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Sample records for jet-cooled molecular ions

  1. An Intense Slit Discharge Source of Jet-Cooled Molecular Ions and Radicals (T(sub rot) less than 30 K)

    NASA Technical Reports Server (NTRS)

    Anderson, David T.; Davis, Scott; Zwier, Timothy S.; Nesbitt, David J.

    1996-01-01

    A novel pulsed, slit supersonic discharge source is described for generating intense jet-cooled densities of radicals (greater than 10(exp 12)/cu cm) and molecular ions (greater than 10(exp 10)/cu cm) under long absorption path (80 cm), supersonically cooled conditions. The design confines the discharge region upstream of the supersonic expansion orifice to achieve efficient rotational cooling down to 30 K or less. The collisionally collimated velocity distribution in the slit discharge geometry yields sub-Doppler spectral linewidths, which for open-shell radicals reveals spin-rotation splittings and broadening due to nuclear hyperfine structure. Application of the slit source for high-resolution, direct IR laser absorption spectroscopy in discharges is demonstrated on species such as OH, H3O(+) and N2H(+).

  2. Jet-cooled molecular radicals in slit supersonic discharges: Sub-Doppler infrared studies of methyl radical

    NASA Astrophysics Data System (ADS)

    Davis, Scott; Anderson, David T.; Duxbury, Geoffrey; Nesbitt, David J.

    1997-10-01

    A novel high-intensity source of jet-cooled molecular radicals is described based on the combination of (i) slit supersonic expansions with (ii) pulsed electric discharges. The electrode bias configuration effectively confines the discharge to a region upstream of the supersonic expansion, which results both in efficient rotational cooling (Trot≈25 K) and high radical densities (>1014/cm3). In conjunction with direct absorption laser probe methods, this discharge source provides a general technique for high-resolution IR studies of jet-cooled radicals. Performance of the slit discharge system is demonstrated on v=1←0 rovibrational transitions in jet-cooled OH radicals, which indicate sub-Doppler linewidths (Δν≈100 MHz) when probed along the slit expansion axis. The enhanced spectral resolution of the slit discharge geometry is utilized to probe the v3=1←0 asymmetric CH stretch vibration-rotation spectra of CH3 radical. Under sub-Doppler conditions, spin-rotation splittings are fully resolved and nuclear hyperfine splittings partially resolved in all of the transitions, permitting the first measure of Fermi contact interactions [af″=-65.5(9) MHz, ɛbb″=-354(5) MHz, af'=-65(2) MHz, ɛbb'=-353(2) MHz] and therefore both the sign and magnitude of spin-polarization effects for CH3 under isolated gas-phase conditions. The results permit direct comparison with high level ab initio calculations, and highlight a clear trend in spin-polarization effects between condensed and gas-phase behavior.

  3. Thermal Management Using Pulsating Jet Cooling Technology

    NASA Astrophysics Data System (ADS)

    Alimohammadi, S.; Dinneen, P.; Persoons, T.; Murray, D. B.

    2014-07-01

    The existing methods of heat removal from compact electronic devises are known to be deficient as the evolving technology demands more power density and accordingly better cooling techniques. Impinging jets can be used as a satisfactory method for thermal management of electronic devices with limited space and volume. Pulsating flows can produce an additional enhancement in heat transfer rate compared to steady flows. This article is part of a comprehensive experimental and numerical study performed on pulsating jet cooling technology. The experimental approach explores heat transfer performance of a pulsating air jet impinging onto a flat surface for nozzle-to-surface distances 1 <= H/D <= 6, Reynolds numbers 1,300 <= Re <= 2,800 pulsation frequency 2Hz <= f <= 65Hz, and Strouhal number 0.0012 <= Sr = fD/Um <= 0.084. The time-resolved velocity at the nozzle exit is measured to quantify the turbulence intensity profile. The numerical methodology is firstly validated using the experimental local Nusselt number distribution for the steady jet with the same geometry and boundary conditions. For a time-averaged Reynolds number of 6,000, the heat transfer enhancement using the pulsating jet for 9Hz <= f <= 55Hz and 0.017 <= Sr <= 0.102 and 1 <= H/D <= 6 are calculated. For the same range of Sr number, the numerical and experimental methods show consistent results.

  4. Molecular ion photofragment spectroscopy

    SciTech Connect

    Bustamente, S.W.

    1983-11-01

    A new molecular ion photofragment spectrometer is described which features a supersonic molecular beam ion source and a radio frequency octapole ion trap interaction region. This unique combination allows several techniques to be applied to the problem of detecting a photon absorption event of a molecular ion. In particular, it may be possible to obtain low resolution survey spectra of exotic molecular ions by using a direct vibrational predissociation process, or by using other more indirect detection methods. The use of the spectrometer is demonstrated by measuring the lifetime of the O/sub 2//sup +/(/sup 4/..pi../sub u/) metastable state which is found to consist of two main components: the /sup 4/..pi../sub 5/2/ and /sup 4/..pi../sub -1/2/ spin components having a long lifetime (approx. 129 ms) and the /sup 4/..pi../sub 3/2/ and /sup 4/..pi../sub 1/2/ spin components having a short lifetime (approx. 6 ms).

  5. Charge exchange molecular ion source

    DOEpatents

    Vella, Michael C.

    2003-06-03

    Ions, particularly molecular ions with multiple dopant nucleons per ion, are produced by charge exchange. An ion source contains a minimum of two regions separated by a physical barrier and utilizes charge exchange to enhance production of a desired ion species. The essential elements are a plasma chamber for production of ions of a first species, a physical separator, and a charge transfer chamber where ions of the first species from the plasma chamber undergo charge exchange or transfer with the reactant atom or molecules to produce ions of a second species. Molecular ions may be produced which are useful for ion implantation.

  6. Stimulated emission pumping spectroscopy of jet-cooled C3

    NASA Astrophysics Data System (ADS)

    Rohlfing, Eric A.; Goldsmith, J. E. M.

    1989-06-01

    We report a dispersed fluorescence spectrum obtained for excitation of a ∑+u-∑+g vibronic band of C3 at 33 588 cm-1, part of a newly discovered electronic system. Rotationally resolved stimulated-emission-pumping spectra of jet-cooled C3 using this ∑+u intermediate state are presented for dumping to the 0v121 (1≤v2≤13) and 6v121 (1≤v2≤5) levels in the 1Σ+g ground state. Vibrational term energies, rotational constants, and l-type doubling parameters are determined for each level.

  7. Sub-Doppler Jet-Cooled Infrared Spectroscopy of ND2H2+ and ND3H+ in the NH Stretch Fundamental Modes

    NASA Astrophysics Data System (ADS)

    Chang, Chih-Hsuan; Nesbitt, David

    2014-06-01

    Sub-Doppler jet-cooled rovibrational spectra of ND3H+, ND2H2+, and NDH3+ ions in various fundamental NH modes were observed and analyzed using difference frequency generation infrared spectroscopy. The ions were generated in the concentration-modulation slit-jet expansion via a H3+ proton transfer mechanism in a discharge mixture of ND3/H2O and H2 gases. NH mode excitation in ND3H+ ion yielded a prominent Q branch feature and parallel band rotational structure. Rotational transitions were confirmed unambiguously by four-line ground state combination differences within frequency measurement accuracy (10 MHz). The band origin was determined to be 3316.8413(9) cm-1. Perturbation in the upper state was observed from analysis of residuals. In the case of ND2H2+, both NH symmetric (b-type) and anti-symmetric (c-type) modes were observed and assigned for the first time, yielding band origins of 3297.5440(1) and 3337.9050(1) cm-1, respectively. The intensity for the two fundamental bands was interpreted with simple context of a bond-dipole model. The present study provided high precision ground state rotational constants (A"=4.85675(4), B"=3.96829(4), C"=3.44667(6) cm-1), which should facilitate microwave searches for isotope-substituted ammonium ions in the regions of interstellar medium, such as dense molecular clouds or younger stellar objects.

  8. Jet-Cooled Emission Spectra of the Xylyl Radicals

    NASA Astrophysics Data System (ADS)

    Selco, J. I.; Carrick, P. G.

    1995-09-01

    Jet-cooled electronic emission spectra from ortho-, meta-, and para-xylyl (methylbenzyl) radicals have been recorded with a corona excited supersonic expansion (CESE) apparatus. A full vibronic analysis of the D1 → D0 transitions for all three isomers has been carried out, allowing for unambiguous assignments of the gas-phase ground state vibrational frequencies. For modes exhibiting progressions (numbering according to Green and Wilson) (11 (18a), 29 (6b), 10 (6a), 9 (1), 25 (3) and 5 (14) in ortho-xylyl; 10 (6b) in meta-xylyl; and 5 (1), 6 (6a), 3 (7a), and 17 (10a) in para-xylyl), anharmonicity constants are calculated and reported. Although CESE excitation of the xylenes (used in this study as precursors) did not result in the interconversion of isomers, it does occur along with homolytic methyl C-H bond dissociation during the formation of the radicals.

  9. High-resolution photoabsorption spectrum of jet-cooled propyne

    SciTech Connect

    Jacovella, U.; Holland, D. M. P.; Boyé-Péronne, S.; Joyeux, D.; Archer, L. E.; Oliveira, N. de; Nahon, L.; Lucchese, R. R.; Xu, Hong; Pratt, S. T.

    2014-09-21

    The absolute photoabsorption cross section of propyne was recorded between 62 000 and 88 000 cm{sup −1} by using the vacuum-ultraviolet, Fourier-transform spectrometer at the Synchrotron Soleil. This cross section spans the region including the lowest Rydberg bands and extends above the Franck-Condon envelope for ionization to the ground electronic state of the propyne cation, X{sup ~+}. Room-temperature spectra were recorded in a flowing cell at 0.9 cm{sup −1} resolution, and jet-cooled spectra were recorded at 1.8 cm{sup −1} resolution and a rotational temperature of ∼100 K. The reduced widths of the rotational band envelopes in the latter spectra reveal new structure and simplify a number of assignments. Although nf Rydberg series have not been assigned previously in the photoabsorption spectrum of propyne, arguments are presented for their potential importance, and the assignment of one nf series is proposed. As expected from previous photoelectron spectra, Rydberg series are also observed above the adiabatic ionization threshold that converge to the v{sub 3}{sup +} = 1 and 2 levels of the C≡C stretching vibration.

  10. Laser-cooled atomic ions as probes of molecular ions

    SciTech Connect

    Brown, Kenneth R.; Viteri, C. Ricardo; Clark, Craig R.; Goeders, James E.; Khanyile, Ncamiso B.; Vittorini, Grahame D.

    2015-01-22

    Trapped laser-cooled atomic ions are a new tool for understanding cold molecular ions. The atomic ions not only sympathetically cool the molecular ions to millikelvin temperatures, but the bright atomic ion fluorescence can also serve as a detector of both molecular reactions and molecular spectra. We are working towards the detection of single molecular ion spectra by sympathetic heating spectroscopy. Sympathetic heating spectroscopy uses the coupled motion of two trapped ions to measure the spectra of one ion by observing changes in the fluorescence of the other ion. Sympathetic heating spectroscopy is a generalization of quantum logic spectroscopy, but does not require ions in the motional ground state or coherent control of the ion internal states. We have recently demonstrated this technique using two isotopes of Ca{sup +} [Phys. Rev. A, 81, 043428 (2010)]. Limits of the method and potential applications for molecular spectroscopy are discussed.

  11. Laser spectroscopy and dynamics of the jet-cooled AsH2 free radical

    NASA Astrophysics Data System (ADS)

    He, Sheng-Gui; Clouthier, Dennis J.

    2007-04-01

    The ÃA12-X˜B12 electronic transition of the jet-cooled AsH2 free radical has been studied by laser-induced fluorescence (LIF), wavelength-resolved emission, and fluorescence lifetime measurements. The radical was produced by a pulsed electric discharge through a mixture of arsine (AsH3) and high pressure argon at the exit of a pulsed valve. Nine vibronic bands were identified by LIF spectroscopy in the 505-400nm region, including a long progression in the bending mode and two bands (101 and 101201) involving the excited state As-H symmetric stretch. Single vibronic level emission spectra showed similar activity in the bending and symmetric stretching frequencies of the ground state. High-resolution spectra of the 000 band exhibited large spin splittings and small, resolved arsenic hyperfine splittings, due to a substantial Fermi contact interaction in the excited state. The rotational constants obtained in the analysis gave effective molecular structures of r0″=1.5183(1)Å, θ0″=90.75(1)° and r0'=1.4830(1)Å, θ0'=123.10(2)°. The excited state fluorescence lifetimes vary dramatically with rovibronic state, from a single value of 1.4μs to many with lifetimes less than 10ns, behavior which the authors interpret as signaling the onset of a predissociative process near the zero-point level of the ground state.

  12. Dispersed Fluorescence Spectroscopy of Jet-Cooled Isobutoxy, 2-METHYL-1-BUTOXY, and Isopentoxy Radicals

    NASA Astrophysics Data System (ADS)

    Reza, Md Asmaul; Reilly, Neil J.; Alam, Jahangir; Mason, Amy; Liu, Jinjun

    2015-06-01

    It is well known that rate constants of certain reactions of alkoxy radicals, e.g., unimolecular dissociation (decomposition by C-C bond fission) and isomerization via 1,5 H-shift, are highly sensitive to the molecular structure. In the present and the next talks, we report dispersed fluorescence (DF) spectra of various alkoxy radicals obtained under supersonic jet-cooled conditions by pumping different vibronic bands of their tilde B ← tilde X laser induced fluorescence (LIF) excitation spectra. This talk focuses on the DF spectra of 2-methyl-1-propoxy (isobutoxy), 2-methyl-1-butoxy, and 3-methyl-1-butoxy (isopentoxy). In all cases, strong CO-stretch progressions were observed, as well as transitions to other vibrational levels, including low-frequency ones. Quantum chemical calculations were carried out to aid the assignment of the DF spectra. Franck-Condon factors were calculated using the ezSpectrum program. Wu, Q.; Liang, G.; Zu, L.; Fang, W. J. Phys. Chem A 2012, 116, 3156-3162. Lin, J.; Wu, Q.; Liang, G.; Zu, L.; Fang, W. RSC Adv. 2012, 2, 583-589. Liang, G.; Liu , C.; Hao, H.; Zu, L.; Fang, W. J. Phys. Chem. A 2013, 117, 13229- 13235. V. Mozhayskiy and A. I. Krylov, http://iopenshell.usc.edu/

  13. Fluorescence lifetimes of jet-cooled tryptophan: elimination of complications from 1La emission

    NASA Astrophysics Data System (ADS)

    Huang, Yuhui; Arnold, Steven; Sulkes, Mark

    1994-08-01

    Fluorescence lifetime measurements can be made on the decay of individual 'frozen' conformers of tryptophan analogs in supersonic gas expansions. These measurements have shown differences in single exponential lifetimes among conformers of a given analog, results which are strongly consistent with the presence of conformation-dependent charge transfer quenching. For jet cooled tryptophan, however, one of the conformers emits from 1La, thereby complicating any interpretation of the results. To remove this problem we considered tryptophan analogs with C-5 substituents, in which all the jet cooled conformers emit from 1Lb. We observed differences in conformer lifetimes similar to cases considered earlier. In the course of this work we discovered that, in contrast to tryptophan, 5- methoxytryptophan shows single exponential decay in solution. Based on additional data for jet cooled samples, we propose the most likely explanation to be substituent induced changes in conformer geometries and populations.

  14. Development of Broad Range Scan Capabilities with Jet Cooled Cavity Ringdown Spectroscopy

    NASA Astrophysics Data System (ADS)

    Codd, Terrance J.; Chen, Ming-Wei; Miller, Terry A.

    2011-06-01

    We have developed a technique for obtaining broad scans, >100 Cm-1, for jet cooled cavity ringdown spectroscopy (CRDS) spectra. Previously the scans of the jet cooled, CRDS apparatus were limited to <10 Cm-1 due to the use of a narrow linewidth radiation source. However, by coupling our jet cooled, CRDS apparatus with a moderate resolution (≃q 0.05 Cm-1) dye laser we are able to greatly increase our rate of data acquisition thereby gaining the capability to perform broad spectral surveys of jet cooled molecules. As a test of the capabilities of the technique we have scanned the tilde{A}-tilde{X} transition of NO_3 previously reported by Deev et al. at room temperature. We believe that this will be a very useful technique to search for transitions of cold molecules whose frequencies are not well known and which later can be studied using high resolution methods. A. Deev, J. Sommar, and M. Okumura, J. Chem. Phys. 122, 224305 (2005).

  15. Photodissociation resonances of jet-cooled NO2 at the dissociation threshold by CW-CRDS.

    PubMed

    Dupré, Patrick

    2015-05-01

    Around 398 nm, the jet-cooled-spectrum of NO2 exhibits a well identified dissociation threshold (D0). Combining the continuous-wave absorption-based cavity ringdown spectroscopy technique and laser induced fluorescence detection, an energy range of ∼25 cm(-1) is analyzed at high resolution around D0. In addition to the usual molecular transitions to long-lived energy levels, ∼115 wider resonances are observed. The position, amplitude, and width of these resonances are determined. The resonance width spreads from ∼0.006 cm(-1) (i.e., ∼450 ps) to ∼0.7 cm(-1) (∼4 ps) with large fluctuations. The identification of at least two ranges of resonance width versus the excess energy can be associated with the opening of the dissociation channels NO2→NO(X(2)Π1/2, v=0, J=1/2+O((3)P2) and NO2→NO(X(2)Π1/2, v=0, J=3/2)+O((3)P2). This analysis corroborates the existence of loose transition states close to the dissociation threshold as reported previously and in agreement with the phase space theory predictions as shown by Tsuchiya's group [Miyawaki et al., J. Chem. Phys. 99, 254-264 (1993)]. The data are analyzed in the light of previously reported frequency- and time-resolved data to provide a robust determination of averaged unimolecular dissociation rate coefficients. The density of reactant levels deduced (ρreac ∼ 11levels/cm(-1)) is discussed versus the density of transitions, the density of resonances, and the density of vibronic levels. PMID:25956098

  16. Molecular ion sources for low energy semiconductor ion implantation (invited).

    PubMed

    Hershcovitch, A; Gushenets, V I; Seleznev, D N; Bugaev, A S; Dugin, S; Oks, E M; Kulevoy, T V; Alexeyenko, O; Kozlov, A; Kropachev, G N; Kuibeda, R P; Minaev, S; Vizir, A; Yushkov, G Yu

    2016-02-01

    Smaller semiconductors require shallow, low energy ion implantation, resulting space charge effects, which reduced beam currents and production rates. To increase production rates, molecular ions are used. Boron and phosphorous (or arsenic) implantation is needed for P-type and N-type semiconductors, respectively. Carborane, which is the most stable molecular boron ion leaves unacceptable carbon residue on extraction grids. A self-cleaning carborane acid compound (C4H12B10O4) was synthesized and utilized in the ITEP Bernas ion source resulting in large carborane ion output, without carbon residue. Pure gaseous processes are desired to enable rapid switch among ion species. Molecular phosphorous was generated by introducing phosphine in dissociators via 4PH3 = P4 + 6H2; generated molecular phosphorous in a pure gaseous process was then injected into the HCEI Calutron-Bernas ion source, from which P4(+) ion beams were extracted. Results from devices and some additional concepts are described. PMID:26932065

  17. Molecular ion sources for low energy semiconductor ion implantation (invited)

    NASA Astrophysics Data System (ADS)

    Hershcovitch, A.; Gushenets, V. I.; Seleznev, D. N.; Bugaev, A. S.; Dugin, S.; Oks, E. M.; Kulevoy, T. V.; Alexeyenko, O.; Kozlov, A.; Kropachev, G. N.; Kuibeda, R. P.; Minaev, S.; Vizir, A.; Yushkov, G. Yu.

    2016-02-01

    Smaller semiconductors require shallow, low energy ion implantation, resulting space charge effects, which reduced beam currents and production rates. To increase production rates, molecular ions are used. Boron and phosphorous (or arsenic) implantation is needed for P-type and N-type semiconductors, respectively. Carborane, which is the most stable molecular boron ion leaves unacceptable carbon residue on extraction grids. A self-cleaning carborane acid compound (C4H12B10O4) was synthesized and utilized in the ITEP Bernas ion source resulting in large carborane ion output, without carbon residue. Pure gaseous processes are desired to enable rapid switch among ion species. Molecular phosphorous was generated by introducing phosphine in dissociators via 4PH3 = P4 + 6H2; generated molecular phosphorous in a pure gaseous process was then injected into the HCEI Calutron-Bernas ion source, from which P4+ ion beams were extracted. Results from devices and some additional concepts are described.

  18. Molecular ions, Rydberg spectroscopy and dynamics

    SciTech Connect

    Jungen, Ch.

    2015-01-22

    Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering.

  19. Cavity QED in a molecular ion trap

    SciTech Connect

    Schuster, D. I.; Bishop, Lev S.; Chuang, I. L.; DeMille, D.; Schoelkopf, R. J.

    2011-01-15

    We propose a class of experiments using rotational states of dipolar molecular ions trapped near an on-chip superconducting microwave cavity. Molecular ions have several advantages over neutral molecules for such cavity quantum electrodynamics experiments. In particular, ions can be loaded easily into deep rf traps and are held independent of their internal state. An analysis of the detection efficiency for, and coherence properties of, the molecular ions is presented. We discuss approaches for manipulating quantum information and performing high-resolution rotational spectroscopy using this system.

  20. Vibronic spectroscopy of jet-cooled hydrogen-bonded clusters

    NASA Astrophysics Data System (ADS)

    Gerhards, M.; Kimpfel, B.; Pohl, M.; Schmitt, M.; Kleinermanns, K.

    1992-07-01

    Mass-selected, two-photon resonant ionisation spectra of supersonically cooled p-cresol · (H 2O) n and phenol · (H 2O) n are reported. Cluster spectra with one, two and three water molecules attached can be unambiguously assigned. A monotonic shift of the electronic spectra with increasing cluster size is not observed here. The spectrum of p-cresol · (H 2O) 1, is red-shifted relative to the free p-cresol spectrum, while the p-cresol · (H 2O) 2,3 electronic origins are blue-shifted relative to p-cresol · (H 2O) 1 but still lie on the red side of the monomer. Simple, highest occupied molecular orbital—lowest unoccupied molecular orbital (HOMO—LUMO) considerations based on an initio calculations show that this can be explained by the inductive effect exerted on the O-atom of p-cresol, which acts as proton donor and acceptor in the H-bonding. The blue shift of n-π* transitions of H-bonded chromophores with carbonyl groups like CH 2O · (H 2O) 1 can be explained similarly. Vibrational spectra of supersonically cooled complexes of p-cresol with H 2O and CH 3OH were further analysed by dispersed fluorescence and stimulated emission, detected by two-colour ionisation dip. In p-cresol · (H 2O) 1, progressions of the intermolecular cluster stretch vibration and its combination bands with intramolecular cluster vibrations were observed with similar frequencies in the S 0 and S 1 states. In p-cresol · (H 2O) 3, further intense intermolecular bands arise, namely the hydrogen-bridge bending and torsion vibrations. This can be attributed to the lower symmetry of these clusters. Ab initio quantum chemical calculations show p-cresol · (H 2O) 3 to have a higher H-bond stretch frequency than p-cresol · (H 2O) 1, because its (unsymmetric) cyclic structure is more rigid. A characteristic pattern of CH 3 torsional bands in p-cresol is observed with complex structures due the CH 3 torsion—overall rotation interaction. Although their appearance is similar, the spacing of

  1. Peltier Refrigerators for Molecular Ion Sources

    NASA Astrophysics Data System (ADS)

    Hershcovitch, Ady

    2008-11-01

    Molecular ion sources have been considered for various applications. In particular, there is considerable effort to develop decaborane and octadecaborane ion sources for the semiconductor industry. Since the invention of the transistor, the trend has been to miniaturize semiconductor devices. As semiconductors become smaller (and get miniaturized), ion energy needed for implantation decreases, since shallow implantation is desired. But, due to space charge (intra-ion repulsion) effects, forming and transporting ion beams becomes a rather difficult task. These problems associated with lower energy ion beams limit implanter ion currents, thus leading to low production rates. One way to tackle the space charge problem is to use singly charged molecular ions. A crucial aspect in generating large molecular ion beam currents is ion source temperature control. Peltier coolers, which have in the past successfully utilized in BaF2 and CSI gamma ray detectors, may be ideal for this application. Clogging prevention of molecular ion sources is also a hurdle, which was overcome with special slots. Both topics are to be presented.

  2. Jet-Cooled Spectroscopy on the Ailes Infrared Beamline of the Synchrotron Radiation Facility Soleil

    NASA Astrophysics Data System (ADS)

    Georges, Robert

    2015-06-01

    . Vervloet, Phys. Chem. Chem. Phys. 15, 10141-10150 (2013) The cyclic ground state structure of the HF trimer revealed by far-infrared jet-cooled Fourier transform spectroscopy. P. Asselin, P. Soulard, B. Madebène, M. Goubet, T. R. Huet, R. Georges, O. Pirali and P. Roy, Phys. Chem. Chem. Phys. 16(10), 4797-806 (2014) Standard free energy of the equilibrium between the trans-monomer and the cyclic-dimer of acetic acid in the gas phase from infrared spectroscopy. M. Goubet, P. Soulard, O. Pirali, P. Asselin, F. Réal, S. Gruet, T. R. Huet, P. Roy and R. Georges, Phys. Chem. Chem. Phys. DOI: 10.1039/c4cp05684a

  3. n,. pi. /sup */ state of jet-cooled benzophenone as studied by sensitized phosphorescence excitation spectroscopy

    SciTech Connect

    Kamei, S.; Sato, T.; Mikami, N.; Ito, M.

    1986-10-23

    The sensitized phosphorescence excitation spectrum of jet-cooled benzophenone due to the S/sub 1/(n,..pi../sup */) produced from S/sub 0/ transition has been measured. It was found that the spectrum consists exclusively of several long progressions of 60 cm/sup -1/ which is the in-phase torsional mode of the phenyl rings. The vibrational analysis and the potential calculation shows that the in the S/sub 1/(n,..pi../sup */) state great geometry changes occur in the dihedral angle between the phenyl rings, the C=O bond distance, and the C-C bonds adjacent to the C=O bond.

  4. Secondary ion mass spectrometry of MCsn+molecular ion complexes

    NASA Astrophysics Data System (ADS)

    Saha, Biswajit; Chakraborty, Purushottam

    2007-05-01

    Excellent detection sensitivity, high dynamic range and good depth resolution make the SIMS technique extremely powerful for the analysis of surfaces and interfaces. However, a serious problem in SIMS analysis is its "matrix effect" that hinders the quantification of a certain species in a sample and consequently, probing the composition of surfaces or interfaces by SIMS is greatly hindered. Appropriate corrective measures are therefore, needed to calibrate the secondary ion currents into respective concentrations for accurate compositional analysis. Working in the MCs+-SIMS mode (M - element to be analyzed, Cs+ - bombarding ions) can circumvent the matrix effect. The quantitative potential of the MCs+-SIMS method is understood by assuming that an MCs+ ion is generated by the combination of a secondary neutral M0 atom with a re-sputtered Cs+ ion in the near-surface region. The emission process for the species M0 is thus decoupled from the subsequent MCs+ ion formation process, in analogy with the ion formation in secondary neutral mass spectrometry (SNMS), resulting in a drastic decrease in matrix effect. Although this technique has found its applicability in direct quantification, it generally suffers from a low useful yield. In such cases, detection of MCsn+(n = 2, 3, …) molecular ions offers a better sensitivity as the yields of such molecular ion complexes have often been found higher than that of MCs+ ions. This is true in most of the cases where the elements are strongly electronegative with respect to cesium. Several works have been reported on the emission of MCsn+molecular ions in the SIMS process, but a complete understanding on the formation mechanism of these ion complexes is still lacking. The kinetic energy distributions of secondary MCsn+molecular ion complexes has been found to be an effective approach to estimate the local instantaneous surface work function changes under various surface exposure conditions, thereby enabling one to elucidate on

  5. Physics with fast molecular-ion beams

    SciTech Connect

    Kanter, E.P.

    1980-01-01

    Fast (MeV) molecular-ion beams provide a unique source of energetic projectile nuclei which are correlated in space and time. The recognition of this property has prompted several recent investigations of various aspects of the interactions of these ions with matter. High-resolution measurements on the fragments resulting from these interactions have already yielded a wealth of new information on such diverse topics as plasma oscillations in solids and stereochemical structures of molecular ions as well as a variety of atomic collision phenomena. The general features of several such experiments will be discussed and recent results will be presented.

  6. Molecular phosphorus ion source for semiconductor technology

    SciTech Connect

    Gushenets V. I.; Hershcovitch A.; Bugaev, A.S.; Oks, E.M.; Kulevoy, T.V.

    2012-02-15

    This paper presents results on the generation of molecular phosphorus ion beams in a hot filament ion source. Solid red phosphorous is evaporated mainly as tetra-atomic molecules up to a temperature of 800 C. Thus, one of the main conditions for producing maximum P{sub 4}{sup +} fraction in the beam is to keep the temperature of the phosphorous oven, the steam line and the discharge chamber walls no greater than 800 C. The prior version of our ion source was equipped with a discharge chamber cooling system. The modified source ensured a P{sub 4}{sup +} ion beam current greater than 30% of the total beam current.

  7. Laser spectroscopy of jet-cooled NiF: Application of Hougen's approximate model for the low-lying electronic states

    NASA Astrophysics Data System (ADS)

    Arsenault, D. L.; Tokaryk, D. W.; Adam, A. G.; Linton, C.

    2016-06-01

    We have taken laser-induced fluorescence spectra of jet-cooled nickel monofluoride formed in a laser-ablation molecular beam source. Dispersed-fluorescence spectroscopy confirms predictions by Hougen (2011) that the parity assignments of levels in the Ω = 1 / 2 state 1570 cm-1 above the ground state should be reversed from those given in Krouti et al. (2002). The quality of the high-resolution spectra was sufficient to measure the [22.9]1.5-X1.5 band for five isotopologues of nickel and the [22.9]1.5-[0.25]0.5 band for molecules containing 58Ni and 60Ni. The spectral line positions for each isotopologue were fit to the Hamiltonian model given by Hougen, which was extended to allow for calculation of the parity-splitting parameter in the ground state.

  8. Spectroscopic observation of jet-cooled 2,5-dichlorobenzyl radical generated by corona discharge

    NASA Astrophysics Data System (ADS)

    Yi, Eun Hye; Yoon, Young Wook; Lee, Sang Kuk

    2014-07-01

    Vibronically excited but jet-cooled 2,5-dichlorobenzyl radical was generated from 2,5-dichlorotoluene precursor in a large excess of helium carrier gas, from which the visible vibronic emission spectrum was recorded. From an analysis of the spectrum observed, it was found that the origin band shows larger shift to red than those expected from mono-substitutions, which has been discussed in terms of orientation of substituents. Also, the electronic energy of the D1 → D0 transition and vibrational mode frequencies at the ground electronic state of the 2,5-dichlorobenzyl radical were determined in comparison with the known vibrational data of precursor and ab initio calculations.

  9. Pyrene measurements in sooting low pressure methane flames by jet-cooled laser-induced fluorescence.

    PubMed

    Wartel, M; Pauwels, J-F; Desgroux, P; Mercier, X

    2011-12-15

    This paper presents in detail the study we carried out concerning the pyrene measurement by jet-cooled laser-induced fluorescence (JCLIF) in different sooting low pressure methane flames. The aim of this paper is both to demonstrate the potentialities of this technique for the measurement of such moderately sized polycyclic aromatic hydrocarbons under sooting flame conditions and to provide new experimental data for the understanding and the development of chemical models of the soot formation processes. Several concentration profiles of pyrene measured in different sooting flame (various pressure and equivalence ratio) are presented. The validation of the JCLIF method for pyrene measurements is explained in detail as well as the calibration procedure, based on the standard addition method, which has been implemented for the quantification of the concentration profiles. Sensitivity lower than 1 ppb was obtained for the measurement of this species under sooting flame conditions. PMID:22029528

  10. Photodissociation resonances of jet-cooled NO{sub 2} at the dissociation threshold by CW-CRDS

    SciTech Connect

    Dupré, Patrick

    2015-05-07

    Around 398 nm, the jet-cooled-spectrum of NO{sub 2} exhibits a well identified dissociation threshold (D{sub 0}). Combining the continuous-wave absorption-based cavity ringdown spectroscopy technique and laser induced fluorescence detection, an energy range of ∼25 cm{sup −1} is analyzed at high resolution around D{sub 0}. In addition to the usual molecular transitions to long-lived energy levels, ∼115 wider resonances are observed. The position, amplitude, and width of these resonances are determined. The resonance width spreads from ∼0.006 cm{sup −1} (i.e., ∼450 ps) to ∼0.7 cm{sup −1} (∼4 ps) with large fluctuations. The identification of at least two ranges of resonance width versus the excess energy can be associated with the opening of the dissociation channels NO{sub 2}→NO(X {sup 2}Π{sub 1/2}, v=0, J=1/2)+O({sup 3}P{sub 2}) and NO{sub 2}→NO(X {sup 2}Π{sub 1/2}, v=0, J=3/2)+O({sup 3}P{sub 2}). This analysis corroborates the existence of loose transition states close to the dissociation threshold as reported previously and in agreement with the phase space theory predictions as shown by Tsuchiya’s group [Miyawaki et al., J. Chem. Phys. 99, 254–264 (1993)]. The data are analyzed in the light of previously reported frequency- and time-resolved data to provide a robust determination of averaged unimolecular dissociation rate coefficients. The density of reactant levels deduced (ρ{sub reac} ∼ 11 levels/cm{sup −1}) is discussed versus the density of transitions, the density of resonances, and the density of vibronic levels.

  11. Dissociative Recombination of Molecular Ions for Astrochemistry

    NASA Astrophysics Data System (ADS)

    Savin, Daniel W.; Novotný, O.; Becker, A.; Buhr, H.; Geppert, W.; Hamberg, M.; Krantz, C.; Kreckel, H.; Schwalm, D.; Spruck, K.; Stützel, J.; Wolf, A.; Yang, B.

    2013-06-01

    Dissociative recombination (DR) of molecular ions is a key chemical process in the cold interstellar medium (ISM). DR affects the composition, charge state, and energy balance of such environments. Astrochemical models of the ISM require reliable total DR cross sections as well as knowledge of the chemical composition and excitation states of the neutral DR products. Theory cannot reliably provide these data. We have systematically measured DR for many astrophysically relevant molecular ions utilizing the TSR storage ring at the Max-Planck-Institute for Nuclear Physics in Heidelberg, Germany. We used the merged ion-electron beam technique combined with an energy- and position-sensitive imaging detector and are able to study DR down to plasma temperatures of 10 K. The DR count rate is used to obtain absolute DR rate coefficient. Additionally we determine the masses of the DR products by measuring their kinetic energy. This allows us to assign particular DR fragmentation channels and to obtain their branching ratios. Moreover, the distribution of detected fragment distances provides information on the kinetic energy released in DR and thus also on the internal excitation of the DR products. All this information is particularly important for understanding DR of heteronuclear polyatomic ions. We will present DR results for several ions recently investigated at TSR. This work is supported in part by NASA and the NSF.

  12. F 3 - molecular ions in fluoride crystals

    NASA Astrophysics Data System (ADS)

    Radzhabov, E. A.

    2016-02-01

    The UV absorption spectra of F 3 - molecular ions in LaF3, SrF2, CaF2, and BaF2 crystals doped with rare-earth elements are studied. Comparison of radiation-colored and additively colored crystals reveals the absorption bands of F 3 - hole centers in the region near 6 eV. Nonempirical calculations of optical transitions agree well with experimental results.

  13. Dissociative Recombination of Molecular Ions for Astrochemistry

    NASA Astrophysics Data System (ADS)

    Novotny, Oldrich; Becker, A.; Buhr, H.; Fleischmann, Andreas; Gamer, Lisa; Geppert, W.; Krantz, C.; Kreckel, H.; Schwalm, D.; Spruck, K.; Wolf, A.; Savin, Daniel Wolf

    2014-06-01

    Dissociative recombination (DR) of molecular ions is a key chemical process in the cold interstellar medium (ISM). DR affects the composition, charge state, and energy balance of such environments. Astrochemical models of the ISM require reliable total DR cross sections as well as knowledge of the chemical composition of the neutral DR products. We have systematically measured DR for many astrophysically relevant molecular ions utilizing the TSR storage ring at the Max-Planck-Institute for Nuclear Physics (MPIK) in Heidelberg, Germany. We used the merged ion-electron beam technique combined with an energy- and position-sensitive imaging detector and are able to study DR down to plasma temperatures as low as 10 K. The DR count rate is used to obtain an absolute merged beams DR rate coefficient from which we can derive a thermal rate coefficient needed for plasma models. Additionally we determine the masses of the DR products by measuring their kinetic energy in the laboratory reference frame. This allows us to assign particular DR fragmentation channels and to obtain their branching ratios. All this information is particularly important for understanding DR of heteronuclear polyatomic ions. We will present DR results for several ions recently investigated at TSR. A new Cryogenic Storage Ring (CSR) is currently being commissioned at MPIK. With the chamber cooled down to ~10 K and a base pressure better than 10-13 mbar, this setup will allow internal cooling of the stored ions down to their rotational ground states, thus opening a new era in DR experiments. New technological challenges arise due to the ultracold, ultra-high vacuum environment of the CSR and thus the detection techniques used at TSR cannot be easily transferred to CSR. We will present new approaches for DR fragment detection in cryogenic environment. This work is supported in part by NASA and the NSF.

  14. Vibronic Spectroscopy of Hetero Dihalo-Benzyl Radicals Generated by Corona Discharge : Jet-Cooled Chlorofluorobenzyl Radicals

    NASA Astrophysics Data System (ADS)

    Yoon, Young; Lee, Sang

    2015-06-01

    The technique of corona excited supersonic jet expansion coupled with a pinhole-type glass nozzle was applied to vibronic spectroscopy of jet-cooled chlorofluorobenzyl radicals for the vibronic assignments and measurements of electronic energies of the D_1 → D_0 transition. The vibronic emission spectra were recorded with a long-path monochromator in the visible region. The 2,3-, 2,4-, and 2.5-chlorofluorobenzyl radicals were generated by corona discharge of corresponding precursor molecules, chlorofluorotoluenes seeded in a large amount of helium carrier gas. The emission spectra show the vibronic bands originating from two benzyl-type radicals, chlorofluorobenzyl and fluorobenzyl benzyl radicals, in which fluorobenzyl radicals were obtained by displacement of Cl by H atom produced by the dissociation of methyl C-H bond. From an analysis of the spectra observed, we could determine the electronic energies in D_1 → D_0 transition and vibrational mode frequencies at the D_0 state of chlorofluorobenzyl radicals which show the origin band of the electronic transition to be shifted to red region, comparing with the parental benzyl radical. The red-shift is highly sensitive to the number, position, and kind of substituents in chlorofluorobenzyl radicals. From the quantitative analysis of the red-shift, it has been found that the additivity rule, discovered recently by Lee group predicts the observation very well. In addition, the negligible contribution of the substituent at the 4-position, the nodal point of the Hückel's molecular orbital theory, can be well describes by the disconnection of substituent from molecular plane of the benzene ring available for delocalized π electrons. In this presentation, I will discuss the spectroscopic observation of new chlorofluorobenzyl radicals and substituent effect on electronic transition energy which is useful for identification of isomeric substituted benzyl radicals. C.~S.~Huh, Y.~W.~Yoon, and S.~K.~Lee, J. Chem

  15. Laser-Induced Fluorescence Spectroscopy of Jet-Cooled t-Butoxy.

    PubMed

    Liu, Jinjun; Reilly, Neil J; Mason, Amy; Miller, Terry A

    2015-12-10

    The vibrational structures of the Ã(2)A1 and X̃(2)E states of t-butoxy were obtained in jet-cooled laser-induced fluorescence (LIF) and dispersed fluorescence (DF) spectroscopic measurements. The observed transitions are assigned based on vibrational frequencies calculated using the complete active space self-consistent field (CASSCF) method and the predicted Franck-Condon factors. The spin-orbit splitting was measured to be 36(5) cm(-1) for the lowest vibrational level of the ground (X̃(2)E) state, which is significantly smaller than that of methoxy, and increases with increasing vibrational quantum number of the CO stretch mode. Vibronic analysis of the DF spectra suggests that Jahn-Teller active modes of the ground-state t-butoxy radical are similar to those of methoxy and would be the same if methyl groups were replaced by hydrogen atoms. The rotational and fine structure of the LIF transition to the first CO stretch overtone level of the Ã(2)A1 state has been simulated using a spectroscopic model first proposed for methoxy, yielding an accurate determination of the rotational constants of both à and X̃ states. PMID:26524342

  16. Resonant two-photon ionization spectroscopy of jet-cooled NiPt

    NASA Astrophysics Data System (ADS)

    Taylor, Scott; Spain, Eileen M.; Morse, Michael D.

    1990-03-01

    Resonant two-photon ionization spectroscopy of jet-cooled NiPt has been used to investigate the possibility of d-electron contributions to the bonding in this species. Based on an abrupt onset of predissociation, the bond strength of NiPt is assigned as D0(NiPt)=2.798±0.003 eV. Comparisons of scans using ArF (6.42 eV) or F2 (7.87 eV) radiation as the ionization laser yield IP(NiPt)=8.02±0.15 eV, from which we derive D0(Ni+-Pt)=2.41±0.15 eV and D0(Ni-Pt+) =3.58±0.35 eV. High resolution studies of the 6-0 and 8-0 bands of one of the three identifiable progressions demonstrate an Ω'=0←Ω`=0 transition with r'e =2.3396±0.0039Å and r″0 =2.2078±0.0023Å. The short bond length and large bond strength of NiPt, as compared to the corresponding values (re=2.330±0.003Å and D0=2.34±0.10 eV) for the coinage metal analog, CuAu, demonstrate significant d-orbital contributions to the bonding in NiPt.

  17. Ground and excited state infrared spectroscopy of jet-cooled radicals: Exploring the photophysics of trihydronaphthyl and inden-2-ylmethyl

    NASA Astrophysics Data System (ADS)

    Kidwell, Nathanael M.; Mehta-Hurt, Deepali N.; Korn, Joseph A.; Sibert, Edwin L.; Zwier, Timothy S.

    2014-06-01

    The alkyl and aromatic CH stretch infrared spectra of inden-2-ylmethyl (I2M, C10H9) and trihydronaphthyl (THN, C10H11) radicals have been recorded under jet-cooled conditions in the ground (D0) and first electronically excited (D1) states using resonant ion-dip infrared (RIDIR) spectroscopy. Previously, the vibronic spectroscopy of a series of C10H9 and C10H11 hydronaphthyl radicals were investigated and their thermochemical properties were evaluated with isomer specificity [J. A. Sebree et al., J. Phys. Chem. A 11, 6255-6262 (2010)]. We show here that one of the m/z 129 spectral carriers characterized in that work was misidentified as 2-hydronaphthyl (2-HN) radical, appearing in a discharge of 1,2-dihydronaphthalene in close proximity to 1-hydronaphthyl radical. The D0-RIDIR spectrum in the alkyl CH stretch region positively identifies the m/z 129 isomer as I2M, whose two-color resonant two-photon ionization (2C-R2PI) spectrum was recently reported by Schmidt and co-workers [T. P. Troy et al., Chem. Sci. 2, 1755-1765 (2011)]. Here, we further characterize the I2M and THN radicals by recording their gas phase IR spectra in the alkyl and aromatic CH stretch regions, and explore the spectroscopic consequences of electronic excitation on the CH stretch absorptions. A local-mode CH stretch Hamiltonian incorporating cubic stretch-bend coupling between anharmonic CH stretches and CH2 scissor modes is utilized to describe their Fermi resonance interactions. Excellent agreement between the experimental and theoretical results facilitates the interpretation of the D0- and D1-state RIDIR spectra of I2M, revealing that upon excitation the alkyl CH stretches decrease in frequency by 70 cm-1, while the allyl-like CH stretches experience a modest blueshift. In comparison, the photophysics of THN are strikingly different in that the IR transitions that possess vibrational motion along the CβH and CδH bonds are absent in the D1-RIDIR spectrum yet are predicted to be present from

  18. Modeling ion sensing in molecular electronics

    NASA Astrophysics Data System (ADS)

    Chen, Caroline J.; Smeu, Manuel; Ratner, Mark A.

    2014-02-01

    We examine the ability of molecules to sense ions by measuring the change in molecular conductance in the presence of such charged species. The detection of protons (H+), alkali metal cations (M+), calcium ions (Ca2+), and hydronium ions (H3O+) is considered. Density functional theory (DFT) is used within the Keldysh non-equilibrium Green's function framework (NEGF) to model electron transport properties of quinolinedithiol (QDT, C9H7NS2), bridging Al electrodes. The geometry of the transport region is relaxed with DFT. The transport properties of the device are modeled with NEGF-DFT to determine if this device can distinguish among the M+ + QDT species containing monovalent cations, where M+ = H+, Li+, Na+, or K+. Because of the asymmetry of QDT in between the two electrodes, both positive and negative biases are considered. The electron transmission function and conductance properties are simulated for electrode biases in the range from -0.5 V to 0.5 V at increments of 0.1 V. Scattering state analysis is used to determine the molecular orbitals that are the main contributors to the peaks in the transmission function near the Fermi level of the electrodes, and current-voltage relationships are obtained. The results show that QDT can be used as a proton detector by measuring transport through it and can conceivably act as a pH sensor in solutions. In addition, QDT may be able to distinguish among different monovalent species. This work suggests an approach to design modern molecular electronic conductance sensors with high sensitivity and specificity using well-established quantum chemistry.

  19. Modeling ion sensing in molecular electronics

    SciTech Connect

    Chen, Caroline J.; Smeu, Manuel Ratner, Mark A.

    2014-02-07

    We examine the ability of molecules to sense ions by measuring the change in molecular conductance in the presence of such charged species. The detection of protons (H{sup +}), alkali metal cations (M{sup +}), calcium ions (Ca{sup 2+}), and hydronium ions (H{sub 3}O{sup +}) is considered. Density functional theory (DFT) is used within the Keldysh non-equilibrium Green's function framework (NEGF) to model electron transport properties of quinolinedithiol (QDT, C{sub 9}H{sub 7}NS{sub 2}), bridging Al electrodes. The geometry of the transport region is relaxed with DFT. The transport properties of the device are modeled with NEGF-DFT to determine if this device can distinguish among the M{sup +} + QDT species containing monovalent cations, where M{sup +} = H{sup +}, Li{sup +}, Na{sup +}, or K{sup +}. Because of the asymmetry of QDT in between the two electrodes, both positive and negative biases are considered. The electron transmission function and conductance properties are simulated for electrode biases in the range from −0.5 V to 0.5 V at increments of 0.1 V. Scattering state analysis is used to determine the molecular orbitals that are the main contributors to the peaks in the transmission function near the Fermi level of the electrodes, and current-voltage relationships are obtained. The results show that QDT can be used as a proton detector by measuring transport through it and can conceivably act as a pH sensor in solutions. In addition, QDT may be able to distinguish among different monovalent species. This work suggests an approach to design modern molecular electronic conductance sensors with high sensitivity and specificity using well-established quantum chemistry.

  20. High-Resolution Spectroscopy of Jet-Cooled Naphthalene: the 000 and 3301 Bands of the A~1B1u<--X~1Ag Transition

    NASA Astrophysics Data System (ADS)

    Joo, Duck-Lae; Takahashi, Rika; O'Reilly, John; Katô, Hajime; Baba, Masaaki

    2002-09-01

    Rotationally resolved excitation spectra of the 0 00 and 33 01 bands of the Ã1B1 u← X˜1Ag electronic transition of naphthalene were measured by a frequency-doubled single-mode tunable laser and a jet-cooled collimated molecular beam. The observed linewidth was 18 MHz, and the absolute wavenumber was determined with an accuracy of better than 0.0002 cm -1. The molecular constants of the X˜1Ag( v=0), Ã1B1 u( v=0), and Ã1B1 u( v33=1) levels were determined and represent the most accurate measurements to date. Three rotational constants were sufficient to fit 3386 lines of J=1-43 and Ka=0-21 with a standard deviation 0.0002 cm -1. This indicates that the molecular structures are rigid both in the X˜1Ag and Ã1B1 u states. When a magnetic field was applied, spectral line broadening was observed for levels with small Ka value in the Ã1B1 u( v33=1) state, and the Zeeman splitting was observed to increase with increasing J. No broadening, however, was observed in the 0 00 band up to H=0.65 T.

  1. Trapped ion simulation of molecular spectrum

    NASA Astrophysics Data System (ADS)

    Shen, Yangchao; Lu, Yao; Zhang, Kuan; Zhang, Shuaining; Huh, Joonsuk; Kim, Kihwan

    2016-05-01

    Boson sampling had been suggested as a classically intractable and quantum mechanically manageable problem via computational complexity theory arguments. Recently, Huh and co-workers proposed theoretically a modified version of boson sampling, which is designed to simulate a molecular problem, as a practical application. Here, we report the experimental implementation of the theoretical proposal with a trapped ion system. As a first demonstration, we perform the quantum simulation of molecular vibronic profile of SO2, which incorporates squeezing, rotation and coherent displacements operations, and the collective projection measurement on phonon modes. This work was supported by the National Basic Research Program of China 11CBA00300, 2011CBA00301, National Natural Science Foundation of China 11374178, 11574002. Basic Science Research Program of Korea NRF-2015R1A6A3A04059773.

  2. Molecular Turnstiles Regulated by Metal Ions.

    PubMed

    Wang, Guangxia; Xiao, Hongmei; He, Jiaojiao; Xiang, Junfeng; Wang, Ying; Chen, Xuebo; Che, Yanke; Jiang, Hua

    2016-04-15

    A family of novel molecular turnstiles 1-3 composed of two stators with pyridyl binding sites and a different-sized triptycene rotor was synthesized. The molecular turnstiles behave in an open state at room temperature in the absence of metal ions but display significantly different closed states in the presence of Ag(+) and Pd(2+). The Ag(+)-mediated turnstiles 1-3Ag exhibited closed states but unreadable bistability at ambient temperature because the Ag(+)-mediated macrocyclic framework is not able to restrict the rotations of the rotors; while temperature was decreased, the macrocyclic frameworks became stable enough to halt the rotations of the rotors, eventually leading to the readable closed states for 1-3Ag. In contrast, Pd(2+)-mediated macrocyclic frameworks are stable, giving rise to a detectable closed state of turnstiles 1-3Pd in a wide range of temperatures. These findings have also been supported by DFT calculations. PMID:26986992

  3. Collective effects in electronic sputtering of organic molecular ions by fast incident cluster ions

    SciTech Connect

    Salehpour, M.; Fishel, D.L.; Hunt, J.E.

    1988-07-15

    The collective sputtering effect of fast primary cluster ions on the yield of secondary molecular ions has been demonstrated for the first time. Results show that the sputtering yield of valine negative molecular ions per incident carbon atom, in a C/sup +//sub n/ incident cluster ion, increases with increasing n. The yield results are interpreted as a direct effect of the enhancement in the electronic stopping power per atom in cluster ions compared to atomic ions.

  4. Spectroscopy and electronic structure of jet-cooled NiPd and PdPt

    NASA Astrophysics Data System (ADS)

    Taylor, Scott; Spain, Eileen M.; Morse, Michael D.

    1990-03-01

    Resonant two-photon ionization spectroscopy of jet-cooled NiPd and PdPt has revealed a dense vibronic spectrum for NiPd and a much more sparse spectrum for PdPt. Four vibrational progressions have been identified for NiPd, and three have been located for PdPt. High resolution investigations of NiPd have established a ground state bond length of r″0 =2.242±0.005 Å with Ω″=2. The observed spectra have been used to bracket the ionization potentials, giving IP(NiPd)=7.18±0.76 eV and IP(PdPt)=8.27±0.38 eV. In contrast to previous work on Ni2, NiPt, and Pt2, no abrupt onset of rapid predissociation is observed for either NiPd or PdPt. A discussion of this result in terms of the expected potential energy curves for the palladium-containing diatomics is presented, which when combined with the frequencies of the highest energy vibronic bands observed yields estimates of D0(NiPd)≊1.46 eV and D0(PdPt)≊1.98 eV. The lack of observable vibronic transitions in Pd2 above 11 375 cm-1 places D0(Pd2) below 1.41 eV, in agreement with Knudsen effusion mass spectrometry. Finally a comparison of the platinum group dimers and the coinage metal dimers is given, demonstrating the increasing importance of d-orbital contributions to the bonding in the platinum group dimers as one moves down the periodic table. The anomalous behavior of the palladium-containing diatomics is also discussed in terms of the highly stable 4d105s0, 1S0 ground state of atomic palladium.

  5. Jet-Cooled Laser-Induced Fluorescence Spectroscopy of T-Butoxy

    NASA Astrophysics Data System (ADS)

    Reilly, Neil J.; Cheng, Lan; Stanton, John F.; Miller, Terry A.; Liu, Jinjun

    2015-06-01

    The vibrational structures of the tilde A ^2A_1 and tilde X ^2E states of t-butoxy were obtained in jet-cooled laser-induced fluorescence (LIF) and dispersed fluorescence (DF) spectroscopic measurements. The observed transitions are assigned based on vibrational frequencies calculated using Complete Active Space Self-Consistent Field (CASSCF) method and the predicted Franck-Condon factors. The spin-orbit (SO) splitting was measured to be 35(5) cm-1 for the lowest vibrational level of the ground (tilde X ^2E) state and increases with increasing vibrational quantum number of the CO stretch mode. Vibronic analysis of the DF spectra suggests that Jahn-Teller (JT)-active modes of the ground-state t-butoxy radical are similar to those of methoxy and would be the same if methyl groups were replaced by hydrogen atoms. Coupled-cluster calculations show that electron delocalization, introduced by the substitution of hydrogens with methyl groups, reduces the electronic contribution of the SO splittings by only around ten percent, and a calculation on the vibronic levels based on quasidiabatic model Hamiltonian clearly attributes the relatively small SO splitting of the tilde X ^2E state of t-butoxy mainly to stronger reduction of orbital angular momentum by the JT-active modes when compared to methoxy. The rotational and fine structure of the LIF transition to the first CO stretch overtone level of the tilde A^2A_1 state has been simulated using a spectroscopic model first proposed for methoxy, yielding an accurate determination of the rotational constants of both tilde A and tilde X states.

  6. 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.

  7. Vibrational Spectroscopy on Trapped Cold Molecular Ions

    NASA Astrophysics Data System (ADS)

    Khanyile, Ncamiso B.; Brown, Kenneth R.

    2014-06-01

    We perform vibrational spectroscopy on the V0←10 overtone of a trapped and sympathetically cooled CaH+ molecular ion using a resonance enhanced two photon dissociation scheme. Our experiments are motivated by theoretical work that proposes comparing the vibrational overtones of CaH^+ with electronic transitions in atoms to detect possible time variation of in the mass ratio of the proton to electron. Due to the nonexistence of experimental data of the transition, we start the search with a broadband femtosecond Ti:Saph laser guided by theoretical calculations. Once the vibrational transition has been identified, we will move to CW lasers to perform rotationally resolved spectroscopy. M. Kajita and Y. Moriwaki, J. Phys. B. At. Mol. Opt.Phys., 42,154022(2009) Private communication

  8. Jet-cooled laser-induced fluorescence spectroscopy of cyclohexoxy: rotational and fine structure of molecules in nearly degenerate electronic States.

    PubMed

    Liu, Jinjun; Miller, Terry A

    2014-12-26

    The rotational structure of the previously observed B̃(2)A' ← X̃(2)A″ and B̃(2)A' ← Ã(2)A' laser-induced fluorescence spectra of jet-cooled cyclohexoxy radical (c-C6H11O) [ Zu, L.; Liu, J.; Tarczay, G.; Dupré, P; Miller, T. A. Jet-cooled laser spectroscopy of the cyclohexoxy radical. J. Chem. Phys. 2004 , 120 , 10579 ] has been analyzed and simulated using a spectroscopic model that includes the coupling between the nearly degenerate X̃ and à states separated by ΔE. The rotational and fine structure of these two states is reproduced by a 2-fold model using one set of molecular constants including rotational constants, spin-rotation constants (ε's), the Coriolis constant (Aζt), the quenched spin-orbit constant (aζed), and the vibronic energy separation between the two states (ΔE0). The energy level structure of both states can also be reproduced using an isolated-state asymmetric top model with rotational constants and effective spin-rotation constants (ε's) and without involving Coriolis and spin-orbit constants. However, the spin-orbit interaction introduces transitions that have no intensity using the isolated-state model but appear in the observed spectra. The line intensities are well simulated using the 2-fold model with an out-of-plane (b-) transition dipole moment for the B̃ ← X̃ transitions and in-plane (a and c) transition dipole moment for the B̃ ← à transitions, requiring the symmetry for the X̃ (Ã) state to be A″ (A'), which is consistent with a previous determination and opposite to that of isopropoxy, the smallest secondary alkoxy radical. The experimentally determined Ã-X̃ separation and the energy level ordering of these two states with different (A' and A″) symmetries are consistent with quantum chemical calculations. The 2-fold model also enables the independent determination of the two contributions to the Ã-X̃ separation: the relativistic spin-orbit interaction (magnetic effect) and the nonrelativistic

  9. High-resolution spectroscopy of jet-cooled CH{sub 5}{sup +}: Progress

    SciTech Connect

    Savage, C.; Dong, F.; Nesbitt, D. J.

    2015-01-22

    Protonated methane (CH{sub 5}{sup +}) is thought to be a highly abundant molecular ion in interstellar medium, as well as a potentially bright μwave- mm wave emitter that could serve as a tracer for methane. This paper describes progress and first successful efforts to obtain a high resolution, supersonically cooled spectrum of CH{sub 5}{sup +} in the 2900-3100 cm{sup −1} region, formed in a slit supersonic discharge at low jet temperatures and with sub-Doppler resolution. Short term precision in frequency measurement (< 5 MHz on an hour time scale) is obtained from a thermally controlled optical transfer cavity servoloop locked onto a frequency stabilized HeNe laser. Long term precision (< 20 MHz day-to-day) due to pressure, temperature and humidity dependent index of refraction effects in the optical transfer cavity is also present and discussed.

  10. Numerical optimization of a multi-jet cooling system for the blown film extrusion

    NASA Astrophysics Data System (ADS)

    Janas, M.; Wortberg, J.

    2015-05-01

    The limiting factor for every extrusion process is the cooling. For the blown film process, this task is usually done by means of a single or dual lip air ring. Prior work has shown that two major effects are responsible for a bad heat transfer. The first one is the interaction between the jet and the ambient air. It reduces the velocity of the jet and enlarges the straight flow. The other one is the formation of a laminar boundary layer on the film surface due to the fast flowing cooling air. In this case, the boundary layer isolates the film and prevents an efficient heat transfer. To improve the heat exchange, a novel cooling approach is developed, called Multi-Jet. The new cooling system uses several slit nozzles over the whole tube formation zone for cooling the film. In contrast to a conventional system, the cooling air is guided vertically on the film surface in different heights to penetrate the boundary sublayer. Simultaneously, a housing of the tube formation zone is practically obtained to reduce the interaction with the ambient air. For the numerical optimization of the Multi-Jet system, a new procedure is developed. First, a prediction model identifies a worth considering cooling configuration. Therefore, the prediction model computes a film curve using the formulation from Zatloukal-Vlcek and the energy balance for the film temperature. Thereafter, the optimized cooling geometry is investigated in detail using a process model for the blown film extrusion that is able to compute a realistic bubble behavior depending on the cooling situation. In this paper, the Multi-Jet cooling system is numerically optimized for several different process states, like mass throughputs and blow-up ratios using one slit nozzle setting. For each process condition, the best cooling result has to be achieved. Therefore, the height of any nozzle over the tube formation zone is adjustable. The other geometrical parameters of the cooling system like the nozzle diameter or the

  11. High-resolution infrared spectrum of jet-cooled methyl acetate in the C=O stretching region: internal rotations of two inequivalent methyl tops.

    PubMed

    Sunahori, Fumie X; Borho, Nicole; Liu, Xunchen; Xu, Yunjie

    2011-12-21

    The jet-cooled high resolution infrared (IR) spectrum of methyl acetate (MA), CH(3)-C(=O)-O-CH(3), in the C=O fundamental band region was recorded by using a rapid scan IR laser spectrometer equipped with an astigmatic multipass cell. No high resolution IR analyses of the ro-vibrational transitions between the ground and non-torsionally excited vibrational states have hitherto been reported for molecules with two inequivalent methyl rotors. Because of the two chemically different methyl tops in MA, i.e., the acetyl -CH(3) and methoxy -CH(3), each rotational energy level is split into more than two torsional sublevels by internal rotations of these methyl groups. We were able to assign ro-vibrational transitions of four torsional species by using the ground state combination differences calculated from the molecular constants of the vibrational ground state recently determined by a global fit of the microwave and millimeter wave lines [M. Tudorie, I. Kleiner, J. T. Hougen, S. Melandri, L. W. Sutikdja, and W. Stahl, J. Mol. Spectrosc. 269, 211 (2011)]. The assigned lines were successfully fitted using the BELGI-Cs-IR program to an overall standard deviation which is comparable to the measurement accuracy. This study is also of interest in understanding the role of methyl rotors in the intramolecular vibrational-energy redistribution processes in mid-size organic molecules. PMID:22191878

  12. The vibrationless Ã←X˜ transition of the jet-cooled deuterated methyl peroxy radical CD3O2 by cavity ringdown spectroscopy

    NASA Astrophysics Data System (ADS)

    Wu, Shenghai; Dupré, Patrick; Rupper, Patrick; Miller, Terry A.

    2007-12-01

    The nearly rotationally resolved spectrum of the ÃA'2←X˜A″2 000 transition of perdeutero methyl peroxy near 1.35μm has been studied via pulsed cavity ringdown spectroscopy. Albeit, this is a weak transition, it is possible to observe the spectrum under jet-cooled conditions (≈15K) by combining a source of narrow-bandwidth radiation (≈250MHz) with a supersonic slit-jet expansion incorporating an electric discharge. The near infrared radiation was obtained by using stimulated Raman scattering and a pulsed, nearly Fourier-transform-limited Ti:sapphire amplifier seeded by a scanable cw Ti:sapphire ring laser. The experimental spectrum has been fitted using a model Hamiltonian that includes the rigid body rotation of an asymmetric top and the spin-rotation interaction. An excellent quality fit was obtained resulting in the determination of 15molecular parameters characterizing the à and X˜ states. Other results reported for CD3O2 include an estimate of the radical concentration and the vibronic transition dipole from the observed absorption intensities. Details about the spectral linewidths are also discussed.

  13. High-resolution infrared spectrum of jet-cooled methyl acetate in the C=O stretching region: Internal rotations of two inequivalent methyl tops

    NASA Astrophysics Data System (ADS)

    Sunahori, Fumie X.; Borho, Nicole; Liu, Xunchen; Xu, Yunjie

    2011-12-01

    The jet-cooled high resolution infrared (IR) spectrum of methyl acetate (MA), CH3-C(=O)-O-CH3, in the C=O fundamental band region was recorded by using a rapid scan IR laser spectrometer equipped with an astigmatic multipass cell. No high resolution IR analyses of the ro-vibrational transitions between the ground and non-torsionally excited vibrational states have hitherto been reported for molecules with two inequivalent methyl rotors. Because of the two chemically different methyl tops in MA, i.e., the acetyl -CH3 and methoxy -CH3, each rotational energy level is split into more than two torsional sublevels by internal rotations of these methyl groups. We were able to assign ro-vibrational transitions of four torsional species by using the ground state combination differences calculated from the molecular constants of the vibrational ground state recently determined by a global fit of the microwave and millimeter wave lines [M. Tudorie, I. Kleiner, J. T. Hougen, S. Melandri, L. W. Sutikdja, and W. Stahl, J. Mol. Spectrosc. 269, 211 (2011)]. The assigned lines were successfully fitted using the BELGI-Cs-IR program to an overall standard deviation which is comparable to the measurement accuracy. This study is also of interest in understanding the role of methyl rotors in the intramolecular vibrational-energy redistribution processes in mid-size organic molecules.

  14. Note: High density pulsed molecular beam for cold ion chemistry

    SciTech Connect

    Kokish, M. G.; Rajagopal, V.; Marler, J. P.; Odom, B. C.

    2014-08-15

    A recent expansion of cold and ultracold molecule applications has led to renewed focus on molecular species preparation under ultrahigh vacuum conditions. Meanwhile, molecular beams have been used to study gas phase chemical reactions for decades. In this paper, we describe an apparatus that uses pulsed molecular beam technology to achieve high local gas densities, leading to faster reaction rates with cold trapped ions. We characterize the beam's spatial profile using the trapped ions themselves. This apparatus could be used for preparation of molecular species by reactions requiring excitation of trapped ion precursors to states with short lifetimes or for obtaining a high reaction rate with minimal increase of background chamber pressure.

  15. Spectroscopy of Jet-Cooled Neutral and Ionized PAHs: Implications for Interstellar Dust

    NASA Technical Reports Server (NTRS)

    Salama, F.; Tan, X.; Biennier, L.; Cami, J.

    2005-01-01

    We present the gas-phase spectroscopy of neutral and ionized polycyclic aromatic hydrocarbons (PAHs) measured in the W-Visible-NIR range in an astrophysically relevant environment. These measurements provide data on PAHs and nanometer sized particles that can now be directly compared to astronomical observations. The harsh physical conditions of the IS medium - characterized by a low temperature, an absence of collisions and strong VUV radiation fields - are simulated in the laborat'ory by associating a molecular beam with an ionizing discharge to generate a cold plasma expansion. PAH ions are formed from the neutral precursors in an isolated environment at low temperature ($\\sim lOO$-K). The spectra of neutral and ionized PAHs are measured using the high sensitivity methods of cavity ring down spectroscopy (CRDS) and multiplex integrated cavity output spectroscopy (MICOS). These experiments provide unique information on the spectra of free, cold large carbon molecules and ions in the gas phase. The electronic bands measured for ionized PAH are found to be intrinsically broad ($\\geq$20 cm$^{-l}$) while the bands associated with the neutral precursors are narrower (of the order of 2 - 10 cm$^{-l}$). The laboratory data are discussed and compared with recent astronomical spectra of large and narrow DIBs and with the spectra of circumstellar environments of selected carbon stars (see contribution of Cami et al.) and the implications for the interstellar PAH population are derived. Preliminary results also show that carbon nanoparticles are formed during the short residence time of the precursors in the plasma. This finding holds great potential for understanding the formation process of interstellar grains.

  16. Moderate Resolution Jet Cooled Cavity Ringdown Spectra of the tilde{A} State of NO_3 Radical

    NASA Astrophysics Data System (ADS)

    Codd, Terrance J.; Chen, Ming-Wei; Roudjane, Mourad; Miller, Terry A.

    2012-06-01

    The tilde{A}-tilde{X} spectrum of NO_3 has been previously observed using cavity ringdown spectroscopy (CRDS) by Andrei Deev et. al under ambient conditions. There the authors assigned a number of vibronic bands in the spectrum. However, under these conditions, hot-bands may be present and the spectrum becomes very congested at frequencies higher than ˜8700 cm-1 due to the density of vibronic states and the overlap of their rotational contours. In order to obtain more information about the tilde{A} state of NO_3 we recently obtained spectra from 7550 cm-1 to over 10000 cm-1 using our moderate resolution (≃ 0.05 cm-1) jet cooled CRDS apparatus. Jet cooling in our apparatus reduces the rotational temperature to <30 K and eliminates vibrational hot bands greatly simplifying the spectrum. We are able to resolve and assign more than 15 vibronic features including a new assignment of the 31_0 band. Analysis of the ν_4 progression shows weak Jahn-Teller coupling in this mode. Anomalous band contours and anharmonic spacings are observed for the ν_1ν_4 combination bands and the cause is being investigated. We also see some features that could belong to vibronically forbidden transitions which may be magnetic dipole allowed. A. Deev, J. Sommar, and M. Okumura, J. Chem. Phys. 122, 224305 (2005)

  17. Performance of water jet cooled silicon monochromators in high power x-ray beams (abstract)

    NASA Astrophysics Data System (ADS)

    Berman, Lonny E.; Hart, Michael

    1992-01-01

    We have fabricated and tested water jet cooled silicon (111) and (220) monochromators specially tailored for extended wiggler beam and concentrated undulator beam power loadings. The tests were made at the X25 27 pole, 1.1 T hybrid wiggler beam line1 at the National Synchrotron Light Source (NSLS). The wiggler-like line-type loading was produced by the direct, unfocused wiggler white beam, in which 300 W of total power in a 60-mm-wide by 5-mm-high [full width at half maximum (FWHM)] cross section were available in the experimental hutch; this represents a typical power density at existing insertion device beam lines. The undulator-like point-type loading was produced by the focused wiggler white beam, generated via reflection of a portion of the direct white beam from a toroidal platinum-coated silicon mirror, resulting in 75 W of total power in a 0.8-mm-wide (FWHM) by 0.45-mm-high (FWHM) cross section in the hutch. This will be a typical power density at next-generation insertion device beam lines. The monochromator design consists of a thin walled silicon box whose bottom is glued to a stainless-steel water manifold; the coolant is delivered through jet tubes directed perpendicular to the underside of the top, diffracting surface of the box.2 Rectangular monochromators with multiple jets were used for the line power loading studies, and cylindrical monochromators with single jets were used for the point power loading studies. Provisions for simple adaptive corrections to compensate for the inevitable beam-induced thermal deformations, consisting of mechanisms to reverse-bend the top surface, and internal heat baffles to frustrate the cooling at the edges of the crystal (to produce an isothermal top surface), were included in the designs. These required approximate matching of the top surface dimensions to the x-ray footprint. To better understand the thermal strain fields, spatial and angular mapping of both fundamental and harmonic Bragg reflections within the

  18. Dissociative recombination of molecular ions with electrons

    NASA Technical Reports Server (NTRS)

    Johnsen, Rainer

    1990-01-01

    An overview is presented for the present state of the art of laboratory measurements of the dissociative recombination of molecular ions with electrons. Most work has focussed on obtaining rates and their temperature dependence, as these are of primary interest for model calculations of ionospheres. A comparison of data obtained using the microwave afterglow method, the flowing afterglow technique, and the merged beam technique shows that generally the agreement is quite good, but there are some serious discrepancies, especially in the case of H(3+) recombination, that need to be resolved. Results of some earlier experimental work need to be reexamined in the light of more recent developments. Such cases are pointed out and a compilation of rate coefficients that have withstood scrutiny is presented. Recent advances in experimental methods, such as the use of laser-in-duced fluorescence, make it possible to identify some neutral products of dissociative recombination. What has been done so far and what results one might expect from future work are briefly reviewed.

  19. Molecular and negative ion production by a standard electron cyclotron resonance ion source

    SciTech Connect

    Racz, R.; Biri, S.; Juhasz, Z.; Sulik, B.

    2012-02-15

    Molecular and negative ion beams, usually produced in special ion sources, play an increasingly important role in fundamental and applied atomic physics. The ATOMKI-ECRIS is a standard ECR ion source, designed to provide highly charged ion (HCI) plasmas and beams. In the present work, H{sup -}, O{sup -}, OH{sup -}, O{sub 2}{sup -}, C{sup -}, C{sub 60}{sup -} negative ions and H{sub 2}{sup +}, H{sub 3}{sup +}, OH{sup +}, H{sub 2}O{sup +}, H{sub 3}O{sup +}, O{sub 2}{sup +} positive molecular ions were generated in this HCI-ECRIS. Without any major modification in the source and without any commonly applied tricks (such as usage of cesium or magnetic filter), negative ion beams of several {mu}A and positive molecular ion beams in the mA range were successfully obtained.

  20. Molecular Ion Beam Transportation for Low Energy Ion Implantation

    SciTech Connect

    Kulevoy, T. V.; Kropachev, G. N.; Seleznev, D. N.; Yakushin, P. E.; Kuibeda, R. P.; Kozlov, A. V.; Koshelev, V. A.; Hershcovitch, A.; Johnson, B. M.; Gushenets, V. I.; Oks, E. M.; Polozov, S. M.; Poole, H. J.

    2011-01-07

    A joint research and development of steady state intense boron ion sources for 100's of electron-volt ion implanters has been in progress for the past five years. Current density limitation associated with extracting and transporting low energy ion beams result in lower beam currents that in turn adversely affects the process throughput. The transport channel with electrostatic lenses for decaborane (B{sub 10}H{sub 14}) and carborane (C{sub 2}B{sub 10}H{sub 12}) ion beams transportation was developed and investigated. The significant increase of ion beam intensity at the beam transport channel output is demonstrated. The transport channel simulation, construction and experimental results of ion beam transportation are presented.

  1. Precision studies of the hydrogen molecular ion and its isotopologues

    NASA Astrophysics Data System (ADS)

    Bekbayev, A. K.; Aznabayev, D. T.; Korobov, V. I.

    2015-08-01

    We present systematic calculations of the leading order relativistic corrections including the hyperfine splitting (HFS) for a wide range of rotational and vibrational states of the HT+ molecular ion. We also calculate the DC and AC Stark effects for the molecular hydrogen ions and H D + in the non-relativistic approximation. The influence of the DC Stark polarizability effect on the hyperfine substates of a ro-vibrational state is carefully analyzed. Our results enable the detailed evaluation of certain systematic shifts of the transition frequencies for the purpose of ultra-high-precision optical, microwave, or radio-frequency spectroscopy of the hydrogen molecular ions in a trap.

  2. An ion mobility mass spectrometer for investigating photoisomerization and photodissociation of molecular ions

    SciTech Connect

    Adamson, B. D.; Coughlan, N. J. A.; Markworth, P. B.; Bieske, E. J.; Continetti, R. E.

    2014-12-15

    An ion mobility mass spectrometry apparatus for investigating the photoisomerization and photodissociation of electrosprayed molecular ions in the gas phase is described. The device consists of a drift tube mobility spectrometer, with access for a laser beam that intercepts the drifting ion packet either coaxially or transversely, followed by a quadrupole mass filter. An ion gate halfway along the drift region allows the instrument to be used as a tandem ion mobility spectrometer, enabling mobility selection of ions prior to irradiation, with the photoisomer ions being separated over the second half of the drift tube. The utility of the device is illustrated with photoisomerization and photodissociation action spectra of carbocyanine molecular cations. The mobility resolution of the device for singly charged ions is typically 80 and it has a mass range of 100-440 Da, with the lower limit determined by the drive frequency for the ion funnels, and the upper limit by the quadrupole mass filter.

  3. Infrared and Electronic Spectroscopy of the Jet-Cooled 5-Methyl-2-furanylmethyl Radical Derived from the Biofuel 2,5-Dimethylfuran.

    PubMed

    Kidwell, Nathanael M; Mehta-Hurt, Deepali N; Korn, Joseph A; Zwier, Timothy S

    2016-08-18

    The electronic and infrared spectra of the 5-methyl-2-furanylmethyl (MFM) radical have been characterized under jet-cooled conditions in the gas phase. This resonance-stabilized radical is formed by H atom loss from one of the methyl groups of 2,5-dimethylfuran (DMF), a promising second-generation biofuel. As a resonance-stabilized radical, it plays an important role in the flame chemistry of DMF. The D0-D1 transition was studied using two-color resonant two-photon ionization (2C-R2PI) spectroscopy. The electronic origin is in the middle of the visible spectrum (21934 cm(-1) = 455.9 nm) and is accompanied by Franck-Condon activity involving the hindered methyl rotor. The frequencies and intensities are fit to a one-dimensional methyl rotor potential, using the calculated form of the ground state potential. The methyl rotor reports sensitively on the local electronic environment and how it changes with electronic excitation, shifting from a preferred ground state orientation with one CH in-plane and anti to the furan oxygen, to an orientation in the excited state in which one CH group is axial to the plane of the furan ring. Ground and excited state alkyl CH stretch infrared spectra are recorded using resonant ion-dip infrared (RIDIR) spectroscopy, offering a complementary view of the methyl group and its response to electronic excitation. Dramatic changes in the CH stretch transitions with electronic state reflect the changing preference for the methyl group orientation. PMID:27456434

  4. High-resolution absorption spectrum of jet-cooled CH3Cl between 70 000 and 85 000 cm-1: New assignments

    NASA Astrophysics Data System (ADS)

    Cossart-Magos, Claudina; Jungen, Martin; Stalder, Joerg; Launay, Françoise

    2005-09-01

    The absorption spectrum of jet-cooled CH3Cl was photographed from 165to117nm (or 60000-85000cm-1, 7.5-10.5eV) at a resolution limit of 0.0008nm (0.3-0.6cm-1 or 0.04-0.08meV). Even in the best structured region of the spectrum, from 70000to85000cm-1 (8.7-10.5eV ), observed bandwidths (full width at half maximum) are large, from 50to150cm-1. No rotational feature could be resolved. The spectrum is dominated by two strong bands near 9eV, 140nm, the D and E bands of Mulliken [J. Chem. Phys. 8, 382 (1940)] or the spectral region D of Price [J. Chem. Phys.4, 539 (1936)]. Their relative intensity is incompatible with previous assignments, namely, to a triplet and a singlet state belonging to the same configuration. On the basis of the present ab initio calculations, those bands are now assigned to two singlet states, the A11 and E1 excited states resulting from the 2e34pe Rydberg configuration. The present calculations also reveal that the two E1 states issued from 2e34sa1 and 2e34pa1 are quasidegenerate and strongly mixed. They should be assigned to the two broad bands near 8eV, 160nm, the B and C bands of Mulliken and Price. Three vibrational modes are observed to be active: the CCl bond stretch ν3(a1), and the CH3 umbrella and rocking vibrations, respectively, ν2(a1) and ν6(e ). The fundamental frequencies deduced are well within the ranges defined by the corresponding values in the neutral and ion ground states. The possibility of a dynamical Jahn-Teller effect induced by the ν6(e) vibrational mode in the E1 Rydberg states is discussed.

  5. Laser-induced fluorescence, dispersed fluorescence and lifetime measurements of jet-cooled chloro-substituted benzyl radicals

    NASA Astrophysics Data System (ADS)

    Hamatani, Satoshi; Tsuji, Kazuhide; Kawai, Akio; Shibuya, Kazuhiko

    2002-07-01

    We measured the laser-induced fluorescence (LIF) and dispersed fluorescence (DF) spectra of jet-cooled α-, o- and m-chlorobenzyl radicals after they were generated by the 193 nm photolysis of the corresponding parent molecules. The vibronically resolved spectra were obtained to analyze their D1-D0 transitions. The fluorescence lifetimes of α-, o-, m- and p-chlorobenzyls in the zeroth vibrational levels of the D1 states were measured to estimate the oscillator strengths of a series of benzyl derivatives. It was found that the α-substitution is inefficient to break the `accidental forbiddenness' of the D1-D0 transition of benzyl, while the ring-substitution enhances the oscillator strength by 50%.

  6. Molecular ion battery: a rechargeable system without using any elemental ions as a charge carrier

    PubMed Central

    Yao, Masaru; Sano, Hikaru; Ando, Hisanori; Kiyobayashi, Tetsu

    2015-01-01

    Is it possible to exceed the lithium redox potential in electrochemical systems? It seems impossible to exceed the lithium potential because the redox potential of the elemental lithium is the lowest among all the elements, which contributes to the high voltage characteristics of the widely used lithium ion battery. However, it should be possible when we use a molecule-based ion which is not reduced even at the lithium potential in principle. Here we propose a new model system using a molecular electrolyte salt with polymer-based active materials in order to verify whether a molecular ion species serves as a charge carrier. Although the potential of the negative-electrode is not yet lower than that of lithium at present, this study reveals that a molecular ion can work as a charge carrier in a battery and the system is certainly a molecular ion-based “rocking chair” type battery. PMID:26043147

  7. Molecular ion battery: a rechargeable system without using any elemental ions as a charge carrier

    NASA Astrophysics Data System (ADS)

    Yao, Masaru; Sano, Hikaru; Ando, Hisanori; Kiyobayashi, Tetsu

    2015-06-01

    Is it possible to exceed the lithium redox potential in electrochemical systems? It seems impossible to exceed the lithium potential because the redox potential of the elemental lithium is the lowest among all the elements, which contributes to the high voltage characteristics of the widely used lithium ion battery. However, it should be possible when we use a molecule-based ion which is not reduced even at the lithium potential in principle. Here we propose a new model system using a molecular electrolyte salt with polymer-based active materials in order to verify whether a molecular ion species serves as a charge carrier. Although the potential of the negative-electrode is not yet lower than that of lithium at present, this study reveals that a molecular ion can work as a charge carrier in a battery and the system is certainly a molecular ion-based “rocking chair” type battery.

  8. Formation of molecular ions by radiative association of cold trapped atoms and ions

    NASA Astrophysics Data System (ADS)

    Dulieu, Olivier; da Silva, Humberto, Jr.; Aymar, Mireille; Raoult, Maurice

    2015-05-01

    Radiative emission during cold collisions between trapped laser-cooled Rb atoms and alkaline-earth ions (Ca+ , Sr+ , Ba+) and Yb+ are studied theoretically, using accurate effective-core-potential based quantum chemistry calculations of potential energy curves and transition dipole moments of the related molecular ions. Radiative association of molecular ions is predicted to occur for all systems with a cross section two to ten times larger than the radiative charge transfer one. Partial and total rate constants are also calculated and compared to available experiments. Narrow shape resonances are expected, which could be detectable at low temperature with an experimental resolution at the limit of the present standards. Vibrational distributions show that the final molecular ions are not created in their ground state level. Supported by the Marie-Curie ITN ``COMIQ: Cold Molecular Ions at the Quantum limit'' of the EU (#607491).

  9. Expansion Discharge Source for Ion Beam Laser Spectroscopy of Cold Molecular Ions

    NASA Astrophysics Data System (ADS)

    Porambo, Michael; Pearson, Jessica; Riccardo, Craig; McCall, Benjamin J.

    2013-06-01

    Molecular ions are important in several fields of research, and spectroscopy acts as a key tool in the study of these ions. However, problems such as low ion abundance, ion-neutral confusion, and spectral congestion due to high internal temperatures can hinder effective spectroscopic studies. To circumvent these problems, we are developing a technique called Sensitive, Cooled, Resolved, Ion BEam Spectroscopy (SCRIBES). This ion beam spectrometer will feature a continuous supersonic expansion discharge source to produce cold molecular ions, electrostatic ion optics to focus the ions into an ion beam and bend the beam away from co-produced neutral molecules, an overlap region for cavity enhanced spectroscopy, and a time-of-flight mass spectrometer. When completed, SCRIBES will be an effective tool for the study of large, fluxional, and complex molecular ions that are difficult to study with other means. The ion beam spectrometer has been successfully implemented with a hot ion source. This talk will focus on the work of integrating a supersonic expansion discharge source into the instrument. To better understand how the source would work in the whole ion beam instrument, characterization studies are being performed with spectroscopy of HN_2^+ in a section of the system to ascertain the rotational temperature of the ion expansion. Attempts are also underway to measure the ion current from a beam formed from the expansion. Once the source in this environment is properly understood, we will reintegrate it to the rest of the ion beam system, completing SCRIBES. A. A. Mills, B. M. Siller, M. W. Porambo, M. Perera, H. Kreckel and B. J. McCall J. Chem. Phys., 135, 224201, (2011). K. N. Crabtree, C. A. Kauffman and B. J. McCall Rev. Sci. Instrum. 81, 086103, (2010).

  10. Observations of molecular ions in the earth's magnetosphere

    NASA Technical Reports Server (NTRS)

    Craven, P. D.; Chappell, C. R.; Kakani, L.; Olsen, R. C.

    1985-01-01

    The retarding ion mass spectrometer on Dynamics Explorer 1 operating over the polar cap during a large magnetic storm has measured fluxes of up to 10 to the 6th ions/sq cm s of the molecular ions N2(+), NO(+), and O2(+). These ions were measured beginning low in the satellite orbit (1.1 earth radii) and extending to about 3 earth radii geocentric altitude. Near perigee, the ions have a rammed distribution indicating a cold Maxwellian plasma (1000-2000 K). The molecular ions gradually shift to a field-aligned distribution at the higher alitudes. An upward flow of 5-10 km/s is found in these field-aligned measurements. The density of the molecular ions is on the order of 2/cu cm at all altitudes, and the energy of the ions generally increases as the satellite moves sunward across the southern polar cap. Kinetic energies of at least 20 eV were found at 2.5 earth-radii geocentric distance.

  11. Understanding ion association states and molecular dynamics using infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Masser, Hanqing

    A molecular level understanding of the ion transport mechanism within polymer electrolytes is crucial to the further development for advanced energy storage applications. This can be achieved by the identification and quantitative measurement of different ion species in the system and further relating them to the ion conductivity. In the first part of this thesis, research is presented towards understanding the ion association states (free ions, ion pairs and ion aggregates) in ionomer systems, and the correlation of ion association states, ion conduction, polymer dynamics, and morphology. Ion conductivity in ionomers can be improved by lowering glass transition temperature, increasing polymer ion solvation ability, and adjusting ionomer structural variables such as ion content, cation type and side chain structure. These effects are studied in three ionomer systems respectively, using a combination of characterization methods. Fourier Transform Infrared Spectroscopy (FTIR) identifies and quantifies the ion association states. Dielectric Spectroscopy (DRS) characterizes ion conductivity and polymer and ion dynamics. X-ray scattering reveals changes in morphology. The influence of a cation solvating plasticizer on a polyester ionomer is systematically investigated with respect to ion association states, ion and polymer dynamics and morphology. A decrease in the number ratio of ion aggregates with increased plasticizer content and a slight increase at elevated temperature are observed in FTIR. Similar results are also detected by X-ray scattering. As determined from dielectric spectroscopy, ion conductivity increases with plasticizer content, in accordance with the decrease in glass transition temperature. Research on copolymer of poly(ethylene oxide) (PEO) and poly(tetramethylene oxide) (PTMO) based ionomers further develops an understanding of the trade-off between ion solvation and segmental dynamics. Upon the incorporation of PTMO, the majority of the PTMO

  12. Theoretical Study of Negative Molecular Ions

    NASA Astrophysics Data System (ADS)

    Simons, Jack

    2011-05-01

    Although this review provides references to tabulations of molecular electron affinities, primarily it focuses on explaining why theory plays an important role in understanding the behavior of anions, explaining the challenges that anions pose to theory, making connections between the theories used to compute electron affinities and the potentials (e.g., charge-dipole, charge-quadrupole, valence attraction and exchange repulsion, dispersion, and polarization) that govern the electron-molecule interaction, and discussing how species with negative electron affinities may possess metastable anion states and how such states should be treated. In addition to references to published literature, many links are given to websites of practicing theoretical chemists who study molecular anions; these links (which appear in boldface) offer the reader a broad avenue to access much more information about molecular anions than can be covered in a review or even through conventional literature sources.

  13. Dissociation Dynamics of Molecular Ions in High dc Electric Field.

    PubMed

    Blum, Ivan; Rigutti, Lorenzo; Vurpillot, François; Vella, Angela; Gaillard, Aurore; Deconihout, Bernard

    2016-05-26

    In an atom probe, molecular ions can be field evaporated from the analyzed material and, then, can dissociate under the very intense electric field close to the field emitter. In this work, field evaporation of ZnO reveals the emission of Zn2O2(2+) ions and their dissociation into ZnO(+) ions. It is shown that the repulsion between the produced ZnO(+) ions is large enough to have a measurable effect on both the ion trajectories and times of flight. Comparison with numerical simulations of the ion trajectories gives information on the lifetime of the parent ions, the energy released by the dissociation and repulsion, and also the dissociation direction. This study not only opens the way to a new method to obtain information on the behavior of molecular ions in high electric fields by using an atom probe, but also opens up the interesting perspective to apply this technique to a wide class of materials and molecules. PMID:27136453

  14. Periodic orbits of the hydrogen molecular ion and their quantization

    SciTech Connect

    Duan, Y.; Yuan, J.; Bao, C.

    1995-11-01

    In a classical study of the hydrogen molecular ion beyond the Born-Oppenheimer approximation (BOA), we have found that segments of trajectories resemble that of the Born-Oppenheimer approximation periodic orbits. The importance of this fact to the classical understanding of chemical bonding leads us to a systematic study of the periodic orbits of the planar hydrogen molecular ion within the BOA. Besides introducing a classification scheme for periodic orbits, we discuss the convergence properties of families of periodic orbits and their bifurcation patterns according to their types. Semiclassical calculations of the density of states based on these periodic orbits yield results in agreement with the exact quantum eigenvalues of the hydrogen molecular ion system.

  15. Optical Pulse-Shaping for Internal Cooling of Molecular Ions

    NASA Astrophysics Data System (ADS)

    Lien, Chien-Yu; Williams, Scott R.; Odom, Brian

    2011-06-01

    We propose a scheme to use pulse-shaped femtosecond lasers to optically cool the internal degrees of freedom of molecular ions. Since this approach relies on cooling rotational and vibrational quanta by exciting an electronic transition, it is most straightforward for molecular ions with diagonal Frank-Condon-Factors. The scheme has the advantage of requiring only tens of microseconds to reach equilibrium without blackbody radiation to redistribute the population. For AlH+, a candidate species, a rate equation simulation shows equilibrium is achieved in 15 μs.

  16. Infrared spectra of small molecular ions trapped in solid neon

    SciTech Connect

    Jacox, Marilyn E.

    2015-01-22

    The infrared spectrum of a molecular ion provides a unique signature for that species, gives information on its structure, and is amenable to remote sensing. It also serves as a comparison standard for refining ab initio calculations. Experiments in this laboratory trap molecular ions in dilute solid solution in neon at 4.2 K in sufficient concentration for observation of their infrared spectra between 450 and 4000 cm{sup !1}. Discharge-excited neon atoms produce cations by photoionization and/or Penning ionization of the parent molecule. The resulting electrons are captured by other molecules, yielding anions which provide for overall charge neutrality of the deposit. Recent observations of ions produced from C{sub 2}H{sub 4} and BF{sub 3} will be discussed. Because of their relatively large possibility of having low-lying excited electronic states, small, symmetric molecular cations are especially vulnerable to breakdown of the Born-Oppenheimer approximation. Some phenomena which can result from this breakdown will be discussed. Ion-molecule reaction rates are sufficiently high that in some systems absorptions of dimer cations and anions are also observed. When H{sub 2} is introduced into the system, the initially-formed ion may react with it. Among the species resulting from such ion-molecule reactions that have recently been studied are O{sub 4}{sup +}, NH{sub 4}{sup +}, HOCO{sup +}, and HCO{sub 2}{sup !}.

  17. Infrared spectra of small molecular ions trapped in solid neon

    NASA Astrophysics Data System (ADS)

    Jacox, Marilyn E.

    2015-01-01

    The infrared spectrum of a molecular ion provides a unique signature for that species, gives information on its structure, and is amenable to remote sensing. It also serves as a comparison standard for refining ab initio calculations. Experiments in this laboratory trap molecular ions in dilute solid solution in neon at 4.2 K in sufficient concentration for observation of their infrared spectra between 450 and 4000 cm!1. Discharge-excited neon atoms produce cations by photoionization and/or Penning ionization of the parent molecule. The resulting electrons are captured by other molecules, yielding anions which provide for overall charge neutrality of the deposit. Recent observations of ions produced from C2H4 and BF3 will be discussed. Because of their relatively large possibility of having low-lying excited electronic states, small, symmetric molecular cations are especially vulnerable to breakdown of the Born-Oppenheimer approximation. Some phenomena which can result from this breakdown will be discussed. Ion-molecule reaction rates are sufficiently high that in some systems absorptions of dimer cations and anions are also observed. When H2 is introduced into the system, the initially-formed ion may react with it. Among the species resulting from such ion-molecule reactions that have recently been studied are O4+, NH4+, HOCO+, and HCO2!.

  18. Jet-Cooled ~A-~X Spectra of the β-HYDROXYETHYLPEROXY and β-HYDROXYETHYLPEROXY-OD Radicals

    NASA Astrophysics Data System (ADS)

    Chen, Ming-Wei; Just, Gabriel M. P.; Codd, Terrance; Miller, Terry A.

    2010-06-01

    The β-hydroxyethylperoxy (HOCH_2CH_2OO, β-HEP) radical in the atmosphere arises from the reaction of ethene (CH_2CH_2) and hydroxyl radical (OH), followed by the reaction with oxygen (O_2). It is also an important intermediate in the oxidation of ethanol, a component of automotive fuel. High-resolution, jet-cooled cavity ring-down spectroscopy (resolution of Δν≈250MHz, considering the instrumental linewidth and the residual Doppler broadening) has been applied to observe the ~A-~X origin band of the most stable conformer of both β-HEP and mono-deuterated β-HEP (DOCH_2CH_2OO, β-HEP-OD). Broadened rotational contours are observed for both isotopologues, but more resolved structure is shown in the β-HEP-OD spectrum. The evolutionary algorithm approach is applied to analyze the spectra, which gives fitted rotational constants and the homogeneous linewidths for both isotopologues using an asymmetric-top model for the rotational Hamiltonian. Evidence corresponding to a narrower homogeneous linewidth in the β-HEP-OD spectra implies that the broad rotational contour of β-HEP likely involves the motion of the hydrogen of the OH group.

  19. Ultrafast excited-state H-atom transfer in jet-cooled 2-(2'-hydroxyphenyl)-oxazole derivatives

    SciTech Connect

    Douhal, A.; Lahmani, F.; Zehnacker-Rentien, A.; Amat-Guerri, F.

    1996-04-01

    The fluorescence excitation and dispersed emission spectra of jet-cooled 2-(2'-hydroxyphenyl)- 4-phenyloxazole (HPPO) and its OH deuterated derivative, DPPO have been investigated. The dispersed fluorescence of both compounds exhibits an identical large Stokes shift. While the excitation spectrum of HPPO is composed of broad overlapping bands, the deuteration of the OH group induces a drastic narrowing of the vibronic structures which are well reproduced by Lorentzian lineshapes corresponding to an homogeneous width ranging from 24 to 30 cm{sup -1} for HPPO and from 3.6 to 9.7 cm{sup -1} for HPPO. The results are interpreted in terms of the occurrence of a fast (> or approx. 4.5x10{sup 12} s{sup -1}) excited-state intramolecular proton-tunnelling-transfer reaction in the enol form producing a keto tautomer through an asymmetric potential energy surface with a small energy barrier. The kinetic isotope effect observed here cannot be described in terms of a monodimensional tunnel effect and may rather involve a multidimensional coordinate involving low frequency motions. 2-(2'-hydroxyphenyl)-4-methyloxazole was also investigated and the influence of complexation on the proton transfer efficiency has been discussed.

  20. Ultrafast excited-state H-atom transfer in jet-cooled 2-(2'-hydroxyphenyl)-oxazole derivatives

    NASA Astrophysics Data System (ADS)

    Douhal, A.; Lahmani, F.; Zehnacker-Rentien, A.; Amat-Guerri, F.

    1996-04-01

    The fluorescence excitation and dispersed emission spectra of jet-cooled 2-(2'-hydroxyphenyl)- 4-phenyloxazole (HPPO) and its OH deuterated derivative, DPPO have been investigated. The dispersed fluorescence of both compounds exhibits an identical large Stokes shift. While the excitation spectrum of HPPO is composed of broad overlapping bands, the deuteration of the OH group induces a drastic narrowing of the vibronic structures which are well reproduced by Lorentzian lineshapes corresponding to an homogeneous width ranging from 24 to 30 cm-1 for HPPO and from 3.6 to 9.7 cm-1 for HPPO. The results are interpreted in terms of the occurrence of a fast (≳4.5×1012 s-1) excited-state intramolecular proton-tunnelling-transfer reaction in the enol form producing a keto tautomer through an asymmetric potential energy surface with a small energy barrier. The kinetic isotope effect observed here cannot be described in terms of a monodimensional tunnel effect and may rather involve a multidimensional coordinate involving low frequency motions. 2-(2'-hydroxyphenyl)-4-methyloxazole was also investigated and the influence of complexation on the proton transfer efficiency has been discussed.

  1. High-resolution absorption cross section measurements of supersonic jet-cooled carbon monoxide between 92.5 and 97.4 nanometers

    NASA Technical Reports Server (NTRS)

    Yoshino, K.; Stark, G.; Esmond, J. R.; Smith, P. L.; Ito, K.; Matsui, T.

    1995-01-01

    High-resolution photoabsorption cross sections for eight CO bands, at wavelengths between 92.5 nm and 97.4 nm, have been measured in a supersonic jet-cooled source (approximately equals 20 K) at the Photon Factory synchrotron radiation facility. New integrated cross sections are reported for four bands between 92.5 nm and 94.2 nm. A low-temperature spectrum of the W(1)-X(0) band (95.6 nm), which was used to determine the absorbing CO column densities, is also presented. Additional jet-cooled cross section measurements were made on the L(0)-X(0), K(0)-X(0), and W(0)-X(0) bands (96.7-97.4 nm) which verify previously published results. A self-consistent set of band oscillator strengths is presented for the eight bands studied.

  2. a Novel Method to Measure Spectra of Cold Molecular Ions

    NASA Astrophysics Data System (ADS)

    Chakrabarty, Satrajit; Holz, Mathias; Campbell, Ewen; Banerjee, Agniva; Gerlich, Dieter; Maier, John P.

    2014-06-01

    A universal method has been developed in our group for measuring the spectra of molecular ions in a 22-pole radio frequency trap at low temperatures. It is based on laser induced inhibition of complex growth (LIICG)1. At low temperatures and high number densities of buffer gas, helium attaches to ions via ternary association. The formation of these weakly bound complexes, however, is inhibited following resonant absorption of the bare molecular ion. The first successful measurements have been demonstrated on the A 2Π_u ← X ^2Σ_g^+ electronic transition of N_2^+, with some thousand N_2^+ ions, helium densities of 1015 cm-3, and storage times of 1 s. The reduction in the number of N_2+-He complexes is the result of an interplay between excitation, radiative and collisional cooling, ternary association, and collision induced dissociation, and is explained using a kinetic model. The method is also applicable to larger molecular species. In this case internal conversion following electronic excitation produces internally "hot" ions, reducing the attachment of helium. The technique is universal because complex formation can be impeded over a wide wavelength range. [1] S. Chakrbarty, M. Holz, E. K. Campbell, A. Banerjee, D. Gerlich, and J. P. Maier, J. Phys. Chem. Lett. 2013, 4, 4051.

  3. A Cartoon in One Dimension of the Hydrogen Molecular Ion

    ERIC Educational Resources Information Center

    Dutta, Sourav; Ganguly, Shreemoyee; Dutta-Roy, Binayak

    2008-01-01

    To illustrate the basic methodology involved in the quantum mechanics of molecules, a one-dimensional caricature of the hydrogen molecular ion (H[superscript +][subscript 2]) is presented, which is exactly solvable, in the Born-Oppenheimer approximation, in terms of elementary functions. The purpose of the exercise is to elucidate in a simple…

  4. Spectroscopy of Benzyl-Type Radicals Generated by Electric Discharge : Jet-Cooled Dichlorobenzyl Radicals

    NASA Astrophysics Data System (ADS)

    Yoon, Young Wook; Lee, Sang Kuk

    2013-06-01

    The technique of corona excited supersonic expansion coupled with a pinhole-type glass nozzle has been proved a useful laser-free spectroscopic tool for observation of vibronic emission spectra of large aromatic molecules, especially for molecular radicals which are long believed to play an important role as a reaction intermediate in aromatic chemical reactions. The vibronic emission spectra recorded with a long-path monochromator exhibit the electronic transition energy in the D_1 → D_0 transition and vibrational mode frequencies at the D_0 state. In this laboratory, all six isomeric dichlorobenzyl radicals have been produced from the corona discharge of corresponding dichlorotoluenes seeded in a large amount of inert carrier gas He. The vibronic emission spectra show very weak intensity due to the existence of Cl atoms in the precursor molecules and possible breakdown of benzene ring by free Cl atoms. Nevertheless, we clearly identified the origin band and a few well-known vibrational modes for each isomer. From an analysis of the spectra observed, we determined the energy of electronic transition and several vibrational modes in the ground electronic state. Also, the red-shift of the origin band from the parental benzyl radical clearly shows the substituent effect of Cl atoms on electronic energy, for which we satisfactorily explain in terms of the shape of the molecular planes and position of the nodal points at a given electronic state, recently developed in this laboratory for identification of isomeric multi-substituted benzyl-type radicals. Y. W. Yoon, C. S. Huh, and S. K. Lee, Chem. Phys. Lett. {550}, 58 (2012). S. K. Lee and S. J. Kim, Chem. Phys. Lett. {412}, 88 (2005).

  5. Utilizing Ion-Mobility Data to Estimate Molecular Masses

    NASA Technical Reports Server (NTRS)

    Duong, Tuan; Kanik, Isik

    2008-01-01

    A method is being developed for utilizing readings of an ion-mobility spectrometer (IMS) to estimate molecular masses of ions that have passed through the spectrometer. The method involves the use of (1) some feature-based descriptors of structures of molecules of interest and (2) reduced ion mobilities calculated from IMS readings as inputs to (3) a neural network. This development is part of a larger effort to enable the use of IMSs as relatively inexpensive, robust, lightweight instruments to identify, via molecular masses, individual compounds or groups of compounds (especially organic compounds) that may be present in specific environments or samples. Potential applications include detection of organic molecules as signs of life on remote planets, modeling and detection of biochemicals of interest in the pharmaceutical and agricultural industries, and detection of chemical and biological hazards in industrial, homeland-security, and industrial settings.

  6. Foil dissociation of fast molecular ions into atomic excited states

    SciTech Connect

    Berry, H.G.; Gay, T.J.; Brooks, R.L.

    1980-01-01

    The intensity and polarizations of light emitted from atomic excited states of dissociated molecular ions were measured. The dissociations are induced when fast molecular ions (50 to 500 keV/amu) are transmitted through thin carbon foils. A calculation of multiple scattering and the Coulomb explosion gives the average internuclear separation of the projectile at the foil surface. Experimentally, the foil thickness is varied to give varying internuclear separations at the foil surface and observe the consequent variation in light yield and optical polarization. Using HeH/sup +/ projectiles, factors of 1 to 5 enhancements of the light yields from n = 3, /sup 1/ /sup 3/P,D states of He I and some He II and H I emissions were observed. The results can be explained in terms of molecular level crossings which provide mixings of the various final states during dissociation of the molecular ions at the exit surface. They suggest a short range surface interaction of the electron pick-up followed by a slow molecular dissociation. Alignment measurements confirm the essential features of the model. Observations of Lyman ..cap alpha.. emission after dissociation of H/sub 2//sup +/ amd H/sub 3//sup +/ show rapid variations in light yield for small internuclear separations at the foil surface.

  7. Candidate molecular ions for an electron electric dipole moment experiment

    SciTech Connect

    Meyer, Edmund R.; Bohn, John L.; Deskevich, Michael P.

    2006-06-15

    This paper is a theoretical work in support of a newly proposed experiment [R. Stutz and E. Cornell, Bull. Am. Soc. Phys. 89, 76 (2004)] that promises greater sensitivity to measurements of the electron's electric dipole moment (EDM) based on the trapping of molecular ions. Such an experiment requires the choice of a suitable molecule that is both experimentally feasible and possesses an expectation of a reasonable EDM signal. We find that the molecular ions PtH{sup +} and HfH{sup +} are both suitable candidates in their low-lying {sup 3}{delta} states. In particular, we anticipate that the effective electric fields generated inside these molecules are approximately 73 and -17 GV/cm, respectively. As a byproduct of this discussion, we also explain how to make estimates of the size of the effective electric field acting in a molecule, using commercially available nonrelativistic molecular structure software.

  8. An experimental and ab initio study of the electronic spectrum of the jet-cooled F{sub 2}BO free radical

    SciTech Connect

    Grimminger, Robert; Clouthier, Dennis J.; Sheridan, Phillip M.

    2014-04-28

    We have studied the B{sup ~} {sup 2}A{sub 1}–X{sup ~} {sup 2}B{sub 2} laser-induced fluorescence (LIF) spectrum of the jet-cooled F{sub 2}BO radical for the first time. The transition consists of a strong 0{sub 0}{sup 0} band at 446.5 nm and eight weak sequence bands to shorter wavelengths. Single vibronic level emission spectra obtained by laser excitation of individual levels of the B{sup ~} state exhibit two electronic transitions: a very weak, sparse B{sup ~}–X{sup ~} band system in the 450–500 nm region and a stronger, more extensive set of B{sup ~} {sup 2}A{sub 1}–A{sup ~} {sup 2}B{sub 1} bands in the 580–650 nm region. We have also performed a series of high level ab initio calculations to predict the electronic energies, molecular structures, vibrational frequencies, and rotational and spin-rotation constants in the X{sup ~} {sup 2}B{sub 2}, A{sup ~2}B{sub 1} and B{sup ~} {sup 2}A{sub 1} electronic states as an aid to the analysis of the experimental data. The theoretical results have been used as input for simulations of the rotationally resolved B{sup ~} {sup 2}A{sub 1}–X{sup ~} {sup 2}B{sub 2} 0{sub 0}{sup 0} LIF band and Franck-Condon profiles of the LIF and single vibronic level emission spectra. The agreement between the simulations obtained with purely ab initio parameters and the experimental spectra validates the geometries calculated for the ground and excited states and the conclusion that the radical has C{sub 2v} symmetry in the X{sup ~}, A{sup ~}, and B{sup ~} states. The spectra provide considerable new information about the vibrational energy levels of the X{sup ~} and A{sup ~} states, but very little for the B{sup ~} state, due to the very restrictive Franck-Condon factors in the LIF spectra.

  9. Spectroscopy and Dynamics of Jet-Cooled Polyynes in a Slit Supersonic Discharge: Sub-Doppler Infrared Studies of Diacetylene HCCCCH.

    PubMed

    Chang, Chih-Hsuan; Nesbitt, David J

    2015-07-16

    Fundamental, bending (ν6, ν7, ν8, ν9), and CC-stretch (ν2, ν3) hot band spectra in the antisymmetric CH stretch (ν4) region near 3330 cm(-1) have been observed and analyzed for jet cooled diacetylene (HC≡C-C≡CH) under sub-Doppler conditions. Diacetylene is generated in situ in the throat of a pulsed supersonic slit expansion by discharge dissociation of acetylene to form ethynyl (C≡CH) + H, followed by radical attack (HC≡CH + C≡C-H) to form HC≡C-C≡CH + H. The combination of (i) sub-Doppler line widths and (ii) absence of spectral congestion permits rotational structure and Coriolis interactions in the ν4 CH stretch fundamental to be observed and analyzed with improved precision. Of particular dynamical interest, the spectra reveal diacteylene formation in highly excited internal vibrational states. Specifically, multiple Π ← Π and Δ ← Δ hot bands built on the ν4 CH stretch fundamental are observed, due to doubly degenerate bending vibrations [cis C≡C-H bend (ν6), trans C-C≡C bend (ν7), trans C≡C-H bend (ν8) and cis C-C≡C bend (ν9)], as well as a heretofore unobserved Σ ← Σ band assigned to excitation of ν2 or 2ν3 CC stretch. Boltzmann analysis yields populations consistent with universally cold rotations (Trot ≈ 15 ± 5 K) and yet superthermal vibrations (Tvib ≈ 85-430 K), the latter of which is quite anomalous for the high collision densities in a slit jet expansion. In order to elucidate the physical mechanism for this excess vibrational excitation, high level ab initio CCSD(T) calculations have been pursued with explicitly correlated basis sets (VnZ-f12; n = 2,3) and extrapolated to the complete basis set (CBS) limit using MOLPRO quantum chemistry software. The results suggest that the extensive hot band structure observed arises from (i) highly exothermic CCH + HCCH addition to yield a strongly bent HCCHCCH radical intermediate (ΔH = -62.6 kcal/mol), followed by (ii) rapid fragmentation over a submerged

  10. Gas feeding molecular phosphorous ion source for semiconductor implanters.

    PubMed

    Gushenets, V I; Oks, E M; Bugaev, A S; Kulevoy, T V; Hershcovitch, A

    2014-02-01

    Phosphorus is a much used dopant in semiconductor technology. Its vapors represent a rather stable tetratomic molecular compound and are produced from one of the most thermodynamically stable allotropic forms of phosphorus-red phosphorus. At vacuum heating temperatures ranging from 325 °C, red phosphorus evaporates solely as P4 molecules (P4/P2 ∼ 2 × 10(5), P4/P ∼ 10(21)). It is for this reason that red phosphorus is best suited as a source of polyatomic molecular ion beams. The paper reports on experimental research in the generation of polyatomic phosphorus ion beams with an alternative P vapor source for which a gaseous compound of phosphorus with hydrogen - phosphine - is used. The ion source is equipped with a specially designed dissociator in which phosphine heated to temperatures close to 700 °C decomposes into molecular hydrogen and phosphorus (P4) and then the reaction products are delivered through a vapor line to the discharge chamber. Experimental data are presented reflecting the influence of the discharge parameters and temperature of the dissociator heater on the mass-charge state of the ion beam. PMID:24593641

  11. Behavior of molecules and molecular ions near a field emitter

    NASA Astrophysics Data System (ADS)

    Gault, Baptiste; Saxey, David W.; Ashton, Michael W.; Sinnott, Susan B.; Chiaramonti, Ann N.; Moody, Michael P.; Schreiber, Daniel K.

    2016-03-01

    The cold emission of particles from surfaces under intense electric fields is a process which underpins a variety of applications including atom probe tomography (APT), an analytical microscopy technique with near-atomic spatial resolution. Increasingly relying on fast laser pulsing to trigger the emission, APT experiments often incorporate the detection of molecular ions emitted from the specimen, in particular from covalently or ionically bonded materials. Notably, it has been proposed that neutral molecules can also be emitted during this process. However, this remains a contentious issue. To investigate the validity of this hypothesis, a careful review of the literature is combined with the development of new methods to treat experimental APT data, the modeling of ion trajectories, and the application of density-functional theory simulations to derive molecular ion energetics. It is shown that the direct thermal emission of neutral molecules is extremely unlikely. However, neutrals can still be formed in the course of an APT experiment by dissociation of metastable molecular ions. This work is a partial contribution of the US Government and therefore is not subject to copyright in the United States.

  12. Molecular imaging of biological tissue using gas cluster ions

    PubMed Central

    Tian, Hua; Wucher, Andreas; Winograd, Nicholas

    2015-01-01

    An Arn+ (n = 1–6000) gas cluster ion source has been utilized to map the chemical distribution of lipids in a mouse brain tissue section. We also show that the signal from high mass species can be further enhanced by doping a small amount of CH4 into the Ar cluster to enhance the ionization of several biologically important molecules. Coupled with secondary ion mass spectrometry instrumentation which utilizes a continuous Ar cluster ion projectile, maximum spatial resolution and maximum mass resolution can be achieved at the same time. With this arrangement, it is possible to achieve chemically resolved molecular ion images at the 4-µm resolution level. The focused Arn+/[Arx(CH4)y]+ beams (4–10 µm) have been applied to the study of untreated mouse brain tissue. A high signal level of molecular ions and salt adducts, mainly from various phosphocholine lipids, has been seen and directly used to map the chemical distribution. The signal intensity obtained using the pure Ar cluster source, the CH4-doped cluster source and C60 is also presented. PMID:26207076

  13. The molecular dynamics simulation of ion-induced ripple growth

    SciTech Connect

    Suele, P.; Heinig, K.-H.

    2009-11-28

    The wavelength-dependence of ion-sputtering induced growth of repetitive nanostructures, such as ripples has been studied by molecular dynamics (MD) simulations in Si. The early stage of the ion erosion driven development of ripples has been simulated on prepatterned Si stripes with a wavy surface. The time evolution of the height function and amplitude of the sinusoidal surface profile has been followed by simulated ion-sputtering. According to Bradley-Harper (BH) theory, we expect correlation between the wavelength of ripples and the stability of them. However, we find that in the small ripple wavelength ({lambda}) regime BH theory fails to reproduce the results obtained by molecular dynamics. We find that at short wavelengths ({lambda}<35 nm) the adatom yield drops hence no surface diffusion takes place which is sufficient for ripple growth. The MD simulations predict that the growth of ripples with {lambda}>35 nm is stabilized in accordance with the available experimental results. According to the simulations, few hundreds of ion impacts in {lambda} long and few nanometers wide Si ripples are sufficient for reaching saturation in surface growth for for {lambda}>35 nm ripples. In another words, ripples in the long wavelength limit seems to be stable against ion-sputtering. A qualitative comparison of our simulation results with recent experimental data on nanopatterning under irradiation is attempted.

  14. Jet-Cooled Laser Spectroscopy of a Jahn-Teller and Pseudo Jahn-Teller Active Molecule: the Nitrate Radical

    NASA Astrophysics Data System (ADS)

    Chen, Ming-Wei; Takematsu, Kana; Okumura, Mitchio; Miller, Terry A.

    2009-06-01

    Well-known as an important intermediate in atmospheric chemistry, the nitrate radical (NO_3) has been extensively studied both experimentally and theoretically. The three energetically lowest electronic states (tilde{X} ^{2}A_{2}^', tilde{A} ^{2}E^'', and tilde{B} ^{2}E^') are strongly coupled by vibronic interactions and hence it is a textbook molecule for understanding the coupling between nearby potential energy surfaces. Such coupling has been treated in considerable detail theoretically. However, corresponding experimental characterization of the interaction is much less detailed. The experimental results primarily consist of IR measurements of vibrational transitions in the ground state. In addition, the electronically forbidden tilde{A}-tilde{X} transition has been observed in ambient temperature CRDS studies. To understand both the Jahn-Teller and pseudo Jahn-Teller coupling in the molecule, further measurements are required with different selection rules and/or higher resolution to resolve the rotational structures of different transitions. In our group, a high-resolution (source Δν≈ 100 MHz in NIR region), jet-cooled CRDS system can be applied to rotationally resolve the electronically forbidden tilde{A}-tilde{X} transition. Furthermore, our high-resolution LIF/SEP system (source Δν≈ 100 MHz) can provide the direct, rotationally resolved measurements of the tilde{B}-tilde{X} and tilde{B}-tilde{A} transitions by operating in the LIF and SEP modes respectively. Such data can provide unambiguous spectral assignments in the tilde{X}, tilde{A} and tilde{B} states. J. F. Stanton, J. Chem. Phys., 126, 134309 (2007) K. Kawaguchi, E. Hirota, T. Ishiwata, and I. Tanaka, J. Chem. Phys., 93, 951 (1990) K. Kawaguchi, T. Ishiwata, E. Hirota, and I. Tanaka, Chem. Phys., 231, 193 (1998) A. Deev, J. Sommar, and M. Okumura, J. Chem. Phys., 122, 224305 (2005) S. Wu, P. Dupré, and T. A. Miller, Phys. Chem. Chem. Phys., 8, 1682, (2006)

  15. Ion-Pair States in Triplet Molecular Hydrogen

    NASA Astrophysics Data System (ADS)

    Setzer, W.; Baker, B. C.; Ashman, S.; Morgan, T. J.

    2016-05-01

    An experimental search is underway to observe the long range triplet ionic states H+ H- of molecular hydrogen. Resonantly enhanced multi-photon ionization of the metastable c 3∏u- 2 pπ state is used access to the R(1)nd1 n = 21 Rydberg state that serves as an intermediate stepping stone state to probe the energy region above the ionization limit with a second tunable laser photon. The metastable state is prepared by electron capture of 6 keV H2+ions in potassium in a molecular beam. Formation of the H+ H- triplet configuration involves triplet excited states of the H- ion, especially the 2p23Pe state, the second bound state of H- predicted to exist with a lifetime long compared to typical auto ionization lifetimes but not yet observed experimentally. Details of the experiment and preliminary results to date will be presented at the conference.

  16. A controllable molecular sieve for Na+ and K+ ions.

    PubMed

    Gong, Xiaojing; Li, Jichen; Xu, Ke; Wang, Jianfeng; Yang, Hui

    2010-02-17

    The selective rate of specific ion transport across nanoporous material is critical to biological and nanofluidic systems. Molecular sieves for ions can be achieved by steric and electrical effects. However, the radii of Na(+) and K(+) are quite similar; they both carry a positive charge, making them difficult to separate. Biological ionic channels contain precisely arranged arrays of amino acids that can efficiently recognize and guide the passage of K(+) or Na(+) across the cell membrane. However, the design of inorganic channels with novel recognition mechanisms that control the ionic selectivity remains a challenge. We present here a design for a controllable ion-selective nanopore (molecular sieve) based on a single-walled carbon nanotube with specially arranged carbonyl oxygen atoms modified inside the nanopore, which was inspired by the structure of potassium channels in membrane spanning proteins (e.g., KcsA). Our molecular dynamics simulations show that the remarkable selectivity is attributed to the hydration structure of Na(+) or K(+) confined in the nanochannels, which can be precisely tuned by different patterns of the carbonyl oxygen atoms. The results also suggest that a confined environment plays a dominant role in the selectivity process. These studies provide a better understanding of the mechanism of ionic selectivity in the KcsA channel and possible technical applications in nanotechnology and biotechnology, including serving as a laboratory-in-nanotube for special chemical interactions and as a high-efficiency nanodevice for purification or desalination of sea and brackish water. PMID:20102186

  17. Atomic and molecular effects on spherically convergent ion flow. II. Multiple molecular species

    NASA Astrophysics Data System (ADS)

    Emmert, Gilbert A.; Santarius, John F.

    2010-01-01

    A theoretical model for the effect of molecular interactions on the flow of molecular ions in spherically convergent geometry where the inner grid (cathode) is at a large negative potential and the outer grid (anode) is grounded has been developed. The model assumes a weakly ionized deuterium plasma composed of D+, D2+, and D3+ ions that interact with the dominant background gas (D2). The interactions included are charge exchange, ionization, and dissociative processes. The formalism developed includes the bouncing motion of the ions in the electrostatic well and sums over all generations of subsequent ions produced by atomic and molecular processes. This leads to a set of two coupled Volterra integral equations, which are solved numerically. From the solution of the Volterra equations, one can obtain quantities of interest, such as the energy spectra of the ions and fast neutral atoms and molecules, and the fusion reaction rate. To provide an experimental test, the model is applied to inertial electrostatic devices and the calculated neutron production rate is compared to previously reported measurements for one University of Wisconsin inertial electrostatic confinement device [D. C. Donovan et al., Fusion Sci. Technol. 56, 507 (2009)]. The results show general agreement with the experimental results, but significant differences remain to be resolved.

  18. 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.

  19. 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.

  20. Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics

    PubMed Central

    Pasi, Marco; Maddocks, John H.; Lavery, Richard

    2015-01-01

    Microsecond molecular dynamics simulations of B-DNA oligomers carried out in an aqueous environment with a physiological salt concentration enable us to perform a detailed analysis of how potassium ions interact with the double helix. The oligomers studied contain all 136 distinct tetranucleotides and we are thus able to make a comprehensive analysis of base sequence effects. Using a recently developed curvilinear helicoidal coordinate method we are able to analyze the details of ion populations and densities within the major and minor grooves and in the space surrounding DNA. The results show higher ion populations than have typically been observed in earlier studies and sequence effects that go beyond the nature of individual base pairs or base pair steps. We also show that, in some special cases, ion distributions converge very slowly and, on a microsecond timescale, do not reflect the symmetry of the corresponding base sequence. PMID:25662221

  1. High Resolution Infrared Spectra of Jet-Cooled Formamide and Formamide Dimer in the C=O Stretch Region

    NASA Astrophysics Data System (ADS)

    Sunahori, Fumie X.; Xu, Yunjie

    2012-06-01

    Formamide (FA) is the simplest molecule with a peptide bond. It has attracted considerable theoretical and spectroscopic attention as a model peptide. The structure of the FA monomer in the ground state was determined to be planar by rotational spectral analyses of several isotopic species. Its high resolution FIR spectrum and IR spectrum in the symmetric N-H stretching region were reported previously. Both matrix isolation and jet-cooled FTIR studies of FA dimer reported spectral evidence for the cyclic C2h symmetric FA dimer bonded by two NH---O bonds, which was predicted to be the most stable structure by ab initio calculations. No high-resolution spectrum of FA dimer, however, has been recorded so far. Our aim in the present study is to study high-resolution IR absorption spectra of both FA and its dimer in the C=O stretching region in order to gain information about the peptide-peptide interactions. IR spectrum of the FA monomer was measured using a rapid scan infrared laser spectrometer equipped with an astigmatic multipass cell. While the monomer band centers at 1754 cm-1, the lines most likely belonging to FA dimer were observed around 1740 cm-1. The spectral assignment of the C=O stretching band of the monomer was made by the means of ground state combination differences. Further data collection and spectral analysis of FA dimer are currently underway. The results will be updated at the conference. E. Hirota, R. Sugisaki, C. J. Nielsen, G. O. Sørensen, J. Mol. Spectrosc. 49, 251, 1974. C. L. Brummel, M. Shen, K. B. Hewett, L. A. Philips, J. Opt. Soc. Am. B, 11, 176, 1994 D. McNaughton, C. J. Evans, S. Lane, C. J. Nielsen, J. Mol. Spectrosc., 193, 104, 1999. A. Mardyukov, E. Sanchez-Garcia, P. Rodziewicz, N. L. Doltsinis, W. Sander, J. Phys. Chem. A., 111, 10552, 2007. M. Albrecht, C. A. Rice, M. A. Suhm, J. Phys. Chem. A., 112, 7530, 2008.

  2. Evidence for ion transport and molecular ion dominance in the Venus ionotail

    NASA Technical Reports Server (NTRS)

    Intriligator, D. S.; Brace, L. H.; Cloutier, P. A.; Grebowsky, J. M.; Hartle, R. E.; Kasprzak, W. T.; Knudsen, W. C.; Strangeway, R. J.

    1994-01-01

    We present analyses from the five Pioneer Venus Orbiter plasma experiments and the plasma wave experiment when a patch of plasma with enhanced densities was encountered in the near-Venus ionotail during atmospheric entry at an altitude of approximately 1100 km in the nightside ionosphere. Our analyses of the thermal and superthermal ion measurements in this plasma feature provides the first evidence that at times molecular ions in the 28-32 amu mass range are dominant over atomic mass species thus yielding evidence for a transport mechanism that reaches into the lower ionosphere. Analysis of plasma analyzer (OPA) observations at this time indicates the presence of ions measured in the rest frame of the spacecraft at approximately 27 and 37 volt energy per unit charge steps. In the rest frame of the planet these superthermal ions are flowing from the dawn direction at speeds (assuming they are O2(+)) of approximately 8 km/s and with a flow component downward (perpendicular to the ecliptic plane) at speeds of approximately 2 km/s. OPA analyses also determine the ion number flux, energy, flow angles, and angular distributions. Plasma wave bursts appear to indicate that plasma density decreases within and on the equatorward edge of the patch of enhanced plasma densities are associated with ion acoustic waves and relative ion streaming.

  3. Resonance Enhanced Multi-Photon Ionization and Uv-Uv Hole-Burning Spectroscopic Studies of Jet-Cooled Acetanilide Derivatives

    NASA Astrophysics Data System (ADS)

    Moon, Ceol Joo; Min, Ahreum; Ahn, Ahreum; Lee, Seung Jun; Choi, Myong Yong; Kim, Seong Keun

    2013-06-01

    Conformational investigations and photochemistry of jet-cooled methacetine (MA) and phenacetine (PA) using one color resonant two-photon ionization (REMPI), UV-UV hole-burning and IR-dip spectroscopy are presented. MA and PA are derivatives of acetanilide, substituted by methoxyl, ethoxyl group in the para position of acetanilide, respectively. Moreover, we have investigated conformational information of the acetanilide derivatives (AAP, MA and PA)-water. In this work, we will present and discuss the solvent effects of the hydroxyl group of acetanilide derivatives in the excited state.

  4. Cryogenic molecular separation system for radioactive 11C ion acceleration

    NASA Astrophysics Data System (ADS)

    Katagiri, K.; Noda, A.; Suzuki, K.; Nagatsu, K.; Boytsov, A. Yu.; Donets, D. E.; Donets, E. D.; Donets, E. E.; Ramzdorf, A. Yu.; Nakao, M.; Hojo, S.; Wakui, T.; Noda, K.

    2015-12-01

    A 11C molecular production/separation system (CMPS) has been developed as part of an isotope separation on line system for simultaneous positron emission tomography imaging and heavy-ion cancer therapy using radioactive 11C ion beams. In the ISOL system, 11CH4 molecules will be produced by proton irradiation and separated from residual air impurities and impurities produced during the irradiation. The CMPS includes two cryogenic traps to separate specific molecules selectively from impurities by using vapor pressure differences among the molecular species. To investigate the fundamental performance of the CMPS, we performed separation experiments with non-radioactive 12CH4 gases, which can simulate the chemical characteristics of 11CH4 gases. We investigated the separation of CH4 molecules from impurities, which will be present as residual gases and are expected to be difficult to separate because the vapor pressure of air molecules is close to that of CH4. We determined the collection/separation efficiencies of the CMPS for various amounts of air impurities and found desirable operating conditions for the CMPS to be used as a molecular separation device in our ISOL system.

  5. Molecular Dynamics Simulations of Ion Equilibration in Ultracold Neutral Plasmas

    NASA Astrophysics Data System (ADS)

    Maksimovic, Nikola; Langin, Thomas; Strickler, Trevor; Killian, Thomas

    2015-11-01

    Understanding transport and equilibration in strongly coupled plasmas is important for modeling plasmas found in extreme environments like inertial confinement fusion plasmas and interiors of gas-giant planets. We use molecular dynamics simulations of Yukawa one component plasmas under periodic boundary conditions to study the evolution of strongly coupled ultracold neutral plasmas (UNPs) at early times. Simulations provide access to observable quantities in strongly coupled plasmas, namely correlation functions. Experimentally, the average velocity of an ion subset with a skewed velocity profile has been used to measure velocity autocorrelation functions and provide access to diffusion coefficients and other transport processes in UNPs. Using the simulation, we verify the experimental measurements of average velocities of ion subsets in UNPs and confirm their agreement with the velocity autocorrelation function. Finally, we examine the collective mode behavior of the ions during their equilibration phase by calculating the longitudinal current correlation function at various times during equilibration. This allows us to study the collective mode coupling behavior of the equilibration of ions in UNPs and its dependence on screening parameter.

  6. Deep-UV biological imaging by lanthanide ion molecular protection

    PubMed Central

    Kumamoto, Yasuaki; Fujita, Katsumasa; Smith, Nicholas Isaac; Kawata, Satoshi

    2015-01-01

    Deep-UV (DUV) light is a sensitive probe for biological molecules such as nucleobases and aromatic amino acids due to specific absorption. However, the use of DUV light for imaging is limited because DUV can destroy or denature target molecules in a sample. Here we show that trivalent ions in the lanthanide group can suppress molecular photodegradation under DUV exposure, enabling a high signal-to-noise ratio and repetitive DUV imaging of nucleobases in cells. Underlying mechanisms of the photodegradation suppression can be excitation relaxation of the DUV-absorptive molecules due to energy transfer to the lanthanide ions, and/or avoiding ionization and reactions with surrounding molecules, including generation of reactive oxygen species, which can modify molecules that are otherwise transparent to DUV light. This approach, directly removing excited energy at the fundamental origin of cellular photodegradation, indicates an important first step towards the practical use of DUV imaging in a variety of biological applications. PMID:26819825

  7. Deep-UV biological imaging by lanthanide ion molecular protection.

    PubMed

    Kumamoto, Yasuaki; Fujita, Katsumasa; Smith, Nicholas Isaac; Kawata, Satoshi

    2016-01-01

    Deep-UV (DUV) light is a sensitive probe for biological molecules such as nucleobases and aromatic amino acids due to specific absorption. However, the use of DUV light for imaging is limited because DUV can destroy or denature target molecules in a sample. Here we show that trivalent ions in the lanthanide group can suppress molecular photodegradation under DUV exposure, enabling a high signal-to-noise ratio and repetitive DUV imaging of nucleobases in cells. Underlying mechanisms of the photodegradation suppression can be excitation relaxation of the DUV-absorptive molecules due to energy transfer to the lanthanide ions, and/or avoiding ionization and reactions with surrounding molecules, including generation of reactive oxygen species, which can modify molecules that are otherwise transparent to DUV light. This approach, directly removing excited energy at the fundamental origin of cellular photodegradation, indicates an important first step towards the practical use of DUV imaging in a variety of biological applications. PMID:26819825

  8. Molecular candidates for cardiac stretch-activated ion channels

    PubMed Central

    Reed, Alistair; Kohl, Peter; Peyronnet, Rémi

    2014-01-01

    The heart is a mechanically-active organ that dynamically senses its own mechanical environment. This environment is constantly changing, on a beat-by-beat basis, with additional modulation by respiratory activity and changes in posture or physical activity, and further overlaid with more slowly occurring physiological (e.g. pregnancy, endurance training) or pathological challenges (e.g. pressure or volume overload). Far from being a simple pump, the heart detects changes in mechanical demand and adjusts its performance accordingly, both via heart rate and stroke volume alteration. Many of the underlying regulatory processes are encoded intracardially, and are thus maintained even in heart transplant recipients. Over the last three decades, molecular substrates of cardiac mechanosensitivity have gained increasing recognition in the scientific and clinical communities. Nonetheless, the processes underlying this phenomenon are still poorly understood. Stretch-activated ion channels (SAC) have been identified as one contributor to mechanosensitive autoregulation of the heartbeat. They also appear to play important roles in the development of cardiac pathologies – most notably stretch-induced arrhythmias. As recently discovered, some established cardiac drugs act, in part at least, via mechanotransduction pathways suggesting SAC as potential therapeutic targets. Clearly, identification of the molecular substrate of cardiac SAC is of clinical importance and a number of candidate proteins have been identified. At the same time, experimental studies have revealed variable–and at times contrasting–results regarding their function. Further complication arises from the fact that many ion channels that are not classically defined as SAC, including voltage and ligand-gated ion channels, can respond to mechanical stimulation. Here, we summarise what is known about the molecular substrate of the main candidates for cardiac SAC, before identifying potential further

  9. Imaging ion and molecular transport at subcellular resolution by secondary ion mass spectrometry

    NASA Astrophysics Data System (ADS)

    Chandra, Subhash; Morrison, George H.

    1995-05-01

    The transport of K+, Na+, and Ca2+ were imaged in individual cells with a Cameca IMS-3f ion microscope. Strict cryogenic frozen freeze-dry sample preparations were employed. Ion redistribution artifacts in conventional chemical preparations are discussed. Cryogenically prepared freeze-fractured freeze-dried cultured cells allowed the three-dimensional ion microscopic imaging of elements. As smaller structures in calcium images can be resolved with the 0.5 [mu]m spatial resolution, correlative techniques are needed to confirm their identity. The potentials of reflected light microscopy, scanning electron microscopy and laser scanning confocal microscopy are discussed for microfeature recognition in freeze-fractured freeze-dried cells. The feasibility of using frozen freeze-dried cells for imaging molecular transport at subcellular resolution was tested. Ion microscopy successfully imaged the transport of the isotopically tagged (13C, 15N) amino acid, -arginine. The labeled amino acid was imaged at mass 28 with a Cs+ primary ion beam as the 28(13C15N)- species. After a 4 h exposure of LLC-PK1 kidney cells to 4 mM labeled arginine, the amino acid was localized throughout the cell with a preferential incorporation into the nucleus and nucleolus. An example is also shown of the ion microscopic imaging of sodium borocaptate, an experimental therapeutic drug for brain tumors, in cryogenically prepared frozen freeze-dried Swiss 3T3 cells.

  10. A new vibrational level of the H2+ molecular ion

    NASA Astrophysics Data System (ADS)

    Carbonell, J.; Lazauskas, R.; Delande, D.; Hilico, L.; Kiliç, S.

    2003-11-01

    A new vibrational level of the H2+ molecular ion with binding energy of 1.09 × 10-9 a.u. approx 30 neV below the first dissociation limit is predicted, using highly accurate numerical non-relativistic quantum calculations, which go beyond the Born-Oppenheimer approximation. It is the first-excited vibrational level v = 1 of the 2pσu electronic state, antisymmetric with respect to the exchange of the two protons, with orbital angular momentum L = 0. It manifests itself as a huge p-H scattering length of a = 750 ± 5 Bohr radii.

  11. Multiple ionization bursts in laser-driven hydrogen molecular ion.

    PubMed

    Takemoto, Norio; Becker, Andreas

    2010-11-12

    Theoretical study on H2(+) in an intense infrared laser field on the attosecond time scale reveals that the molecular ion shows multiple bursts of ionization within a half-cycle of the laser field oscillation, in contrast to the widely accepted tunnel ionization picture for an atom. These bursts are found to be induced by transient localization of the electron at one of the nuclei, and a relation between the time instants of the localization and the vector potential of the laser light is derived. A scheme is proposed to probe the localization dynamics by an extreme ultraviolet laser pulse. PMID:21231228

  12. High-precision spectroscopy of hydrogen molecular ions

    NASA Astrophysics Data System (ADS)

    Zhong, Zhen-Xiang; Tong, Xin; Yan, Zong-Chao; Shi, Ting-Yun

    2015-05-01

    In this paper, we overview recent advances in high-precision structure calculations of the hydrogen molecular ions ( and HD+), including nonrelativistic energy eigenvalues and relativistic and quantum electrodynamic corrections. In combination with high-precision measurements, it is feasible to precisely determine a molecular-based value of the proton-to-electron mass ratio. An experimental scheme is presented for measuring the rovibrational transition frequency (v,L) : (0,0) → (6,1) in HD+, which is currently underway at the Wuhan Institute of Physics and Mathematics. Project supported by the National Natural Science Foundation of China (Grants Nos. 11474316, 11004221, 10974224, and 11274348), the “Hundred Talent Program” of Chinese Academy of Sciences. Yan Zong-Chao was supported by NSERC, SHARCnet, ACEnet of Canada, and the CAS/SAFEA International Partnership Program for Creative Research Teams.

  13. Energetic atomic and molecular ions in Saturn's magnetosphere

    SciTech Connect

    Hamilton, D.C.; Brown, D.C.; Gloeckler, G.; Axford, W.I.

    1983-11-01

    We present observations and anlysis of the composition, energy spectra and spatial distribution of energetic ions (> or approx. =0.2 MeV/nucleon) in Saturn's magnetosphere outside of approx.4 R/sub S/. Our results are based on data from the low-energy particle telescope (LEPT), one of the two sensors of the low-energy charged particle (LECP) experiment on Voyager 1 and 2. The major species, in order of abundance, are H, H/sub 2//sup +/, He, H/sub 3//sup +/, C, and O. The energy spectra of the magnetospheric ions are typically very soft (..gamma..approx.6-7), with an apparent cutoff in energy/charge at 1--2 MeV/e. From the abundance ratios we conclude that the energetic He, C, and O ions have a solar wind origin. The molecular hydrogen ions H/sub 2//sup +/, and H/sub 3//sup +/ probably originate from Saturn's upper ionosphere. The protons can originate from the solar wind, the ionosphere or the hydrogen atom torus in Saturn's outer magnetosphere. The local H/sup +/ sources apparently were dominant at the time of Voyager 1 encouter, but the solar wind may also have been an important source at the time of Voyager 2. To explain the fact that the energetic heavy ions (Z> or =6, E> or approx. =0.2 MeV/nucleon) are apparently of solar wind origin, an acceleration process that favors ions with small mass/charge ionized solar wind particles even though singly or doubly charged local ions (e.g. O/sup +/, O/sup + +/, N/sup +/, etc.) have been observed to be much more abundant in the low-energy magnetospheric plasma. Energization may involve a two-step process of electrostatic iacceleration in the tail region combined with inward radial diffusion. The fluxes of all species decreased inside the orbit of Dione and were nearlly wiped out in the ''slot'' region within the orbit of Tethys.

  14. Photoionization and photofragmentation of the C60+ molecular ion

    NASA Astrophysics Data System (ADS)

    Baral, K. K.; Aryal, N. B.; Esteves-Macaluso, D. A.; Thomas, C. M.; Hellhund, J.; Lomsadze, R.; Kilcoyne, A. L. D.; Müller, A.; Schippers, S.; Phaneuf, R. A.

    2016-03-01

    Cross-section measurements are reported for single and double photoionization of C60+ ions in the photon energy range 18-150 eV accompanied by the loss of zero to seven pairs of carbon atoms, as well as for fragmentation without ionization resulting in loss of two to eight pairs of C atoms in the photon energy range 18-65 eV. Absolute measurements were performed by merging a beam of C60+ molecular ions with a beam of monochromatized synchrotron radiation. Product channels involving dissociation yielding smaller fullerene fragment ions account for nearly half of the total measured oscillator strength in this energy range. The sum of cross sections for the measured product channels is compared to a published calculation of the total photoabsorption cross section of neutral C60 based on time-dependent density-functional theory. This comparison and an accounting of oscillator strengths indicate that with the exception of C58+, the most important product channels resulting from photoabsorption were accounted for in the experiment. Threshold energies for the successive removal of carbon atom pairs accompanying photoionization are also determined from the measurements.

  15. Photodissociation spectroscopy of the dysprosium monochloride molecular ion.

    PubMed

    Dunning, Alexander; Petrov, Alexander; Schowalter, Steven J; Puri, Prateek; Kotochigova, Svetlana; Hudson, Eric R

    2015-09-28

    We have performed a combined experimental and theoretical study of the photodissociation cross section of the molecular ion DyCl(+). The photodissociation cross section for the photon energy range 35,500 cm(-1) to 47,500 cm(-1) is measured using an integrated ion trap and time-of-flight mass spectrometer; we observe a broad, asymmetric profile that is peaked near 43,000 cm(-1). The theoretical cross section is determined from electronic potentials and transition dipole moments calculated using the relativistic configuration-interaction valence-bond and coupled-cluster methods. The electronic structure of DyCl(+) is extremely complex due to the presence of multiple open electronic shells, including the 4f(10) configuration. The molecule has nine attractive potentials with ionically bonded electrons and 99 repulsive potentials dissociating to a ground state Dy(+) ion and Cl atom. We explain the lack of symmetry in the cross section as due to multiple contributions from one-electron-dominated transitions between the vibrational ground state and several resolved repulsive excited states. PMID:26429013

  16. Photodissociation spectroscopy of the dysprosium monochloride molecular ion

    NASA Astrophysics Data System (ADS)

    Dunning, Alexander; Petrov, Alexander; Schowalter, Steven J.; Puri, Prateek; Kotochigova, Svetlana; Hudson, Eric R.

    2015-09-01

    We have performed a combined experimental and theoretical study of the photodissociation cross section of the molecular ion DyCl+. The photodissociation cross section for the photon energy range 35 500 cm-1 to 47 500 cm-1 is measured using an integrated ion trap and time-of-flight mass spectrometer; we observe a broad, asymmetric profile that is peaked near 43 000 cm-1. The theoretical cross section is determined from electronic potentials and transition dipole moments calculated using the relativistic configuration-interaction valence-bond and coupled-cluster methods. The electronic structure of DyCl+ is extremely complex due to the presence of multiple open electronic shells, including the 4f10 configuration. The molecule has nine attractive potentials with ionically bonded electrons and 99 repulsive potentials dissociating to a ground state Dy+ ion and Cl atom. We explain the lack of symmetry in the cross section as due to multiple contributions from one-electron-dominated transitions between the vibrational ground state and several resolved repulsive excited states.

  17. Photodissociation spectroscopy of the dysprosium monochloride molecular ion

    SciTech Connect

    Dunning, Alexander Schowalter, Steven J.; Puri, Prateek; Hudson, Eric R.; Petrov, Alexander; Kotochigova, Svetlana

    2015-09-28

    We have performed a combined experimental and theoretical study of the photodissociation cross section of the molecular ion DyCl{sup +}. The photodissociation cross section for the photon energy range 35 500 cm{sup −1} to 47 500 cm{sup −1} is measured using an integrated ion trap and time-of-flight mass spectrometer; we observe a broad, asymmetric profile that is peaked near 43 000 cm{sup −1}. The theoretical cross section is determined from electronic potentials and transition dipole moments calculated using the relativistic configuration-interaction valence-bond and coupled-cluster methods. The electronic structure of DyCl{sup +} is extremely complex due to the presence of multiple open electronic shells, including the 4f{sup 10} configuration. The molecule has nine attractive potentials with ionically bonded electrons and 99 repulsive potentials dissociating to a ground state Dy{sup +} ion and Cl atom. We explain the lack of symmetry in the cross section as due to multiple contributions from one-electron-dominated transitions between the vibrational ground state and several resolved repulsive excited states.

  18. Development of a sensitive mid-infrared spectrometer for the study of cooled molecular ions

    NASA Astrophysics Data System (ADS)

    Porambo, Michael W.

    The study of molecular ions is relevant to many areas of scientific interest. Mid-infrared laser spectroscopy functions as a useful tool for understanding the role of molecular ions in these areas. To this end, a broadly tunable mid-infrared difference frequency generation noise-immune cavity-enhanced optical heterodyne molecular spectroscopy (NICE-OHMS) system has been developed and characterized through rovibrational spectroscopy of methane. In addition, an attempt was made to use this spectrometer to probe molecular ions focused into an ion beam. Challenges inherent to laboratory molecular ion spectroscopy, such as quantum dilution at high internal temperatures and low ion number density, have been addressed through the development of an instrument that produces rotationally cooled molecular ions coupled to the highly sensitive spectroscopic technique NICE-OHMS. The instrument was first explored as an extension of an ion beam spectrometer by the integration of a continuous supersonic expansion discharge source for the production of the cooled molecular ions. Issues with the implementation led to the re- design of the instrument for spectroscopically probing a supersonic expansion discharge directly with NICE-OHMS. After implementing discharge modulation of the supersonic expansion source, spectra of rotationally cooled H(3/+) and HN(+/2) were acquired. This instrumental development and preliminary spectroscopy has paved the way for a new method for the sensitive spectroscopic study of cooled molecular ions that will aid further insight into these chemical species in many fields.

  19. Ion and Molecular Recognition Using Aryl–Ethynyl Scaffolding

    PubMed Central

    Vonnegut, Chris L.; Tresca, Blakely W.

    2015-01-01

    The aryl–ethynyl linkage has been extensively employed in the construction of hosts for a variety of guests. Uses range from ion detection (e.g., of metal cations in the environment or industrial waste and of anions prevalent in nature), to molecular mimics for biological systems, and to applications targeting future safety issues (such as CO2 capture and indicators for the manufacture of chemical weapons). This Focus Review examines the utilization of the aryl–ethynyl linkage in engineering host molecules for a variety of different guests, and how the alkyne unit plays an integral part as both a rigid scaffolding section in host geometry design as well as a linker to allow conjugative communication between discrete π-electron systems. PMID:25586943

  20. Molecular Dynamical Study on Ion Channeling through Peptide Nanotube

    NASA Astrophysics Data System (ADS)

    Sumiya, Norihito; Igami, Daiki; Takeda, Kyozaburo

    2011-12-01

    We theoretically study the possibility of ion channeling through peptide nanotubes (PNTs). After designing the minimal peptide nanorings (PNRs) and their aggregated form (peptide nanotubes, PNT) computationally, we carry out molecular dynamics (MD) calculations for cation channeling. The present MD calculations show that cation channeling through PNTs occurs. Furthermore, inter-ring hydrogen bonds (HBs) survive and maintain the tubular form of PNTs during cation channeling. We introduce mobility such that cation channeling can be evaluated quantitatively. As the ionic radius of the cation becomes smaller, the effective relaxation time τ becomes larger. Accordingly, mobilities of 10-2˜10-3[cm2/volt/sec] are calculated. In contrast, when an anion (F-) passes through the PNT, the inter-ring HBs are broken, thus inducing breakdown of the peptide backbone. Consequently, H atoms from the broken HBs surround the channeling anion (F-) and halt its motion.

  1. Molecular ions in the protostellar shock L1157-B1

    NASA Astrophysics Data System (ADS)

    Podio, L.; Lefloch, B.; Ceccarelli, C.; Codella, C.; Bachiller, R.

    2014-05-01

    Aims: We perform a complete census of molecular ions with an abundance greater than ~10-10 in the protostellar shock L1157-B1. This allows us to study the ionisation structure and chemistry of the shock. Methods: An unbiased high-sensitivity survey of L1157-B1 performed with the IRAM-30 m and Herschel/HIFI as part of the CHESS and ASAI large programmes allows searching for molecular ions emission. Then, by means of a radiative transfer code in the large velocity gradient approximation, the gas physical conditions and fractional abundances of molecular ions are derived. The latter are compared with estimates of steady-state abundances in the cloud and their evolution in the shock calculated with the chemical model Astrochem. Results: We detect emission from HCO+, H13CO+, N2H+, HCS+, and for the first time in a shock, from HOCO+ and SO+. The bulk of the emission peaks at blue-shifted velocity, ~0.5-3 km s -1 with respect to systemic, has a width of ~3-7 km s-1 and is associated with the outflow cavities (Tkin ~ 20-70 K, nH2 ~ 105 cm-3). A high-velocity component up to -40 km s-1, associated with the primary jet, is detected in the HCO+ 1-0 line. Observed HCO+ and N2H+ abundances (XHCO+ ~ 0.7-3 × 10-8, XN2H+ ~ 0.4-8 × 10-9) agree with steady-state abundances in the cloud and with their evolution in the compressed and heated gas in the shock for cosmic rays ionisation rate ζ = 3 × 10-16 s-1. HOCO+, SO+, and HCS+ observed abundances (XHOCO+ ~ 10-9, XSO+ ~ 8 × 10-10, XHCS+ ~ 3-7 × 10-10), instead, are 1-2 orders of magnitude larger than predicted in the cloud; on the other hand, they are strongly enhanced on timescales shorter than the shock age (~2000 years) if CO2, S or H2S, and OCS are sputtered off the dust grains in the shock. Conclusions: The performed analysis indicates that HCO+ and N2H+ are a fossil record of pre-shock gas in the outflow cavity, whilst HOCO+, SO+, and HCS+ are effective shock tracers that can be used to infer the amount of CO2 and sulphur

  2. Ion and molecular recognition using aryl-ethynyl scaffolding.

    PubMed

    Vonnegut, Chris L; Tresca, Blakely W; Johnson, Darren W; Haley, Michael M

    2015-03-01

    The aryl-ethynyl linkage has been extensively employed in the construction of hosts for a variety of guests. Uses range from ion detection (e.g., of metal cations in the environment or industrial waste and of anions prevalent in nature), to molecular mimics for biological systems, and to applications targeting future safety issues (such as CO2 capture and indicators for the manufacture of chemical weapons). This Focus Review examines the utilization of the aryl-ethynyl linkage in engineering host molecules for a variety of different guests, and how the alkyne unit plays an integral part as both a rigid scaffolding section in host geometry design as well as a linker to allow conjugative communication between discrete π-electron systems. PMID:25586943

  3. Cluster ion beam profiling of organics by secondary ion mass spectrometry--does sodium affect the molecular ion intensity at interfaces?

    PubMed

    Green, Felicia M; Gilmore, Ian S; Seah, Martin P

    2008-12-01

    The use of cluster ion beam sputtering for depth profiling organic materials is of growing technological importance and is a very active area of research. At the 44th IUVSTA Workshop on "Sputtering and Ion Emission by Cluster Ion Beams", recent results were presented of a cluster ion beam depth profile of a thin organic molecular layer on a silicon wafer substrate. Those data showed that the intensity of molecular secondary ions is observed to increase at the interface and this was explained in terms of the higher stopping power in the substrate and a consequently higher sputtering yield and even higher secondary ion molecular sputtering yield. An alternative hypothesis was postulated in the workshop discussion which may be paraphrased as: "under primary ion bombardment of an organic layer, mobile ions such as sodium may migrate to the interface with the inorganic substrate and this enhancement of the sodium concentration increases the ionisation probability, so increasing the molecular ion yield observed at the interface". It is important to understand if measurement artefacts occur at interfaces for quantification as these are of great technological relevance - for example, the concentration of drug in a drug delivery system. Here, we evaluate the above hypothesis using a sample that exhibits regions of high and low sodium concentration at both the organic surface and the interface with the silicon wafer substrate. There is no evidence to support the hypothesis that the probability of molecular secondary ion ionisation is related to the sodium concentration at these levels. PMID:19039819

  4. Molecular designs for controlling the local environments around metal ions.

    PubMed

    Cook, Sarah A; Borovik, A S

    2015-08-18

    The functions of metal complexes are directly linked to the local environment in which they are housed; modifications to the local environment (or secondary coordination sphere) are known to produce changes in key properties of the metal centers that can affect reactivity. Noncovalent interactions are the most common and influential forces that regulate the properties of secondary coordination spheres, which leads to complexities in structure that are often difficult to achieve in synthetic systems. Using key architectural features from the active sites of metalloproteins as inspiration, we have developed molecular systems that enforce intramolecular hydrogen bonds (H-bonds) around a metal center via incorporation of H-bond donors and acceptors into rigid ligand scaffolds. We have utilized these molecular species to probe mechanistic aspects of biological dioxygen activation and water oxidation. This Account describes the stabilization and characterization of unusual M-oxo and heterobimetallic complexes. These types of species have been implicated in a range of oxidative processes in biology but are often difficult to study because of their inherent reactivity. Our H-bonding ligand systems allowed us to prepare an Fe(III)-oxo species directly from the activation of O2 that was subsequently oxidized to form a monomeric Fe(IV)-oxo species with an S = 2 spin state, similar to those species proposed as key intermediates in non-heme monooxygenases. We also demonstrated that a single Mn(III)-oxo center that was prepared from water could be converted to a high-spin Mn(V)-oxo species via stepwise oxidation, a process that mimics the oxidative charging of the oxygen-evolving complex (OEC) of photosystem II. Current mechanisms for photosynthetic O-O bond formation invoke a Mn(IV)-oxyl species rather than the isoelectronic Mn(V)-oxo system as the key oxidant based on computational studies. However, there is no experimental information to support the existence of a Mn

  5. Polarizabilities and Other Properties of the td Muons Molecular Ion

    NASA Technical Reports Server (NTRS)

    Bhatia, A. K.; Drachman, Richard J.; Fisher, Richard R. (Technical Monitor)

    2001-01-01

    Wavefunctions of Hylleraas type were used earlier to calculate energy levels of muonic systems. Recently, we found in the case of the molecular ions H2+, D2+ and HD+ that it was necessary to include high powers of the internuclear distance in the Hylleraas functions to localize the nuclear motion when treating the ions as three-body systems without invoking the Born-Oppenheimer approximation. We try the same approach in a muonic system, td(mu-). Improved convergence is obtained for J = 0 and 1 states for shorter expansions when we use this type of generalized Hylleraas function, but as the expansion length increases the high powers are no longer useful. We obtain good energy values for the two lowest J = 0 and J = 1 states and compare them with the best earlier calculations. Expectation values are obtained for various operators, the Fermi contact parameters, and the permanent quadrupole moment. The cusp conditions are also calculated. The polarizability of the ground state is then calculated using second-order perturbation theory with intermediate J = 1 pseudostates. It should be possible to measure the polarizability by observing Rydberg states of atoms with td(mu-) acting as the nucleus.

  6. Molecular lanthanide single-ion magnets: from bulk to submonolayers.

    PubMed

    Dreiser, J

    2015-05-13

    Single-ion magnets (SIMs) are mononuclear molecular complexes exhibiting slow relaxation of magnetization. They are currently attracting a lot of interest because of potential applications in spintronics and quantum information processing. However, exploiting SIMs in, e.g. molecule-inorganic hybrid devices requires a fundamental understanding of the effects of molecule-substrate interactions on the SIM magnetic properties. In this review the properties of lanthanide SIMs in the bulk crystalline phase and deposited on surfaces in the (sub)monolayer regime are discussed. As a starting point trivalent lanthanide ions in a ligand field will be described, and the challenges in characterizing the ligand field are illustrated with a focus on several spectroscopic techniques which are able to give direct information on the ligand-field split energy levels. Moreover, the dominant mechanisms of magnetization relaxation in the bulk phase are discussed followed by an overview of SIMs relevant for surface deposition. Further, a short introduction will be given on x-ray absorption spectroscopy, x-ray magnetic circular dichroism and scanning tunneling microscopy. Finally, the recent experiments on surface-deposited SIMs will be reviewed, along with a discussion of future perspectives. PMID:25893740

  7. Molecular dynamics simulation of graphene bombardment with Si ion

    NASA Astrophysics Data System (ADS)

    Qin, Xin-Mao; Gao, Ting-Hong; Yan, Wan-Jun; Guo, Xiao-Tian; Xie, Quan

    2014-03-01

    Molecular dynamics simulations with Tersoff-Ziegler-Biersack-Littmark (Tersoff-ZBL) potential and adaptive intermolecular reactive empirical bond order (AIREBO) potential are performed to study the effect of irradiated graphene with silicon ion at several positions and energy levels of 0.1-1000 eV. The simulations reveal four processes: absorption, replacement, transmission and damage. At energies below 110 eV, the dominant process is absorption. For atom in group (a), the process that takes place is replacement, in which the silicon ion removes one carbon atom and occupies the place of the eliminated atom at the incident energy of 72-370 eV. Transmission is present at energies above 100 eV for atom in group (d). Damage is a very important process in current bombardment, and there are four types of defects: single vacancy, replacement-single vacancy, double vacancy and nanopore. The simulations provide a fundamental understanding of the silicon bombardment of graphene, and the parameters required to develop graphene-based devices by controlling defect formation.

  8. Ab initio molecular dynamics calculations of ion hydration free energies

    SciTech Connect

    Leung, Kevin; Rempe, Susan B.; Lilienfeld, O. Anatole von

    2009-05-28

    We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or '{lambda}-path' technique to compute the intrinsic hydration free energies of Li{sup +}, Cl{sup -}, and Ag{sup +} ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential ({phi}) contributions, we obtain absolute AIMD hydration free energies ({Delta}G{sub hyd}) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model {phi} predictions. The sums of Li{sup +}/Cl{sup -} and Ag{sup +}/Cl{sup -} AIMD {Delta}G{sub hyd}, which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag{sup +}+Ni{sup +}{yields}Ag+Ni{sup 2+} in water. The predictions for this reaction suggest that existing estimates of {Delta}G{sub hyd} for unstable radiolysis intermediates such as Ni{sup +} may need to be extensively revised.

  9. Novel Metal Ion Based Estrogen Mimics for Molecular Imaging

    SciTech Connect

    Rajagopalan, Raghavan

    2006-01-30

    The overall objective of the SBIR Phase I proposal is to prepare and evaluate a new class of {sup 99m}Tc or {sup 94m}Tc containing estrogen-like small molecules ('estrogen mimics') for SPECT or PET molecular imaging of estrogen receptor positive (ER+) tumors. In this approach, the metal ion is integrated into the estrone skeleton by isosteric substitution of a carbon atom in the steroidal structure to give new class of mimics that are topologically similar to the native estrogen (Fig. 1). Although both N{sub 2}S{sub 2} and N{sub 3}S mimics 1 and 2 were considered as target structures, molecular modeling study revealed that the presence of the acetyl group at position-15 in the N{sub 3}S mimic 2 causes steric hinderance toward binding of 2 to SHBG. Therefore, initial efforts were directed at the synthesis and evaluation of the N{sub 2}S{sub 2} mimic 1.

  10. Spectroscopic identification of isomeric jet-cooled benzyl-type radicals formed from 3-fluoro-o-xylene by corona discharge

    NASA Astrophysics Data System (ADS)

    Yoon, Young Wook; Chae, Sang Youl; Lee, Sang Kuk

    2013-10-01

    By means of a pinhole-type glass nozzle designed for supersonic jet expansion along with corona discharge, vibronically excited but jet-cooled isomeric benzyl-type radicals were generated from the precursor 3-fluoro-o-xylene. The visible vibronic emission spectrum was recorded from the discharge system with a long-path monochromator. From an analysis of the spectrum observed, we identified the formation of two isomers, 2-methyl-3-fluorobenzyl and 2-methyl-6-fluorobenzyl radicals in the corona discharge of precursor, and determined for the first time the electronic energy in the D1 → D0 transition and vibrational mode frequencies in the D0 state for both isomers.

  11. Jet-cooled laser-induced fluorescence spectroscopy of ScH: Observation of an Ω‧=2-Ω″=1 transition

    NASA Astrophysics Data System (ADS)

    Mukund, Sheo; Bhattacharyya, Soumen; Nakhate, S. G.

    2014-11-01

    New bands of scandium monohydride at origins 17,914.5 and 17,942.3 cm-1 have been observed in a jet-cooled beam with laser-induced fluorescence spectroscopy. Mass-selected resonant photoionization spectroscopy also confirmed the carrier of the band as ScH. The rotational analysis indicated that both transitions at 17,914.5 and 17,942.3 cm-1 are of Ω‧=2-Ω″=1 type with vibrational assignments (0,0) and (1,1) respectively. The assigned g3Φ2-a3Δ1 excitation is the first observed triplet-triplet transition in ScH.

  12. Plant sunscreens in the UV-B: ultraviolet spectroscopy of jet-cooled sinapoyl malate, sinapic acid, and sinapate ester derivatives.

    PubMed

    Dean, Jacob C; Kusaka, Ryoji; Walsh, Patrick S; Allais, Florent; Zwier, Timothy S

    2014-10-22

    Ultraviolet spectroscopy of sinapoyl malate, an essential UV-B screening agent in plants, was carried out in the cold, isolated environment of a supersonic expansion to explore its intrinsic UV spectral properties in detail. Despite these conditions, sinapoyl malate displays anomalous spectral broadening extending well over 1000 cm(-1) in the UV-B region, presenting the tantalizing prospect that nature's selection of UV-B sunscreen is based in part on the inherent quantum mechanical features of its excited states. Jet-cooling provides an ideal setting in which to explore this topic, where complications from intermolecular interactions are eliminated. In order to better understand the structural causes of this behavior, the UV spectroscopy of a series of sinapate esters was undertaken and compared with ab initio calculations, starting with the simplest sinapate chromophore sinapic acid, and building up the ester side chain to sinapoyl malate. This "deconstruction" approach provided insight into the active mechanism intrinsic to sinapoyl malate, which is tentatively attributed to mixing of the bright V ((1)ππ*) state with an adiabatically lower (1)nπ* state which, according to calculations, shows unique charge-transfer characteristics brought on by the electron-rich malate side chain. All members of the series absorb strongly in the UV-B region, but significant differences emerge in the appearance of the spectrum among the series, with derivatives most closely associated with sinapoyl malate showing characteristic broadening even under jet-cooled conditions. The long vibronic progressions, conformational distribution, and large oscillator strength of the V (ππ*) transition in sinapates makes them ideal candidates for their role as UV-B screening agents in plants. PMID:25295994

  13. Improved electron ionization ion source for the detection of supersonic molecular beams

    NASA Astrophysics Data System (ADS)

    Amirav, Aviv; Fialkov, Alexander; Gordin, Alexander

    2002-08-01

    An improved electron ionization (EI) ion source is described, based on the modification of a Brink-type EI ion source through the addition of a second cage with a fine mesh outside the ion chamber. The added outer cage shields the inner ion cage (ionization zone) against the penetration of the filament and electron repeller potentials, and thus results in the provision of ions with narrower ion energy distribution, hence improved ion-beam quality. The closer to zero electrical field inside the ion cage enables improved filtration (rejection) of ions that are produced from vacuum background compounds, based on difference in ion energies of beam and background species. The improved background ion filtration and ion-beam quality resulted in 2.6 times higher mass spectrometric ion signal, combined with 6.4 times better signal to noise ratio, in comparison with the same ion source having a single cage. The dual cage ion source further provides a smaller or no reduction of the electron emission current upon lowering the electron energy for achieving softer EI and/or electron attachment ionization. It also improves the long-term mass spectral and signal reproducibility and enables fast, automated change of the electron energy. Consequently, the dual cage EI ion source is especially effective for use with gas chromatography mass spectrometry with supersonic molecular beams (SMB), liquid chromatography mass spectrometry with SMB, ion guns with SMB, and any other experimental systems with SMB or nonthermal molecular beams.

  14. Nonlinear effects in desorption of valine with fast incident molecular ions

    SciTech Connect

    Salehpour, M.; Fishel, D.L.; Hunt, J.E.

    1988-12-15

    Fast molecular ions as primary particles have been used to study secondary-ion desorption from organic layers. The secondary molecular-ion yield of the amino acid valine (molecular weight, 117) has been measured as a function of the velocity of primary atomic and molecular incident ions. The primary ions used were C/sup +/, O/sup +/, Ar/sup +/, C/sub 2//sup +/, O/sub 2//sup +/ , CO/sup +/, CO/sub 2//sup +/, CH/sup +/, CH/sub 3//sup +/, CF/sup +/, CF/sub 3//sup +/, C/sub 3/F/sub 5//sup +/, and C/sub 4/F/sub 7//sup +/ in the energy range 600 keV--3.7 MeV. The secondary molecular-ion yields, when compared to yields for atomic constituents, unambiguously show that collective effects exist in desorption with incident molecular ions. Results are discussed in the framework of enhancement in the electronic stopping power per atom for molecular ions due to the vicinage of the fast-moving charges in the material. The resulting high-yield enhancements, especially with the use of large incident ions such as C/sub 3/F/sub 5//sup +/ and C/sub 4/F/sub 7//sup +/, are very encouraging for the future of mass spectrometry of large organic molecules.

  15. Laser mass spectrometry of biological molecular ions produced by matrix assisted laser desorption ionization (MALDI)

    NASA Astrophysics Data System (ADS)

    Jia, W. J.; Kosmidis, C.; Ledingham, K. W. D.; Scott, C. T. J.; Singhal, R. P.

    1996-10-01

    A tandem reflectron laser mass spectrometer is used for investigations of the photo fragmentation of molecular ions. The observed fragmentation patterns for 2,5-dihydrobenzoic acid and its fragments ions are analysed. PTH-trytophan and PTH-valine ions, generated by MALDI, are photodissociated and their fragmentation pattern is discussed.

  16. Mechanism of fragmentation and atomization of molecular ions in gasdynamic transport cell

    NASA Astrophysics Data System (ADS)

    Bazhenov, A. N.; Bulovich, S. V.; Gall, L. N.; Kretinina, A. V.; Lapushkin, M. N.; Gall, N. R.

    2010-04-01

    The fragmentation of molecular ions formed upon the electrospraying of a sample and transported through the gasdynamic system of a mass spectrometer equipped with an IESAP (Ion Extraction from Solution at Atmospheric Pressure) source has been experimentally studied. It is established that ion fragmentation in a Kantorowicz-Gray type cell takes place in the immediate vicinity of a skimmer port, apparently, as a result of collisions between ions (accelerated in an electric field) and stagnant gas. Molecular mechanisms of fragmentation are considered and it is concluded that this process can take place in a single ion-molecule collision event.

  17. On the sources of energization of molecular ions at ionospheric altitudes

    SciTech Connect

    Peterson, W.K.; Abe, T.; Fukunishi, H.; Greffen, M.J.; Hayakawa, H.; Kasahara, Y.; Kimura, I.; Matsuoka, A.; Mukai, T.; Nagatsuma, T. ||||

    1994-12-01

    During geomagnetically active times, the suprathermal mass spectrometer on the Akebono satellite frequency observes upflowing molecular ions (NO(+), N2(+), O2(+)) in the 2-3 Earth radii geocentric distance regions in the auroral zone. Molecular ions originating at ionospheric altitudes must acquire an energy of the order of 10 eV in order to overcome gravitation and reach altitudes greater than 2 R(sub E). This energy must be acquired in a time short compared with the local dissociative recombination lifetime of the ions; the latter is of the order of minutes in the F region ionosphere (300-500 km altitude). Upflowing molecular ions thus provide a test particle probe into the mechanisms responsible for heavy ion escape from the ionosphere. In this paper we analyze the extensive complement of plasma, field, and wave data obtained on the Akebono satellite in a number of upflowing molecular ion events observed at high altitudes (5000-10,000 km). We use these data to investigate the source of energization of the molecular ions at ionospheric altitudes. We show that Joule heating and ion resonance heating do not transfer enough energy or do not transfer it fast enough to account for the observed fluxes of upflowing molecular ions. We found that the observed field-aligned currents were too weak to support large-scale field-aligned current instabilities at ionospheric altitudes.

  18. Counter-ion distribution around flexible polyelectrolytes having different molecular architecture.

    PubMed

    Chremos, Alexandros; Douglas, Jack F

    2016-03-21

    We explore the monovalent counter-ion distribution around flexible highly-charged polyelectrolytes with different molecular architectures (linear chains, stars, and unknotted and trefoil rings) using molecular dynamics simulations that include an explicit solvent that interacts with the polyelectrolyte. In particular, we find that the molecular topology influences the fraction of counter-ions transiently associating with the polyelectrolyte on a scale of the order of the chain segments, forming a "condensed" counter-ion interfacial layer. As with the hydrogen bonding of water to proteins and other polymers, the persistence time of these interfacial "bound" counter-ions is relatively short, O(1 ps), and we characterize the fluctuations in the number of the counter-ions populating the interfacial layer. We also find that the counter-ions are distributed in a non-uniform fashion on the polyelectrolyte backbone, forming dynamical clusters whose form and average size is sensitive to molecular architecture. In addition, we find that the residual bound counter-ions, not located in either the interfacial layer or the bulk solution, form a diffuse ionic cloud around the polyelectrolyte due to the uncompensated polyelectrolyte charge along the backbone. Generally charge valence strongly influences the extent of the diffuse counter-ion cloud, but in the case of monovalent counter-ions, we find that the size of the diffuse counter-ion cloud nearly coincides with the polyelectrolyte radius of gyration, independent of molecular topology. PMID:26864861

  19. Photovoltaic lithium-ion battery fabricated by molecular precursor method

    NASA Astrophysics Data System (ADS)

    Nagai, Hiroki; Suzuki, Tatsuya; Takahashi, Yoshihisa; Sato, Mitsunobu

    2016-06-01

    A novel thin-film lithium-ion battery (LIB) which can be charged by the light irradiation was fabricated by molecular precursor method. The unprecedented, translucent thin-film LIB, fabricated on a fluorine-doped tin oxide pre-coated glass substrate, was attained by using the active materials, titania for anode and LiCoO2 for cathode, respectively. The averaged potential at 2.04V was observed by applying a constant current of 0.2mA. Then, that at 1.82V was detected after 60s during the sequential self-discharge process. The charging voltage of the assembled battery was 1.38V with irradiation of 1-sun, the self-discharge voltage was 1.37V. Based on the calibration curve of the charging voltages over constant currents ranging from 0-1.0mA, the detected value can be theoretically reduced to the charging operation by applying a constant current of approximately 60μA. The charge and discharge of this device was stable voltage at least 30 cycles. The two-in-one device can simultaneously generate and store electricity from solar light, the renewable energy source, and may be applied in smart windows for distributed power system according to on-site demand.

  20. Molecular ions in the laboratory and in space

    SciTech Connect

    McCarthy, Michael C.

    2015-01-22

    Molecular ions play a central role in the gas-phase chemistry of the interstellar medium; they also provide information on the physical conditions in astronomical sources (e.g., fractional ionization), and in some cases can be used to infer the abundance of nonpolar molecules such as N{sub 2} and CO{sub 2} which can not be observed in the radio band. During the past four years, the rotational spectra of six carbon-chain anions (C{sub 2}H{sup −}, C{sub 4}H{sup −}, C{sub 6}H{sup −}, C{sub 8}H{sup −}, CN{sup −}, C{sub 3}N{sup −}), NCO{sup −} and seven protonated species (HSCO{sup +}, HSCS{sup +}, cis- and trans-HOSO{sup +}, H{sub 2}NCO{sup +}, HNCOH{sup +}, and HNNO{sup +}) have been detected in our laboratory. On the basis of dedicated astronomical searches, all of the carbon-chain anions except C{sub 2}H{sup −} have now been identified in space. In addition to highlighting recent work on carbon-chain anions and protonated HSO{sub 2}{sup +}, efforts to better understand the distribution of anions in space using C{sub 6}H{sup −} as a tracer for negative charge are described.

  1. Molecular dynamics simulation of ion focusing and crowdion formation in self-ion-irradiated Fe

    NASA Astrophysics Data System (ADS)

    Chen, Di; Shao, Lin

    2012-02-01

    We have used molecular dynamics (MD) simulation to investigate damage and defect development in a <1 0 0> Fe substrate upon 2 keV Fe ion bombardment. The damage cascade formation is accompanied by atomic shifting over a limited distance along the direction of one atomic row, which leads to formation of crowdions aligned with <1 1 1> direction. At the end of structural relaxation and defect recombination, crowdions lead to formation of dumbbell defects - a type of vacancy-interstitial complexes having one vacancy between a pair of slightly displaced interstitials. The dumbbell defects are initially oriented along <1 1 1> direction. After a typical period of 0.2 ps, some dumbbell defects rotate towards <1 1 0> direction. Crowdion and dumbbell defect formation influence the time dependent damage buildups.

  2. Superstatistical velocity distributions of cold trapped ions in molecular-dynamics simulations

    NASA Astrophysics Data System (ADS)

    Rouse, I.; Willitsch, S.

    2015-11-01

    We present a realistic molecular-dynamics treatment of laser-cooled ions in radio-frequency ion traps which avoids previously made simplifications such as modeling laser cooling as a friction force and combining individual heating mechanisms into a single effective heating force. Based on this implementation, we show that infrequent energetic collisions of single ions with background gas molecules lead to pronounced heating of the entire ion ensemble and a time-varying secular ensemble temperature, which manifests itself in a superstatistical time-averaged velocity distribution of the ions. The effect of this finding on the experimental determination of ion temperatures and rate constants for cold chemical reactions is discussed.

  3. Molecular recognition of organic ammonium ions in solution using synthetic receptors

    PubMed Central

    Späth, Andreas

    2010-01-01

    Summary Ammonium ions are ubiquitous in chemistry and molecular biology. Considerable efforts have been undertaken to develop synthetic receptors for their selective molecular recognition. The type of host compounds for organic ammonium ion binding span a wide range from crown ethers to calixarenes to metal complexes. Typical intermolecular interactions are hydrogen bonds, electrostatic and cation–π interactions, hydrophobic interactions or reversible covalent bond formation. In this review we discuss the different classes of synthetic receptors for organic ammonium ion recognition and illustrate the scope and limitations of each class with selected examples from the recent literature. The molecular recognition of ammonium ions in amino acids is included and the enantioselective binding of chiral ammonium ions by synthetic receptors is also covered. In our conclusion we compare the strengths and weaknesses of the different types of ammonium ion receptors which may help to select the best approach for specific applications. PMID:20502608

  4. Interaction of monovalent ions with the water liquid-vapor interface - A molecular dynamics study

    NASA Technical Reports Server (NTRS)

    Wilson, Michael A.; Pohorille, Andrew

    1991-01-01

    Results of molecular dynamics calculations are presented for a series of ions at infinite dilution near the water liquid-vapor interface. The free energies of ion transfer from the bulk to the interface are discussed, as are the accompanying changes of water structure at the surface and ion mobilities as a function of their proximity to the interface. It is shown that simple dielectric models do not provide an accurate description of ions at the water surface. The results of the study should be useful in the development of better models incorporating the shape and molecular structure of the interface.

  5. Hybrid molecular ions emitted from CO-NH3 ice bombarded by fission fragments

    NASA Astrophysics Data System (ADS)

    Martinez, R.; Ponciano, C. R.; Farenzena, L. S.; Iza, P.; Homem, M. G. Pe; Naves de Brito, A.; da Silveira, E. F.; Wien, K.

    2007-05-01

    CO-NH3 ice at 25 K is bombarded by 65 MeV fission fragments and the emitted secondary ions are analyzed by time-of-flight mass spectrometry. The yields of the specific ion species (those formed only from CO or from NH3 molecules) and of the hybrid ion species (formed from both CO and NH3 molecules) are determined as a function of the ice temperature. The time-temperature dependence of desorption yields has been used for secondary ion identification because its behavior characterizes the ion's origin around the sublimation temperature of CO ice (~30 K). The mass spectrum of positive ions measured before CO sublimation is decomposed into three spectra corresponding to CO specific ions, NH3 specific ions and hybrid molecular ions, respectively. The observed spectrum after CO sublimation is very similar to that of a pure NH3 specific spectrum. The total yield of all positive hybrid molecular ions over 600 u mass range is found to be about 2 ions/impact: 20% of this is attributed to N and NH3 containing ions and 80% are ions having the CnOmHl+ structure. The ions Cnions is about 20 times lower than that of positive ions, the most abundant species being the cyanide ion CN-. Observation of cluster ions based on (HCN)n indicates the formation of hydrogen cyanide.

  6. Non-destructive state detection for quantum logic spectroscopy of molecular ions.

    PubMed

    Wolf, Fabian; Wan, Yong; Heip, Jan C; Gebert, Florian; Shi, Chunyan; Schmidt, Piet O

    2016-02-25

    Precision laser spectroscopy of cold and trapped molecular ions is a powerful tool in fundamental physics--used, for example, in determining fundamental constants, testing for their possible variation in the laboratory, and searching for a possible electric dipole moment of the electron. However, the absence of cycling transitions in molecules poses a challenge for direct laser cooling of the ions, and for controlling and detecting their quantum states. Previously used state-detection techniques based on photodissociation or chemical reactions are destructive and therefore inefficient, restricting the achievable resolution in laser spectroscopy. Here, we experimentally demonstrate non-destructive detection of the quantum state of a single trapped molecular ion through its strong Coulomb coupling to a well controlled, co-trapped atomic ion. An algorithm based on a state-dependent optical dipole force changes the internal state of the atom according to the internal state of the molecule. We show that individual quantum states in the molecular ion can be distinguished by the strength of their coupling to the optical dipole force. We also observe quantum jumps (induced by black-body radiation) between rotational states of a single molecular ion. Using the detuning dependence of the state-detection signal, we implement a variant of quantum logic spectroscopy of a molecular resonance. Our state-detection technique is relevant to a wide range of molecular ions, and could be applied to state-controlled quantum chemistry and to spectroscopic investigations of molecules that serve as probes for interstellar clouds. PMID:26855427

  7. Formation and fragmentation of quadruply charged molecular ions by intense femtosecond laser pulses.

    PubMed

    Yatsuhashi, Tomoyuki; Nakashima, Nobuaki

    2010-07-22

    We investigated the formation and fragmentation of multiply charged molecular ions of several aromatic molecules by intense nonresonant femtosecond laser pulses of 1.4 mum with a 130 fs pulse duration (up to 2 x 10(14) W cm(-2)). Quadruply charged states were produced for 2,3-benzofluorene and triphenylene molecular ion in large abundance, whereas naphthalene and 1,1'-binaphthyl resulted only in up to triply charged molecular ions. The laser wavelength was nonresonant with regard to the electronic transitions of the neutral molecules, and the degree of fragmentation was strongly correlated with the absorption of the singly charged cation radical. Little fragmentation was observed for naphthalene (off-resonant with cation), whereas heavy fragmentation was observed in the case of 1,1'-binaphthyl (resonant with cation). The degree of H(2) (2H) and 2H(2) (4H) elimination from molecular ions increased as the charge states increased in all the molecules examined. A striking difference was found between triply and quadruply charged 2,3-benzofluorene: significant suppression of molecular ions with loss of odd number of hydrogen was observed in the quadruply charged ions. The Coulomb explosion of protons in the quadruply charged state and succeeding fragmentation resulted in the formation of triply charged molecular ions with an odd number of hydrogens. The hydrogen elimination mechanism in the highly charged state is discussed. PMID:20578764

  8. Heavy atom nitroxyl radicals. VI. The electronic spectrum of jet-cooled H2PO, the prototypical phosphoryl free radical

    NASA Astrophysics Data System (ADS)

    Gharaibeh, Mohammed A.; Clouthier, Dennis J.; Tarroni, Riccardo

    2011-12-01

    The previously unknown electronic spectrum of the H2PO free radical has been identified in the 407-337 nm region using a combination of laser-induced fluorescence and single vibronic level emission spectroscopy. High level ab initio predictions of the properties of the ground and first two excited doublet states were used to identify the spectral region in which to search for the electronic transition and were used to aid in the analysis of the data. The band system is assigned as the {tilde B}2A'-{tilde X}2A' electronic transition which involves promotion of an electron from the π to the π* molecular orbital. The excited state r0 molecular structure was determined by rotational analysis of high resolution LIF spectra to be r(PO) = 1.6710(2) Å, r(PH) = 1.4280(6) Å, θ(HPO) = 105.68(7)°, θ(HPH) = 93.3(2)°, and the out-of-plane angle = 66.8(2)°. The structural changes on electronic excitation, which include substantial increases in the PO bond length and out-of-plane angle, are as expected based on molecular orbital theory and our previous studies of the isoelectronic H2AsO, Cl2PS, and F2PS free radicals.

  9. The molecular motion of bovine serum albumin under physiological conditions is ion specific.

    PubMed

    Medda, Luca; Monduzzi, Maura; Salis, Andrea

    2015-04-18

    Specific ion effects on the Brownian molecular motion of BSA protein under physiological conditions are investigated. New useful insights into Hofmeister phenomena related to electrolyte-protein interactions are presented. PMID:25782536

  10. ION AND MOLECULE SENSORS USING MOLECULAR RECOGNITION IN LUMINESCENT, CONDUCTIVE POLYMERS

    EPA Science Inventory

    This program integrates three individual, highly interactive projects that will use molecular recognition strategies to develop sensor technology based on luminescent, conductive polymers that contain sites for binding specific molecules or ions in the presence of related molecul...

  11. Efficient rotational cooling of Coulomb-crystallized molecular ions by a helium buffer gas.

    PubMed

    Hansen, A K; Versolato, O O; Kłosowski, L; Kristensen, S B; Gingell, A; Schwarz, M; Windberger, A; Ullrich, J; López-Urrutia, J R Crespo; Drewsen, M

    2014-04-01

    The preparation of cold molecules is of great importance in many contexts, such as fundamental physics investigations, high-resolution spectroscopy of complex molecules, cold chemistry and astrochemistry. One versatile and widely applied method to cool molecules is helium buffer-gas cooling in either a supersonic beam expansion or a cryogenic trap environment. Another more recent method applicable to trapped molecular ions relies on sympathetic translational cooling, through collisional interactions with co-trapped, laser-cooled atomic ions, into spatially ordered structures called Coulomb crystals, combined with laser-controlled internal-state preparation. Here we present experimental results on helium buffer-gas cooling of the rotational degrees of freedom of MgH(+) molecular ions, which have been trapped and sympathetically cooled in a cryogenic linear radio-frequency quadrupole trap. With helium collision rates of only about ten per second--that is, four to five orders of magnitude lower than in typical buffer-gas cooling settings--we have cooled a single molecular ion to a rotational temperature of 7.5(+0.9)(-0.7) kelvin, the lowest such temperature so far measured. In addition, by varying the shape of, or the number of atomic and molecular ions in, larger Coulomb crystals, or both, we have tuned the effective rotational temperature from about 7 kelvin to about 60 kelvin by changing the translational micromotion energy of the ions. The extremely low helium collision rate may allow for sympathetic sideband cooling of single molecular ions, and eventually make quantum-logic spectroscopy of buffer-gas-cooled molecular ions feasible. Furthermore, application of the present cooling scheme to complex molecular ions should enable single- or few-state manipulations of individual molecules of biological interest. PMID:24670662

  12. An experimental and theoretical study of the Ã(2)A(″)Π-X̃(2)A(') band system of the jet-cooled HBBr/DBBr free radical.

    PubMed

    Gharaibeh, Mohammed; Clouthier, Dennis J; Tarroni, Riccardo

    2016-06-21

    The electronic spectra of the HBBr and DBBr free radicals have been studied in depth. These species were prepared in a pulsed electric discharge jet using a precursor mixture of BBr3 vapor and H2 or D2 in high pressure argon. Transitions to the electronic excited state of the jet-cooled radicals were probed with laser-induced fluorescence and the ground state energy levels were measured from the single vibronic level emission spectra. HBBr has an extensive band system in the red which involves a linear-bent transition between the two Renner-Teller components of what would be a (2)Π state at linearity. We have used high level ab initio theory to calculate potential energy surfaces for the bent (2)A' ground state and the linear Ã(2)A(″)Π excited state and we have determined the ro-vibronic energy levels variationally, including spin orbit effects. The correspondence between the computed and experimentally observed transition frequencies, upper state level symmetries, and H and B isotope shifts was used to make reliable assignments. We have shown that the ground state barriers to linearity, which range from 10 000 cm(-1) in HBF to 2700 cm(-1) in BH2, are inversely related to the energy of the first excited (2)Σ ((2)A') electronic state. This suggests that a vibronic coupling mechanism is responsible for the nonlinear equilibrium geometries of the ground states of the HBX free radicals. PMID:27334164

  13. Isomer discrimination of PAHs formed in sooting flames by jet-cooled laser-induced fluorescence: application to the measurement of pyrene and fluoranthene

    NASA Astrophysics Data System (ADS)

    Mouton, Thomas; Mercier, Xavier; Desgroux, Pascale

    2016-05-01

    Jet-cooled laser-induced fluorescence is a spectroscopic method, specifically developed for the study of PAHs formed in flames. This technique has already been used to measure different aromatic species in sooting low-pressure methane flames such as benzene, naphthalene, and pyrene. The use of the LIF technique to excite PAHs drastically cooled down inside a supersonic jet offers the possibility to get selective and quantitative profiles of PAHs sampled from sooting flames. In this paper, we demonstrate the ability of this experimental method to separate the contribution of two mass isomers generated in sooting flames which are the pyrene and the fluoranthene. The selectivity of the method is demonstrated by studying the spectral properties of these species. The method is then applied to the measurement of both these species in two sooting flames with different equivalence ratios and stabilized at 200 torr (26.65 kPa). The sensitivity of the technique has been found to reach a few ppb in the case of fluoranthene measurements.

  14. An experimental and theoretical study of the A˜ 2A″Π -X˜ 2A' band system of the jet-cooled HBBr/DBBr free radical

    NASA Astrophysics Data System (ADS)

    Gharaibeh, Mohammed; Clouthier, Dennis J.; Tarroni, Riccardo

    2016-06-01

    The electronic spectra of the HBBr and DBBr free radicals have been studied in depth. These species were prepared in a pulsed electric discharge jet using a precursor mixture of BBr3 vapor and H2 or D2 in high pressure argon. Transitions to the electronic excited state of the jet-cooled radicals were probed with laser-induced fluorescence and the ground state energy levels were measured from the single vibronic level emission spectra. HBBr has an extensive band system in the red which involves a linear-bent transition between the two Renner-Teller components of what would be a 2Π state at linearity. We have used high level ab initio theory to calculate potential energy surfaces for the bent 2A' ground state and the linear A˜ 2A″Π excited state and we have determined the ro-vibronic energy levels variationally, including spin orbit effects. The correspondence between the computed and experimentally observed transition frequencies, upper state level symmetries, and H and B isotope shifts was used to make reliable assignments. We have shown that the ground state barriers to linearity, which range from 10 000 cm-1 in HBF to 2700 cm-1 in BH2, are inversely related to the energy of the first excited 2Σ (2A') electronic state. This suggests that a vibronic coupling mechanism is responsible for the nonlinear equilibrium geometries of the ground states of the HBX free radicals.

  15. Generalized Langevin models of molecular dynamics simulations with applications to ion channels

    NASA Astrophysics Data System (ADS)

    Gordon, Dan; Krishnamurthy, Vikram; Chung, Shin-Ho

    2009-10-01

    We present a new methodology, which combines molecular dynamics and stochastic dynamics, for modeling the permeation of ions across biological ion channels. Using molecular dynamics, a free energy profile is determined for the ion(s) in the channel, and the distribution of random and frictional forces is measured over discrete segments of the ion channel. The parameters thus determined are used in stochastic dynamics simulations based on the nonlinear generalized Langevin equation. We first provide the theoretical basis of this procedure, which we refer to as "distributional molecular dynamics," and detail the methods for estimating the parameters from molecular dynamics to be used in stochastic dynamics. We test the technique by applying it to study the dynamics of ion permeation across the gramicidin pore. Given the known difficulty in modeling the conduction of ions in gramicidin using classical molecular dynamics, there is a degree of uncertainty regarding the validity of the MD-derived potential of mean force (PMF) for gramicidin. Using our techniques and systematically changing the PMF, we are able to reverse engineer a modified PMF which gives a current-voltage curve closely matching experimental results.

  16. Infrared laser spectroscopy of jet-cooled carbon clusters: the nu 5 band of linear C9

    NASA Technical Reports Server (NTRS)

    Van Orden, A.; Provencal, R. A.; Keutsch, F. N.; Saykally, R. J.

    1996-01-01

    The nu 5 antisymmetric stretching vibration of 1 sigma+g C9 has been observed using direct infrared diode laser absorption spectroscopy of a pulsed supersonic cluster beam. Twenty-eight rovibrational transitions measured in the region of 2079-2081 cm-1 were assigned to this band. A combined least squares fit of these transitions with previously reported nu 6 transitions yielded the following molecular constants for the nu 5 band: nu 0 = 2 079.673 58(17) cm-1, B"= 0.014 321 4(10) cm-1, and B'=0.014 288 9(10) cm-1. The IR intensity of the nu 5 band relative to nu 6 was found to be 0.108 +/- 0.006. Theoretical predictions for the relative intensities vary widely depending upon the level of theory employed, and the experimental value reported here is in reasonable agreement only with the result obtained from the most sophisticated ab initio calculation considered (CCSD).

  17. Molecular microenvironments: Solvent interactions with nucleic acid bases and ions

    NASA Technical Reports Server (NTRS)

    Macelroy, R. D.; Pohorille, A.

    1986-01-01

    The possibility of reconstructing plausible sequences of events in prebiotic molecular evolution is limited by the lack of fossil remains. However, with hindsight, one goal of molecular evolution was obvious: the development of molecular systems that became constituents of living systems. By understanding the interactions among molecules that are likely to have been present in the prebiotic environment, and that could have served as components in protobiotic molecular systems, plausible evolutionary sequences can be suggested. When stable aggregations of molecules form, a net decrease in free energy is observed in the system. Such changes occur when solvent molecules interact among themselves, as well as when they interact with organic species. A significant decrease in free energy, in systems of solvent and organic molecules, is due to entropy changes in the solvent. Entropy-driven interactioins played a major role in the organization of prebiotic systems, and understanding the energetics of them is essential to understanding molecular evolution.

  18. Method and source for producing a high concentration of positively charged molecular hydrogen or deuterium ions

    DOEpatents

    Ehlers, Kenneth W.; Leung, Ka-Ngo

    1988-01-01

    A high concentration of positive molecular ions of hydrogen or deuterium gas is extracted from a positive ion source having a short path length of extracted ions, relative to the mean free path of the gas molecules, to minimize the production of other ion species by collision between the positive ions and gas molecules. The ion source has arrays of permanent magnets to produce a multi-cusp magnetic field in regions remote from the plasma grid and the electron emitters, for largely confining the plasma to the space therebetween. The ion source has a chamber which is short in length, relative to its transverse dimensions, and the electron emitters are at an even shorter distance from the plasma grid, which contains one or more extraction apertures.

  19. ARTEMIS observations of terrestrial ionospheric molecular ion outflow at the Moon

    NASA Astrophysics Data System (ADS)

    Poppe, A. R.; Fillingim, M. O.; Halekas, J. S.; Raeder, J.; Angelopoulos, V.

    2016-07-01

    The Acceleration, Reconnection, Turbulence, and Electrodynamics of the Moon's Interaction with the Sun (ARTEMIS) spacecraft observes outflowing molecular ionospheric ions at lunar distances in the terrestrial magnetotail. The heavy ion fluxes are observed during geomagnetically disturbed times and consist of mainly molecular species (N2+, NO+, and O2+, approximately masses 28-32 amu) on the order of 105-106 cm-2 s-1 at nearly identical velocities as concurrently present protons. By performing backward particle tracing in time-dependent electromagnetic fields from the magnetohydrodynamic Open Global Geospace Circulation Model of the terrestrial magnetosphere, we show that the ions escape the inner magnetosphere through magnetopause shadowing near noon and are subsequently accelerated to common velocities down the low-latitude boundary layer to lunar distances. At the Moon, the observed molecular ion outflow can sputter significant fluxes of neutral species into the lunar exosphere while also delivering nitrogen and oxygen to the lunar volatile inventory.

  20. 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.

  1. Out-of-plane low-frequency vibrations and nonradiative decay in the 1ππ* state of jet-cooled 5-methylcytosine.

    PubMed

    Trachsel, Maria A; Lobsiger, Simon; Leutwyler, Samuel

    2012-09-13

    We investigate the UV vibronic spectrum and excited-state nonradiative processes of jet-cooled 5-methylcytosine (5MCyt) using two-color resonant two-photon ionization spectroscopy at 0.3 and 0.05 cm(–1) resolution. In contrast to cytosine, which shows only five bands above its electronic origin, the lowest electronic transition of 5MCyt exhibits about 25 low-frequency vibronic bands that extend to 0(0)(0) + 450 cm(–1), allowing to extract detailed information on the excited-state electronic and nuclear structure. Most bands are overtones and combinations of the out-of-plane vibrations ν'(1), ν'(2), and ν'(3). Their large intensities reflect butterfly-, boat-, and twist-deformations of the 5MCyt framework upon electronic excitation. From the rotational contours of the 0(0)(0), 1(0)(2), 2(0)(2), and 3(0)(2) bands, the transition is found to be polarized along the in-plane a/b axes, characteristic of a (1)ππ* transition. Approximate second-order coupled-cluster (CC2) and time-dependent B3LYP calculations both predict that 5MCyt undergoes an out-of-plane deformation in its (1)ππ* (S(2)) state but both methods overestimate the out-of-plane ν'(1), ν'(2), and ν'(3) vibrational frequencies by a factor of 3–5. The TD-B3LYP (1)ππ* transition dipole moment direction is 10%:90% a:b, in good agreement with experiment. From the Lorentzian line shape contributions needed to fit the rotational contours, a lower limit to the 5MCyt (1)ππ* state lifetime at the 0(0)(0), 1(0)(2), 2(0)(2), and 3(0)(2) bands is determined as τ ≥ 30 ps. These values are in stark contrast to the ultrafast (picosecond) lifetimes measured for jet-cooled cytosine by femtosecond pump–probe techniques. They also confirm the observation from the R2PI spectrum that 5-methylation of cytosine increases its excited-state lifetime. The higher out-of-plane overtone and combination bands disappear from the spectrum by ~460 cm(–1), signaling the onset of lifetimes τ < 0.5 ps, induced by

  2. Studies on Molecular and Ion Transport in Silicalite Membranes and Applications as Ion Separator for Redox Flow Battery

    NASA Astrophysics Data System (ADS)

    Yang, Ruidong

    Microporous zeolite membranes have been widely studied for molecular separations based on size exclusion or preferential adsorption-diffusion mechanisms. The MFI-type zeolite membranes were also demonstrated for brine water desalination by molecular sieving effect. In this research, the pure silica MFI-type zeolite (i.e. silicalite) membrane has been for the first time demonstrated for selective permeation of hydrated proton (i.e. H3O+) in acidic electrolyte solutions. The silicalite membrane allows for permeation of H 3O+ ions, but is inaccessible to the large hydrated multivalent vanadium ions due to steric effect. The silicalite membrane has been further demonstrated as an effective ion separator in the all-vanadium redox flow battery (RFB).The silicalite is nonionic and its proton conductivity relies on the electric field-driven H3O+ transport through the sub nanometer-sized pores under the RFB operation conditions. The silicalite membrane displayed a significantly reduced self-discharge rate because of its high proton-to-vanadium ion transport selectivity. However, the nonionic nature of the silicalite membrane and very small diffusion channel size render low proton conductivity and is therefore inefficient as ion exchange membranes (IEMs) for practical applications. The proton transport efficiency may be improved by reducing the membrane thickness. However, the zeolite thin films are extremely fragile and must be supported on mechanically strong and rigid porous substrates. In this work, silicalite-Nafion composite membranes were synthesized to achieve a colloidal silicalite skin on the Nafion thin film base. The "colloidal zeolite-ionic polymer" layered composite membrane combines the advantages of high proton-selectivity of the zeolite layer and the mechanical flexibility and low proton transport resistance of the ionic polymer membrane. The composite membrane exhibited higher proton/vanadium ion separation selectivity and lower electrical resistance than

  3. Jet-Cooled Cavity Ring-Down Spectroscopy of the ~a ^2E^"-~X ^2A_2^' Vibronic Transition of NO_3

    NASA Astrophysics Data System (ADS)

    Chen, Ming-Wei; Just, Gabriel M. P.; Codd, Terrance; Miller, Terry A.

    2010-06-01

    The three energetically lowest electronic states (~X 2A2^', ~A 2E^", and ~B 2E^') of NO_3 are strongly coupled by vibronic interactions and have been treated in considerable detail theoretically. Corresponding experimental characterization of the interaction is much less detailed. Previous experimental results primarily consist of IR measurements of vibrational transitions in the ground state. In addition, the electronically forbidden ~A-~X transition has been observed in ambient temperature CRDS studies. A slit-jet nozzle with a high voltage pulsed discharge has been applied to produce the NO_3 radical by dissociating the N-O bond of N_2O_5, and the jet-cooled NO_3 CRDS absorption spectrum has been successfully observed with a high-resolution laser source (Δν≈250MHz, intrinsic resolution considering the instrumental linewidth and the residual Doppler broadening in the jet). The 4^1_0 band (parallel band) shows complex rotational structure which is presently being analyzed. The 2^1_0 band has also been measured as an example of a perpendicular band. Besides the ν_2 and ν_4 vibronic bands, the vibronically forbidden origin band (0^0_0 band) has been recorded under the same experimental conditions. The weakly observed ~A-~X origin band is likely either a magnetic dipole or an electric quardrupole transition. J. F. Stanton, J. Chem. Phys., 126, 134309 (2007) K. Kawaguchi, E. Hirota, T. Ishiwata, and I. Tanaka, J. Chem. Phys., 93, 951 (1990) K. Kawaguchi, T. Ishiwata, E. Hirota, and I. Tanaka, Chem. Phys., 231, 193 (1998) A. Deev, J. Sommar, and M. Okumura, J. Chem. Phys., 122, 224305 (2005) E. Hirota, T. Ishiwata, K. Kawaguchi, M. Fujitake, N. Ohashi, I. Tanaka, J. Chem. Phys., 107, 2829 (1997)

  4. Jet-cooled infrared spectroscopy in slit supersonic discharges: symmetric and antisymmetric CH2 stretching modes of fluoromethyl (CH2F) radical.

    PubMed

    Whitney, Erin S; Dong, Feng; Nesbitt, David J

    2006-08-01

    The combination of shot noise-limited direct absorption spectroscopy with long-path-length slit supersonic discharges has been used to obtain first high-resolution infrared spectra for jet-cooled CH2F radicals in the symmetric (nu1) and antisymmetric (nu5) CH2 stretching modes. Spectral assignment has yielded refined lower- and upper-state rotational constants and fine-structure parameters from least-squares fits to the sub-Doppler line shapes for individual transitions. The rotational constants provide indications of large amplitude vibrational averaging over a low-barrier double minimum inversion-bending potential. This behavior is confirmed by high-level coupled cluster singles/doubles/triples calculations extrapolated to the complete basis set limit and adiabatically corrected for zero point energy. The calculations predict a nonplanar equilibrium structure (theta approximately 29 degrees, where theta is defined to be 180 degrees minus the angle between the C-F bond and the CH2 plane) with a 132 cm(-1) barrier to planarity and a vibrational bend frequency (nu(bend) approximately 276 cm(-1)), in good agreement with previous microwave estimates (nu(bend) = 300 (30) cm(-1)) by Hirota and co-workers [Y. Endo et al., J. Chem. Phys. 79, 1605 (1983)]. The nearly 2:1 ratio of absorption intensities for the symmetric versus antisymmetric bands is in good agreement with density functional theory calculations, but in sixfold contrast with simple local mode CH2 bond dipole predictions of 1:3. This discrepancy arises from a surprisingly strong dependence of the symmetric stretch intensity on the inversion bend angle and provides further experimental support for a nonplanar equilibrium structure. PMID:16942210

  5. Probabilistic rotational state preparation of a single molecular ion though consecutive partial projection measurements

    NASA Astrophysics Data System (ADS)

    Drewsen, Michael

    2016-05-01

    Fully quantum state prepared molecular ions are of interest for a wide range of research fields, including ultra-cold chemistry, ultra-high resolution spectroscopy for test of fundamental physics, and quantum information science. Cooling of the translational degrees of freedom of trapped molecular ions into the millikelvin range has become routine through Coulomb interactions with simultaneously trapped and Doppler laser-cooled atomic ions, and recently it has even become possible to prepare a single molecular ion in its absolute ground state with respect to its quantized motion in the external trapping potential. With respect to the internal rovibrational degrees of freedom, significant progress towards single quantum state preparation has as well recently been realized by a series of complementary methods. In the talk, a novel method for probabilistic rotational state preparation of polar molecular ions based on consecutive partial projection measurements will be discussed. Results of state preparation of vibrational cold single MgH+ ions in the rotational ground or first excited state with maximum likelihood estimated populations of 0.98 and 0.95, respectively, will be presented.

  6. Experiments on Interactions of Electrons with Molecular Ions in Fusion and Astrophysical Plasmas

    NASA Astrophysics Data System (ADS)

    Bannister, M. E.; Aliabadi, H.; Bahati, E. M.; Fogle, M. R.; Krstić, P.; Vane, C. R.; Ehlerding, A.; Geppert, W.; Hellberg, F.; Zhaunerchyk, V.; Larsson, M.; Thomas, R. D.

    2007-08-01

    Through beam-beam experiments at the Multicharged Ion Research Facility (MIRF) at Oak Ridge National Laboratory (ORNL) and at the CRYRING heavy ion storage ring at Stockholm University, we are seeking to formulate a more complete picture of electron-impact dissociation of molecular ions. These inelastic collisions play important roles in many low temperature plasmas such as in divertors of fusion devices and in astrophysical environments. An electron-ion crossed beams experiment at ORNL investigates the dissociative excitation and dissociative ionization of molecular ions from a few eV up to 100 eV. Measurements on dissociative recombination (DR) experiments are made at CRYRING, where chemical branching fractions and fragmentation dynamics are studied. Taking advantage of a 250-kV acceleration platform at the MIRF, a merged electron-ion beams energy loss apparatus is employed to study DR down to zero energy. Recent results on the dissociation of molecular ions of importance in fusion and astrophysics are presented.

  7. Molecular dynamics simulations of swift heavy ion induced defect recovery in SiC

    SciTech Connect

    Backman, Marie; Toulemonde, Marcel; Pakarinen, Olli H; Juslin, Niklas; Djurabekova, Flyura; Nordlund, Kai; Debelle, Aurelien; Weber, William J

    2013-01-01

    Swift heavy ions induce a high density of electronic excitations that can cause the formation of amorphous ion tracks in insulators. No ion tracks have been observed in the semiconductor SiC, but recent experimental work suggests that irradiation damaged SiC can undergo defect recovery under swift heavy ion irradiation. It is believed that local heating of the lattice due to the electronic energy deposition can anneal, and thereby recover, some of the disordered structure. We simulate the local heating due to the ions by the inelastic thermal spike model and perform molecular dynamics simulations of dierent model damage states to study the defect recovery on an atomistic level. We find significant recovery of point defects and a disordered layer, as well as recrystallization at the amorphous-to-crystalline interface of an amorphous layer. The simulation results support the swift heavy ion annealing hypothesis.Swift heavy ions induce a high density of electronic excitations that can cause the formation of amorphous ion tracks in insulators. No ion tracks have been observed in the semiconductor SiC, but recent experimental work suggests that irradiation damaged SiC can undergo defect recovery under swift heavy ion irradiation. It is believed that local heating of the lattice due to the electronic energy deposition can anneal, and thereby recover, some of the disordered structure. We simulate the local heating due to the ions by the inelastic thermal spike model and perform molecular dynamics simulations of dierent model damage states to study the defect recovery on an atomistic level. We find significant recovery of point defects and a disordered layer, as well as recrystallization at the amorphous-to-crystalline interface of an amorphous layer. The simulation results support the swift heavy ion annealing hypothesis.

  8. Production of lanthanide molecular ion beams by fluorination technique

    NASA Astrophysics Data System (ADS)

    Roussière, B.; Deloncle, I.; Barré-Boscher, N.; Cardona, M. A.; Cheikh Mhamed, M.; Corbin, T.; Cottereau, E.; Croizet, H.; Dimitrov, B.; Essabaa, S.; Gavrilov, G.; Gottardo, A.; Goutev, N.; Guillot, J.; Hojman, D.; Lau, C.; Roccia, S.; Tusseau-Nenez, S.; Verney, D.; Yavahchova, M.; the ALTO collaboration

    2016-06-01

    Systematic off-line fluorination studies on all the stable lanthanide isotopes have been performed. The results are presented as a function of various parameters such as the target temperature, the type of ion source used (hot plasma or surface ionization) and the quantity of CF4 introduced. The first on-line measurements allowed us to determine the optimal experimental conditions for producing radioactive lanthanide isotopes.

  9. Ion Channels in Plant Bioenergetic Organelles, Chloroplasts and Mitochondria: From Molecular Identification to Function.

    PubMed

    Carraretto, Luca; Teardo, Enrico; Checchetto, Vanessa; Finazzi, Giovanni; Uozumi, Nobuyuki; Szabo, Ildiko

    2016-03-01

    Recent technical advances in electrophysiological measurements, organelle-targeted fluorescence imaging, and organelle proteomics have pushed the research of ion transport a step forward in the case of the plant bioenergetic organelles, chloroplasts and mitochondria, leading to the molecular identification and functional characterization of several ion transport systems in recent years. Here we focus on channels that mediate relatively high-rate ion and water flux and summarize the current knowledge in this field, focusing on targeting mechanisms, proteomics, electrophysiology, and physiological function. In addition, since chloroplasts evolved from a cyanobacterial ancestor, we give an overview of the information available about cyanobacterial ion channels and discuss the evolutionary origin of chloroplast channels. The recent molecular identification of some of these ion channels allowed their physiological functions to be studied using genetically modified Arabidopsis plants and cyanobacteria. The view is emerging that alteration of chloroplast and mitochondrial ion homeostasis leads to organelle dysfunction, which in turn significantly affects the energy metabolism of the whole organism. Clear-cut identification of genes encoding for channels in these organelles, however, remains a major challenge in this rapidly developing field. Multiple strategies including bioinformatics, cell biology, electrophysiology, use of organelle-targeted ion-sensitive probes, genetics, and identification of signals eliciting specific ion fluxes across organelle membranes should provide a better understanding of the physiological role of organellar channels and their contribution to signaling pathways in plants in the future. PMID:26751960

  10. 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...

  11. Ab initio investigation of electronic properties of the magnesium hydride molecular ion.

    PubMed

    Khemiri, Noura; Dardouri, Riadh; Oujia, Brahim; Gadéa, Florent Xavier

    2013-09-12

    In this work, adiabatic potential energy curves, spectroscopic constants, dipole moments, and vibrational levels for numerous electronic states of magnesium hydride molecular ion (MgH(+)) are computed. These properties are determined by the use of an ab initio method involving a nonempirical pseudopotential for the magnesium core (Mg), the core polarization potential (CPP), the l-dependent cutoff functions and the full valence configuration interaction (FCI). The molecular ion is thus treated as a two-electron system. Our calculations on the MgH(+) molecular ion extend previous theoretical works to numerous electronic excited states in the various symmetries. A good agreement with the available theoretical and experimental works is obtained for the spectroscopic constants, the adiabatic potential energy curves, and the dipole moments for the lowest states of MgH(+). PMID:23944679

  12. Molecular Interactions in 1-Ethyl-3-methylimidazolium Acetate Ion Pair: A Density Functional Study

    NASA Astrophysics Data System (ADS)

    Dhumal, Nilesh R.; Kim, Hyung J.; Kiefer, Johannes

    2009-08-01

    The density functional method is used to obtain the molecular structure, electron density topography, and vibrational frequencies of the ion pair 1-ethyl-3-methylimidazolium acetate. Different conformers are simulated on the basis of molecular interactions between the 1-ethyl-3-methylimidazolium cation and acetate anion. The lowest energy conformers exhibit strong C-H···O interionic interactions compared with other conformers. Characteristic vibrational frequencies of the ion pair and their shifts with respect to free ions are analyzed via the natural bond orbitals and difference electron density maps coupled with molecular electron density topology. Theoretically scaled vibrational frequencies are also compared with the spontaneous Raman scattering and attenuated total reflection infrared absorption measurements.

  13. Measurement of the density profile of pure and seeded molecular beams by femtosecond ion imaging

    SciTech Connect

    Meng, Congsen; Janssen, Maurice H. M.

    2015-02-15

    Here, we report on femtosecond ion imaging experiments to measure the density profile of a pulsed supersonic molecular beam. Ion images are measured for both a molecular beam and bulk gas under identical experimental conditions via femtosecond multiphoton ionization of Xe atoms. We report the density profile of the molecular beam, and the measured absolute density is compared with theoretical calculations of the centre line beam density. Subsequently, we discuss reasons accounting for the differences between measurements and calculations and propose that strong skimmer interference is the most probable cause for the differences. Furthermore, we report on experiments measuring the centre line density of seeded supersonic beams. The femtosecond ion images show that seeding the heavy Xe atom at low relative seed fractions (1%-10%) in a light carrier gas like Ne results in strong relative enhancements of up to two orders of magnitude.

  14. Molecular hydrogen ion elimination from alkyl iodides under strong laser beam irradiation

    NASA Astrophysics Data System (ADS)

    Kosmidis, C.; Kaziannis, S.; Siozos, P.; Lyras, A.; Robson, L.; Ledingham, K. W. D.; McKenna, P.; Jaroszynski, D. A.

    2006-01-01

    The elimination of H2+ from alkyl iodides under strong (up to 5 × 1015 W cm-2) laser irradiation is studied by means of time-of-flight mass spectrometry. The study has been performed by using 60 fs ([lambda] = 800 nm) and 35 ps ([lambda] = 1064, 532, 355 and 266 nm) laser pulses. It is concluded that the H2+ ions are ejected from ionic states via Coulomb explosion processes. The molecular rearrangement leading to H2+ formation is attributed to a tunneling process through a H transfer barrier. For the case of methyl iodide, about 10% of the doubly charged parent ions undergo molecular rearrangement. From a comparison of the H2+/H+ ion yield ratio of the studied molecules, it turns out that the H2+ formation from H atoms bonded to a terminal carbon atom is more efficient than that arising from H atoms bonded to central C atoms of the molecular chain.

  15. Measurement of the density profile of pure and seeded molecular beams by femtosecond ion imaging.

    PubMed

    Meng, Congsen; Janssen, Maurice H M

    2015-02-01

    Here, we report on femtosecond ion imaging experiments to measure the density profile of a pulsed supersonic molecular beam. Ion images are measured for both a molecular beam and bulk gas under identical experimental conditions via femtosecond multiphoton ionization of Xe atoms. We report the density profile of the molecular beam, and the measured absolute density is compared with theoretical calculations of the centre line beam density. Subsequently, we discuss reasons accounting for the differences between measurements and calculations and propose that strong skimmer interference is the most probable cause for the differences. Furthermore, we report on experiments measuring the centre line density of seeded supersonic beams. The femtosecond ion images show that seeding the heavy Xe atom at low relative seed fractions (1%-10%) in a light carrier gas like Ne results in strong relative enhancements of up to two orders of magnitude. PMID:25725826

  16. Spatial decomposition of molecular ions within 3D atom probe reconstructions.

    PubMed

    Breen, Andrew; Moody, Michael P; Gault, Baptiste; Ceguerra, Anna V; Xie, Kelvin Y; Du, Sichao; Ringer, Simon P

    2013-09-01

    Two methods for separating the constituent atoms of molecular ions within atom probe tomography reconstructions are presented. The Gaussian Separation Method efficiently deconvolutes molecular ions containing two constituent atoms and is tested on simulated data before being applied to an experimental HSLA steel dataset containing NbN. The Delaunay Separation Method extends separation to larger complex ions and is also tested on simulated data before being applied to an experimental GaAs dataset containing many large (>3 atoms) complex ions. First nearest neighbour (1NN) distributions and images of the reconstruction before and after the separations are used to show the effect of the algorithms and their validity and practicality are also discussed. PMID:23522847

  17. Hydrogen molecular ions: new schemes for metrology and fundamental physics tests

    NASA Astrophysics Data System (ADS)

    Karr, Jean-Philippe; Patra, Sayan; Koelemeij, Jeroen C. J.; Heinrich, Johannes; Sillitoe, Nicolas; Douillet, Albane; Hilico, Laurent

    2016-06-01

    High-accuracy spectroscopy of hydrogen molecular ions has important applications for the metrology of fundamental constants and tests of fundamental theories. Up to now, the experimental resolution has not surpassed the part-per-billion range. We discuss two methods by which it could be improved by a huge factor. Firstly, the feasibility of Doppler-free quasidegenerate two-photon spectroscopy of trapped and sympathetically cooled ensembles of HD+ ions is discussed, and it is shown that rovibrational transitions may be detected with a good signal-to-noise ratio. Secondly, the performance of a molecular quantum-logic ion clock based on a single Be+-H2 + ion pair is analyzed in detail. Such a clock could allow testing the constancy of the proton-to-electron mass ratio at the 10-17/yr level.

  18. Generation of circularly polarized attosecond pulses by intense ultrashort laser pulses from extended asymmetric molecular ions

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Bandrauk, André D.

    2011-08-01

    We present a method for generation of single circularly polarized attosecond pulses in extended asymmetric HHe2+ molecular ions. By employing an intense ultrashort circularly polarized laser pulse with intensity 4.0×1014 W/cm2, wavelength 400 nm, and duration 10 optical cycles, molecular high-order-harmonic generation (MHOHG) spectra with multiple plateaus exhibit characters of circular polarization. Using a classical laser-induced collision model, double collisions of continuum electrons first with neighboring ions and then second with parent ions are presented at a particular internuclear distance and confirmed from numerical solutions of a time-dependent Schrödinger equation. We analyze the MHOHG spectra with a Gabor time window and find that, due to the asymmetry of HHe2+, a single collision trajectory of continuum electrons with ions can produce circularly polarized harmonics, leading to single circularly polarized attosecond pulses for specific internuclear distances.

  19. Generation of circularly polarized attosecond pulses by intense ultrashort laser pulses from extended asymmetric molecular ions

    SciTech Connect

    Yuan, Kai-Jun; Bandrauk, Andre D.

    2011-08-15

    We present a method for generation of single circularly polarized attosecond pulses in extended asymmetric HHe{sup 2+} molecular ions. By employing an intense ultrashort circularly polarized laser pulse with intensity 4.0x10{sup 14} W/cm{sup 2}, wavelength 400 nm, and duration 10 optical cycles, molecular high-order-harmonic generation (MHOHG) spectra with multiple plateaus exhibit characters of circular polarization. Using a classical laser-induced collision model, double collisions of continuum electrons first with neighboring ions and then second with parent ions are presented at a particular internuclear distance and confirmed from numerical solutions of a time-dependent Schroedinger equation. We analyze the MHOHG spectra with a Gabor time window and find that, due to the asymmetry of HHe{sup 2+}, a single collision trajectory of continuum electrons with ions can produce circularly polarized harmonics, leading to single circularly polarized attosecond pulses for specific internuclear distances.

  20. Three-dimensional momentum imaging of delayed dissociation of metastable molecular ions

    NASA Astrophysics Data System (ADS)

    Malakar, Y.; Jochim, Bethany; Erdwien, Reid; Carnes, K. D.; Pearson, W. L.; Rudenko, A.; Ben-Itzhak, I.

    2016-05-01

    Coincidence three-dimensional momentum imaging has been a powerful technique in studies of molecular fragmentation following ionization by ultrashort intense laser pulses, fast ion or electron impact, etc. On occasion, the fragmentation process of the intermediate molecular ion can be delayed by a significant fraction of the flight time to the detector due to the presence of metastable states. We focus on the signatures of delayed dissociation into an ion pair observed in coincidence spectra obtained using cold target recoil ion momentum spectrometry (COLTRIMS). Moreover, we present a method for recovering the complete 3D momenta of the dissociating fragments as well as the time delay of the dissociation. Laser-induced dissociation of hydrocarbon dications, for example C2 H42+ --> H+ + C2 H3+,is used to demonstrate the method. Supported by the Chemical Sciences, Geosciences, and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U. S. Department of Energy.

  1. 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 ...

  2. Millimeter-Wave Spectroscopic and Collisional Studies of Molecules and Molecular Ions

    NASA Astrophysics Data System (ADS)

    Pearson, John Christoffersen

    1995-01-01

    Molecular spectroscopy in the millimeter- and submillimeter-wave regions is an important tool in molecular physics. Information on molecular motions and interactions is obtained from spectroscopic studies of energy levels and collisions. This information and the data from which it is derived are essential in remote sensing of the atmosphere and the interstellar medium. Remote sensing at submillimeter wavelengths is now possible, making higher frequency and quantum number measurements of known interstellar species like water, propionitrile and ethyl alcohol necessary. Remote sensing improvements have also facilitated the need for spectral data on suspected interstellar molecules like propylene. The desire to extract quantitative information from atmospheric remote sensing has resulted in the need for a better understanding of the molecular interactions that cause pressure broadening. The use of a cold molecular ion to magnify the effects of intermolecular interactions has serious implications for pressure broadening theory. The measurement and analysis of rotational spectra of the asymmetric rotors water and propionitrile and the internal rotors propylene and ethyl alcohol are presented. These investigations provide the data and analysis necessary for astronomical observation. The ethyl alcohol investigation is the first experimental millimeter-wave study of a molecule with an asymmetric internal rotor. This study provides the data necessary for detailed theoretical modeling of this type of problem. A novel new experimental technique for generating and studying molecular ions is presented. The first temperature dependent microwave pressure broadening study of a molecular ion colliding with a neutral molecule, HCO^{+} on H_2 , is presented.

  3. Ultra-sensitive high-precision spectroscopy of a fast molecular ion beam

    SciTech Connect

    Mills, Andrew A.; Siller, Brian M.; Porambo, Michael W.; Perera, Manori; Kreckel, Holger; McCall, Benjamin J.

    2011-12-14

    Direct spectroscopy of a fast molecular ion beam offers many advantages over competing techniques, including the generality of the approach to any molecular ion, the complete elimination of spectral confusion due to neutral molecules, and the mass identification of individual spectral lines. The major challenge is the intrinsic weakness of absorption or dispersion signals resulting from the relatively low number density of ions in the beam. Direct spectroscopy of an ion beam was pioneered by Saykally and co-workers in the late 1980s, but has not been attempted since that time. Here, we present the design and construction of an ion beam spectrometer with several improvements over the Saykally design. The ion beam and its characterization have been improved by adopting recent advances in electrostatic optics, along with a time-of-flight mass spectrometer that can be used simultaneously with optical spectroscopy. As a proof of concept, a noise-immune cavity-enhanced optical heterodyne molecular spectroscopy (NICE-OHMS) setup with a noise equivalent absorption of {approx}2 x 10{sup -11} cm{sup -1} Hz{sup -1/2} has been used to observe several transitions of the Meinel 1-0 band of N{sub 2}{sup +} with linewidths of {approx}120 MHz. An optical frequency comb has been used for absolute frequency calibration of transition frequencies to within {approx}8 MHz. This work represents the first direct spectroscopy of an electronic transition in an ion beam, and also represents a major step toward the development of routine infrared spectroscopy of rotationally cooled molecular ions.

  4. The roles of electronic and nuclear stopping in the desorption valine negative molecular ions

    SciTech Connect

    Hunt, J.E.; Salehpour, M.; Fishel, D.L.; Tou, J.C.

    1988-01-01

    The yield of valine negative molecular ions has been measured as a function of Xe/sup +/, Kr/sup +/, and Ar/sup +/ primary ion velocity. The electronic and nuclear stopping powers are comparable in magnitude and opposite in slope in the experimental velocity region. The yield data are explained in terms of electronic stopping power alone, with no contribution from nuclear stopping power within the experimental error. Low molecular weight atomic species are found to be best described by a nuclear stopping power related process. 18 refs., 3 figs.

  5. Double-modulation spectroscopy of molecular ions - Eliminating the background in velocity-modulation spectroscopy

    NASA Technical Reports Server (NTRS)

    Lan, Guang; Tholl, Hans Dieter; Farley, John W.

    1991-01-01

    Velocity-modulation spectroscopy is an established technique for performing laser absorption spectroscopy of molecular ions in a discharge. However, such experiments are often plagued by a coherent background signal arising from emission from the discharge or from electronic pickup. Fluctuations in the background can obscure the desired signal. A simple technique using amplitude modulation of the laser and two lock-in amplifiers in series to detect the signal is demonstrated. The background and background fluctuations are thereby eliminated, facilitating the detection of molecular ions.

  6. Ion exhange and molecular sorption of oxalic acid with a highly basic anion exchanger

    NASA Astrophysics Data System (ADS)

    Krisilova, E. V.; Oros, G. Yu.; Krisilov, A. V.; Selemenev, V. F.

    2014-04-01

    Ab initio modeling of a matrix fragment of resin and geometry optimization of the molecular structure of oxalic acid were performed. The isotherm of oxalic acid sorption with AV-17-8 anion exchange resin was obtained by the variable concentrations technique. The ion-exchange and molecular components of sorbate fixation with the ion exchanger were determined. The hydration of the highly basic anion exchanger that absorbed different quantities of dicarboxylic acid was evaluated by the centrifuging method. The dependence of the amount of water and sorbate concentration in the resin was linear antibatic.

  7. Improvement of Contact Resistance with Molecular Ion Implantation

    SciTech Connect

    Lee, Kyung Won; Lee, Jin Ku; Oh, Jae Geun; Ju, Min Ae; Jeon, Seung Joon; Ku, Ja Chun; Park, Sung Ki; Huh, Tae Hoon; Kim, Steve; Ra, Geum Joo; Harris, Mark A.; Reece, Ronald N.; Yoon, Dae Ho

    2008-11-03

    Basic characteristics of ClusterBoron (B{sub 18}H{sub 22}) implantation were investigated for improving contact resistance in DRAM devices. Generally, {sup 49}BF{sub 2} has been widely used for contact implant application in DRAM manufacturing because of its higher productivity compared to monomer boron ({sup 11}B). However, because of limited activation in a low thermal budget ({approx}800 deg. C) anneal, the sheet resistance was saturated for doses over 5x10{sup 15} ions/cm{sup 2}. Although many investigations have been reported, such as {sup 30}BF implant mixed implant with monomer boron etc., no practical solution has been found for dramatic improvement of contact resistance in a productive manner. B{sub 18}H{sub 22} was developed to overcome the productivity limitations encountered in low energy, high dose boron implantation and the limited activation of {sup 49}BF{sub 2} due to co-implanted fluorine. In this study, basic characterization of the B{sub 18}H{sub 22} contact implant was performed through sheet resistance, SIMS (Secondary Ion Mass Spectrometry) and XTEM (cross-sectional transmission electron microscopy). The B{sub 18}H{sub 22} implants showed lower sheet resistance than conventional {sup 49}BF{sub 2} for 5x10{sup 15} ions/cm{sup 2} on bare wafer tests. Through XTEM study, we found the activation behavior of both B{sub 18}H{sub 22} and {sup 49}BF{sub 2} were directly related with the amorphous layer thickness and residual defects from low thermal budget anneal. PMOS contact resistance in the sub-70 nm device by B{sub 18}H{sub 22} implantation showed considerable improvement (about 30%), showing B{sub 18}H{sub 22} could replace the BF{sub 2} for contact implant in contact resistance implant.

  8. Toward Molecular 4f Single-Ion Magnet Qubits.

    PubMed

    Pedersen, Kasper S; Ariciu, Ana-Maria; McAdams, Simon; Weihe, Høgni; Bendix, Jesper; Tuna, Floriana; Piligkos, Stergios

    2016-05-11

    Quantum coherence is detected in the 4f single-ion magnet (SIM) Yb(trensal), by isotope selective pulsed EPR spectroscopy on an oriented single crystal. At X-band, the spin-lattice relaxation (T1) and phase memory (Tm) times are found to be independent of the nuclei bearing, or not, a nuclear spin. The observation of Rabi oscillations of the spin echo demonstrates the possibility to coherently manipulate the system for more than 70 rotations. This renders Yb(trensal), a sublimable and chemically modifiable SIM, an excellent candidate for quantum information processing. PMID:27105449

  9. Changes in the molecular ion yield and fragmentation of peptides under various primary ions in ToF-SIMS and matrix-enhanced ToF-SIMS.

    PubMed

    Körsgen, Martin; Tyler, Bonnie J; Pelster, Andreas; Lipinsky, Dieter; Dreisewerd, Klaus; Arlinghaus, Heinrich F

    2016-06-01

    Time of flight secondary ion mass spectrometry (ToF-SIMS) is a powerful technique for the nanoanalysis of biological samples, but improvements in sensitivity are needed in order to detect large biomolecules, such as peptides, on the individual cell level at physiological concentrations. Two promising options to improve the sensitivity of SIMS to large peptides are the use of cluster primary ions to increase desorption of intact molecules or the use of matrix-assisted laser desorption/ionization (MALDI) matrices to increase the ionization probability. In this paper, the authors have combined these two approaches in order to improve understanding of the interaction between ionization and fragmentation processes. The peptides bradykinin and melittin were prepared as neat monolayers on silicon, in a Dextran-40 matrix and in two common MALDI matrices, 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxy cinnamic acid (HCCA). ToF-SIMS spectra of these samples were collected using a range of small Bi cluster primary ions and large Ar cluster primary ions. The trends observed in the molecular ion yield and the [M+H](+)/C4H8N(+) ratio with primary ion cluster size were sample system dependent. The molecular ion yield of the bradykinin was maximized by using 30 keV Bi3 (+) primary ions in a DHB matrix but in the HCCA matrix, the maximum molecular ion yield was obtained by using 30 keV Bi7 (+) primary ions. In contrast, the molecular ion yield for melittin in both matrices was greatest using 20 keV Ar2000 (+) primary ions. Improvements in the molecular ion yield were only loosely correlated with a decrease in small fragment ions. The data indicate a complex interplay between desorption processes and ion formation processes which mean that the optimal analytical conditions depend on both the target analyte and the matrix. PMID:26829968

  10. Reversing Molecular Ion Formation for Quantum Simulations in a Coulomb Crystal of Be+ Ions

    NASA Astrophysics Data System (ADS)

    Sawyer, Brian; Bohnet, Justin; Britton, Joseph; Bollinger, John

    2015-05-01

    For more than a decade, the internal states of cold, trapped atomic ions have been used as qubits for quantum logic operations. Penning traps allow for confinement and manipulation of very large ion crystals (>> 100) in 1D, 2D, or 3D configurations. Quantum simulation experiments with 2D crystals in Penning traps rely on engineered couplings between Be+ internal spin and collective ion motion perpendicular to the crystal plane. High-fidelity quantum logic operations require precise knowledge of the crystal mode structure, but mode eigenfrequencies and eigenvectors can shift over time as impurity hydride ions (i.e. BeH+) are formed in the crystal via chemistry with background H2 molecules in the vacuum chamber. To mitigate this, we have demonstrated a single-photon photodissociation scheme for BeH+ that efficiently recovers Be+ ions within the crystal. A commercial excimer laser operating at 157 nm provides the photodissociation light, and we note that a 193 nm excimer should efficiently recover Mg+ and Al+ from their respective hydride species, making this technique applicable to a wide range of ion species used in quantum information experiments. Supported by a NIST-NRC Fellowship.

  11. Ion-beam assisted deposition of thin molybdenum films studied by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Robbemond, Arie; Thijsse, Barend J.

    1997-05-01

    We report results obtained by molecular dynamics simulation of low energy argon-ion assisted growth of thin molybdenum films (≈ 20 Å). The effects of a single ion impact are discussed, but more particularly we consider film growth from a manufacturing viewpoint and examine the properties of the completed films. Results for ion-beam assisted deposition are compared with those for unassisted growth (i.e. physical vapor deposition). Surface orientation, atomic displacements, surface roughness, sputtering, point defects, and the influence of off-normal atom incidence are discussed.

  12. Vibrational Spectroscopy of Sympathetically Cooled CaH^+ Molecular Ions

    NASA Astrophysics Data System (ADS)

    Khanyile, Ncamiso B.; Goeders, James E.; Brown, Kenneth R.

    2013-06-01

    The search for time variation in the fundamental constants of nature such as the fine structure constant(α) and the proton/electron mass ratio(μ), is an area of active research. Comparing the vibrational overtones of CaH^+ with electronic transitions in atoms has been proposed as a means to detect possible time variation of μ Before these precision measurements can be realized, the survey spectroscopy needs to be performed. We describe our experiments using a Coulomb crystal of sympathetically cooled CaH^+ and laser-cooled Ca^+ ions to measure the vibrational overtones by resonance-enhanced multiphoton photo-dissociation (REMPD) in a linear Paul trap. The dissociation of CaH^+ is detected by observing the change in the crystal composition by monitoring the Ca^+ fluorescence. Future single ion experiments for the precision measurement are also discussed. J. Uzan, Rev. Mod. Phys. 75, 403 (2003). M. Kajita and Y. Moriwaki, J. Phys. B: At. Mol. Opt. Phys. 42, 154022(2009).

  13. When electrons meet molecular ions and what happens next: dissociative recombination from interstellar molecular clouds to internal combustion engines.

    PubMed

    Thomas, Richard D

    2008-01-01

    The interaction of matter with its environment is the driving force behind the evolution of 99% of the observed matter in the universe. The majority of the visible universe exists in a state of weak ionization, the so called fourth state of matter: plasma. Plasmas are ubiquitous, from those occurring naturally; interstellar molecular clouds, cometary comae, circumstellar shells, to those which are anthropic in origin; flames, combustion engines and fusion reactors. The evolution of these plasmas is driven by the interaction of the plasma constituents, the ions, and the electrons. One of the most important subsets of these reactions is electron-molecular ion recombination. This process is significant for two very important reasons. It is an ionization reducing reaction, removing two ionised species and producing neutral products. Furthermore, these products may themselves be reactive radical species which can then further drive the evolution of the plasma. The rate at which the electron reacts with the ion depends on many parameters, for examples the collision energy, the internal energy of the ion, and the structure of the ion itself. Measuring these properties together with the manner in which the system breaks up is therefore critical if the evolution of the environment is to be understood at all. Several techniques have been developed to study just such reactions to obtain the necessary information on the parameters. In this paper the focus will be on one the most recently developed of these, the Ion Storage Ring, together with the detection tools and techniques used to extract the necessary information from the reaction. PMID:18618616

  14. Rotational dynamics of a diatomic molecular ion in a Paul trap

    SciTech Connect

    Hashemloo, A.; Dion, C. M.

    2015-11-28

    We present models for a heteronuclear diatomic molecular ion in a linear Paul trap in a rigid-rotor approximation, one purely classical and the other where the center-of-mass motion is treated classically, while rotational motion is quantized. We study the rotational dynamics and their influence on the motion of the center-of-mass, in the presence of the coupling between the permanent dipole moment of the ion and the trapping electric field. We show that the presence of the permanent dipole moment affects the trajectory of the ion and that it departs from the Mathieu equation solution found for atomic ions. For the case of quantum rotations, we also evidence the effect of the above-mentioned coupling on the rotational states of the ion.

  15. Rotational dynamics of a diatomic molecular ion in a Paul trap.

    PubMed

    Hashemloo, A; Dion, C M

    2015-11-28

    We present models for a heteronuclear diatomic molecular ion in a linear Paul trap in a rigid-rotor approximation, one purely classical and the other where the center-of-mass motion is treated classically, while rotational motion is quantized. We study the rotational dynamics and their influence on the motion of the center-of-mass, in the presence of the coupling between the permanent dipole moment of the ion and the trapping electric field. We show that the presence of the permanent dipole moment affects the trajectory of the ion and that it departs from the Mathieu equation solution found for atomic ions. For the case of quantum rotations, we also evidence the effect of the above-mentioned coupling on the rotational states of the ion. PMID:26627960

  16. Ion Transport through Membrane-Spanning Nanopores Studied by Molecular Dynamics Simulations and Continuum Electrostatics Calculations

    PubMed Central

    Peter, Christine; Hummer, Gerhard

    2005-01-01

    Narrow hydrophobic regions are a common feature of biological channels, with possible roles in ion-channel gating. We study the principles that govern ion transport through narrow hydrophobic membrane pores by molecular dynamics simulation of model membranes formed of hexagonally packed carbon nanotubes. We focus on the factors that determine the energetics of ion translocation through such nonpolar nanopores and compare the resulting free-energy barriers for pores with different diameters corresponding to the gating regions in closed and open forms of potassium channels. Our model system also allows us to compare the results from molecular dynamics simulations directly to continuum electrostatics calculations. Both simulations and continuum calculations show that subnanometer wide pores pose a huge free-energy barrier for ions, but a small increase in the pore diameter to ∼1 nm nearly eliminates that barrier. We also find that in those wider channels the ion mobility is comparable to that in the bulk phase. By calculating local electrostatic potentials, we show that the long range Coulomb interactions of ions are strongly screened in the wide water-filled channels. Whereas continuum calculations capture the overall energetics reasonably well, the local water structure, which is not accounted for in this model, leads to interesting effects such as the preference of hydrated ions to move along the pore wall rather than through the center of the pore. PMID:16006629

  17. Building up water-wire clusters: isomer-selective ultraviolet and infrared spectra of jet-cooled 2-aminopurine (H2O)n, n = 2 and 3.

    PubMed

    Lobsiger, Simon; Sinha, Rajeev K; Leutwyler, Samuel

    2013-10-17

    2-Aminopurine (2AP) is an adenine analogue with a high fluorescence quantum yield in water solution, which renders it a useful real-time probe of DNA structure. We report the ultraviolet (UV) and infrared (IR) spectra of size-selected and jet-cooled 9H-2AP·(H2O)n clusters with n = 2 and 3. Mass- and species-specific UV/UV holeburning spectroscopy allows to separate the UV spectra of four cluster isomers in the 31,200–33,000 cm(–1) spectral region with electronic band origins at 31339, 31450, 31891, and 32163 cm(–1). Using IR/UV depletion spectroscopy in combination with B3LYP calculated harmonic vibrational frequencies, the H-bonding topologies of two isomers of the n = 2 and of two isomers of the n = 3 cluster are identified. One n = 2 isomer (denoted 2A) forms a water dimer chain between the N9H and N3 atoms at the sugar-edge site, the other isomer (denoted 2D) binds one H2O at the sugar-edge site and the other at the trans-amino site between the N1 atom and the NH2 group. For 2-aminopurine·(H2O)3, one isomer (denoted 3A) forms an H-bonded water wire at the sugar-edge site, while isomer 3B accommodates two H2O molecules at the sugar-edge and one at the trans-amino site. The approximate second-order coupled cluster (CC2) method predicts the adiabatic S1 ← S0 transitions of 9H-2-aminopurine and six water cluster isomers with n = 1–3 in very good agreement with the experimental 0(0)(0) frequencies, with differences of <0.6%. The stabilization of the S1(ππ*) state of 2-aminopurine by water clusters is highly regiospecific: Isomers with one or two H2O molecules H-bonded in the trans-amino position induce large spectra red shifts, corresponding to 1ππ* state stabilization of 10–12 kJ/mol, while water-wire cluster solvation at the sugar-edge leads to much smaller stabilization. The evolution of the IR spectra of the water-wire clusters with n = 1–3 that are H-bonded to the sugar-edge site is discussed. Qualitatively different regions (denoted I to IV

  18. High resolution spectroscopy of jet cooled phenyl radical: The ν1 and ν2 a1 symmetry C-H stretching modes

    NASA Astrophysics Data System (ADS)

    Chang, Chih-Hsuan; Nesbitt, David J.

    2016-07-01

    A series of CH stretch modes in phenyl radical (C6H5) has been investigated via high resolution infrared spectroscopy at sub-Doppler resolution (˜60 MHz) in a supersonic discharge slit jet expansion. Two fundamental vibrations of a1 symmetry, ν1 and ν2, are observed and rotationally analyzed for the first time, corresponding to in-phase and out-of-phase symmetric CH stretch excitation at the ortho/meta/para and ortho/para C atoms with respect to the radical center. The ν1 and ν2 band origins are determined to be 3073.968 50(8) cm-1 and 3062.264 80(7) cm-1, respectively, which both agree within 5 cm-1 with theoretical anharmonic scaling predictions based on density functional B3LYP/6-311g++(3df,3dp) calculations. Integrated band strengths for each of the CH stretch bands are analyzed, with the relative intensities agreeing remarkably well with theoretical predictions. Frequency comparison with previous low resolution Ar-matrix spectroscopy [A. V. Friderichsen et al., J. Am. Chem. Soc. 123, 1977 (2001)] reveals a nearly uniform Δν ≈ + 10-12 cm-1 blue shift between gas phase and Ar matrix values for ν1 and ν2. This differs substantially from the much smaller red shift (Δν ≈ - 1 cm-1) reported for the ν19 mode, and suggests a simple physical model in terms of vibrational mode symmetry and crowding due to the matrix environment. Finally, the infrared phenyl spectra are well described by a simple asymmetric rigid rotor Hamiltonian and show no evidence for spectral congestion due to intramolecular vibrational coupling, which bodes well for high resolution studies of other ring radicals and polycyclic aromatic hydrocarbons. In summary, the combination of slit jet discharge methods with high resolution infrared lasers enables spectroscopic investigation of even highly reactive combustion and interstellar radical intermediates under gas phase, jet-cooled (Trot ≈ 11 K) conditions.

  19. High resolution spectroscopy of jet cooled phenyl radical: The ν1 and ν2 a1 symmetry C-H stretching modes.

    PubMed

    Chang, Chih-Hsuan; Nesbitt, David J

    2016-07-28

    A series of CH stretch modes in phenyl radical (C6H5) has been investigated via high resolution infrared spectroscopy at sub-Doppler resolution (∼60 MHz) in a supersonic discharge slit jet expansion. Two fundamental vibrations of a1 symmetry, ν1 and ν2, are observed and rotationally analyzed for the first time, corresponding to in-phase and out-of-phase symmetric CH stretch excitation at the ortho/meta/para and ortho/para C atoms with respect to the radical center. The ν1 and ν2 band origins are determined to be 3073.968 50(8) cm(-1) and 3062.264 80(7) cm(-1), respectively, which both agree within 5 cm(-1) with theoretical anharmonic scaling predictions based on density functional B3LYP/6-311g++(3df,3dp) calculations. Integrated band strengths for each of the CH stretch bands are analyzed, with the relative intensities agreeing remarkably well with theoretical predictions. Frequency comparison with previous low resolution Ar-matrix spectroscopy [A. V. Friderichsen et al., J. Am. Chem. Soc. 123, 1977 (2001)] reveals a nearly uniform Δν ≈ + 10-12 cm(-1) blue shift between gas phase and Ar matrix values for ν1 and ν2. This differs substantially from the much smaller red shift (Δν ≈ - 1 cm(-1)) reported for the ν19 mode, and suggests a simple physical model in terms of vibrational mode symmetry and crowding due to the matrix environment. Finally, the infrared phenyl spectra are well described by a simple asymmetric rigid rotor Hamiltonian and show no evidence for spectral congestion due to intramolecular vibrational coupling, which bodes well for high resolution studies of other ring radicals and polycyclic aromatic hydrocarbons. In summary, the combination of slit jet discharge methods with high resolution infrared lasers enables spectroscopic investigation of even highly reactive combustion and interstellar radical intermediates under gas phase, jet-cooled (Trot ≈ 11 K) conditions. PMID:27475358

  20. Kinetic Stability of Non-IPR Fullerene Molecular Ions.

    PubMed

    Aihara, Jun-ichi; Nakagami, Yuto; Sekine, Rika

    2015-06-18

    Many fullerenes that violate the isolated pentagon rule (IPR) form stable metallofullerenes. In general, a fullerene cage is kinetically stabilized by acquiring a given number of electrons. Kinetic stability of negatively charged non-IPR fullerenes, including the recently isolated endohedral metallofullerene with a heptagonal face, was rationalized in terms of bond resonance energy (BRE). Interestingly, molecular anions of conventional fullerenes found in most isolated metallofullerenes are kinetically stable with large positive BREs for all CC bonds. As we pointed out in 1993, the IPR does not apply to charged fullerenes because π-bonds shared by two five-membered rings are aromatized to varying extents. PMID:26020361

  1. Molecular mobility, morphology, and ion conduction in ionomers for electroactive devices

    NASA Astrophysics Data System (ADS)

    Tudryn, Gregory J.

    aggregation process in Na ionomers as ionic dipoles thermally randomize and lower the measured dielectric constant of the medium, leading to further aggregation. We observe amplified microphase-separation through ionic groups preferentially solvated by PEO chains, as seen in block copolymers with added salt. Even at 25%PEO / 75%PTMO the ionomers have VFT temperature dependence of conducting ion mobility, meaning that the 25% PEO/ion microphase is still continuous A model is developed to describe the frequency dependent storage and loss modulus and the delay in Rouse motion due to ion association lifetime, as functions of ion content and molecular weight for our low molecular weight ionomers. The ion rearrangement relaxation in dielectric spectroscopy is clearly the ion association lifetime that controls terminal dynamics in linear viscoelasticity, allowing a simple sticky Rouse model, using the most-probable distribution based on NMR Mn, to fully describe master curves of the frequency dependent storage and loss modulus. Using insight from ionic interaction strength, ionic liquids are used as counterions, effectively plasticizing the ionomers without added solvent. Ionic interactions were weakened with increasing counterion size, and with modification of cations using ether-oxygen, promoting self-solvation, which increases conducting ion density by an order of magnitude. Room temperature ionic liquids were subsequently used in combination with NafionRTM membranes as electroactive substrates to correlate ion transport to morphology as a function of volume fraction of ionic liquid. This study illuminated the critical volume uptake of ionic liquid in Nafion, identifying percolation of ionic pathways and a significant increase in dielectric constant at low frequencies, indicating an increase in the number density of ions capable of polarizing at the electrode surface. Consequently, the fundamental information obtained about the structure-property relations of ionomers can be used

  2. Photochemistry and molecular ions in carbon-rich circumstellar envelopes

    NASA Technical Reports Server (NTRS)

    Glassgold, A. E.; Mamon, G. A.; Omont, A.; Lucas, R.

    1987-01-01

    An earlier theory of ionization of C-rich circumstellar envelopes based on the photochemical model is extended to include the temperature dependence of ion-molecule reactions with polar molecules, particularly HCN, and line self-shielding of CO dissociating radiation. The results are applied to the abundances of HCO(+) and HNC in C-rich circumstellar envelopes. With standard parameters for IRC + 10216, the model is found to be consistent with the new upper limit to the antenna temperature of the J = 1-0 line of HCO(+) obtained with the IRAM 30-m telescope. The photochemical model provides a natural explanation of the relatively large ratio of HCN to HNC observed for C-rich circumstellar envelopes, and good agreement is obtained for the H(C-13)N/HNC antenna temperature ratio measured for IRC + 10216.

  3. Lifetimes and stabilities of familiar explosives molecular adduct complexes during ion mobility measurements

    PubMed Central

    McKenzie, Alan; DeBord, John Daniel; Ridgeway, Mark; Park, Melvin; Eiceman, Gary; Fernandez-Lima, Francisco

    2015-01-01

    Trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS) was utilized for the separation and identification of familiar explosives in complex mixtures. For the first time, molecular adduct complex lifetimes, relative stability, binding energies and candidate structures are reported for familiar explosives. Experimental and theoretical results showed that the adduct size and reactivity, complex binding energy and the explosive structure tailors the stability of the molecular adduct complex. TIMS flexibility to adapt the mobility separation as a function of the molecular adduct complex stability (i.e., short or long IMS experiments / low or high IMS resolution) permits targeted measurements of explosives in complex mixtures with higher confidence levels. PMID:26153567

  4. Indirect Terahertz Spectroscopy of Molecular Ions Using Highly Accurate and Precise Mid-Ir Spectroscopy

    NASA Astrophysics Data System (ADS)

    Mills, Andrew A.; Ford, Kyle B.; Kreckel, Holger; Perera, Manori; Crabtree, Kyle N.; McCall, Benjamin J.

    2009-06-01

    With the advent of Herschel and SOFIA, laboratory methods capable of providing molecular rest frequencies in the terahertz and sub-millimeter regime are increasingly important. As of yet, it has been difficult to perform spectroscopy in this wavelength region due to the limited availability of radiation sources, optics, and detectors. Our goal is to provide accurate THz rest frequencies for molecular ions by combining previously recorded microwave transitions with combination differences obtained from high precision mid-IR spectroscopy. We are constructing a Sensitive Resolved Ion Beam Spectroscopy setup which will harness the benefits of kinematic compression in a molecular ion beam to enable very high resolution spectroscopy. This ion beam is interrogated by continuous-wave cavity ringdown spectroscopy using a home-made widely tunable difference frequency laser that utilizes two near-IR lasers and a periodically-poled lithium niobate crystal. Here, we report our efforts to optimize our ion beam spectrometer and to perform high-precision and high-accuracy frequency measurements using an optical frequency comb. footnote

  5. Rotational energy of the hydrogen molecular ion in a magnetic field

    SciTech Connect

    Maluendes, S.A.; Fernandez, F.M.; Castro, E.A.

    1983-10-01

    A general method which combines hypervirial relations with the Hellmann-Feynman theorem and perturbation theory is applied in order to calculate the rotational eigenvalues of the hydrogen molecular ion in a magnetic field. Analytical expressions as well as numerical results are presented for both low and high field strengths.

  6. Resonance-Raman-scattering spectroscopy for the halogen-molecular-ion centers in alkali halides

    NASA Astrophysics Data System (ADS)

    Suzuki, T.; Tanimura, K.; Itoh, N.

    1993-10-01

    We have measured the Raman scattering in resonance with the bonding-to-antibonding transitions of two types of dihalogen-molecular-ion centers in alkali halides, the VK and H centers; the molecular ion occupies two adjacent halogen sites in the former and a single halogen site in the latter. It is found that the stretching-vibration frequency of the molecular ion is higher by more than 30% for the H center than for the VK center. The hardening is ascribed to the bond tightening due to the Madelung potential. Although the Raman line due to the stretching vibration consists of a single line in most alkali halides, two closely lying lines are observed for the H centers in alkali halides with small alkali-metal to halogen radius ratio and also for the VK center in NaCl. The paired-line structure is ascribed to the coupling of the stretching vibration of the halogen molecular ion with the lattice.

  7. Modeling of ion complexation and extraction using substructural molecular fragments

    PubMed

    Solov'ev; Varnek; Wipff

    2000-05-01

    A substructural molecular fragment (SMF) method has been developed to model the relationships between the structure of organic molecules and their thermodynamic parameters of complexation or extraction. The method is based on the splitting of a molecule into fragments, and on calculations of their contributions to a given property. It uses two types of fragments: atom/bond sequences and "augmented atoms" (atoms with their nearest neighbors). The SMF approach is tested on physical properties of C2-C9 alkanes (boiling point, molar volume, molar refraction, heat of vaporization, surface tension, melting point, critical temperature, and critical pressures) and on octanol/water partition coefficients. Then, it is applied to the assessment of (i) complexation stability constants of alkali cations with crown ethers and phosphoryl-containing podands, and of beta-cyclodextrins with mono- and 1,4-disubstituted benzenes, and (ii) solvent extraction constants for the complexes of uranyl cation by phosphoryl-containing ligands. PMID:10850791

  8. Dysregulation of transition metal ion homeostasis is the molecular basis for cadmium toxicity in Streptococcus pneumoniae

    PubMed Central

    Begg, Stephanie L.; Eijkelkamp, Bart A.; Luo, Zhenyao; Couñago, Rafael M.; Morey, Jacqueline R.; Maher, Megan J.; Ong, Cheryl-lynn Y.; McEwan, Alastair G.; Kobe, Bostjan; O’Mara, Megan L.; Paton, James C.; McDevitt, Christopher A.

    2015-01-01

    Cadmium is a transition metal ion that is highly toxic in biological systems. Although relatively rare in the Earth’s crust, anthropogenic release of cadmium since industrialization has increased biogeochemical cycling and the abundance of the ion in the biosphere. Despite this, the molecular basis of its toxicity remains unclear. Here we combine metal-accumulation assays, high-resolution structural data and biochemical analyses to show that cadmium toxicity, in Streptococcus pneumoniae, occurs via perturbation of first row transition metal ion homeostasis. We show that cadmium uptake reduces the millimolar cellular accumulation of manganese and zinc, and thereby increases sensitivity to oxidative stress. Despite this, high cellular concentrations of cadmium (~17 mM) are tolerated, with negligible impact on growth or sensitivity to oxidative stress, when manganese and glutathione are abundant. Collectively, this work provides insight into the molecular basis of cadmium toxicity in prokaryotes, and the connection between cadmium accumulation and oxidative stress. PMID:25731976

  9. Rotationsal and vibrational spectra of molecular ions: Feasibility of laboratory and astrophysical observation

    NASA Technical Reports Server (NTRS)

    Woods, R. C.; Certain, P. R.; Bernstein, R. B.

    1974-01-01

    The rotational spectra of a number of small molecular ions should be detectable in the microwave or millimeter wave regions in laboratory experiments using currently available techniques. The dipole moments and absorption coefficients of polar diatomics CO(+) and NO(+) as well as asymmetric isotopically enriched species, like O-18O-16(+), NE-20NE-22(+), and OC-18 O-16(+) are calculated to be sufficiently large to allow observation of their spectra. In addition to the detailed molecular structure information which such spectral data would provide, precise knowledge of the transition frequencies would render likely the detection of certain of these ions in the interstellar sources or in planetary atmospheres. All of these ions also possess vibrational spectra which should be detectable in the infrared region in laboratory or astrophysical sources.

  10. Systematics in a measurement of the electron's electric dipole moment using trapped molecular ions

    NASA Astrophysics Data System (ADS)

    Grau, Matt; Cossel, Kevin; Cairncross, William; Gresh, Dan; Zhou, Yan; Ye, Jun; Cornell, Eric

    2015-05-01

    A precision measurement of the electron's electric dipole moment (EDM) has important implications for physics beyond the Standard Model. Trapped molecular ions offer high sensitivity in such an experiment because of the large effective electric fields and long coherence times that are possible. Our experiment uses Ramsey spectroscopy of HfF+ ions in a linear RF trap with rotating bias fields, achieving coherence times beyond 1 second for 1000 trapped ions. Compared to other electron EDM experiments that use molecular beams, we will be sensitive to a different class of systematic errors. In this work we investigate systematic errors arising from all fields involved in the experiment, including the trapping and polarizing electric fields, magnetic field gradients, and motional effects such as geometric phases. This work was supported by NIST and NSF.

  11. Properties of solvate shells and the mobility of ions, according to molecular dynamics data

    NASA Astrophysics Data System (ADS)

    Lankin, A. V.; Norman, G. E.; Orekhov, M. A.

    2016-05-01

    The solvate shells of an ion, its velocity autocorrelation function, and diffusion coefficient D are found, and the interrelations between them are analyzed. A single ion in the system of atoms of a liquid is considered a model system. The interaction between the ion and atoms of the liquid is described by polarization potential U( r); the interaction between atoms of the liquid alone is described by the Lennard-Jones potential. A classical molecular dynamics method is used. Five solvate shells around the ion are found, and the lifetimes of atoms on each shell are calculated. It is found that the velocity autocorrelation function is of a vibrating nature. The spectrum of the autocorrelator and the frequency of cluster vibrations in a linear approximation are compared. Dependences D on parameters of potential U( r) are found. No dependence D on the ion mass is found; this is explained by solvation. The Einstein-Stokes formula and the HSK approximation are used in discussing the results. It is shown that at small radii of the ion, dependence D on parameters U( r) is described by such a model. When the ion radius is increased, the deviation from this dependence and an increase in D are observed. The results are compared to experimental mobilities of O 2 - and Ar 2 + ions in liquid argon.

  12. 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

  13. Theoretical study of swift molecular ions specularly reflected from solid surfaces under glancing angle of incidence

    NASA Astrophysics Data System (ADS)

    Song, Yuan-Hong; Wang, You-Nian; Mišković, Z. L.

    2005-04-01

    We develop a theoretical model to study grazing scattering of fast diatomic molecular ions from a solid surface, based on the dielectric response formalism within the specular reflection model, where the plasmon pole approximation for dielectric function is employed to describe the single-particle and the collective excitations of the electron gas at the surface. Evolution of the bound-electron densities at the constituent ions of a molecule in the course of scattering is described by an approach similar to recent implementation of the Brandt-Kitagawa model for single-ion surface grazing scattering. We solve numerically the equations of motion for the constituent ions and obtain the ion scattering trajectories in the presence of Coulomb explosion modified by the surface wake potential, for the initial molecular-axis orientations in either random directions or along the beam. Vicinage effect on the total energy loss is discussed on the basis of analyzing the position-dependent stopping powers of individual ions and the interferences in the electron excitations of the substrate.

  14. A Investigation of a Possible Molecular Effect in Ion Atom Collision Using a Gaseous Argon Target

    NASA Astrophysics Data System (ADS)

    Arora, Sanjeev

    1992-01-01

    The present work deals with an investigation of the molecular effect, which is defined as the difference in experimental results using isotachic atomic ion and molecular ion beams in ion atom collisions. Previous studies have dealt almost exclusively with total cross section measurements. This thesis explores the idea that the molecular effect may be more pronounced in the differential ionization probability of the target atoms. Also, a gaseous argon target of sufficiently low density was used in order to ensure that the two correlated protons in the H _2^{+} beam did not interact with two adjacent target atoms simultaneously. We report that, contrary to the expectations noted above, the molecular effect in the K shell differential ionization probability of argon for scattering angles up to 90^circ appears to be no more than the molecular effect in the total ionization probability. The uncertainity in our results is statistical in nature and can be improved upon by running the experiment for a longer duration of time.

  15. Angle-resolved intensity and energy distributions of positive and negative hydrogen ions released from tungsten surface by molecular hydrogen ion impact

    NASA Astrophysics Data System (ADS)

    Kato, S.; Tanaka, N.; Sasao, M.; Kisaki, M.; Tsumori, K.; Nishiura, M.; Matsumoto, Y.; Kenmotsu, T.; Wada, M.; Yamaoka, H.

    2015-08-01

    Hydrogen ion reflection properties have been investigated following the injection of H+, H2+ and H3+ ions onto a polycrystalline W surface. Angle- and energy-resolved intensity distributions of both scattered H+ and H- ions are measured by a magnetic momentum analyzer. We have detected atomic hydrogen ions reflected from the surface, while molecular hydrogen ions are unobserved within our detection limit. The reflected hydrogen ion energy is approximately less than one-third of the incident beam energy for H3+ ion injection and less than a half of that for H2+ ion injection. Other reflection properties are very similar to those of monoatomic H+ ion injection. Experimental results are compared to the classical trajectory simulations using the ACAT code based on the binary collision approximation.

  16. Heavy ion induced mutations in mammalian cells: Cross sections and molecular analysis

    NASA Technical Reports Server (NTRS)

    Stoll, U.; Schmidt, P.; Schneider, E.; Kiefer, J.

    1994-01-01

    Our investigations of heavy ion-induced mutations in mammalian cells, which had been begun a few years ago, were systematically continued. For the first time, it was possible to cover a large LET range with a few kinds of ions. To do this, both UNILAC and SIS were used to yield comparable data for a large energy range. This is a necessary condition for a comprehensive description of the influence of such ion parameters as energy and LET. In these experiments, the induced resistance against the poison 6-thioguanin (6-TG), which is linked to the HPRT locus on the genome, is being used as mutation system. In addition to the mutation-induction cross-section measurements, the molecular changes of the DNA are being investigated by means of Multiplex PCR ('Polymerase Chain Reaction') gene amplification. From these experiments we expect further elucidation of the mutation-inducing mechanisms composing the biological action of heavy-ion radiation.

  17. Development of a Submillimeter Multipass Spectrometer for the Study of Molecular Ions

    NASA Astrophysics Data System (ADS)

    Carroll, A.; Rocher, B.; Laas, J. C.; Deprince, B. A.; Hays, B.; Weaver, S. L. Widicus; Lang, S.

    2012-06-01

    We have developed a multipass spectrometer for the submillimeter spectral region that is being used to study molecular ions through gas phase spectroscopy. The optical configuration is based on the design of Perry and coworkers that was implemented in the optical regime. To our knowledge, this is the first implementation of this optical configuration at long wavelengths. The setup involves two nearly concentric spherical mirrors that focus the multiple beam passes into a small area, or ``waist'', in the middle of the sample chamber. A supersonic molecular beam is coupled to the setup so that the molecular beam crosses the optical path at the waist. Initial studies have focused on neutral test molecules to probe the physical properties of the molecular beam under various arrangements of the molecular source relative to the optical path. Current studies focus on coupling a plasma discharge source to the setup to enable the study of molecular ions. Here we present the design of this instrument, compare the spectrometer capabilities to a traditional single pass spectrometer, and discuss the results of initial spectroscopic studies.

  18. Effect of Zn(2+) ions on the assembly of amylin oligomers: insight into the molecular mechanisms.

    PubMed

    Wineman-Fisher, Vered; Miller, Yifat

    2016-08-01

    Amylin is an endocrine hormone and is a member of the family of amyloid peptides and proteins that emerge as potential scaffolds by self-assembly processes. Zn(2+) ions can bind to amylin peptides to form self-assembled Zn(2+)-amylin oligomers. In the current work the binding sites of Zn(2+) ions in the self-assembled amylin oligomers at various concentrations of zinc have been investigated. Our results yield two conclusions. First, in the absence of Zn(2+) ions polymorphic states (i.e. various classes of amylin oligomers) are obtained, but when Zn(2+) ions bind to amylin peptides to form Zn(2+)-amylin oligomers, the polymorphism is decreased, i.e. Zn(2+) ions bind only to specific classes of amylin. At low concentrations of Zn(2+) ions the polymorphism is smaller than at high concentrations. Second, the structural features of the self-assembled amylin oligomers are not affected by the presence of Zn(2+) ions. This study proposes new molecular mechanisms of the self-assembly of Zn(2+)-amylin oligomers. PMID:27425207

  19. Fourier transform spectroscopy of the Swan (d(sup 3)pi(sub g) - a(sup 3)pi(sub u)) system of the jet-cooled C2 molecule

    NASA Technical Reports Server (NTRS)

    Prasad, C. V. V.; Bernath, P. F.

    1994-01-01

    The Swan (d(sup 3)pi(sub g) - a(sup 3)pi(sub u)) system of the C2 molecule was produced in a jet-cooled corona excited supersonic expansion of helium using diazoacetonitrile as a percursor molecule. This spectrum was recorded using the McMath Fourier transform spectrometer of the National Solar Observatory at Kitt Peak. A total of nine bands with v prime = 0 to 3 and v prime prime = 0 to 4 in the range 16,570-22,760/cm were observed and rotationally analyzed. The C2 molecules in this source had a rotational temperature of only 90 K so that only the low-J lines were present in the spectrum. In some sense the low temperatures in the jet source simulate conditions in the interstellar medium. The Swan system of C2 was also produced in a composite wall hollow cathode made Al4C3/Cu, and the rotational structure of the 1-0, 2-1, 3-2, 0-0, and 1-1 bands were analyzed. The data obtained from both these spectra were fitted together along with some recently published line positions. The rotational constants, lambda doubling parameters and the vibrational constants were estimated from this global fit. Our work on jet-cooled C2 follows similar work on the violet and red systems of CN. A summary of this CN work is also presented. also presented.

  20. Calculations of fast ion collisions with multi-center molecular targets

    NASA Astrophysics Data System (ADS)

    Kirchner, Tom

    2011-05-01

    The theoretical treatment of ion-molecule collisions is challenging for several reasons: the systems have many degrees of freedom, a rather complex geometry, and the electron dynamics might be nonperturbative and involve electron-electron interaction effects. However, the interest in accurate calculations has been growing recently. An important reason for this development is the relevance of ion-molecule collisions for a number of fields, such as atmospheric science, and the understanding of radiation damage of biological tissue. We have developed a new approach to meet these challenges. It disregards rovibrational motion, but it does address the multi-center geometry of the system and the generally nonperturbative nature of the electron dynamics. The key ingredients are an expansion of the initially populated molecular orbitals in terms of a single-center basis and a spectral representation of the molecular Hamiltonian. This facilitates a separation of molecular geometry and collision dynamics and makes it possible to use well-established ion-atom methods with relatively minor modifications. We have extended our basis generator method to deal with the collision dynamics and report on results for ionization and fragmentation of water molecules by proton and He+ ion impact over wide ranges of collision energies. For the case of He+ impact this will include a discussion of effects due to the presence of the projectile electron. This work has been supported by the Natural Sciences and Engineering Research Council of Canada.

  1. Ion-water and ion-polypeptide correlations in a gramicidin-like channel. A molecular dynamics study.

    PubMed Central

    Jordan, P C

    1990-01-01

    This work describes a molecular dynamics study of ion-water and ion-polypeptide correlation in a model gramicidin-like channel (the polyglycine analogue) based upon interaction between polarizable, multipolar groups. The model suggests that the vicinity of the dimer junction and of the ethanolamine tail are regions of unusual flexibility. Cs+ binds weakly in the mouth of the channel: there it coordinates five water molecules and the #11CO group with which it interacts strongly and is ideally aligned. In the channel interior it is generally pentacoordinate; at the dimer junction, because of increased channel flexibility, it again becomes essentially hexacoordinate. The ion is also strongly coupled to the #13 CO but not to either #9 or #15, consistent with 13C NMR data. Water in the channel interior is strikingly different from bulk water; it has a much lower mean dipole moment. This correlates with our observation (which differs from that of previous studies) that water-water angular correlations do not persist within the channel, a result independent of ion occupancy or ionic polarity. In agreement with streaming potential measurements, there are seven single file water molecules associated with Cs+ permeation; one of these is always in direct contact with bulk water. At the mouth of an ion-free channel, there is a pattern of dipole moment alteration among the polar groups. Due to differential interaction with water, exo-carbonyls have unusually large dipole moments whereas those of the endo-carbonyls are low. The computed potential of mean force for CS+ translocation is qualitatively reasonable. However, it only exhibits a weakly articulated binding site and it does not quantitatively account for channel energetics. Correction for membrane polarization reduces, but does not eliminate, these problems. PMID:1705448

  2. 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.

  3. Molecularly imprinted porous beads for the selective removal of copper ions.

    PubMed

    Younis, M Rizwan; Bajwa, Sadia Z; Lieberzeit, Peter A; Khan, Waheed S; Mujahid, Adnan; Ihsan, Ayesha; Rehman, Asma

    2016-02-01

    In the present work, novel molecularly imprinted polymer porous beads for the selective separation of copper ions have been synthesized by combining two material-structuring techniques, namely, molecular imprinting and oil-in-water-in-oil emulsion polymerization. This method produces monodisperse spherical beads with an average diameter of ∼2-3 mm, in contrast to adsorbents produced in the traditional way of grinding and sieving. Field-emission scanning electron microscopy indicates that the beads are porous in nature with interconnected pores of about 25-50 μm. Brunner-Emmett-Teller analysis shows that the ion-imprinted beads possess a high surface area (8.05 m(2) /g), and the total pore volume is determined to be 0.00823 cm(3) /g. As a result of the highly porous nature and ion-imprinting, the beads exhibit a superior adsorption capacity (84 mg/g) towards copper than the non-imprinted material (22 mg/g). Furthermore, selectivity studies indicate that imprinted beads show splendid recognizing ability, that is, nearly fourfold greater selective binding for Cu(2+) in comparison to the other bivalent ions such as Mn(2+) , Ni(2+) , Co(2+) , and Ca(2+) . The imprinted composite beads prepared in this study possess uniform porous morphology and may open up new possibilities for the selective removal of copper ions from waste water/contaminated matrices. PMID:26632078

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

    PubMed Central

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

    2015-01-01

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

  5. Combining molecular dynamics and an electrodiffusion model to calculate ion channel conductance.

    PubMed

    Wilson, Michael A; Nguyen, Thuy Hien; Pohorille, Andrew

    2014-12-14

    Establishing the relation between the structures and functions of protein ion channels, which are protein assemblies that facilitate transmembrane ion transport through water-filled pores, is at the forefront of biological and medical sciences. A reliable way to determine whether our understanding of this relation is satisfactory is to reproduce the measured ionic conductance over a broad range of applied voltages. This can be done in molecular dynamics simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. Since this approach is computationally very expensive we develop a markedly more efficient alternative in which molecular dynamics is combined with an electrodiffusion equation. This alternative approach applies if steady-state ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. The theory refers only to line densities of ions in the channel and, therefore, avoids ambiguities related to determining the surface area of the channel near its endpoints or other procedures connecting the line and bulk ion densities. We apply the theory to a simple, model system based on the trichotoxin channel. We test the assumptions of the electrodiffusion equation, and determine the precision and consistency of the calculated conductance. We demonstrate that it is possible to calculate current/voltage dependence and accurately reconstruct the underlying (equilibrium) free energy profile, all from molecular dynamics simulations at a single voltage. The approach developed here applies to other channels that satisfy the conditions of the electrodiffusion equation. PMID:25494790

  6. Combining molecular dynamics and an electrodiffusion model to calculate ion channel conductance

    NASA Astrophysics Data System (ADS)

    Wilson, Michael A.; Nguyen, Thuy Hien; Pohorille, Andrew

    2014-12-01

    Establishing the relation between the structures and functions of protein ion channels, which are protein assemblies that facilitate transmembrane ion transport through water-filled pores, is at the forefront of biological and medical sciences. A reliable way to determine whether our understanding of this relation is satisfactory is to reproduce the measured ionic conductance over a broad range of applied voltages. This can be done in molecular dynamics simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. Since this approach is computationally very expensive we develop a markedly more efficient alternative in which molecular dynamics is combined with an electrodiffusion equation. This alternative approach applies if steady-state ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. The theory refers only to line densities of ions in the channel and, therefore, avoids ambiguities related to determining the surface area of the channel near its endpoints or other procedures connecting the line and bulk ion densities. We apply the theory to a simple, model system based on the trichotoxin channel. We test the assumptions of the electrodiffusion equation, and determine the precision and consistency of the calculated conductance. We demonstrate that it is possible to calculate current/voltage dependence and accurately reconstruct the underlying (equilibrium) free energy profile, all from molecular dynamics simulations at a single voltage. The approach developed here applies to other channels that satisfy the conditions of the electrodiffusion equation.

  7. Cluster secondary ion mass spectrometry and the temperature dependence of molecular depth profiles.

    PubMed

    Mao, Dan; Wucher, Andreas; Brenes, Daniel A; Lu, Caiyan; Winograd, Nicholas

    2012-05-01

    The quality of molecular depth profiles created by erosion of organic materials by cluster ion beams exhibits a strong dependence upon temperature. To elucidate the fundamental nature of this dependence, we employ the Irganox 3114/1010 organic delta-layer reference material as a model system. This delta-layer system is interrogated using a 40 keV C(60)(+) primary ion beam. Parameters associated with the depth profile such as depth resolution, uniformity of sputtering yield, and topography are evaluated between 90 and 300 K using a unique wedge-crater beveling strategy that allows these parameters to be determined as a function of erosion depth from atomic force microscope (AFM) measurements. The results show that the erosion rate calibration performed using the known Δ-layer depth in connection with the fluence needed to reach the peak of the corresponding secondary ion mass spectrometry (SIMS) signal response is misleading. Moreover, we show that the degradation of depth resolution is linked to a decrease of the average erosion rate and the buildup of surface topography in a thermally activated manner. This underlying process starts to influence the depth profile above a threshold temperature between 210 and 250 K for the system studied here. Below that threshold, the process is inhibited and steady-state conditions are reached with constant erosion rate, depth resolution, and molecular secondary ion signals from both the matrix and the Δ-layers. In particular, the results indicate that further reduction of the temperature below 90 K does not lead to further improvement of the depth profile. Above the threshold, the process becomes stronger at higher temperature, leading to an immediate decrease of the molecular secondary ion signals. This signal decay is most pronounced for the highest m/z ions but is less for the smaller m/z ions, indicating a shift toward small fragments by accumulation of chemical damage. The erosion rate decay and surface roughness buildup

  8. Ion Pair in Extreme Aqueous Environments, Molecular-Based and Electric Conductance Approaches

    SciTech Connect

    Chialvo, Ariel A; Gruszkiewicz, Miroslaw {Mirek} S; Simonson, J Michael {Mike}; Palmer, Donald; Cole, David R

    2009-01-01

    We determine by molecular-based simulation the density profiles of the Na+!Cl! ion-pair association constant in steam environments along three supercritical isotherms to interrogate the behavior of ion speciation in dilute aqueous solutions at extreme conditions. Moreover, we describe a new ultra-sensitive flow-through electric conductance apparatus designed to bridge the gap between the currently lowest steam-density conditions at which we are experimentally able to attain electric conductance measurements and the theoretically-reachable zero-density limit. Finally, we highlight important modeling challenges encountered near the zero-density limit and discuss ways to overcome them.

  9. Molecular structure studies by 3D imaging of fast ion beams

    SciTech Connect

    Kanter, E.P.; Vager, Z.; Both, G.; Cooney, P.J.; Faibis, A.; Koenig, W.; Zabransky, B.J.; Zajfman, D.

    1986-01-01

    The use of the Coulomb-explosion technique combined with a radically new multi-particle detector, extremely thin film targets, and low-excitation ion source has enabled, for the first time, direct measurements of the complete stereochemistry of complex polyatomic molecular ions. We outline the methods used and present results for protonated acetylene (C/sub 2/H/sub 3//sup +/) and the methane cation (CH/sub 4//sup +/) as examples. We demonstrate the techniques by which these methods can be generalized to determine directly vibrational motions in polyatomic molecules. 24 refs., 4 figs.

  10. Heterogeneous behavior of metalloproteins toward metal ion binding and selectivity: insights from molecular dynamics studies.

    PubMed

    Gogoi, Prerana; Chandravanshi, Monika; Mandal, Suraj Kumar; Srivastava, Ambuj; Kanaujia, Shankar Prasad

    2016-07-01

    About one-third of the existing proteins require metal ions as cofactors for their catalytic activities and structural complexities. While many of them bind only to a specific metal, others bind to multiple (different) metal ions. However, the exact mechanism of their metal preference has not been deduced to clarity. In this study, we used molecular dynamics (MD) simulations to investigate whether a cognate metal (bound to the structure) can be replaced with other similar metal ions. We have chosen seven different proteins (phospholipase A2, sucrose phosphatase, pyrazinamidase, cysteine dioxygenase (CDO), plastocyanin, monoclonal anti-CD4 antibody Q425, and synaptotagmin 1 C2B domain) bound to seven different divalent metal ions (Ca(2+), Mg(2+), Zn(2+), Fe(2+), Cu(2+), Ba(2+), and Sr(2+), respectively). In total, 49 MD simulations each of 50 ns were performed and each trajectory was analyzed independently. Results demonstrate that in some cases, cognate metal ions can be exchanged with similar metal ions. On the contrary, some proteins show binding affinity specifically to their cognate metal ions. Surprisingly, two proteins CDO and plastocyanin which are known to bind Fe(2+) and Cu(2+), respectively, do not exhibit binding affinity to any metal ion. Furthermore, the study reveals that in some cases, the active site topology remains rigid even without cognate metals, whereas, some require them for their active site stability. Thus, it will be interesting to experimentally verify the accuracy of these observations obtained computationally. Moreover, the study can help in designing novel active sites for proteins to sequester metal ions particularly of toxic nature. PMID:26248730

  11. Adsorption of hydrated halide ions on charged electrodes: Molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Glosli, James N.; Philpott, Michael R.

    1993-04-01

    Constant temperature molecular dynamics has been used to simulate the adsorption of hydrated halide ion X(-) = F(-), Cl(-), Br(-), and I(-), and lithium ion Li(+) on a flat uniformly charged surfaces. The simulations were done with either 214 water molecules and two ions (Li(+) and X(-)) in a box 2.362 nm deep or with 430 water molecules and the two ions in a box 4.320 nm deep. The boxes were periodically replicated in the xy directions. The magnitude of the surface charge on the box end was + or - 0.11 c/nm(sup 2), corresponding to an electric field of 2 x 10(exp 7) V/cm. The lateral dimensions of the simulation cell were 1.862 nm x 1.862 nm (x times y) in each case. All of the water molecules and ions interacted with the end walls via a weak 9 - 3 potential. The ST2 water model and parameters optimized for alkali halides interacting with the model ST2 water molecule were used in the calculations. Common practices of truncating the interactions at a finite distance (0.82 nm) and switching off Coulomb interactions at small distances were followed. The temperature was set at T = 2.411 kJ/mole (290 K). Some of the properties calculated were: distribution density profiles for ions and water across the gap important for comparisons iwth Gouy-Chapman theory, adsorbed ion-water pair correlation functions, the number of water molecules in the first and second hydration shells of the ions as a function of time. The time spent by a water molecule in the hydration shell was calculated to be approximately ten times longer for lithium than any other ion. The correlation between distance from the electrode and hydration number was studied and generally found to be pronounced for the larger anions.

  12. Ab initio molecular dynamics simulations of organic electrolytes, electrodes, and lithium ion transport for Li-ion batteries

    NASA Astrophysics Data System (ADS)

    Kent, P. R. C.; Ganesh, P.; Jiang, De-En; Borodin, O.

    2012-02-01

    Optimizing the choice of electrolyte in lithium ion batteries and an understanding of the solid-electrolyte interphase (SEI) is required to optimize the balance between high-energy storage, high rate capability, and lifetime. We perform accurate ab initio molecular-dynamics simulations of common cyclic carbonates and LiPF6 to build solvation models which explain available Neutron and NMR spectroscopies. Our results corroborate why ethylene carbonate is a preferred choice for battery applications over propylene carbonate and how mixtures with dimethyl carbonate improve Li-ion diffusion. We study the role of functionalization of graphite-anode edges on the reducibility of the electrolyte and the ease of Li-ion intercalation at the initial stages of SEI formation. We find that oxygen terminated edges readily act as strong reductive sites, while hydrogen terminated edges are less reactive and allow faster Li diffusion. Orientational ordering of the solvent molecules precedes reduction at the interphase. Inorganic reductive components are seen to readily migrate to the anode edges, leading to increased surface passivation of the anode. We are currently quantifying Li-intercalation barriers across realistic SEI models, and progress along these lines will be presented.

  13. Ejection of solvated ions from electrosprayed methanol/water nanodroplets studied by molecular dynamics simulations.

    PubMed

    Ahadi, Elias; Konermann, Lars

    2011-06-22

    The ejection of solvated small ions from nanometer-sized droplets plays a central role during electrospray ionization (ESI). Molecular dynamics (MD) simulations can provide insights into the nanodroplet behavior. Earlier MD studies have largely focused on aqueous systems, whereas most practical ESI applications involve the use of organic cosolvents. We conduct simulations on mixed water/methanol droplets that carry excess NH(4)(+) ions. Methanol is found to compromise the H-bonding network, resulting in greatly increased rates of ion ejection and solvent evaporation. Considerable differences in the water and methanol escape rates cause time-dependent changes in droplet composition. Segregation occurs at low methanol concentration, such that layered droplets with a methanol-enriched periphery are formed. This phenomenon will enhance the partitioning of analyte molecules, with possible implications for their ESI efficiencies. Solvated ions are ejected from the tip of surface protrusions. Solvent bridging prior to ion secession is more extensive for methanol/water droplets than for purely aqueous systems. The ejection of solvated NH(4)(+) is visualized as diffusion-mediated escape from a metastable basin. The process involves thermally activated crossing of a ~30 kJ mol(-1) free energy barrier, in close agreement with the predictions of the classical ion evaporation model. PMID:21591733

  14. Molecular dispersion energy parameters for alkali and halide ions in aqueous solution.

    PubMed

    Reiser, S; Deublein, S; Vrabec, J; Hasse, H

    2014-01-28

    Thermodynamic properties of aqueous solutions containing alkali and halide ions are determined by molecular simulation. The following ions are studied: Li(+), Na(+), K(+), Rb(+), Cs(+), F(-), Cl(-), Br(-), and I(-). The employed ion force fields consist of one Lennard-Jones (LJ) site and one concentric point charge with a magnitude of ±1 e. The SPC/E model is used for water. The LJ size parameter of the ion models is taken from Deublein et al. [J. Chem. Phys. 136, 084501 (2012)], while the LJ energy parameter is determined in the present study based on experimental self-diffusion coefficient data of the alkali cations and the halide anions in aqueous solutions as well as the position of the first maximum of the radial distribution function of water around the ions. On the basis of these force field parameters, the electric conductivity, the hydration dynamics of water molecules around the ions, and the enthalpy of hydration is predicted. Considering a wide range of salinity, this study is conducted at temperatures of 293.15 and 298.15 K and a pressure of 1 bar. PMID:25669552

  15. Molecular dispersion energy parameters for alkali and halide ions in aqueous solution

    SciTech Connect

    Reiser, S.; Deublein, S.; Hasse, H.; Vrabec, J.

    2014-01-28

    Thermodynamic properties of aqueous solutions containing alkali and halide ions are determined by molecular simulation. The following ions are studied: Li{sup +}, Na{sup +}, K{sup +}, Rb{sup +}, Cs{sup +}, F{sup −}, Cl{sup −}, Br{sup −}, and I{sup −}. The employed ion force fields consist of one Lennard-Jones (LJ) site and one concentric point charge with a magnitude of ±1 e. The SPC/E model is used for water. The LJ size parameter of the ion models is taken from Deublein et al. [J. Chem. Phys. 136, 084501 (2012)], while the LJ energy parameter is determined in the present study based on experimental self-diffusion coefficient data of the alkali cations and the halide anions in aqueous solutions as well as the position of the first maximum of the radial distribution function of water around the ions. On the basis of these force field parameters, the electric conductivity, the hydration dynamics of water molecules around the ions, and the enthalpy of hydration is predicted. Considering a wide range of salinity, this study is conducted at temperatures of 293.15 and 298.15 K and a pressure of 1 bar.

  16. Dipole moments and orientation polarizabilities of diatomic molecular ions for precision atomic mass measurement

    NASA Astrophysics Data System (ADS)

    Cheng, Michelle; Brown, John M.; Rosmus, Pavel; Linguerri, Roberto; Komiha, Najia; Myers, Edmund G.

    2007-01-01

    In high precision Penning trap mass spectrometry the cyclotron frequency of a polarizable ion is perturbed due to the Stark interaction with the motional electric field. For polar diatomic molecular ions, which have adjacent rotational levels of opposite parity, these shifts can be particularly large—especially for the lowest rotational levels, which are those occupied by ions stored for many hours in cryogenic Penning traps. In order to provide corrections to precision atomic mass measurements, we consider the calculation of orientation polarizabilities of CO+ and the positive ions of the first and second row diatomic hydrides, LiH+ to ArH+ . Dipole moments for these ions have been calculated using the restricted coupled cluster method with perturbative triples and large basis sets. Using these dipoles and an effective Hamiltonian, we have obtained rotational-state dependent polarizabilities of the open-shell diatomic ions CO+ , NH+ , OH+ , FH+ , PH+ , SH+ , and ClH+ . Results are given for those rotational levels that are significantly populated at 4.2K , for magnetic fields up to 10T . For the remaining first and second row hydride cations, polarizabilities at the magnetic fields of interest can be obtained from a simple formula valid for closed-shell molecules. Conversely, in cases where the polarizability shifts can be measured, our results enable experimental determination of dipole moments.

  17. Ion transport in the gramicidin channel: molecular dynamics study of single and double occupancy.

    PubMed Central

    Roux, B; Prod'hom, B; Karplus, M

    1995-01-01

    The structural and thermodynamic factors responsible for the singly and doubly occupied saturation states of the gramicidin channel are investigated with molecular dynamics simulations and free energy perturbation methods. The relative free energy of binding of all of the five common cations Li+, Na+, K+, Rb+, and Cs+ is calculated in the singly and doubly occupied channel and in bulk water. The atomic system, which includes the gramicidin channel, a model membrane made of neutral Lennard-Jones particles and 190 explicit water molecules to form the bulk region, is similar to the one used in previous work to calculate the free energy profile of a Na+ ion along the axis of the channel. In all of the calculations, the ions are positioned in the main binding sites located near the entrances of the channel. The calculations reveal that the doubly occupied state is relatively more favorable for the larger ions. Thermodynamic decomposition is used to show that the origin of the trend observed in the calculations is due to the loss of favorable interactions between the ion and the single file water molecules inside the channel. Small ions are better solvated by the internal water molecules in the singly occupied state than in the doubly occupied state; bigger ions are solvated almost as well in both occupation states. Water-channel interactions play a role in the channel response. The observed trends are related to general thermodynamical properties of electrolyte solutions. Images FIGURE 2 PMID:7538804

  18. Molecular dynamics simulations of silicon chloride ion incidence during Si etching in Cl-based plasmas

    NASA Astrophysics Data System (ADS)

    Nakazaki, Nobuya; Takao, Yoshinori; Eriguchi, Koji; Ono, Kouichi

    2014-05-01

    Classical molecular dynamics (MD) simulations have been performed for SiClx+ (x = 0-4) ions incident on Si(100) surfaces, using an improved Stillinger-Weber (SW) potential form, to understand the surface reaction kinetics of etch byproduct ion incidence during Si etching in Cl-based plasmas. The ions were normally incident on surfaces with translational energies in the range of Ei = 20-500 eV, and the surface reaction kinetics of Clx+ (x = 1, 2) ion incidence were also simulated for reference. The etch yields and thresholds presently simulated were in agreement with the experimental results previously reported for the respective ion beam incidences on Si. Numerical results indicated that the etch yields y* per halogen (or per constituent Cl atom of incident ions), thresholds, surface coverages of Cl atoms adsorbed, and thicknesses of chlorinated surface layers are almost the same, when compared at the same translational energy e_{\\text{i}}^{*} per halogen; moreover, the stoichiometries of product species desorbed, stoichiometries of chlorinated surface layers, and their depth profiles are also similar when compared at the same e_{\\text{i}}^{*}. Thus, it follows that the etching characteristics for SiClx+ as well as Clx+ incidences on Si are determined primarily or scaled universally by e_{\\text{i}}^{*}, unless the deposition is significant at low Ei or e_{\\text{i}}^{*} for SiCl+ and SiCl2+.

  19. Promoting the Adsorption of Metal Ions on Kaolinite by Defect Sites: A Molecular Dynamics Study

    PubMed Central

    Li, Xiong; Li, Hang; Yang, Gang

    2015-01-01

    Defect sites exist abundantly in minerals and play a crucial role for a variety of important processes. Here molecular dynamics simulations are used to comprehensively investigate the adsorption behaviors, stabilities and mechanisms of metal ions on defective minerals, considering different ionic concentrations, defect sizes and contents. Outer-sphere adsorbed Pb2+ ions predominate for all models (regular and defective), while inner-sphere Na+ ions, which exist sporadically only at concentrated solutions for regular models, govern the adsorption for all defective models. Adsorption quantities and stabilities of metal ions on kaolinite are fundamentally promoted by defect sites, thus explaining the experimental observations. Defect sites improve the stabilities of both inner- and outer-sphere adsorption, and (quasi) inner-sphere Pb2+ ions emerge only at defect sites that reinforce the interactions. Adsorption configurations are greatly altered by defect sites but respond weakly by changing defect sizes or contents. Both adsorption quantities and stabilities are enhanced by increasing defect sizes or contents, while ionic concentrations mainly affect adsorption quantities. We also find that adsorption of metal ions and anions can be promoted by each other and proceeds in a collaborative mechanism. Results thus obtained are beneficial to comprehend related processes for all types of minerals. PMID:26403873

  20. A Novel Methodology for Metal Ion Separation Based on Molecularly Imprinting

    SciTech Connect

    Zuo, Xiaobin; Mosha, Donnati; Hassan, Mansour M.; Givens, Richard S.; Busch, Daryle H.

    2004-03-31

    The siderophore-based extraction of iron from the soil by bacteria is proposed as a model for a new separation methodology labeled the soil poutice, a molecular device that would selectively retrieve the complex of a targeted metal ion. In this report we described the synthesis and characterization of molecularly imprinted polymers and their application in the specific recognition of macrocyclic metal complexes. The imprinting is based on non-covalent interactions such as hydrogen bonding, electrostatic attractions and minor metal-ligand coordination. Good rebinding capacity for the imprinting metal complex was observed in acetonitrile as well as in water. The polymers are resistant to strong acids and oxidizing agents and showed an increase of rebinding capacity during cycles of reuse. The imprinting procedure, combined with the previously known selective chelation of macrocyclic ligands, supports the feasibility of a new methodology that can be used to extract waste metal ions effectively and selectively from soils and ground water.

  1. Confinement of the hydrogen molecular ion H2+ under a magnetic field inside a spheroid

    NASA Astrophysics Data System (ADS)

    Molinar, Martin

    2010-03-01

    A study of the confinement of the hydrogen molecular ion H2+ is done. The molecular ion is subject to the action of a magnetic field. In the Born -- Oppenheimer approximation, we solve numerically the Schr"odinger's equation, using trial functions and one algorithm that allows us to calculate the energies for different given values of the confinement parameters. We use the variational method in order to estimate the energy of the ground state. Some properties of the system as the pressure exerted by the confinement, the polarizability in the approximations of Kirkwood and Buckingham and the energies of the vibrational states are calculated. The behavior of the internuclear separation is analyzed for the geometry considered.

  2. Molecular ion-pair states in ungerade H{sub 2}

    SciTech Connect

    Kirrander, Adam; Jungen, Christian

    2011-11-15

    Molecular ion-pair states are analogs of electronic Rydberg states, but with the electron replaced by a much heavier ion. We calculate ab initio the long-range vibrational H{sup +}H{sup -} ion-pair states in H{sub 2} for ungerade {sup 1}{Sigma}{sub u}{sup +} symmetry, corresponding to recent observations by Ekey and McCormack [Phys. Rev. A 84, 020501 (2011)]. The overall trends in the experiment are reproduced and many peaks can be assigned. The calculations yield interloper resonances corresponding to vibrational states trapped inside the barriers on the potential-energy curves 5,6 {sup 1}{Sigma}{sub u}{sup +}.

  3. 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

  4. Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

    PubMed Central

    2016-01-01

    Molecular dynamics (MD) simulations of ions (K+, Na+, Ca2+ and Cl−) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain. PMID:27118886

  5. A SEARCH FOR CO-EVOLVING ION AND NEUTRAL GAS SPECIES IN PRESTELLAR MOLECULAR CLOUD CORES

    SciTech Connect

    Tassis, Konstantinos; Hezareh, Talayeh; Willacy, Karen

    2012-11-20

    A comparison between the widths of ion and neutral molecule spectral lines has been recently used to estimate the strength of the magnetic field in turbulent star-forming regions. However, the ion (HCO{sup +}) and neutral (HCN) species used in such studies may not be necessarily co-evolving at every scale and density, and thus, may not trace the same regions. Here, we use coupled chemical/dynamical models of evolving prestellar molecular cloud cores including non-equilibrium chemistry, with and without magnetic fields, to study the spatial distribution of HCO{sup +} and HCN, which have been used in observations of spectral line width differences to date. In addition, we seek new ion-neutral pairs that are good candidates for such observations, because they have similar evolution and are approximately co-spatial in our models. We identify three such good candidate pairs: HCO{sup +}/NO, HCO{sup +}/CO, and NO{sup +}/NO.

  6. Nonlinear effects in defect production by atomic and molecular ion implantation

    SciTech Connect

    David, C. Dholakia, Manan; Chandra, Sharat; Nair, K. G. M.; Panigrahi, B. K.; Amirthapandian, S.; Amarendra, G.; Varghese Anto, C.; Santhana Raman, P.; Kennedy, John

    2015-01-07

    This report deals with studies concerning vacancy related defects created in silicon due to implantation of 200 keV per atom aluminium and its molecular ions up to a plurality of 4. The depth profiles of vacancy defects in samples in their as implanted condition are carried out by Doppler broadening spectroscopy using low energy positron beams. In contrast to studies in the literature reporting a progressive increase in damage with plurality, implantation of aluminium atomic and molecular ions up to Al{sub 3}, resulted in production of similar concentration of vacancy defects. However, a drastic increase in vacancy defects is observed due to Al{sub 4} implantation. The observed behavioural trend with respect to plurality has even translated to the number of vacancies locked in vacancy clusters, as determined through gold labelling experiments. The impact of aluminium atomic and molecular ions simulated using MD showed a monotonic increase in production of vacancy defects for cluster sizes up to 4. The trend in damage production with plurality has been explained on the basis of a defect evolution scheme in which for medium defect concentrations, there is a saturation of the as-implanted damage and an increase for higher defect concentrations.

  7. Nonlinear effects in defect production by atomic and molecular ion implantation

    NASA Astrophysics Data System (ADS)

    David, C.; Varghese Anto, C.; Dholakia, Manan; Chandra, Sharat; Nair, K. G. M.; Panigrahi, B. K.; Santhana Raman, P.; Amirthapandian, S.; Amarendra, G.; Kennedy, John

    2015-01-01

    This report deals with studies concerning vacancy related defects created in silicon due to implantation of 200 keV per atom aluminium and its molecular ions up to a plurality of 4. The depth profiles of vacancy defects in samples in their as implanted condition are carried out by Doppler broadening spectroscopy using low energy positron beams. In contrast to studies in the literature reporting a progressive increase in damage with plurality, implantation of aluminium atomic and molecular ions up to Al3, resulted in production of similar concentration of vacancy defects. However, a drastic increase in vacancy defects is observed due to Al4 implantation. The observed behavioural trend with respect to plurality has even translated to the number of vacancies locked in vacancy clusters, as determined through gold labelling experiments. The impact of aluminium atomic and molecular ions simulated using MD showed a monotonic increase in production of vacancy defects for cluster sizes up to 4. The trend in damage production with plurality has been explained on the basis of a defect evolution scheme in which for medium defect concentrations, there is a saturation of the as-implanted damage and an increase for higher defect concentrations.

  8. Molecular Dynamics Simulation of the Antiamoebin Ion Channel: Linking Structure and Conductance

    NASA Technical Reports Server (NTRS)

    Wilson, Michael A.; Wei, Chenyu; Bjelkmar, Paer; Wallace, B. A.; Pohorille, Andrew

    2011-01-01

    Molecular dynamics simulations were carried out in order to ascertain which of the potential multimeric forms of the transmembrane peptaibol channel, antiamoebin, is consistant with its measured conductance. Estimates of the conductance obtained through counting ions that cross the channel and by solving the Nernst-Planck equation yield consistent results, indicating that the motion of ions inside the channel can be satisfactorily described as diffusive.The calculated conductance of octameric channels is markedly higher than the conductance measured in single channel recordings, whereas the tetramer appears to be non-conducting. The conductance of the hexamer was estimated to be 115+/-34 pS and 74+/-20 pS, at 150 mV and 75 mV, respectively, in satisfactory agreement with the value of 90 pS measured at 75 mV. On this basis we propose that the antiamoebin channel consists of six monomers. Its pore is large enough to accommodate K(+) and Cl(-) with their first solvation shells intact. The free energy barrier encountered by K(+) is only 2.2 kcal/mol whereas Cl(-) encounters a substantially higher barrier of nearly 5 kcal/mol. This difference makes the channel selective for cations. Ion crossing events are shown to be uncorrelated and follow Poisson statistics. keywords: ion channels, peptaibols, channel conductance, molecular dynamics

  9. Effect of molecular weight on ion diffusion and transference number in poly(ethylene oxide)

    NASA Astrophysics Data System (ADS)

    Timachova, Ksenia; Balsara, Nitash

    2015-03-01

    Solid polymer electrolytes are of great interest for their potential use in high specific energy, solid-state batteries, however, salt transport properties in polymer electrolytes have not been comprehensively addressed over a wide range of molecular weights. Poly(ethylene oxide) (PEO) has been the most widely studied polymer electrolyte due to its high solvation of lithium salts and low glass transition temperature. This study presents measurements of the transport properties of lithium bis(trifluoromethanesulfone)imide (LiTFSI) in PEO at both the high concentration present in functional electrolytes and in the dilute limit for a large range of PEO molecular weights. Individual diffusion coefficients of the Li + and TFSI- ions were measured using pulsed-field gradient nuclear magnetic resonance and the cation transference number was calculated. The diffusion coefficients, transference number, and conductivity as a function of molecular weight and salt concentration provide a complete set of transport properties for PEO.

  10. Complexation of tetrandrine with calcium ion probed by various spectroscopic methods and molecular modeling

    NASA Astrophysics Data System (ADS)

    Stanculescu, Ioana; Mandravel, Cristina; Landy, David; Woisel, Patrice; Surpateanu, Gheorghe

    2003-07-01

    The formation of the complex between tetrandrine and the calcium ion, in solution, was studied using FTIR, UV-Vis, 1H NMR, 13C NMR and electrospray mass spectroscopy spectroscopic methods and molecular modeling. The calcium salts used were: Ca(ClO 4) 2·4H 2O and Ca(Picrate) 2 in the solvents: acetonitrile (CH 3CN), deuterated acetonitrile (CD 3CN) and tetrahydrofurane (THF). The determined complex stability constant was: 20277±67 dm 3 mol -1 and corresponding free energy Δ G0=-5.820±0.002 kcal mol -1. The molecular simulation of the complex formation with the MM3 Augmented force field integrated in CAChe provided useful data about its energy. Combining the experimental results and molecular modeling we propose a model for the structure of tetrandrine-Ca complex with an eight coordinated geometry.

  11. Scattering and Sputtering Processes of Ar^+ and Cu^+ Ions on Cu Surfaces: Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Abrams, Cameron; Graves, David B.

    1998-10-01

    A better understanding of how energetic Ar^+ and Cu^+ ions from plasmas interact with copper surfaces is crucial for further development of metallization technologies. We present results of molecular dynamics (MD) simulations of Ar^+ and Cu^+ ions impacting model Cu surfaces with a variety of impact energies (50 - 200 eV) and angles. We modeled Cu-Cu interactions using the EAM potential energy function (PEF) and Ar-Cu interactions using the ZBL PEF.(K. Gärtner et al.), Nucl. Instr. Meth. Phys. Res. B 102, 183 (1995). We report the total sputtering and reflection yields for these energies and angles. We report spatial distributions of sputter and reflection yields with respect to angle of ejection, and compare our MD results to recent experimental findings.(C. Doughty, S. M. Gorbatkin, and L. A. Berry, J. Appl. Phys. 82), 1868 (1997). The effects of changing ion energy and angle on these quantities are discussed. For example, we observe that the sputter yield for Ar^+ on Cu decreases as the Ar^+ ion's incident angle is increased from 30^circ to 60^circ from normal. These results shed light on the dynamics of low energy ion/metal surface interactions and provide a useful databases for use in profile evolution simulations of Cu seed layer deposition and trench/via fill.

  12. Electron emission and molecular fragmentation during hydrogen and deuterium ion impact on carbon surfaces

    NASA Astrophysics Data System (ADS)

    Qayyum, A.; Schustereder, W.; Mair, C.; Scheier, P.; Märk, T. D.; Cernusca, S.; Winter, HP.; Aumayr, F.

    2003-03-01

    Molecular fragmentation and electron emission during hydrogen ion impact on graphite surfaces has been investigated in the eV to keV impact energy region typical for fusion edge plasma conditions. As a target surface graphite tiles for the Tokamak experiment Tore Supra in CEA-Cadarache/France and highly oriented pyrolytic graphite (HOPG) have been used. For both surfaces studied, the experimentally observed threshold for electron emission is at about 50 eV/amu impact energy. Electron emission from the high conductivity side of the carbon tile is 15-20% less as compared to its low conductivity side, whereas results for HOPG are generally between these two cases. Deuterium and hydrogen ions are almost equally effective in liberating electrons from graphite when comparing results for the same impact velocity. Surface-induced dissociation of deuterium ions D 3+ upon impact on Tore Supra graphite tiles, in the collision energy range of 20-100 eV, produced only atomic fragment ions D +. The other possible fragment ion D 2+ could not be observed.

  13. Ion implantation on ultra high molecular weight polyethylene (UHMWPE) for medical prosthesis

    NASA Astrophysics Data System (ADS)

    Torrisi, L.; Visco, A. M.; Valenza, A.

    2003-09-01

    In order to improve the wear resistance of ultra high molecular weight polyethylene (UHMWPE). a surface modification is induced by ion implantation of different ions at 300 keV energy with doses ranging between 10(14)-10(17) ions/cm(2). Wear measurements, in terms of weight loss, are performed with a "pin on disc" friction machine, these tests measure the wear property of the UHMWPE against a metallic probe before and after the ion implantation treatment, Results demonstrate that in the implanted samples the wear resistance increases by about 76% with respect to the non-irradiated samples. The irradiated polymeric layer was characterized with the mass quadrupole spectrometry. Raman spectroscopy, infrared absorption analysis, scanning electron microscopy, atomic force microscopy and calorimetric analysis. The results suggest that wear decrease effect can be attributed to the ion bombardment inducing a high carbon surface concentration and cross-linking effects in the irradiated polymeric layer. The irradiated UHMWPE surfaces find special applications in the field of the mobile prosthesis such as hip joints.

  14. Molecular Dynamics Simulations of Ion Transport and Mechanisms in Polymer Nanocomposites

    NASA Astrophysics Data System (ADS)

    Mogurampelly, Santosh; Ganesan, Venkat

    2015-03-01

    Using all atom molecular dynamics and trajectory-extending kinetic Monte Carlo simulations, we study the influence of Al2O3 nanoparticles on the transport properties of Li+ ions in polymer electrolytes consisting of polyethylene oxide (PEO) melt solvated with LiBF4 salt. We observe that the nanoparticles have a strong influence on polymer segmental dynamics which in turn correlates with the mobility of Li+ ions. Explicitly, polymer segmental relaxation times and Li+ ion residence times around polymer were found to increase with the addition of nanoparticles. We also observe that increasing short range repulsive interactions between nanoparticles and polymer membrane leads to increasing polymer dynamics and ion mobility. Overall, our simulation results suggest that nanoparticle induced changes in conformational and dynamic properties of the polymer influences the ion mobilities in polymer electrolytes and suggests possible directions for using such findings to improve the polymer matrix conductivity. The authors acknowledge the Texas Advanced Computing Center (TACC) at The University of Texas at Austin for providing computing resources that have contributed to the research.

  15. Molecular dynamics simulation of the damage production in Al (110) surface with slow argon ions

    NASA Astrophysics Data System (ADS)

    Valkealahti, S.; Nieminen, R. M.

    We have developed a molecular dynamics simulation program to gain more insight into the sputtering process, especially the damage produced by it. We have studied the sputtering of aluminium (110) surface with argon ions. The Morse pair potentail was used for Al-Al interaction, the Lennard-Jones potential for Ar-Ar interaction and both the Molière potential and the universal potential of Ziegler et al. for Ar-Al interaction. An electronic friction term proportional to the particle velocities was also used. The studied incident argon ion energies and angles were 200 and 400 eV and 0° (normal), 25°, 45° and 75°, respectively. The calculated sputtering yield and the overall shape and the mean depth of the vacancy profiles agree with the experimental results. The obtained profiles contain a narrow peak within the topmost atomic layers, followed by a weak tail deeper in the material. The intersitial and argon ion distributions are much more spread out at larger depths. The total number of vacancies per incident Ar + ion varies from 0 to 7, increasing as function of Ar + ion energy.

  16. Chemistry induced by energetic ions in water ice mixed with molecular nitrogen and oxygen

    NASA Astrophysics Data System (ADS)

    Boduch, Ph.; Domaracka, A.; Fulvio, D.; Langlinay, T.; Lv, X. Y.; Palumbo, M. E.; Rothard, H.; Strazzulla, G.

    2012-08-01

    Context. Several molecular species have been observed as frozen gases in cold environments such as grains in the interstellar/circumstellar medium or icy objects in the outer solar system. Because N2 and O2 are homonuclear, symmetric molecules are not easily observed. It is therefore relevant to find indirect methods to prove their presence from astronomical observations. Aims: Here we investigate one of the possible indirect methods, namely the formation of specific molecules by cosmic ion bombardment of ices in astrophysical environments that contain O2 and N2. The observation of these molecules in astronomical environments could act as a trojan horse to detect the presence of frozen molecular oxygen and/or nitrogen. Methods: We have conducted ion bombardment experiments of frozen O2, H2O and their mixtures with N2 at the laboratories of CIMAP-GANIL at Caen (France) and LASp at Catania (Italy). Different ions (13C2+, Ar2+ and H+) and energies (30-200 keV) have been used. Results: We have found that 13CO2 is formed when carbon ions are implanted in ices containing H2O and/or O2. Ozone and nitrogen oxides (NO, N2O, NO2) are formed in the studied ices containing O2 and N2 with different relative abundances. Conclusions: We suggest that ozone and nitrogen oxides are present and have to be searched for in some specific environments such as dense clouds in the interstellar medium and the surfaces of Pluto, Charon and Triton. Their observation could demonstrate the presence of molecular oxygen and/or nitrogen. A possible interest for the observations of atmospheres in exo-planetary objects is also discussed.

  17. High-resolution room temperature and jet-cooled spectroscopic investigation of 15NH3 in the ν1+ν3 band region (1.51 μm)

    NASA Astrophysics Data System (ADS)

    Földes, T.; Vanfleteren, T.; Rizopoulos, A.; Herman, M.; Vander Auwera, J.; Softley, T. P.; Di Lonardo, G.; Fusina, L.

    2016-08-01

    Spectra of 99% isotopically pure 15NH3 were recorded using cavity ring-down (CRD, 6567-6639 cm-1) and Fourier transform (FT, 6350-6985 cm-1) spectroscopy under jet cooled and room temperature conditions, respectively. Measured line positions on both data sets improve on literature values, in particular by one order of magnitude for the ν1+ν3 band. A room temperature list of line positions, with approximate line intensities, is provided, much more complete and precise than presently available. Line broadening effects in the CRD spectrum allowed lines with J‧‧‧- values between 0 and 3 to be identified. Ground state combination differences were used to refine the assignments, further assisted by intensity ratios between the two data sets. Reliable values for J, K and inversion symmetry of the ground state vibrational levels, as well as further information on a/s doublets could be obtained, updating and extending literature assignments.

  18. Ions interacting with complex molecular systems: The effect of a surrounding environment

    NASA Astrophysics Data System (ADS)

    Zettergren, Henning

    2015-07-01

    This paper highlight results from studies of keV-ion impact on complex molecules and molecular clusters, which have been carried out at the ARIBE facility in Caen (France) during the last decade. Studies of fullerenes, Polycyclic Aromatic Hydrocarbons (PAHs), and biomolecules are reviewed with focus on the effect of a surrounding environment when ions interact with weakly bound clusters of theses species. One common result is that charge and energy are rapidly shared between the individual molecules in the clusters, in contrast to e.g. weakly bound atomic clusters where the charge stay localized to a few atoms from which the electrons are removed during the collisions. Another important finding is that ion collisions may induce reactions within clusters such as e.g. proton transfer and different types of molecular growth processes. In the latter case, these processes may be driven by prompt non-statistical atom knockouts in billiard-ball like atom-atom collisions favouring highly reactive fragments. In contrast, statistical fragmentation in general yields different and less reactive fragments.

  19. 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

  20. Cryogenic molecular separation system for radioactive {sup 11}C ion acceleration

    SciTech Connect

    Katagiri, K.; Noda, A.; Suzuki, K.; Nagatsu, K.; Nakao, M.; Hojo, S.; Wakui, T.; Noda, K.; Boytsov, A. Yu.; Donets, D. E.; Donets, E. D.; Donets, E. E.; Ramzdorf, A. Yu.

    2015-12-15

    A {sup 11}C molecular production/separation system (CMPS) has been developed as part of an isotope separation on line system for simultaneous positron emission tomography imaging and heavy-ion cancer therapy using radioactive {sup 11}C ion beams. In the ISOL system, {sup 11}CH{sub 4} molecules will be produced by proton irradiation and separated from residual air impurities and impurities produced during the irradiation. The CMPS includes two cryogenic traps to separate specific molecules selectively from impurities by using vapor pressure differences among the molecular species. To investigate the fundamental performance of the CMPS, we performed separation experiments with non-radioactive {sup 12}CH{sub 4} gases, which can simulate the chemical characteristics of {sup 11}CH{sub 4} gases. We investigated the separation of CH{sub 4} molecules from impurities, which will be present as residual gases and are expected to be difficult to separate because the vapor pressure of air molecules is close to that of CH{sub 4}. We determined the collection/separation efficiencies of the CMPS for various amounts of air impurities and found desirable operating conditions for the CMPS to be used as a molecular separation device in our ISOL system.

  1. 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

  2. Predissociation of high-lying Rydberg states of molecular iodine via ion-pair states

    SciTech Connect

    Bogomolov, Alexandr S.; Grüner, Barbara; Mudrich, Marcel; Kochubei, Sergei A.; Baklanov, Alexey V.

    2014-03-28

    Velocity map imaging of the photofragments arising from two-photon photoexcitation of molecular iodine in the energy range 73 500–74 500 cm{sup −1} covering the bands of high-lying gerade Rydberg states [{sup 2}Π{sub 1/2}]{sub c}6d;0{sub g}{sup +} and [{sup 2}Π{sub 1/2}]{sub c}6d;2{sub g} has been applied. The ion signal was dominated by the atomic fragment ion I{sup +}. Up to 5 dissociation channels yielding I{sup +} ions with different kinetic energies were observed when the I{sub 2} molecule was excited within discrete peaks of Rydberg states and their satellites in this region. One of these channels gives rise to images of I{sup +} and I{sup −} ions with equal kinetic energy indicating predissociation of I{sub 2} via ion-pair states. The contribution of this channel was up to about 50% of the total I{sup +} signal. The four other channels correspond to predissociation via lower lying Rydberg states giving rise to excited iodine atoms providing I{sup +} ions by subsequent one-photon ionization by the same laser pulse. The ratio of these channels varied from peak to peak in the spectrum but their total ionic signal was always much higher than the signal of (2 + 1) resonance enhanced multi-photon ionization of I{sub 2}, which was previously considered to be the origin of ionic signal in this spectral range. The first-tier E0{sub g}{sup +} and D{sup ′}2{sub g} ion-pair states are concluded to be responsible for predissociation of Rydberg states [{sup 2}Π{sub 1/2}]{sub c}6d;0{sub g}{sup +} and [{sup 2}Π{sub 1/2}]{sub c}6d;2{sub g}, respectively. Further predissociation of these ion-pair states via lower lying Rydberg states gives rise to excited I(5s{sup 2}5p{sup 4}6s{sup 1}) atoms responsible for major part of ion signal. The isotropic angular distribution of the photofragment recoil directions observed for all channels indicates that the studied Rydberg states are long-lived compared with the rotational period of the I{sub 2} molecule.

  3. FTICR/MS studies of gas-phase actinide ion reactions: fundamental chemical and physical properties of atomic and molecular actinide ions and neutrals

    NASA Astrophysics Data System (ADS)

    Gibson, J. K.; Haire, R. G.; Marçalo, J.; Santos, M.; Leal, J. P.; Pires de Matos, A.; Tyagi, R.; Mrozik, M. K.; Pitzer, R. M.; Bursten, B. E.

    2007-10-01

    Fundamental aspects of the chemical and physical properties of atomic and molecular actinide ions and neutrals are being examined by Fourier transform ion cyclotron resonance mass spectrometry (FTICR/MS). To date, gas-phase reactivity studies of bare and ligated An+ and An2+ ions, where An = Th, Pa, U, Np, Pu, Am, and Cm, with oxidants and with hydrocarbons have been performed. Among the information that has been deduced from these studies are thermodynamic properties of neutral and ionic actinide oxide molecules and the role of the 5f electrons in actinide chemistry. Parallel theoretical studies of selected actinide molecular ions have also been carried out to substantiate the interpretation of the experimental observations.

  4. Ion distributions near dielectric interfaces from Car-Parrinello molecular dynamics

    NASA Astrophysics Data System (ADS)

    Jadhao, Vikram; Solis, Francisco; Olvera de La Cruz, Monica

    2013-03-01

    Free charges in media characterized by different dielectric constants and separated by thin boundaries are basic models for studying phenomena in both biological and synthetic materials. Knowing the distributions of ions near the dielectric interfaces between these media is crucial towards understanding the structural and physical properties of these systems. We present a new Car-Parrinello molecular dynamics method for simulating charges in heterogeneous media and computing such distributions. This method is founded on a true energy functional of induced charge density which enables the replacement of the expensive solution of the Poisson equation at each simulation step with an on-the-fly computation of polarization effects. Our simulations track the exact induced density at all times and demonstrate excellent energy conservation. The method is applied to study models of a charged colloid in polar solvent, ions near a liquid-liquid emulsion droplet, and charged biological macromolecule in aqueous solution. Results for ionic density profiles for different dielectric contrasts, ion concentrations, ion valencies, and different interfacial shapes are presented. We thank DDR&E and the AFOSR Award No. FA9550-10-1-0167 and NSF Grant Nos. DMR-0805330 and DMR-0907781

  5. A metal–ion-responsive adhesive material via switching of molecular recognition properties

    PubMed Central

    Nakamura, Takashi; Takashima, Yoshinori; Hashidzume, Akihito; Yamaguchi, Hiroyasu; Harada, Akira

    2014-01-01

    Common adhesives stick to a wide range of materials immediately after they are applied to the surfaces. To prevent indiscriminate sticking, smart adhesive materials that adhere to a specific target surface only under particular conditions are desired. Here we report a polymer hydrogel modified with both β-cyclodextrin (βCD) and 2,2′-bipyridyl (bpy) moieties (βCD–bpy gel) as a functional adhesive material responding to metal ions as chemical stimuli. The adhesive property of βCD–bpy gel based on interfacial molecular recognition is expressed by complexation of metal ions to bpy that controlled dissociation of supramolecular cross-linking of βCD–bpy. Moreover, adhesion of βCD–bpy gel exhibits selectivity on the kinds of metal ions, depending on the efficiency of metal–bpy complexes in cross-linking. Transduction of two independent chemical signals (metal ions and host–guest interactions) is achieved in this adhesion system, which leads to the development of highly orthogonal macroscopic joining of multiple objects. PMID:25099995

  6. UV Photodissociation of Proline-containing Peptide Ions: Insights from Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Girod, Marion; Sanader, Zeljka; Vojkovic, Marin; Antoine, Rodolphe; MacAleese, Luke; Lemoine, Jérôme; Bonacic-Koutecky, Vlasta; Dugourd, Philippe

    2015-03-01

    UV photodissociation of proline-containing peptide ions leads to unusual product ions. In this paper, we report laser-induced dissociation of a series of proline-containing peptides at 213 nm. We observe specific fragmentation pathways corresponding to the formation of (y-2), (a + 2) and (b + 2) fragment ions. This was not observed at 266 nm or for peptides which do not contain proline residues. In order to obtain insights into the fragmentation dynamics at 213 nm, a small peptide (RPK for arginine-proline-lysine) was studied both theoretically and experimentally. Calculations of absorption spectra and non-adiabatic molecular dynamics (MD) were made. Second and third excited singlet states, S2 and S3, lie close to 213 nm. Non-adiabatic MD simulation starting from S2 and S3 shows that these transitions are followed by C-C and C-N bond activation close to the proline residue. After this first relaxation step, consecutive rearrangements and proton transfers are required to produce unusual (y-2), (a + 2) and (b + 2) fragment ions. These fragmentation mechanisms were confirmed by H/D exchange experiments.

  7. Molecular dynamics simulation of bipartite bimetallic clusters under low-energy argon ion bombardment

    NASA Astrophysics Data System (ADS)

    Shirokorad, D. V.; Kornich, G. V.; Buga, S. G.

    2016-02-01

    The evolution of bipartite bimetallic atomic clusters within 5 ps under bombardment with monoenergetic argon ions at the initial energy ranging from 1 eV to 1.4 keV has been simulated by the classical molecular dynamics method with a target obtained from Ni‒Al and Cu‒Au clusters consisting of 78 and 390 atoms, equally divided between the corresponding monometallic parts, the simulated pairs of which have different heats of intermixing. The changes in the potential energy and temperature, the sputtering yields, and the intensity of the ion-stimulated movement of atoms at the interface of the monometallic parts of clusters of both sizes have been determined as functions of the energy of the bombardment.

  8. Molecular dynamics simulation of silicon oxidation enhanced by energetic hydrogen ion irradiation

    NASA Astrophysics Data System (ADS)

    Mizotani, Kohei; Isobe, Michiro; Fukasawa, Masanaga; Nagahata, Kazunori; Tatsumi, Tetsuya; Hamaguchi, Satoshi

    2015-04-01

    Molecular dynamics numerical simulations have been performed to clarify the mechanism of enhanced oxidation in Si during silicon gate etching by HBr/O2 plasmas. Such enhanced oxidation sometimes manifests itself as Si recess during gate etching processes. When a Si substrate is subject to energetic ion bombardment together with a flux of radical species, our study has identified the cause of such enhanced oxidation in Si as enhanced O diffusion arising from the momentum transfer from energetic H atoms to O atoms on the surface or in the subsurface of the Si substrate. No chemical effect such as hydrogenation of Si plays a role for the enhanced oxidation. Simulation results are found to be in good agreement with earlier experimental observations of ion-irradiation-enhanced oxidation obtained by beam experiments.

  9. Dissociative recombination of stored and phase-spaced cooled molecular ions in CRYRING

    SciTech Connect

    Larsson, M.; Sundstroem, G.; Carlson, M.; Danared, H.; Kaellberg, A.; Rensfelt, K.G.; af Ugglas, M.; Brostroem, L.; Mannervik, S.; Sigray, P.; Filevich, A.; Datz, S.; Mowat, J.R.

    1993-11-01

    Ion storage rings offer several advantages for studies of recombination of molecular ions by electrons, a process which in general leads to dissociation. During the last year dissociative recombination of H{sub 3}{sup +}, HD{sup +}, H{sub 2}{sup +}, D{sub 2}{sup +}, {sup 3}HeH{sup +}, {sup 4}HeH{sup +} and {sup 4}HeD{sup +} have been studied in storage rings in Stockholm, Heidelberg, Tokyo and Aarhus. Only a fraction of the results obtained at these places have been processed to the point where they have been published in the literature. Hence, the discussion of some of the results in this article must be regarded as tentative.

  10. A fluorescent aptasensor for potassium ion detection-based triple-helix molecular switch.

    PubMed

    Verdian-Doghaei, A; Housaindokht, M R; Abnous, Kh

    2014-12-01

    Here, a biosensor based on a quadruplex-forming aptamer for the determination of potassium ion (K(+)) is presented. The aptamer was used as a molecular recognition element; it was adjacent to two arm fragments and a dual-labeled oligonucleotide serving as a signal transduction probe (STP) that is complementary of the arm fragment sequence. In the presence of K(+), the aptamer was displaced from the STP, which was accompanied by decreased signal. The quenching percentage of fluorescence intensity was proportional to the concentration of K(+) in the range of 0.05 to 1.4mM. A detection limit of 0.014 mM was achieved. Furthermore, other metal ions, such as Na(+), Li(+), NH4(+), Mg(2+), and Ca(2+), caused no notable interference on the detection of K(+). PMID:25173515

  11. A Time-Distinguished Analysis of the Harmonic Structure from a Model Molecular Ion

    NASA Astrophysics Data System (ADS)

    Yang, Yu-Jun; Chen, Gao; Chen, Ji-Gen; Zhu, Qi-Ren

    2004-04-01

    We present high-order harmonic generation spectra resulted from a single-electron model molecular ion exposed to intense laser fields by numerically solving a one-dimensional time-dependent Schrödinger equation. There are three plateaus in the spectra and the maximal cutoff energy is Ip+8.5Up, when the inter-nuclear distance R equals pialpha0/2. Here Ip is the ionization potential and Up = E02/(4omega2) is the ponderomotive potential with E0 and omega being the laser electric field amplitude and the central frequency. The harmonic structures are well interpreted by a modified three-step model in which the effects of the electron reflected by the non-parent ion are stressed.

  12. The rotation of NO3- as a probe of molecular ion - water interactions

    NASA Astrophysics Data System (ADS)

    Thøgersen, J.; Nielsen, J. B.; Knak Jensen, S.; Keiding, S. R.; Odelius, M.; Ogden, T.; Réhault, J.; Helbing, J.

    2013-03-01

    The hydration dynamics of aqueous nitrate, NO3-(aq), is studied by 2D-IR spectroscopy, UV-IR- and UV-UV transient absorption spectroscopy. The experimental results are compared to Car-Parinello molecular dynamics (MD) simulations. The 2D-IR measurements and MD simulations of the non-degenerate asymmetric stretch vibrations of nitrate reveal an intermodal energy exchange occurring on a 0.2 ps time scale related to hydrogen bond fluctuations. The transient absorption measurements find that the nitrate ions rotate in 2 ps. The MD simulations indicate that the ion rotation is associated with the formation of new hydrogen bonds. The 2 ps rotation time thus indicates that the hydration shell of aqueous nitrate is rather labile.

  13. Static and dynamic properties of confined, cold ion plasmas: MD (molecular dynamics) simulations

    SciTech Connect

    Schiffer, J.P.

    1989-01-01

    Some four years ago it was suggested that in the new generation of heavy ion accelerator storage rings for multiply charged ions, being planned in Europe, one may well attain internal temperatures that would correspond to very cold plasmas. Since that time, the techniques of electron or laser cooling of such beams has evolved and it may well be possible to reach temperatures corresponding to a plasma coupling parameter {Gamma} >> 100. I was fortunate to have had an opportunity to collaborate during 1986-87 with my former colleague Aneesur Rahman, of Molecular Dynamics fame, and we adapted the MD method to the calculation of the properties of cold confined plasmas. After Rahman's premature death two years ago I have continued the exploration of these systems and would like to summarize the results here. 9 refs., 10 figs.

  14. Pairing mechanism among ionic liquid ions in aqueous solutions. A molecular dynamics study

    SciTech Connect

    Annapureddy, Harsha V.; Dang, Liem X.

    2013-07-18

    In this study, we carried out molecular dynamics simulations to examine the molecular mechanism for ionic liquid pair association in aqueous solutions. We chose the commonly studied imidazolium-based ionic liquid pairs. We computed potentials of mean force (PMF) for four systems—1,3-dimethlylimidazoliumchloride; 1,3-dimethlylimidazolium iodide; 1-methly-3-octylimidazolium chloride; and 1-methly-3-octylimidazolium iodide. Our PMF studies show a stronger interaction for the ion pairs of systems involving dimethlylimidazolium as the cation species compared to that of the systems containing octylimidazolium. This result indicates a decrease in ion-pair association as the cation alkyl tail length increases. We also studied the kinetics of ion-pair dissociation using different rate theories such as the Grote-Hynes and Kramer’s theories. As expected, the computed rate results significantly deviated from results obtained from transition state theory because it does not account for dynamical solvent effects. Dissociative barrier curvatures are found to be very small for the systems investigated because the transmission coefficients computed using Grote-Hynes theory and Kramer’s theory are approximately equal. Our analysis of the rotational dynamics of cations revealed that the time scales for molecular reorientation are longer for cations with longer alkyl tails. This work was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences (BES), Division of Chemical Sciences, Geosciences, and Biosciences. Pacific Northwest National Laboratory is a multiprogram national laboratory operated for DOE by Battelle. The calculations were carried out using computer resources provided by BES.

  15. Sodium ion interactions with aqueous glucose: insights from quantum mechanics, molecular dynamics, and experiment.

    PubMed

    Mayes, Heather B; Tian, Jianhui; Nolte, Michael W; Shanks, Brent H; Beckham, Gregg T; Gnanakaran, S; Broadbelt, Linda J

    2014-02-27

    In the last several decades, significant efforts have been conducted to understand the fundamental reactivity of glucose derived from plant biomass in various chemical environments for conversion to renewable fuels and chemicals. For reactions of glucose in water, it is known that inorganic salts naturally present in biomass alter the product distribution in various deconstruction processes. However, the molecular-level interactions of alkali metal ions and glucose are unknown. These interactions are of physiological interest as well, for example, as they relate to cation-glucose cotransport. Here, we employ quantum mechanics (QM) to understand the interaction of a prevalent alkali metal, sodium, with glucose from a structural and thermodynamic perspective. The effect on β-glucose is subtle: a sodium ion perturbs bond lengths and atomic partial charges less than rotating a hydroxymethyl group. In contrast, the presence of a sodium ion significantly perturbs the partial charges of α-glucose anomeric and ring oxygens. Molecular dynamics (MD) simulations provide dynamic sampling in explicit water, and both the QM and the MD results show that sodium ions associate at many positions with respect to glucose with reasonably equivalent propensity. This promiscuous binding nature of Na(+) suggests that computational studies of glucose reactions in the presence of inorganic salts need to ensure thorough sampling of the cation positions, in addition to sampling glucose rotamers. The effect of NaCl on the relative populations of the anomers is experimentally quantified with light polarimetry. These results support the computational findings that Na(+) interacts similarly with α- and β-glucose. PMID:24308866

  16. Molecular Dynamics Study of Gramicidin A in Lipid Bilayer: Electrostatic Map and Ion Conduction

    NASA Astrophysics Data System (ADS)

    Saito, Hiroaki; Iwayama, Masashi; Kawaguchi, Kazutomo; Mizukami, Taku; Miyakawa, Takeshi; Takasu, Masako; Nagao, Hidemi

    The electrostatic potential (ESP) of gramicidin A (GA) in the DMPC lipid bilayers with/without an external uniform electrostatic field was investigated by molecular dynamics (MD) simulation. We found that the ESP profile with an external electrostatic field became step shape. The water and polar groups of the lipid and GA are rearranged in order to restore a flat ESP in the water bulk and GA channel interior. The reorientation of the polar head group enhances the ESP difference between each hydration regions of the membrane, and this should yield an increase of ion conductance through the GA channel.

  17. 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.

  18. Fabrication of carbon nanotube nanogap electrodes by helium ion sputtering for molecular contacts

    SciTech Connect

    Thiele, Cornelius; Vieker, Henning; Beyer, André; Gölzhäuser, Armin; Flavel, Benjamin S.; Hennrich, Frank; Muñoz Torres, David; Eaton, Thomas R.; Mayor, Marcel; Kappes, Manfred M.; Löhneysen, Hilbert v.; and others

    2014-03-10

    Carbon nanotube nanogaps have been used to contact individual organic molecules. However, the reliable fabrication of a truly nanometer-sized gap remains a challenge. We use helium ion beam lithography to sputter nanogaps of only (2.8 ± 0.6) nm size into single metallic carbon nanotubes embedded in a device geometry. The high reproducibility of the gap size formation provides a reliable nanogap electrode testbed for contacting small organic molecules. To demonstrate the functionality of these nanogap electrodes, we integrate oligo(phenylene ethynylene) molecular rods, and measure resistance before and after gap formation and with and without contacted molecules.

  19. Adsorption of hydrated halide ions on charged electrodes. Molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Glosli, James N.; Philpott, Michael R.

    1993-06-01

    Constant temperature molecular dynamics has been used to simulate the adsorption of hydrated halide ions X-=F-, Cl-, Br- and I-, and lithium ion Li+ on flat uniformly charged surfaces. The simulations were done with either 214 water molecules and two ions (Li+ and X-) in a box 2.362 nm deep or with 430 water molecules and the two ions in a box 4.320 nm deep. The boxes were periodically replicated in the xy directions. The magnitude of the surface charge on the box ends was ±0.11 e/(nm)2, corresponding to an electric field of 2×107 V/cm. The lateral dimensions of the simulation cell were 1.862 nm×1.862 nm (x×y) in each case. All of the water molecules and ions interacted with the end walls via a weak 9-3 potential. The Stillinger ST2 water model and parameters optimized for alkali halides interacting with the model ST2 water molecule were used in the calculations. Common particles of truncating the interactions at a finite distance (0.82 nm) and switching off Coulomb interactions at small distances were followed. The temperature was set at T=2.411 kJ/mol (290 K). Some of the properties calculated were distribution density profiles for ions and water across the gap important for comparisons with Gouy-Chapman theory, adsorbed ion-water pair correlation functions, and the number of water molecules in the first and second hydration shells of the ions as a function of time. The time spent by a water molecule in the hydration shell was calculated to be approximately ten times longer for lithium than any other ion. The correlation between distance from the electrode and hydration number was studied and generally found to be pronounced for the larger anions. Comparison of the dynamics of the common ion Li+ for different anions revealed the subtle influence of a transcell interaction in the 2.362 nm thick film. In the given field, the smallest ions Li+ and F- remained fully solvated at all times. Chloride behaved quite differently. Part of the time this ion was far

  20. Discovery of energetic molecular ions (NO/sup +/ and O/sub 2//sup +/) in the storm time ring current

    SciTech Connect

    Klecker, B.; Moebius, E.; Hovestadt, D.; Scholer, M.; Gloeckler, G.; Ipavich, F.M.

    1986-07-01

    A few hours after the onset of a large geomagnetic storm on September 4, 1984, energetic molecular ions in the mass range 28--32, predminantly NO/sup +/ and O/sub 2//sup +/, have been discovered in the outer ring current at L--7. The data have been obtained with the time-of-flight spectrometer SULEICA on the AMPTE/IRM spacecraft. We find at 160 keV/e a mean abundance ratio of the molecular ions relative to O/sup +/ ions of 0.031 +- 0.004. During quiet times no molecular ions are observed, the 1 sigma upper limit of the ratio derived by averaging over several quiet periods is 0.003. The observations demonstrate the injection of ionospheric plasma into the storm time ring current and the subsequent acceleration to energies of several hundred keV on a time scale of a few hours after the onset of the magnetic storm.

  1. Molecular Mechanisms of ZnO Nanoparticle Dispersion in Solution: Modeling of Surfactant Association, Electrostatic Shielding and Counter Ion Dynamics

    PubMed Central

    Duchstein, Patrick; Milek, Theodor; Zahn, Dirk

    2015-01-01

    Molecular models of 5 nm sized ZnO/Zn(OH)2 core-shell nanoparticles in ethanolic solution were derived as scale-up models (based on an earlier model created from ion-by-ion aggregation and self-organization) and subjected to mechanistic analyses of surface stabilization by block-copolymers. The latter comprise a poly-methacrylate chain accounting for strong surfactant association to the nanoparticle by hydrogen bonding and salt-bridges. While dangling poly-ethylene oxide chains provide only a limited degree of sterical hindering to nanoparticle agglomeration, the key mechanism of surface stabilization is electrostatic shielding arising from the acrylates and a halo of Na+ counter ions associated to the nanoparticle. Molecular dynamics simulations reveal different solvent shells and distance-dependent mobility of ions and solvent molecules. From this, we provide a molecular rationale of effective particle size, net charge and polarizability of the nanoparticles in solution. PMID:25962096

  2. Molecular mechanism of acetylcholine receptor-controlled ion translocation across cell membranes

    PubMed Central

    Cash, Derek J.; Hess, George P.

    1980-01-01

    Two molecular processes, the binding of acetylcholine to the membrane-bound acetylcholine receptor protein and the receptor-controlled flux rates of specific inorganic ions, are essential in determining the electrical membrane potential of nerve and muscle cells. The measurements reported establish the relationship between the two processes: the acetylcholine receptor-controlled transmembrane ion flux of 86Rb+ and the concentration of carbamoylcholine, a stable analog of acetylcholine. A 200-fold concentration range of carbamoylcholine was used. The flux was measured in the millisecond-to-minute time region by using a quench flow technique with membrane vesicles prepared from the electric organ of Electrophorus electricus in eel Ringer's solution at pH 7.0 and 1°C. The technique makes possible the study of the transmembrane transport of specific ions, with variable known internal and external ion concentrations, in a system in which a determinable number of receptors is exposed to a known concentration of ligand. The response curve of ion flux to ligand was sigmoidal with an average maximum rate of 84 sec-1. Carbamoylcholine induced inactivation of the receptor with a maximum rate of 2.7 sec-1 and a different ligand dependence so that it was fast relative to ion flux at low ligand concentration but slow relative to ion flux at high ligand concentration. The simplest model that fits the data consists of receptor in the active and inactive states in ligand-controlled equilibria. Receptor inactivation occurs with one or two ligand molecules bound. For channel opening, two ligand molecules bound to the active state are required, and cooperativity results from the channel opening process itself. With carbamoylcholine, apparently, the equilibrium position for the channel opening step is only one-fourth open. The integrated rate equation, based on the model, predicts the time dependence of receptor-controlled ion flux over the concentration range of carbamoylcholine

  3. Elucidation of Drug Metabolite Structural Isomers Using Molecular Modeling Coupled with Ion Mobility Mass Spectrometry.

    PubMed

    Reading, Eamonn; Munoz-Muriedas, Jordi; Roberts, Andrew D; Dear, Gordon J; Robinson, Carol V; Beaumont, Claire

    2016-02-16

    Ion mobility-mass spectrometry (IM-MS) in combination with molecular modeling offers the potential for small molecule structural isomer identification by measurement of their gas phase collision cross sections (CCSs). Successful application of this approach to drug metabolite identification would facilitate resource reduction, including animal usage, and may benefit other areas of pharmaceutical structural characterization including impurity profiling and degradation chemistry. However, the conformational behavior of drug molecules and their metabolites in the gas phase is poorly understood. Here the gas phase conformational space of drug and drug-like molecules has been investigated as well as the influence of protonation and adduct formation on the conformations of drug metabolite structural isomers. The use of CCSs, measured from IM-MS and molecular modeling information, for the structural identification of drug metabolites has also been critically assessed. Detection of structural isomers of drug metabolites using IM-MS is demonstrated and, in addition, a molecular modeling approach has been developed offering rapid conformational searching and energy assessment of candidate structures which agree with experimental CCSs. Here it is illustrated that isomers must possess markedly dissimilar CCS values for structural differentiation, the existence and extent of CCS differences being ionization state and molecule dependent. The results present that IM-MS and molecular modeling can inform on the identity of drug metabolites and highlight the limitations of this approach in differentiating structural isomers. PMID:26752623

  4. The ejection of triatomic molecular hydrogen ions H3+ produced by the interaction of benzene molecules with ultrafast laser pulses

    NASA Astrophysics Data System (ADS)

    Kaziannis, S.; Liontos, I.; Karras, G.; Corsi, C.; Bellini, M.; Kosmidis, C.

    2009-10-01

    The ejection process of triatomic molecular hydrogen ions produced by the interaction of benzene with ultrafast laser pulses of moderate strong intensity (˜1014 W/cm2) is studied by means of TOF mass spectrometry. The H3+ formation can only take place through the rupture of two C-H bonds and the migration of hydrogen atoms within the molecular structure. The H3+ fragments are released with high kinetic energy (typically 2-8 eV) and at laser intensities ≥1014 W/cm2, well above that required for the double ionization of benzene, suggesting that its formation is taking place within multiply charged parent ions. The relative ejection efficiency of H3+ molecular hydrogen ions with respect to the atomic ones is found to be strongly decreasing as a function of the laser intensity and pulse duration (67-25 fs). It is concluded that the H3+ formation is only feasible within parent molecular precursors of relatively low charged states and before significant elongation of their structure takes place, while the higher multiply charged molecular ions preferentially dissociate into H+ ions. The ejection of H2+ ions is also discussed in comparison to the production of H3+ and H+ ions. Finally, by recording the mass spectra of two deuterium label isotopes of benzene (1,2-C6H4D2, 1,4-C6H4D2) it is verified that the ejection efficiency of some molecular fragments, such as D2H+, DH+, is dependent on the specific position of hydrogen atoms in the molecular skeleton prior dissociation.

  5. Dark electrochemistry and photoelectrochemistry of molecularly doped ion-exchange polymer blends

    SciTech Connect

    Crouch, A.M.; Ordonez, I.; Langford, C.H.; Lawrence, M.F.

    1988-10-20

    Ion-exchange polymer blends have been shown to produce modified electrode surfaces with high affinities for ionic reactants. The main feature of these blends is their spontaneous tendency to segregate into hydrophilic and hydrophobic domains. It is now believed that, when appropriate dye molecules are incorporated into such films and then illuminated, these systems operate under both ionic and dry electronic conduction mechanisms. The dark electrochemical measurements performed on an ion-exchange polymer containing ZnTPPS/sup 4 -/, ZnTPP, ZnPc(OPh)/sub 4/, or CuPcTS/sub 4-/, in contact with a Fe(CN)/sub 6//sup 3-/4-/ redox solution, show that the dye molecules within the film are immobile and that the high ion-exchange capability is maintained. The photoelectrochemical results obtained with the dye-loaded films indicate that electrons may be transferred from the photoexcited dyes to the polymer matrix and transported to the SnO/sub 2/ substrate electrode. The oxidized dye molecules are reduced by accepting electrons from the Fe(CN)/sub 6//sup 4 -/ species. The electronic conduction following charge separation is assumed to be intimately related to the ion-exchange polymer's tendency to segregate into hydrophilic and hydrophobic domains and also the excited-state energetics of the dye. A model which invokes the existence of large distributions of molecular ion states is proposed to explain the conduction of electrons through the hydrophobic domains of the polymer film and a detailed energy level diagram is presented to summarize the overall situation.

  6. Semiconductor-based heterostructure formation using low energy ion beams: Ion beam deposition (IBD) and combined ion and molecular beam deposition (CIMD)

    SciTech Connect

    Herbots, N.; Hellman, O.C.; Cullen, P.A.; Vancauwenberghe, O.

    1988-09-15

    In our previous work, we investigated the use of ion beam deposition (IBD) to grow epitaxial films at temperatures lower than those used in thermal processing (less than 500/sup 0/C). Presently, we have applied IBD to the growth of dense (6.4 x 10/sup 22/ atom/cm/sup 3/) silicon dioxide thin films at 400/sup 0/C. Through these experiments we have found several clues to the microscopic processes leading to the formation of thin film phases by low energy ions. Using Monte-Carlo simulations, we have found that low energy collision cascades in silicon have unique features such as a high probability of relocation events that refill vacancies as they are created. Our results show that the combination of a low defect density in low energy collision cascades with the high mobility of interstitials in covalent materials can be used to athermally generate atomic displacements tha can lead to ordering. These displacements can lead to epitaxial ordering at substrate temperatures below the minimum temperature necessary for molecular beam epitaxy (550/sup 0/C). It can also lead to the formation of high quality silicon dioxide at temperatures well below that of thermal oxidation in silicon (i.e. <850/sup 0/C). A growth model which we derive from these observations provides a fundamental understanding of how atomic collisions can be used to induce epitaxy or compound formation at low temperatures.

  7. Tuning Piezo ion channels to detect molecular-scale movements relevant for fine touch

    PubMed Central

    Poole, Kate; Herget, Regina; Lapatsina, Liudmila; Ngo, Ha-Duong; Lewin, Gary R.

    2014-01-01

    In sensory neurons, mechanotransduction is sensitive, fast and requires mechanosensitive ion channels. Here we develop a new method to directly monitor mechanotransduction at defined regions of the cell-substrate interface. We show that molecular-scale (~13 nm) displacements are sufficient to gate mechanosensitive currents in mouse touch receptors. Using neurons from knockout mice, we show that displacement thresholds increase by one order of magnitude in the absence of stomatin-like protein 3 (STOML3). Piezo1 is the founding member of a class of mammalian stretch-activated ion channels, and we show that STOML3, but not other stomatin-domain proteins, brings the activation threshold for Piezo1 and Piezo2 currents down to ~10 nm. Structure–function experiments localize the Piezo modulatory activity of STOML3 to the stomatin domain, and higher-order scaffolds are a prerequisite for function. STOML3 is the first potent modulator of Piezo channels that tunes the sensitivity of mechanically gated channels to detect molecular-scale stimuli relevant for fine touch. PMID:24662763

  8. Observation of electric-dipole-forbidden infrared transitions in cold molecular ions

    NASA Astrophysics Data System (ADS)

    Germann, Matthias; Tong, Xin; Willitsch, Stefan

    2014-11-01

    Spectroscopic transitions in atoms and molecules that are not allowed within the electric-dipole approximation, but occur because of higher-order terms in the interaction between matter and radiation, are termed dipole-forbidden. These transitions are extremely weak and therefore exhibit very small natural linewidths. Dipole-forbidden optical transitions in atoms form the basis of next-generation atomic clocks and of high-fidelity qubits used in quantum information processors and quantum simulators. In molecules, however, such transitions are much less characterized, reflecting the considerable challenges to address them. Here, we report direct observation of dipole-forbidden, electric-quadrupole-allowed infrared (IR) transitions in a molecular ion. Their detection was enabled by the very long interrogation times of several minutes afforded by the sympathetic cooling of individual quantum-state-selected molecular ions into the nearly perturbation-free environment of a Coulomb crystal. The present work paves the way for new mid-IR frequency standards and precision spectroscopic measurements on single molecules in the IR domain.

  9. Metal ion mediated synthesis of molecularly imprinted polymers targeting tetracyclines in aqueous samples.

    PubMed

    Qu, Guorun; Zheng, Sulian; Liu, Yumin; Xie, Wei; Wu, Aibo; Zhang, Dabing

    2009-10-01

    Molecularly imprinted polymers (MIPs) prepared in water-containing systems are more appropriate as adsorption materials in analyte extraction from biological samples. However, water as a polar solvent involved in the synthesis of MIPs frequently disrupts non-covalent interactions, and causes non-specific binding. In this study Fe(2+) was used as mediator to prepare MIPs, targeting tetracyclines (TCs) of tetracycline (TC), oxytetracycline (OTC) and chlortetracycline (CTC), with TC as template molecule and methacrylic acid (MAA) as functional monomer. The subsequent binding assay indicated that Fe(2+) was responsible for substantially improved specific binding in recognition of TCs by decreasing the non-specific binding. Spectrophotometric analysis suggested the existence of the strong interactions among TC, metal ions and MAA in the mixture of methanol and water. Moreover, mass spectrometric measurements verified that Fe(2+) could bridge between TC and MAA to form a ternary complex of one TC, one Fe(2+) and four MAAs with a mass of 844.857. Furthermore, combined with molecularly imprinted solid-phase extraction (MISPE) for sample pretreatment, HPLC-UV analysis data revealed good performance of the obtained MIPs as adsorbents. The recoveries of TC, OTC and CTC in urine samples were 80.1-91.6%, 78.4-89.3% and 78.2-86.2%, respectively. This research strategy provides an example for preparation of desirable water-compatible MIPs extracting target drugs from aqueous samples by introducing metal ion as mediator into conventional polymerization system. PMID:19726243

  10. Isolation of Ion-Driven Conformations in Diphenylacetylene Molecular Switches Using Cryogenic Infrared Spectroscopy

    NASA Astrophysics Data System (ADS)

    Wolk, Arron B.; Garand, Etienne; Jones, Ian M.; Kamrath, Michael Z.; Hamilton, Rew; Johnson, Mark A.

    2012-06-01

    We report the infrared predissociation spectra of a family of ionic diphenylacetylene molecular switch complexes. The electrosprayed complexes were trapped and cooled in a cryogenic (10K) quadrupole ion trap and tagged with molecular deuterium. The infrared spectra of the vibrationally cold species reveal sharp transitions over a wide energy range (800 - 3800 cm-1), facilitating comparison to harmonic spectra. The evolution of the band pattern upon derivatization of the complexes exposes the signatures of the amide, urea, and carbonyl functionalities, enabling unambiguous identification of the non-covalent interactions that control the secondary structure of the molecule. Complexation with the tetramethylammonium cation reveals a conformation analogous to that of the neutral molecule, while halide ion attachment induces a conformational change similar to that observed earlier in solution. In several cases, both the donor and acceptor groups involved in the multidentate H-bonds are observed, providing a microscopic mechanical picture of the interactions at play. I. Jones, and A. Hamilton, Angew. Chem. Intl. Edit. 50, 4597 (2011).

  11. Molecular force transduction by ion channels – diversity and unifying principles

    PubMed Central

    Sukharev, Sergei; Sachs, Frederick

    2012-01-01

    Summary Cells perceive force through a variety of molecular sensors, of which the mechanosensitive ion channels are the most efficient and act the fastest. These channels apparently evolved to prevent osmotic lysis of the cell as a result of metabolite accumulation and/or external changes in osmolarity. From this simple beginning, nature developed specific mechanosensitive enzymes that allow us to hear, maintain balance, feel touch and regulate many systemic variables, such as blood pressure. For a channel to be mechanosensitive it needs to respond to mechanical stresses by changing its shape between the closed and open states. In that way, forces within the lipid bilayer or within a protein link can do work on the channel and stabilize its state. Ion channels have the highest turnover rates of all enzymes, and they can act as both sensors and effectors, providing the necessary fluxes to relieve osmotic pressure, shift the membrane potential or initiate chemical signaling. In this Commentary, we focus on the common mechanisms by which mechanical forces and the local environment can regulate membrane protein structure, and more specifically, mechanosensitive ion channels. PMID:22797911

  12. Stability and migration of metal ions in G4-wires by molecular dynamics simulations.

    PubMed

    Cavallari, Manuela; Calzolari, Arrigo; Garbesi, Anna; Di Felice, Rosa

    2006-12-28

    We present a molecular dynamics investigation of guanine quadruple helices based on classical force fields. We analyze the dependence of the helical conformation on various compositional factors, such as the length of the G4-wire, as well as the incorporation into the helix channel of alkali ions of different species and in different amounts. In compliance with previous indications, our results suggest that monovalent alkali cations assist the stability of the quadruplex arrangement against disruption on the few nanoseconds time scale in the order of increasing van der Waals radius. Whereas very short G4-wire fragments immediately unfold in the absence of coordinating metal ions or in the presence of tiny ions (e.g., Li+) in agreement with the experimental evidence that empty short guanine quadruplexes are not formed in any synthetic conditions, our simulations show that longer empty helices do not discompose. This finding supports the possibility of producing long G4-wires with different guanine-cation stoichiometries than those routinely known. The classical trajectories allow us to identify different stationary axial sites for the different metal species, which are confirmed by complementary quantum calculations. PMID:17181293

  13. Molecular Dynamics Simulation of the Antiamoebin Ion Channel: Linking Structure and Conductance

    PubMed Central

    Wilson, Michael A.; Wei, Chenyu; Bjelkmar, Pär; Wallace, B.A.; Pohorille, Andrew

    2011-01-01

    Molecular-dynamics simulations were carried out to ascertain which of the potential multimeric forms of the transmembrane peptaibol channel, antiamoebin, is consistent with its measured conductance. Estimates of the conductance obtained through counting ions that cross the channel and by solving the Nernst-Planck equation yield consistent results, indicating that the motion of ions inside the channel can be satisfactorily described as diffusive. The calculated conductance of octameric channels is markedly higher than the conductance measured in single channel recordings, whereas the tetramer appears to be nonconducting. The conductance of the hexamer was estimated to be 115 ± 34 pS and 74 ± 20 pS, at 150 mV and 75 mV, respectively, in satisfactory agreement with the value of 90 pS measured at 75 mV. On this basis, we propose that the antiamoebin channel consists of six monomers. Its pore is large enough to accommodate K+ and Cl− with their first solvation shells intact. The free energy barrier encountered by K+ is only 2.2 kcal/mol whereas Cl− encounters a substantially higher barrier of nearly 5 kcal/mol. This difference makes the channel selective for cations. Ion crossing events are shown to be uncorrelated and follow Poisson statistics. PMID:21575573

  14. Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics

    PubMed Central

    2016-01-01

    We compare the performance of five magnesium (Mg2+) ion models in simulations of an RNA stem loop which has an experimentally determined divalent ion dependent conformational shift. We show that despite their differences in parametrization and resulting van der Waals terms, including differences in the functional form of the nonbonded potential, when the RNA adopts its folded conformation, all models behave similarly across ten independent microsecond length simulations with each ion model. However, when the entire structure ensemble is accounted for, chelation of Mg2+ to RNA is seen in three of the five models, most egregiously and likely artifactual in simulations using a 12-6-4 model for the Lennard-Jones potential. Despite the simple nature of the fixed point-charge and van der Waals sphere models employed, and with the exception of the likely oversampled directed chelation of the 12-6-4 potential models, RNA–Mg2+ interactions via first shell water molecules are surprisingly well described by modern parameters, allowing us to observe the spontaneous conformational shift from Mg2+ free RNA to Mg2+ associated RNA structure in unrestrained molecular dynamics simulations. PMID:27294370

  15. Fragmentation of molecular adsorbates by electron and ion bombardment: methoxy chemistry on Al(111)

    SciTech Connect

    Basu, P.; Chen, J.G.; Ng, L.; Colaianni, M.L.; Yates, J.T.

    1988-08-15

    High-resolution electron-energy-loss spectroscopy (HR)EELS has been used successfully to provide direct spectroscopic evidence regarding details of the molecular fragmentation of methoxy (CH3O) on Al(lll) caused by energetic electron and ion beams. Chemisorbed methoxy on Al(lll) is produced by heating of absorbed CH3OH. Irradiation of CH3O(a) by either energetic (approx 300 eV) electrons or Ar+ ions results in C-O and C-H bond scission with simultaneous formation of Al-O and Al-C bonds. During electron stimulated desorption the CH3O(a) species undergo sequential fragmentation first to CHx groups that are captured by the surface and in the final decay process to adsorbed carbon. C-O bonds in CH3O9a) are depleted preferentially compared to C-H bonds in CHx(a) species. The electron-induced sequential fragmentation of the patent CH3 group (from methoxy) to resultant CHx(a) occurs with an efficiency approx. 3 orders of magnitude greater than the subsequent process of CHx(a)=C(a). Cross sections for various bond scission processes in electron and ion bombardment have been estimated.

  16. Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics.

    PubMed

    Bergonzo, Christina; Hall, Kathleen B; Cheatham, Thomas E

    2016-07-12

    We compare the performance of five magnesium (Mg(2+)) ion models in simulations of an RNA stem loop which has an experimentally determined divalent ion dependent conformational shift. We show that despite their differences in parametrization and resulting van der Waals terms, including differences in the functional form of the nonbonded potential, when the RNA adopts its folded conformation, all models behave similarly across ten independent microsecond length simulations with each ion model. However, when the entire structure ensemble is accounted for, chelation of Mg(2+) to RNA is seen in three of the five models, most egregiously and likely artifactual in simulations using a 12-6-4 model for the Lennard-Jones potential. Despite the simple nature of the fixed point-charge and van der Waals sphere models employed, and with the exception of the likely oversampled directed chelation of the 12-6-4 potential models, RNA-Mg(2+) interactions via first shell water molecules are surprisingly well described by modern parameters, allowing us to observe the spontaneous conformational shift from Mg(2+) free RNA to Mg(2+) associated RNA structure in unrestrained molecular dynamics simulations. PMID:27294370

  17. Improvement of the gas cluster ion beam-(GCIB)-based molecular secondary ion mass spectroscopy (SIMS) depth profile with O2(+) cosputtering.

    PubMed

    Chu, Yi-Hsuan; Liao, Hua-Yang; Lin, Kang-Yi; Chang, Hsun-Yun; Kao, Wei-Lun; Kuo, Ding-Yuan; You, Yun-Wen; Chu, Kuo-Jui; Wu, Chen-Yi; Shyue, Jing-Jong

    2016-04-21

    Over the last decade, cluster ion beams have displayed their capability to analyze organic materials and biological specimens. Compared with atomic ion beams, cluster ion beams non-linearly enhance the sputter yield, suppress damage accumulation and generate high mass fragments during sputtering. These properties allow successful Secondary Ion Mass Spectroscopy (SIMS) analysis of soft materials beyond the static limit. Because the intensity of high mass molecular ions is intrinsically low, enhancing the intensity of these secondary ions while preserving the sample in its original state is the key to highly sensitive molecular depth profiles. In this work, bulk poly(ethylene terephthalate) (PET) was used as a model material and analyzed using Time-of-Flight SIMS (ToF-SIMS) with a pulsed Bi3(2+) primary ion. The optimized hardware of a 10 kV Ar2500(+) Gas Cluster Ion Beam (GCIB) with a low kinetic energy (200-500 V) oxygen ion (O2(+)) as a cosputter beam was employed for generating depth profiles and for examining the effect of beam parameters. The results were then quantitatively analyzed using an established erosion model. It was found that the ion intensity of the PET monomer ([M + H](+)) and its large molecular fragment ([M - C2H4O + H](+)) steadily declined during single GCIB sputtering, with distortion of the distribution information. However, under an optimized GCIB-O2(+) cosputter, the secondary ion intensity quickly reached a steady state and retained >95% intensity with respect to the pristine surface, although the damage cross-section was larger than that of single GCIB sputtering. This improvement was due to the oxidation of molecules and the formation of -OH groups that serve as proton donors to particles emitted from the surface. As a result, the ionization yield was enhanced and damage to the chemical structure was masked. Although O2(+) is known to alter the chemical structure and cause damage accumulation, the concurrently used GCIB could

  18. Iron Oxide Nanoparticle-Micelles (ION-Micelles) for Sensitive (Molecular) Magnetic Particle Imaging and Magnetic Resonance Imaging

    PubMed Central

    Starmans, Lucas W. E.; Burdinski, Dirk; Haex, Nicole P. M.; Moonen, Rik P. M.; Strijkers, Gustav J.; Nicolay, Klaas; Grüll, Holger

    2013-01-01

    Background Iron oxide nanoparticles (IONs) are a promising nanoplatform for contrast-enhanced MRI. Recently, magnetic particle imaging (MPI) was introduced as a new imaging modality, which is able to directly visualize magnetic particles and could serve as a more sensitive and quantitative alternative to MRI. However, MPI requires magnetic particles with specific magnetic properties for optimal use. Current commercially available iron oxide formulations perform suboptimal in MPI, which is triggering research into optimized synthesis strategies. Most synthesis procedures aim at size control of iron oxide nanoparticles rather than control over the magnetic properties. In this study, we report on the synthesis, characterization and application of a novel ION platform for sensitive MPI and MRI. Methods and Results IONs were synthesized using a thermal-decomposition method and subsequently phase-transferred by encapsulation into lipidic micelles (ION-Micelles). Next, the material and magnetic properties of the ION-Micelles were analyzed. Most notably, vibrating sample magnetometry measurements showed that the effective magnetic core size of the IONs is 16 nm. In addition, magnetic particle spectrometry (MPS) measurements were performed. MPS is essentially zero-dimensional MPI and therefore allows to probe the potential of iron oxide formulations for MPI. ION-Micelles induced up to 200 times higher signal in MPS measurements than commercially available iron oxide formulations (Endorem, Resovist and Sinerem) and thus likely allow for significantly more sensitive MPI. In addition, the potential of the ION-Micelle platform for molecular MPI and MRI was showcased by MPS and MRI measurements of fibrin-binding peptide functionalized ION-Micelles (FibPep-ION-Micelles) bound to blood clots. Conclusions The presented data underlines the potential of the ION-Micelle nanoplatform for sensitive (molecular) MPI and warrants further investigation of the FibPep-ION-Micelle platform for

  19. Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields.

    PubMed

    Yoo, Jejoong; Wilson, James; Aksimentiev, Aleksei

    2016-10-01

    Calcium ions (Ca(2+) ) play key roles in various fundamental biological processes such as cell signaling and brain function. Molecular dynamics (MD) simulations have been used to study such interactions, however, the accuracy of the Ca(2+) models provided by the standard MD force fields has not been rigorously tested. Here, we assess the performance of the Ca(2+) models from the most popular classical force fields AMBER and CHARMM by computing the osmotic pressure of model compounds and the free energy of DNA-DNA interactions. In the simulations performed using the two standard models, Ca(2+) ions are seen to form artificial clusters with chloride, acetate, and phosphate species; the osmotic pressure of CaAc2 and CaCl2 solutions is a small fraction of the experimental values for both force fields. Using the standard parameterization of Ca(2+) ions in the simulations of Ca(2+) -mediated DNA-DNA interactions leads to qualitatively wrong outcomes: both AMBER and CHARMM simulations suggest strong inter-DNA attraction whereas, in experiment, DNA molecules repel one another. The artificial attraction of Ca(2+) to DNA phosphate is strong enough to affect the direction of the electric field-driven translocation of DNA through a solid-state nanopore. To address these shortcomings of the standard Ca(2+) model, we introduce a custom model of a hydrated Ca(2+) ion and show that using our model brings the results of the above MD simulations in quantitative agreement with experiment. Our improved model of Ca(2+) can be readily applied to MD simulations of various biomolecular systems, including nucleic acids, proteins and lipid bilayer membranes. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 752-763, 2016. PMID:27144470

  20. Density functional theory and molecular dynamics study of the uranyl ion (UO₂)²⁺.

    PubMed

    Rodríguez-Jeangros, Nicolás; Seminario, Jorge M

    2014-03-01

    The detection of uranium is very important, especially in water and, more importantly, in the form of uranyl ion (UO₂)²⁺, which is one of its most abundant moieties. Here, we report analyses and simulations of uranyl in water using ab initio modified force fields for water with improved parameters and charges of uranyl. We use a TIP4P model, which allows us to obtain accurate water properties such as the boiling point and the second and third shells of water molecules in the radial distribution function thanks to a fictitious charge that corrects the 3-point models by reproducing the exact dipole moment of the water molecule. We also introduced non-bonded interaction parameters for the water-uranyl intermolecular force field. Special care was taken in testing the effect of a range of uranyl charges on the structure of uranyl-water complexes. Atomic charges of the solvated ion in water were obtained using density functional theory (DFT) calculations taking into account the presence of nitrate ions in the solution, forming a neutral ensemble. DFT-based force fields were calculated in such a way that water properties, such as the boiling point or the pair distribution function stand. Finally, molecular dynamics simulations of a water box containing uranyl cations and nitrate anions are performed at room temperature. The three peaks in the oxygen-oxygen radial distribution function for water were found to be kept in the presence of uranyl thanks to the improvement of interaction parameters and charges. Also, we found three shells of water molecules surrounding the uranyl ion instead of two as was previously thought. PMID:24573498

  1. Fluorescent DNAzyme biosensors for metal ions based on catalytic molecular beacons.

    PubMed

    Liu, Juewen; Lu, Yi

    2006-01-01

    In this chapter, methods for designing metal ion sensors using fluorophore- and quencher-labeled DNAzymes are discussed. In contrast to the classical molecular beacon method based on binding, the methods described here utilize catalytic cleavage to release the fluorophore for detection and quantification, making it possible to take advantage of catalytic turnovers for signal amplification. Unlike classical molecular beacons that detect only nucleic acids, catalytic molecular beacons can be applied to different DNAzymes to detect a broad range of analytes. The methods described are based on the finding that almost all known trans-cleaving DNAzymes share a similar structure comprised of a catalytic DNAzyme core flanked by two substrate recognition arms. Using a typical DNAzyme called the "8-17" DNAzyme as an example, the design of highly sensitive and selective Pb2+ sensors is described in detail. The initial design employs a single fluorophore-quencher pair in close proximity, with the fluorophore on the 5'-end of the substrate and the quencher on the 3'-end of the enzyme. Although this sensor is highly sensitive and selective at 4 degrees C, high background fluorescence is observed at higher temperatures. Therefore a new design with an additional quencher attached to the 3'-end of the substrate is employed to suppress background fluorescence. The dual quencher method allows the sensor to perform at ambient temperatures with a high signal-to-noise ratio. PMID:16785634

  2. Metal Oxide Nanosensors Using Polymeric Membranes, Enzymes and Antibody Receptors as Ion and Molecular Recognition Elements

    PubMed Central

    Willander, Magnus; Khun, Kimleang; Ibupoto, Zafar Hussain

    2014-01-01

    The concept of recognition and biofunctionality has attracted increasing interest in the fields of chemistry and material sciences. Advances in the field of nanotechnology for the synthesis of desired metal oxide nanostructures have provided a solid platform for the integration of nanoelectronic devices. These nanoelectronics-based devices have the ability to recognize molecular species of living organisms, and they have created the possibility for advanced chemical sensing functionalities with low limits of detection in the nanomolar range. In this review, various metal oxides, such as ZnO-, CuO-, and NiO-based nanosensors, are described using different methods (receptors) of functionalization for molecular and ion recognition. These functionalized metal oxide surfaces with a specific receptor involve either a complex formation between the receptor and the analyte or an electrostatic interaction during the chemical sensing of analytes. Metal oxide nanostructures are considered revolutionary nanomaterials that have a specific surface for the immobilization of biomolecules with much needed orientation, good conformation and enhanced biological activity which further improve the sensing properties of nanosensors. Metal oxide nanostructures are associated with certain unique optical, electrical and molecular characteristics in addition to unique functionalities and surface charge features which shows attractive platforms for interfacing biorecognition elements with effective transducing properties for signal amplification. There is a great opportunity in the near future for metal oxide nanostructure-based miniaturization and the development of engineering sensor devices. PMID:24841244

  3. Nanojets, electrospray, and ion field evaporation: molecular dynamics simulations and laboratory experiments.

    PubMed

    Luedtke, W D; Landman, Uzi; Chiu, Y-H; Levandier, D J; Dressler, R A; Sok, S; Gordon, M S

    2008-10-01

    The energetics, interfacial properties, instabilities, and fragmentation patterns of electrosprays made from formamide salt solutions are investigated in a mass spectrometric vacuum electrospray experiment and using molecular dynamics (MD) simulations. The electrospray source is operated in a Taylor cone-jet mode, with the nanojet that forms being characterized by high surface-normal electric field strengths in the vicinity of 1 V/nm. Mass-to-charge ratios were determined for both positive and negative currents sprayed from NaI-formamide solutions with solute-solvent mole ratios of 1:8.4 and 1:36.9, and from KI-formamide solutions with mole ratios of 1:41 and 1:83. The molecular dynamics simulations were conducted on isolated 10 nm NaI-formamide droplets at mole ratios of 1:8 and 1:16. The droplet was subjected to a uniform electric field with strengths ranging between 0.5 and 1.5 V/nm. Both the experiments and simulations demonstrate a mixed charge emission regime where field-induced desorption of solvated ions and charged droplets occurs. The macroscopic parameters, such as average mass-to-charge ratio and maximum surface-normal field strengths deduced from the simulations are found to be in good agreement with the experimental work and consistent with electrohydrodynamic theory of cone-jets. The observed mass spectrometric Na (+) and I (-) solvated ion distributions are consistent with a thermal evaporation process, and are correctly reproduced by the simulation after incorporation of the different flight times and unimolecular ion dissociation rates in the analysis. Alignment of formamide dipoles and field-induced reorganization of the positive and negative ionic charges in the interfacial region are both found to contribute to the surface-normal field near the points of charge emission. In the simulations the majority of cluster ions are found to be emitted from the tip of the jet rather than from the neck region next to the Taylor cone. This finding is

  4. Molecular Depth Profiling of Sucrose Films: A Comparative Study of C₆₀n⁺ Ions and Traditional Cs⁺ and O₂⁺ Ions

    SciTech Connect

    Zhu, Zihua; Nachimuthu, Ponnusamy; Lea, Alan S.

    2009-10-15

    Time-of-flight secondary ion mass spectrometry (ToF-SIMS) depth profiling of sucrose thin films were investigated using 10 keV C60+, 20 keV C602+, 30 keV C603+, 250 eV, 500 eV and 1000 eV Cs+ and O2+ as sputtering ions. With C60n+ ions, the molecular ion signal initially decreases, and reaches a steady-state that is about 38-51% of its original intensity, depending on the energy of the C60n+ ions. On the contrary, with Cs+ and O2+ sputtering, molecular ion signals decrease quickly to the noise level, even using low energy (250 eV) sputtering ions. In addition, the sucrose/Si interface by C60+ sputtering is much narrower than that of Cs+ and O2+ sputtering. To understand the mechanisms of sputtering-induced damage by these ions, X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) were used to characterize the bottoms of these sputter craters. XPS data show very little chemical change in the C60+ sputter crater, while considerable amorphous carbon was found in the O2+ and Cs+ sputter craters, indicating extensive decomposition of the sucrose molecules. AFM images show a very flat bottom in the C60+ sputter crater, while the Cs+ and O2+ sputter crater bottoms are significantly rougher than that of the C60+ sputter crater. Based on above data, we developed a simple model to explain different damage mechanisms during sputtering process.

  5. Coulomb crystals in a cryogenic Paul trap for sympathetic cooling of molecular ions and highly charged ions

    NASA Astrophysics Data System (ADS)

    Windberger, A.; Schwarz, M.; Versolato, O. O.; Baumann, T.; Bekker, H.; Schmöger, L.; Hansen, A. K.; Gingell, A. D.; Klosowski, L.; Kristensen, S.; Schmidt, P. O.; Ullrich, J.; Drewsen, M.; Crespo López-Urrutia, J. R.

    2013-03-01

    Electron beam ion traps used for spectroscopy of highly charged ions (HCI) produce a deep trapping potential leading to high temperatures of the stored ions, and thus limiting the achievable spectral resolution. A novel device at the Max-Planck-Institut für Kernphysik, the Cryogenic linear Paul Trap Experiment (CryPTEx), attached to an electron beam ion trap, provides a new experimental platform to overcome these limitations. The trap assembly operates at a temperature of 4 K and offers optical access for quantum manipulation and imaging of the trapped ions. Since forbidden optical transitions in HCI do not support direct laser cooling, sympathetic cooling with Coulomb crystals of singly charged ions such as Be+ or Mg+ will be applied in order to reach the natural linewidth of optical forbidden transitions in HCI of interest. With the added advantage of long ion trapping times resulting from residual gas pressures of H2 at 4 K below 10-15 mbar, CryPTEx has been commissioned in collaboration with the Ion Trap Group in Århus using rovibrationally cooled MgH+ ions. Strong suppression of the black body radiation at the trap center, ion storage times of about 28 hours, and largely enhanced population of the rovibrational ground state were achieved.

  6. Production of NaCa+ molecular ions in the ground state from cold atom-ion mixtures by photoassociation via an intermediate state

    NASA Astrophysics Data System (ADS)

    Gacesa, Marko; Montgomery, John A.; Michels, H. Harvey; Côté, Robin

    2016-07-01

    We present a theoretical analysis of optical pathways for formation of cold ground-state (NaCa) + molecular ions via an intermediate state. The formation schemes are based on ab initio potential energy curves and transition dipole moments calculated using effective-core-potential methods of quantum chemistry. In the proposed approach, starting from a mixture of cold trapped Ca+ ions immersed into an ultracold gas of Na atoms, (NaCa) + molecular ions are photoassociated in the excited E +1Σ electronic state and allowed to spontaneously decay either to the ground electronic state or an intermediate state from which the population is transferred to the ground state via an additional optical excitation. By analyzing all possible pathways, we find that the efficiency of a two-photon scheme, via either the B +1Σ or C +1Σ potential, is sufficient to produce significant quantities of ground-state (NaCa) + molecular ions. A single-step process results in lower formation rates that would require either a high-density sample or a very intense photoassociation laser to be viable.

  7. Molecular Ions and Other Exotic Molecules in Space: A Coordinated Astronomical, Laboratory, and Theoretical Study

    NASA Astrophysics Data System (ADS)

    McCarthy, Michael

    This proposal request funds to continue a laboratory program in close coordination with radio astronomical observations dedicated to the study of highly reactive molecular ions, radicals, and metastable isomers that are thought to be key intermediates in rich interstellar and circumstellar sources. Determining the carriers of strong unidentified lines, such as U617.6 which has recently been observed with the Herschel space satellite, is the type of problem in laboratory astrophysics that our group is particularly adept at, and will be also emphasized in the upcoming grant period. Most new molecular species will be detected using microwave cavity rotational spectroscopy, followed either by microwave/millimeter-wave double resonance or millimeter/THz absorption to better characterize the rotational spectra in bands where Herschel and SOFIA operate. Using this combined approach, the rotational spectra of a number of ions of astronomical interest such as the cis- and trans isomers of HOSO+, H2NCO+, HNCOH+, H2CCHCNH+, C3N-, and NCO- have recently been detected in our laboratory, as have metastable isomers or derivatives of isocyanic acid, HNCO. As a result of this work, HOCN, HSCN, TiO2, and several molecular anions have been identified for the first time in space in the span of only a few years. Emphasis in the upcoming grant period will be placed on the detection of diatomic and small polyatomic ions such as SiH+, SiN-, CN+, NCS-, etc., other prototypical ions, including protonated benzene C6H7+, and silicon- and phosphorus-bearing species of astronomical interest. On the assumption that U617.6 is the fundamental b-type transition of a small polyatomic molecule, systematic searches for species of the form XOH, where X is likely either an atom or diatomic, will be given high priority because slightly bent species with this functional group (e.g., NNOH+, SiOH, etc.) possess an A rotational constants of about the right magnitude. Instrumental refinement will also be

  8. Precision spectroscopy of the molecular ion HD{sup +}: Control of Zeeman shifts

    SciTech Connect

    Bakalov, Dimitar; Korobov, Vladimir; Schiller, Stephan

    2010-11-15

    Precision spectroscopy on cold molecules can potentially enable novel tests of fundamental laws of physics and alternative determination of some fundamental constants. Realizing this potential requires a thorough understanding of the systematic effects that shift the energy levels of molecules. We have performed a complete ab initio calculation of the magnetic field effects for a particular system, the molecular hydrogen ion HD{sup +}. Different spectroscopic schemes have been considered, and several transitions, all accessible by modern radiation sources and exhibiting well controllable or negligible Zeeman shift, have been identified. Thus, HD{sup +} is a candidate for the determination of the ratio of electron-to-nuclear reduced mass, and for tests of its time independence.

  9. Molecular conformation changes of PET films under high-energy Ar ion bombardment

    NASA Astrophysics Data System (ADS)

    Liu, Changlong; Jin, Yunfan; Zhu, Zhiyong; Sun, Youmei; Hou, Mingdong; Wang, Zhiguang; Wang, Yanbin; Zhang, Chonghong; Chen, Xiaoxi; Liu, Jie; Li, Baoquan

    2000-06-01

    Investigation of the surface modification in molecular structure of semicrystalline polyethylene terephthalate (PET) films induced by Ar ion bombardment is presented. The PET samples are analysed by using Fourier transform infrared spectroscopy (FTIR), X-ray diffractometer (XRD), and X-ray photoelectron spectroscopy (XPS). A significant loss of crystallinity is observed, which is related to the configuration transformation of ethylene glycol residue from the trans into the gauche. Chain scissions are observed at the para position of di-substituted benzene rings, -CO bonds and C-O bonds. The C-O bonds are destroyed more selectively than -CO bonds. The benzene ring structures show only small change under irradiation and do not participate in degradation process. Extra CC bonds and alkyne end groups are created above a critical dose of 4.0 MGy. The results are briefly discussed.

  10. Electron-impact dissociation cross sections of vibrationally excited He_{2}^{+} molecular ion

    NASA Astrophysics Data System (ADS)

    Celiberto, R.; Baluja, K. L.; Janev, R. K.; Laporta, V.

    2016-01-01

    Electron-impact cross sections for the dissociation process of vibrationally excited He2+ molecular ion, as a function of the incident electron energy are calculated for the dissociative transition \\text{X}{{ }2}Σu+\\to \\text{A}{{ }2}Σg+ by using the R-matrix method in the adiabatic-nuclei approximation. The potential energy curves for the involved electronic states and transition dipole moment, also calculated with the R-matrix method, were found to be in good agreement with the results reported in literature. The vibrationally resolved dissociation cross sections of He2+(v) exhibit a resonant structure around 7 eV. The observed strong variation of the magnitude of this structure with the vibrational level is explained in terms of the overlap of initial and final (continuum) state wave functions in the Franck–Condon region.

  11. The composition of heavy molecular ions inside the ionopause of Comet Halley

    NASA Technical Reports Server (NTRS)

    Mitchell, David L.; Lin, R. P.; Anderson, K. A.; Carlson, C. W.; Curtis, D. W.; Korth, A.; Reme, H.; Sauvaud, J. A.; Duston, C.; Mendis, D. A.

    1989-01-01

    The RPA2-PICCA instrument aboard the Giotto spacecraft obtained 10-210 amu mass spectral of cold thermal molecular ions in the coma of Comet Halley. The dissociation products of the long chain formaldehyde polymer polyoxymethylene (POM) have recently been proposed as the dominant complex molecules in the coma of Comet Halley; however, POM alone cannot account for all of the features of the high resolution spectrum. An important component of the dust at Comet Halley is particles highly enriched in carbon, hydrogen, oxygen, and nitrogen relative to the composition of carbonaceous chondrites. Since this dust could be a source for the heavy molecules observed by PICCA, a search was conducted for other chemical species by determining all the molecules with mass between 20 and 120 amu which can be made from the relatively abundant C, H, O, and N, without regard to chemical structure.

  12. Effect of Molecular Weight on the Ion Transport Mechanism in Polymerized Ionic Liquids

    SciTech Connect

    Fan, Fei; Wang, Weiyu; Holt, Adam P; Feng, Hongbo; Uhrig, David; Lu, Xinyi; Hong, Tao; Wang, Yangyang; Kang, Nam-Goo; Mays, Jimmy; Sokolov, Alexei P

    2016-01-01

    The unique properties of ionic liquids (ILs) have made them promising candidates for electrochemical applications. Polymerization of the corresponding ILs results in a new class of materials called polymerized ionic liquids (PolyILs). Though PolyILs offer the possibility to combine the high conductivity of ILs and the high mechanical strength of polymers, their conductivities are typically much lower than that of the corresponding small molecule ILs. In the present work, seven PolyILs were synthesized having degrees of polymerization ranging from 1 to 333, corresponding to molecular weights (MW) from 482 to 160 400 g/mol. Depolarized dynamic light scattering, broadband dielectric spectroscopy, rheology, and differential scanning calorimetry were employed to systematically study the influence of MW on the mechanism of ionic transport and segmental dynamics in these materials. The modified Walden plot analysis reveals that the ion conductivity transforms from being closely coupled with structural relaxation to being strongly decoupled from it as MW increases.

  13. Broadband Velocity Modulation Spectroscopy of Molecular Ions for Use in the Jila Electron Edm Experiment

    NASA Astrophysics Data System (ADS)

    Gresh, Daniel N.; Cossel, Kevin C.; Cornell, Eric A.; Ye, Jun

    2013-06-01

    The JILA electron electric dipole moment (eEDM) experiment will use a low-lying, metastable ^3Δ_1 state in trapped molecular ions of HfF^+ or ThF^+. Prior to this work, the low-lying states of these molecules had been investigated by PFI-ZEKE spectroscopy. However, there were no detailed studies of the electronic structure. The recently developed technique of frequency comb velocity modulation spectroscopy (VMS) provides broad-bandwidth, high-resolution, ion-sensitive spectroscopy, allowing the acquisition of 150 cm^{-1} of continuous spectra in 30 minutes over 1500 simultaneous channels. By supplementing this technique with cw-laser VMS, we have investigated the electronic structure of HfF^+ in the frequency range of 9950 to 14600 cm^{-1}, accurately fitting and assigning 16 rovibronic transitions involving 8 different electronic states including the X^1Σ^+ and a^3Δ_1 states. In addition, an observed ^3Π_{0+} state with coupling to both the X and a states has been used in the actual eEDM experiment to coherently transfer population from the rovibronic ground state of HfF^+ to the eEDM science state. Furthermore, we report on current efforts of applying frequency comb VMS at 700 - 900 nm to the study of ThF^+, which has a lower energy ^3Δ_1 state and a greater effective electric field, and will provide increased sensitivity for a measurement of the eEDM. A. E. Leanhardt et. al., Journal of Molecular Spectroscopy 270, 1-25 (2011). B. J. Barker, I. O. Antonov, M. C. Heaven, K. A. Peterson, Journal of Chemical Physics 136, 104305 (2012). L. C. Sinclair, K. C. Cossel, T. Coffey, J. Ye, E. A. Cornell, Physical Review Letters 107, 093002 (2011). K.C. Cossel et. al., Chemical Physics Letters 546, 1-11 (2012).

  14. Molecular Heterogeneity of Ewing Sarcoma as Detected by Ion Torrent Sequencing

    PubMed Central

    Zhang, Nana; Liu, Haijing; Yue, Guanjun; Zhang, Yan; You, Jiangfeng; Wang, Hua

    2016-01-01

    Ewing sarcoma (ES) is the second most common malignant bone and soft tissue tumor in children and adolescents. Despite advances in comprehensive treatment, patients with ES metastases still suffer poor outcomes, thus, emphasizing the need for detailed genetic profiles of ES patients to identify suitable molecular biomarkers for improved prognosis and development of effective and targeted therapies. In this study, the next generation sequencing Ion AmpliSeq™ Cancer Hotspot Panel v2 was used to identify cancer-related gene mutations in the tissue samples from 20 ES patients. This platform targeted 207 amplicons of 2800 loci in 50 cancer-related genes. Among the 20 tissue specimens, 62 nonsynonymous hotspot mutations were identified in 26 cancer-related genes, revealing the molecular heterogeneity of ES. Among these, five novel mutations in cancer-related genes (KDR, STK11, MLH1, KRAS, and PTPN11) were detected in ES, and these mutations were confirmed with traditional Sanger sequencing. ES patients with KDR, STK11, and MLH1 mutations had higher Ki-67 proliferation indices than the ES patients lacking such mutations. Notably, more than half of the ES patients harbored one or two possible ‘druggable’ mutations that have been previously linked to a clinical cancer treatment option. Our results provided the foundation to not only elucidate possible mechanisms involved in ES pathogenesis but also indicated the utility of Ion Torrent sequencing as a sensitive and cost-effective tool to screen key oncogenes and tumor suppressors in order to develop personalized therapy for ES patients. PMID:27077911

  15. Inner-shell photoexcitations as probes of the molecular ions CH+, OH+, and SiH+: Measurements and theory

    NASA Astrophysics Data System (ADS)

    Mosnier, J.-P.; Kennedy, E. T.; van Kampen, P.; Cubaynes, D.; Guilbaud, S.; Sisourat, N.; Puglisi, A.; Carniato, S.; Bizau, J.-M.

    2016-06-01

    Spectral probes for the CH+, OH+, and SiH+ hydride molecular ions that play key roles in astrophysics and plasma processes are presented. The merged-beam technique at the SOLEIL synchrotron was used to record the photoionization (ion yield) spectra of CH+, OH+, and SiH+ and that of their parent atomic ions, in the K -shell and L -shell regions, respectively. Energies and oscillator strengths for the K α (CH+ and OH+) and L α (SiH+) transitions were determined from the spectra. Ab initio calculations interpret the experimental data in terms of contributions from ground and excited valence electronic states.

  16. Molecular Dynamics Simulation of Ion Solvation in Polymer Melts: Effects of Dielectric Inhomogeneity and Chain Connectivity on Solvation Energy of Ions

    NASA Astrophysics Data System (ADS)

    Liu, Lijun; Nakamura, Issei

    We study the ion solvation in block copolymer melts and polymer blends using molecular dynamics simulations. In our simulations, polymers are formed through the connection of beads that provide the dielectric response. Thus, we highlight the effect of the dielectric contrast between different species on the solvation energy of ions. We demonstrate the local enrichment of higher-dielectric components near ions, which corresponds well with the result of mean-field theories. Moreover, the chain connectivity significantly affects the reorientation of molecular dipoles in response to the electrostatic field from ions. Thus, we illustrate the marked difference in the solvation energy between the block copolymer and polymer blend. Importantly, the solvation energy substantially depends on the chain length of the polymers, in stark contrast to the Born solvation energy. We also show that our simulation results exhibit striking similarity to the result of the recent self-consistent mean field theories. However, for strongly correlated dipoles and ions, our simulations provide qualitatively opposite behaviors to these results, suggesting further development of the theoretical frameworks. This work was supported by the National Natural Science Foundation of China (21474112 and 21404103). We are grateful to the Computing Center of Jilin Province for essential support.

  17. Ion and molecule sensors using molecular recognition in luminescent, conductive polymers. FY 1997 year-end progress report

    SciTech Connect

    Wasielewski, M.R.

    1997-01-01

    'The purpose of this project is to use molecular recognition strategies to develop sensor technology based on luminescent, conductive polymers that contain sites for binding specific molecules or ions in the presence of related molecules or ions. Selective binding of a particular molecule or ion of interest to these polymers will result in a large change in their luminescence and/or conductivity, which can be used to both qualitatively and quantitatively sense the presence of the bound molecules or ions. The main thrusts and accomplishments in the first year of this project involve developing polymer syntheses that yield conjugated polymers to which a wide variety of ligands for metal ion binding can be readily incorporated.'

  18. A combined electron-ion spectrometer for studying complete kinematics of molecular dissociation upon shell selective ionization

    SciTech Connect

    Saha, K.; Banerjee, S. B.; Bapat, B.

    2013-07-15

    A combined electron-ion spectrometer has been built to study dissociation kinematics of molecular ions upon various electronic decay processes ensuing from ionization of neutral molecules. The apparatus can be used with various ionization agents. Ion time-of-flight (ToF) spectra arising from various electronic decay processes are acquired by triggering the ToF measurement in coincidence with energy analyzed electrons. The design and the performance of the spectrometer in a photoionization experiment is presented in detail. Electron spectra and ion time of flight spectra resulting from valence and 2p{sub 1/2} ionization of Argon and those from valence ionization of CO are presented to demonstrate the capability of the instrument. The fragment ion spectra show remarkable differences (both kinematic and cross sectional) dependent on the energy of the ejected electron, corresponding to various electron loss and decay mechanisms in dissociative photoionization of molecules.

  19. A molecular dynamics study of phase transition in strongly coupled pair-ion plasmas

    SciTech Connect

    Baruah, Swati; Ganesh, R.; Avinash, K.

    2015-08-15

    Existence of phase transition in strongly coupled pair-ion plasmas with soft core is investigated. Extensive Molecular Dynamics (MD) simulations are performed in the canonical ensemble, for such plasmas, at different temperatures, to analyze phase stability. Our studies show interesting phase co-existence between liquid-like and vapor-like phases. The different phases are identified by calculating the ensemble averaged density. This and the corresponding critical properties are calculated directly from MD simulation. The critical temperature of vapor-liquid coexistence is obtained, and the corresponding critical value of density is also estimated for different sizes of the soft core. We have used a novel method that allows the location of phase coexistence through a constant density simulation in which the temperature is changed in a single time-step (quenching) in order to place the system in a thermodynamically and mechanically unstable state, resulting in spontaneous separation of two coexisting phases. The results obtained from this temperature quench MD method also show the coexistence of vapor-liquid phase in pair-ion plasmas. The critical exponents obtained directly from MD simulation are found to be in close agreement with the values predicted by a mean-field theory.

  20. Molecular Dynamics simulation of Ru flattening by Gas Cluster Ion Beam

    NASA Astrophysics Data System (ADS)

    Matsukuma, Masaaki; Matsuzaki, Kazuyoshi; Inaba, Kenji; Miura, Ryuji; Suzuki, Ai; Hatakeyama, Nozomu; Miyamoto, Akira

    2014-10-01

    Noble metals such as platinum or ruthenium have been hardly used in the semiconductor devices in spite of their physical and electrical properties, because they were hard to process. High energy monomer ion beams which can cut hard materials may induce structural damages. A gas cluster ion beam (GCIB) consists of a few thousands of atoms or molecules and is accelerated up to several tens keV. GCIB is able to realize localized high energy deposition with low energy per components in the cluster. This means that each component in clusters cannot have enough energy to react with surface. On the other hand, the clusters with tens keV of kinetic energy may make a high reactive field at the hypocenter areas. In consequence it is expected that the GCIB irradiation should achieve the metal processing with low damage. Recently flattening of Ru thin films using GCIB is reported. We conducted molecular dynamics simulation of GCIB incident to Ru surface with the in-house interatomic potential models obtained based on the quantum chemical calculations and found that the internal degree of freedom of a cluster played important roles during the GCIB bombardment.

  1. Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields

    USGS Publications Warehouse

    Lee, M.W.; Meuwly, M.

    2013-01-01

    The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.

  2. Molecular Dynamics Modeling of Ion Adsorption to the Basal Surfaces of Kaolinite

    SciTech Connect

    Vasconcelos, Igor F.; Bunker, Bruce A.; Cygan, Randall T.

    2008-06-06

    Molecular dynamics simulation is used to study the mechanisms involved in the adsorption of various ions to the basal surfaces of kaolinite. Analysis of simulation data indicates that cations and anions adsorb preferably on the siloxane and gibbsite surfaces of kaolinite, respectively. Strong inner-sphere adsorption of chlorine at aluminum vacancies on the gibbsite surface and the occurrence of chlorine-driven inner-sphere adsorption of cesium and sodium on the gibbsite surface for high ionic strengths are observed. Cesium ions form strong inner-sphere complexes at ditrigonal cavities on the siloxane surface. Outer-sphere cesium is highly mobile and only weak adsorption may occur. A small amount of sodium adsorbs on the siloxane surface as inner-sphere complexes at less clearly defined sites. Like cesium, sodium only forms very weak outer-sphere complexes on this surface. Inner-sphere complexes of cadmium and lead do not occur on either surface. Relatively strong outer-sphere cadmium and lead complexes are present on the siloxane surface at ditrigonal cavities.

  3. Ultrafast spectroscopy of the aqueous chloride ion studied by quantum molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Borgis, Daniel; Staib, Arnulf

    1996-11-01

    The dynamics of the photodetachment of an electron from a chloride ion in water induced by excitation of the lowest charge-transfer-to-solvent state is explored by using quantum molecular dynamics simulations. The ejected electron is described in terms of floating Gaussian orbitals, and solvent electronic polarization effects are accounted for in a fully self-consistent way. The simulation results point to a two-step photodissociation mechanism: the formation of a metastable electron - atom pair on a subpicosecond time-scale followed on a picosecond time-scale by the competition between two different reaction channels, (i) a diffusive barrier-impeded dissociation of the pair, yielding a solvated halogen atom and a free electron, and (ii) a non-radiative quantum recombination, eventually leading to the chloride ion in its ground state. The computed transient absorption spectra are compatible with the experimental data either at early times during the formation of the electron - atom pair or at longer times when dissociation - recombination occurs.

  4. Novel Ion-Exchange Coagulants Remove More Low Molecular Weight Organics than Traditional Coagulants.

    PubMed

    Zhao, Huazhang; Wang, Lei; Hanigan, David; Westerhoff, Paul; Ni, Jinren

    2016-04-01

    Low molecular weight (MW) charged organic matter is poorly removed by conventional coagulants but contributes to disinfection byproduct formation during chlorination of drinking waters. We hypothesized that CIEX, a new Al-based hybrid coagulant with ion-exchange functional groups, would be new mechanistic approach to remove low MW organic matter during coagulation and would perform better than polyaluminum chloride (PACl) or metal-salt based coagulants. We measured coagulation performance using dissolved organic carbon (DOC) in a high hardness surface water. CIEX achieved excellent turbidity removal and removed 20% to 46% more DOC than FeCl3, Al2(SO4)3, or PACl, depending on dose. The improved DOC removal was attributable to better removal of low MW organic matter (<2 kDa). We further studied removal mechanisms in a model water containing a low MW organic acid (salicylic acid (SA)). CIEX achieved high removal of organic acids (>90% of SA) independent of pH, whereas removal by metal salts was lower (<15%) and was strongly pH dependent. CIEX ion-exchange capability is facilitated by its covalently bound quaternary ammonium group, which conventional coagulants lack. Plus, unlike other cationic polymers that react with chloramines to form N-nitrosodimethylamine (NDMA), CIEX has a low molar yield (9.3 × 10(-7) mol NDMA per mol CIEX-N). PMID:26974542

  5. Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields.

    PubMed

    Lee, Myung Won; Meuwly, Markus

    2013-12-14

    The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories. PMID:24170171

  6. Conversion of an atomic to a molecular argon ion and low pressure argon relaxation

    NASA Astrophysics Data System (ADS)

    M, N. Stankov; A, P. Jovanović; V, Lj Marković; S, N. Stamenković

    2016-01-01

    The dominant process in relaxation of DC glow discharge between two plane parallel electrodes in argon at pressure 200 Pa is analyzed by measuring the breakdown time delay and by analytical and numerical models. By using the approximate analytical model it is found that the relaxation in a range from 20 to 60 ms in afterglow is dominated by ions, produced by atomic-to-molecular conversion of Ar+ ions in the first several milliseconds after the cessation of the discharge. This conversion is confirmed by the presence of double-Gaussian distribution for the formative time delay, as well as conversion maxima in a set of memory curves measured in different conditions. Finally, the numerical one-dimensional (1D) model for determining the number densities of dominant particles in stationary DC glow discharge and two-dimensional (2D) model for the relaxation are used to confirm the previous assumptions and to determine the corresponding collision and transport coefficients of dominant species and processes. Project supported by the Ministry of Education, Science and Technological Development of the Republic of Serbia (Grant No. ON171025).

  7. Exploring ion induced folding of a single-stranded DNA oligomer from molecular simulation studies.

    PubMed

    Chakraborty, Kaushik; Khatua, Prabir; Bandyopadhyay, Sanjoy

    2016-06-21

    One crucial issue in DNA hydration is the effect of salts on its conformational features. This has relevance in biology as cations present in the cellular environment shield the negative charges on the DNA backbone, thereby reducing the repulsive force between them. By screening the negative charges along the backbone, cations stabilize the folded structure of DNA. To study the effect of the added salt on single-stranded DNA (ss-DNA) conformations, we have performed room temperature molecular dynamics simulations of an aqueous solution containing the ss-DNA dodecamer with the 5'-CGCGAATTCGCG-3' sequence in the presence of 0.2, 0.5, and 0.8 M NaCl. Our calculations reveal that in the presence of the salt, the DNA molecule forms more collapsed coil-like conformations due to the screening of negative charges along the backbone. Additionally, we demonstrated that the formation of an octahedral inner-sphere complex by the strongly bound ion plays an important role in the stabilization of such folded conformation of DNA. Importantly, it is found that ion-DNA interactions can also explain the formation of non-sequential base stackings with longer lifetimes. Such non-sequential base stackings further stabilize the collapsed coil-like folded form of the DNA oligomer. PMID:27241311

  8. Molecular-dynamics simulation of the effect of ions on a liquid-liquid interface for a partially miscible mixture

    NASA Astrophysics Data System (ADS)

    Wardle, Kent E.; Carlson, Eric; Henderson, Douglas; Rowley, Richard L.

    2004-04-01

    Molecular-dynamics simulations were performed to model the effect of added salt ions on the liquid-liquid interface in a partially miscible system. Simulations of the interface between saturated phases of a model 1-hexanol+water system show a bilayer structure of 1-hexanol molecules at the interface with -OH heads of the first layer directed into the water phase and the opposite orientation for the second layer. The alignment of the polar -OH groups at the interface stabilizes a charge separation of sodium and chloride ions when salt is introduced into the aqueous phase, producing an electrical double layer. Chloride ions aggregate nearer the interface and sodium ions move toward the bulk water phase, consistent with the explanation that the -OH alignment presents a region of partial positive charges to which the hydrated chloride atoms are attracted. Ions near the interface were found to be less solvated than those in the bulk phase. An electric field was also applied to drive ions through the interface. Ions crossing the interface tended to shed water molecules as they entered the hexanol bilayer, leaving a trail of water molecules. Stabilization and facilitated transport of the ion by interactions with the second layer of hexanol molecules appeared to be an important step in the mechanism of sodium ion transport.

  9. Shallow junction characteristics due to low temperature BGe molecular ion implantation into silicon

    NASA Astrophysics Data System (ADS)

    Liang, J. H.; Wu, C. H.

    2014-08-01

    In this study, shallow junction characteristics produced by implanting 2 × 1015 cm-2 77 keV BGe molecular ions into n-type <1 0 0> silicon wafers at liquid nitrogen temperature (LT) and room temperature (RT) were investigated. Post-annealing methods employed consisted of furnace annealing (FA) at 550 °C for 0.5, 1, 2, and 3 h and rapid thermal annealing (RTA) at 1050 °C for 25 s. In particular, one-step (FA) and two-step (FA + RTA) post-annealing treatments were conducted. The shallow junction characteristics that were examined included junction depth, sheet resistance, crystalline recovery, and damage microstructure, and were measured using secondary ion mass spectrometry (SIMS), a four-point probe, Raman scattering spectroscopy (RSS), and cross-sectional transmission electron microscopy (XTEM), respectively. The as-implanted results revealed that the LT specimen retains a greater amount of implantation damage than the RT one does due to the occurrence of less in situ annealing in the former during ion implantation. However, the as-annealed results indicated that the shallow junction characteristics of the LT specimens are superior to those of the RT ones when annealing time in FA is greater than 1 h, which is caused by a greater solid phase epitaxial growth (SPEG) rate in the former to anneal out more damage during annealing. Notably, an annealing time of 3 h in FA is needed in order to achieve optimal crystalline recovery and electrical activation in both the one- and two-step post-annealing treatments under investigation. The same holds for both the LT and RT implantations.

  10. Role of ion-pair states in the predissociation dynamics of Rydberg states of molecular iodine.

    PubMed

    von Vangerow, J; Bogomolov, A S; Dozmorov, N V; Schomas, D; Stienkemeier, F; Baklanov, A V; Mudrich, M

    2016-07-28

    Using femtosecond pump-probe ion imaging spectroscopy, we establish the key role of I(+) + I(-) ion-pair (IP) states in the predissociation dynamics of molecular iodine I2 excited to Rydberg states. Two-photon excitation of Rydberg states lying above the lowest IP state dissociation threshold (1st tier) is found to be followed by direct parallel transitions into IP states of the 1st tier asymptotically correlating to a pair of I ions in their lowest states I(+)((3)P2) + I(-)((1)S0), of the 2nd tier correlating to I(+)((3)P0) + I(-)((1)S0), and of the 3rd tier correlating to I(+)((1)D2) + I(-)((1)S0). Predissociation via the 1st tier proceeds presumably with a delay of 1.6-1.7 ps which is close to the vibrational period in the 3rd tier state (3rd tier-mediated process). The 2nd tier IP state is concluded to be the main precursor for predissociation via lower lying Rydberg states proceeding with a characteristic time of 7-8 ps and giving rise to Rydberg atoms I(5s(2)5p(4)6s(1)). The channel generating I((2)P3/2) + I((2)P1/2) atoms with total kinetic energy corresponding to one-photon excitation is found to proceed via a pump - dump mechanism with dramatic change of angular anisotropy of this channel as compared with earlier nanosecond experiments. PMID:27353150

  11. Jet Cooled Laser Induced Fluorescence Spectroscopy of FCH2CH2O and Other Photo-Fragments of XCH2CH2ONO (X=F, Cl, Br, Oh)

    NASA Astrophysics Data System (ADS)

    Chhantyal-Pun, Rabi; Chen, Ming-Wei; Miller, Terry A.

    2011-06-01

    HOCH2CH2O is one of the prototypical hydroxyalkoxy intermediates formed in the OH mediated oxidation of olefins in the atmosphere. Specifically, HOCH2CH2O is produced from NO assisted reduction of HOCH2CH2OO which in turn is formed by the OH mediated oxidation of ethene in the atmosphere. Halogen substituted ethoxy can be a model to study the hydroxy substituted ethoxy. Our group has successfully studied different primary, secondary and unsaturated alkoxy radicals using Laser Induced Fluorescence technique (LIF) coupled with supersonic free jet expansion in the past. In this talk we will present the jet cooled LIF spectrum of FCH2CH2O. FCH2CH2O was produced in the jet by 351nm photodissociation of FCH2CH2ONO. Aided by ab inito calculations and past experiments, we were able to assign our spectrum to different conformers of FCH2CH2O based on the G(±120°) and T(O°) orientations of the OCCF dihedral angle. Besides FCH2CH2O, we also found transitions belonging to HCHO and CH2CHO from FCH2CH2ONO photodissociation. HCHO and CH2CHO were also found in Cl, Br and OH substituted precursors.

  12. Molecular harmonic extension and enhancement from H2 + ions in the presence of spatially inhomogeneous fields

    NASA Astrophysics Data System (ADS)

    Feng, Liqiang

    2015-11-01

    Molecular high-order harmonic generation from the H2 + ion driven by spatial inhomogeneous fields consisting of the chirped pulse and a terahertz pulse has been theoretically investigated by numerically solving the non-Born-Oppenheimer time-dependent Schrödinger equation. It shows that with the introduction of the chirp as well as the spatial inhomogeneity of the pulse, not only the harmonic cutoff is remarkably extended, but also the single short quantum path is selected to contribute to the harmonic spectra. Moreover, through investigation the effects of the laser and the molecular parameters on the inhomogeneous harmonic generation, we found 1.92- and 3.3-dB enhanced fields for the chirp-free and chirped inhomogeneous pulses, respectively. Isotopic effect shows that intense harmonics can be generated from the lighter molecule. Furthermore, with the enhancement of the initial vibrational state and by properly adding a terahertz controlling pulse, the harmonic yield is enhanced by almost five orders of magnitude compared with the initial single chirped case. As a result, a 362-eV supercontinuum (which corresponds to a 4.0-dB laser field enhancement) with five orders of magnitude improvement is obtained. Finally, by properly superposing the harmonics, a series of intense extreme ultraviolet pulses with durations from 22 to 52 as can be produced.

  13. Dissociation and ionization in capture of antiprotons by the hydrogen molecular ion

    NASA Astrophysics Data System (ADS)

    Cohen, James S.

    2005-05-01

    Antiprotonic atoms and anti-hydrogen are hot areas of current experimental research. Cross sections for antiproton capture will soon be measured directly for the first time by the ASACUSA collaboration at the CERN antiproton decelerator and trap. In the present work [1], cross sections and initial quantum number distributions are calculated for capture of the antiproton (p) and the negative muon (^-) by the hydrogen molecular ion H2^+ using the fermion molecular dynamics (FMD) method. The capture of p is found to be almost entirely adiabatic, occurring via target dissociation without ionization, but nonadiabatic effects are found to play a significant role in the capture of ^-, especially at the higher capture energies. Generally good agreement is obtained with the recent adiabatic classical-trajectory Monte Carlo (CTMC-a) calculation of Sakimoto [2]. The capture properties of H2^+ are shown to be completely different from those previously calculated for both the H atom and neutral H2 molecule. Proposed experiments [3] on p capture by H, H2 and H2^+, at the same relative collision energies, will provide a major test of our theoretical understanding [4].[1] J.S. Cohen, J. Phys. B (to be published).[2] K. Sakimoto, J. Phys. B 37, 2255 (2004).[3] Y. Yamazaki et al., Nucl. Instrum. Methods B 154, 174 (1999); 214, 196 (2004); Hyperfine Interact. 138, 141 (2001).[4] J.S. Cohen, Rep. Prog. Phys. 67, 1769 (2004).

  14. A recoil ion momentum spectrometer for molecular and atomic fragmentation studies.

    PubMed

    Khan, Arnab; Tribedi, Lokesh C; Misra, Deepankar

    2015-04-01

    We report the development and performance studies of a newly built recoil ion momentum spectrometer for the study of atomic and molecular fragmentation dynamics in gas phase upon the impact of charged particles and photons. The present design is a two-stage Wiley-McLaren type spectrometer which satisfies both time and velocity focusing conditions and is capable of measuring singly charged ionic fragments up-to 13 eV in all directions. An electrostatic lens has been introduced in order to achieve velocity imaging. Effects of the lens on time-of-flight as well as on the position have been investigated in detail, both, by simulation and in experiment. We have used 120 keV proton beam on molecular nitrogen gas target. Complete momentum distributions and kinetic energy release distributions have been derived from the measured position and time-of-flight spectra. Along with this, the kinetic energy release spectra of fragmentation of doubly ionized nitrogen molecule upon various projectile impacts are presented. PMID:25933839

  15. Progress of a new instrument to study molecular dynamics of interstellar ion-neutral reactions

    NASA Astrophysics Data System (ADS)

    Perera, Manori; Roenitz, Kevin; Lamm, Ben; Rudd, Lydia; Justl, Andrew; Landeweer, Steven; Roadman, Danny; Koscielniak, Justyna; Sonnenberger, Andrew

    2016-06-01

    Astrochemistry, a relatively young field of research, addresses a gap in our understanding of molecular evolution in space. With many space missions gathering data, the number of unresolved spectral lines is growing rapidly. Each year there are about three new molecules that are identified in the interstellar medium (ISM). However, our understanding of molecular processes, branching ratios, and rates are at a beginner level. For instance, we do not yet understand the chemical processes associated with the creation and evolution of even the most basic prebiotic molecules such as water and methanol in space. One of the important steps toward understanding the chemistry of the ISM is to identify, through laboratory and theoretical work, a list of potential target molecules that are likely to exist in the ISM. This work describes experimental progress towards building a spectrometer that is able to produce complex cold ions that will react with cooled neutral molecules under conditions similar to those in space. I plan to present the instrumental progress and how astronomical reaction dynamic needs will be met using the instrument, and the present status of the instrument and measurements in my lab.

  16. A recoil ion momentum spectrometer for molecular and atomic fragmentation studies

    SciTech Connect

    Khan, Arnab; Tribedi, Lokesh C.; Misra, Deepankar

    2015-04-15

    We report the development and performance studies of a newly built recoil ion momentum spectrometer for the study of atomic and molecular fragmentation dynamics in gas phase upon the impact of charged particles and photons. The present design is a two-stage Wiley-McLaren type spectrometer which satisfies both time and velocity focusing conditions and is capable of measuring singly charged ionic fragments up-to 13 eV in all directions. An electrostatic lens has been introduced in order to achieve velocity imaging. Effects of the lens on time-of-flight as well as on the position have been investigated in detail, both, by simulation and in experiment. We have used 120 keV proton beam on molecular nitrogen gas target. Complete momentum distributions and kinetic energy release distributions have been derived from the measured position and time-of-flight spectra. Along with this, the kinetic energy release spectra of fragmentation of doubly ionized nitrogen molecule upon various projectile impacts are presented.

  17. Molecular-state treatment of collisions between protons and He/sup +/ ions

    SciTech Connect

    Winter, T.G.; Hatton, G.J.; Lane, N.F.

    1980-09-01

    Cross sections have been calculated for electron transfer into all states of H in collisions of protons and /sup 4/He/sup +/ ions at center-of-mass energies from 1.6 to 14 keV. Excitation of the 2s, 2p/sub 0/, and 2p/sub 1/ states of He/sup +/ has also been considered. The coupled-molecular-state calculations incorporate matrix elements and potential curves determined previously for up to ten molecular states 1ssigma, 2ssigma, ..., 3ddelta and up to 22 states 1ssigma, 2ssigma, ..., 4fphi 5gsigma, 5g..pi.. in treatments with and without plane-wave translational factors, respectively. The departure from rectilinear trajectories has been estimated to affect the electron-transfer cross sections by less than 7% at energies above 1.6 keV. The present results show very good agreement with the magnitude and structure of a recent experimental cross-section curve.

  18. Photophysical processes of triplet states and radical ions in pure and molecularly doped polymers. Final report

    SciTech Connect

    Burkhart, R.D.

    1998-01-01

    Both the past and current objectives are to learn how to control the rate and direction of triplet exciton migration in both pure and molecularly doped polymer systems. Since triplet excimers are efficient traps for migrating excitons, a secondary objective has been to characterize these excimers with a view toward their use as rate modifiers or excited state quenchers. Further objectives included those stated above as past and current objectives but with an additional goal. The authors learned that fluid solutions of many of the nitrogen containing chromophores with which they work produce both radical cations and anions upon excimer laser excitation. They also learned that a phosphorus analogue behaves similarly. At this time the mechanism of charge generation in these systems is not well established but they do know that the electronically excited states and radical ions can potentially interconvert. They wanted to find out whether or not the pure or molecularly doped polymer systems could be used in a step-wise sequence involving light absorption followed by charge generation. All of their activities are oriented toward the potential end use of polymeric systems in the conversion of light energy to perform various types of useful work.

  19. Early stages of insulin fibrillogenesis examined with ion mobility mass spectrometry and molecular modelling.

    PubMed

    Cole, Harriet; Porrini, Massimiliano; Morris, Ryan; Smith, Tom; Kalapothakis, Jason; Weidt, Stefan; Mackay, C Logan; MacPhee, Cait E; Barran, Perdita E

    2015-10-21

    A prevalent type of protein misfolding causes the formation of β-sheet-rich structures known as amyloid fibrils. Research into the mechanisms of fibril formation has implications for both disease prevention and nanoscale templating technologies. This investigation into the aggregation of insulin utilises ion mobility mass spectrometry coupled with molecular modelling to identify and characterise oligomers formed during the 'lag' phase that precedes fibril growth. High resolution mass spectrometry and collision induced dissociation is used to unequivocally assign species as m/z coincident multimers or confomers, providing a robust analytical approach that supports the use of molecular dynamics to atomistically resolve the observed oligomers. We show that insulin oligomerises to form species In where 2 ≤ n ≤ 12 and within this set of oligomers we delineate over 60 distinct conformations, the most dominant of which are compact species. Modelling trained with experimental data suggests that the dominant compact dimers are enriched in β-sheet secondary structure and dominated by hydrophobic interactions, and provides a linear relationship between Rg and collision cross section. This approach provides detailed insight to the early stages of assembly of this much studied amyloidogenic protein, and can be used to inform models of nucleation and growth. PMID:26369607

  20. A First Principles Molecular Dynamics Study Of Calcium Ion In Water

    SciTech Connect

    Lightstone, F; Schwegler, E; Allesch, M; Gygi, F; Galli, G

    2005-01-28

    In this work we report on Car-Parrinello simulations of the divalent calcium ion in water, aimed at understanding the structure of the hydration shell and at comparing theoretical results with a series of recent experiments. Our paper shows some of the progress in the investigation of aqueous solutions brought about by the advent of ab initio molecular dynamics and highlights the importance of accessing subtle details of ion-water interactions from first-principles. Calcium plays a vital role in many biological systems, including signal transduction, blood clotting and cell division. In particular, calcium ions are known to interact strongly with proteins as they tend to bind well to both negatively charged (e.g. in aspartate and glutamate) and uncharged oxygens (e.g. in main-chain carbonyls). The ability of calcium to coordinate multiple ligands (from 6 to 8 oxygen atoms) with an asymmetric coordination shell enables it to cross-link different segments of a protein and induce large conformational changes. The great biochemical importance of the calcium ion has led to a number of studies to determine its hydration shell and its preferred coordination number in water. Experimental studies have used a variety of techniques, including XRD, EXAFS, and neutron diffraction to elucidate the coordination of Ca{sup 2+} in water. The range of coordination numbers (n{sub C}) inferred by X-ray diffraction studies varies from 6 to 8, and is consistent with that reported in EXAFS experiments (8 and 7.2). A wider range of values (6 to 10) was found in early neutron diffraction studies, depending on concentration, while a more recent measurement by Badyal, et al. reports a value close to 7. In addition to experimental measurements, many theoretical studies have been carried out to investigate the solvation of Ca{sup 2+} in water and have also reported a wide range of coordination numbers. Most of the classical molecular dynamics (MD) and QM/MM simulations report n{sub C} in the

  1. Counter-ion specificity explored in abnormal expansion of supra-molecular aggregates in aqueous solution of alkaline metal salts.

    PubMed

    Huang, Ningdong; Tao, Jiaojiao; Wei, Shenghui; Chen, Mingming; Wei, Chengsha; Li, Liangbin

    2015-09-21

    Ionic effects in aqueous solution of macro-ions showing specificity and unconventional characters, respectively, receive a lot of interests recently; however, the complexity of specific ion effects in unconventional phenomena remains ambiguous. In this study, the effects of univalent ions on aggregation of supra-molecular nano-fibrils with charged carboxylate groups on the surface as a prototype of macro-ions are investigated by Small Angle X-ray Scattering (SAXS) in aqueous solutions of alkaline metal chlorides. It is found that the columnar bundles of charged fibrils are expanded in certain salt concentration range contradicting the conventional screening effects of salts. The degree of expansion is dominated by cations as Na(+) induces drastic effects in comparison to rather gentle changes from K(+) and Cs(+). The specific cations effects observed by SAXS correlate with the pH behavior of the solutions, an indicator of surface charge, or number of carboxylate groups along the supra-molecular fibrils. It is postulated that while Na(+) with stronger affinity to carboxylates apparently reduces the surface charge, K(+) and Cs(+) only weakly interact with carboxylates and induce minor changes, accounting for the cation-sensitive aggregation behavior of fibrils observed by SAXS. By probing the bundling aggregation of charged supra-molecular nano-fibrils in salty water, we provide direct evidence of specific counter-ion effects in unusual expansion caused by univalent salts. PMID:26395732

  2. Dependence of the Rate of LiF Ion-Pairing on the Description of Molecular Interaction.

    PubMed

    Pluhařová, Eva; Baer, Marcel D; Schenter, Gregory K; Jungwirth, Pavel; Mundy, Christopher J

    2016-03-01

    We present an analysis of the dynamics of ion-pairing of lithium fluoride (LiF) in aqueous solvent using both detailed molecular simulation as well as reduced models within a generalized Langevin equation (GLE) framework. We explored the sensitivity of the ion-pairing phenomena to the details of descriptions of molecular interaction, comparing two empirical potentials to explicit quantum based density functional theory. We find quantitative differences in the potentials of mean force for ion-pairing as well as time dependent frictions that lead to variations in the rate constant and reactive flux correlation functions. These details reflect differences in solvent response to ion-pairing between different representations of molecular interaction and influence anharmonicity of the dynamic response. We find that the short-time anharmonic response is recovered with a GLE parametrization. Recovery of the details of long time response may require extensions to the reduced model. We show that the utility of using a reduced model leads to a straightforward application of variational transition state theory concepts to the condensed phase system. The significance of this is reflected in the analysis of committor distributions and the variation of planar hypersurfaces, leading to an improved understanding of factors that determine the rate of LiF ion-pairing. PMID:26501355

  3. Three dimensional imaging technique suitable for the measurements of the internal energies of asymmetrical diatomic molecular ions

    NASA Astrophysics Data System (ADS)

    Sauza, J. B.; Panchenko, D. I.; Duot, A. C.; Strom, R. A.; Andrianarijaona, V. M.

    2015-05-01

    We propose a three dimensional imaging technique that could be used to measure the internal energy of asymmetrical diatomic molecular ions such as HeH+ and CO+. The detection scheme is similar to the one used for symmetrical diatomic molecular ions, which accesses the internal energy of the ion through the kinetic energy release in a resonant dissociative charge transfer (see for instance). In that technique, the fragments hit two detectors which send the positions of the impacts along with the difference between the times of impacts to a computer. The computed kinetic energy release is related to the vibrational excitation level of the initial molecular ion. In the case of an asymmetrical ion, the lighter fragment has a higher recoil velocity and goes further away transversally from the center of mass direction. The heavier fragment would not hit the first detector if the beam is judiciously misaligned. Therefore, we make distinction between the two particles. Details of the technique will be presented. Authors wish to give special thanks to Pacific Union College Student Senate for their financial support.

  4. Counter-ion binding and mobility in the presence of hydrophobic polyions – combining molecular dynamics simulations and NMR

    NASA Astrophysics Data System (ADS)

    Druchok, Maksym; Malikova, Natalie; Rollet, Anne-Laure; Vlachy, Vojko

    2016-06-01

    Counter-ion binding and mobility in aqueous solutions of partially hydrophobic ionene oligoions is studied here by a combination of all-atomic molecular dynamics (MD) simulations and NMR (19F and 81Br nuclei) measurements. We present results for 12, 12-ionenes in the presence of different halide ions (F-, Cl-, Br- and I-), as well as their mixtures; the latter allowing us to probe counter-ion selectivity of these oligoions. We consolidate both structural and dynamic information, in particular simulated radial distribution functions and average residence times of counter-ions in the vicinity of ionenes and NMR data in the form of counter-ion chemical shift and self-diffusion coefficients. On one hand, previously reported enthalpy of dilution and mixing measurements show a reverse counter-ion sequence for 12, 12-ionenes with respect to their less hydrophobic 3, 3- and 6, 6- analogues. On the other hand, the current MD and NMR data, reflecting the counter-ion binding tendencies to the ionene chain, give evidence for the same ordering as that observed by MD for 3, 3-ionenes. This is not seen as a contradiction and can be rationalized on the basis of increasing chain hydrophobicity, which has different consequences for enthalpy and ion-binding. The latter is reflecting free energy changes and as such includes both enthalpic and entropic contributions.

  5. Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel

    PubMed Central

    Ulmschneider, Martin B.; Bagnéris, Claire; McCusker, Emily C.; DeCaen, Paul G.; Delling, Markus; Clapham, David E.; Ulmschneider, Jakob P.; Wallace, B. A.

    2013-01-01

    The crystal structure of the open conformation of a bacterial voltage-gated sodium channel pore from Magnetococcus sp. (NaVMs) has provided the basis for a molecular dynamics study defining the channel’s full ion translocation pathway and conductance process, selectivity, electrophysiological characteristics, and ion-binding sites. Microsecond molecular dynamics simulations permitted a complete time-course characterization of the protein in a membrane system, capturing the plethora of conductance events and revealing a complex mixture of single and multi-ion phenomena with decoupled rapid bidirectional water transport. The simulations suggest specific localization sites for the sodium ions, which correspond with experimentally determined electron density found in the selectivity filter of the crystal structure. These studies have also allowed us to identify the ion conductance mechanism and its relation to water movement for the NavMs channel pore and to make realistic predictions of its conductance properties. The calculated single-channel conductance and selectivity ratio correspond closely with the electrophysiology measurements of the NavMs channel expressed in HEK 293 cells. The ion translocation process seen in this voltage-gated sodium channel is clearly different from that exhibited by members of the closely related family of voltage-gated potassium channels and also differs considerably from existing proposals for the conductance process in sodium channels. These studies simulate sodium channel conductance based on an experimentally determined structure of a sodium channel pore that has a completely open transmembrane pathway and activation gate. PMID:23542377

  6. Ion-ion repulsion and entropic effects on Na+ transport in Na2Ni2TeO6: Molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Sau, Kartik

    2016-05-01

    Molecular dynamics (MD) study of Na+ transport in Na2Ni2TeO6 is performed systematically with varying strengths of Na+-Na+ repulsions. This virtual experiment is performed to understand the physics of the ion transport. The optimal short range Na-Na repulsion exhibits highest Na+ diffusion. The Na+ occupancy shows a systematic shift in favor of higher energy and the connecting channels between the interstitial sites are thicker as the short range repulsion between Na+ is increased. The microscopic energy barriers, covering volume in the population distribution profile of the Na+ as well as its site occupancy suggest increasing role of entropic factors for higher ion-ion repulsion.

  7. Structural characterization of saturated branched chain fatty acid methyl esters by collisional dissociation of molecular ions generated by electron ionization.

    PubMed

    Ran-Ressler, Rinat R; Lawrence, Peter; Brenna, J Thomas

    2012-01-01

    Saturated branched chain fatty acids (BCFA) are present as complex mixtures in numerous biological samples. The traditional method for structure elucidation, electron ionization (EI) mass spectrometry, sometimes does not unambiguously enable assignment of branching in isomeric BCFA. Zirrolli and Murphy (Zirrolli , J. A. , and R. A. Murphy. 1993. Low-energy tandem mass spectrometry of the molecular ion derived from fatty acid methyl esters: a novel method for analysis of branched-chain fatty acids. J. Am. Soc. Mass Spectrom. 4: 223-229.) showed that the molecular ions of four BCFA methyl ester (BCFAME) yield highly characteristic fragments upon collisional dissociation using a triple quadrupole instrument. Here, we confirm and extend these results by analysis using a tabletop 3-D ion trap for activated molecular ion EI-MS/MS to 30 BCFAME. iso-BCFAME produces a prominent ion (30-100% of base peak) for [M-43] (M-C₃H₇), corresponding to the terminal isopropyl moiety in the original iso-BCFAME. Anteiso-FAME yield prominent ions (20-100% of base peak) corresponding to losses on both side of the methyl branch, [M-29] and [M-57], and tend to produce more prominent m/z 115 peaks corresponding to a cyclization product around the ester. Dimethyl and tetramethyl FAME, with branches separated by at least one methylene group, yield fragment on both sides of the sites of methyl branches that are more than 6 C away from the carboxyl carbon. EI-MS/MS yields uniquely specific ions that enable highly confident structural identification and quantification of BCFAME. PMID:22021637

  8. Molecular dynamics study of linear and comb-like polyelectrolytes in aqueous solution: effect of Ca2+ ions

    NASA Astrophysics Data System (ADS)

    Tong, Kefeng; Song, Xingfu; Sun, Shuying; Xu, Yanxia; Yu, Jianguo

    2014-08-01

    All-atom molecular dynamics simulations were employed to provide microscopic mechanism for the salt tolerance of polyelectrolytes dispersants. The conformational variation of polyelectrolytes and interactions between COO- groups and counterions/water molecules were also studied via radius of gyration and pair correlations functions. Sodium polyacrylate (NaPA) and sodium salts of poly(acrylic acid)-poly(ethylene oxide) (NaPA-PEO) were selected as the representative linear and comb-like polyelectrolyte, respectively. The results show that Ca2+ ions interact with COO- groups much stronger than Na+ ions and can bring ion-bridging interaction between intermolecular COO- groups in the NaPA systems. While in the NaPA-PEO systems, the introduced PEO side chains can prevent backbone chains from ion-bridging interactions and weaken the conformational changes. The present results can help in selecting and designing new-type efficient polyelectrolyte dispersants with good salt tolerance.

  9. Effect of Na+ and Ca2+ ions on a lipid Langmuir monolayer: an atomistic description by molecular dynamics simulations.

    PubMed

    Giner Casares, Juan José; Camacho, Luis; Martín-Romero, Maria Teresa; López Cascales, José Javier

    2008-12-01

    Studying the effect of alkali and alkaline-earth metal cations on Langmuir monolayers is relevant from biophysical and nanotechnological points of view. In this work, the effect of Na(+) and Ca(2+) on a model of an anionic Langmuir lipid monolayer of dimyristoylphosphatidate (DMPA(-)) is studied by molecular dynamics simulations. The influence of the type of cation on lipid structure, lipid-lipid interactions, and lipid ordering is analyzed in terms of electrostatic interactions. It is found that for a lipid monolayer in its solid phase, the effect of the cations on the properties of the lipid monolayer can be neglected. The influence of the cations is enhanced for the lipid monolayer in its gas phase, where sodium ions show a high degree of dehydration compared with calcium ions. This loss of hydration shell is partly compensated by the formation of lipid-ion-lipid bridges. This difference is ascribed to the higher charge-to-radius ratio q/r for Ca(2+), which makes ion dehydration less favorable compared to Na(+). Owing to the different dehydration behavior of sodium and calcium ions, diminished lipid-lipid coordination, lipid-ion coordination, and lipid ordering are observed for Ca(2+) compared to Na(+). Furthermore, for both gas and solid phases of the lipid Langmuir monolayers, lipid conformation and ion dehydration across the lipid/water interface are studied. PMID:19012310

  10. A Mechanism for Ion Transport Across the Water/Dichloromethane Interface: A Molecular Dynamics Study Using Polarizable Potential Models

    SciTech Connect

    Dang, Liem X. )

    2001-02-01

    In this work, we used molecular dynamics techniques and mean force approaches to compute the ion transfer free energy for the water/dichloromethane liquid-liquid interface. We used polarizable potential models to describe the interactions among the species, and both forward and reverse directions were carried out to estimate the error bar of the computed free energy results. Based on the results of our calculations, we have proposed a mechanism that describes the transport of a chlorine ion across the interface. The computed ion transfer free energy is 14 & No.177; 2 kcal/mol, which is in reasonable agreement with the experimentally reported value of 10 kcal/mol. A smooth transition from the aqueous phase to the non-aqueous phase on the free energy profile clearly indicates that the ion transfer mechanism is a nonactivated process. The computed hydration number for the chlorine ion indicates that some water molecules are associated with the ion inside the non-aqueous phase. This result is in excellent agreement with the experimental interpretation of the ion transfer mechanism reported recently by Osakai et al. (J. Phys. Chem. 1997, 101, 8341).

  11. 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.

  12. Effect of calcium ions on the density of lecithin and its effective molecular volume in lecithin-water dispersions.

    PubMed

    Yeap, Pei Koon; Lim, Koon Ong; Chong, Chon Sing; Teng, Tjoon Tow

    2008-01-01

    As the packing structure of lipid molecules in the liposomes will vary in the presence of ions, it is expected that the density of lipid and the effective volume of lipid molecules in the dispersions will also vary, albeit minutely. Density measurements of lipid-water dispersions with the addition of Ca(2+) ions were determined accurately. The effect of Ca(2+) ions on the molecular packing structure of the liposomes was elucidated from the results obtained. The results for the density of the lecithin in the dispersions with and without the addition of Ca(2+) ions are, respectively, 1.0782 and 1.0579 g cm(-3) at 25 degrees C; and 1.0048 and 0.9961 g cm(-3) at 50 degrees C. The average values of the effective molecular volume of lecithin in the dispersions with and without the addition of Ca(2+) ions are, respectively, 1.131E-21 and 1.152E-21 cm(3) at 25 degrees C; and 1.213E-21 and 1.224E-21 cm(3) at 50 degrees C. PMID:17963698

  13. Atom ejection from a fast-ion track: A molecular-dynamics study

    SciTech Connect

    Urbassek, H.M. ); Kafemann, H. ); Johnson, R.E. )

    1994-01-01

    As a model for atom ejection from fast-ion tracks, molecular-dynamics simulations of a cylindrical track of energized particles are performed. An idealized situation is studied where every atom in a cylindrical track of radius [ital R][sub 0] is energized with energy [ital E][sub 0]. The emission yield [ital Y]([ital E][sub 0],[ital R][sub 0]) shows the existence of two ejection regimes. If the particle energy [ital E][sub 0] is below the sublimation energy [ital U] of the material, a threshold regime is seen in which [ital Y] rises roughly like the third power of [ital E][sub 0]; for high-energy densities [ital E][sub 0][approx gt][ital U], the yield rises much more slowly, roughly linearly. In both cases, ejected particles mostly originate from the track, rather than from its surroundings, and from the first or the first few monolayers. The behavior found is interpreted here in terms of emission due to a pressure-driven jet (linear regime) or due to a pressure pulse (threshold regime). These both behave differently from the often-used thermal-spike sputtering model.

  14. From hopanoids to cholesterol: Molecular clocks of pentameric ligand-gated ion channels.

    PubMed

    Barrantes, Francisco J; Fantini, Jacques

    2016-07-01

    Pentameric ligand-gated ion channels (pLGICs) and their lipid microenvironments appear to have acquired mutually adaptive traits along evolution: 1) the three-ring architecture of their transmembrane (TM) region; 2) the ability of the outermost TM ring to convey lipid signals to the middle ring, which passes them on to the central pore ring, and 3) consensus motifs for sterol recognition in all pLGICs. Hopanoids are triterpenoid fossil lipids that constitute invaluable biomarkers for tracing evolution at the molecular scale. The cyanobacterium Gloeobacter violaceus is the oldest known living organism in which the X-ray structure of its pLGIC, GLIC, reveals the presence of the above attributes and, as discussed in this review, the ability to bind hopanoids. ELIC, the pLGIC from the bacillus Erwinia chrysanthemi is the only other known case to date. Both prokaryotes lack cholesterol but their pLGICs exhibit the same sterol motifs as mammalian pLGIC. This remarkable conservation suggests that the association of sterols and hopanoid surrogate molecules arose from the early need in prokaryotes to stabilize pLGIC TM regions by means of relatively rigid lipid molecules. The conservation of these phenotypic traits along such a long phylogenetic span leads us to suggest the possible co-evolution of these sterols with pLGICs. PMID:27084463

  15. Aqua Ions-Graphene Interfacial and Confinement Behavior: Insights from isobaric-isothermal molecular dynamics

    SciTech Connect

    Chialvo, Ariel A; Cummings, Peter T

    2011-01-01

    We carry out a systematic micro-structural characterization of the solidfluid interface (SFI) of water and simple metal chloride aqueous solutions in contact with a free standing plate or with two such plates separated by an inter-plate distance 0 ! h( ) ! 30 at ambient conditions via isothermalisobaric molecular dynamics. With this characterization we target the interrogation of the system in search for answers to fundamental questions regarding the structure of the external and internal (confined) SFI s, the effect of the differential hydration behavior among species and its link to species expulsion from confinement. For water at ambient conditions we found that the structure of the external SFI s is independent of the interplate distance h in the range 0 ! h( ) ! 30 , i.e., the absence of wallmediated correlation effects between external and internal SFI s, and that for h < 9 the slit-pores de-wet. Moreover, we observed a selective expulsion of ions caused by the differential hydration between the anion and the cations with a consequent charging of the slit-pore. All these observations were interpreted in terms of the axial profiles for precisely defined order parameters including tetrahedral configuration, hydrogen bonding, and species coordination numbers.

  16. Detection of a new interstellar molecular ion, H2COH+ (protonated formaldehyde).

    PubMed

    Ohishi, M; Ishikawa, S I; Amano, T; Oka, H; Irvine, W M; Dickens, J E; Ziurys, L M; Apponi, A J

    1996-11-01

    A new interstellar molecular ion, H2COH+ (protonated formaldehyde), has been detected toward Sgr B2, Orion KL, W51, and possibly in NGC 7538 and DR21(OH). Six transitions were detected in Sgr B2(M). The 1(1,0)-1(0,1) transition was detected in all sources listed above. Searches were also made toward the cold, dark clouds TMC-1 and L134N, Orion (3N, 1E), and a red giant, IRC + 10216, without success. The excitation temperatures of H2COH+ are calculated to be 60-110 K, and the column densities are on the order of 10(12)-10(14) cm-2 in Sgr B2, Orion KL, and W51. The fractional abundance of H2COH+ is on the order of 10(-11) to 10-(9), and the ratio of H2COH+ to H2CO is in the range 0.001-0.5 in these objects. The values in Orion KL seem to be consistent with the "early time" values of recent model calculations by Lee, Bettens, & Herbst, but they appear to be higher than the model values in Sgr B2 and W51 even if we take the large uncertainties of column densities of H2CO into account. We suggest production routes starting from CH3OH may play an important role in the formation of H2COH+. PMID:11541244

  17. Metastable structures and isotope exchange reactions in polyoxometalate ions provide a molecular view of oxide dissolution.

    PubMed

    Rustad, James R; Casey, William H

    2012-03-01

    Reactions involving minerals and glasses in water are slow and difficult to probe spectroscopically but are fundamental to the performance of oxide materials in green technologies such as automotive thermoelectric power generation, CO2 capture and storage and water-oxidation catalysis; these must be made from geochemically common elements and operate in hydrous environments. Polyoxometalate ions (POMs) have structures similar to condensed oxide phases and can be used as molecular models of the oxide/water interface. Oxygen atoms in POM exchange isotopes at different rates, but, at present, there is no basis for predicting how the coordination environment and metal substitution influences rates and mechanisms. Here we identify low-energy metastable configurations that form from the breaking of weak bonds between metals and underlying highly coordinated oxygen atoms, followed by facile hydroxide, hydronium or water addition. The mediation of oxygen exchange by these stuffed structures suggests a new view of the relationship between structure and reactivity at the oxide/solution interface. PMID:22231599

  18. Molecular Mapping of General Anesthetic Sites in a Voltage-Gated Ion Channel

    PubMed Central

    Barber, Annika F.; Liang, Qiansheng; Amaral, Cristiano; Treptow, Werner; Covarrubias, Manuel

    2011-01-01

    Several voltage-gated ion channels are modulated by clinically relevant doses of general anesthetics. However, the structural basis of this modulation is not well understood. Previous work suggested that n-alcohols and inhaled anesthetics stabilize the closed state of the Shaw2 voltage-gated (Kv) channel (K-Shaw2) by directly interacting with a discrete channel site. We hypothesize that the inhibition of K-Shaw2 channels by general anesthetics is governed by interactions between binding and effector sites involving components of the channel's activation gate. To investigate this hypothesis, we applied Ala/Val scanning mutagenesis to the S4-S5 linker and the post-PVP S6 segment, and conducted electrophysiological analysis to evaluate the energetic impact of the mutations on the inhibition of the K-Shaw2 channel by 1-butanol and halothane. These analyses identified residues that determine an apparent binding cooperativity and residue pairs that act in concert to modulate gating upon anesthetic binding. In some instances, due to their critical location, key residues also influence channel gating. Complementing these results, molecular dynamics simulations and in silico docking experiments helped us visualize possible anesthetic sites and interactions. We conclude that the inhibition of K-Shaw2 by general anesthetics results from allosteric interactions between distinct but contiguous binding and effector sites involving inter- and intrasubunit interfaces. PMID:21961587

  19. Custom-tailored adsorbers: A molecular dynamics study on optimal design of ion exchange chromatography material.

    PubMed

    Lang, Katharina M H; Kittelmann, Jörg; Pilgram, Florian; Osberghaus, Anna; Hubbuch, Jürgen

    2015-09-25

    The performance of functionalized materials, e.g., ion exchange resins, depends on multiple resin characteristics, such as type of ligand, ligand density, the pore accessibility for a molecule, and backbone characteristics. Therefore, the screening and identification process for optimal resin characteristics for separation is very time and material consuming. Previous studies on the influence of resin characteristics have focused on an experimental approach and to a lesser extent on the mechanistic understanding of the adsorption mechanism. In this in silico study, a previously developed molecular dynamics (MD) tool is used, which simulates any given biomolecule on resins with varying ligand densities. We describe a set of simulations and experiments with four proteins and six resins varying in ligand density, and show that simulations and experiments correlate well in a wide range of ligand density. With this new approach simulations can be used as pre-experimental screening for optimal adsorber characteristics, reducing the actual number of screening experiments, which results in a faster and more knowledge-based development of custom-tailored adsorbers. PMID:26319376

  20. Effect of Molecular Weight on the Ion Transport Mechanism in Polymerized Ionic Liquids

    DOE PAGESBeta

    Fan, Fei; Wang, Weiyu; Holt, Adam P.; Feng, Hongbo; Uhrig, David; Lu, Xinyi; Hong, Tao; Wang, Yangyang; Kang, Nam-Goo; Mays, Jimmy; et al

    2016-06-07

    The unique properties of ionic liquids (ILs) have made them promising candidates for electrochemical applications. Polymerization of the corresponding ILs results in a new class of materials called polymerized ionic liquids (PolyILs). Though PolyILs offer the possibility to combine the high conductivity of ILs and the high mechanical strength of polymers, their conductivities are typically much lower than that of the corresponding small molecule ILs. In this study, seven PolyILs were synthesized having degrees of polymerization ranging from 1 to 333, corresponding to molecular weights (MW) from 482 to 160 400 g/mol. Depolarized dynamic light scattering, broadband dielectric spectroscopy, rheology,more » and differential scanning calorimetry were employed to systematically study the influence of MW on the mechanism of ionic transport and segmental dynamics in these materials. Finally, the modified Walden plot analysis reveals that the ion conductivity transforms from being closely coupled with structural relaxation to being strongly decoupled from it as MW increases.« less

  1. Communication: Rigidity of the molecular ion H{sub 5}{sup +}

    SciTech Connect

    Fábri, Csaba

    2014-02-07

    The fourth-age quantum chemical code GENIUSH is used for the variational determination of rotational-vibrational energy levels corresponding to reduced- and full-dimensional models of H{sub 5}{sup +}, a molecular ion exhibiting several strongly coupled large-amplitude motions. The computations are supplemented with one- and two-dimensional analytic results which help to understand the peculiar rovibrational energy-level structure computed correctly for the first time. An unusual aspect of the results is that the canonical Eckart-embedding of molecule-fixed axes, a cornerstone of the computational spectroscopy of semirigid molecules, is found to be inadequate. Furthermore, it is shown that while the 1D “active torsion” model provides proper results when compared to the full, 9D treatment, models excluding the torsion have limited physical significance. The structure of the rovibrational energy levels of H{sub 5}{sup +} proves that this is a prototypical astructural molecule: the rotational and vibrational level spacings are of the same order of magnitude and the level structure drastically deviates from that computed via perturbed rigid-rotor and harmonic-oscillator models.

  2. An investigation on the mechanism of sublimed DHB matrix on molecular ion yields in SIMS imaging of brain tissue.

    PubMed

    Dowlatshahi Pour, Masoumeh; Malmberg, Per; Ewing, Andrew

    2016-05-01

    We have characterized the use of sublimation to deposit matrix-assisted laser desorption/ionization (MALDI) matrices in secondary ion mass spectrometry (SIMS) analysis, i.e. matrix-enhanced SIMS (ME-SIMS), a common surface modification method to enhance sensitivity for larger molecules and to increase the production of intact molecular ions. We use sublimation to apply a thin layer of a conventional MALDI matrix, 2,5-dihydroxybenzoic acid (DHB), onto rat brain cerebellum tissue to show how this technique can be used to enhance molecular yields in SIMS while still retaining a lateral resolution around 2 μm and also to investigate the mechanism of this enhancement. The results here illustrate that cholesterol, which is a dominant lipid species in the brain, is decreased on the tissue surface after deposition of matrix, particularly in white matter. The decrease of cholesterol is followed by an increased ion yield of several other lipid species. Depth profiling of the sublimed rat brain reveals that the lipid species are de facto extracted by the DHB matrix and concentrated in the top most layers of the sublimed matrix. This extraction/concentration of lipids directly leads to an increase of higher mass lipid ion yield. It is also possible that the decrease of cholesterol decreases the potential suppression of ion yield caused by cholesterol migration to the tissue surface. This result provides us with significant insights into the possible mechanisms involved when using sublimation to deposit this matrix in ME-SIMS. Graphical Abstract Schematic representation of the enhancement on the molecular ion yields in SIMS by deposition of DHB matrix on the brain tissue using sublimation. PMID:26922337

  3. Atomic and molecular effects on spherically convergent ion flow. I. Single atomic species

    SciTech Connect

    Emmert, G. A.; Santarius, J. F.

    2010-01-15

    A formalism for analyzing the effect of ion-neutral gas interactions on the flow of ions between nearly transparent electrodes in spherical geometry has been developed for atomic ions in a weakly ionized plasma, so that the important atomic effects are charge exchange and ion impact ionization. The formalism is applied to spherical, gridded, inertial-electrostatic confinement (IEC) devices. The formalism yields detailed information about the energy spectra of the ions and fast neutral atoms, and the resulting fusion rate for {sup 3}He ions in a background {sup 3}He gas. The results are illustrated with an example calculation for the Wisconsin IEC device operating on {sup 3}He.

  4. Theoretical and experimental studies of the molecular orbital bonding coefficients for Cu2+ ion in cesium hydrogen oxalate single crystals

    NASA Astrophysics Data System (ADS)

    Kalfaoǧlu, Emel; Karabulut, Bünyamin

    2016-03-01

    Electron paramagnetic resonance (EPR) and optical absorption spectra of Cu2+ ions in cesium hydrogen oxalate single crystals have been investigated at room temperature. The spin-Hamiltonian parameters (g and A), have been determined. Crystalline field around the Cu2+ ion is almost axially symmetric. The results show a single paramagnetic site which confirms the triclinic crystal symmetry. Molecular orbital bonding coefficients are studied from the EPR and optical data. Theoretical octahedral field parameter and the tetragonal field parameters have been evaluated from the superposition model. Using these parameters, various bonding parameters are analyzed and the nature of bonding in the complex is discussed. The theoretical results are supported by experimental results.

  5. Improvement in the assessment of direct and facilitated ion transfers by electrochemically induced redox transformations of common molecular probes.

    PubMed

    Zhou, Min; Gan, Shiyu; Zhong, Lijie; Dong, Xiandui; Ulstrup, Jens; Han, Dongxue; Niu, Li

    2012-03-14

    A new strategy based on a thick organic film modified electrode allowed us, for the first time, to explore the voltammetric processes for a series of hydrophilic ions by electrochemically induced redox transformations of common molecular probes. During the limited time available for voltammetry, this thick organic film ensured that the generated product of the molecular probe, which is within a limited diffusion layer, was kept far away from the aqueous-organic solvent interface; therefore, regardless of the degree of hydrophobicity, the generated product never participates in ion exchange across the interface and the charge neutrality of the organic film (containing an extremely hydrophobic electrolyte) can only be maintained by the injection of ions from the aqueous phase. Taking advantage of this fact, common redox probes, such as ferrocene (Fc) and 7,7,8,8-tetracyanoquinodimethane (TCNQ), which are almost useless for both three-phase electrode (TPE) and thin-layer cyclic voltammetry (TLCV) methods, can induce the transfer of numerous highly hydrophilic anions and cations. Consequently, the majority of their Gibbs transfer energies have been accurately determined for the first time to the best of our knowledge. With this in mind, using TCNQ as a redox probe to induce facilitated cation transfer, a stategy that is more advantageous than traditional methods has been developed. The main advantages are that: (i) voltammetric experiments performed on this system were free from the polarized potential window (ppw) in the aqueous phase and, as a result, this allowed the assessment of weakly assisted ion transfers, which appear at the terminal of the ppw at single polarized interfaces; (ii) without introducing the tetraphenylarsonium-tetraphenylborate (TPAs-TPB) thermodynamic assumption, one can conveniently evaluate both the association constant and the stoichiometric parameter between the ion and its ionophore by comparison of their direct and facilitated ion transfer

  6. Molecular dynamics simulation exploration of cooperative migration mechanism of calcium ions in sarcoplasmic reticulum Ca2+-ATPase.

    PubMed

    Huang, Yongqi; Li, Huifang; Bu, Yuxiang

    2009-10-01

    Calcium ATPase is a member of the P-type ATPase, and it pumps calcium ions from the cytoplasm into the reticulum against a concentration gradient. Several X-ray structures of different conformations have been solved in recent years, providing basis for elucidating the active transport mechanism of Ca2+ ions. In this work, molecular dynamics (MD) simulations were performed at atomic level to investigate the dynamical process of calcium ions moving from the outer mouth of the protein to their binding sites. Five initial locations of Ca2+ ions were considered, and the simulations lasted for 2 or 6 ns, respectively. Specific pathways leading to the binding sites and large structural rearrangements around binding sites caused by uptake of calcium ions were identified. A cooperative binding mechanism was observed from our simulation. Firstly, the first Ca2+ ion binds to site I, and then, the second Ca2+ ion approaches. The interactions between the second Ca2+ and the residues around site I disturb the binding state of site I and weaken its binding ability for the first bound Ca2+. Because of the electrostatic repulsion of the second Ca2+ and the electrostatic attraction of site II, the first bound Ca2+ shifts from site I to site II. Concertedly, the second Ca2+ binds to site I, forming a binding state with two Ca2+ ions, one at site I and the other at site II. Both of Glu908 and Asp800 coordinate with the two Ca2+ ions simultaneously during the concerted binding process, which is believed to be the hinge to achieve the concerted binding. In our simulations, four amino acid residues that serve as the channel to link the outer mouth and the binding sites during the binding process were recognized, namely Tyr837, Tyr763, Asn911, and Ser767. The analyses regarding the activity of the proteins via mutations of some key residues also supported our cooperative mechanism. PMID:19242958

  7. Lithium ion solvation and diffusion in bulk organic electrolytes from first-principles and classical reactive molecular dynamics.

    PubMed

    Ong, Mitchell T; Verners, Osvalds; Draeger, Erik W; van Duin, Adri C T; Lordi, Vincenzo; Pask, John E

    2015-01-29

    Lithium-ion battery performance is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact both the solvation and diffusivity of Li ions. In this work, we used first-principles molecular dynamics to examine the solvation and diffusion of Li ions in the bulk organic solvents ethylene carbonate (EC), ethyl methyl carbonate (EMC), and a mixture of EC and EMC. We found that Li ions are solvated by either carbonyl or ether oxygen atoms of the solvents and sometimes by the PF6(-) anion. Li(+) prefers a tetrahedrally coordinated first solvation shell regardless of which species are involved, with the specific preferred solvation structure dependent on the organic solvent. In addition, we calculated Li diffusion coefficients in each electrolyte, finding slightly larger diffusivities in the linear carbonate EMC compared to the cyclic carbonate EC. The magnitude of the diffusion coefficient correlates with the strength of Li(+) solvation. Corresponding analysis for the PF6(-) anion shows greater diffusivity associated with a weakly bound, poorly defined first solvation shell. These results can be used to aid in the design of new electrolytes to improve Li-ion battery performance. PMID:25523643

  8. Ion Pair Asociation in Ultra Supercritical Aqueous Environments: Successful Interplay between Conductance Experiment, Theory and Molecular Simulation.

    SciTech Connect

    Chialvo, Ariel A; Gruszkiewicz, Miroslaw {Mirek} S; Cole, David R

    2010-01-01

    We discuss the interplay between theory, molecular simulation and electric conductance experiments as an important tool for the extraction of ion-pair interaction potentials to make possible the bridging of the density gap between the lowest experimentally attainable conductance measurement and the theoretically reachable zero-density limit of the ion-pair association constant. Then, we predict the density dependence of the Na+!Cl! pair association constant in ultra supercritical steam environments by constraint molecular dynamics simulation over state conditions relevant to the new generation of ultra-supercritical steam power plants. Finally, we draw attention to relevant modeling challenges associated to the behavior of these systems around the zero-density limit and discuss ways to overcome them.

  9. The Study of the Nuclear Motion in D{sub 2}{sup +} Molecular Ion By Using the Harmonic Spectra

    SciTech Connect

    Daniele, R.; Castiglia, G.; Corso, P. P.; Fiordilino, E.; Orlando, G.; Persico, F.; Morales, F.

    2007-12-26

    In this paper we show how it is possible to investigate the nuclei dynamics of a D{sub 2}{sup +} molecular ion by using the high harmonic generation spectra emitted by the system when subjected to an intense laser field. In particular, the emitted spectra contains, in addition to the usual odd harmonic peaks, additional satellite peaks whose frequency spacing is equal to the vibrational frequency of the nuclei.

  10. Computation of the hindrance factor for the diffusion for nanoconfined ions: molecular dynamics simulations versus continuum-based models

    NASA Astrophysics Data System (ADS)

    Zhu, Haochen; Ghoufi, Aziz; Szymczyk, Anthony; Balannec, Béatrice; Morineau, Denis

    2012-06-01

    We report the self-diffusion coefficients and hindrance factor for the diffusion of ions into cylindrical hydrophilic silica nanopores (hydrated silica) determined from molecular dynamics (MD) simulations. We make a comparison with the hindered diffusion coefficients used in continuum-based models of nanofiltration (NF). Hindrance factors for diffusion estimated from the macroscopic hydrodynamic theory were found to be in fair quantitative agreement with MD simulations for a protonated pore, but they strongly overestimate diffusion inside a deprotonated pore.

  11. Ion Pairing and Counterion Condensation in Aqueous Electrolyte and Poly-electrolyte Solutions: Insights from Molecular Simulation

    SciTech Connect

    Chialvo, Ariel A; Simonson, J Michael {Mike}

    2007-01-01

    We discuss the molecular-based study of ion-pair formation in LiCl aqueous solutions and its implications on the interpretation of the raw data from neutron diffraction with isotopic substitution experiments, the counterion condensation in aqueous polyelectrolyte solutions comprising short-chain lithium poly-styrene sulfonate (Li{sup +}-PSS{sup -}), as well as their interplay leading to the occurrence of 'like-charge' attractive interactions in the presence of salts of polyvalent counterions.

  12. Different routes, same pathways: Molecular mechanisms under silver ion and nanoparticle exposures in the soil sentinel Eisenia fetida.

    PubMed

    Novo, Marta; Lahive, Elma; Díez-Ortiz, María; Matzke, Marianne; Morgan, Andrew J; Spurgeon, David J; Svendsen, Claus; Kille, Peter

    2015-10-01

    Use of nanotechnology products is increasing; with silver (Ag) nanoparticles particularly widely used. A key uncertainty surrounding the risk assessment of AgNPs is whether their effects are driven through the same mechanism of action that underlies the toxic effects of Ag ions. We present the first full transcriptome study of the effects of Ag ions and NPs in an ecotoxicological model soil invertebrate, the earthworm Eisenia fetida. Gene expression analyses indicated similar mechanisms for both silver forms with toxicity being exerted through pathways related to ribosome function, sugar and protein metabolism, molecular stress, disruption of energy production and histones. The main difference seen between Ag ions and NPs was associated with potential toxicokinetic effects related to cellular internalisation and communication, with pathways related to endocytosis and cilia being significantly enriched. These results point to a common final toxicodynamic response, but initial internalisation driven by different exposure routes and toxicokinetic mechanisms. PMID:26204059

  13. Design of a novel metal binding peptide by molecular dynamics simulation to sequester Cu and Zn ions

    PubMed Central

    Mahnam, K.; Saffar, B.; Mobini-Dehkordi, M.; Fassihi, A.; Mohammadi, A.

    2014-01-01

    Heavy metal toxicity has serious adverse effects on the environment. The metal sequestering characteristics of a novel metal binding peptide (Glu-Cys)11 Gly+linker+hexahistidine (EC11:His6) was investigated to determine if it can absorb Cu2+ or Zn2+ cations. Molecular dynamics simulations were carried out using a model of 6 Cu2+ or Zn2+ and other ions enclosed in a fully hydrated simulation box with the designed peptide. Totally, 240 nano second (ns) simulations were done in three phases. Results showed that the selected linker is able to separate two domains of this peptide and that the carboxyl oxygens of Glu residues of EC11 in the designed peptide can absorb these ions. Sequestration of Cu2+ or Zn2+ ions by the designed peptide does not change overall tertiary and secondary structures of peptide. PMID:25598801

  14. Molecular Dynamics Simulation Study of Parallel Telomeric DNA Quadruplexes at Different Ionic Strengths: Evaluation of Water and Ion Models.

    PubMed

    Rebič, Matúš; Laaksonen, Aatto; Šponer, Jiří; Uličný, Jozef; Mocci, Francesca

    2016-08-01

    Most molecular dynamics (MD) simulations of DNA quadruplexes have been performed under minimal salt conditions using the Åqvist potential parameters for the cation with the TIP3P water model. Recently, this combination of parameters has been reported to be problematic for the stability of quadruplex DNA, especially caused by the ion interactions inside or near the quadruplex channel. Here, we verify how the choice of ion parameters and water model can affect the quadruplex structural stability and the interactions with the ions outside the channel. We have performed a series of MD simulations of the human full-parallel telomeric quadruplex by neutralizing its negative charge with K(+) ions. Three combinations of different cation potential parameters and water models have been used: (a) Åqvist ion parameters, TIP3P water model; (b) Joung and Cheatham ion parameters, TIP3P water model; and (c) Joung and Cheatham ion parameters, TIP4Pew water model. For the combinations (b) and (c), the effect of the ionic strength has been evaluated by adding increasing amounts of KCl salt (50, 100, and 200 mM). Two independent simulations using the Åqvist parameters with the TIP3P model show that this combination is clearly less suited for the studied quadruplex with K(+) as counterions. In both simulations, one ion escapes from the channel, followed by significant deformation of the structure, leading to deviating conformation compared to that in the reference crystallographic data. For the other combinations of ion and water potentials, no tendency is observed for the channel ions to escape from the quadruplex channel. In addition, the internal mobility of the three loops, torsion angles, and counterion affinity have been investigated at varied salt concentrations. In summary, the selection of ion and water models is crucial as it can affect both the structure and dynamics as well as the interactions of the quadruplex with its counterions. The results obtained with the TIP4Pew

  15. Molecular basis of ion permeability in a voltage-gated sodium channel.

    PubMed

    Naylor, Claire E; Bagnéris, Claire; DeCaen, Paul G; Sula, Altin; Scaglione, Antonella; Clapham, David E; Wallace, B A

    2016-04-15

    Voltage-gated sodium channels are essential for electrical signalling across cell membranes. They exhibit strong selectivities for sodium ions over other cations, enabling the finely tuned cascade of events associated with action potentials. This paper describes the ion permeability characteristics and the crystal structure of a prokaryotic sodium channel, showing for the first time the detailed locations of sodium ions in the selectivity filter of a sodium channel. Electrostatic calculations based on the structure are consistent with the relative cation permeability ratios (Na(+) ≈ Li(+) ≫ K(+), Ca(2+), Mg(2+)) measured for these channels. In an E178D selectivity filter mutant constructed to have altered ion selectivities, the sodium ion binding site nearest the extracellular side is missing. Unlike potassium ions in potassium channels, the sodium ions in these channels appear to be hydrated and are associated with side chains of the selectivity filter residues, rather than polypeptide backbones. PMID:26873592

  16. Effect of lithium and sodium ions on a charged membrane of dipalmitoylphosphatidylserine: a study by molecular dynamics simulation.

    PubMed

    López Cascales, J J; García de la Torre, J

    1997-12-01

    We describe a series of molecular dynamics simulations performed on a model of charged lipid bilayer (dipalmitoylphosphatidylserine) and water, in presence of sodium and lithium ions, with an atomic detail. The structure of the lipid membranes was strongly affected by the presence of lithium, as manifested by the observation of a transition from a disordered to a gel state. Concerning the mechanism of such a transition, it was associated to the dehydration that we detected in the lipid-water interface in the presence of lithium. This dehydration introduced an increase in the lipid-lipid interactions, and as a consequence, a diminution of the disorder of the membrane. When both types of ions are present in the aqueous phase, lithium shown a special affinity for the lipid membrane displacing almost all the sodium ions toward the middle of the water layer. As a result, we observed remarkable differences in the atom and electric field distributions across the lipid membrane. Concerning the diffusion and orientation of water molecules across the lipid-water interface, we also observed a strong dependency of the type ion. On the other hand, the mobility and the hydration shell of lithium and sodium ions are strongly perturbed by the presence of the charged lipid bilayer. The lipid layer was responsible for a dehydration of the ions compared to bulk water. This dehydration was compensated by an increase of coordination number of the ions with the lipid oxygens. Also, the residence times of water in the first hydration shell of lithium and sodium ions are perturbed by the presence of the lipid membrane. PMID:9408167

  17. Solvent controlled ion association in structured copolymers: Molecular dynamics simulations in dilute solutions

    NASA Astrophysics Data System (ADS)

    Aryal, Dipak; Perahia, Dvora; Grest, Gary S.

    2015-09-01

    Tailoring the nature of individual segments within ion containing block co-polymers is one critical design tool to achieve desired properties. The local structure including the size and distribution of the ionic blocks, as well as the long range correlations, are crucial for their transport ability. Here, we present molecular dynamics simulations on the effects of varying the concentrations of the ionizable groups on the conformations of pentablock ionomer that consist of a center block of ionic sulfonated styrene tethered to polyethylene and terminated by a bulky substituted styrene in dilute solutions. Sulfonation fractions f (0 ≤ f ≤ 0.55), spanning the range from ionomer to polyelectrolytes, were studied. Results for the equilibrium conformation of the chains in water and a 1:1 mixture of cyclohexane and heptane are compared to that in implicit poor solvents with dielectric constants ɛ = 1.0 and 77.73. In water, the pentablock collapses with the sulfonated groups on the outer surface. As f increases, the ionic, center block increasingly segregates from the hydrophobic regions. In the 1:1 mixture of cyclohexane and heptane, the flexible blocks swell, while the center ionic block collapses for f > 0. For f = 0, all blocks swell. In both implicit poor solvents, the pentablock collapses into a nearly spherical shape for all f. The sodium counterions disperse widely throughout the simulation cell for both water and ɛ = 77.73, whereas for ɛ = 1.0 and mixture of cyclohexane and heptane, the counterions largely condense onto the collapsed pentablock.

  18. Radiative properties of molecular nitrogen ions produced by helium Penning ionization and argon effects

    NASA Technical Reports Server (NTRS)

    Miller, George, III; Song, Kyo-Dong

    1994-01-01

    The development of hypersonic aerospace vehicles requires a better understanding on the thermal and chemical nonequilibrium kinetics of participating species in shock layers. The computational fluid dynamic (CFD) codes developed for such flowfields overestimate the radiation in the spectral region of 300 - 600 nm. A speculation for this overestimation is that inclusion of Ar, CO2, and H2O at the upper atmosphere flight region makes a significant impact on radiative kinetics of molecular nitrogen ions. To define the effects of minority species on the radiative kinetics of N2(+), an experimental setup was made by using the helium Penning ionization. The vibrational and rotational temperature were measured by mapping the vibrational and rotational distributions of N2(+) emission with high spectroscopic resolution and absolute intensity measurements. Measured vibrational temperatures were in the range from 18,000 to 36,000 K, and rotational temperatures were in the range from 300 to 370 K. The irradiance of 391.44 nm line and rotational and vibrational temperatures were analyzed to define argon and CO2 effects on the N2(+) emission. When Ar or CO2 is injected with N2, the rotational temperature did not change. The irradiances were reduced by 34 percent and 78 percent for the 50 percent of mixture of Ar and CO2, respectively. The vibrational temperatures were increased by 24.1 percent and 82.9 percent for the 50 percent of mixture of Ar and CO2, respectively. It appears that there are no significant effects from small concentrations of Ar and CO2 at the upper atmosphere flight region.

  19. Molecular Dynamics Investigation of Ion Sorption and Permeation in Desalination Membranes.

    PubMed

    Kolev, Vesselin; Freger, Viatcheslav

    2015-11-01

    With the purpose of gaining insights into the mechanisms of ion uptake and permeation in desalination membranes, MD investigation of a model polyamide membrane was carried out. A relatively large membrane (45K atoms) was assembled, which closely matched real desalination membrane in terms of chemistry and water permeability. Simulations demonstrate that the mechanism of ion uptake distinctly differs from mean-field approaches assuming a smeared excluding Donnan potential. Ion sorption on charged sites in the membrane phase appears to be highly localized, due to electrostatic forces dominating over translational entropy. Moreover, sorption on partial atomic charges becomes possible as well, which greatly enhances salt (co-ion) uptake and weakens the effect of fixed charges on salt exclusion. This could explain high ion uptake measured in polyamide membranes for both co- and counterions and variations of ion sorption and permeation at low salt concentrations. On the other hand, present simulations greatly overestimate ion permeability, which could be explained by a more open structure than in real membranes, in which dense polyamide fragments may efficiently block ion permeation. Unfortunately, MD cannot analyze ion uptake and permeation in dense fragments containing too few ions, which calls for new approaches to studying barrier properties of polyamide. PMID:26451495

  20. Continuous Supersonic Expansion Discharge Source for High-Precision Mid-Infrared Spectroscopy of Cold Molecular Ions

    NASA Astrophysics Data System (ADS)

    Talicska, Courtney; Porambo, Michael; McCall, Benjamin J.

    2015-06-01

    The low temperatures and pressures of the interstellar medium provide an ideal environment for gas phase ion-neutral reactions that play an essential role in the chemistry of the universe. High-precision laboratory spectra of molecular ions are necessary to facilitate new astronomical discoveries and provide a deeper understanding of interstellar chemistry, but forming ions in measurable quantities in the laboratory has proved challenging. Even when cryogenically cooled, the high temperatures and pressures of typical discharge cells lead to diluted and congested spectra from which extracting chemical information is difficult. Here we overcome this challenge by coupling an electric discharge to a continuous supersonic expansion source to form ions cooled to low temperatures. The ion production abilities of the source have been demonstrated previously as ion densities on the order of 1010-1012 cm-3 have been observed for H3+.a With a smaller rotational constant and the expectation that it will be formed with comparable densities, HN2+ is used as a reliable measure of the cooling abilities of the source. Ions are probed through the use of a widely tunable mid-infrared (3-5 μm) spectrometer based on light formed by difference frequency generation and noise-immune cavity-enhanced optical heterodyne molecular spectroscopy (NICE-OHMS).b To improve the sensitivity of the instrument the discharge is electrically modulated and the signal is fed into a lock-in amplifier before being recorded by a custom data acquisition program. Rovibrational transitions of H3+ and HN2+ have been recorded, giving rotational temperatures of 80-120 K and 35-40 K, respectively. With verification that the source is producing rotationally cold ions, we move toward the study of primary ions of more astronomical significance, including H2CO+. aK. N. Crabtree, C. A. Kaufman, and B. J. McCall, Rev. Sci. Instrum. 81, 086103 (2010). bM. W. Porambo, B. M. Siller, J. M. Pearson, and B. J. McCall, Opt

  1. Pairing preferences of the model mono-valence mono-atomic ions investigated by molecular simulation

    SciTech Connect

    Zhang, Qiang; Zhang, Ruiting; Zhao, Ying; Li, HuanHuan; Zhuang, Wei E-mail: gaoyq@pku.edu.cn; Gao, Yi Qin E-mail: gaoyq@pku.edu.cn

    2014-05-14

    We carried out a series of potential of mean force calculations to study the pairing preferences of a series of model mono-atomic 1:1 ions with evenly varied sizes. The probabilities of forming the contact ion pair (CIP) and the single water separate ion pair (SIP) were presented in the two-dimensional plots with respect to the ion sizes. The pairing preferences reflected in these plots largely agree with the empirical rule of matching ion sizes in the small and big size regions. In the region that the ion sizes are close to the size of the water molecule; however, a significant deviation from this conventional rule is observed. Our further analysis indicated that this deviation originates from the competition between CIP and the water bridging SIP state. The competition is mainly an enthalpy modulated phenomenon in which the existing of the water bridging plays a significant role.

  2. Glancing-angle ion enhanced surface diffusion on gaAs(001) during molecular beam epitaxy.

    PubMed

    DeLuca, P M; Ruthe, K C; Barnett, S A

    2001-01-01

    We describe the effects of glancing incidence 3-4 keV Ar ion bombardment on homoepitaxial growth on vicinal GaAs(001). The average adatom lifetime on surface terraces, measured during growth using specular ion scattering, decreased monotonically with increasing ion current density. The results indicated that surface diffusivity was increased by the ions. The ion beam also suppressed growth oscillations and decreased the film surface roughness. This indicates a change from two-dimensional island nucleation to step-flow growth due to increased adatom surface diffusivity. A simple model, involving direct momentum transfer from ions to adatoms, is shown to be consistent with the measured enhanced diffusion. PMID:11177806

  3. Molecular dynamics study of radiation damage and microstructure evolution of zigzag single-walled carbon nanotubes under carbon ion incidence

    NASA Astrophysics Data System (ADS)

    Li, Huan; Tang, Xiaobin; Chen, Feida; Huang, Hai; Liu, Jian; Chen, Da

    2016-07-01

    The radiation damage and microstructure evolution of different zigzag single-walled carbon nanotubes (SWCNTs) were investigated under incident carbon ion by molecular dynamics (MD) simulations. The radiation damage of SWCNTs under incident carbon ion with energy ranging from 25 eV to 1 keV at 300 K showed many differences at different incident sites, and the defect production increased to the maximum value with the increase in incident ion energy, and slightly decreased but stayed fairly stable within the majority of the energy range. The maximum damage of SWCNTs appeared when the incident ion energy reached 200 eV and the level of damage was directly proportional to incident ion fluence. The radiation damage was also studied at 100 K and 700 K and the defect production decreased distinctly with rising temperature because radiation-induced defects would anneal and recombine by saturating dangling bonds and reconstructing carbon network at the higher temperature. Furthermore, the stability of a large-diameter tube surpassed that of a thin one under the same radiation environments.

  4. Infrared spectroscopy of molecular ions in selected rotational and spin-orbit states.

    PubMed

    Jacovella, U; Agner, J A; Schmutz, H; Deiglmayr, J; Merkt, F

    2016-07-01

    First results are presented obtained with an experimental setup developed to record IR spectra of rotationally state-selected ions. The method we use is a state-selective version of a method developed by Schlemmer et al. [Int. J. Mass Spectrom. 185, 589 (1999); J. Chem. Phys. 117, 2068 (2002)] to record IR spectra of ions. Ions are produced in specific rotational levels using mass-analyzed-threshold-ionization spectroscopy. The state-selected ions generated by pulsed-field ionization of Rydberg states of high principal quantum number (n ≈ 200) are extracted toward an octupole ion guide containing a neutral target gas. Prior to entering the octupole, the ions are excited by an IR laser. The target gas is chosen so that only excited ions react to form product ions. These product ions are detected mass selectively as a function of the IR laser wavenumber. To illustrate this method, we present IR spectra of C2H2 (+) in selected rotational levels of the (2)Πu,3/2 and (2)Πu,1/2 spin-orbit components of the vibronic ground state. PMID:27394102

  5. Infrared spectroscopy of molecular ions in selected rotational and spin-orbit states

    NASA Astrophysics Data System (ADS)

    Jacovella, U.; Agner, J. A.; Schmutz, H.; Deiglmayr, J.; Merkt, F.

    2016-07-01

    First results are presented obtained with an experimental setup developed to record IR spectra of rotationally state-selected ions. The method we use is a state-selective version of a method developed by Schlemmer et al. [Int. J. Mass Spectrom. 185, 589 (1999); J. Chem. Phys. 117, 2068 (2002)] to record IR spectra of ions. Ions are produced in specific rotational levels using mass-analyzed-threshold-ionization spectroscopy. The state-selected ions generated by pulsed-field ionization of Rydberg states of high principal quantum number (n ≈ 200) are extracted toward an octupole ion guide containing a neutral target gas. Prior to entering the octupole, the ions are excited by an IR laser. The target gas is chosen so that only excited ions react to form product ions. These product ions are detected mass selectively as a function of the IR laser wavenumber. To illustrate this method, we present IR spectra of C 2 H2 + in selected rotational levels of the 2Πu,3/2 and 2Πu,1/2 spin-orbit components of the vibronic ground state.

  6. Fragmentation of peptide negative molecular ions induced by resonance electron capture

    PubMed Central

    Vasil’ev, Yury V.; Figard, Benjamin J.; Morré, Jeff; Deinzer, Max L.

    2009-01-01

    A simple robust method to study resonance gas-phase reactions between neutral peptides of low volatility and free electrons has been designed and implemented. Resonance electron capture (REC) experiments were performed by several neutral model peptides and two naturally occurring peptides. The assignment of negative ions (NIs) formed in these gas-phase reactions was based on high mass-resolving power experiments. From these accurate mass measurements, it was concluded that fragment NIs formed by low (1–2 eV) energy REC are of the same types as those observed in electron capture∕transfer dissociation, where the positive charge is a factor. The main feature resulting from these REC experiments by peptides is the occurrence of zn−1 ions, which are invariably of the highest abundances in the negative ion mass spectra of larger peptides. [M–H]− NIs presumably the carboxylate anion structure dominate the REC spectra of smaller peptides. There was no evidence for the occurrence of the complementary reaction, i.e., the formations of cn+1 ions. Instead, cn ions arose without hydrogen∕proton transfer albeit with lower abundances than that observed for zn−1 ions. Only the amide forms of small peptides showed more abundant ion peaks for the cn ions than for the zn−1 ions. The mechanisms for the N–Cα bond cleavage are discussed. PMID:19655877

  7. Characterization of sputtering products during graphite exposure to deuterium ions by molecular dynamics

    NASA Astrophysics Data System (ADS)

    Marian, Jaime; Zepeda-Ruiz, Luis A.; Couto, Nicole; Bringa, Eduardo M.; Gilmer, George H.; Stangeby, Peter C.; Rognlien, Thomas D.

    2007-02-01

    We study sputtering by 100eV deuterium irradiation on deuterated amorphous carbon layers at 300K using molecular dynamics (MD) simulations. Two main results are reported here. First, a special mechanism for carbon release—additional to and distinct from the standard definitions for physical and chemical sputtering of carbon by hydrogen isotopes—has been identified and quantified. This process, here termed ion induced release of unsaturated hydrocarbons (IRUH's), is primarily due to a recently identified atomic collision process where momentum from an impacting particle is transferred approximately perpendicular to the C-C bond, severing it. For the prescribed conditions, the IRUH yield has been found to be comparable to that of standard physical and chemical sputtering, the former being also consistently and simultaneously calculated here. IRUH release of single C atoms does not involve any hydrogenic chemistry and is therefore properly considered to be a distinct and additive type of physical sputtering to that of standard physical sputtering. For 100eV D+ the single C yields of the two physical sputtering mechanisms have been found to be approximately equal. IRUH release of carbon is directly from the surface region of the solid and is separate from, and additional to, standard chemical sputtering (not included in these MD calculations), which typically produces saturated hydrocarbons such as CD4, from regions extending over the stopping depth of the deuteron in the solid. IRUH is evidently included in experimental measurements of total sputtering yield, e.g., by weight loss. The average energy of IRUH carbon products is about 1eV and the angular distribution is consistent with a cosine distribution. Second, it is found that for the standard physically sputtered single C atoms the energy distribution is roughly consistent with the widely used Thompson distribution—this despite the fact that the assumptions on which the Thompson distribution is based are not

  8. Charge transport and magnetoresistance of G4-DNA molecular device modulated by counter ions and dephasing effect

    NASA Astrophysics Data System (ADS)

    Kang, Da-wei; Sun, Meng-le; Zuo, Zheng-wei; Wang, Hui-xian; Lv, Shi-jie; Li, Xin-zhong; Li, Li-ben

    2016-02-01

    The charge transport properties of the G4-DNA molecular device in the presence of counter ions and dephasing effect are investigated based on the Green function method and Landauer-Büttiker theory. The currents through the G4-DNA molecular device depend on the interference patterns at different coupling configurations. There is an effective electrostatic interaction between the counter ions and the G4-DNA molecule which introduces disorder into the on-site energies of G bases. The current through the device can be enhanced by the small disorder which avoids the strong interference of electrons at the same energy in some coupling configurations, however the diagonal disorder can suppress the overall current due to the Anderson localization of charge carriers when the disorder is large. In the presence of dephasing effect the current through the device at all coupling configurations can be enhanced as a result of the phase coherence losing of electron. As for the magnetic field response, the magnetoresistance of the device is always suppressed by the counter ions and dephasing effect.

  9. Secondary Ion Mass Spectrometry Imaging of Molecular Distributions in Cultured Neurons and their Processes: Comparative Analysis of Sample Preparation

    PubMed Central

    Tucker, Kevin R.; Li, Zhen; Rubakhin, Stanislav S.; Sweedler, Jonathan V.

    2012-01-01

    Neurons often exhibit a complex chemical distribution and topography; therefore, sample preparation protocols that preserve structures ranging from relatively large cell somata to small neurites and growth cones are an important factor in secondary ion mass spectrometry (SIMS) imaging studies. Here, SIMS was used to investigate the subcellular localization of lipids and lipophilic species in neurons from Aplysia californica. Using individual neurons cultured on silicon wafers, we compared and optimized several SIMS sampling approaches. After an initial step to remove the high salt culturing media, formaldehyde, paraformaldehyde and glycerol, and various combinations thereof, were tested for their ability to achieve cell stabilization during and after the removal of extracellular media. These treatments improved the preservation of cellular morphology as visualized with SIMS imaging. For analytes >250 Da, coating the cell surface with a 3.2 nm-thick gold layer increased the ion intensity; multiple analytes previously not observed or observed at low abundance were detected, including intact cholesterol and vitamin E molecular ions. However, once a sample was coated, many of the lower molecular mass (<200 Da) analyte signals were suppressed. The optimum approach depended on the analyte being studied, and these approaches included rinsing with water and cell stabilization with glycerol and 4% paraformaldehyde. The sample preparation methods described here enhance SIMS imaging of processes of individual cultured neurons over a broad mass range with enhanced image contrast. PMID:22930440

  10. Secondary ion mass spectrometry imaging of molecular distributions in cultured neurons and their processes: comparative analysis of sample preparation.

    PubMed

    Tucker, Kevin R; Li, Zhen; Rubakhin, Stanislav S; Sweedler, Jonathan V

    2012-11-01

    Neurons often exhibit a complex chemical distribution and topography; therefore, sample preparation protocols that preserve structures ranging from relatively large cell somata to small neurites and growth cones are important factors in secondary ion mass spectrometry (SIMS) imaging studies. Here, SIMS was used to investigate the subcellular localization of lipids and lipophilic species in neurons from Aplysia californica. Using individual neurons cultured on silicon wafers, we compared and optimized several SIMS sampling approaches. After an initial step to remove the high salt culturing media, formaldehyde, paraformaldehyde, and glycerol, and various combinations thereof, were tested for their ability to achieve cell stabilization during and after the removal of extracellular media. These treatments improved the preservation of cellular morphology as visualized with SIMS imaging. For analytes >250 Da, coating the cell surface with a 3.2 nm-thick gold layer increased the ion intensity; multiple analytes previously not observed or observed at low abundance were detected, including intact cholesterol and vitamin E molecular ions. However, once a sample was coated, many of the lower molecular mass (<200 Da) analyte signals were suppressed. The optimum approach depended on the analyte being studied; the approaches evaluated included rinsing with water and cell stabilization with glycerol and 4 % paraformaldehyde. The sample preparation methods described here enhance SIMS imaging of processes of individual cultured neurons over a broad mass range with enhanced image contrast. PMID:22930440

  11. Secondary Ion Mass Spectrometry Imaging of Molecular Distributions in Cultured Neurons and Their Processes: Comparative Analysis of Sample Preparation

    NASA Astrophysics Data System (ADS)

    Tucker, Kevin R.; Li, Zhen; Rubakhin, Stanislav S.; Sweedler, Jonathan V.

    2012-11-01

    Neurons often exhibit a complex chemical distribution and topography; therefore, sample preparation protocols that preserve structures ranging from relatively large cell somata to small neurites and growth cones are important factors in secondary ion mass spectrometry (SIMS) imaging studies. Here, SIMS was used to investigate the subcellular localization of lipids and lipophilic species in neurons from Aplysia californica. Using individual neurons cultured on silicon wafers, we compared and optimized several SIMS sampling approaches. After an initial step to remove the high salt culturing media, formaldehyde, paraformaldehyde, and glycerol, and various combinations thereof, were tested for their ability to achieve cell stabilization during and after the removal of extracellular media. These treatments improved the preservation of cellular morphology as visualized with SIMS imaging. For analytes >250 Da, coating the cell surface with a 3.2 nm-thick gold layer increased the ion intensity; multiple analytes previously not observed or observed at low abundance were detected, including intact cholesterol and vitamin E molecular ions. However, once a sample was coated, many of the lower molecular mass (<200 Da) analyte signals were suppressed. The optimum approach depended on the analyte being studied; the approaches evaluated included rinsing with water and cell stabilization with glycerol and 4 % paraformaldehyde. The sample preparation methods described here enhance SIMS imaging of processes of individual cultured neurons over a broad mass range with enhanced image contrast.

  12. Interpretation of the vibrational energy level structure of the astructural molecular ion H5 + and all of its deuterated isotopomers

    NASA Astrophysics Data System (ADS)

    Sarka, János; Császár, Attila G.

    2016-04-01

    Variational nuclear motion computations, employing an exact kinetic energy operator and two different potential energy surfaces, are performed to study the first 60 vibrational states of the molecular ion H 5+ ≡ [H2-H-H2]+ and all of its deuterated isotopologues and isotopomers, altogether 12 species. Detailed investigation of the vibrational wavefunctions mostly results in physically intuitive labels not only for the fundamentals but also for the overtone and combination states computed. The torsional motion associated with the left and right diatomics appears to be well separated from the other vibrational degrees of freedom for all species. The unusual structure of the higher-lying bending states and the heavy mixing of the internal motions is partly due to the astructural character of all these molecular ions. The existence of distinct isotopomers in the H 5 - n Dn + , n = 1-4 cases, in the energy range studied, is confirmed. Two rules determine the stability order of the isotopomers: first, when possible, H prefers to stay in the middle of the ions rather than at the sides, and, second, the isotopomer with a homonuclear diatomic at the side is always lower in energy. The large number of precise vibrational energies of the present study, as well as the detailed assignment of the states, should serve as benchmarks for future studies by more approximate nuclear-motion treatments, such as diffusion Monte Carlo and multiconfiguration time-dependent Hartree.

  13. 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

  14. Molecular mechanism of ATP binding and ion channel activation in P2X receptors

    SciTech Connect

    Hattori, Motoyuki; Gouaux, Eric

    2012-10-24

    P2X receptors are trimeric ATP-activated ion channels permeable to Na{sup +}, K{sup +} and Ca{sup 2+}. The seven P2X receptor subtypes are implicated in physiological processes that include modulation of synaptic transmission, contraction of smooth muscle, secretion of chemical transmitters and regulation of immune responses. Despite the importance of P2X receptors in cellular physiology, the three-dimensional composition of the ATP-binding site, the structural mechanism of ATP-dependent ion channel gating and the architecture of the open ion channel pore are unknown. Here we report the crystal structure of the zebrafish P2X4 receptor in complex with ATP and a new structure of the apo receptor. The agonist-bound structure reveals a previously unseen ATP-binding motif and an open ion channel pore. ATP binding induces cleft closure of the nucleotide-binding pocket, flexing of the lower body {beta}-sheet and a radial expansion of the extracellular vestibule. The structural widening of the extracellular vestibule is directly coupled to the opening of the ion channel pore by way of an iris-like expansion of the transmembrane helices. The structural delineation of the ATP-binding site and the ion channel pore, together with the conformational changes associated with ion channel gating, will stimulate development of new pharmacological agents.

  15. Thermodynamic model for electron emission and negative- and positive-ion formation in keV molecular collisions

    NASA Astrophysics Data System (ADS)

    Juhász, Z.

    2016-08-01

    A statistical-type model is developed to describe the ion production and electron emission in collisions of (molecular) ions with atoms. The model is based on the Boltzmann population of the bound electronic energy levels of the quasimolecule formed in the collision and the discretized continuum. The discretization of the continuum is implemented by a free-electron gas in a box model assuming an effective square potential of the quasimolecule. The temperature of the electron gas is calculated by taking into account a thermodynamically adiabatic process due to the change of the effective volume of the quasimolecule as the system evolves. The system may undergo a transition with a small probability from the discretized continuum to the states of the complementary continuum. It is assumed that these states are decoupled from the thermodynamic time development. The decoupled states overwhelmingly determine the yield of the asymptotically observed fragment ions. The main motivation of this work is to describe the recently observed H- ion production in O H++Ar collisions. The obtained differential cross sections for H- formation, cation production, and electron emission are close to the experimental ones. Calculations for the atomic systems O++Ar and H++Ar are also in reasonable agreement with the experiments indicating that the model can be applied to a wide class of collisions.

  16. Molecular Dynamics Analysis of Ion Incident Energy and Angle Dependences of Si etching with Cl, Br, and HBr beams

    NASA Astrophysics Data System (ADS)

    Nakazaki, Nobuya; Tsuda, Hirotaka; Takao, Yoshinori; Eriguchi, Koji; Ono, Kouichi

    2011-10-01

    Profile anomalies and surface roughness are now critical issues to be resolved in the plasma etching of nanometer-scale microelectronic devices, which in turn requires a better understanding of the effects of the ion incident angle on surface reaction kinetics. For example, the line edge and line width roughness of feature sidewalls and the roughness of bottom surfaces of the feature are assumed to be caused by the angular distribution of incident ions onto feature surfaces. This paper presents a classical molecular dynamics (MD) simulation of Si(100) etching by Cl+, Br+, and HBr+ ion beams with different incident energies (Ei = 20-300 eV) and angles (θ = 0°-90°), where an improved Stillinger-Weber interatomic potential model is used for Si/halogen interactions. The results indicated that the surface reaction kinetics exhibit a characteristic of the ion-enhanced etching at lower energies, where the etch yield is maximum at normal incidence, while a characteristics of the physical sputtering at higher energies, where the yield is maximum at off-normal incidence.

  17. Molecular Structures and Ion Mobility Cross Sections: Analysis of the Effects of He and N2 Buffer Gas.

    PubMed

    Bleiholder, Christian; Johnson, Nicholas R; Contreras, Stephanie; Wyttenbach, Thomas; Bowers, Michael T

    2015-07-21

    An empirically observed correlation between ion mobility cross sections in helium and nitrogen buffer gases was examined as a function of temperature, molecular size, and shape. Experimental cross sections were determined for tetraglycine, bradykinin, angiotensin 2, melittin, and ubiquitin at 300 K and in the range from 80 to 550 K on home-built instruments and calculated by the projection superposition approximation (PSA) method. The PSA was also used to predict cross sections for larger systems such as human pancreatic alpha-amylase, concanavalin, Pichia pastoris lysyl oxidase, and Klebsiella pneumoniae acetolactate synthase. The data show that the ratio of cross sections in helium and nitrogen depends significantly on the temperature of the buffer gas as well as the size and shape of the analyte ion. Therefore, the analysis of the data indicates that a simple formula that seeks to quantitatively relate the momentum transfer cross sections observed in two distinct buffer gases lacks a sound physical basis. PMID:26076363

  18. Study of the population inversion mechanisms and superradiance on ion transitions of molecular nitrogen in the filament

    NASA Astrophysics Data System (ADS)

    Ivanov, N. G.; Losev, V. F.; Prokop'ev, V. E.

    2015-12-01

    The experimental results of the inversion population mechanisms study in the resonant electronic transition B3Πg-A3Σu+ of nitrogen ions by optically pumped of air and pure nitrogen by femtosecond laser pulse at a wavelength of 950 nm are presented. It is shown that the inversion results from selective settling of N2+(B2Σu+, v' =0) excited state by multiphoton excitation of the autoionization states of the nitrogen molecule with energy of 18.7 eV. Seed photon for superradiance at transitions of molecular nitrogen ions are photons the axial supercontinuum occurring in the filament on the respective wavelengths. The mode of the superradiance at a wavelength λ = 358.4 nm referred to the transition of the CN molecules was realized.

  19. Coupling mechanical forces to electrical signaling: molecular motors and the intracellular transport of ion channels.

    PubMed

    Barry, Joshua; Gu, Chen

    2013-04-01

    Proper localization of various ion channels is fundamental to neuronal functions, including postsynaptic potential plasticity, dendritic integration, action potential initiation and propagation, and neurotransmitter release. Microtubule-based forward transport mediated by kinesin motors plays a key role in placing ion channel proteins to correct subcellular compartments. PDZ- and coiled-coil-domain proteins function as adaptor proteins linking ionotropic glutamate and GABA receptors to various kinesin motors, respectively. Recent studies show that several voltage-gated ion channel/transporter proteins directly bind to kinesins during forward transport. Three major regulatory mechanisms underlying intracellular transport of ion channels are also revealed. These studies contribute to understanding how mechanical forces are coupled to electrical signaling and illuminating pathogenic mechanisms in neurodegenerative diseases. PMID:22910031

  20. Coupling Mechanical Forces to Electrical Signaling: Molecular Motors and the Intracellular Transport of Ion Channels

    PubMed Central

    Barry, Joshua; Gu, Chen

    2013-01-01

    Proper localization of various ion channels is fundamental to neuronal functions, including postsynaptic potential plasticity, dendritic integration, action potential initiation and propagation, and neurotransmitter release. Microtubule-based forward transport mediated by kinesin motors plays a key role in placing ion channel proteins to correct subcellular compartments. PDZ- and coiled-coil-domain proteins function as adaptor proteins linking ionotropic glutamate and GABA receptors to various kinesin motors, respectively. Recent studies show that several voltage-gated ion channel/transporter proteins directly bind to kinesins during forward transport. Three major regulatory mechanisms underlying intracellular transport of ion channels are also revealed. These studies contribute to understanding how mechanical forces are coupled to electrical signaling and illuminating pathogenic mechanisms in neurodegenerative diseases. PMID:22910031

  1. Solid State Structures of Alkali Metal Ion Complexes Formed by Low-Molecular-Weight Ligands of Biological Relevance.

    PubMed

    Aoki, Katsuyuki; Murayama, Kazutaka; Hu, Ning-Hai

    2016-01-01

    This chapter provides structural data, mainly metal binding sites/modes, observed in crystal structures of alkali metal ion complexes containing low-molecular-weight ligands of biological relevance, mostly obtained from the Cambridge Structural Database (the CSD version 5.35 updated to February 2014). These ligands include (i) amino acids and small peptides, (ii) nucleic acid constituents (excluding quadruplexes and other oligonucleotides), (iii) simple carbohydrates, and (iv) naturally occurring antibiotic ionophores. For some representative complexes of these ligands, some details on the environment of the metal coordination and structural characteristics are described. PMID:26860299

  2. Three-dimensional ordering of cold ion beams in a storage ring: A molecular-dynamics simulation study

    SciTech Connect

    Yuri, Yosuke

    2015-06-29

    Three-dimensional (3D) ordering of a charged-particle beams circulating in a storage ring is systematically studied with a molecular-dynamics simulation code. An ion beam can exhibit a 3D ordered configuration at ultralow temperature as a result of powerful 3D laser cooling. Various unique characteristics of the ordered beams, different from those of crystalline beams, are revealed in detail, such as the single-particle motion in the transverse and longitudinal directions, and the dependence of the tune depression and the Coulomb coupling constant on the operating points.

  3. On the physiological/pathological link between Aβ peptide, cholesterol, calcium ions and membrane deformation: A molecular dynamics study.

    PubMed

    Pannuzzo, Martina

    2016-06-01

    The dynamic interplay between cholesterol, asymmetrically (at physiological condition) or symmetrically (hallmark of aging) distributed in membrane, and β amyloid peptides is investigated by a computational approach. The drawn overall picture, starting from the very appearance of β amyloid peptides and going through their self-assembling into potentially toxic oligomeric species, reinforces some of the experimental and theoretical shots recently reported in literature, while new important molecular hints on the physiological role played by the β amyloid peptide are proposed. The so dreaded formation of amyloid pores selective for the passage of calcium ions could in fact explain their physiological concomitant recruitment in the regulation of synaptic plasticity. PMID:27003127

  4. Reconsideration of metal surface sputtering due to bombardment of high-energy argon ion particles: a molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Kammara, Kishore K.; Kumar, Rakesh; Donbosco, Ferdin S.

    2016-03-01

    Some interesting aspects of metal surface sputtering phenomenon are numerically investigated in this work using the molecular dynamics approach. Along with that, we have carried out a critical analysis of the interaction potentials typically used for modeling. Two metallic surfaces, viz., copper, Cu(100), and nickel, Ni(100), are chosen for study that are bombarded by argon ions at various energies and angles of projection. The sputtering yield is calculated by performing molecular dynamics simulations, and the same is compared with experiments and theoretical predictions wherever possible. Furthermore, other interesting parameters like the kinetic energy, velocity, and scattering angle distribution for sputtered and incident atoms are presented and discussed. Through different case studies, the present work emphasizes on the importance of interaction model used for metal surface modeling for a realistic numerical reproduction of the complex metal surface sputtering process.

  5. Direct mapping of recoil in the ion-pair dissociation of molecular oxygen by a femtosecond depletion method.

    PubMed

    Baklanov, Alexey V; Janssen, Liesbeth M C; Parker, David H; Poisson, Lionel; Soep, Benoit; Mestdagh, Jean-Michel; Gobert, Olivier

    2008-12-01

    Time-resolved dynamics of the photodissociation of molecular oxygen, O(2), via the (3)Sigma(u) (-) ion-pair state have been studied with femtosecond time resolution using a pump-probe scheme in combination with velocity map imaging of the resulting O(+) and O(-) ions. The fourth harmonic of a femtosecond titanium-sapphire (Ti:sapphire) laser (lambda approximately 205 nm) was found to cause three-photon pumping of O(2) to a level at 18.1 eV. The parallel character of the observed O(+) and O(-) images allowed us to conclude that dissociation takes place on the (3)Sigma(u) (-) ion-pair state. The 815 nm fundamental of the Ti:sapphire laser used as probe was found to cause two-photon electron photodetachment starting from the O(2) ion-pair state, giving rise to (O((3)P)+O(+)((4)S)) products. This was revealed by the observed depletion of the yield of the O(-) anion and the appearance of a new O(+) cation signal with a kinetic energy E(transl)(O(+)) dependent on the time delay between the pump and probe lasers. This time-delay dependence of the dissociation dynamics on the ion-pair state has also been simulated, and the experimental and simulated results coincide very well over the experimental delay-time interval from about 130 fs to 20 ps where two- or one-photon photodetachment takes place, corresponding to a change in the R(O(+),O(-)) interatomic distance from 12 to about 900 A. This is one of the first implementations of a depletion scheme in femtosecond pump-probe experiments which could prove to be quite versatile and applicable to many femtosecond time-scale experiments. PMID:19063560

  6. The molecular mechanism of ion-dependent gating in secondary transporters.

    PubMed

    Zhao, Chunfeng; Noskov, Sergei Yu

    2013-10-01

    LeuT-like fold Na-dependent secondary active transporters form a large family of integral membrane proteins that transport various substrates against their concentration gradient across lipid membranes, using the free energy stored in the downhill concentration gradient of sodium ions. These transporters play an active role in synaptic transmission, the delivery of key nutrients, and the maintenance of osmotic pressure inside the cell. It is generally believed that binding of an ion and/or a substrate drives the conformational dynamics of the transporter. However, the exact mechanism for converting ion binding into useful work has yet to be established. Using a multi-dimensional path sampling (string-method) followed by all-atom free energy simulations, we established the principal thermodynamic and kinetic components governing the ion-dependent conformational dynamics of a LeuT-like fold transporter, the sodium/benzyl-hydantoin symporter Mhp1, for an entire conformational cycle. We found that inward-facing and outward-facing states of Mhp1 display nearly the same free energies with an ion absent from the Na2 site conserved across the LeuT-like fold transporters. The barrier separating an apo-state from inward-facing or outward-facing states of the transporter is very low, suggesting stochastic gating in the absence of ion/substrate bound. In contrast, the binding of a Na2 ion shifts the free energy stabilizing the outward-facing state and promoting substrate binding. Our results indicate that ion binding to the Na2 site may also play a key role in the intracellular thin gate dynamics modulation by altering its interactions with the transmembrane helix 5 (TM5). The Potential of Mean Force (PMF) computations for a substrate entrance displays two energy minima that correspond to the locations of the main binding site S1 and proposed allosteric S2 binding site. However, it was found that substrate's binds to the site S1 ∼5 kcal/mol more favorable than that to the

  7. Method and source for producing a high concentration of positively charged molecular hydrogen or deuterium ions

    DOEpatents

    Ehlers, K.W.; Leung, K.N.

    1983-07-26

    One principal object of the present invention is to provide a novel method and apparatus for generating a high concentration of H/sub 2//sup +/ or D/sub 2//sup +/ ions by using a new and improved multicusp ion source. The basic principle in achieving a high percentage of H/sub 2//sup +/ or D/sub 2//sup +/ ions is to extract them from the source as soon as they are produced. Otherwise they will react with background gas molecules to form tri-atomic ions H/sub 3//sup +/ or D/sub 3//sup +/ or be dissociated by electrons. The former reaction H/sub 2//sup +/ + H/sub 2/ ..-->.. H/sub 3//sup +/ + H can have a very short mean free path length lambda. Assuming a background neutral gas density of approximately 3.3 x 10/sup 13/ cm/sup -3/ and a cross-section sigma of approximately 6 x 10/sup -15/ cm/sup 2/, lambda = (n/sub 0/ sigma)/sup -1/ is estimated to be about 5 cm. Thus the distance traversed by the H/sub 2//sup +/ ion before it arrives at the extractor electrode cannot exceed this value. This in turn sets a limit on the length of the source chamber.

  8. Development of a High Resolution Analyzing Magnet System for Heavy Molecular Ions

    NASA Astrophysics Data System (ADS)

    Ghazaly, Mohamed O. A. El; Dehnel, Morgan; Defrance, Pierre

    At the King Abdulaziz City for Science and Technology (KACST, Saudi Arabia), a versatile ion-beam injector was constructed to provide the electrostatic storage ring with the required high-quality ion beams. In order to remove the ambiguity over the ion mass due to the exclusive application of electric fields in the set-up, the injector is being equipped with a high resolution mass analyzing magnet. A high resolution Analyzing Magnet System has been designed to provide a singly-charged ion beam of kinetic energy up to 50 keV, mass up to 1500 Amu, and with the mass resolution fixed to Δm/m =1:1500. The system includes specific entrance and exit slits, designed to sustain the required mass resolution. Furthermore, specific focusing and shaping optics have been added upstream and downstream the system, in order to monitor and adapt the shape of the ion beam at the entrance and exit of the system, respectively. The present paper gives an overview on the design of this mass analyzing magnet system together with the upstream/downstream adapting optics.

  9. Targeting the untargeted in molecular phenomics with structurally-selective ion mobility-mass spectrometry.

    PubMed

    May, Jody Christopher; Gant-Branum, Randi Lee; McLean, John Allen

    2016-06-01

    Systems-wide molecular phenomics is rapidly expanding through technological advances in instrumentation and bioinformatics. Strategies such as structural mass spectrometry, which utilizes size and shape measurements with molecular weight, serve to characterize the sum of molecular expression in biological contexts, where broad-scale measurements are made that are interpreted through big data statistical techniques to reveal underlying patterns corresponding to phenotype. The data density, data dimensionality, data projection, and data interrogation are all critical aspects of these approaches to turn data into salient information. Untargeted molecular phenomics is already having a dramatic impact in discovery science from drug discovery to synthetic biology. It is evident that these emerging techniques will integrate closely in broad efforts aimed at precision medicine. PMID:27132126

  10. [Molecular dynamics simulations of migration of ions and molecules through the acetylcholine receptor channel].

    PubMed

    Shaĭtan, K V; Li, A; Tershkina, K B; Kirpichnikov, M P

    2007-01-01

    A dynamic model of the channel of an acetylcholine receptor in a closed state has been proposed. The channel is formed by five a-helices of subunit M2 and stabilized by the cyclic hydrocarbon (CH2)105. The migration of charged and unchanged van der Waals particles with a diameter of 7.72 A equivalent to the diameter of a hydrated sodium ion has been studied. The migration occurred by the action of external force applied to the complex along the channel axis. In the closed state, the inhibition of ions is due to two components: electrostatic interaction and steric constraints. The van der Waals channel gate is formed by residues 13'-A-Val255, B-Val261, C-Val269, D-Val255, and E-Ile264, and the negatively changed residues occurring in the upper part of the channel have a great effect on ion selectivity. PMID:17633536

  11. Ion and electron beam processing of condensed molecular solids to form thin films

    SciTech Connect

    Ruckman, M.W.; Strongin, M.; Mowlem, J.K.; Moore, J.F.; Strongin, D.R.

    1992-12-31

    Electron and ion beams can be used to deposit thin films and etch surfaces using gas phase precursors. However, the generation of undesirable gas phase products and the diffusion of the reactive species beyond the region irradiated by the electron or ion beam can limit selectivity. In this paper, the feasibility of processing condensed precursors such as diborane, tri-methyl aluminum, ammonia and water at 78 K with low energy ( 100--1000 eV) electron and ion beams (Ar{sup +}, N{sub 2}{sup +} and H{sub 2}{sup +}) ranging in current density from 50 nA to several {mu}a per cm{sup 2} is examined. It was found that boron, boron nitride and stoichiometric aluminum oxide films could be deposited from the condensed volatile; species using charged particle beams and some of the physical and chemical aspects and limitations of this new technique are discussed.

  12. Ion and electron beam processing of condensed molecular solids to form thin films

    SciTech Connect

    Ruckman, M.W.; Strongin, M. ); Mowlem, J.K.; Moore, J.F.; Strongin, D.R. . Dept. of Chemistry)

    1992-01-01

    Electron and ion beams can be used to deposit thin films and etch surfaces using gas phase precursors. However, the generation of undesirable gas phase products and the diffusion of the reactive species beyond the region irradiated by the electron or ion beam can limit selectivity. In this paper, the feasibility of processing condensed precursors such as diborane, tri-methyl aluminum, ammonia and water at 78 K with low energy ( 100--1000 eV) electron and ion beams (Ar[sup +], N[sub 2][sup +] and H[sub 2][sup +]) ranging in current density from 50 nA to several [mu]a per cm[sup 2] is examined. It was found that boron, boron nitride and stoichiometric aluminum oxide films could be deposited from the condensed volatile; species using charged particle beams and some of the physical and chemical aspects and limitations of this new technique are discussed.

  13. Electronic structure and noncovalent interactions within ion-radical complexes of N-(2-furylmethyl)aniline molecular ions.

    PubMed

    Vallejo Narváez, Wilmer E; Rocha-Rinza, Tomás

    2015-03-12

    We investigate the electronic structure and noncovalent interactions within cation-radical complexes that are relevant in the electron impact mass spectrometry of N-(2-furylmethyl)anilines, 4-R-C6H4-NH-CH2-C4H3O with (R = -H, -OCH3, -CH3, -F, -Cl, -Br). In particular, we consider the reactive intermediates that precede the final products of two previously suggested dissociation pathways for these systems, i.e., (i) a direct cleavage of the NH-CH2 bond and (ii) an isomerization/fragmentation mechanism. The study is performed by means of correlated calculations (UCCSD and UMP2) together with density functionals (UM06 an UM06-2x) along with the triple-ζ quality basis set 6-311++G(2d,2p). In addition, we carried out a topological analysis of the electron density in accordance with the quantum theory of atoms in molecules (QTAIM) together with the examination of the noncovalent interaction (NCI) index. In contrast with previous studies based on the UB3LYP approximation, we could determine the transition states associated with both fragmentation pathways. The Rice-Ramsperger-Kassel-Marcus theory, used to determine the relative importance of these dissociation mechanisms, indicates that whereas the direct cleavage and the isomerization/fragmentation reaction routes have similar constant rates at low energy, the former prevails when the energy of the system is increased. The QTAIM analysis reveals that the charge of the cation-radical complex is mainly located on either a furfuryl (direct cleavage mechanism) or a pyrylium (isomerization/fragmentation pathway) ion and that these units interact with a neutral radical aniline moiety. The localization of the positive charge in either a furfuryl or pyrylium cation is in agreement with the preminecence of the m/z = 81 fragment in the mass spectrometry of N-(2-furylmethyl)anilines. Moreover, the QTAIM properties indicate that the α unpaired electron of the system is principally distributed over the nitrogen and the ortho and

  14. Modelling rotations, vibrations, and rovibrational couplings in astructural molecules - a case study based on the H+5 molecular ion

    NASA Astrophysics Data System (ADS)

    Sarka, János; Fábri, Csaba; Szidarovszky, Tamás; Császár, Attila G.; Lin, Zhou; McCoy, Anne B.

    2015-07-01

    One-dimensional (1D) and two-dimensional (2D) models are investigated, which help to understand the unusual rovibrational energy-level structure of the astronomically relevant and chemically interesting astructural molecular ion H+5. Due to the very low hindering barrier characterising the 1D torsion-only vibrational model of H+5, this model yields strongly divergent energy levels. The results obtained using a realistic model for the torsion potential, including the computed (near) degeneracies, can be rationalised in terms of the model with no barrier. Coupling of the torsional motion with a single rotational degree of freedom is also investigated in detail. It is shown how the embedding-dependent rovibrational models yield energy levels that can be rationalised via the 2D vibrational model containing two independent torsions. Insight into the complex rovibrational energy level structure of the models and of H+5 is gained via variational nuclear motion and diffusion Monte Carlo computations and by the analysis of the wavefunctions they provide. The modelling results describing the transition from the zero barrier limit to the large barrier limit should prove to be useful for the important class of molecules and molecular ions that contain two weakly coupled internal rotors.

  15. Molecular Mechanisms of Ultrafiltration Membrane Fouling in Polymer-Flooding Wastewater Treatment: Role of Ions in Polymeric Fouling.

    PubMed

    Liu, Guicai; Yu, Shuili; Yang, Haijun; Hu, Jun; Zhang, Yi; He, Bo; Li, Lei; Liu, Zhiyuan

    2016-02-01

    Polymer (i.e., anionic polyacrylamide (APAM)) fouling of polyvinylidene fluoride (PVDF) ultrafiltration (UF) membranes and its relationships to intermolecular interactions were investigated using atomic force microscopy (AFM). Distinct relations were obtained between the AFM force spectroscopy measurements and calculated fouling resistance over the concentration polarization layer (CPL) and gel layer (GL). The measured maximum adhesion forces (Fad,max) were closely correlated with the CPL resistance (Rp), and the proposed molecular packing property (largely based on the shape of AFM force spectroscopy curve) of the APAM chains was related to the GL resistance (Rg). Calcium ions (Ca(2+)) and sodium ions (Na(+)) caused more severe fouling. In the presence of Ca(2+), the large Rp corresponded to high foulant-foulant Fad,max, resulting in high flux loss. In addition, the Rg with Ca(2+) was minor, but the flux recovery rate after chemical cleaning was the lowest, indicating that Ca(2+) created more challenges in GL cleaning. With Na(+), the fouling behavior was complicated and concentration-dependent. The GL structures with Na(+), which might correspond to the proposed molecular packing states among APAM chains, played essential roles in membrane fouling and GL cleaning. PMID:26735590

  16. Using a superconducting tunnel junction detector to measure the secondary electron emission efficiency for a microchannel plate detector bombarded by large molecular ions

    PubMed

    Westmacott; Frank; Labov; Benner

    2000-01-01

    An energy-sensitive superconducting tunnel junction (STJ) detector was used to measure the secondary electron emission efficiency, epsilon(e), for a microchannel plate (MCP) detector bombarded by large (up to 66 kDa), slow moving (<40 km/s) molecular ions. The method used is new and provides a more direct procedure for measuring the efficiency of secondary electron emission from a surface. Both detectors were exposed simultaneously to nearly identical ion fluxes. By exposing only a small area of the MCP detector to ions, such that the area exposed was effectively the same as the size of the STJ detector, the number of ions detected with each detector were directly comparable. The STJ detector is 100% efficient for detecting ions in the energy regime investigated and therefore it can be used to measure the detection efficiency and secondary electron emission efficiency of the MCP. The results are consistent with measurements made by other groups and provide further characterization of the loss in sensitivity noted previously when MCP detectors have been used to detect high-mass ions. Individual molecular ions of mass 66 kDa with 30 keV kinetic energy were measured to have about a 5% probability of producing one or more electrons when impacting the MCP. When ion energy was reduced to 10 keV, the detection probability decreased to 1 %. The secondary electron yield was calculated from the secondary electron emission efficiency and found to scale linearly with the mass of the impinging molecular ion and to about the fourth power of ion velocity. Secondary electrons were observed for primary ion impacts >5 km/s, regardless of mass, and no evidence of a velocity (detection) threshold was observed. Copyright 2000 John Wiley & Sons, Ltd. PMID:11006596

  17. Coordination and Hydrolysis of Plutonium Ions in Aqueous Solution using Car-Parrinello Molecular Dynamics Free Energy Simulations

    SciTech Connect

    Odoh, Samuel O.; Bylaska, Eric J.; De Jong, Wibe A.

    2013-11-27

    Car-Parrinello molecular dynamics (CPMD) simulations have been used to examine the hydration structures, coordination energetics and the first hydrolysis constants of Pu3+, Pu4+, PuO2+ and PuO22+ ions in aqueous solution at 300 K. The coordination numbers and structural properties of the first shell of these ions are in good agreement with available experimental estimates. The hexavalent PuO22+ species is coordinated to 5 aquo ligands while the pentavalent PuO2+ complex is coordinated to 4 aquo ligands. The Pu3+ and Pu4+ ions are both coordinated to 8 water molecules. The first hydrolysis constants obtained for Pu3+ and PuO22+ are 6.65 and 5.70 respectively, all within 0.3 pH units of the experimental values (6.90 and 5.50 respectively). The hydrolysis constant of Pu4+, 0.17, disagrees with the value of -0.60 in the most recent update of the Nuclear Energy Agency Thermochemical Database (NEA-TDB) but supports recent experimental findings. The hydrolysis constant of PuO2+, 9.51, supports the experimental results of Bennett et al. (Radiochim. Act. 1992, 56, 15). A correlation between the pKa of the first hydrolysis reaction and the effective charge of the plutonium center was found.

  18. Molecular origin of high free energy barriers for alkali metal ion transfer through ionic liquid-graphene electrode interfaces.

    PubMed

    Ivaništšev, Vladislav; Méndez-Morales, Trinidad; Lynden-Bell, Ruth M; Cabeza, Oscar; Gallego, Luis J; Varela, Luis M; Fedorov, Maxim V

    2016-01-14

    In this work we study mechanisms of solvent-mediated ion interactions with charged surfaces in ionic liquids by molecular dynamics simulations, in an attempt to reveal the main trends that determine ion-electrode interactions in ionic liquids. We compare the interfacial behaviour of Li(+) and K(+) at a charged graphene sheet in a room temperature ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate, and its mixtures with lithium and potassium tetrafluoroborate salts. Our results show that there are dense interfacial solvation structures in these electrolytes that lead to the formation of high free energy barriers for these alkali metal cations between the bulk and direct contact with the negatively charged surface. We show that the stronger solvation of Li(+) in the ionic liquid leads to the formation of significantly higher interfacial free energy barriers for Li(+) than for K(+). The high free energy barriers observed in our simulations can explain the generally high interfacial resistance in electrochemical storage devices that use ionic liquid-based electrolytes. Overcoming these barriers is the rate-limiting step in the interfacial transport of alkali metal ions and, hence, appears to be a major drawback for a generalised application of ionic liquids in electrochemistry. Some plausible strategies for future theoretical and experimental work for tuning them are suggested. PMID:26661060

  19. Molecular dynamics simulations of void and helium bubble stability in amorphous silicon during heavy-ion bombardment

    SciTech Connect

    Okuniewski, Maria A.; Ashkenazy, Yinon; Heuser, Brent J.; Averback, Robert S.

    2004-10-15

    A study of void and helium (He) bubble stability in amorphous silicon (a-Si) subjected to heavy-ion bombardment was conducted with molecular dynamics simulations. The effects of incident ion energy, incident ion direction, and He pressure were investigated. He bubbles with pressures equal to or greater than 0.1 kbar were found to be stable during isotropic 2 keV xenon (Xe) irradiation. Bubbles with pressures below this limit collapsed completely. On the other hand, voids and bubbles of all pressures were stable following unidirectional 2 keV Xe bombardment. In this case, the voids and bubbles became elongated and resisted closure, a phenomenon attributed to the inability of liquid Si to wet the flat, low-curvature internal surfaces of the open-volume defect. The void closure rates varied from 55 to 180 A/dpa as the Xe projectile energy increased from 0.2 keV to 2 keV, respectively. An analytical model based on a viscous flow mechanism is presented to describe the behavior associated with the slowest closure rate. The faster rates are attributed to pressure-induced convective flow into the void.

  20. Effect of bound state of water on hydronium ion mobility in hydrated Nafion using molecular dynamics simulations

    SciTech Connect

    Mabuchi, Takuya; Tokumasu, Takashi

    2014-09-14

    We have performed a detailed analysis of the structural properties of the sulfonate groups in terms of isolated and overlapped solvation shells in the nanostructure of hydrated Nafion membrane using classical molecular dynamics simulations. Our simulations have demonstrated the correlation between the two different areas in bound water region, i.e., the first solvation shell, and the vehicular transport of hydronium ions at different water contents. We have employed a model of the Nafion membrane using the improved force field, which is newly modified and validated by comparing the density and water diffusivity with those obtained experimentally. The first solvation shells were classified into the two types, the isolated area and the overlapped area. The mean residence times of solvent molecules explicitly showed the different behaviors in each of those areas in terms of the vehicular transport of protons: the diffusivity of classical hydronium ions in the overlapped area dominates their total diffusion at lower water contents while that in the isolated area dominates for their diffusion at higher water contents. The results provided insights into the importance role of those areas in the solvation shells for the diffusivity of vehicular transport of hydronium ions in hydrated Nafion membrane.

  1. High-precision laser and rf spectroscopy of atomic, molecular, and slow ion beams

    SciTech Connect

    Childs, W.J.; Goodman, L.S.; Sen, A.

    1987-01-01

    Interesting new results were obtained in 1986 in high-precision Laser-rf studies of neutral atoms, neutral molecules, and atomic ions. Because of their novelty, the ionic results are discussed at some length and then summarize briefly results in the other two areas.

  2. Effects of Bisphenol A on ion channels: Experimental evidence and molecular mechanisms.

    PubMed

    Soriano, Sergi; Ripoll, Cristina; Alonso-Magdalena, Paloma; Fuentes, Esther; Quesada, Ivan; Nadal, Angel; Martinez-Pinna, Juan

    2016-07-01

    Bisphenol A (BPA) is an endocrine-disrupting chemical (EDC) produced in huge quantities in the manufacture of polycarbonate plastics and epoxy resins. It is present in most humans in developed countries, acting as a xenoestrogen and it is considered an environmental risk factor associated to several diseases. Among the whole array of identified mechanisms by which BPA can interfere with physiological processes in living organisms, changes on ion channel activity is one of the most poorly understood. There is still little evidence about BPA regulation of ion channel expression and function. However, this information is key to understand how BPA disrupts excitable and non-excitable cells, including neurons, endocrine cells and muscle cells. This report is the result of a comprehensive literature review on the effects of BPA on ion channels. We conclude that there is evidence to say that these important molecules may be key end-points for EDCs acting as xenoestrogens. However, more research on channel-mediated BPA effects is needed. Particularly, mechanistic studies to unravel the pathophysiological actions of BPA on ion channels at environmentally relevant doses. PMID:26930576

  3. Effects of molecular model, ionic strength, divalent ions, and hydrophobic interaction on human neurofilament conformation

    NASA Astrophysics Data System (ADS)

    Lee, Joonseong; Kim, Seonghoon; Chang, Rakwoo; Jayanthi, Lakshmi; Gebremichael, Yeshitila

    2013-01-01

    The present study examines the effects of the model dependence, ionic strength, divalent ions, and hydrophobic interaction on the structural organization of the human neurofilament (NF) brush, using canonical ensemble Monte Carlo (MC) simulations of a coarse-grained model with the amino-acid resolution. The model simplifies the interactions between the NF core and the sidearm or between the sidearms by the sum of excluded volume, electrostatic, and hydrophobic interactions, where both monovalent salt ions and solvents are implicitly incorporated into the electrostatic interaction potential. Several important observations are made from the MC simulations of the coarse-grained model NF systems. First, the mean-field type description of monovalent salt ions works reasonably well in the NF system. Second, the manner by which the NF sidearms are arranged on the surface of the NF backbone core has little influence on the lateral extension of NF sidearms. Third, the lateral extension of the NF sidearms is highly affected by the ionic strength of the system: at low ionic strength, NF-M is most extended but at high ionic strength, NF-H is more stretched out because of the effective screening of the electrostatic interaction. Fourth, the presence of Ca2 + ions induces the attraction between negatively charged residues, which leads to the contraction of the overall NF extension. Finally, the introduction of hydrophobic interaction does not change the general structural organization of the NF sidearms except that the overall extension is contracted.

  4. Molecular formulae of marine and terrigenous dissolved organic matter detected by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry

    NASA Astrophysics Data System (ADS)

    Koch, Boris P.; Witt, Matthias; Engbrodt, Ralph; Dittmar, Thorsten; Kattner, Gerhard

    2005-07-01

    The chemical structure of refractory marine dissolved organic matter (DOM) is still largely unknown. Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR-MS) was used to resolve the complex mixtures of DOM and provide valuable information on elemental compositions on a molecular scale. We characterized and compared DOM from two sharply contrasting aquatic environments, algal-derived DOM from the Weddell Sea (Antarctica) and terrigenous DOM from pore water of a tropical mangrove area in northern Brazil. Several thousand molecular formulas in the mass range of 300-600 Da were identified and reproduced in element ratio plots. On the basis of molecular elemental composition and double-bond equivalents (DBE) we calculated an average composition for marine DOM. O/C ratios in the marine samples were lower (0.36 ± 0.01) than in the mangrove pore-water sample (0.42). A small proportion of chemical formulas with higher molecular mass in the marine samples were characterized by very low O/C and H/C ratios probably reflecting amphiphilic properties. The average number of unsaturations in the marine samples was surprisingly high (DBE = 9.9; mangrove pore water: DBE = 9.4) most likely due to a significant contribution of carbonyl carbon. There was no significant difference in elemental composition between surface and deep-water DOM in the Weddell Sea. Although there were some molecules with unique marine elemental composition, there was a conspicuous degree of similarity between the terrigenous and algal-derived end members. Approximately one third of the molecular formulas were present in all marine as well as in the mangrove samples. We infer that different forms of microbial degradation ultimately lead to similar structural features that are intrinsically refractory, independent of the source of the organic matter and the environmental conditions where degradation took place.

  5. Explanation of efficient quenching of molecular ion vibrational motion by ultracold atoms.

    PubMed

    Stoecklin, Thierry; Halvick, Philippe; Gannouni, Mohamed Achref; Hochlaf, Majdi; Kotochigova, Svetlana; Hudson, Eric R

    2016-01-01

    Buffer gas cooling of molecules to cold and ultracold temperatures is a promising technique for realizing a host of scientific and technological opportunities. Unfortunately, experiments using cryogenic buffer gases have found that although the molecular motion and rotation are quickly cooled, the molecular vibration relaxes at impractically long timescales. Here, we theoretically explain the recently observed exception to this rule: efficient vibrational cooling of BaCl(+) by a laser-cooled Ca buffer gas. We perform intense close-coupling calculations that agree with the experimental result, and use both quantum defect theory and a statistical capture model to provide an intuitive understanding of the system. This result establishes that, in contrast to the commonly held opinion, there exists a large class of systems that exhibit efficient vibrational cooling and therefore supports a new route to realize the long-sought opportunities offered by molecular structure. PMID:27088647

  6. Explanation of efficient quenching of molecular ion vibrational motion by ultracold atoms

    NASA Astrophysics Data System (ADS)

    Stoecklin, Thierry; Halvick, Philippe; Gannouni, Mohamed Achref; Hochlaf, Majdi; Kotochigova, Svetlana; Hudson, Eric R.

    2016-04-01

    Buffer gas cooling of molecules to cold and ultracold temperatures is a promising technique for realizing a host of scientific and technological opportunities. Unfortunately, experiments using cryogenic buffer gases have found that although the molecular motion and rotation are quickly cooled, the molecular vibration relaxes at impractically long timescales. Here, we theoretically explain the recently observed exception to this rule: efficient vibrational cooling of BaCl+ by a laser-cooled Ca buffer gas. We perform intense close-coupling calculations that agree with the experimental result, and use both quantum defect theory and a statistical capture model to provide an intuitive understanding of the system. This result establishes that, in contrast to the commonly held opinion, there exists a large class of systems that exhibit efficient vibrational cooling and therefore supports a new route to realize the long-sought opportunities offered by molecular structure.

  7. Explanation of efficient quenching of molecular ion vibrational motion by ultracold atoms

    PubMed Central

    Stoecklin, Thierry; Halvick, Philippe; Gannouni, Mohamed Achref; Hochlaf, Majdi; Kotochigova, Svetlana; Hudson, Eric R.

    2016-01-01

    Buffer gas cooling of molecules to cold and ultracold temperatures is a promising technique for realizing a host of scientific and technological opportunities. Unfortunately, experiments using cryogenic buffer gases have found that although the molecular motion and rotation are quickly cooled, the molecular vibration relaxes at impractically long timescales. Here, we theoretically explain the recently observed exception to this rule: efficient vibrational cooling of BaCl+ by a laser-cooled Ca buffer gas. We perform intense close-coupling calculations that agree with the experimental result, and use both quantum defect theory and a statistical capture model to provide an intuitive understanding of the system. This result establishes that, in contrast to the commonly held opinion, there exists a large class of systems that exhibit efficient vibrational cooling and therefore supports a new route to realize the long-sought opportunities offered by molecular structure. PMID:27088647

  8. Effect of ion structure on conductivity in lithium-doped ionic liquid electrolytes: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Liu, Hongjun; Maginn, Edward

    2013-09-01

    Molecular dynamics simulations were performed to examine the role cation and anion structure have on the performance of ionic liquid (IL) electrolytes for lithium conduction over the temperature range of 320-450 K. Two model ionic liquids were studied: 1-butyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide ([bmim][Tf2N]) and 1-butyl-4-methylpyridinium pyrrolide ([bmpyr][pyl]) doped with Li[Tf2N] and Li[pyl], respectively. The results have demonstrated that the Li+ doped IL containing the planar [bmpyr] cation paired with the planar [pyl] anion significantly outperformed the [bmim][Tf2N] IL. The different coordination of Li+ with the [Tf2N]- or [pyl]- anions produces a remarkable change in IL structure with a concomitant effect on the transport of all ions. For the doped [bmim][Tf2N], each Li+ is coordinated by four oxygen atoms from [Tf2N]- anions. Formation of a rigid structure between Li+ and [Tf2N]- induces a decrease in the mobility of all ions. In contrast, for the doped [bmpyr][pyl], each Li+ is coordinated by two nitrogen atoms from [pyl]- anions. The original alternating structure cation|anion|cation in the neat [bmpyr][pyl] is replaced by another alternating structure cation|anion|Li+|anion|cation in the doped [bmpyr][pyl]. Increases of Li+ mole fraction in doped [bmpyr][pyl] affects the dynamics to a much lesser extent compared with [bmim][Tf2N] and leads to reduced diffusivities of cations and anions, but little change in the dynamics of Li+. More importantly, the calculations predict that the Li+ ion conductivity of doped [bmpyr][pyl] is comparable to that observed in organic liquid electrolytes and is about an order of magnitude higher than that of doped [bmim][Tf2N]. Such Li+ conductivity improvement suggests that this and related ILs may be promising candidates for use as electrolytes in lithium ion batteries and capacitors.

  9. Single-ion hydration thermodynamics from clusters to bulk solutions: Recent insights from molecular modeling

    DOE PAGESBeta

    Vlcek, Lukas; Chialvo, Ariel A.

    2016-01-03

    The importance of single-ion hydration thermodynamic properties for understanding the driving forces of aqueous electrolyte processes, along with the impossibility of their direct experimental measurement, have prompted a large number of experimental, theoretical, and computational studies aimed at separating the cation and anion contributions. Here we provide an overview of historical approaches based on extrathermodynamic assumptions and more recent computational studies of single-ion hydration in order to evaluate the approximations involved in these methods, quantify their accuracy, reliability, and limitations in the light of the latest developments. Finally, we also offer new insights into the factors that influence the accuracymore » of ion–water interaction models and our views on possible ways to fill this substantial knowledge gap in aqueous physical chemistry.« less

  10. Influence of ions on genome packaging and ejection: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Ali, I.; Marenduzzo, D.

    2011-09-01

    We, theoretically, investigate the effect of ions on the packing and ejection dynamics of flexible and semiflexible polymers from spherical viral capsids. We find that when the polymer charge is less screened, or the Debye length increases (corresponding to a buffer with low concentration of a monovalent salt, such as Na+), the packing becomes more difficult and it may stop midway. Ejection, instead, proceeds more easily if the electrostatic screening is small. On the other hand, more screening (corresponding, for example, to the addition of divalent ions such as Mg2 +) results in easier packing and slower ejection. We interpret this as resulting from electrostatic forces among the various polymer sections, which can be tuned with the type of salt present in the solution. We also discuss how the DNA structure inside the capsid changes due to screened electrostatic interactions.

  11. Emerging Molecular Mechanisms of Signal Transduction in Pentameric Ligand-Gated Ion Channels.

    PubMed

    Nemecz, Ákos; Prevost, Marie S; Menny, Anaïs; Corringer, Pierre-Jean

    2016-05-01

    Nicotinic acetylcholine, serotonin type 3, γ-amminobutyric acid type A, and glycine receptors are major players of human neuronal communication. They belong to the family of pentameric ligand-gated ion channels, sharing a highly conserved modular 3D structure. Recently, high-resolution structures of both open- and closed-pore conformations have been solved for a bacterial, an invertebrate, and a vertebrate receptor in this family. These data suggest that a common gating mechanism occurs, coupling neurotransmitter binding to pore opening, but they also pinpoint significant differences among subtypes. In this Review, we summarize the structural and functional data in light of these gating models and speculate about their mechanistic consequences on ion permeation, pathological mutations, as well as functional regulation by orthosteric and allosteric effectors. PMID:27151638

  12. 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.

  13. Increasing measurement sensitivity for the electron's electric dipole moment using trapped molecular ions

    NASA Astrophysics Data System (ADS)

    Zhou, Yan; Gresh, Daniel; Cairncross, William; Grau, Matt; Ng, Kia Boon; Ni, Yiqi; Cornell, Eric; Ye, Jun

    2016-05-01

    Based on our latest measurements of the electron's electric dipole moment (eEDM) using trapped HfF+ ions, after 100 hours of data collection, the statistical error still dominates in our overall uncertainty budget. Overcoming the bottleneck of limited statistical sensitivity can increase the precision of the eEDM measurement directly. Here, we present the progress of three ongoing experiments: (1) applying STImulated Raman Adiabatic Passage (STIRAP) with rotating linear polarization for increased coherent population transfer from the ground X1Σ+ state to the eEDM-sensitive 3Δ1 state; (2) implementing a new ion-counting detector toward shot-noise limited sensitivity with significant suppression technical noise; (3) exploring the possibility of using the ground 3Δ1 state of ThF+ ions to realize a larger effective electric field and a longer coherence time. These experiments provide a route towards an order of magnitude increase in statistical sensitivity in the second generation of measurements.

  14. Initiating Molecular Growth in the Interstellar Medium via Dimeric Complexes of Observed Ions and Molecules

    NASA Technical Reports Server (NTRS)

    Bera, Partha P.; Head-Gordon, Martin; Lee, Timothy J.

    2011-01-01

    A feasible initiation step for particle growth in the interstellar medium (ISM) is simulated by means of ab quantum chemistry methods. The systems studied are dimer ions formed by pairing nitrogen containing small molecules known to exist in the ISM with ions of unsaturated hydrocarbons or vice versa. Complexation energies, structures of ensuing complexes and electronic excitation spectra of the encounter complexes are estimated using various quantum chemistry methods. Moller-Plesset perturbation theory (MP2, Z-averaged perturbation theory (ZAP2), coupled cluster singles and doubles with perturbative triples corrections (CCSD(T)), and density functional theory (DFT) methods (B3LYP) were employed along with the correlation consistent cc-pVTZ and aug-cc-pVTZ basis sets. Two types of complexes are predicted. One type of complex has electrostatic binding with moderate (7-20 kcal per mol) binding energies, that are nonetheless significantly stronger than typical van der Waals interactions between molecules of this size. The other type of complex develops strong covalent bonds between the fragments. Cyclic isomers of the nitrogen containing complexes are produced very easily by ion-molecule reactions. Some of these complexes show intense ultraviolet visible spectra for electronic transitions with large oscillator strengths at the B3LYP, omegaB97, and equations of motion coupled cluster (EOM-CCSD) levels. The open shell nitrogen containing carbonaceous complexes especially exhibit a large oscillator strength electronic transition in the visible region of the electromagnetic spectrum.

  15. An energy-filtering device coupled to a quadrupole mass spectrometer for soft-landing molecular ions on surfaces with controlled energy

    SciTech Connect

    Bodin, A.; Laloo, R.; Abeilhou, P.; Guiraud, L.; Gauthier, S.; Martrou, D.

    2013-09-15

    We have developed an energy-filtering device coupled to a quadrupole mass spectrometer to deposit ionized molecules on surfaces with controlled energy in ultra high vacuum environment. Extensive numerical simulations as well as direct measurements show that the ion beam flying out of a quadrupole exhibits a high-energy tail decreasing slowly up to several hundred eV. This energy distribution renders impossible any direct soft-landing deposition of molecular ions. To remove this high-energy tail by energy filtering, a 127° electrostatic sector and a specific triplet lenses were designed and added after the last quadrupole of a triple quadrupole mass spectrometer. The results obtained with this energy-filtering device show clearly the elimination of the high-energy tail. The ion beam that impinges on the sample surface satisfies now the soft-landing criterion for molecular ions, opening new research opportunities in the numerous scientific domains involving charges adsorbed on insulating surfaces.

  16. Effect of Increasing Molecular Weight on the A and B blocks of a Single-ion-conducting Block Copolymer Electrolyte for Lithium Batteries

    NASA Astrophysics Data System (ADS)

    Rojas, Adriana; Inceoglu, Sebnem; Thakker, Kanav; Mackay, Nikolaus; Balsara, Nitash

    Single-ion-conducting block copolymer electrolytes are desirable for lithium metal batteries due to their ability to eliminate salt concentration gradients across the electrolyte; i.e., the lithium ion transference number is approximately unity. A series of poly(ethylene oxide)- b-poly(styrenesulfonyllithium(trifluoromethylsulfonyl)imide) (PEO- b-PSLiTFSI) copolymers was studied wherein the molecular weights of both blocks were varied. Small angle x-ray scattering and ac impedance spectroscopy were used to probe the dependence of ionic conductivity on morphology. Preliminary work suggests that increasing the molecular weights of the blocks results in increased disorder and lower conductivity.

  17. Investigation of structural and dynamical properties of hafnium(IV) ion in liquid ammonia: An ab initio QM/MM molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Suwardi; Pranowo, Harno Dwi; Armunanto, Ria

    2015-09-01

    The structure and dynamics of Hf4+ ion in liquid ammonia have been investigated by an ab initio quantum mechanics molecular mechanics (QM/MM) molecular dynamics simulation. The structural data was obtained in terms of radial distribution, coordination number and angular distribution, and then the dynamics in mean ligand residence time. The Hf4+ ion is coordinated by five ammonia molecules in the first solvation shell showing a distorted square pyramidal structure with an average Hf4+-N distance of 2.38 Å. No ammonia ligand was observed for exchange processes between the first and second shells.

  18. Growth of 3C-SiC( 1 0 0 ) thin films on Si( 1 0 0 ) by the molecular ion beam deposition

    NASA Astrophysics Data System (ADS)

    Matsumoto, Takashi; Kiuchi, Masato; Sugimoto, Satoshi; Goto, Seiichi

    2001-11-01

    Silicon carbide (SiC) thin films were produced on Si(1 0 0) at low growth temperatures of 750-1000°C, using the molecular ion beam deposition (IBD) technique with a precursor of organosilicon ions. The ions extracted at 25 keV were mass selected, and decelerated to 100 eV. The precursor of methylsilicenium ions (SiCH 3+), which has a Si-C bond in the molecular structure, was generated from dimethylsilane (SiH 2(CH 3) 2). The energy distribution of SiCH 3+ ions was measured by a PPM421 plasma process monitor. It was confirmed that the energy distributions were 100±1 eV. The chemical bondings and surface structures of SiC thin films were analyzed by Raman spectroscopy and reflection high-energy electron diffraction (RHEED). In the Raman spectrum, a peak at 796 cm -1 was assigned to transverse optic phonon scattering in 3C-SiC. As a result of the analysis of RHEED patterns, 3C-SiC(1 0 0) were formed on Si(1 0 0) substrates. Using the molecular IBD technique with the precursor of methylsilicenium ions, the formation of SiC thin films is available on Si(1 0 0) at low temperature (750°C).

  19. Ion Association in High-Temperature Aqueous HCl Solutions. A Molecular Simulation Study

    SciTech Connect

    Chialvo, A.A.; Cummings, P.T.; Mesmer, R.E.; Simonson, J.M.

    1999-10-30

    The profiles of the potential of mean force for the Cl- - H3O+ pair, as predicted by two ab initio models, are determined by constraint molecular dynamics simulation at a near-critical condition. The corresponding association constants are then determined and compared with that from conductance measurements to test the reliability of the current simulation models for HCl.

  20. Molecular pathophysiology and pharmacology of the voltage-sensing module of neuronal ion channels

    PubMed Central

    Miceli, Francesco; Soldovieri, Maria Virginia; Ambrosino, Paolo; De Maria, Michela; Manocchio, Laura; Medoro, Alessandro; Taglialatela, Maurizio

    2015-01-01

    Voltage-gated ion channels (VGICs) are membrane proteins that switch from a closed to open state in response to changes in membrane potential, thus enabling ion fluxes across the cell membranes. The mechanism that regulate the structural rearrangements occurring in VGICs in response to changes in membrane potential still remains one of the most challenging topic of modern biophysics. Na+, Ca2+ and K+ voltage-gated channels are structurally formed by the assembly of four similar domains, each comprising six transmembrane segments. Each domain can be divided into two main regions: the Pore Module (PM) and the Voltage-Sensing Module (VSM). The PM (helices S5 and S6 and intervening linker) is responsible for gate opening and ion selectivity; by contrast, the VSM, comprising the first four transmembrane helices (S1–S4), undergoes the first conformational changes in response to membrane voltage variations. In particular, the S4 segment of each domain, which contains several positively charged residues interspersed with hydrophobic amino acids, is located within the membrane electric field and plays an essential role in voltage sensing. In neurons, specific gating properties of each channel subtype underlie a variety of biological events, ranging from the generation and propagation of electrical impulses, to the secretion of neurotransmitters and to the regulation of gene expression. Given the important functional role played by the VSM in neuronal VGICs, it is not surprising that various VSM mutations affecting the gating process of these channels are responsible for human diseases, and that compounds acting on the VSM have emerged as important investigational tools with great therapeutic potential. In the present review we will briefly describe the most recent discoveries concerning how the VSM exerts its function, how genetically inherited diseases caused by mutations occurring in the VSM affects gating in VGICs, and how several classes of drugs and toxins

  1. Some Dynamical Features of Molecular Fragmentation by Electrons and Swift Ions

    NASA Astrophysics Data System (ADS)

    Montenegro, E. C.; Sigaud, L.; Wolff, W.; Luna, H.; Natalia, Ferreira

    To date, the large majority of studies on molecular fragmentation by swift charged particles have been carried out using simple molecules, for which reliable Potential Energy Curves are available to interpret the measured fragmentation yields. For complex molecules the scenario is quite different and such guidance is not available, obscuring even a simple organization of the data which are currently obtained for a large variety of molecules of biological or technological interest. In this work we show that a general and relatively simple methodology can be used to obtain a broader picture of the fragmentation pattern of an arbitrary molecule. The electronic ionization or excitation cross section of a given molecular orbital, which is the first part of the fragmentation process, can be well scaled by a simple and general procedure at high projectile velocities. The fragmentation fractions arising from each molecular orbital can then be achieved by matching the calculated ionization with the measured fragmentation cross sections. Examples for Oxygen, Chlorodifluoromethane and Pyrimidine molecules are presented.

  2. Ion-exchange molecularly imprinted polymer for the extraction of negatively charged acesulfame from wastewater samples.

    PubMed

    Zarejousheghani, Mashaalah; Schrader, Steffi; Möder, Monika; Lorenz, Pierre; Borsdorf, Helko

    2015-09-11

    Acesulfame is a known indicator that is used to identify the introduction of domestic wastewater into water systems. It is negatively charged and highly water-soluble at environmental pH values. In this study, a molecularly imprinted polymer (MIP) was synthesized for negatively charged acesulfame and successfully applied for the selective solid phase extraction (SPE) of acesulfame from influent and effluent wastewater samples. (Vinylbenzyl)trimethylammonium chloride (VBTA) was used as a novel phase transfer reagent, which enhanced the solubility of negatively charged acesulfame in the organic solvent (porogen) and served as a functional monomer in MIP synthesis. Different molecularly imprinted polymers were synthesized to optimize the extraction capability of acesulfame. The different materials were evaluated using equilibrium rebinding experiments, selectivity experiments and scanning electron microscopy (SEM). The most efficient MIP was used in a molecularly imprinted-solid phase extraction (MISPE) protocol to extract acesulfame from wastewater samples. Using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS-MS) analysis, detection and quantification limits were achieved at 0.12μgL(-1) and 0.35μgL(-1), respectively. Certain cross selectivity for the chemical compounds containing negatively charged sulfonamide functional group was observed during selectivity experiments. PMID:26256920

  3. Molecular structure and vibrational spectra of dithionite ion by ab initio calculations

    NASA Astrophysics Data System (ADS)

    Leszczynski, Jerzy; Zerner, Michael C.

    1989-07-01

    The structure of the dithionite ion, S 2O 42-, is examined using quantum chemical calculations. These studies strongly suggest that only the C 2h (trans) isomer is stable in solution. The C 2v (cis) form reported in Na 2S 2O 4·2H 2O is stabilized by crystal forces. The calculated vibrational spectrum of the C 2h form is in excellent agreement with that observed in aqueous solution. Taking into account the negative frequency calculated for the C 2v structure yields a calculated spectrum in good agreement with that observed for the crystal.

  4. Warm target recoil ion momentum spectroscopy for fragmentation of molecular hydrogen by ultrashort laser pulses.

    PubMed

    Liu, Jia; Wu, Jian; Czasch, Achim; Zeng, Heping

    2009-07-20

    We demonstrate warm target recoil ion momentum spectroscopy for the fragmentation dynamics of the warm hydrogen molecules at room temperature. The thermal movement effect of the warm molecule is removed by using a correction algorithm in the momentum space. Based on the reconstructed three-dimensional momentum vectors as well as the kinetic energy release spectra, different vibrational states of the H(2)(+) ground state are clearly visible and the internuclear separation for charge resonance enhanced ionization of the second electron is identified. The results show adequate accordance with the former experiments using other techniques. PMID:19654636

  5. Analysis of testosterone in human urine using molecularly imprinted solid-phase extraction and corona discharge ion mobility spectrometry.

    PubMed

    Mirmahdieh, Shiva; Mardihallaj, Azam; Hashemian, Zahra; Razavizadeh, Jalal; Ghaziaskar, Hassan; Khayamian, Taghi

    2011-01-01

    Analysis of testosterone was accomplished using corona discharge ion mobility spectrometry. Molecular imprinted polymer was used for the extraction and pre-concentration of testosterone. Analytical parameters including precision, dynamic range and detection limit were obtained. The linear dynamic range was from 10 to 250 ng/mL and the limit of detection was 0.9 ng/mL. The proposed method was used for analysis of testosterone in urine samples. A urine sample from a 3-year-old girl was used as the blank. The RSD was below 10%. The obtained results from the method were also compared with the standard method for analysis of testosterone using SPE-HPLC analysis. The results demonstrate the accuracy of the method. PMID:21171183

  6. Formation and atomic configuration of binary metallic glasses studied by ion beam mixing and molecular dynamics simulation

    SciTech Connect

    Tai, K. P.; Gao, N.; Dai, X. D.; Li, J. H.; Liu, B. X.

    2007-06-15

    Metallic glasses are obtained in an immiscible Ag-Nb system with overall composition ranging from 25 to 90 at. % of Nb by ion beam mixing. Interestingly, the diffraction analysis shows that the formed Nb-rich metallic glass features are two distinct atomic configurations. In atomistic modeling, an n-body Ag-Nb potential is derived, under the assistance of ab initio calculation, and then applied in molecular dynamics simulations. An atomic configuration is discovered, i.e., an icositetrahedral ordering, and as well as an icosahedral ordering observed in the Ag-Nb metallic glasses and in some previously reported systems. Simulations confirm that the two dominate local atomic packing units are formed through a structural phase transition from the Nb-based bcc and fcc solid solutions, respectively, suggesting a concept of structural heredity that the crystalline structure of the constituent metals play a decisive role in determining the atomic structure of the resultant metallic glasses.

  7. Comparison of AlN films grown by RF magnetron sputtering and ion-assisted molecular beam epitaxy

    SciTech Connect

    Chan, J.; Fu, T.; Cheung, N.W.; Ross, J.; Newman, N.; Rubin, M.

    1993-04-01

    Crystalline aluminum nitride (AlN) thin films were formed on various substrates by using RF magnetron sputtering of an A1 target in a nitrogen plasma and also by ion-assisted molecular beam epitaxy (IAMBE). Basal-oriented AlN/(111) Si showed a degradation of crystallinity with increased substrate temperature from 550 to 770 C, while the crystallinity of AlN/(0001) A1{sub 2}O{sub 3} samples improved from 700 to 850 C. The optical absorption characteristics of the AlN/(0001) A1{sub 2}O{sub 3} films as grown by both deposition methods revealed a decrease in subbandgap absorption with increased substrate temperature.

  8. Biased interface between solid ion conductor LiBH{sub 4} and lithium metal: A first principles molecular dynamics study

    SciTech Connect

    Ikeshoji, Tamio; Ando, Yasunobu; Otani, Minoru; Tsuchida, Eiji; Takagi, Shigeyuki; Matsuo, Motoaki; Orimo, Shin-ichi

    2013-09-23

    We use first-principles molecular dynamics to study the electrochemical solid-solid interface between lithium metal and lithium electrolyte LiBH{sub 4}. An external bias is applied by using an effective screening medium. We observe large polarization in the LiBH{sub 4}, because the lithium cations in LiBH{sub 4} are shifted more on one side of the double-well potential of Li{sup +}. This results in a large potential drop in the interface region and a large double-layer capacity corresponding to ca. 70 μF/cm{sup 2}. H-coordination to the Li atoms plays an important role in the charge-transfer reaction and ion transfer.

  9. Molecular dynamics study on Ar ion bombardment effects in amorphous SiO{sub 2} deposition processes

    SciTech Connect

    Taguchi, Masafumi; Hamaguchi, Satoshi

    2006-12-15

    Argon ion bombardment effects on growing amorphous SiO{sub 2} films during reactive sputtering deposition processes were examined based on molecular dynamics (MD) and Monte Carlo (MC) simulation techniques. The system we have considered here is a film that is subject to energetic Ar bombardment while it is formed by surface reactions of Si and O atoms separately supplied at low kinetic energies. It has been found that (1) Ar injections preferentially sputter O atoms from the surface over Si and (2) also have a compressing effect on the growing film during the deposition process. In other words, our MD/MC simulations have demonstrated at the atomic level that, with higher energy Ar injections, an amorphous SiO{sub 2} film grown in a reactive sputtering deposition process is denser and more Si rich.

  10. Removal of the metal ions from aqueous solutions by nanoscaled low molecular pectin isolated from seagrass Phyllospadix iwatensis.

    PubMed

    Khozhaenko, Elena; Kovalev, Valeri; Podkorytova, Elena; Khotimchenko, Maksim

    2016-09-15

    Pectins from sea grasses are considered as promising substances with pronounced metal-binding activity. Due to the high molecular weight and heterogeneous structure, the use of pectins for removal of metal ions is difficult. Technology of directed pectin degradation was developed and homogenous degraded nanoscaled pectin polymers were synthesized. Experimental samples of degraded pectin isolated from Phyllospadix iwatensis were tested for their metal binding activity in comparison with native pectin from this seagrass and commercial citrus pectin. The metal uptake of all pectin compounds was highest within the pH range from 4.0 to 6.0. The Langmuir, Freundlich and BET sorption models were applied to describe the isotherms and constants. Results showed that depolymerized pectin exerts highest lead and cadmium binding activity with pronounced affinity. All pectin compounds were suggested to be favorable sorbents. Therefore, it can be concluded that degraded pectin is a prospective material for creation of metal-removing water treatment systems. PMID:26848015

  11. Nonadiabatic molecular dynamics simulations of the photofragmentation and geminate recombination dynamics in size-selected I2- . Arn cluster ions

    NASA Astrophysics Data System (ADS)

    Batista, V. S.; Coker, D. F.

    1997-05-01

    We investigate the photodissociation, geminate recombination and relaxation dynamics in size-selected I2-ṡArn cluster ions using a coupled quantum-classical molecular dynamics method and a model Hamiltonian gained from diatomics-in-ionic systems. We calculate photofragmentation yields of various charged product clusters of the dissociated I-ṡArf or recombined I2-ṡArf' forms as a function of precursor cluster size and find almost quantitative agreement with experimental results. The trends in photofragmentation are explained in terms of various participating electronically nonadiabatic channels coupled with vibrational relaxation on these different surfaces. We also explore the role of long range electrostatic interactions and underlying precursor cluster geometry on the photofragmentation dynamics.

  12. Molecular dynamics (MD) study on the electrochemical properties of electrolytes in lithium-ion battery (LIB) applications

    NASA Astrophysics Data System (ADS)

    Salami, Negin

    While the high energy density and the power along with longer cycle life and less requirements of maintenance distinguish the rechargeable lithium-ion batteries (LIBs) from other energy storage devices, development of an electrolyte of LIBs with optimized properties still constitutes a challenge towards next-generation LIB systems with robust electrochemical performance. The electrolytes serve as the medium to provide ionic conduction path between the electrodes as their basic function. Conductivity of the solutions are mainly affected by their transport properties and the electrolyte electrode/separator interfacial phenomena. Although many contributions on thermodynamic properties of the electrolytes consist of alkyl carbonates mixed with salts have been previously studied, relatively little information is known regarding the correlation between interfacial properties of the electrolyte -electrode/separator with electrochemical properties of the cell. In this study, therefore, we present the impacts of salt concentration and temperature-dependent properties of LIBs on wetting behavior of various electrolytes, i.e., ethyl methyl carbonate (EMC), diethyl carbonate (DEC), and propylene carbonate (PC), in contact with the graphite anode and polyethylene (PE)/polypropylene (PP) separator using molecular dynamics (MD) computational technique. The results based on MD computations affirm the general consistent dependency of interfacial tension energies to polarity of the solvents in DEC, EMC, and PC electrolytes contained 1 M LiPF6 salt. The PC systems interestingly showed inverse trend due to the special stacking motifs of PC layers that may increase the interfacial electrostatic interactions. Temperature did not show significant effect on the interfacial energies of linear solvents whereas PC exhibited more tendency to interact with the graphite anode at T = 25 C compared to the similar solution at 0 C. Moreover, the electrolytes that incorporated same solvents had

  13. Integrated Molecular and Microscopic Scale Insight into Morphology and Ion Dynamics in Ca2+-Mediated Natural Organic Matter Floccs

    SciTech Connect

    Bowers, Geoffrey M.; Argersinger, Haley E.; Reddy, Venkataswara; Johnson, Timothy A.; Arey, Bruce W.; Bowden, Mark E.; Kirkpatrick, Robert J.

    2015-08-06

    Combined X-ray diffraction (XRD), helium ion microscopy (HeIM), and Ca-43 nuclear magnetic resonance (NMR) results provide novel insight into the nano- and microstructure of flocculated NOM; the molecular-scale interaction among natural organic matter (NOM), dissolved Ca2+ ions, and water in NOM floccs; and the effects of pH and ionic strength on these characteristics. Suwannee River humic acid (HA), fulvic acid (FA), and NOM flocculated from Ca2+ bearing solutions share similar morphological characteristics on the 100 nm to micron scales, including micron-sized equant fragments and rounded, rough areas with features on the 100 nm scale. HeIM suggests that the NOM floccs are built from a fundamental spheroidal structure that is similar to 10 nm in diameter, in agreement with published AFM and small-angle X-ray scattering results. Calcium is incorporated into these floccs at 100% relative humidity in a wide range of disordered structural environments, with basic pH leading to shorter mean Ca-O distances and lower mean coordination numbers with respect to floccs formed under acidic conditions. The NMR results show that dynamical processes involving water and Ca2+ occurring at frequencies >10(4) Hz are important for hydrated OM floccs, in agreement with published molecular dynamics simulations of OM in solution. From the NMR results, we find evidence for two Ca2+ dynamic averaging mechanisms: one related to rapid exchange (>100 kHz) between surface proximity-restricted (those within 5 angstrom of a surface) and bulk solution environments when excess Ca2+ is present in the pore solution when pore water is unfrozen and a second consisting of intermediate scale (tens of kHz) site exchange among strongly sorbed inner-sphere sites when excess Ca2+ is absent and the carboxylic and phenolic functional groups of the NOM are deprotonated.

  14. Rovibrational molecular populations, atoms, and negative ions in H2 and D2 magnetic multicusp discharges

    NASA Astrophysics Data System (ADS)

    Pealat, M.; Taran, J.-P. E.; Bacal, M.; Hillion, F.

    1985-06-01

    Coherent anti-Stokes Raman scattering is applied to the study of rovibrational populations in magnetic multicusp H2 and D2 discharges. This subject is of interest to negative hydrogen-ion formation by volume plasma processes. The populations of high-lying rotational states (J greater than 5) in the vibrational levels v = 0, 1, and 2 are found to be significantly higher than expected from the Boltzmann law. In H2 the net populations of the first four vibrational levels follow approximately the Boltzmann law, with the vibrational temperature of 2390 K (in a 90 V-10 A discharge at 55 micro bar). In similar discharge conditions, the population of the state v = 3 in D2 is higher than expected from the Boltzmann law. In the presence of the discharge a deficiency in H2 and D2 molecule density was observed and was attributed to the possible presence of H and D atoms. This was verified by an independent measurement of the atomic fraction and temperature. The density of negative ions, measured by the photodetachment technique, is also reported.

  15. Static Properties and Stark Effect of the Ground State of the HD Molecular Ion

    NASA Technical Reports Server (NTRS)

    Bhatia, A. K.; Drachman, Richard J.

    1999-01-01

    We have calculated static properties of the ground state of the HD(+) ion and its lowest-lying P-state without making use of the Born-Oppenheimer approximation, as was done in the case of H2(+) and D2(+) [Phys. Rev. A 58, 2787 (1998)]. The ion is treated as a three-body system whose ground state is spherically symmetric. The wavefunction is of generalized Hylleraas type, but it is necessary to include high powers of the internuclear distance to localize the nuclear motion. We obtain good values of the energies of the ground S-state and lowest P-state and compare them with earlier calculations. Expectation values are obtained for various operators, the Fermi contact parameters, and the permanent quadrupole moment. The cusp conditions are also calculated. The polarizability was then calculated using second-order perturbation theory with intermediate P pseudostates. Since the nuclei in HD(+) are not of equal mass there is dipole coupling between the lowest two rotational states, which are almost degenerate. This situation is carefully analyzed, and the Stark shift is calculated variationally as a function of the applied electric field.

  16. Molecular mechanism of the assembly of an acid-sensing receptor ion channel complex.

    PubMed

    Yu, Yong; Ulbrich, Maximilian H; Li, Ming-Hui; Dobbins, Scott; Zhang, Wei K; Tong, Liang; Isacoff, Ehud Y; Yang, Jian

    2012-01-01

    Polycystic kidney disease (PKD) family proteins associate with transient receptor potential (TRP) channel family proteins to form functionally important complexes. PKD proteins differ from known ion channel-forming proteins and are generally thought to act as membrane receptors. Here we find that PKD1L3, a PKD protein, functions as a channel-forming subunit in an acid-sensing heteromeric complex formed by PKD1L3 and TRPP3, a TRP channel protein. Single amino-acid mutations in the putative pore region of both proteins alter the channel's ion selectivity. The PKD1L3/TRPP3 complex in the plasma membrane of live cells contains one PKD1L3 and three TRPP3. A TRPP3 C-terminal coiled-coil domain forms a trimer in solution and in crystal, and has a crucial role in the assembly and surface expression of the PKD1L3/TRPP3 complex. These results demonstrate that PKD subunits constitute a new class of channel-forming proteins, enriching our understanding of the function of PKD proteins and PKD/TRPP complexes. PMID:23212381

  17. The Reorientation Mechanism of Hydroxide Ions in Water: A Molecular Dynamics Study

    SciTech Connect

    Sun, Xiuquan; Yoo, Soohaeng; Xantheas, Sotiris S.; Dang, Liem X.

    2009-10-19

    simulations with polarizable potential models. Two major solvation structures of OH- were suggested by our study. One of which has four accepted hydrogen bonds from water and the other has five accepted hydrogen bonds. A weak hydrogen bond donated by the hydroxide ion was observed in our simulations. The simulated reorientation relaxation times of OH- are in qualitative agreement with CTTS experiments. We propose a two-step mechanism for the reorientation of hydroxide ions in water. First, the reorientation of OH- is initiated by the coupled translation with water molecules in its first solvation shell. Second, the OH- hydrogen relaxes to the minimum energy state. The rate-limiting step in this mechanism is the first step, translation diffusion of the first solvation shell water molecules. The activation energies of reorientation of OH- and translation of H2O determined from our simulations are 22.5 and 18.5 kJ/mol, respectively. These values fall in the range of the measured data. This work was supported by the US Department of energy's Office of Basic Energy Sciences, Chemical Sciences program. Pacific Northwest national Laboratory is operated by Battelle for the US Department of Energy.

  18. Modulation of acid-sensing ion channels: molecular mechanisms and therapeutic potential

    PubMed Central

    Chu, Xiang-Ping; Papasian, Christopher J; Wang, John Q; Xiong, Zhi-Gang

    2011-01-01

    Increases in extracellular proton concentrations, which takes place in physiological conditions such as synaptic signaling and pathological conditions such as tissue inflammation, ischemic stroke, traumatic brain injury, and epileptic seizure, activates a unique family of membrane ion channels; the acid-sensing ion channels (ASICs). All ASICs belong to amiloride-sensitive degenerin/epithelial Na+ channel superfamily. Four genes encoded at seven sub-units have been identified. ASICs are expressed primarily in neurons and have been shown to play critical roles in synaptic plasticity, learning/memory, fear conditioning, sensory transduction, pain perception, ischemic brain injury, seizure, and other neurological as well as psychological disorders. Although protons are the primary activator for ASICs, the properties and/or level of expression of these channels are modulated dramatically by neuropeptides, di-and polyvalent cations, inflammatory mediators, associated proteins, and protein phosphorylations, etc. Modulation of ASICs can result in profound changes in the activities and functions of these channels in both physiological and pathological processes. In this article, we provide an up to date review on the modulations of ASICs by exogenous agents and endogenous signaling molecules. A better understanding of how ASICs can be modulated should help define new strategies to counteract the deleterious effects of dysregulated ASIC activity. PMID:22162785

  19. ESA IBER-2 Molecular and Cellular Changes in Human Endothelial Cells in Response to Nickel Ion Irradiation (CORALS project)

    NASA Astrophysics Data System (ADS)

    Moreels, M.; Quintens, R.; De Vos, W.; Beck, M.; Tabury, K.; Suetens, A.; Abouelaradat, K.; Dieriks, B.; Ernst, E.; Lee, R.; Lambert, C.; Van Oostveldt, P.; Baatout, S.

    2013-02-01

    On Earth, most radiation exposures (medical and natural background) consist of low-linear energy transfer (LET) photons. In space, astronauts are exposed to higher doses and to more varied types of radiation. Cosmic radiation mainly consists of high-energy protons and high-Z and -energy (HZE) particles. These high-LET particles are predicted to account for most of the radiation induced health effects. In this regard, further analysis of the biological effects of HZE particles is essential. In the present study, endothelial cells were irradiated with different doses of nickel ions produced in the synchrotron at GSI (Darmstadt, Germany). After different time points, RNA was extracted for genome-wide analysis and supernatants were collected for multiplex cytokine assay. DNA double strand breaks were detected using γH2AX staining. Our results demonstrated that nickel irradiation induced molecular and cellular changes in human endothelial cells. Further analysis is ongoing to confirm the obtained data and to further explore the biological effects after nickel ion exposure.

  20. Characterization of methyl methacrylate oligomers using secondary ion mass spectrometry, APCI mass spectrometry and molecular orbital theory

    NASA Astrophysics Data System (ADS)

    Takeuchi, T.; Iwai, K.; Momoji, K.; Miyamoto, I.; Saiki, K.; Hashimoto, K.

    2003-01-01

    The ionization efficiency and fragmentation mechanism of methyl methacrylate (MMA) oligomers (3-mer˜8-mer) were investigated by using secondary ion mass spectrometry (SIMS) and APCI mass spectrometry (APCI-MS). Protonation and fragmentation mechanisms of MMA oligomers were clarified by using molecular orbital (MO) methods. MMA oligomers were synthesized in anionic polymerization, and the oligomers were fractionated into 3-mer˜8-mer using gel permeation chromatography (GPC). In SIMS of MMA oligomers (3-mer˜8-mer), [MH] +, [MH-CH 3OH] +, [MH-methyl formate] + and [MH-2CH 3OH-methyl formate] + appeared. The peak intensities of adduct ions [M+Li] +, [M+Na] + and [M+K] + increased with the increase of the polymerization degree. The optimized geometries and H +, Li +, Na + and K + affinities of MMA monomer (1-mer), dimer (2-mer), and trimer (3-mer) were calculated using the PM3 and ab initio MO methods. The calculated H +, Li +, Na + and K + affinities increased in order of 1-mer, 2-mer and 3-mer of MMA.

  1. Does Thermal Breathing Affect Collision Cross Sections of Gas-Phase Peptide Ions? An Ab Initio Molecular Dynamics Study.

    PubMed

    Pepin, Robert; Petrone, Alessio; Laszlo, Kenneth J; Bush, Matthew F; Li, Xiaosong; Tureček, František

    2016-07-21

    Ab initio molecular dynamics (AIMD) with density functional theory (DFT) was applied to explore conformational motions and collision cross sections (Ω) of folded (2) and extended (7) conformers of doubly charged peptide ions, (Ala-Ala-Leu-Arg + 2H)(2+), in the gas phase at 300 and 473 K. The experimental Ω of (Ala-Ala-Leu-Arg +2H)(2+) was measured as 149 ± 1.2 Å(2) at 298 K. Thermally distributed mean values of Ω for 2 and 7 at 300 and 473 K were only 0.8-1.1% larger than for the equilibrium 0 K structures. Long (>10 ps) trajectory calculations indicated entropy-driven conformational change of 2 to 7 that occurred at random within a ∼ 4 ps time window. The experimental Ω was found to fit the calculated population averaged values for 2 and 7, indicating a rapid conformer interconversion. Overall, thermal breathing had only a minor effect on the peptide ion collision cross sections. PMID:27389035

  2. Molecular dynamics study of ion capture from water by a model ionophore, tetraprotonated cryptand SC24

    NASA Technical Reports Server (NTRS)

    Owenson, Brian; Macelroy, Robert D.; Pohorille, Andrew

    1988-01-01

    The molecular dynamics of chloride capture from water by the tetraprotonated cryptand SC24 has been studied for the cases of 19 distances between the criptand and the chloride. The chloride capture is found to be characterized by a rapid cooperative change in the conformation of the cryptand when the Cl(-) begins to enter the ligand and just as it encounters the energy barrier. The conformational transition is associated with a shift of three N-H bonds from the pure endo orientation, such that they point toward the chloride.

  3. Molecular basis for convergent evolution of glutamate recognition by pentameric ligand-gated ion channels

    PubMed Central

    Lynagh, Timothy; Beech, Robin N.; Lalande, Maryline J.; Keller, Kevin; Cromer, Brett A.; Wolstenholme, Adrian J.; Laube, Bodo

    2015-01-01

    Glutamate is an indispensable neurotransmitter, triggering postsynaptic signals upon recognition by postsynaptic receptors. We questioned the phylogenetic position and the molecular details of when and where glutamate recognition arose in the glutamate-gated chloride channels. Experiments revealed that glutamate recognition requires an arginine residue in the base of the binding site, which originated at least three distinct times according to phylogenetic analysis. Most remarkably, the arginine emerged on the principal face of the binding site in the Lophotrochozoan lineage, but 65 amino acids upstream, on the complementary face, in the Ecdysozoan lineage. This combined experimental and computational approach throws new light on the evolution of synaptic signalling. PMID:25708000

  4. Photoionization study of quasibound states of doubly charged molecular nitrogen ions

    NASA Astrophysics Data System (ADS)

    Hellner, L.; Besnard, M. J.; Dujardin, G.; Malinovich, Y.

    1988-01-01

    Doubly charged N 22+ ions were produced by double photoionization of neutral nitrogen molecules with the synchrotron radiation from ACO as a photon source of variable energy in the 40-70 eV range. From the double photoionization spectrum the threshold energy of the stable X 1Σ g+ state was found at 43.1 ± 0.1 eV. The D 1Σ g+ → X 1Σ g+ emission observed by using a photoion-photon of fluorescence coincidence (PIFCO) experiment. The onset energy of this emitting D 1Σ u+ state at 50.5 eV, was deduced from the variation of the fluorescence efficiency as a function of the excitation photon energy. The lifetime of this emitting state was measured to be τ = 8 ± 3 ns.

  5. Population Redistribution Among Multiple Electronic States of Molecular Nitrogen Ions in Strong Laser Fields.

    PubMed

    Yao, Jinping; Jiang, Shicheng; Chu, Wei; Zeng, Bin; Wu, Chengyin; Lu, Ruifeng; Li, Ziting; Xie, Hongqiang; Li, Guihua; Yu, Chao; Wang, Zhanshan; Jiang, Hongbing; Gong, Qihuang; Cheng, Ya

    2016-04-01

    We carry out a combined theoretical and experimental investigation on the population distributions in the ground and excited states of tunnel-ionized nitrogen molecules at various driver wavelengths in the near- and midinfrared range. Our results reveal that efficient couplings (i.e., population exchanges) between the ground N_{2}^{+}(X^{2}Σ_{g}^{+}) state and the excited N_{2}^{+}(A^{2}Π_{u}) and N_{2}^{+}(B^{2}Σ_{u}^{+}) states occur in strong laser fields. The couplings result in a population inversion between the N_{2}^{+}(X^{2}Σ_{g}^{+}) and N_{2}^{+}(B^{2}Σ_{u}^{+}) states at wavelengths near 800 nm, which is verified by our experimental observation of the amplification of a seed at ∼391  nm. The result provides insight into the mechanism of free-space nitrogen ion lasers generated in remote air with strong femtosecond laser pulses. PMID:27104707

  6. Electron Capture Processes Following Collisions of He^2+ Ions with Molecular Targets

    NASA Astrophysics Data System (ADS)

    Abu-Haija, O.

    2005-05-01

    Energy-gain spectra, absolute state-selective and total cross sections have been measured for single-electron capture processes in collisions of He^2+ ions with O2, H2O, CO2, N2, and NH3 at impact energies between 100 eV and 1600 eV and scattering angles between 0^o and 6^o using the translational energy-gain spectroscopy (TES) technique. As apparent from the translational energy-gain measurements, single-electron capture (SEC) from O2 and H2O proceeds by both dissociative and non-dissociative channels, whereas for N2 and CO2 only dissociative SEC has been observed. However, for NH3 the non-dissociative SEC channel is found to be predominantly populated. Total cross sections have also been compared with available measurements and theoretical calculations based on Landua-Zener model and Demkov model.

  7. Theoretical Hyperfine Structure of the Molecular Hydrogen Ion at the 1 ppm Level.

    PubMed

    Korobov, Vladimir I; Koelemeij, J C J; Hilico, L; Karr, J-Ph

    2016-02-01

    We revisit the mα^{6}(m/M) order corrections to the hyperfine splitting in the H_{2}^{+} ion and find a hitherto unrecognized second-order relativistic contribution associated with the vibrational motion of the nuclei. Inclusion of this correction term produces theoretical predictions which are in excellent agreement with experimental data [K. B. Jefferts, Phys. Rev. Lett. 23, 1476 (1969)], thereby concluding a nearly 50-year-long theoretical quest to explain the experimental results within their 1-ppm error. The agreement between the theory and experiment corroborates the proton structural properties as derived from the hyperfine structure of atomic hydrogen. Our work furthermore indicates that, for future improvements, a full three-body evaluation of the mα^{6}(m/M) correction term will be mandatory. PMID:26894709

  8. Theoretical Hyperfine Structure of the Molecular Hydrogen Ion at the 1 ppm Level

    NASA Astrophysics Data System (ADS)

    Korobov, Vladimir I.; Koelemeij, J. C. J.; Hilico, L.; Karr, J.-Ph.

    2016-02-01

    We revisit the m α6(m /M ) order corrections to the hyperfine splitting in the H2+ ion and find a hitherto unrecognized second-order relativistic contribution associated with the vibrational motion of the nuclei. Inclusion of this correction term produces theoretical predictions which are in excellent agreement with experimental data [K. B. Jefferts, Phys. Rev. Lett. 23, 1476 (1969)], thereby concluding a nearly 50-year-long theoretical quest to explain the experimental results within their 1-ppm error. The agreement between the theory and experiment corroborates the proton structural properties as derived from the hyperfine structure of atomic hydrogen. Our work furthermore indicates that, for future improvements, a full three-body evaluation of the m α6(m /M ) correction term will be mandatory.

  9. Population Redistribution Among Multiple Electronic States of Molecular Nitrogen Ions in Strong Laser Fields

    NASA Astrophysics Data System (ADS)

    Yao, Jinping; Jiang, Shicheng; Chu, Wei; Zeng, Bin; Wu, Chengyin; Lu, Ruifeng; Li, Ziting; Xie, Hongqiang; Li, Guihua; Yu, Chao; Wang, Zhanshan; Jiang, Hongbing; Gong, Qihuang; Cheng, Ya

    2016-04-01

    We carry out a combined theoretical and experimental investigation on the population distributions in the ground and excited states of tunnel-ionized nitrogen molecules at various driver wavelengths in the near- and midinfrared range. Our results reveal that efficient couplings (i.e., population exchanges) between the ground N2+(X2Σg+) state and the excited N2+(A2Πu) and N2+(B2Σu+) states occur in strong laser fields. The couplings result in a population inversion between the N2+(X2Σg+) and N2+(B2Σu+) states at wavelengths near 800 nm, which is verified by our experimental observation of the amplification of a seed at ˜391 nm . The result provides insight into the mechanism of free-space nitrogen ion lasers generated in remote air with strong femtosecond laser pulses.

  10. Spectroscopy, calorimetry and molecular simulation studies on the interaction of catalase with copper ion.

    PubMed

    Hao, Fang; Jing, Mingyang; Zhao, Xingchen; Liu, Rutao

    2015-02-01

    In this research, the binding mechanism of Cu(2+) to bovine liver catalase (BLC) was studied by fluorescence spectroscopy, ultraviolet-visible (UV-vis) absorption spectroscopy, circular dichroism (CD) spectroscopy, isothermal titration calorimetry (ITC) and molecular docking methods. The cellar experiment was firstly carried out to investigate the inhibition effect of catalase. During the fluorescence quenching study, after correcting the inner filter effect (IFE), the fluorescence of BLC was found to be quenched by Cu(2+). The quenching mechanism was determined by fluorescence lifetime measurement, and was confirmed to be the dynamic mode. The secondary structure content of BLC was changed by the addition of Cu(2+), as revealed by UV-vis absorption and CD spectra, which further induces the decrease in BLC activity. Molecular simulation study indicates that Cu(2+) is located between two β-sheets and two random coils of BLC near to the heme group, and interacts with His 74 and Ser 113 residues near a hydrophilic area. The decrease of α-helix and the binding of His 74 are considered to be the major reason for the inhibition of BLC activity caused by Cu(2+). The ITC results indicate that the binding stoichiometry of Cu(2+) to catalase is 11.4. Moreover, the binding of Cu(2+) to BLC destroyed H-bonds, which was confirmed by the CD result. PMID:25618814

  11. Ab initio molecular dynamics simulations of ion-solid interactions in zirconate pyrochlores

    DOE PAGESBeta

    Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen; Zu, X. T.

    2015-01-31

    In this paper, an ab initio molecular dynamics method is employed to study low energy recoil events in zirconate pyrochlores (A2Zr2O7, A = La, Nd and Sm). It shows that both cations and anions in Nd2Zr2O7 and Sm2Zr2O7 are generally more likely to be displaced than those in La2Zr2O7. The damage end states mainly consist of Frenkel pair defects, and the Frenkel pair formation energies in Nd2Zr2O7 and Sm2Zr2O7 are lower than those in La2Zr2O7. These results suggest that the order–disorder structural transition more easily occurs in Nd2Zr2O7 and Sm2Zr2O7 resulting in a defect-fluorite structure, which agrees well with experimentalmore » observations. Our calculations indicate that oxygen migration from 48f and 8b to 8a sites is dominant under low energy irradiation. A number of new defects, including four types of cation Frenkel pairs and six types of anion Frenkel pairs, are revealed by ab initio molecular dynamics simulations. The present findings may help to advance the fundamental understanding of the irradiation response behavior of zirconate pyrochlores.« less

  12. Analysis of fusaric acid in maize using molecularly imprinted solid phase extraction (MISPE) clean-up and ion-pair LC with diode array UV detection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fusaric acid is a phytotoxin and mycotoxin occasionally found in maize contaminated with Fusarium fungi. A selective sample clean-up procedure was developed to detect fusaric acid in maize using molecularly imprinted solid phase extraction (MISPE) clean-up coupled with ion-pair liquid chromatography...

  13. Analysis of angular distribution of fragments in relativistic heavy-ion collisions by quantum molecular dynamics

    NASA Astrophysics Data System (ADS)

    Ogawa, Tatsuhiko; Sato, Tatsuhiko; Hashimoto, Shintaro; Niita, Koji

    2016-05-01

    To predict angular distribution of fragments produced in nucleusnucleus collisions, JAERI quantum molecular dynamics model (JQMD) was improved. Because JQMD underestimated fragments in the forward angle, which were mainly produced by peripheral collisions, JQMD was revised so as to simulate peripheral collisions accurately. Density-dependent in-medium effect and relativistic effect on nucleonnucleon interactions were incorporated for this purpose. The revised version of JQMD coupled with a statistical decay model was used to calculate differential fragment production cross sections measured in earlier studies. Comparison of the measured data and calculation by the revised and old JQMD showed that the revised JQMD can predict fragment angular distribution better than old JQMD. Particularly, agreement of fragment yield in the forward angle is substantially improved.

  14. Detection of a Noble Gas Molecular Ion, 36ArH+, in the Crab Nebula

    NASA Astrophysics Data System (ADS)

    Barlow, M. J.; Swinyard, B. M.; Owen, P. J.; Cernicharo, J.; Gomez, H. L.; Ivison, R. J.; Krause, O.; Lim, T. L.; Matsuura, M.; Miller, S.; Olofsson, G.; Polehampton, E. T.

    2013-12-01

    Noble gas molecules have not hitherto been detected in space. From spectra obtained with the Herschel Space Observatory, we report the detection of emission in the 617.5- and 1234.6-gigahertz J = 1-0 and 2-1 rotational lines of 36ArH+ at several positions in the Crab Nebula, a supernova remnant known to contain both molecular hydrogen and regions of enhanced ionized argon emission. Argon-36 is believed to have originated from explosive nucleosynthesis in massive stars during core-collapse supernova events. Its detection in the Crab Nebula, the product of such a supernova event, confirms this expectation. The likely excitation mechanism for the observed 36ArH+ emission lines is electron collisions in partially ionized regions with electron densities of a few hundred per centimeter cubed.

  15. Detection of a noble gas molecular ion, 36ArH+, in the Crab Nebula.

    PubMed

    Barlow, M J; Swinyard, B M; Owen, P J; Cernicharo, J; Gomez, H L; Ivison, R J; Krause, O; Lim, T L; Matsuura, M; Miller, S; Olofsson, G; Polehampton, E T

    2013-12-13

    Noble gas molecules have not hitherto been detected in space. From spectra obtained with the Herschel Space Observatory, we report the detection of emission in the 617.5- and 1234.6-gigahertz J = 1-0 and 2-1 rotational lines of (36)ArH(+) at several positions in the Crab Nebula, a supernova remnant known to contain both molecular hydrogen and regions of enhanced ionized argon emission. Argon-36 is believed to have originated from explosive nucleosynthesis in massive stars during core-collapse supernova events. Its detection in the Crab Nebula, the product of such a supernova event, confirms this expectation. The likely excitation mechanism for the observed (36)ArH(+) emission lines is electron collisions in partially ionized regions with electron densities of a few hundred per centimeter cubed. PMID:24337290

  16. A molecular dynamics study on slow ion interactions with the polycyclic aromatic hydrocarbon molecule anthracene

    SciTech Connect

    Postma, J.; Hoekstra, R.; Schlathölter, T.; Tielens, A. G. G. M.

    2014-03-01

    Atomic collisions with polycyclic aromatic hydrocarbon (PAH) molecules are astrophysically particularly relevant for collision energies of less than 1 keV. In this regime, the interaction dynamics are dominated by elastic interactions. We have employed a molecular dynamics simulation based on analytical interaction potentials to model the interaction of low energy hydrogen and helium projectiles with isolated anthracene (C{sub 14}H{sub 10}) molecules. This approach allows for a very detailed investigation of the elastic interaction dynamics on an event by event basis. From the simulation data the threshold projectile kinetic energies above which direct C atom knock out sets in were determined. Anthracene differential energy transfer cross sections and total (dissociation) cross sections were computed for a wide range of projectile kinetic energies. The obtained results are interpreted in the context of PAH destruction in astrophysical environments.

  17. Ion adsorption and diffusion in smectite: Molecular, pore, and continuum scale views

    NASA Astrophysics Data System (ADS)

    Tinnacher, Ruth M.; Holmboe, Michael; Tournassat, Christophe; Bourg, Ian C.; Davis, James A.

    2016-03-01

    Clay-rich media have been proposed as engineered barrier materials or host rocks for high level radioactive waste repositories in several countries. Hence, a detailed understanding of adsorption and diffusion in these materials is needed, not only for radioactive contaminants, but also for predominant earth metals, which can affect radionuclide speciation and diffusion. The prediction of adsorption and diffusion in clay-rich media, however, is complicated by the similarity between the width of clay nanopores and the thickness of the electrical double layer (EDL) at charged clay mineral-water interfaces. Because of this similarity, the distinction between 'bulk liquid' water and 'surface' water (i.e., EDL water) in clayey media can be ambiguous. Hence, the goal of this study was to examine the ability of existing pore scale conceptual models (single porosity models) to link molecular and macroscopic scale data on adsorption and diffusion in compacted smectite. Macroscopic scale measurements of the adsorption and diffusion of calcium, bromide, and tritiated water in Na-montmorillonite were modeled using a multi-component reactive transport approach while testing a variety of conceptual models of pore scale properties (adsorption and diffusion in individual pores). Molecular dynamics (MD) simulations were carried out under conditions similar to those of our macroscopic scale diffusion experiments to help constrain the pore scale models. Our results indicate that single porosity models cannot be simultaneously consistent with our MD simulation results and our macroscopic scale diffusion data. A dual porosity model, which allows for the existence of a significant fraction of bulk liquid water-even at conditions where the average pore width is only a few nanometers-may be required to describe both pore scale and macroscopic scale data.

  18. A Distonic Radical-Ion for Detection of Traces of Adventitious Molecular Oxygen (O2) in Collision Gases Used in Tandem Mass Spectrometers

    NASA Astrophysics Data System (ADS)

    Jariwala, Freneil B.; Hibbs, John A.; Weisbecker, Carl S.; Ressler, John; Khade, Rahul L.; Zhang, Yong; Attygalle, Athula B.

    2014-09-01

    We describe a diagnostic ion that enables rapid semiquantitative evaluation of the degree of oxygen contamination in the collision gases used in tandem mass spectrometers. Upon collision-induced dissociation (CID), the m/z 359 positive ion generated from the analgesic etoricoxib undergoes a facile loss of a methyl sulfone radical [•SO2(CH3); 79-Da] to produce a distonic radical cation of m/z 280. The product-ion spectrum of this m/z 280 ion, recorded under low-energy activation on tandem-in-space QqQ or QqTof mass spectrometers using nitrogen from a generator as the collision gas, or tandem-in-time ion-trap (LCQ, LTQ) mass spectrometers using purified helium as the buffer gas, showed two unexpected peaks at m/z 312 and 295. This enigmatic m/z 312 ion, which bears a mass-to-charge ratio higher than that of the precursor ion, represented an addition of molecular oxygen (O2) to the precursor ion. The exceptional affinity of the m/z 280 radical cation towards oxygen was deployed to develop a method to determine the oxygen content in collision gases.

  19. Molecular and functional characterization of acid-sensing ion channel (ASIC) 1b.

    PubMed

    Bässler, E L; Ngo-Anh, T J; Geisler, H S; Ruppersberg, J P; Gründer, S

    2001-09-01

    Acid-sensing ion channels (ASICs) are activated by extracellular protons and are involved in neurotransmission in the central nervous system, in pain perception, as well as in mechanotransduction. Six different ASIC subunits have been cloned to date, which are encoded by four genes (ASIC1-ASIC4). Proton-gated currents have been described in isolated neurons from sensory ganglia as well as from central nervous system. However, it is largely unclear which of the cloned ASIC subunits underlie these native proton-gated currents. Recently, a splice variant, ASIC-beta, has been described for ASIC1a. In this variant about one-third of the protein is exchanged at the N terminus. Here we show that ASIC-beta has a longer N terminus than previously reported, extending the sequence divergence between ASIC1a and this new variant (ASIC1b). We investigated in detail kinetic and selectivity properties of ASIC1b in comparison to ASIC1a. Kinetics is similar for ASIC1b and ASIC1a. Ca(2+) permeability of ASIC1a is low, whereas ASIC1b is impermeable to Ca(2+). Currents through ASIC1a resemble currents, which have been described in sensory and central neurons, whereas the significance of ASIC1b remains to be established. Moreover, we show that a pre-transmembrane 1 domain controls the permeability to divalent cations in ASIC1, contributing to our understanding of the pore structure of these channels. PMID:11448963

  20. Molecular mechanisms of Cys-loop ion channel receptor modulation by ivermectin

    PubMed Central

    Lynagh, Timothy; Lynch, Joseph W.

    2012-01-01

    Ivermectin is an anthelmintic drug that works by inhibiting neuronal activity and muscular contractility in arthropods and nematodes. It works by activating glutamate-gated chloride channels (GluClRs) at nanomolar concentrations. These receptors, found exclusively in invertebrates, belong to the pentameric Cys-loop receptor family of ligand-gated ion channels (LGICs). Higher (micromolar) concentrations of ivermectin also activate or modulate vertebrate Cys-loop receptors, including the excitatory nicotinic and the inhibitory GABA type-A and glycine receptors (GlyRs). An X-ray crystal structure of ivermectin complexed with the C. elegans α GluClR demonstrated that ivermectin binds to the transmembrane domain in a cleft at the interface of adjacent subunits. It also identified three hydrogen bonds thought to attach ivermectin to its site. Site-directed mutagenesis and voltage-clamp electrophysiology have also been employed to probe the binding site for ivermectin in α1 GlyRs. These have raised doubts as to whether the hydrogen bonds are essential for high ivermectin potency. Due to its lipophilic nature, it is likely that ivermectin accumulates in the membrane and binds reversibly (i.e., weakly) to its site. Several lines of evidence suggest that ivermectin opens the channel pore via a structural change distinct from that induced by the neurotransmitter agonist. Conformational changes occurring at locations distant from the pore can be probed using voltage-clamp fluorometry (VCF), a technique which involves quantitating agonist-induced fluorescence changes from environmentally sensitive fluorophores covalently attached to receptor domains of interest. This technique has demonstrated that ivermectin induces a global conformational change that propagates from the transmembrane domain to the neurotransmitter binding site, thus suggesting a mechanism by which ivermectin potentiates neurotransmitter-gated currents. Together, this information provides new insights into

  1. Differential fluorescence from molecularly imprinted polymers containing europium ions as a transducer element

    NASA Astrophysics Data System (ADS)

    Pestov, Dmitry; Anderson, John; Tepper, Gary

    2006-10-01

    Molecularly imprinted polymers (MIPs) have the potential to provide a unique combination of high chemical selectivity and environmental stability and are, therefore, being widely studied in chemical sensor applications. Optical interrogation of the MIP-chemical interaction is very convenient for the detection of fluorescent compounds, but is problematic for the detection of non-fluorescent species. Doping MIPs with Eu3+ is one approach that can facilitate the optical detection of non-fluorescent species. Eu3+ has absorption in the near UV and the doped MIP can, therefore, be excited with a commercially available laser diode at 375nm. In the present paper MIPs doped with Eu3+ and imprinted to methyl salicylate (MES), a chemical warfare agent simulant, were prepared in the form of a thin film on a quartz substrate. Non-imprinted (Blank) polymer films were also prepared using the same imprinting procedure, but without introducing the MES template. Both polymers were tested to MES and the structurally similar compound methyl 3,5-dimethylbenzoate (DMB) in hexane. For MES, the fluorescence intensity of the MIP was significantly stronger than for the Blank, while for the methyl 3,5-dimethylbenzoate, the Blank polymer exhibited the stronger fluorescence signal. A portable chemical sensor employing differential fluorescence from MIP/Blank polymer pairs is under development and allows target discrimination without the need for spectroscopic analysis of the emission spectra.

  2. Characterization of the molecular species of glycerophospholipids from rabbit kidney: an alternative approach to the determination of the fatty acyl chain position by negative ion fast atom bombardment combined with mass-analysed ion kinetic energy analysis.

    PubMed

    Chen, S; Curcuruto, O; Catinella, S; Traldi, P; Menon, G

    1992-12-01

    An alternative approach to identifying fatty acid chain position in the molecular species of glycerophospholipids has been studied and developed. The fatty acyl groups esterified to the glycerol backbone in isomeric glycerophosphatidyl-choline, -serine and -ethanolamine as well as glycerophosphatidic acid can be detected by the presence of a pair of anions derived from phosphatidic acid parent ions (M minus the polar head groups in glycerophospholipids), designed to be [M--polar head--R2COOH]- and [M--polar head--R2CO--H]-, produced by negative ion fast atom bombardment combined with mass-analysed ion kinetic energy analysis. Because of the significant abundance of [M--polar head--R2COOH]- anion, fatty acid chains differing by 2 Da can be distinguished by accurate measurements of the electrostatic voltage related to this ion. Three-volt differences can be evidenced. Using this approach, the molecular species of glycerophosphatidyl-choline, -serine, -ethanolamine and -inositol from rabbit kidney were characterized after the separation of both class and species by normal and reversed-phase high-performance liquid chromatography, respectively. We identified 11 arachidonoyl-containing molecular species of glycerophospholipids and the other 17 lipid molecules in this biological material. A couple of 1- alkenyl-2-arachidonoyl-sn-glycerol-3-phosphoethanolamine species, identified as plasmalogen GPE 16:0-20:4 and plasmalogen GPE 18:0-20:4, were found for the first time in rabbit kidney. PMID:1477110

  3. Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel

    PubMed Central

    Bjelkmar, Pär; Niemelä, Perttu S.; Vattulainen, Ilpo; Lindahl, Erik

    2009-01-01

    Structure and dynamics of voltage-gated ion channels, in particular the motion of the S4 helix, is a highly interesting and hotly debated topic in current membrane protein research. It has critical implications for insertion and stabilization of membrane proteins as well as for finding how transitions occur in membrane proteins—not to mention numerous applications in drug design. Here, we present a full 1 µs atomic-detail molecular dynamics simulation of an integral Kv1.2 ion channel, comprising 120,000 atoms. By applying 0.052 V/nm of hyperpolarization, we observe structural rearrangements, including up to 120° rotation of the S4 segment, changes in hydrogen-bonding patterns, but only low amounts of translation. A smaller rotation (∼35°) of the extracellular end of all S4 segments is present also in a reference 0.5 µs simulation without applied field, which indicates that the crystal structure might be slightly different from the natural state of the voltage sensor. The conformation change upon hyperpolarization is closely coupled to an increase in 310 helix contents in S4, starting from the intracellular side. This could support a model for transition from the crystal structure where the hyperpolarization destabilizes S4–lipid hydrogen bonds, which leads to the helix rotating to keep the arginine side chains away from the hydrophobic phase, and the driving force for final relaxation by downward translation is partly entropic, which would explain the slow process. The coordinates of the transmembrane part of the simulated channel actually stay closer to the recently determined higher-resolution Kv1.2 chimera channel than the starting structure for the entire second half of the simulation (0.5–1 µs). Together with lipids binding in matching positions and significant thinning of the membrane also observed in experiments, this provides additional support for the predictive power of microsecond-scale membrane protein simulations. PMID:19229308

  4. First-principles molecular dynamics simulations of uranyl ion interaction at the water/rutile TiO2(110) interface

    NASA Astrophysics Data System (ADS)

    Sebbari, K.; Roques, J.; Simoni, E.; Domain, C.; Perron, H.; Catalette, H.

    2012-08-01

    The effects of temperature and solvation on uranyl ion adsorption at the water/rutile TiO2(110) interface are investigated by Density Functional Theory (DFT) in both static and Born-Oppenheimer molecular dynamics approaches. According to experimental observations, uranyl ion can form two surface complexes in a pH range from 1.5 to 4.5. Based on these observations, the structures of the complexes at 293 K are first calculated in agreement with vacuum static calculations. Then, an increase in temperature (293 to 425 K) induces the reinforcement of uranyl ion adsorption due to the release of water molecules from the solvation shell of uranyl ion. Finally, temperature can modify the nature of the surface species.

  5. Dissociation of multicharged CO molecular ions produced in collisions with 97-MeV Ar14+: Total-kinetic-energy distributions

    NASA Astrophysics Data System (ADS)

    Sampoll, G.; Watson, R. L.; Heber, O.; Horvat, V.; Wohrer, K.; Chabot, M.

    1992-03-01

    Transient molecular ions of COq+ (where q=2-7) were produced in single collisions of 97-MeV Ar14+ projectiles with neutral CO molecules. The resulting dissociation products were identified by coincidence time-of-flight spectroscopy in which the time of flight of the first ion to reach the detector and the time difference between the first ion and its partner were recorded event by event. An iterative matrix-transformation procedure was employed to convert the time-difference spectra for the prominent dissociation channels into total-kinetic-energy distributions. Analysis of the total-kinetic-energy distributions and comparisons with the available data for CO2+ and CO3+ from synchrotron radiation experiments led to the conclusion that ionization by Ar-ion impact populates states having considerably higher excitation energies than those accessed by photoionization.

  6. Understanding Ion Binding Affinity and Selectivity in β-Parvalbumin Using Molecular Dynamics and Mean Spherical Approximation Theory.

    PubMed

    Kucharski, Amir N; Scott, Caitlin E; Davis, Jonathan P; Kekenes-Huskey, Peter M

    2016-08-25

    Parvalbumin (PV) is a globular calcium (Ca(2+))-selective protein expressed in a variety of biological tissues. Our computational studies of the rat β-parvalbumin (β-PV) isoform seek to elucidate the molecular thermodynamics of Ca(2+) versus magnesium (Mg(2+)) binding at the protein's two EF-hand motifs. Specifically, we have utilized molecular dynamics (MD) simulations and a mean-field electrolyte model (mean spherical approximation (MSA) theory) to delineate how the EF-hand scaffold controls the "local" thermodynamics of Ca(2+) binding selectivity over Mg(2+). Our MD simulations provide the probability density of metal-chelating oxygens within the EF-hand scaffolds for both Ca(2+) and Mg(2+), as well the conformational strain induced by Mg(2+) relative to Ca(2+) binding. MSA theory utilizes the binding domain oxygen and charge distributions to predict the chemical potential of ion binding, as well as their corresponding concentrations within the binding domain. We find that the electrostatic and steric contributions toward ion binding were similar for Mg(2+) and Ca(2+), yet the latter was 5.5 kcal/mol lower in enthalpy when internal strain within the EF hand was considered. We therefore speculate that beyond differences in dehydration energies for the Ca(2+) versus Mg(2+), strain induced in the β-PV EF hand by cation binding significantly contributes to the nearly 10,000-fold difference in binding affinity reported in the literature. We further complemented our analyses of local factors governing cation binding selectivity with whole-protein (global) contributions, such as interhelical residue-residue contacts and solvent exposure of hydrophobic surface. These contributions were found to be comparable for both Ca(2+)- and Mg(2+)-bound β-PV, which may implicate local factors, EF-hand strain, and dehydration, in providing the primary means of selectivity. We anticipate these methods could be used to estimate metal binding thermodynamics across a broad range of

  7. The alpha-5 segment of Bacillus thuringiensis delta-endotoxin: in vitro activity, ion channel formation and molecular modelling.

    PubMed Central

    Gazit, E; Bach, D; Kerr, I D; Sansom, M S; Chejanovsky, N; Shai, Y

    1994-01-01

    A peptide with a sequence corresponding to the highly conserved alpha-5 segment of the Cry delta-endotoxin family (amino acids 193-215 of Bacillus thuringiensis CryIIIA [Gazit and Shai (1993) Biochemistry 32, 3429-3436]), was investigated with respect to its interaction with insect membranes, cytotoxicity in vitro towards Spodoptera frugiperda (Sf-9) cells, and its propensity to form ion channels in planar lipid membranes (PLMs). Selectively labelled analogues of alpha-5 at either the N-terminal amino acid or the epsilon-amine of its lysine, were used to monitor the interaction of the peptides with insect membranes. The fluorescent emission spectra of the 7-nitrobenz-2-oxa-1,3-diazole-4-yl (NBD)-labelled alpha-5 peptides displayed a blue shift upon binding to insect (Spodoptera littoralis) mid-gut membranes, reflecting the relocation of the fluorescent probes to an environment of increased apolarity, i.e. within the lipidic constituent of the membrane. Moreover, midgut membrane-bound NBD-labelled alpha-5 peptides were protected from enzymic proteolysis. Functional characterization of alpha-5 has revealed that it is cytotoxic to Sf-9 insect cells, and that it forms ion channels in PLMs with conductances ranging from 30 to 1000 pS. A proline-substituted analogue of alpha-5 is less cytolytic and slightly more exposed to enzymic digestion. Molecular modelling utilizing simulated annealing via molecular dynamics suggests that a transbilayer pore may be formed by alpha-5 monomers that assemble to form a left-handed coiled coil of approximately parallel helices. These findings further support a role for alpha-5 in the toxic mechanism of delta-endotoxins, and assign alpha-5 as one of the transmembrane helices which form the toxic pore. The suggested role is consistent with the recent finding that cleavage of CryIVB delta-endotoxin in a loop between alpha-5 and alpha-6 is highly important for its larvicidal activity [Angsuthanasombat, Crickmore and Ellar (1993) FEMS

  8. [The Ion Identification and Molecular Logic Gate of a Thiacalix[4]arene Fluorescent Probe].

    PubMed

    Wu, Fu-yong; Yu, Mei; Mu, Lan; Zeng, Xi; Wang, Rui-xiao; Takehiko Yamato

    2016-01-01

    A disubstituted phthalimide-based thiacalix[4] arene derivative (probe s1) was synthesized from cone 1, 3-thiacalix[4] arene and hydroxyethyl phthalimide, with benzyl appended the lower edge of thiacalix[4]-arene by triazole ring in the 2,4 position. The relative fluorescence quantum yield of probe s1 is 0.43 in CH3CN solvent. The strong fluorescence emission of probe s1 at 390 nm wavelength can be selectively quenched by Fe3+ in DMF/H2O solution. Similarly, the presence of I- also induced a significant fluorescence quenching of probe s1 at 310 nm wavelength in CH3CN solution. Spectral titration and isothermal titration calorimetry were showed that probe s1 with Fe3+ or I- both form 1 : 1 complexes, the binding constants up to 10(5) and coordinate process were spontaneous. The linear ranges of fluorescence detect Fe3+ or I- were 1.0 x 10(-7) - 1.6 x 10(-4) mol x L(-1) and 1.0 x 10(-7) - 8.5 x 10(-5) mol x L(-1), detection limits were up to 2.30 x 10(-8) mol x L(-1) and 1.17 x 10(-8) mol x L(-1), respectively. Meanwhile, take advantage of identification and coordination action, a logic circuit constructed at the molecular level by controlling two input signals of Fe3+ and F-, which causing probe s1 cycling of fluorescence emission or quenching. IR spectrum speculated that the nitrogen atoms of triazole groups are involved in the complexation with Fe3+, while the hydrogen atoms of triazole groups were complexed with I- by hydrogen bonding. PMID:27228760

  9. Phycodnavirus potassium ion channel proteins question the virus molecular piracy hypothesis.

    PubMed

    Hamacher, Kay; Greiner, Timo; Ogata, Hiroyuki; Van Etten, James L; Gebhardt, Manuela; Villarreal, Luis P; Cosentino, Cristian; Moroni, Anna; Thiel, Gerhard

    2012-01-01

    Phycodnaviruses are large dsDNA, algal-infecting viruses that encode many genes with homologs in prokaryotes and eukaryotes. Among the viral gene products are the smallest proteins known to form functional K(+) channels. To determine if these viral K(+) channels are the product of molecular piracy from their hosts, we compared the sequences of the K(+) channel pore modules from seven phycodnaviruses to the K(+) channels from Chlorella variabilis and Ectocarpus siliculosus, whose genomes have recently been sequenced. C. variabilis is the host for two of the viruses PBCV-1 and NY-2A and E. siliculosus is the host for the virus EsV-1. Systematic phylogenetic analyses consistently indicate that the viral K(+) channels are not related to any lineage of the host channel homologs and that they are more closely related to each other than to their host homologs. A consensus sequence of the viral channels resembles a protein of unknown function from a proteobacterium. However, the bacterial protein lacks the consensus motif of all K(+) channels and it does not form a functional channel in yeast, suggesting that the viral channels did not come from a proteobacterium. Collectively, our results indicate that the viruses did not acquire their K(+) channel-encoding genes from their current algal hosts by gene transfer; thus alternative explanations are required. One possibility is that the viral genes arose from ancient organisms, which served as their hosts before the viruses developed their current host specificity. Alternatively the viral proteins could be the origin of K(+) channels in algae and perhaps even all cellular organisms. PMID:22685610

  10. Biophysics and Molecular Biology of Cardiac Ion Channels for the Safety Pharmacologist.

    PubMed

    Pugsley, Michael K; Curtis, Michael J; Hayes, Eric S

    2015-01-01

    Cardiac safety pharmacology is a continuously evolving discipline that uses the basic principles of pharmacology in a regulatory-driven process to generate data to inform risk/benefit assessment of a new chemical entity (NCE). The aim of cardiac safety pharmacology is to characterise the pharmacodynamic/pharmacokinetic (PK/PD) relationship of a drug's adverse effects on the heart using continuously evolving methodology. Unlike Toxicology, safety pharmacology includes within its remit a regulatory requirement to predict the risk of rare cardiotoxic (potentially lethal) events such as torsades de pointes (TdP), which is statistically associated with drug-induced changes in the QT interval of the ECG due to blockade of I Kr or K v11.1 current encoded by hERG. This gives safety pharmacology its unique character. The key issues for the safety pharmacology assessment of a drug on the heart are detection of an adverse effect liability, projection of the data into safety margin calculation and clinical safety monitoring. This chapter will briefly review the current cardiac safety pharmacology paradigm outlined in the ICH S7A and ICH S7B guidance documents and the non-clinical models and methods used in the evaluation of new chemical entities in order to define the integrated risk assessment for submission to regulatory authorities. An overview of how the present cardiac paradigm was developed will be discussed, explaining how it was based upon marketing authorisation withdrawal of many non-cardiovascular compounds due to unanticipated proarrhythmic effects. The role of related biomarkers (of cardiac repolarisation, e.g. prolongation of the QT interval of the ECG) will be considered. We will also provide an overview of the 'non-hERG-centric' concepts utilised in the evolving comprehensive in vitro proarrhythmia assay (CIPA) that details conduct of the proposed ion channel battery test, use of human stem cells and application of in silico models to early cardiac safety

  11. Ion condensation behavior and dynamics of water molecules surrounding the sodium poly(methacrylic acid) chain in water: a molecular dynamics study.

    PubMed

    Chung, Yung-Ting; Huang, Ching-I

    2012-03-28

    All-atom molecular dynamics simulations are used to study the condensation behavior of monovalent (Na(+)) and multivalent (Ca(2+)) salt counterions associated with the co-ions (Cl(-)) surrounding the charged poly(methacrylic acid) (PMAA) chain in water. The study is extended to the influences on chain conformation, local arrangement, and dynamics of water in the highly diluted aqueous solutions. We find that even when the salt ions are monovalent, they attract more than one charged monomer and act as a bridging agent within the chain, as the multivalent salt ions. In principle, the salt ions bridge between not only the "non-adjacent" but also the "adjacent" charged monomers, leading to a more coil-like and a locally stretched conformation, respectively. With an increase in the salt concentration, the amount of coiled-type condensed ions increase and reach a maximum when the chain conformation becomes the most collapsed; whereas, the stretched-type shows an opposite trend. Our results show that the attractive interactions through the condensed salt ions between the non-adjacent monomers are responsible for the conformational collapse. When the salt concentration increases high enough, a significant increase for the stretched-type condensed ions makes an expansion effect on the chain. These stretched-type salt ions, followed by the adsorption of the co-ions and water molecules, tend to form a multilayer organization outside surrounding the PMAA chain. Thus, the expansion degree of the chain conformation is greatly limited. When only the monovalent Na(+) ions are present in the solutions, water molecules are primarily adsorbed into either the condensed Na(+) ions or the COO(-) groups. These adsorbed water molecules form hydrogen bonds with each other and enhance the local bridging behavior associated with the Na(+) condensation on the resultant chain conformation. With an increase in the amount of multivalent Ca(2+) salt ions, more water molecules are bonded directly

  12. Molecular characterization of inhibiting biochar water-extractable substances using electrospray ionization fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Smith, Cameron R; Sleighter, Rachel L; Hatcher, Patrick G; Lee, James W

    2013-01-01

    Biochar has gained significant interest worldwide for its potential use as both a carbon sequestration technique and soil amendment. Recently, research has shown that pinewood-derived biochar water extracts inhibited the growth of aquatic photosynthetic microorganisms, both prokaryotic and eukaryotic algae, while chicken litter- and peanut shell-derived biochar water extracts showed no growth inhibition. With the use of electrodialysis, the pinewood-derived biochar water extract is separated into 3 fractions (anode-isolated, center chamber retained, and cathode-isolated substances) all with varying toxic effects. Because of its ultrahigh resolution and mass precision, electrospray ionization (ESI) coupled to Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) is utilized in this study to analyze biochar water extracts at a molecular level to enhance our understanding of the toxic nature of pinewood-derived biochar water extracts as compared to benign peanut shell-derived biochar water extracts. The molecular composition of pinewood-derived biochar water extracts shows unique carbohydrate ligneous components and sulfur containing condensed ligneous components that are both absent from the peanut shell water extracts and more prevalent in the anode-isolated substances. Using Kendrick mass defect analysis, we also determine that the most likely inhibitor species contain carboxyl and hydroxyl homologous series, both of which are characteristic functional groups hypothesized in our previous research for the inhibitor species. We have suggested that inhibition of aquatic photosynthetic microorganism growth is most likely due to degraded lignin-like species rich in oxygen containing functionalities. From the study conducted here, we show the potential of ultrahigh resolution FTICR-MS as a valuable analytical technique for determining whether certain biochars are safe and benign for use as carbon sequestration and soil amendment. PMID:24180747

  13. Collision cross section prediction of deprotonated phenolics in a travelling-wave ion mobility spectrometer using molecular descriptors and chemometrics.

    PubMed

    Gonzales, Gerard Bryan; Smagghe, Guy; Coelus, Sofie; Adriaenssens, Dieter; De Winter, Karel; Desmet, Tom; Raes, Katleen; Van Camp, John

    2016-06-14

    The combination of ion mobility and mass spectrometry (MS) affords significant improvements over conventional MS/MS, especially in the characterization of isomeric metabolites due to the differences in their collision cross sections (CCS). Experimentally obtained CCS values are typically matched with theoretical CCS values from Trajectory Method (TM) and/or Projection Approximation (PA) calculations. In this paper, predictive models for CCS of deprotonated phenolics were developed using molecular descriptors and chemometric tools, stepwise multiple linear regression (SMLR), principal components regression (PCR), and partial least squares regression (PLS). A total of 102 molecular descriptors were generated and reduced to 28 after employing a feature selection tool, composed of mass, topological descriptors, Jurs descriptors and shadow indices. Therefore, the generated models considered the effects of mass, 3D conformation and partial charge distribution on CCS, which are the main parameters for either TM or PA (only 3D conformation) calculations. All three techniques yielded highly predictive models for both the training (R(2)SMLR = 0.9911; R(2)PCR = 0.9917; R(2)PLS = 0.9918) and validation datasets (R(2)SMLR = 0.9489; R(2)PCR = 0.9761; R(2)PLS = 0.9760). Also, the high cross validated R(2) values indicate that the generated models are robust and highly predictive (Q(2)SMLR = 0.9859; Q(2)PCR = 0.9748; Q(2)PLS = 0.9760). The predictions were also very comparable to the results from TM calculations using modified mobcal (N2). Most importantly, this method offered a rapid (<10 min) alternative to TM calculations without compromising predictive ability. These methods could therefore be used in routine analysis and could be easily integrated to metabolite identification platforms. PMID:27181646

  14. Identification and analysis of low molecular weight dissolved organic carbon in subglacial basal ice ecosystems by ion chromatography

    NASA Astrophysics Data System (ADS)

    Lawson, E. C.; Wadham, J. L.; Lis, G. P.; Tranter, M.; Pickard, A. E.; Stibal, M.; Dewsbury, P.; Fitzsimons, S.

    2015-08-01

    Glacial runoff is an important source of dissolved organic carbon (DOC) for downstream heterotrophic activity, despite the low overall DOC concentrations. This is because of the abundance of bioavailable, low molecular weight (LMW) DOC species. However, the provenance and character of LMW-DOC is not fully understood. We investigated the abundance and composition of DOC in subglacial environments via a molecular level DOC analysis of basal ice, which forms by water/sediment freeze-on to the glacier sole. Spectrofluorometry and a novel ion chromatographic method, which has been little utilised in glacial science for LMW-DOC determinations, were employed to identify and quantify the major LMW fractions (free amino acids, carbohydrates and carboxylic acids) in basal ice from four glaciers, each with a different basal debris type. Basal ice from Joyce Glacier (Antarctica) was unique in that 98 % of the LMW-DOC was derived from the extremely diverse FAA pool, comprising 14 FAAs. LMW-DOC concentrations in basal ice were dependent on the bioavailability of the overridden organic carbon (OC), which in turn, was influenced by the type of overridden material. Mean LMW-DOC concentrations in basal ice from Russell Glacier (Greenland), Finsterwalderbreen (Svalbard) and Engabreen (Norway) were low (0-417 nM C), attributed to the relatively refractory nature of the OC in the overridden paleosols and bedrock. In contrast, mean LMW-DOC concentrations were an order of magnitude higher (4430 nM C) in basal ice from Joyce Glacier, a reflection of the high bioavailability of the overridden lacustrine material (>17 % of the sediment OC comprised extractable carbohydrates, a proxy for bioavailable OC). We find that the overridden material may act as a direct (via abiotic leaching) and indirect (via microbial cycling) source of DOC to the subglacial environment and provides a range of LMW-DOC compounds that may stimulate microbial activity in wet sediments in current subglacial

  15. Formation rate for Rb 2 + molecular ions created in collisions of Rb Rydberg and ground-state atoms

    NASA Astrophysics Data System (ADS)

    Stanojevic, Jovica; Côté, Robin

    2016-05-01

    We calculate the formation rate of the molecular Rb2+ion in its various bound states produced in the associative ionization of a Rydberg and a ground-state atom. Before the formation takes place, the colliding atoms are accelerated by an attractive force between the collision partners. In this way the ground-state atom is first captured by the Rydberg electron and then guided towards the positive ion-core where a molecular ion is subsequently formed. As recently demonstrated, this process results in giant collisional cross sections for the molecular ion formation, with the cross sections essentially determined by the size of the Rydberg atom. For sufficient high principal quantum numbers and atomic densities, many ground-state atoms are already located inside the Rydberg atom and ready to participate in the associative ionization. The same process can occur between a Rydberg and a ground-state atom that form a long-range Rydberg molecule, possibly contributing to the shortening of the lifetimes of Rydberg atoms and molecules. Partial support from the US Army Research Office (ARO-MURI W911NF-14-1-0378), and from NSF (Grant No. PHY-1415560).

  16. The coupling between stability and ion pair formation in magnesium electrolytes from first-principles quantum mechanics and classical molecular dynamics

    SciTech Connect

    Rajput, Nav Nidhi; Qu, Xiaohuui; Sa, Niya; Burrell, Anthony K.; Persson, Kristin A.

    2015-03-11

    In this work we uncover a novel effect between concentration dependent ion pair formation and anion stability at reducing potentials, e.g., at the metal anode. Through comprehensive calculations using both first-principles as well as well-benchmarked classical molecular dynamics over a matrix of electrolytes, covering solvents and salt anions with a broad range in chemistry, we elucidate systematic correlations between molecular level interactions and composite electrolyte properties, such as electrochemical stability, solvation structure, and dynamics. We find that Mg electrolytes are highly prone to ion pair formation, even at modest concentrations, for a wide range of solvents with different dielectric constants, which have implications for dynamics as well as charge transfer. Specifically, we observe that, at Mg metal potentials, the ion pair undergoes partial reduction at the Mg cation center (Mg2+ -> Mg+), which competes with the charge transfer mechanism and can activate the anion to render it susceptible to decomposition. Specifically, TFSI exhibits a significant bond weakening while paired with the transient, partially reduced Mg+. In contrast, BH4 and BF4 are shown to be chemically stable in a reduced ion pair configuration. Furthermore, we observe that higher order glymes as well as DMSO improve the solubility of Mg salts, but only the longer glyme chains reduce the dynamics of the ions in solution. This information provides critical design metrics for future electrolytes as it elucidates a close connection between bulk solvation and cathodic stability as well as the dynamics of the salt.

  17. Time-of-Flight Secondary Ion Mass Spectrometry based Molecular Histology of Human Spinal Cord Tissue and Motor Neurons

    PubMed Central

    Hanrieder, Jörg; Malmberg, Per; Lindberg, Olle R.; Fletcher, John S.; Ewing, Andrew G.

    2013-01-01

    Secondary ion mass spectrometry is a powerful method for imaging biological samples with high spatial resolution. Whole section ToF SIMS scans and multivariate data analysis have been performed on human spinal cord in order to delineate anatomical regions of interest based on their chemical distribution pattern. ToF SIMS analysis of thoracic spinal cord sections was performed at 5µm resolution within 2 hours. Multivariate image analysis by means of principal component analysis and maximum auto correlation factor analysis resulted in detection of more than 400 m/z peaks that were found to be significantly changed. Here, the results show characteristic biochemical distributions that are well in line with major histological regions, including grey and white matter. As an approach for iterative segmentation, we further evaluated previously outlined regions of interest as identified by multivariate image analysis. Here, further discrimination of the grey matter into ventral, lateral and dorsal neuroanatomical regions was observed. TOF SIMS imaging has been carried out at submicron resolution obtaining localization and characterization of spinal motor neurons based on their chemical fingerprint, including neurotransmitter precursors that serve as molecular indicators for motor neuron integrity. Thus, TOF SIMS can be used as an approach for chemical histology and pathology. SIMS holds immense potential for investigating the subcellular mechanisms underlying spinal cord related diseases including chronic pain and amyotrophic lateral sclerosis. PMID:23947367

  18. Volumetric intensity dependence on the formation of molecular and atomic ions within a high intensity laser focus.

    PubMed

    Robson, Lynne; Ledingham, Kenneth W D; McKenna, Paul; McCanny, Thomas; Shimizu, Seiji; Yang, Jiamin M; Wahlström, Claes-Göran; Lopez-Martens, Rodrigo; Varju, Katalin; Johnsson, Per; Mauritsson, Johan

    2005-01-01

    The mechanism of atomic and molecular ionization in intense, ultra-short laser fields is a subject which continues to receive considerable attention. An inherent difficulty with techniques involving the tight focus of a laser beam is the continuous distribution of intensities contained within the focus, which can vary over several orders of magnitude. The present study adopts time of flight mass spectrometry coupled with a high intensity (8 x 10(15) Wcm(-2)), ultra-short (20 fs) pulse laser in order to investigate the ionization and dissociation of the aromatic molecule benzene-d1 (C(6)H(5)D) as a function of intensity within a focused laser beam, by scanning the laser focus in the direction of propagation, while detecting ions produced only in a "thin" slice (400 and 800 microm) of the focus. The resultant TOF mass spectra varies significantly, highlighting the dependence on the range of specific intensities accessed and their volumetric weightings on the ionization/dissociation pathways accessed. PMID:15653366

  19. Theoretical prediction of the potential curves for the lowest-lying states of the C2 + molecular ion

    NASA Astrophysics Data System (ADS)

    Petrongolo, Carlo; Bruna, Pablo J.; Peyerimhoff, Sigrid D.; Buenker, Robert J.

    1981-04-01

    Ab initio MRD-CI potential curves have been calculated for C2+ in its first 16 electronic states and vertical transition energies Tv have been computed for a number of higher-lying species, all of which correlate with the first dissociation limit C(3Pg)+C+(2Pu). The ground state of this molecular ion is found to be X 4Σg- while the first excited state is 1 2Πu, with a calculated Te value of 0.84 eV. On the basis of this work the C2 I.P. value known experimentally is ascribed to the a 3Πu→1 2Πu process while the transition involving both ground states appears to be difficult to detect experimentlly. Thus, the measured De value for C+2 should involve fragmentation of the 1 2Πu states as well. A comparison with previous calculations which attempt to estimate the correlation energies of the various C+2 states in a semiempirical manner shows very large discrepancies, both in the transition energies themselves and in the ordering of these states. Finally the assignment for the Meinel experimental band system at 4.98 eV as a 2Σ-g←2Πu transition in C+2 is not supported by the present theoretical study.

  20. Atomic/Molecular Layer Deposition of Lithium Terephthalate Thin Films as High Rate Capability Li-Ion Battery Anodes.

    PubMed

    Nisula, Mikko; Karppinen, Maarit

    2016-02-10

    We demonstrate the fabrication of high-quality electrochemically active organic lithium electrode thin films by the currently strongly emerging combined atomic/molecular layer deposition (ALD/MLD) technique using lithium terephthalate, a recently found anode material for lithium-ion battery (LIB), as a proof-of-the-concept material. Our deposition process for Li-terephthalate is shown to well comply with the basic principles of ALD-type growth including the sequential self-saturated surface reactions, a necessity when aiming at micro-LIB devices with three-dimensional architectures. The as-deposited films are found crystalline across the deposition temperature range of 200-280 °C, which is a trait highly desired for an electrode material but rather unusual for hybrid inorganic-organic thin films. Excellent rate capability is ascertained for the Li-terephthalate films with no conductive additives required. The electrode performance can be further enhanced by depositing a thin protective LiPON solid-state electrolyte layer on top of Li-terephthalate; this yields highly stable structures with capacity retention of over 97% after 200 charge/discharge cycles at 3.2 C. PMID:26812433