion can drastically alter the structure, changing the potential maximum by an order of magnitude. For a fixed Mach number, a critical density ratio of light to heavy ions is found at which the potential maximum changes discontinuously from a value large enough to reflect the light ions to one which allows them to traverse the shock front and enter the downstream flow. The downstream oscillatory structure normally seen in a shock is completely quenched by dissipation due to light ion reflection at concentrations of 3-8% He in an Ar plasma for typical electron to ion temperature ratios and Mach number values.

  13. 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

  14. Structural determination of intact proteins using mass spectrometry

    DOEpatents

    Kruppa, Gary; Schoeniger, Joseph S.; Young, Malin M.

    2008-05-06

    The present invention relates to novel methods of determining the sequence and structure of proteins. Specifically, the present invention allows for the analysis of intact proteins within a mass spectrometer. Therefore, preparatory separations need not be performed prior to introducing a protein sample into the mass spectrometer. Also disclosed herein are new instrumental developments for enhancing the signal from the desired modified proteins, methods for producing controlled protein fragments in the mass spectrometer, eliminating complex microseparations, and protein preparatory chemical steps necessary for cross-linking based protein structure determination.Additionally, the preferred method of the present invention involves the determination of protein structures utilizing a top-down analysis of protein structures to search for covalent modifications. In the preferred method, intact proteins are ionized and fragmented within the mass spectrometer.

  15. Fluorescent carbon quantum dot hydrogels for direct determination of silver ions.

    PubMed

    Cayuela, A; Soriano, M L; Kennedy, S R; Steed, J W; Valcárcel, M

    2016-05-01

    The paper reports for the first time the direct determination of silver ion (Ag(+)) using luminescent Carbon Quantum Dot hydrogels (CQDGs). Carbon Quantum Dots (CQDs) with different superficial moieties (passivate-CQDs with carboxylic groups, thiol-CQDs and amine-CQDs) were used to prepare hybrid gels using a low molecular weight hydrogelator (LMWG). The use of the gels results in considerable fluorescence enhancement and also markedly influences selectivity. The most selective CQDG system for Ag(+) ion detection proved to be those containing carboxylic groups onto their surface. The selectivity towards Ag(+) ions is possibly due to its flexible coordination sphere compared with other metal ions. This fluorescent sensing platform is based on the strong Ag-O interaction which can quench the photoluminescence of passivate-CQDs (p-CQDs) through charge transfer. The limit of detection (LOD) and quantification (LOQ) of the proposed method were 0.55 and 1.83µgmL(-1), respectively, being applied in river water samples. PMID:26946015

  16. Fine Structure in Swift Heavy Ion Tracks in Amorphous SiO2

    NASA Astrophysics Data System (ADS)

    Kluth, P.; Schnohr, C. S.; Pakarinen, O. H.; Djurabekova, F.; Sprouster, D. J.; Giulian, R.; Ridgway, M. C.; Byrne, A. P.; Trautmann, C.; Cookson, D. J.; Nordlund, K.; Toulemonde, M.

    2008-10-01

    We report on the observation of a fine structure in ion tracks in amorphous SiO2 using small angle x-ray scattering measurements. Tracks were generated by high energy ion irradiation with Au and Xe between 27 MeV and 1.43 GeV. In agreement with molecular dynamics simulations, the tracks consist of a core characterized by a significant density deficit compared to unirradiated material, surrounded by a high density shell. The structure is consistent with a frozen-in pressure wave originating from the center of the ion track as a result of a thermal spike.

  17. 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.

  18. 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.

  19. 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.

  20. The progress made in determining the Mycobacterium tuberculosis structural proteome

    PubMed Central

    Hecker, Michael

    2011-01-01

    Mycobacterium tuberculosis is a highly infectious pathogen that is still responsible for millions of deaths annually. Effectively treating this disease typically requires a course of antibiotics, most of which were developed decades ago. These drugs are, however, not effective against persistent tubercle bacilli and the emergence of drug-resistant stains threatens to make many of them obsolete. The identification of new drug targets, allowing the development of new potential drugs, is therefore imperative. Both proteomics and structural biology have important roles to play in this process, the former as a means of identifying promising drug targets and the latter allowing understanding of protein function and protein–drug interactions at atomic resolution. The determination of M. tuberculosis protein structures has been a goal of the scientific community for the last decade, who have aimed to supply a large amount of structural data that can be used in structure-based approaches for drug discovery and design. Only since the genome sequence of M. tuberculosis has been available has the determination of large numbers of tuberculosis protein structures been possible. Currently, the molecular structures of 8.5% of all the pathogen's protein-encoding ORFs have been determined. In this review, we look at the progress made in determining the M. tuberculosis structural proteome and the impact this has had on the development of potential new drugs, as well as the discovery of the function of crucial mycobaterial proteins. PMID:21674801

  1. Structural Variations and Solvent Structure of r(UGGGGU) Quadruplexes Stabilized by Sr2+ Ions

    PubMed Central

    Fyfe, Alastair C.; Dunten, Pete W.; Martick, Monika M.; Scott, William G.

    2015-01-01

    Guanine-rich sequences can, under appropriate conditions, adopt a distinctive, four-stranded, helical fold known as a G-quadruplex. Interest in quadruplex folds has grown in recent years as evidence of their biological relevance has accumulated from both sequence analysis and function-specific assays. The folds are unusually stable and their formation appears to require close management to maintain cell health; regulatory failure correlates with genomic instability and a number of cancer phenotypes. Biologically relevant quadruplex folds are anticipated to form transiently in mRNA and in single-stranded, unwound DNA. To elucidate factors, including bound solvent, that contribute to the stability of RNA quadruplexes, we examine, by X-ray crystallography and small-angle X-ray scattering, the structure of a previously reported tetramolecular quadruplex, UGGGGU stabilized by Sr2+ ions. Crystal forms of the octameric assembly formed by this sequence exhibit unusually strong diffraction and anomalous signal enabling the construction of reliable models to a resolution of 0.88 Å. The solvent structure confirms hydration patterns reported for other nucleic acid helical conformations and provides support for the greater stability of RNA quadruplexes relative to DNA. Novel features detected in the octameric RNA assembly include a new crystal form, evidence of multiple conformations and structural variations in the 3′ U tetrad, including one that leads to the formation of a hydrated internal cavity. PMID:25861762

  2. Characterization of ion-irradiation-induced nanodot structures on InP surfaces by atom probe tomography.

    PubMed

    Gnaser, Hubert; Radny, Tobias

    2015-12-01

    Surfaces of InP were bombarded by 1.9 keV Ar(+) ions under normal incidence. The total accumulated ion fluence the samples were exposed to was varied from 1 × 10(17) cm(-2) to 3 × 10(18)cm(-2) and ion flux densities f of (0.4-2) × 10(14) cm(-2) s(-1) were used. Nanodot structures were found to evolve on the surface from these ion irradiations, their dimensions however, depend on the specific bombardment conditions. The resulting surface morphology was examined by atomic force microscopy (AFM). As a function of ion fluence, the mean radius, height, and spacing of the dots can be fitted by power-law dependences. In order to determine possible local compositional changes in these nanostructures induced by ion impact, selected samples were prepared for atom probe tomography (APT). The results indicate that by APT the composition of individual InP nanodots evolving under ion bombardment could be examined with atomic spatial resolution. At the InP surface, the values of the In/P concentration ratio are distinctly higher over a distance of ~1 nm and amount to 1.3-1.8. However, several aspects critical for the analyses were identified: (i) because of the small dimensions of these nanostructures a successful tip preparation proved very challenging. (ii) The elemental compositions obtained from APT were found to be influenced pronouncedly by the laser pulse energy; typically, low energies result in the correct stoichiometry whereas high ones lead to an inhomogeneous evaporation from the tips and deviations from the nominal composition. (iii) Depending again on the laser energy, a prolific emission of Pn cluster ions was observed, with n ≤ 11. PMID:25980895

  3. 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.

  4. 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.

  5. 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.

  6. Differential potentiometric determination of perchlorate and iodide ions in industrial wastes

    SciTech Connect

    Kolbyagin, N.P.; Vlasova, E.G.; Zhilina, O.D.; Renkova, Z.S.

    1986-12-01

    The determination of perchlorates and iodides present together in industrial wastes is hampered by the fact that these anions either are precipitated by the same organic reagents or form colored complexes with similar absorption maxima. Determining them by separation or by deducting one from their sum is a multi-step analysis which takes more time and decreases accuracy. In this paper, the authors report a rapid, single-step determination of co-present perchlorate and iodide by precipitative titration with nitron solution and potentiometric indication of the equivalence point by a perchlorate-selective membrane electrode. The perchlorate and iodide determinations were unaffected by surfactant, suspensions, and ions not precipitated with nitron. A single analysis takes 15-20 minutes. This method may also be used for analyzing single salts.

  7. Structure and characteristics of ions in hot plasma

    NASA Astrophysics Data System (ADS)

    Vainshtein, Leonid Abramovich; Shevel'Ko, Viacheslav Petrovich

    Methods for calculating the radiation and collision characteristics of atoms and ions, such as oscillator forces, transition probabilities, and interaction cross sections and velocities, are presented in a systematic manner. The book contains a large amount of reference data that are essential in nuclear physics, laser spectroscopy, astrophysics, and theory of atomic spectra and collisions. A computer program written in FORTRAN for calculating the characteristics of atoms is included.

  8. Carbohydrate polymers as constituents of exopolymer substances in seawater, their complexing properties towards copper ions, surface and catalytic activity determined by electrochemical methods.

    PubMed

    Plavšić, Marta; Strmečki, Slađana

    2016-01-01

    The goal of this study was to investigate to which extent polysaccharides (PS) contribute to the complexing capacity for copper ion (LT), to determine their property of surface activity and evaluate their capability to cause the catalytic hydrogen evolution wave (peak "H") due to their adsorption and the catalytic groups in their structure. Complexing capacities and apparent stability constants (Kapp) were measured electrochemically for model polysaccharides (PS): carrageenans (κ-, ι- and λ-), chondroitin sulfate, dextran, dextran sulfate, Na-alginate and humic material. Cu-complexing capacities were determined for Na-alginate (logKapp=8.32) and chondroitin sulphate (logKapp=8.14). PS adsorb on different surfaces due to their amphyphylic properties and on that way they could increase the interaction of copper ions with these surfaces by forming the surface complexes with Cu ions. PMID:26453850

  9. 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.

  10. Method and apparatus for determining clay counter-ion concentration in shaly sands

    SciTech Connect

    Scala, C.

    1987-10-06

    This patent describes a method for determining, in situ, clay counter-ion concentrations in a fluid bearing shaly sand earth formation penetrated by a well borehole, comprising the steps of: (a) detecting in a well borehole at a particular depth level natural gamma radiation emanating from the earth formations penetrated by the borehole as count rate signals. Then separating the detected gamma radiation signals into an energy spectrum of naturally occurring gamma radiation count rate signals as a function of energy and generating signals representative of the energy spectrum of the count rates of naturally occurring gamma radiation at the particular depth level; (b) comparing the representative count rate signals with standard gamma ray energy spectra representative of natural radioactive elements found in the earth formations penetrated by a well borehole. Thereby separating out gamma ray count rates attributable to at least uranium U, thorium Th, and potassium K occurring in the earth formations; (c) measuring the porosity phi of the earth formation at the particular depth level and normalizing the count rates attributable to uranium U and thorium Th at the particular depth level; (d) determining the clay counter ion concentration Q/sub v/ of the earth formations at the particular depth level by using a predetermined functional relationship and obtaining a signal representative of Q/sub v/ at the particular depth level; and, (e) recording the representative clay counter-ion concentration Q/sub v/ signal as a function of borehole depth.

  11. 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. PMID:25308690

  12. Modular calibrant sets for the structural analysis of nucleic acids by ion mobility spectrometry mass spectrometry.

    PubMed

    Lippens, Jennifer L; Ranganathan, Srivathsan V; D'Esposito, Rebecca J; Fabris, Daniele

    2016-06-20

    This study explored the use of modular nucleic acid (NA) standards to generate calibration curves capable of translating primary ion mobility readouts into corresponding collision cross section (CCS) data. Putative calibrants consisted of single- (ss) and double-stranded (ds) oligo-deoxynucleotides reaching up to ∼40 kDa in size (i.e., 64 bp) and ∼5700 Å(2) in CCS. To ensure self-consistency among reference CCS values, computational data obtained in house were preferred to any experimental or computational data from disparate sources. Such values were obtained by molecular dynamics (MD) simulations and either the exact hard sphere scattering (EHSS) or the projection superposition approximation (PSA) methods, and then plotted against the corresponding experimental values to generate separate calibration curves. Their performance was evaluated on the basis of their correlation coefficients and ability to provide values that matched the CCS of selected test samples mimicking typical unknowns. The results indicated that the predictive power benefited from the exclusion of higher charged species that were more susceptible to the destabilizing effects of Coulombic repulsion. The results revealed discrepancies between EHSS and PSA data that were ascribable to the different approximations used to describe the ion mobility process. Within the boundaries defined by these approximations and the challenges of modeling NA structure in a solvent-free environment, the calibrant sets enabled the experimental determination of CCS with excellent reproducibility (precision) and error (accuracy), which will support the analysis of progressively larger NA samples of biological significance. PMID:27152369

  13. 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.

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

    SciTech Connect

    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 suggests that there are preferred Si <100> interstitial splits. 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±0.4×10e-19 m2/sec.

  15. Etching and structural changes in nitrogen plasma immersion ion implanted polystyrene films

    NASA Astrophysics Data System (ADS)

    Gan, B. K.; Bilek, M. M. M.; Kondyurin, A.; Mizuno, K.; McKenzie, D. R.

    2006-06-01

    Plasma immersion ion implantation (PIII), with nitrogen ions of energy 20 keV in the fluence range of 5 × 1014-2 × 1016 ions cm-2, is used to modify 100 nm thin films of polystyrene on silicon wafer substrates. Ellipsometry is used to study changes in thickness with etching and changes in optical constants. Two distinctly different etch rates are observed as the polymer structure is modified. FTIR spectroscopy data reveals the structural changes, including changes in aromatic and aliphatic groups and oxidation and carbonisation processes, occurring in the polystyrene film as a function of the ion fluence. The transformation to a dense amorphous carbon-like material was observed to progress through an intermediate structural form containing a high concentration of Cdbnd C and Cdbnd O bonds.

  16. Purification, Biochemical Analysis, and Structure Determination of JmjC Lysine Demethylases.

    PubMed

    Krishnan, S; Trievel, R C

    2016-01-01

    Jumonji C (JmjC) lysine demethylases (KDMs) catalyze the site- and state-specific demethylation of lysine residues in histone and nonhistone protein substrates. These enzymes have been implicated in diverse genomic processes, including epigenetic gene regulation, DNA damage response, DNA replication, and regulation of heterochromatin structure. In addition, a number of JmjC KDMs contribute to the incidence of numerous cancers, rendering them targets for the development of novel chemotherapeutic drugs. Using the JMJD2 KDM subfamily as representative examples, this chapter outlines strategies for purifying highly active, recombinant JmjC KDMs lacking inhibitory transition metal ions, characterizing kinetic parameters of these enzymes using a coupled fluorescent assay, and determining crystal structures of the enzymes in complex with methylated histone peptides. Together, these approaches provide a foundation for structural and biochemical characterization of the JmjC KDMs and facilitate efforts to identify small molecule inhibitors through high-throughput screening and structure-guided design. PMID:27372758

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

    DOE PAGESBeta

    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

  18. 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.

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

    PubMed Central

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

    2015-01-01

    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. PMID:25945580

  20. Monolithic octadecylsilyl-silica gel column for the high-speed ion chromatographic determination of acidity.

    PubMed

    Xu, Qun; Tanaka, Kazuhiko; Mori, Masanobu; Helaleh, Murad I H; Hu, Wenzhi; Hasebe, Kiyoshi; Toada, Hiroshi

    2003-05-16

    A monolithic ODS-silica gel column modified by saturating it with lithium dodecylsulfate (Li-DS) was used to demonstrate the high-speed separation of H+ from other mono- and divalent cations, such as Na+, NH4+, K+, Mg2+ and Ca2+ using ion chromatography (IC). Using a 5 mM EDTA-2K solution containing 0.10 mM Li-DS (pH 4.80) as eluent, H+ was eluted with a sharp and symmetrical peak within 1.0 min before other cations at a flow-rate of 1.5 ml min(-1). The rapid elution of H+ and its conductimetric detection could be attributed to the presence of EDTA (HY2-), which can convert H+ ions as anions. i.e. H(+) + H2Y(2-) --> H3Y(-). The acidity of rainwater and deionized water samples was determined using this IC system with satisfactory results. PMID:12830891

  1. 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.

  2. Using Data to Determine the Initial Conditions in Heavy Ion Collisions

    NASA Astrophysics Data System (ADS)

    Soltz, Ron; Garishvili, Irakli; Abelev, Betty

    2012-10-01

    We have developed a framework, the Comprehensive Heavy Ion Model Evaluation Reporting Algorithm (CHIMERA) to determine the optimal model and initial conditions of heavy ion collisions by comparing to data from a variety of observables. We have used this framework to study simple participant and binary collisions scaling in the presence of pre-equilibrium flow in the context of the VH2 2D+1 viscous hydrodynamic model with UrQMD afterburner for data from RHIC. We have also used this framework to explore the significance of variations in the equation of state. We have recently begun to apply this framework to a new hydro-solver tools known as CHOMBO, which incorporates adaptive mesh refinement techniques that are well suited to the study of initial state fluctuations. We will review results from using CHIMERA with VH2, and discuss future plans for using CHOMBO to study initial state fluctuations.

  3. Determination of surfactant sodium lauryl ether sulfate by ion pairing chromatography with suppressed conductivity detection

    SciTech Connect

    Ye, M.Y.; Walkup, R.G.; Hill, K.D. )

    1994-01-01

    A method for the determination of the anionic Steol CS-330 surfactant is described. CS-330 is a complex mixture of oligomers due to the various sizes of fatty alcohols and the number of moles of the ethoxylation. The main component of CS-330 is sodium lauryl ether sulfate (SLES). Since a SLES molecule has a hydrophilic sulfate head and a hydrophobic alkyl ethoxyl tail, it is very difficult to separate these molecules with conventional reverse phase chromatography or ion exchange chromatography. This work uses ion pairing chromatography with suppressed conductivity detection. The separation of oligomers in CS-330 is achieved. SLES does not have UV-absorbing chromophores, therefore an optical detector is not very sensitive. Suppressed conductivity detection technique significantly increases sensitivity and a quantitation limit of 56.60 ppm is achieved.

  4. Why do the Abundances of Ions Generated by MALDI Look Thermally Determined?

    NASA Astrophysics Data System (ADS)

    Bae, Yong Jin; Choe, Joong Chul; Moon, Jeong Hee; Kim, Myung Soo

    2013-11-01

    In a previous study ( J. Mass Spectrom. 48, 299-305, 2013), we observed that the abundance of each ion in a matrix-assisted laser desorption ionization (MALDI) spectrum looked thermally determined. To find out the explanation for the phenomenon, we estimated the ionization efficiency and the reaction quotient (QA) for the autoprotolysis of matrix, M + M → [M + H]+ + [M - H]-, from the temperature-controlled laser desorption ionization spectra of α-cyano-4-hydroxycinnamic acid (CHCA) and 2,5-dihydroxybenzoic acid (DHB). We also evaluated the equilibrium constants (KA) for the autoprotolysis at various temperatures by quantum chemical calculation. Primary ion formation via various thermal models followed by autoprotolysis-recombination was compatible with the observations. The upper limit of the effective temperature of the plume where autoprotolysis-recombination occurs was estimated by equating QA with the calculated equilibrium constant. [Figure not available: see fulltext.

  5. Ion chromatographic determination of phosphorus soluble in different extracting media in fertilizers.

    PubMed

    Mazzei, Raffaele Antonio; Scuppa, Stefano

    2006-01-01

    A new method based on ion chromatography (IC) was developed for the determination of phosphorus in fertilizers. Fertilizers were extracted with water, mineral acids, and 2% formic acid, 2% citric acid, and neutral ammonium citrate solutions according to European Regulation No. 2003/2003 of the European Parliament and the Council of October 13, 2003, or the Decree of the Italian Agriculture Minister of June 17, 2002; the extracts were analyzed by direct injection, after simple filtration, by IC on an IonPac AS19 (250 x 4 mm id) column, using a KOH (21-50-21 mM) gradient and suppressed conductivity detection. The calibration plot was linear over the range of 5-50 mg/L (r(2) of >0.999). The method was evaluated by comparison with a gravimetric method according to established norms. Associated uncertainty at the 95% confidence level was established as 0.47% for the determination of 3-46% P2O5 by IC. A good chromatographic separation of phosphorus forms such as phosphates and phosphites, and some other important anions like nitrates, chlorides, and sulfates present in many commercial fertilizers was also possible, with a linear response over the range of 5-50 mg/L. After a more complete validation, this IC determination of phosphorus could replace more tedious methods such as those using gravimetric determinations. PMID:17042171

  6. 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.

  7. 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. PMID:26807492

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

    DOE PAGESBeta

    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)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

  9. Plasma screening effects on the electronic structure of multiply charged Al ions using Debye and ion-sphere models

    NASA Astrophysics Data System (ADS)

    Das, Madhulita; Sahoo, B. K.; Pal, Sourav

    2016-05-01

    We analyze atomic structures of plasma-embedded aluminum (Al) atom and its ions in the weak- and strong-coupling regimes. The plasma screening effects in these atomic systems are accounted for using the Debye and ion-sphere (IS) potentials for the weakly and strongly coupled plasmas, respectively. Within the Debye model, special attention is given to investigate the spherical and nonspherical plasma screening effects considering in the electron-electron interaction potential. The relativistic coupled-cluster (RCC) method has been employed to describe the relativistic and electronic correlation effects in the above atomic systems. The variations in the ionization potentials (IPs) and excitation energies (EEs) of the plasma-embedded Al ions are presented. It is found that the atomic systems exhibit more stability when the exact screening effects are taken into account. It is also shown that in the presence of a strongly coupled plasma environment, the highly ionized Al ions show blueshifts and redshifts in the spectral lines of the transitions between the states with the same and different principal quantum numbers, respectively. Comparison among the results obtained from the Debye and IS models are also carried out considering similar plasma conditions.

  10. Optical and structural properties of YF3 thin films prepared by ion-assisted deposition or ion beam sputtering techniques

    NASA Astrophysics Data System (ADS)

    Robic, Jean-Yves; Muffato, Viviane; Chaton, Patrick; Ida, Michel; Berger, M.

    1994-11-01

    The properties of materials in thin films are strongly dependent on the coating techniques and on the technological parameters. We have investigated about some optical and structural properties of YF3 thin films prepared using different energetic techniques: ion assisted deposition (IAD) and ion beam sputtering (IBS). The properties of the thin films obtained by these energetic processes are compared to the properties obtained by classical electron beam evaporation. In classical evaporation, the optical properties in the visible range depend on the temperature of the deposition and on the incidence of the vapor flux. The optical properties are correlated with the density of the films measured by Rutherford backscattering. In the case of IAD, the influence on optical properties, both in the visible and in the infrared range, of some technological parameters (pressure, ion energy and ion density) are illustrated. The refractive index and the extinction coefficient have been obtained by spectrophotometry. Furthermore, we show that IBS may lead to YF3 layers of high density.

  11. 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. PMID:21730162

  12. 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.

  13. 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. PMID:26614803

  14. Local structural properties of Co-ion-implanted ZnO nanorods

    NASA Astrophysics Data System (ADS)

    Park, C. I.; Jin, Zhenlan; Jeong, E. S.; Hwang, I. H.; Han, S. W.

    2013-12-01

    We examined the local structural properties around Co and Zn ions in Co-ion-implanted ZnO nanorods by using an X-ray absorption fine structure (XAFS) analysis. Vertically-aligned ZnO nanorods were synthesized on Al2O3 substrates by using a catalyst-free metal-organic chemicalvapor deposition. Co ions (Co+ and Co2+) with energies of 50 and 100 keV and fluxes of 1013 and 1015 particles/cm2 were implanted in the ZnO nanorods, and the ion-implanted ZnO nanorods were annealed at 400-650°C. X-ray absorption near edge structure (XANES) analyses demonstrated that the chemical valence state of the Co ions were mostly 2+. An extended XAFS (EXAFS) analysis revealed that the Co ions were mostly substituted at the Zn sites of ZnO nanorods at a Coion flux of 1015 particles/cm2. However, at a flux of 1013 particles/cm2, Co ions formed Co-O and Co-Co clusters. These results were in contrast to the Co distribution in Co-added ZnO predicted by using a Monte Carlo method.

  15. 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.

  16. Highly selective and sensitive spectrophotometric determination of trace amounts of silver ion in surfactant media using 2-mercaptobenzoxazole.

    PubMed

    Ghaedi, M; Daneshfar, A; Shokrollahi, A; Ghaedi, H; Arvin Pili, F

    2007-09-01

    A simple and accurate spectrophotometric method for determination of trace amounts of silver ion in tap and wastewater solution and photographic solutions has been described. The spectrophotometric determination of silver ion using 2-mercaptobenzoxazole (MBO) in the presence of Triton X-100 as nonionic surfactant has been carried out. The Beer's law is obeyed over the concentration range of 0.1-9.0 microg mL(-1) of Ag+ ion with the detection limits of 1.6 ng mL(-1). The influence of type and amount of surfactant, pH, complexation time and amount of ligand on sensitivity of method were optimized. Finally the repeatability, accuracy and the effect of interfering ions on the determination of silver ion were evaluated. There is a good agreement between results of proposed method and atomic absorption spectrometry. PMID:17970312

  17. In cellulo structure determination of a novel cypovirus polyhedrin

    SciTech Connect

    Axford, Danny; Ji, Xiaoyun; Stuart, David I.; Sutton, Geoff

    2014-05-01

    The crystal structure of a previously unsolved type of cypovirus polyhedrin has been determined from data collected directly from frozen live insect cells. This work demonstrates that with the use of a microfocus synchrotron beam the structure of a novel viral polyhedrin could be successfully determined from microcrystals within cells, removing the preparatory step of sample isolation and maintaining a favourable biological environment. The data obtained are of high quality, comparable to that obtained from isolated crystals, and enabled a facile structure determination. A small but significant difference is observed between the unit-cell parameters and the mosaic spread of in cellulo and isolated crystals, suggesting that even these robust crystals are adversely affected by removal from the cell.

  18. Structure Determination of Membrane Proteins by Nuclear Magnetic Resonance Spectroscopy

    NASA Astrophysics Data System (ADS)

    Opella, Stanley J.

    2013-06-01

    Many biological membranes consist of 50% or more (by weight) membrane proteins, which constitute approximately one-third of all proteins expressed in biological organisms. Helical membrane proteins function as receptors, enzymes, and transporters, among other unique cellular roles. Additionally, most drugs have membrane proteins as their receptors, notably the superfamily of G protein-coupled receptors with seven transmembrane helices. Determining the structures of membrane proteins is a daunting task because of the effects of the membrane environment; specifically, it has been difficult to combine biologically compatible environments with the requirements for the established methods of structure determination. There is strong motivation to determine the structures in their native phospholipid bilayer environment so that perturbations from nonnatural lipids and phases do not have to be taken into account. At present, the only method that can work with proteins in liquid crystalline phospholipid bilayers is solid-state NMR spectroscopy.

  19. Structure Determination of Membrane Proteins by Nuclear Magnetic Resonance Spectroscopy

    PubMed Central

    Opella, Stanley J.

    2014-01-01

    Many biological membranes consist of 50% or more (by weight) membrane proteins, which constitute approximately one-third of all proteins expressed in biological organisms. Helical membrane proteins function as receptors, enzymes, and transporters, among other unique cellular roles. Additionally, most drugs have membrane proteins as their receptors, notably the superfamily of G protein–coupled receptors with seven transmembrane helices. Determining the structures of membrane proteins is a daunting task because of the effects of the membrane environment; specifically, it has been difficult to combine biologically compatible environments with the requirements for the established methods of structure determination. There is strong motivation to determine the structures in their native phospholipid bilayer environment so that perturbations from nonnatural lipids and phases do not have to be taken into account. At present, the only method that can work with proteins in liquid crystalline phospholipid bilayers is solid-state NMR spectroscopy. PMID:23577669

  20. 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.

  1. Structure of the pentameric ligand-gated ion channel ELIC cocrystallized with its competitive antagonist acetylcholine

    PubMed Central

    Pan, Jianjun; Chen, Qiang; Willenbring, Dan; Yoshida, Ken; Tillman, Tommy; Kashlan, Ossama B.; Cohen, Aina; Kong, Xiang-Peng; Xu, Yan; Tang, Pei

    2012-01-01

    ELIC, the pentameric ligand-gated ion channel from Erwinia chrysanthemi, is a prototype for Cys-loop receptors. Here we show that acetylcholine is a competitive antagonist for ELIC. We determine the acetylcholine–ELIC cocrystal structure to a 2.9-Å resolution and find that acetylcholine binding to an aromatic cage at the subunit interface induces a significant contraction of loop C and other structural rearrangements in the extracellular domain. The side chain of the pore-lining residue F247 reorients and the pore size consequently enlarges, but the channel remains closed. We attribute the inability of acetylcholine to activate ELIC primarily to weak cation-π and electrostatic interactions in the pocket, because an acetylcholine derivative with a simple quaternary-to-tertiary ammonium substitution activates the channel. This study presents a compelling case for understanding the structural underpinning of the functional relationship between agonism and competitive antagonism in the Cys-loop receptors, providing a new framework for developing novel therapeutic drugs. PMID:22395605

  2. Electromagnetic solitary structures in dense electron-positron-ion magnetoplasmas

    NASA Astrophysics Data System (ADS)

    Masood, W.; Hussain, S.; Rizvi, H.; Mushtaq, A.; Ayub, M.

    2010-12-01

    The linear and nonlinear propagation characteristics of low-frequency obliquely propagating magnetoacoustic waves in dense electron-positron-ion magnetoplasmas are studied in this paper by using the quantum magnetohydrodynamic (QMHD) model. A quantum Kadomtsev-Petviashvili (KP) equation is derived by using the reductive perturbation technique. The dependence of the fast and slow magnetoacoustic solitary waves on the positron concentration, the obliqueness parameter θ and the magnetic field is also investigated. The present investigation may have relevance to dense astrophysical environments where the quantum effects are expected to dominate.

  3. High-resolution heavy ion track structure imaging

    NASA Astrophysics Data System (ADS)

    Laczko, G.; Dangendorf, V.; Krämer, M.; Schardt, D.; Tittelmeier, K.

    2004-12-01

    Radiation action in matter depends on the details of the spatial distribution of energy transfer events on the nanometer scale. In this contribution, we present an instrument for experimental investigation of spatial ionisation patterns of ions in matter. The experimental system is based on a time projection chamber with a parallel drift field, parallel-plate charge and light amplification layers and optical readout with an image-intensified CCD camera (OPtical Avalanche Chamber (OPAC)). The chamber is operated with low pressure gas (4-40 hPa) to achieve a resolution of down to 50 nm in tissue density. Preliminary results of measurements and simulations are presented.

  4. Mixing and Matching Detergents for Membrane Protein NMR Structure Determination

    SciTech Connect

    Columbus, Linda; Lipfert, Jan; Jambunathan, Kalyani; Fox, Daniel A.; Sim, Adelene Y.L.; Doniach, Sebastian; Lesley, Scott A.

    2009-10-21

    One major obstacle to membrane protein structure determination is the selection of a detergent micelle that mimics the native lipid bilayer. Currently, detergents are selected by exhaustive screening because the effects of protein-detergent interactions on protein structure are poorly understood. In this study, the structure and dynamics of an integral membrane protein in different detergents is investigated by nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy and small-angle X-ray scattering (SAXS). The results suggest that matching of the micelle dimensions to the protein's hydrophobic surface avoids exchange processes that reduce the completeness of the NMR observations. Based on these dimensions, several mixed micelles were designed that improved the completeness of NMR observations. These findings provide a basis for the rational design of mixed micelles that may advance membrane protein structure determination by NMR.

  5. 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…

  6. 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...

  7. 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.

  8. Determinants of Market Structure and the Airline Industry

    NASA Technical Reports Server (NTRS)

    Raduchel, W.

    1972-01-01

    The general economic determinants of market structure are outlined with special reference to the airline industry. Included are the following facets: absolute size of firms; distributions of firms by size; concentration; entry barriers; product and service differentiation; diversification; degrees of competition; vertical integration; market boundaries; and economies of scale. Also examined are the static and dynamic properties of market structure in terms of mergers, government policies, and economic growth conditions.

  9. Solution structure of a designed cyclic peptide ligand for nickel and copper ions

    PubMed Central

    Eshelman, Matthew R.; Aldous, Amanda R.; Neupane, Kosh P.; Kritzer, Joshua A.

    2014-01-01

    Nuclear magnetic resonance (NMR) spectroscopy was used to study a cyclic peptide derived from the amino-terminal copper-and-nickel-binding (ATCUN) motif. The three-dimensional structure of the unliganded peptide in aqueous solution was solved by simulated annealing using distance constraints derived from Nuclear Overhauser Effects. A structural model for the Ni(II)-bound complex was also produced based on NMR evidence and prior spectroscopic data, which are consistent with crystal structures of linear ATCUN complexes. Structural interpolation, or “morphing,” was used to understand the transition of this highly structured cyclic peptide from its unliganded structure to its metal-ion-bound structure. PMID:25414527

  10. Experimental Test of Instability-Enhanced Collisional Friction for Determining Ion Loss in Two Ion Species Plasmas

    SciTech Connect

    Yip, Chi-Shung; Hershkowitz, Noah; Severn, Greg

    2010-06-04

    Recent experiments have shown that ions in weakly collisional plasmas containing two ion species of comparable densities nearly reach a common velocity at the sheath edge. A new theory suggests that collisional friction between the two ion species enhanced by two stream instability reduces the drift velocity of each ion species relative to each other near the sheath edge and finds that the difference in velocities at the sheath edge depends on the relative concentrations of the species. It is small 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, ion drift velocities were measured with laser-induced fluorescence in argon-xenon plasmas. We show that the predictions are in excellent agreement with the first experimental tests of the new model.

  11. 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.

  12. 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.

  13. Ion chromatography to detect salts in stone structures and to assess salt removal methods

    NASA Astrophysics Data System (ADS)

    Alvarez de Buergo, M.; Lopez-Arce, P.; Fort, R.

    2012-04-01

    Stone - and in general all materials- from built heritage is very often damaged by salt crystallisation processes. Such processes usually derive into a loss of material compactness, as salts - given specific conditions and parameters- crystallize inside the material pores, exerting a pressure against the material pore walls higher than what they can resist - similar to the effect of liquid water when converts to solid water or ice-, thus breaking and disrupting the material by generating fissures and increasing the pore volume ratio, loosing its initial cohesion. When these deterioration processes take place inside a structure, salts - from different sources: material itself, restoration materials, from the ground, etc.- may come up to the stone surface - either temporarily or in permanently-, from beneath it, as efflorescences, depending mainly on the microclimatic conditions of the environment and the salts source. Efflorescences can be analysed and their nature identified (e.g. by means of X ray diffraction, in which the mineralogical composition of the salt is obtained), which can be, general, of aid not only for restoration but for preventive conservation measures. But what we do not know a priori when only characterising salt compounds- is the extent of the damage due to the presence of salts inside a structure (sub- and cryptoefflorescences). In this work we present a procedure in which the depth of the salt content can be measured, and its nature identified, based on the use of the ion chromatography technique. This technique allows identifying the existing ions in a specific sample, both anions and cations. The procedure consists of drilling (with a drilling core ranging from 5 to 8 mm in diameter, therefore causing the minimum damage to the material) in a same point at different depths from the surface and several depths from the bottom. The samples obtained are analysed and the ion content determined, qualitative and quantitatively. By means of a

  14. Studies of the substorm on March 12, 1991: 1. Structure of substorm activity and auroral ions

    NASA Astrophysics Data System (ADS)

    Lazutin, L. L.; Kozelova, T. V.; Meredith, N. P.; Danielides, M.; Kozelov, B. V.; Jussila, J.; Korth, A.

    2007-02-01

    The substorm on March 12, 1991 is studied using the data of ground-based network of magnetometers, all-sky cameras and TV recordings of aurora, and measurements of particle fluxes and magnetic field onboard a satellite in the equatorial plane. The structure of substorm activity and the dynamics of auroral ions of the central plasma sheet (CPS) and energetic quasi-trapped ions related to the substorm are considered in the first part. It is shown that several sharp changes in the fluxes and pitch-angle distribution of the ions which form the substorm ion injection precede a dipolarization of the magnetic field and increases of energetic electrons, and coincide with the activation of aurora registered 20° eastward from the satellite. A conclusion is drawn about different mechanisms of the substorm acceleration (injection) of electrons and ions.

  15. Influence of Kilo-Electron Oxygen Ion Irradiation on Structural, Electrical and Optical Properties of CdTe Thin Films

    NASA Astrophysics Data System (ADS)

    Honey, Shehla; Thema, F. T.; Bhatti, M. T.; Ishaq, A.; Naseem, Shahzad; Maaza, M.

    2016-09-01

    In this paper, effect of oxygen (O+) ion irradiation on the properties of polycrystalline cubic structure CdTe thin films has been investigated. CdTe thin films were irradiated with O+ ions of energy 80keV at different fluence ranging from 1×1015 to 5×1016 ion/cm2 at room temperature. At 1×1015 ion/cm2 O+ ions fluence, the CdTe structure was maintained while XRD peaks of cubic phase were shifted toward lower angles. At 5×1016 ion/cm2 O+ ions fluence, cubic structure of CdTe thin films was transformed into hexagonal structure. In addition, electrical resistivity and optical bandgap were decreased with increasing O+ ion beam irradiation.

  16. 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

    2016-07-01

    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.

  17. 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.

  18. Determination of fluoride using ion-selective electrodes in the presence of aluminum.

    PubMed

    Borjigin, Siqingaowa; Ashimura, Yuuta; Yoshioka, Toshiaki; Mizoguchi, Tadaaki

    2009-12-01

    We describe a method for determining fluoride with ion-selective electrodes (ISEs). Tartrate and Tris-based total ionic strength adjustment buffers (TISABs) were found to lower the interference from aluminum to a greater extent than conventional citrate-based TISABs. We adopted a solid TISAB addition method that is simple to perform, and can be carried out without lowering the level of fluoride. The apparent recovery of fluoride was 95% or higher, even at 500 mg L(-1) of Al3+ when a tartrate and Tris-based TISAB was used. Interferences from common ions were not observed at 100 mg L(-1) levels. We determined the fluoride content in solid silicate samples with ISEs without preliminary steam distillation after alkali fusion processing. Adding a solid TISAB mixture consisting of tartaric acid, sodium tartrate, and Tris, however, eliminated any interference from high levels of aluminum and sodium and potassium carbonates. The proposed analytical method was also applied to the determination of fluoride in geochemical reference samples. PMID:20009331

  19. Acoustic double layer structures in dense magnetized electron-positron-ion plasmas

    SciTech Connect

    Akhtar, N.; Mahmood, S.

    2011-11-15

    The acoustic double layer structures are studied using quantum hydrodynamic model in dense magnetized electron-positron-ion plasmas. The extended Korteweg-de Vries is derived using reductive perturbation method. It is found that increase in the ion concentration in dense magnetized electron-positron plasmas increases the amplitude as well as the steepness of the double layer structure. However, increase in the magnetic field strength and decrease in the obliqueness of the nonlinear acoustic wave enhances only the steepness of the double layer structures. The numerical results have also been shown by using the data of the outer layer regions of white dwarfs given in the literature.

  20. Crystal structures reveal the molecular basis of ion translocation in sodium/proton antiporters.

    PubMed

    Coincon, Mathieu; Uzdavinys, Povilas; Nji, Emmanuel; Dotson, David L; Winkelmann, Iven; Abdul-Hussein, Saba; Cameron, Alexander D; Beckstein, Oliver; Drew, David

    2016-03-01

    To fully understand the transport mechanism of Na(+)/H(+) exchangers, it is necessary to clearly establish the global rearrangements required to facilitate ion translocation. Currently, two different transport models have been proposed. Some reports have suggested that structural isomerization is achieved through large elevator-like rearrangements similar to those seen in the structurally unrelated sodium-coupled glutamate-transporter homolog GltPh. Others have proposed that only small domain movements are required for ion exchange, and a conventional rocking-bundle model has been proposed instead. Here, to resolve these differences, we report atomic-resolution structures of the same Na(+)/H(+) antiporter (NapA from Thermus thermophilus) in both outward- and inward-facing conformations. These data combined with cross-linking, molecular dynamics simulations and isothermal calorimetry suggest that Na(+)/H(+) antiporters provide alternating access to the ion-binding site by using elevator-like structural transitions. PMID:26828964