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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. Electronic Spectra of the Jet-Cooled Acetaminophen

    NASA Astrophysics Data System (ADS)

    Lee, Seung Jun; Min, Ahreum; Kim, Yusic; Choi, Myong Yong; Chang, Jinyoung; Lee, Sang Hak; Kim, Seong Keun

    2010-06-01

    Resonant two-photon ionization (R2PI), laser induced fluorescence (LIF) and UV-UV double resonance spectra of the jet-cooled acetaminophen, widely used as a pain reliever and fever reducer, were obtained in the gas phase. Conformational characterizations for acetaminophen will be presented with an aid of spectroscopic techniques and DFT B3LYP calculations.

  3. Fluorescence excitation spectrum and solvent-assisted conformational isomerization (SACI) of jet-cooled acetaminophen

    NASA Astrophysics Data System (ADS)

    Sohn, Woon Yong; Kang, Jeong Seok; Lee, So Young; Kang, Hyuk

    2013-08-01

    Fluorescence excitation spectrum of jet-cooled acetaminophen was obtained. When AAP was expanded with a buffer gas containing 0.3-1.1% of water, absorption peaks of the less stable trans conformer was significantly reduced by solvent-assisted conformational isomerization (SACI), which is confirmed by a separately measured UV-UV hole burning spectroscopy. It is also confirmed by quantum mechanical calculation and RRKM calculation that it is energetically and kinetically possible to induce SACI in AAP with water. The SACI mechanism suggests a possible pathway that acetaminophen can adopt an active conformation in vivo, which is need for molecular recognition and drug activity.

  4. Jet Cooled Rotational Studies of Dipeptides

    NASA Astrophysics Data System (ADS)

    Cabezas, C.; Mata, M. Varela S.; López, J. C.; Alonso, J. L.

    2011-06-01

    Rotational spectra of Gly-Pro and Pro-Gly dipeptides have been examined with laser ablation molecular beam Fourier transform microwave (LA-MB-FTMW) spectroscopy. Three conformers for Gly-Pro and one for Pro-Gly have been unequivocally identified in the supersonic expansion by the comparison of the experimental rotational and 14N (I=1) nuclear quadrupole coupling constants with those predicted by ab initio methods. The quadrupole hyperfine structure of two 14N nuclei has been totally resolved and it allows to experimentally characterize the main intramolecular forces which stabilize the assigned conformers. The biomimetic molecule Ac-Ala-NH_2 has been also studied. The C_7 and C_5 peptide conformations (intramolecularly hydrogen-bonded seven- or five-membered cycle, respectively) have been unequivocally identified in the supersonic expansion. The ability to identify peptide conformations suggest that it soon may be possible to explore the structures of larger peptides using LA-MB-FTMW spectroscopy. J. L. Alonso, C. Pérez, M. E. Sanz, J. C. López, S. Blanco, Phys. Chem. Chem. Phys. 11,617-627 (2009)and references therein

  5. 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).

  6. 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.

  7. Photodetachment-photoelectron spectroscopy of jet-cooled chrysene

    NASA Astrophysics Data System (ADS)

    Tschurl, Martin; Boesl, Ulrich

    2006-03-01

    Jet-cooled chrysene anions have been produced by attachment of slow laser-induced photoelectrons. The molecules have been studied by photodetachment-photoelectron spectroscopy using various wavelengths of the detachment laser. The adiabatic electron affinity of chrysene was directly determined to be 0.32 +/- 0.01 eV. In the S0 state of neutral chrysene two different vibrational modes are visible. Both are assigned to breathing modes of the aromatic ring system. In addition, the first excited triplet state is observed and a singlet triplet energy gap of 2.64 +/- 0.01 eV has been determined. In this state it was also possible to resolve a vibrational mode. At 355 nm an anion resonance was found that ended up in vibrationally highly excited neutral chrysene. As an explanation a special relaxation pathway is suggested.

  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. Jet-Cooled Chlorofluorobenzyl Radicals: Spectroscopy and Mechanism

    NASA Astrophysics Data System (ADS)

    Yoon, Young; Lee, Sang

    2016-06-01

    Whereas the benzyl radical, a prototypic aromatic free radical, has been the subject of numerous spectroscopic studies, halo-substituted benzyl radicals have received less attention, due to the difficulties associated with production of radicals from precursors. In particular, chloro-substituted benzyl radicals have been much less studied because of the weak visible emission intensity and weak C-Cl bond dissociation energy. The jet-cooled chlorofluorobenzyl radicals were generated in a technique of corona excited supersonic jet expansion using a pinhole-type glass nozzle for the vibronic assignments and measurements of electronic energies of the D_1 → D_0 transition. The 2,4-,2.5-, and 2.6- chlorofluorobenzyl radicals were generated by corona discharge of corresponding precursors, chlorofluorotoluenes seeded in a large amount of helium carrier gas. The vibronic emission spectra were recorded with a long-path monochromator in the visible region. The emission spectra show the vibronic bands originating from two types of benzyl-type radicals, chlorofluorobenzyl and fluorobenzyl benzyl radicals, in which fluorobenzyl radicals were obtained by displacement of Cl by H produced by dissociation of methyl C-H bond. From the 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. From the quantitative analysis of the red-shift, it has been found that the additivity rule can be applied to dihalo-substituted benzyl radicals. In this presentation, the dissociation process of precursors in corona discharge is discussed in terms of bond dissociation energy as well as the spectroscopic analysis of the radicals. C. S. Huh, Y. W. Yoon, and S. K. Lee, J. Chem. Phys. 136, 174306 (2012). Y. W. Huh, S. Y. Chae, and S. K. Lee, Chem

  11. 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/

  12. 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.

  13. 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).

  14. A study of jet-cooled exciplex formation

    SciTech Connect

    Deperasinska, Irena

    1996-04-01

    The characteristic of different types of isomeric forms of molecular exciplexes is presented on the base of semiempirical calculations of potential energy surfaces for molecular complexes, formed between anthracene (AN) and N,N-diethylaniline (DEA), naphthalene (NA) and triethylamine (TEA) and tetracyanobenzene (TCNB) and mesitylene (MS)

  15. 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.

  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.

  17. Electronic spectrum of jet cooled SiCN

    NASA Astrophysics Data System (ADS)

    Fukushima, Masaru; Ishiwata, Takashi

    2016-09-01

    We have generated SiCN in a supersonic free expansion, and measured the laser induced fluorescence (LIF) spectrum. Prior to the experiments, ab initio calculations were carried out to obtain the information necessary for searching for the LIF signals. In addition to the X ˜ 2Π state, the optimized structures of three excited states, 2Δ, 2Σ+, and 2Σ-, have been obtained. Guided by the predictions, the LIF excitation spectrum of SiCN was observed in the UV region. The rotational structure of the 00 0 band with the origin, 29 261.639 cm-1, indicated that the electronic transition is A ˜ 2Δ- X ˜ 2Π. The spin-orbit (SO) constants of the X ˜ 2Π and A ˜ 2Δ states were determined to be 140.824 and 4.944 cm-1, respectively. In the A ˜ 2Δ state, the Fermi resonance between the (0, 20, 0) 2Δ and (0, 00, 1) 2Δ vibronic levels was identified. The molecular constants of the X ˜ 2Π state were determined through the simultaneous analysis of the combination differences derived from the present LIF data with the previously reported rotational transitions. The spectroscopic parameters of the A ˜ 2Δ state were also obtained from the analysis where the constants of the X ˜ 2Π state, derived above, were fixed at those values.

  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. Snapshot of highly charged molecular ions

    NASA Astrophysics Data System (ADS)

    Shiromaru, H.; Nishide, T.; Kitamura, T.; Rajgara, F. A.; Sanderson, J. S.; Achiba, Y.; Kobayashi, N.

    2000-02-01

    Explosive fragmentation of highly charged molecular ions has been studied by a position sensitive time-of-flight (TOF) technique. The highly charged molecular ions of CO2, NO2, and CD4 were produced by 90-120 keV collisions of Arn+ (n=6,8). By the detailed analysis of the 3-dimensional velocity vectors of the fragment ions, molecular images at the instant of multiple ionization are "reconstructed," which are consistent with known structure of the neutral molecules. This in turn means that the dissociation of the highly charged ions is reasonably described by the pure Coulomb explosion scheme.

  20. 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.

  1. 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.

  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. Secondary ion mass spectrometry: Polyatomic and molecular ion emission

    NASA Astrophysics Data System (ADS)

    Colton, Richard J.; Ross, Mark M.; Kidwell, David A.

    1986-03-01

    Secondary ion mass spectrometry (SIMS) has become a diverse tool for the study of many substances such as metals, semiconductors, inorganic compounds and organic compounds, including polymers and biomolecules. This paper discusses the formation and emission of polyatomic and molecular ions from surfaces of these materials. The mass, energy, and abundance distribution of cluster ions emitted from various solids — Van der Waals, molecular, metallic, ionic and covalent — are compared. Trends in their emission patterns are discussed in terms of a recombination or a direct emission mechanism. For example, the ion abundance of cluster ions sputtered from metals decreases monotonically with increasing cluster size due to a decreasing formation probability for large clusters. The emission from metal oxides, however, shows a broad distribution of M mO ±n cluster ions whose formation can be described by both recombination and direct emission mechanisms. Covalently bonded molecules tend to eject as intact species. The emission of molecular ions is also discussed with respect to the method of ionization and the various sample preparation and matrix-assisted and derivatization procedures used. For example, the emission of molecular ions from metal surfaces is strongly influenced by the nature of the adsorption site; and matrix-assisted and derivatization procedures enhance the ionization efficiency of the analyte.

  4. 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.

  5. Carbon-based ion and molecular channels

    NASA Astrophysics Data System (ADS)

    Sint, Kyaw; Wang, Boyang; Kral, Petr

    2008-03-01

    We design ion and molecular channels based on layered carboneous materials, with chemically-functionalized pore entrances. Our molecular dynamics simulations demonstrate that these ultra-narrow pores, with diameters around 1 nm, are highly selective to the charges and sizes of the passing (Na^+ and Cl^-) ions and short alkanes. We demonstrate that the molecular flows through these pores can be easily controlled by electrical and mechanical means. These artificial pores could be integrated in fluidic nanodevices and lab-on-a-chip techniques with numerous potential applications. [1] Kyaw Sint, Boyang Wang and Petr Kral, submitted. [2] Boyang Wang and Petr Kral, JACS 128, 15984 (2006).

  6. Molecular phosphorus ion source for semiconductor technologya)

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

    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 P4+ 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 P4+ ion beam current greater than 30% of the total beam current.

  7. 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.

  8. 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.

  9. Identification of Structural Motifs of Imidazolium Based Ionic Liquids from Jet-Cooled Infrared Spectroscopy.

    NASA Astrophysics Data System (ADS)

    Young, Justin W.; Booth, Ryan S.; Annesley, Christopher; Stearns, Jaime A.

    2016-06-01

    Highly variable and potentially revolutionary, ionic liquids (IL) are a class of molecules with potential for numerous Air Force applications such as satellite propulsion, but the complex nature of IL structure and intermolecular interactions makes it difficult to adequately predict structure-property relationships in order to make new IL-based technology a reality. For example, methylation of imidazolium ionic liquids leads to a substantial increase in viscosity but the underlying physical mechanism is not understood. In addition the role of hydrogen bonding in ILs, especially its relationship to macroscopic properties, is a matter of ongoing research. Here, structural motifs are identified from jet-cooled infrared spectra of different imidazolium based ionic liquids, such as 1-ethyl-3-methylimidazolium bis(trifluoromethyl-sulfonyl)imide. Measurements of the C-H stretches indicate three structural families present in the gas phase.

  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. Molecular phosphorus ion source for semiconductor technology

    SciTech Connect

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

  12. 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.

  13. Multipass laser mass spectrometer with extreme jet-cooled pulsed gas

    SciTech Connect

    Kirihara, Naotoshi; Takahashi, Kenji; Kitada, Norifumi; Tanaka, Mizuho; Suzuki, Yasuo

    2006-09-15

    We have developed a photon accumulated laser mass spectrometer that enables us to identify isomers of polychlorinated dibenzo-p-dioxin and polychlorinated dibenzofuran. This system is comprised of a high temperature (230 deg. C) pulsed gas injector (PGI), multimirror multipath system (MMS), and the conventional time-of-flight mass spectrometer. The PGI induces the formation of a choked supersonic jet gas pulse that cools down to a temperature to restrain fragmentation and reduces vibrational and rotational thermal noises. The results suggest that the excited lifetime numbers and fragment dynamics of these species change completely with jet cooling of molecules. The MMS enhances the soft ionization efficiency (by a factor of 1000 over a single path system) through photon accumulation by extending the irradiation duration (to about 40 ns) and volume, and it further minimizes fragmentation by carefully controlling the laser intensity distribution within the ionization volume. For the typical isomer 2,3,4,7,8-pentachlorodibenzofuran, the system achieved a detection threshold (S/N ratio=3) of 410 ppq (equivalent to 4.4 ng/N m{sup 3})

  14. The UV Spectroscopy of Jet-Cooled 3-PHENYL-2-PROPYNENITRILE

    NASA Astrophysics Data System (ADS)

    Jawad, Khadija M.; Zwier, Timothy S.

    2016-06-01

    The atmosphere of Saturn's moon Titan is replete with hydrocarbons and nitriles, but knowledge of the formation and sink processes as well as the identities of molecules on the large end of photochemical models of the atmosphere is very limited. 3-phenyl-2-propynenitrile (Ph-C≡C-C≡N) is of potential importance in this atmosphere because it is a likely product of photochemical reaction between cyanoacetylene and benzene, bringing together two of the key functional groups in Titan's atmosphere in a single molecule. We present the UV spectrum of this molecule in the gas phase, under jet-cooled conditions, using 2-color resonant two-photon ionization. The spectrum was recorded from 292-208nm, taking advantage of the wide tunability of a BBO-based OPO as the excitation source. On its long wavelength end, the spectrum has sharp transitions arising from a ΠΠ* transition characteristic of a phenyl derivative, while deeper into the UV the spectrum is broadened in a manner reminiscent of cyanoacteylene.

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

    PubMed

    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

  16. 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

  17. 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.

  18. 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.

  19. Infrared Cavity Ringdown Laser Absorption Spectroscopy of jet-cooled clusters

    NASA Astrophysics Data System (ADS)

    Provencal, Robert Allen

    Infrared Cavity Ringdown Laser Absorption Spectroscopy (IR-CRLAS) employing stimulated Raman scattering (SRS) of pulsed dye lasers as the tunable IR source has been developed. This technique allows highly sensitive (ca. 1 ppm fractional absorption) direct absorption measurements to be performed in the 2-8 μm spectral range with complete wavelength coverage. Basic CR-LAS principles and essential SRS theory are reviewed. IR- CRLAS spectrometers based on both a Raman shifted dye laser and a pulsed Alexandrite ring laser are described. The IR-CRLAS spectrometer has been used in a comparative study of the O-H-stretching vibrations of small alcohol clusters. Results indicate an increase in the hydrogen bond strength as the alcohol chain length increases. An IR-CRLAS investigation of the aromatic C-H stretches of benzene and berizene/methane mixtures, performed in an effort to provide experimental support for a theoretically proposed ``antihydrogen bond'', produced negative results. Similarly, negative results from a visible CRLAS search for water cluster absorptions in connection with the anomalous atmospheric absorption of solar radiation are presented. Infrared laser spectroscopic studies of the structures and bonding in jet-cooled carbon clusters are discussed. The measurement and analysis of a rovibrational band at 2074 cm-1, tentatively assigned to linear C10 is presented. The astrophysical significance of carbon clusters is also discussed in conjunction with the first detection of a non polar molecule (C3) in a cold interstellar dust forming region, performed using far-infrared heterodyne spectroscopy aboard the Kuiper Airborne Observatory.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Accelerator mass spectrometry of molecular ions

    NASA Astrophysics Data System (ADS)

    Golser, Robin; Gnaser, Hubert; Kutschera, Walter; Priller, Alfred; Steier, Peter; Vockenhuber, Christof; Wallner, Anton

    2005-10-01

    The use of tandem accelerators for accelerator mass spectrometry (AMS) allows to literally "analyze" molecules. When a molecular ion with mass M and charge Q is injected at the low-energy side, it is efficiently broken up into its atomic constituents during the stripping process in the terminal. At the high-energy side the positively charged atomic ions are again analyzed by their mass-to-charge ratio and by their energy in the detector (and eventually by their nuclear charge, too). We show the usefulness of the AMS method by identifying unambiguously the doubly-charged negative molecule (43Ca19F4)2- for the first time. It considerably eases the task that the total mass M = 119 is odd, so the di-anion is injected at the half-integer mass-to-charge ratio M/Q = 59.5, where no singly charged ions can interfere. The full power of AMS is needed when we try to proof the existence of di-anions with an integer M/Q, e.g. (23Na35Cl3)2-, whose stability is of interest for atomic physics theory.

  5. 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.

  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. 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

  8. Normal modes of 4-aminobenzonitrile (4-ABN). A comparison of PM3 calculations with experimental jet-cooled spectroscopy

    NASA Astrophysics Data System (ADS)

    Yu, Haiping; Joslin, Evelyn; Zain, Sharifuddin M.; Rzepa, Henry; Phillips, David

    1993-12-01

    The geometry and the normal modes of 4-aminobenzonitrile (4-ABN) in the ground and first excited states have been computed using PM3 formulation. These calculated results, together with previous vapour phase absorption and infrared studies, are used to examine the vibrational modes in the laser-induced fluorescence (LIF) excitation and emission spectra of jet-cooled 4-ABN. The calculated vibrational frequencies of the normal modes show good agreement with experiment both for the electronic ground and the first excited states, but there is a relatively large discrepancy in the position of the electronic origin transition.

  9. 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

  10. 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.

  11. 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)

  12. Jet cooled NO 2 intra cavity laser absorption spectroscopy (ICLAS) between 11200 and 16150 cm -1

    NASA Astrophysics Data System (ADS)

    Georges, R.; Delon, A.; Bylicki, F.; Jost, R.; Campargue, A.; Charvat, A.; Chenevier, M.; Stoeckel, F.

    1995-01-01

    We have combined the high sensitivity of the ICLAS technique with the rotational cooling effect of a slit jet expansion in order to observe and to understand the visible and near infrared NO 2 spectrum. By this way, an equivalent absorption pathlength of several kilometers through rotationally cooled molecules has been achieved. Due to the vibronic interaction between the two lowest electronic states, X˜ 2A 1 and à 2B 2, this spectrum is vibronically dense and complex. Moreover, the dense room temperature rotational structure is perturbed by additional rovibronic interactions. In contrast, the rotational analysis of our jet cooled spectrum is straightforward. The NO 2 absorption spectrum is vanishing to the IR but, owing to the high sensitivity of the ICLAS technique, we have been able to record the NO 2 spectrum down to 11200 cm -1 with a new Ti:sapphire ICLAS spectrometer. As a result 249 2B 2 vibronic bands have been observed (175 cold bands and 74 hot bands) in the 11200-16150 cm -1 energy range. Due to the cooling effect of the slit jet we have reduced the rotational temperature down to about 12 K and at this temperature the K = 0 subbands are dominant. Consequently, we have analysed only the K = 0 manifold for N ⩽ 7 of each vibronic band. The dynamical range of the band intensities is about one thousand. Due to the strong vibronic interaction between the X˜ 2A 1 and à 2B 2 electronic states, we observed not only the a 1 vibrational levels of the à 2B 2 state but also the b 2 vibrational levels of the X˜ 2A 1 state interacting with the previous ones. By comparison with the calculated density of states, we conclude that we have observed about 65% of the total number of 2B 2 vibronic levels located in the studied range. However, there are more missing levels in the IR because of the weakness of the spectrum in this range. The correlation properties of this set of vibronic levels have been analysed calculating the power spectrum of the absorption stick

  13. The excited-state structure, vibrations, lifetimes, and nonradiative dynamics of jet-cooled 1-methylcytosine

    NASA Astrophysics Data System (ADS)

    Trachsel, Maria A.; Wiedmer, Timo; Blaser, Susan; Frey, Hans-Martin; Li, Quansong; Ruiz-Barragan, Sergi; Blancafort, Lluís; Leutwyler, Samuel

    2016-10-01

    We have investigated the S0 → S1 UV vibronic spectrum and time-resolved S1 state dynamics of jet-cooled amino-keto 1-methylcytosine (1MCyt) using two-color resonant two-photon ionization, UV/UV holeburning and depletion spectroscopies, as well as nanosecond and picosecond time-resolved pump/delayed ionization measurements. The experimental study is complemented with spin-component-scaled second-order coupled-cluster and multistate complete active space second order perturbation ab initio calculations. Above the weak electronic origin of 1MCyt at 31 852 cm-1 about 20 intense vibronic bands are observed. These are interpreted as methyl group torsional transitions coupled to out-of-plane ring vibrations, in agreement with the methyl group rotation and out-of-plane distortions upon 1ππ∗ excitation predicted by the calculations. The methyl torsion and ν1 ' (butterfly) vibrations are strongly coupled, in the S1 state. The S0 → S1 vibronic spectrum breaks off at a vibrational excess energy Eexc ˜ 500 cm-1, indicating that a barrier in front of the ethylene-type S1⇝S0 conical intersection is exceeded, which is calculated to lie at Eexc = 366 cm-1. The S1⇝S0 internal conversion rate constant increases from kIC = 2 ṡ 109 s-1 near the S1(v = 0) level to 1 ṡ 1011 s-1 at Eexc = 516 cm-1. The 1ππ∗ state of 1MCyt also relaxes into the lower-lying triplet T1 (3ππ∗) state by intersystem crossing (ISC); the calculated spin-orbit coupling (SOC) value is 2.4 cm-1. The ISC rate constant is 10-100 times lower than kIC; it increases from kISC = 2 ṡ 108 s-1 near S1(v = 0) to kISC = 2 ṡ 109 s-1 at Eexc = 516 cm-1. The T1 state energy is determined from the onset of the time-delayed photoionization efficiency curve as 25 600 ± 500 cm-1. The T2 (3nπ∗) state lies >1500 cm-1 above S1(v = 0), so S1⇝T2 ISC cannot occur, despite the large SOC parameter of 10.6 cm-1. An upper limit to the adiabatic ionization energy of 1MCyt is determined as 8.41 ± 0.02 e

  14. Excited-state structure, vibrations, and nonradiative relaxation of jet-cooled 5-fluorocytosine.

    PubMed

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

    2014-03-20

    The S0 → S1 vibronic spectrum and S1 state nonradiative relaxation of jet-cooled keto-amino 5-fluorocytosine (5FCyt) are investigated by two-color resonant two-photon ionization spectroscopy at 0.3 and 0.05 cm(–1) resolution. The 0(0)(0) rotational band contour is polarized in-plane, implying that the electronic transition is (1)ππ*. The electronic transition dipole moment orientation and the changes of rotational constants agree closely with the SCS-CC2 calculated values for the (1)ππ* (S1) transition of 5FCyt. The spectral region from 0 to 300 cm(–1) is dominated by overtone and combination bands of the out-of-plane ν1′ (boat), ν2′ (butterfly), and ν3′ (HN–C6H twist) vibrations, implying that the pyrimidinone frame is distorted out-of-plane by the (1)ππ* excitation, in agreement with SCS-CC2 calculations. The number of vibronic bands rises strongly around +350 cm(–1); this is attributed to the (1)ππ* state barrier to planarity that corresponds to the central maximum of the double-minimum out-of-plane vibrational potentials along the ν1′, ν2′, and ν3′ coordinates, which gives rise to a high density of vibronic excitations. At +1200 cm(–1), rapid nonradiative relaxation (k(nr) ≥ 10(12) s(–1)) sets in, which we interpret as the height of the (1)ππ* state barrier in front of the lowest S1/S0 conical intersection. This barrier in 5FCyt is 3 times higher than that in cytosine. The lifetimes of the ν′ = 0, 2ν1′, 2ν2′, 2ν1′ + 2ν2′, 4ν2′, and 2ν1′ + 4ν2′ levels are determined from Lorentzian widths fitted to the rotational band contours and are τ ≥ 75 ps for ν′ = 0, decreasing to τ ≥ 55 ps at the 2ν1′ + 4ν2′ level at +234 cm(–1). These gas-phase lifetimes are twice those of S1 state cytosine and 10–100 times those of the other canonical nucleobases in the gas phase. On the other hand, the 5FCyt gas-phase lifetime is close to the 73 ps lifetime in room-temperature solvents. This lack of

  15. 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

  16. Secondary Molecular Ion Emission In Binary Projectile-Surface Collisions

    NASA Astrophysics Data System (ADS)

    Jalowy, T.; Neugebauer, R.; Farenzena, L. S.; Collado, V. M.; Schmidt-Böcking, H.; da Silveira, E. F.; Groeneveld, K. O.

    2003-08-01

    Secondary molecular ions, emitted from a LiF target bombarded by a MeV argon beam, are analyzed by a XY-TOF detection system. This new method allows, for each emitted ion, simultaneous measurement of its time-of flight (TOF) and its impact coordinates (XY) on the detector surface, after acceleration by a homogenous electric field. Angular distributions and initial velocities for atomic (H+ , Li+, C+) and for molecular (Hn+, CmHn+) ions are determined. The analysis reveals different emission processes, among them a unexpected emission of fast molecular ions from binary collisions.

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

    PubMed

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

    2014-08-01

    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.

  18. 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.

  19. Rotational relaxation of molecular ions in a buffer gas

    NASA Astrophysics Data System (ADS)

    Pérez-Ríos, Jesús; Robicheaux, F.

    2016-09-01

    The scattering properties regarding the rotational degrees of freedom of a molecular ion in the presence of a buffer gas of helium are investigated. This study is undertaken within the framework of the infinite-order sudden approximation for rotational transitions, which is shown to be applicable to a large variety of molecular ions in a buffer gas of helium at fairly low temperatures. The results derived from the present approach have potential applications in cold chemistry and molecular quantum logic spectroscopy.

  20. 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.

  1. 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.

  2. 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

  3. 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%.

  4. 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.

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

    PubMed

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

    2015-06-04

    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.

  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. 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).

  8. 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.

  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. New molecular ions in spectra of comet P/Halley

    NASA Technical Reports Server (NTRS)

    Wyckoff, S.; Wehinger, P. A.; Spinrad, Hyron; Belton, M. J. S.

    1986-01-01

    Spectroscopic observations (4000 to 7000 A) were obtained of comet P/Halley near the time of the spacecraft encounters in March 1986. Molecular ion emission features were observed in the long-slit CCD spectra. Additional spectroscopic observations obtained in April 1986 confirm the presence of many new ion features in the plasma tail. It is proposed that CO2(+) be identified with the new features in the 4000 to 4350 A region. The other unidentified ion features may be attributable to a single ion species.

  12. Resonant two-photon ionization spectroscopy of jet-cooled UN: Determination of the ground state

    NASA Astrophysics Data System (ADS)

    Matthew, Daniel J.; Morse, Michael D.

    2013-05-01

    The optical transitions of supersonically cooled uranium nitride (UN) have been investigated in the range from 19 200 to 23 900 cm-1 using resonant two-photon ionization spectroscopy. A large number of bands have been observed, of which seven have been rotationally resolved and analyzed. All are found to arise from the same state, which is presumably the ground state of the molecule. From the analysis of the bands, the ground state has Ω = 3.5, with a bond length of 1.7650(12) Å. Comparisons to the known isovalent molecules are made, and the variations in ground state configuration are explained in terms of the configurational reordering that occurs with changes in the nuclear and ligand charges. It is concluded that the UN molecule is best considered as a U3+N3- species in which the closed shell nitride ligand interacts with a U3+ ion. The ground state of the molecule derives from a U3+ ion in its 7s15f 2 atomic configuration.

  13. High Resolution Infrared Spectra of Plasma Jet-Cooled - and Triacetylene in the C-H Stretch Region by CW Cavity Ring-Down Spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhao, D.; Guss, J.; Walsh, A.; Doney, K.; Linnartz, H.

    2013-06-01

    Polyacetylenes form an important series of unsaturated hydrocarbons that are of astrophysical interest. Small polyacetylenes have been detected from infrared observations in dense atmosphere of Titan and in a protoplanetary nebula CRL 618. We present here high-resolution mid-infrared spectra of diacetylene (HC_{4}H) and triacetylene (HC_{6}H) that are recorded in a supersonically expanded pulsed planar plasma using an ultra-sensitive detection technique. This method uses an all fiber-laser-based optical parametric oscillator (OPO), in combination with continuous wave cavity ring-down spectroscopy (cw-CRDS) as a direct absorption detection tool. A hardware-based multi-trigger concept is developed to apply cw-CRDS to pulsed plasmas. Vibrationally hot but rotationally cold HC_{4}H and HC_{6}H are produced by discharging a C_{2}H_{2}/He/Ar gas mixture which is supersonically expanded into a vacuum chamber through a slit discharge nozzle. Experimental spectra are recorded at a resolution of ˜100 MHz in the 3305-3340 cm^{-1} region, which is characteristic of the C-H stretch vibrations of HC_{4}H and HC_{6}H. Jet-cooling in our experiment reduces the rotational temperature of both HC_{4}H and HC_{6}H to <20 K. In total, ˜2000 lines are measured. More than fourteen (vibrationally hot) bands for HC_{4}H and four bands for HC_{6}H are assigned based on Loomis-Wood diagrams, and nearly half of these bands are analyzed for the first time. For both molecules improved and new molecular constants of a series of vibrational levels are presented. The accurate molecular data reported here, particularly those for low-lying (bending) vibrational levels may be used to interpret the ro-vibrational transitions in the FIR and submillimeter/THz region. D. Zhao, J. Guss, A. Walsh, H. Linnartz Chem. Phys. Lett., {dx.doi.org/10.1016/j.cplett.2013.02.025}, in press, 2013.

  14. Sub-Doppler Slit Jet Discharge Spectroscopy of Jet Cooled Polyacetylenes: the Anti-Symmetric CH Stretch Mode of Triacetylene

    NASA Astrophysics Data System (ADS)

    Chang, Chih-Hsuan; Roberts, Melanie A.; Nesbitt, David J.

    2013-06-01

    Growth of polyacetylenic molecules in acetylene flames is thought to play a central role in combustion chemistry and formation of soot, as well as the chemistry of gas clouds in the interstellar medium. In this talk, we present results from first sub-Doppler, high resolution infrared spectroscopic studies on triacetylene. In particular, we explore the fundamental anti-symmetric CH stretching mode (v_5) of jet-cooled triacetylene in a pulsed slit discharge, where the "{in-situ} synthesis" arises from a discharge of trace(0.1-1%) acetylene/rare gas mixtures followed by rapid CCH + HCCH chemistry in the supersonic expansion environment. The band origin of this mode is determined to be 3329.0544(2) cm^{-1}. At high resolution, a series of avoided energy level crossings arising from rotational perturbations are observed and ascribed to perpendicular Coriolis mixing with a near degenerate manifold of Π vibrational symmetry. The energy level patterns are successfully analyzed to reveal spectroscopic constants and Coriolis coupling matrix elements for the perturbing manifold. In addition, a weak Π-Π hot band progression due to thermal population in the slit jet is observed and assigned. D. McNaughton and D. N. Bruget, J. Mol. Spectrosc.150, 620 (1991) K. Matsumura, K. Kawaguchi, D. McNaughton, and D. N. Bruget, J. Mol. Spectrosc.158, 489 (1993)

  15. Analysis of the Cavity Ringdown Spectra of the Smallest Jet-Cooled Alkyl Peroxy Radicals Using a Evolutionary Algorithm

    NASA Astrophysics Data System (ADS)

    Just, Gabriel M. P.; Rupper, Patrick; Miller, Terry A.; Meerts, W. Leo

    2009-06-01

    Alkyl peroxy radicals long have been well known to bekey intermediates in atmospheric chemistry as well as in low temperature combustion. For the last several years, our group has generated a data set for these radicals using room temperature cavity ringdown spectroscopy. We have recently extended our investigations of these radicals to obtain a similar data set of spectra under jet cooled conditions using a quasi-Fourier-transform-limited laser source, a supersonic slit jet expansion, and a discharge. We were able to observe partially rotationally resolved spectra of isomers and conformers of several peroxy radicals such as methyl peroxy, CH_3O_2/CD_3O_2, ethyl peroxy, C_2H_5O_2 and C_2D_5O_2, propyl peroxy, C_3H_7O_2, and phenyl peroxy, C_6H_5O_2. To analyze our results we employed a new approach by using the evolutionary algorithm method, whereby we can effectively use both the frequency and the intensity information contained in the experimental spectra. This presentation will focus on the results from our fitted spectra which were obtained using this semi-automated method and will demonstrate the power of our technique .

  16. Dispersed-Fluorescence Spectroscopy of Jet-Cooled Calcium Ethoxide Radical (CaOC_2H_5)

    NASA Astrophysics Data System (ADS)

    Paul, Anam C.; Reza, Md Asmaul; Liu, Jinjun

    2016-06-01

    Metal-containing free radicals are important intermediates in metal-surface reactions and in the interaction between metals and organic molecules. In the present work, dispersed fluorescence (DF) spectra of the calcium ethoxide radical (CaOC_2H_5) have been obtained by pumping the {tilde A^2}{A}' ← {tilde X^2}{A}' and the {tilde B^2}{A}'' ← {tilde X^2}{A}' origin bands in its laser-induced fluorescence (LIF) spectrum. CaOC_2H_5 radicals were produced by 1064 nm laser ablation of calcium grains in the presence of ethanol under jet-cooled conditions. Dominant transitions in the vibrationally resolved DF spectra are well reproduced using Franck-Condon factors predicted by complete active space self-consistent (CASSCF) calculations. Differences in transition intensities between the {tilde A^2}{A}' → {tilde X^2}{A}' and the {tilde B^2}{A}'' → {tilde X^2}{A}' DF spectra are attributed to the pseudo-Jahn-Teller interaction between the tilde A ^2 A' and the tilde B ^2 A'' states. Collision-induced population transfer between these two excited electronic states results in additional peaks in the DF spectra.

  17. Quantitative measurement of naphthalene in low-pressure flames by jet-cooled laser-induced fluorescence

    NASA Astrophysics Data System (ADS)

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

    2010-09-01

    We have recently developed a new laser based set-up (Jet-Cooled Laser-Induced Fluorescence) for the analysis of aromatic compounds generated in flames. This method relies on the extraction of the species from the flame via a thin microprobe and their direct analysis inside a supersonic free jet by Laser-Induced Fluorescence (LIF). Under the supersonic conditions of the jet, the vibronic spectra of the molecules become structured as the possibility of electronic transitions is reduced, allowing their selective detection by LIF. In addition, due to the very low quenching efficiency inside the jet, LIF signals can be directly related to the population of the probed species and easily calibrated into absolute concentrations. All of the work presented here has been carried out for naphthalene, which is an important PAH involved in soot formation mechanisms. The calibration procedure is described in detail. We also report a detailed study of the quantitative features of the technique, in particular cooling efficiencies and collision rates as well as some additional potential factors that could bias the quantitative aspect of the method. Finally, the possibilities of the technique for the measurement of PAH within flames in the presence of soot particles along with its accuracy and reproducibility are demonstrated by recording naphthalene mole fractions profiles in several rich CH4/O2/N2 flames. A detection limit of the order of a ppb is demonstrated under flame conditions with and without the presence of soot particles.

  18. Infrared laser absorption spectroscopy of the ν7 band of jet-cooled iron pentacarbonyl

    NASA Astrophysics Data System (ADS)

    Loroño, M.; Cruse, H. A.; Davies, P. B.

    2000-02-01

    The ν7 parallel band of Fe(CO) 5 has been measured in the 620 cm -1 region using high-resolution diode laser absorption spectroscopy in a free jet expansion. A comparison with simulated band profiles indicated a rotational temperature of between 2 and 3 K in the jet. At these temperatures the K-structure of the Q-branch is partly resolved. The following molecular parameters were obtained: ν0=619.95747(12) cm -1, B7=0.026743(2) cm -1, A7=0.030721(1) cm -1. Approximate values of the quartic centrifugal distortion constants were also obtained from fitting the spectra.

  19. Low fragment polyatomic molecular ion source by using permanent magnets

    NASA Astrophysics Data System (ADS)

    Takeuchi, Mitsuaki; Hayashi, Kyouhei; Imanaka, Kousuke; Ryuto, Hiromichi; Takaoka, Gikan H.

    2014-02-01

    Electron-ionization-type polyatomic molecular ion source with low fragment was developed by using a pair of ring-shaped Sm-Co magnets. The magnets were placed forward and backward side of ionization part to confine electrons extracted from a thermionic cathode. Calculated electron trajectory of the developed ion source was 20 times longer than that of an ordinary outer filament configuration that has no magnetic confinement. Mass spectra of the molecular ions generated from n-tetradecane (C14H30) gas exhibited 4 times larger intensity than that of the ordinary configuration in a range of mass/charge from 93 to 210 u. This indicates that suppression of fragment ion was obtained by increase of low energy electrons resulted from the electron confinement.

  20. Low fragment polyatomic molecular ion source by using permanent magnets.

    PubMed

    Takeuchi, Mitsuaki; Hayashi, Kyouhei; Imanaka, Kousuke; Ryuto, Hiromichi; Takaoka, Gikan H

    2014-02-01

    Electron-ionization-type polyatomic molecular ion source with low fragment was developed by using a pair of ring-shaped Sm-Co magnets. The magnets were placed forward and backward side of ionization part to confine electrons extracted from a thermionic cathode. Calculated electron trajectory of the developed ion source was 20 times longer than that of an ordinary outer filament configuration that has no magnetic confinement. Mass spectra of the molecular ions generated from n-tetradecane (C14H30) gas exhibited 4 times larger intensity than that of the ordinary configuration in a range of mass/charge from 93 to 210 u. This indicates that suppression of fragment ion was obtained by increase of low energy electrons resulted from the electron confinement. PMID:24593425

  1. 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.

  2. 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 !}.

  3. 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.

  4. 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.

  5. 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.

  6. Molecular secondary ion mass spectrometry: New dimensions in chemical characterization

    NASA Astrophysics Data System (ADS)

    Colton, Richard J.; Campana, Joseph E.; Kidwell, David A.; Ross, Mark M.; Wyatt, Jeffrey R.

    1985-04-01

    Secondary ion mass spectrometry (SIMS) has become a diverse tool for the study of many substances other than metals and semiconductors. This paper discusses the emission of polyatomic and molecular ions from surfaces that contain various inorganic and organic compounds including polymers and biomolecules. The mass and abundance distribution of cluster ions emitted from various solids — Van der Waals, metallic, ionic and covalent — are compared. Trends in the emission patterns are discussed in terms of a recombination or direct emission mechanism. The emission of molecular ions is also discussed with respect to the method of ionization and the various sample preparation and matrix-assisted procedures used. The matrices include various solid-state and liquid matrices such as ammonium chloride, charcoal, glycerol and gallium. Various chemical derivatization procedures have been developed to enhance the sensitivity of molecular SIMS and to detect selectively components in mixtures. The procedures are demonstrated for the low-level detection of airborne contaminants from paints, for the analysis of drugs in biological fluids, and for the sequencing of biomolecules such as peptides and sugars. The emission of characteristic fragment ions from the surfaces of polymers is also described for thick, insulating films.

  7. 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)

  8. 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…

  9. 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.

  10. Ab Initio Molecular Dynamics Study on the Interactions between Carboxylate Ions and Metal Ions in Water.

    PubMed

    Mehandzhiyski, Aleksandar Y; Riccardi, Enrico; van Erp, Titus S; Trinh, Thuat T; Grimes, Brian A

    2015-08-20

    The interaction between a carboxylate anion (deprotonated propanoic acid) and the divalent Mg(2+), Ca(2+), Sr(2+), Ba(2+) metal ions is studied via ab initio molecular dynamics. The main focus of the study is the selectivity of the carboxylate-metal ion interaction in aqueous solution. The interaction is modeled by explicitly accounting for the solvent molecules on a DFT level. The hydration energies of the metal ions along with their diffusion and mobility coefficients are determined and a trend correlated with their ionic radius is found. Subsequently, a series of 16 constrained molecular dynamics simulations for every ion is performed, and the interaction free energy is obtained from thermodynamic integration of the forces between the metal ion and the carboxylate ion. The results indicate that the magnesium ion interacts most strongly with the carboxylate, followed by calcium, strontium, and barium. Because the interaction free energy is not enough to explain the selectivity of the reaction observed experimentally, more detailed analysis is performed on the simulation trajectories to understand the steric changes in the reaction complex during dissociation. The solvent dynamics appear to play an important role during the dissociation of the complex and also in the observed selectivity behavior of the divalent ions.

  11. 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.

  12. A rotary nano ion pump: a molecular dynamics study.

    PubMed

    Lohrasebi, A; Feshanjerdi, M

    2012-09-01

    The dynamics of a rotary nano ion pump, inspired by the F (0) part of the F(0)F(1)-ATP synthase biomolecular motor, were investigated. This nanopump is composed of a rotor, which is constructed of two carbon nanotubes with benzene rings, and a stator, which is made of six graphene sheets. The molecular dynamics (MD) method was used to simulate the dynamics of the ion nanopump. When the rotor of the nanopump rotates mechanically, an ion gradient will be generated between the two sides of the nanopump. It is shown that the ion gradient generated by the nanopump is dependant on parameters such as the rotary frequency of the rotor, temperature and the amounts and locations of the positive and negative charges of the stator part of the nanopump. Also, an electrical potential difference is generated between the two sides of the pump as a result of its operation.

  13. Gas feeding molecular phosphorous ion source for semiconductor implanters

    NASA Astrophysics Data System (ADS)

    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 × 105, P4/P ˜ 1021). 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.

  14. 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.

  15. 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

  16. Precision Spectroscopy on Single Cold Trapped Molecular Nitrogen Ions

    NASA Astrophysics Data System (ADS)

    Hegi, Gregor; Najafian, Kaveh; Germann, Matthias; Sergachev, Ilia; Willitsch, Stefan

    2016-06-01

    The ability to precisely control and manipulate single cold trapped particles has enabled spectroscopic studies on narrow transitions of ions at unprecedented levels of precision. This has opened up a wide range of applications, from tests of fundamental physical concepts, e.g., possible time-variations of fundamental constants, to new and improved frequency standards. So far most of these experiments have concentrated on atomic ions. Recently, however, attention has also been focused on molecular species, and molecular nitrogen ions have been identified as promising candidates for testing a possible time-variation of the proton/electron mass ratio. Here, we report progress towards precision-spectroscopic studies on dipole-forbidden vibrational transitions in single trapped N2+ ions. Our approach relies on the state-selective generation of single N2+ ions, subsequent infrared excitation using high intensity, narrow-band quantum-cascade lasers and a quantum-logic scheme for non-destructive state readout. We also characterize processes limiting the state lifetimes in our experiment, which impair the measurement fidelity. P. O. Schmidt et. al., Science 309 (2005), 749. M. Kajita et. al., Phys. Rev. A 89 (2014), 032509 M. Germann , X. Tong, S. Willitsch, Nature Physics 10 (2014), 820. X. Tong, A. Winney, S. Willitsch, Phys. Rev. Lett. 105 (2010), 143001

  17. 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

  18. Determination of ion quantity by using low-temperature ion density theory and molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Du, Li-Jun; Song, Hong-Fang; Li, Hai-Xia; Chen, Shao-Long; Chen, Ting; Sun, Huan-Yao; Huang, Yao; Tong, Xin; Guan, Hua; Gao, Ke-Lin

    2015-11-01

    In this paper, we report a method by which the ion quantity is estimated rapidly with an accuracy of 4%. This finding is based on the low-temperature ion density theory and combined with the ion crystal size obtained from experiment with the precision of a micrometer. The method is objective, straightforward, and independent of the molecular dynamics (MD) simulation. The result can be used as the reference for the MD simulation, and the method can improve the reliability and precision of MD simulation. This method is very helpful for intensively studying ion crystal, such as phase transition, spatial configuration, temporal evolution, dynamic character, cooling efficiency, and the temperature limit of the ions. Project supported by the National Basic Research Program of China (Grant Nos. 2012CB821301 and 2010CB832803), the National Natural Science Foundation of China (Grant Nos. 11004222 and 91121016), and the Chinese Academy of Sciences.

  19. Laser induced fluorescence and resonant two-photon ionization spectroscopy of jet-cooled 1-hydroxy-9,10-anthraquinone

    NASA Astrophysics Data System (ADS)

    Cho, Sung Haeng; Huh, Hyun; Kim, Hyung Min; Kim, Choong Ik; Kim, Nam Joon; Kim, Seong Keun

    2005-01-01

    We carried out laser induced fluorescence and resonance enhanced two-color two-photon ionization spectroscopy of jet-cooled 1-hydroxy-9,10-anthraquinone (1-HAQ). The 0-0 band transition to the lowest electronically excited state was found to be at 461.98 nm (21 646 cm-1). A well-resolved vibronic structure was observed up to 1100 cm-1 above the 0-0 band, followed by a rather broad absorption band in the higher frequency region. Dispersed fluorescence spectra were also obtained. Single vibronic level emissions from the 0-0 band showed Stokes-shifted emission spectra. The peak at 2940 cm-1 to the red of the origin in the emission spectra was assigned as the OH stretching vibration in the ground state, whose combination bands with the C=O bending and stretching vibrations were also seen in the emission spectra. In contrast to the excitation spectrum, no significant vibronic activity was found for low frequency fundamental vibrations of the ground state in the emission spectrum. The spectral features of the fluorescence excitation and emission spectra indicate that a significant change takes place in the intramolecular hydrogen bonding structure upon transition to the excited state, such as often seen in the excited state proton (or hydrogen) transfer. We suggest that the electronically excited state of interest has a double minimum potential of the 9,10-quinone and the 1,10-quinone forms, the latter of which, the proton-transferred form of 1-HAQ, is lower in energy. On the other hand, ab initio calculations at the B3LYP/6-31G(d,p) level predicted that the electronic ground state has a single minimum potential distorted along the reaction coordinate of tautomerization. The 9,10-quinone form of 1-HAQ is the lowest energy structure in the ground state, with the 1,10-quinone form lying ˜5000 cm-1 above it. The intramolecular hydrogen bond of the 9,10-quinone was found to be unusually strong, with an estimated bond energy of ˜13 kcal/mol (˜4500 cm-1), probably due to

  20. 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.

  1. Ion motions in molecular dynamics simulations on DNA

    NASA Astrophysics Data System (ADS)

    Ponomarev, Sergei Y.; Thayer, Kelly M.; Beveridge, David L.

    2004-10-01

    Counterions play a significant role in DNA structure and function, and molecular dynamics (MD) simulations offer the prospect of detailed description of the dynamical structure of ions at the molecular level. However, the motions of mobile counterions are notably slow to converge in MD on DNA. Obtaining accurate and reliable MD simulations requires knowing just how much sampling is required for convergence of each of the properties of interest. To address this issue, MD on a d(CGCGAATTCGCG) duplex in a dilute aqueous solution of water and 22 Na+ counterions was performed until convergence was achieved. The calculated first shell ion occupancies and DNA-Na+ radial distribution functions were computed as a function of time to assess convergence, and compared with relaxation times of the DNA internal parameters shift, slide, rise, tilt, roll, and twist. The sequence dependence of fractional occupancies of ions in the major and minor grooves of the DNA is examined, and the possibility of correlation between ion proximity and DNA minor groove widths is investigated.

  2. 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

  3. 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.

  4. 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

  5. Jet-cooled spectroscopy of the α-methylbenzyl radical: probing the state-dependent effects of methyl rocking against a radical site.

    PubMed

    Kidwell, Nathanael M; Reilly, Neil J; Nebgen, Ben; Mehta-Hurt, Deepali N; Hoehn, Ross D; Kokkin, Damian L; McCarthy, Michael C; Slipchenko, Lyudmila V; Zwier, Timothy S

    2013-12-19

    The state-dependent spectroscopy of α-methylbenzyl radical (α-MeBz) has been studied under jet-cooled conditions. Two-color resonant two-photon ionization (2C-R2PI), laser-induced fluorescence, and dispersed fluorescence spectra were obtained for the D0-D1 electronic transition of this prototypical resonance-stabilized radical in which the methyl group is immediately adjacent to the primary radical site. Extensive Franck-Condon activity in hindered rotor levels was observed in the excitation spectrum, reflecting a reorientation of the methyl group upon electronic excitation. Dispersed fluorescence spectra from the set of internal rotor levels are combined with the excitation spectrum to obtain a global fit of the barrier heights and angular change of the methyl group in both D0 and D1 states. The best-fit methyl rotor potential in the ground electronic state (D0) is a flat-topped 3-fold potential (V3" = 151 cm(-1), V6" = 34 cm(-1)) while the D1 state has a lower barrier (V3' = 72 cm(-1), V6' = 15 cm(-1)) with Δφ = ± π/3, π, consistent with a reorientation of the methyl group upon electronic excitation. The ground state results are compared with calculations carried out at the DFT B3LYP level of theory using the 6-311+G(d,p) basis set, and a variety of excited state calculations are carried out to compare against experiment. The preferred geometry of the methyl rotor in the ground state is anti, which switches to syn in the D1 state and in the cation. The calculations uncover a subtle combination of effects that contribute to the shift in orientation and change in barrier in the excited state relative to ground state. Steric interaction favors the anti conformation, while hyperconjugation is greater in the syn orientation. The presence of a second excited state close by D1 is postulated to influence the methyl rotor properties. A resonant ion-dip infrared (RIDIR) spectrum in the alkyl and aromatic CH stretch regions was also recorded, probing in a

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. Molecular mass and location of the most abundant peak of the molecular ion isotopomeric cluster.

    PubMed

    Goraczko, Andrzej J

    2005-09-01

    The location of the most abundant peak of the molecular-ion pattern often differs from the molecular mass published in scientific databases. The location is also distinct from the value expected from average atomic masses. The cause of this phenomenon is a large number of atoms of carbon, sulfur, chlorine, bromine, silicon and boron. This due to the natural isotope abundances of some elements forming organic compounds. A parameter called location of the most abundant peak of an isotopometric cluster (LAPIC) denotes the location of the most abundant (the main) peak of an isotopomeric cluster, which is determined, e.g., by mass spectrometry and can be important for medium- and high-molecular mass compounds. The equations for LAPIC calculation are presented for elements usually observed in organic compounds. The LAPIC with elemental formula helps effectively, e.g., in mass spectra interpretation since the prediction of LAPIC allows the correct connection of the main peak of the investigated ion with the expected ion formula and the mass of the ion considered. This solution can be a substitute for the much more complex method of isotopometric analysis applied in mass spectra interpretation. [Figure: see text]. Differences of the most abundant peak location (Delta LAPIC(C)=f(n)) for carbon aggregates C(n).

  12. 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

  13. Multiple Ionization Bursts in Laser-Driven Hydrogen Molecular Ion

    SciTech Connect

    Takemoto, Norio; Becker, Andreas

    2010-11-12

    Theoretical study on H{sub 2}{sup +} 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.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. Jet-Cooled Excitation Spectra of Large Benzannulated Benzyl Radicals: 9-ANTHRACENYLMETHYL (C_{15}H_{11}) and 1-PYRENYLMETHYL (C_{17}H_{11})

    NASA Astrophysics Data System (ADS)

    O'Connor, Gerard D.; Bacskay, George B.; Woodhouse, Gabrielle V. G.; Troy, Tyler P.; Nauta, Klaas; Kable, Scott H.; Schmidt, Timothy W.

    2013-06-01

    The jet-cooled D_1 ← D_0 excitation spectra of two benzannulated benzyl radicals (BBRs), 9-anthracenylmethyl (9-AnMe) and 1-pyrenylmethyl (9-PyMe), have been obtained using mass-resolved resonant two-colour two-photon ionization spectroscopy (R2C2PI). Analysis of the spectra in view of symmetry and calculated vibrational frequencies indicate significant vibronic coupling. From the spectrum of 9-AnMe we elucidate significant anharmonicity in the excited state. This anharmonic behaviour is examined computationally through both TDDFT and ab initio methods. Excited state properties of 9-AnMe and 1-PyMe are examined with reference to the existing spectra of smaller BBRs. Trends in the observed spectra of BBRs allow spectroscopic properties of larger BBRs to be predicted. These predictions suggest the D_1 ← D_0 transitions of large BBRs are unlikely to be carriers of the diffuse interstellar bands.

  19. 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.

  20. 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

  1. Molecular dynamics simulation of reactive ion etching of Si by energetic Cl ions

    SciTech Connect

    Hanson, D.E.; Voter, A.F.; Kress, J.D.

    1997-10-01

    We report results from molecular dynamics simulations of the etching of a Si surface by energetic Cl atoms (15eV{le}E{le}200eV). We find that the energy dependence of the Si yield (number of Si atoms desorbed per incident Cl ion) is in reasonable agreement with recent experiments and with previous simulations performed up to 50 eV. We also investigate the variation of the Si yield with the impact angle of incidence, the stoichiometry of the desorbed material, and the effect of a thermal background Cl flux to the surface in the presence of an ion flux at 50 eV. Surface roughening due to etching was observed and the calculated rms roughness is in reasonable agreement with experiments. {copyright} {ital 1997 American Institute of Physics.}

  2. 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

  3. 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

  4. 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.

  5. 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

  6. 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

  7. Electron-Impact Dissociation of Hydrocarbon Molecular Ions

    SciTech Connect

    Bannister, Mark E; Schultz, David Robert

    2014-01-01

    Absolute cross sections for electron-impact dissociation of CH_x^+ (x=1,2,3) producing CH_y^+ (y=0,1,2) fragment ions were measured in the 3-100 eV range using a crossed electron-ion beams technique with total uncertainties of about 11% near the cross section peaks. For CH^+ dissociation, although the measured energy dependence agrees well with two sets of storage ring measurements, the magnitude of the present results lies about 15% to 25% below the other results at the cross section peak near 40 eV. For dissociation of CH_2^+, the cross sections are nearly identical for energies above 15 eV, but they are dramatically different at lower energies. The CH^+ channel exhibits a strong peak rising from an observed threshold of about 6 eV; the C^+ channel is relatively flat down to the lowest measured energy. For dissociation of CH_3^+ and CD_3^+, good agreement is found with other results reported for the CH^+ fragment, but some differences are found for the CD_2^+ and C^+ fragments. A pilot study has also been undertaken to assess the feasibility of applying a molecular dynamics approach to treat the full range of electron-hydrocarbon dissociation processes, especially for energies above a few eV, in order to provide an overarching theoretical model that can be readily applied. Comparison with the experimental data for CH^+ shows favorable agreement.

  8. 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.

  9. 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.

  10. 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.

  11. Molecular dynamics simulations of water within models of ion channels.

    PubMed Central

    Breed, J; Sankararamakrishnan, R; Kerr, I D; Sansom, M S

    1996-01-01

    The transbilayer pores formed by ion channel proteins contain extended columns of water molecules. The dynamic properties of such waters have been suggested to differ from those of water in its bulk state. Molecular dynamics simulations of ion channel models solvated within and at the mouths of their pores are used to investigate the dynamics and structure of intra-pore water. Three classes of channel model are investigated: a) parallel bundles of hydrophobic (Ala20) alpha-helices; b) eight-stranded hydrophobic (Ala10) antiparallel beta-barrels; and c) parallel bundles of amphipathic alpha-helices (namely, delta-toxin, alamethicin, and nicotinic acetylcholine receptor M2 helix). The self-diffusion coefficients of water molecules within the pores are reduced significantly relative to bulk water in all of the models. Water rotational reorientation rates are also reduced within the pores, particularly in those pores formed by alpha-helix bundles. In the narrowest pore (that of the Ala20 pentameric helix bundle) self-diffusion coefficients and reorientation rates of intra-pore waters are reduced by approximately an order of magnitude relative to bulk solvent. In Ala20 helix bundles the water dipoles orient antiparallel to the helix dipoles. Such dipole/dipole interaction between water and pore may explain how water-filled ion channels may be formed by hydrophobic helices. In the bundles of amphipathic helices the orientation of water dipoles is modulated by the presence of charged side chains. No preferential orientation of water dipoles relative to the pore axis is observed in the hydrophobic beta-barrel models. Images FIGURE 1 FIGURE 5 FIGURE 7 PMID:8785323

  12. 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.

  13. 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.

  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. 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.

  16. Mid-Infrared Nice-Ohms Spectrometer for the Study of Cold Molecular Ions

    NASA Astrophysics Data System (ADS)

    Porambo, Michael; Pearson, Jessica; Talicska, Courtney; McCall, Benjamin J.

    2014-06-01

    Molecular ions are involved in the chemistry of many interesting systems, such as the atmosphere, combustion reactions, and the interstellar medium. Challenging aspects of studying molecular ions spectroscopically include producing ions in enough abundance and, for large or fluxional ions, overcoming the problem of quantum dilution at high vibrational and rotational temperature. Furthermore, highly precise transition frequencies are needed to answer many questions involving molecular ions, such as the presence of specific candidate ions in the interstellar medium. To address these challenges, we have constructed a mid-infrared spectrometer that uses a difference frequency generation (DFG) light source to probe cooled molecular ions produced in a continuous supersonic expansion discharge source. The cooling of the ions achieved through supersonic expansion mitigates the problem of quantum dilution. High sensitivity to detect the 1012 ions per cm3 produced is accomplished through the use of noise-immune cavity-enhanced optical heterodyne molecular spectroscopy (NICE-OHMS) as a detection technique. Finally, an optical frequency comb is used to measure the transition frequencies of molecular ions precisely. This talk will present the current status of the instrument and preliminary studies to optimize and characterize its performance. Initial studies of room temperature methane allowed us to verify the use of NICE-OHMS for inferring rotational temperature of a molecular sample through Boltzmann plot analysis. Spectroscopy of H_3^+ and HN_2^+ extended this temperature verification to molecular ions. Future work on H_2CO^+, with the goal of determining its rovibrational transitions to a precision on the order of 1 MHz to aid in astronomical detection, will also be presented.

  17. 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.

  18. 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

  19. 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.

  20. The complex spectrum of a "simple" free radical: the Ã-X̃ band system of the jet-cooled boron difluoride free radical.

    PubMed

    Yang, Jie; Ellis, Blaine; Clouthier, Dennis J

    2011-09-01

    The near-ultraviolet band system of the jet-cooled boron difluoride free radical has been studied by a combination of laser-induced fluorescence and single vibronic level wavelength resolved emission spectroscopies. The radical was produced in a supersonic discharge jet using a precursor mixture of 1%-3% of BF(3) or (10)BF(3) in high pressure argon. A large number of bands were found in the 340-286 nm region and assigned as transitions from the X̃(2)A(1) ground state to the lower Renner-Teller component of the Ã(2)Π excited state, based on our previous ab initio potential energy surface predictions, matching the emission spectra Franck-Condon profiles of (11)BF(2) and (10)BF(2), and comparison of observed and calculated boron isotope effects. Several bands have been rotationally analyzed providing ground state structural parameters of r(0)('') (BF) = 1.3102(9) Å and θ(0)('') (FBF) = 119.7(6)°. The ground state totally symmetric vibrational energy levels of both boron isotopologues have also been measured and assigned up to energies of more than 8000 cm(-1). Although BF(2) might be considered to be a "simple" free radical, understanding the details of its electronic spectrum remains a major challenge for both theory and experiment.

  1. Infrared and ultraviolet laser spectroscopy of jet-cooled substituted salicylic acids; substitution effects on the excited state intramolecular proton transfer in salicylic acid

    NASA Astrophysics Data System (ADS)

    Abd El-Hakam Abou El-Nasr, E.; Fujii, A.; Ebata, T.; Mikami, N.

    Substitution effects on the excited state intramolecular proton transfer (ESIPT) in the salicylic acid (SA) frame were studied by electronic and infrared spectroscopy of jet-cooled 5-methoxylsalicylic acid (5-MeOSA), 5-methylsalicylic acid (5-MeSA), 5-fluorosalicylic acid (5-FSA), 6-fluorosalicylic acid (6-FSA), and methyl salicylate (MS). Infrared spectra were measured in the 3 µm region for both the electronic ground (S0) and first excited (S1) states. The electronic excitation/emission spectra of 5-MeSA and 6-FSA showed the typical spectral features of ESIPT, which have been found in the spectra of SA. On the other hand, 5-MeOSA and 5-FSA exhibit a mirror-image relation between their excitation and emission spectra, which has been regarded as a result of the suppression of ESIPT. Despite such a remarkable difference among the electronic spectra, IR spectroscopy shows that a drastic change of the phenolic OH stretching vibration does occur upon electronic excitation of all substituted SAs, that is, the phenolic OH band of all the SAs disappears from the 3 µm region, indicating a large elongation of the phenolic O-H bond (over 0.1 Å) in S1. This result means that the intramolecular hydrogen bond strength is remarkably enhanced by electronic excitation in all the substituted SAs. Substitution effects on ESIPT in dimers are also discussed.

  2. 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

  3. 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.

  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. Ultrafast electronic motion in hydrogen molecular ions induced by a high power intense laser

    NASA Astrophysics Data System (ADS)

    Mineo, H.; Teranishi, Y.; Chao, S. D.; Lin, S. H.

    2010-10-01

    In this Letter we report a method for controlling electronic localization in a molecular ion, on an attosecond time scale, using a high-intensity laser, based on two different excitation mechanisms. One takes place during ionization, and the other takes place sequentially, following ionization. The electronic excited states of the hydrogen molecular ion are created during ionization by taking the configuration interaction mixing of neutral molecules into account. We detect the ultrafast oscillatory electronic motion between two atoms in a hydrogen molecular ion occurring due to the creation of excited states during the course of ionization.

  6. Bound-Free and Bound-Bound Spectroscopy of Cold Trapped Molecular Ions

    NASA Astrophysics Data System (ADS)

    Wester, Roland

    2016-06-01

    Cryogenic radiofrequency ion traps have become a versatile tool to study the spectroscopy and state-selected collision dynamics of molecular ions. Different types of action spectroscopy have been developed to obtain a precise and sensitive spectroscopic signature. In this talk I will give an introduction to molecular ion spectroscopy in multipole traps. Then I will present recent experimental and theoretical investigations from our group on photodetachment spectroscopy and state-selected collisions of cold OH- anions colliding with helium and hydrogen. Based on these results we performed high resolution terahertz spectroscopy on the two lowest rotational transitions of OD-. Work is in progress to extend the rotational spectroscopy to polyatomic molecular anions.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. Exploring Ion-Ion Interactions in Aqueous Solutions by a Combination of Molecular Dynamics and Neutron Scattering.

    PubMed

    Kohagen, Miriam; Pluhařová, Eva; Mason, Philip E; Jungwirth, Pavel

    2015-05-01

    Recent advances in computational and experimental techniques have allowed for accurate description of ion pairing in aqueous solutions. Free energy methods based on ab initio molecular dynamics, as well as on force fields accounting effectively for electronic polarization, can provide quantitative information about the structures and occurrences of individual types of ion pairs. When properly benchmarked against electronic structure calculations for model systems and against structural experiments, in particular neutron scattering, such force field simulations represent a powerful tool for elucidating interactions of salt ions in complex biological aqueous environments. PMID:26263314

  13. Exploring Ion-Ion Interactions in Aqueous Solutions by a Combination of Molecular Dynamics and Neutron Scattering.

    PubMed

    Kohagen, Miriam; Pluhařová, Eva; Mason, Philip E; Jungwirth, Pavel

    2015-05-01

    Recent advances in computational and experimental techniques have allowed for accurate description of ion pairing in aqueous solutions. Free energy methods based on ab initio molecular dynamics, as well as on force fields accounting effectively for electronic polarization, can provide quantitative information about the structures and occurrences of individual types of ion pairs. When properly benchmarked against electronic structure calculations for model systems and against structural experiments, in particular neutron scattering, such force field simulations represent a powerful tool for elucidating interactions of salt ions in complex biological aqueous environments.

  14. How alkali metal ion binding alters the conformation preferences of gramicidin A: a molecular dynamics and ion mobility study.

    PubMed

    Chen, Liuxi; Gao, Yi Qin; Russell, David H

    2012-01-12

    Here, we present a systematic study combing electrospray ionization-ion mobility experiments and an enhanced sampling molecular dynamics, specifically integrated tempering sampling molecular dynamics simulations (ITS-MDS), to explore the conformations of alkali metal ion (Na, K, and Cs) adducts of gramicidin A (GA) in vacuo. Folding simulation is performed to obtain inherent conformational preferences of neutral GA to provide insights about how the binding of metal ions influences the intrinsic conformations of GA. The comparison between conformations of neutral GA and alkali metal ion adducts reveals a high degree of structural similarity, especially between neutral GA and [GA + Na](+); however, the structural similarities decrease as ionic radius of the metal increases. Collision cross section (CCS) profiles for [GA + Na](+) and [GA + Cs](+) ions obtained from by ITS-MDS compare favorably with the experimental CCS, but there are significant differences from CCS profiles for [GA + K](+) ions. Such discrepancies between the calculated and measured CCS profiles for [GA + K](+) are discussed in terms of limitations in the simulation force field as well as possible size-dependent coordination of the [GA + K](+) ion complex.

  15. The modeling of cobalt ions adsorption on molecular sieves and zeolite AW-300

    NASA Astrophysics Data System (ADS)

    ćiçek, Ekrem; Aras, Erdal; Dede, Bülent; Kılıç, Ahmet

    2013-12-01

    High concentration heavy metals in the environment can cause serious problem on human health. Cobalt is a heavy metal that has a large application in different fields. In the present work, we aimed to investigate the adsorption of the cobalt ions from aqueous solutions on molecular sieves and zeolite AW-300. Molecular sieves and zeolites were activated at 873 K for two hours before the adsorption experiment. UV-Visible spectrometer was used to measure concentrations of cobalt ions. All adsorption experiments were performed according to statistical designs for response surface methodological approach. A response surface analysis was guided to advance understand the interactions between adsorbent dose and initial concentration of cobalt ions. The removal efficiencies of cobalt ions on sorbents were characterized. The results indicated that molecular sieves and zeolite AW-300 can be used to remove cobalt ions from aqueous solutions.

  16. Single Molecular Ion Spectroscopy: Towards Precision Measurements on CaH+

    NASA Astrophysics Data System (ADS)

    Brown, Kenneth R.; Khanyile, Ncamiso B.; Rugango, Rene; Shu, Gang; Calvin, Aaron

    2016-06-01

    Precision spectroscopy of molecular ions has applications in astrochemistry, quantum state controlled chemical reactions, and measurements of fundamental constants. While spectroscopy of molecular ions is challenging, we present techniques to study molecular ions co-trapped with laser-cooled atomic ions in ion traps. We recently demonstrated the measurement of the ν' = 10 ← ν = 0 and ν' =9 ← ν = 0 overtone transitions in CaH+ using resonant two photon dissociation. This technique is extended to the 21Σ ← 11Σ electronic transition, which should be rotationally resolvable. This resolution will allow further investigation into the internal state control of CaH+ by techniques such as optical pumping, cryogenic cooling, and buffer gas cooling. N. B. Khanyile, et. al. Nat. Commun. 6 7825 (2015).

  17. Rotational spectra, conformational structures, and dipole moments of thiodiglycol by jet-cooled FTMW and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Xu, Li-Hong; Liu, Qiang; Suenram, R. D.; Lovas, F. J.; Hight Walker, A. R.; Jensen, J. O.; Samuels, A. C.

    2004-12-01

    The rotational spectra of three low-energy conformers of thiodiglycol (TDG) (HOCH 2CH 2SCH 2CH 2OH) have been measured in a molecular beam using a pulsed-nozzle Fourier-transform microwave spectrometer. To determine the likely conformational structures with ab initio approach, conformational structures of 2-(ethylthio)ethanol (HOEES) (CH 3CH 2SCH 2CH 2OH) were used as starting points together with the consideration of possible intramolecular hydrogen bonding in TDG. Three lower-energy conformers have been found for TDG at the MP2=Full/6311G** level and ab initio results agree nicely with experimentally determined rotational constants. In addition, Stark measurements were performed for two of the three conformers for dipole moment determinations, adding to our confidence of the conformational structure matches between experimental observations and ab initio calculations. Of the three lower-energy conformers, one displays a compact folded-like structure with strong hydrogen bonding between the two hydroxyl groups and the central sulfide atom. Two other conformers have relatively open chain-like structures with hydrogen bonding between each of the hydroxyl groups to the central sulfur atom, of which one has pure b-type dipole moment according to the ab initio results.

  18. Zero kinetic energy photoelectron spectroscopy of jet cooled benzo[a]pyrene from resonantly enhanced multiphoton ionization

    NASA Astrophysics Data System (ADS)

    Zhang, Jie; Harthcock, Colin; Han, Fangyuan; Kong, Wei

    2011-12-01

    We report zero kinetic energy (ZEKE) photoelectron spectroscopy of benzo[a]pyrene (BaP) via resonantly enhanced multiphoton ionization (REMPI). Our analysis concentrates on the vibrational modes of the first excited state (S1) and those of the ground cationic state (D0). Similar to pyrene, another peri-condensed polycyclic aromatic hydrocarbon we have investigated, the first two electronically excited states of BaP exhibit extensive configuration interactions. However, the two electronic states are of the same symmetry, hence vibronic coupling does not introduce any out-of-plane modes in the REMPI spectrum, and Franck-Condon analysis is qualitatively satisfactory. The ZEKE spectra from the in-plane modes observed in the REMPI spectrum demonstrate strong propensity in preserving the vibrational excitation of the intermediate state. Although several additional bands in combination with the vibrational mode of the intermediate state are identifiable, they are much lower in intensity. This observation implies that the molecular structure of BaP has a tremendous capability to accommodate changes in charge density. All observed bands of the cation are IR active, establishing the role of ZEKE spectroscopy in mapping out far infrared bands for astrophysical applications.

  19. 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.

  20. The Adiabatic Ionization Energy and Triplet T1 Energy of Jet-Cooled Keto-Amino Cytosine.

    PubMed

    Lobsiger, Simon; Leutwyler, Samuel

    2012-12-01

    Gas-phase cytosine exists in five different tautomer/rotamer forms 1, 2a, 2b, 3a, and 3b. We determine the threshold ionization energy (IE) of the keto-amino tautomer 1 as 8.73 ± 0.02 eV, using resonant two-photon ionization mass spectrometry in a supersonic molecular beam via the (1)ππ* excited state. This is the first IE threshold measurement for the biologically relevant tautomer 1. The IE of the thermal gas-phase mixture of cytosine has been measured as 8.60 ± 0.05 eV by Kostko et al. using single-photon VUV photoionization [Phys. Chem. Chem. Phys., 2010, 12, 2860]. Given the tautomer distribution and ionization energies calculated in that work, our determination of the keto-amino tautomer IE implies that the IE measured by Kostko et al. is dominated by the enol-amino tautomers 2a and 2b. Upon excitation of keto-amino cytosine to its (1)ππ* state, relaxation occurs to a lower-lying long-lived state. The IE threshold measured via this state places its energy about 0.69 eV below the (1)ππ* state, in good agreement with the triplet T1 energy of keto-amino cytosine calculated by several high-level ab initio methods. The identification of keto-amino cytosine T1 is the basis for characterizing the intersystem crossing rates into and the photochemical reactions of this long-lived state.

  1. Comparison between Free and Immobilized Ion Effects on Hydrophobic Interactions: A Molecular Dynamics Study.

    PubMed

    Huang, Kai; Gast, Sebastian; Ma, C Derek; Abbott, Nicholas L; Szlufarska, Izabela

    2015-10-15

    Fundamental studies of the effect of specific ions on hydrophobic interactions are driven by the need to understand phenomena such as hydrophobically driven self-assembly or protein folding. Using β-peptide-inspired nanorods, we investigate the effects of both free ions (dissolved salts) and proximally immobilized ions on hydrophobic interactions. We find that the free ion effect is correlated with the water density fluctuation near a nonpolar molecular surface, showing that such fluctuation can be an indicator of hydrophobic interactions in the case of solution additives. In the case of immobilized ion, our results demonstrate that hydrophobic interactions can be switched on and off by choosing different spatial arrangements of proximal ions on a nanorod. For globally amphiphilic nanorods, we find that the magnitude of the interaction can be further tuned using proximal ions with varying ionic sizes. In general, univalent proximal anions are found to weaken hydrophobic interactions. This is in contrast to the effect of free ions, which according to our simulations strengthen hydrophobic interactions. In addition, immobilized anions of increasing ionic size do not follow the same ordering (Hofmeister-like ranking) as free ions when it comes to their impact on hydrophobic interactions. The immobilized ion effect is not simply correlated with the water density fluctuation near the nonpolar side of the amphiphilic nanorod. We propose a molecular picture that explains the contrasting effects of immobilized versus free ions.

  2. High-resolution rovibrational spectroscopy of jet-cooled phenyl radical: the ν19 out-of-phase symmetric CH stretch.

    PubMed

    Buckingham, Grant T; Chang, Chih-Hsuan; Nesbitt, David J

    2013-10-01

    Phenyl radical has been studied via sub-Doppler infrared spectroscopy in a slit supersonic discharge expansion source, with assignments for the highest frequency b2 out-of-phase C-H symmetric stretch vibration (ν19) unambiguously confirmed by ≤6 MHz (0.0002 cm(-1)) agreement with microwave ground state combination differences of McMahon et al. [Astrophys. J. 2003, 590, L61-64]. Least squares analysis of over 100 resolved rovibrational peaks in the sub-Doppler spectrum to a Watson Hamiltonian yields precision excited-state rotational constants and a vibrational band origin (ν0 = 3071.8915(4) cm(-1)) consistent with a surprisingly small red-shift (0.9 cm(-1)) with respect to Ar matrix isolation studies of Ellison and co-workers [J. Am. Chem. Soc. 2001, 123, 1977]. Nuclear spin weights and inertial defects confirm the vibrationally averaged planarity and (2)A1 rovibronic symmetry of phenyl radical, with analysis of the rotational constants consistent with a modest C2v distortion of the carbon backbone frame due to partial sp rehybridization of the σ C radical-center. Most importantly, despite the number of atoms (N = 11) and vibrational modes (3N - 6 = 27), phenyl radical exhibits a remarkably clean jet cooled high-resolution IR spectrum that shows no evidence of intramolecular vibrational relaxation (IVR) phenomena such as local or nonlocal perturbations due to strongly coupled nearby dark states. This provides strong support for the feasibility of high-resolution infrared spectroscopy in other aromatic hydrocarbon radical systems.

  3. High Resolution Rovibrational Spectroscopy of Jet-Cooled Phenyl Radical: the ν_{19} Out-Of Symmetric C-H Stretch

    NASA Astrophysics Data System (ADS)

    Buckingham, Grant T.; Chang, Chih-Hsuan; Nesbitt, David J.

    2013-06-01

    Phenyl radical has been studied via sub-Doppler infrared spectroscopy in a slit supersonic discharge expansion source, with assignments for the highest frequency b_{2} out-of-phase C-H symmetric stretch vibration (ν_{19}) unambiguously confirmed by ≤ 6 MHz (0.0002 cm^{-1}) agreement with microwave ground state combination differences of McMahon et al. [Astrophys. J. 590, L61-64 (2003)]. Least squares analysis of > 100 resolved rovibrational peaks in the sub-Doppler spectrum to a Watson Hamiltonian yields precision exited-state rotational constants and a vibrational band origin (ν_{0} = 3071.8915(4) cm^{-1}) consistent with a surprisingly small red-shift (0.9 cm^{-1}) with respect to Ar matrix isolation studies of Ellison and coworkers [J. Am. Chem. Soc. 123, 1977 (2001)]. Nuclear spin weights and inertial defects confirm the vibrationally averaged planarity and ^{2}A_{1} rovibronic symmetry of phenyl radical, with analysis of the rotational constants consistent with a modest C_{2v} distortion of the carbon backbone frame due to partial sp rehybridization of the σ C radical-center. Most importantly, despite the number of atoms (N = 11) and vibrational modes (3N-6 = 27), phenyl radical exhibits a remarkably clean jet cooled high resolution IR spectrum that shows no evidence of intramolecular vibrational relaxation (IVR) phenomena such as local or non-local perturbations due to strongly coupled nearby dark states. This provides strong support for the feasibility of high resolution infrared spectroscopy in other cyclic aromatic hydrocarbon radical systems.

  4. High-Resolution Rovibrational Spectroscopy of Jet-Cooled Phenyl Radical: The ν19 Out-of-Phase Symmetric CH Stretch

    NASA Astrophysics Data System (ADS)

    Buckingham, Grant T.; Chang, Chih-Hsuan; Nesbitt, David J.

    2013-10-01

    Phenyl radical has been studied via sub-Doppler infrared spectroscopy in a slit supersonic discharge expansion source, with assignments for the highest frequency b2 out-of-phase C-H symmetric stretch vibration (-19) unambiguously confirmed by ≤6 MHz (0.0002 cm-1) agreement with microwave ground state combination differences of McMahon et al. [Astrophys. J. 2003, 590, L61-64]. Least squares analysis of over 100 resolved rovibrational peaks in the sub-Doppler spectrum to a Watson Hamiltonian yields precision excited-state rotational constants and a vibrational band origin (-0 = 3071.8915(4) cm-1) consistent with a surprisingly small red-shift (0.9 cm-1) with respect to Ar matrix isolation studies of Ellison and co-workers [J. Am. Chem. Soc. 2001, 123, 1977]. Nuclear spin weights and inertial defects confirm the vibrationally averaged planarity and 2A1 rovibronic symmetry of phenyl radical, with analysis of the rotational constants consistent with a modest C2v distortion of the carbon backbone frame due to partial sp rehybridization of the σ C radical-center. Most importantly, despite the number of atoms (N = 11) and vibrational modes (3N - 6 = 27), phenyl radical exhibits a remarkably clean jet cooled high-resolution IR spectrum that shows no evidence of intramolecular vibrational relaxation (IVR) phenomena such as local or nonlocal perturbations due to strongly coupled nearby dark states. This provides strong support for the feasibility of high-resolution infrared spectroscopy in other aromatic hydrocarbon radical systems.

  5. An optical-optical double resonance probe of the lowest triplet state of jet-cooled thiophosgene: Rovibronic structures and electronic relaxation

    NASA Astrophysics Data System (ADS)

    Fujiwara, Takashige; Lim, Edward C.; Judge, Richard H.; Moule, David C.

    2006-03-01

    The vibrational structure, rotational structure, and electronic relaxation of the "dark" T1A23(n,π*) state of jet-cooled thiophosgene have been investigated by two-color S2←T1←S0 optical-optical double resonance (OODR) spectroscopy, which monitors the S2→S0 fluorescence generated by S2←T1 excitation. This method is capable of isolating the T1 vibrational structure into a1, b1, and b2 symmetry blocks. The fluorescence-detected vibrational structure of the Tz spin state of T1 shows that the CS stretching frequency as well as the barrier height for pyramidal deformation are significantly greater in the A23(n,π*) state than in the corresponding A21(n,π*) state. The differing vibrational parameters of the T1 thiophosgene relative to the S1 thiophosgene can be attributed to the motions of unpaired electrons that are better correlated when they are in the excited singlet state than when they are in the triplet state of same electron configuration. A set of T1 structural parameters and the information concerning the T1 spin states have been obtained from least-square fittings of the rotationally resolved T1←S0 excitation spectrum. The nearly degenerate ∣x⟩ and ∣y⟩ spin states are well removed from ∣z⟩ spin component, indicating that T1 thiophosgene is a good example of case (ab) coupling. The decay of the ∣z⟩ spin state of T1 thiophosgene, obtained from time-resolved S2←T1←S0 OODR experiment, is characteristic of strong-coupling intermediate-case decay in which an initial rapid decay is followed by recurrences and/or a long-lived quasiexponential decay.

  6. 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)

  7. Spectroscopy of jet-cooled AlMn and trends in the electronic structure of the 3d transition metal aluminides

    NASA Astrophysics Data System (ADS)

    Behm, Jane M.; Morse, Michael D.

    1994-10-01

    Jet-cooled diatomic AlMn has been spectroscopically investigated and is shown to possess a 5Πi ground state deriving from the Al (3s23p1,2P0)+Mn (3d54s2,6S) separated atom limit. This implies that the aluminum atom favors a 3pπ approach to the manganese atom, a result that is in agreement with previous studies on the related AlCa and AlZn molecules. The ground state bond length has been measured as 2.6384±0.0010 Å, a value which includes corrections due to spin-uncoupling effects in the X 5Πi state. It is suggested that the 5Πi state emerges as the ground state due to a particularly favorable configuration interaction with a low-lying 5Πi state that derives from the interaction of Al (3s23p1,2P0)+Mn [3d6(5D)4s1,6D]. Combination of the atoms in this excited state leads to a strong σ2 covalent bond via a 3pσAl-4sσMn interaction, which causes this excited electronic state to drop in energy so that it is expected to lie within a few thousand cm-1 of the ground electronic state. Following a discussion of the spectroscopic results on AlMn, an overall summary of the spectroscopic results on the 3d series of transition metal aluminides is presented, along with predictions of the ground electronic states of the as yet unobserved AlSc, AlTi, and AlFe molecules.

  8. 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.

  9. Enhancement of the molecular ion yield in plasma desorption mass spectrometry using explosive matrices.

    PubMed

    Zubarev, R A; Håkansson, P; Sundqvist, B; Talrose, V L

    1997-01-01

    The working hypothesis of this study was that the chemical energy of matrix material may be released, although only on a microscale, under MeV ion bombardment and may assist ejection of large intact bioorganic molecules. To test the hypothesis, the performance of several common explosives, as matrices in plasma desorption mass spectrometry, was compared to the standard matrix, nitrocellulose (NC), which is also a high explosive. Two explosives, RDX and HMX, were found to be new, effective matrices for peptides and proteins. While the performance of RDX was comparable with that of nitrocellulose, HMX gave a superior molecular ion yield and a higher average charge state of desorbed molecular ions compared with NC. Noth RDX and HMX have a similar chemical composition and structure, although the latter is a more powerful explosive. The measured total ion yield allows the conclusion that the increase in the amount of ejected material, due to the chemical energy release in high explosives under MeV ion bombardment, is limited, perhaps to a factor of 2 to 3. The fact that not all tested explosives gave molecular ions from peptides and proteins suggests that other factors, such as gas-phase chemistry, may play a significant role in molecular ion formation.

  10. 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.

  11. Physics with colder molecular ions: The Heidelberg Cryogenic Storage Ring CSR

    NASA Astrophysics Data System (ADS)

    Zajfman, D.; Wolf, A.; Schwalm, D.; Orlov, D. A.; Grieser, M.; von Hahn, R.; Welsch, C. P.; Crespo Lopez-Urrutia, J. R.; Schröter, C. D.; Urbain, X.; Ullrich, J.

    2005-01-01

    A novel cryogenic electrostatic storage ring is planned to be built at the Max-Planck Institute for Nuclear Physics in Heidelberg. The machine is expected to operate at low temperatures (~2K) and to store beams with kinetic energies between 20 to 300 keV. An electron target based on cooled photocathode technology will serve as a major tool for the study of reactions between molecular ions and electrons. Moreover, atomic beams can be merged and crossed with the stored ion beams allowing for atom molecular-ion collision studies at very low up to high relative energies. The proposed experimental program, centered around the physics of cold molecular ions, is shortly outlined.

  12. 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.

  13. Possible Observation of the Thermal Desorption of Excited Molecular Ions from Hot Graphite

    NASA Astrophysics Data System (ADS)

    Gee, Philip; Ehrenreich, Thomas; Lozano, Juan; Kessel, Quentin; Pollack, Edward; Smith, Winthrop

    2002-05-01

    In perhaps the first experiment to determine the energies of ions thermally desorbed from positively biased graphite,^1 ion energies are measured which appear to be inconsistent with the bias applied to the graphite. The energies are consistent however, with the desorption of a molecular ion, perhaps KH^+, which then dissociates after leaving the surface. Hence, we suggest that molecular ions may be thermally desorbed in excited states. This research was supported by the Connecticut Space Grant Consortium under NASA EPSCOR grant No. NCC5-601. 1. J. Lozano, Q.C. Kessel, E. Pollack and W.W. Smith, "Ion Beam Emission of Charged Particles from Hot Graphite" in shape Application of Accelerators in Research and Industry - Sixteenth International Conference, edited by J.L. Duggan and I.L. Morgan, AIP CP (576), 1044-1046 (2001)

  14. 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

  15. Molecular Modeling of Mechanosensory Ion Channel Structural and Functional Features

    PubMed Central

    Gessmann, Renate; Kourtis, Nikos; Petratos, Kyriacos; Tavernarakis, Nektarios

    2010-01-01

    The DEG/ENaC (Degenerin/Epithelial Sodium Channel) protein family comprises related ion channel subunits from all metazoans, including humans. Members of this protein family play roles in several important biological processes such as transduction of mechanical stimuli, sodium re-absorption and blood pressure regulation. Several blocks of amino acid sequence are conserved in DEG/ENaC proteins, but structure/function relations in this channel class are poorly understood. Given the considerable experimental limitations associated with the crystallization of integral membrane proteins, knowledge-based modeling is often the only route towards obtaining reliable structural information. To gain insight into the structural characteristics of DEG/ENaC ion channels, we derived three-dimensional models of MEC-4 and UNC-8, based on the available crystal structures of ASIC1 (Acid Sensing Ion Channel 1). MEC-4 and UNC-8 are two DEG/ENaC family members involved in mechanosensation and proprioception respectively, in the nematode Caenorhabditis elegans. We used these models to examine the structural effects of specific mutations that alter channel function in vivo. The trimeric MEC-4 model provides insight into the mechanism by which gain-of-function mutations cause structural alterations that result in increased channel permeability, which trigger cell degeneration. Our analysis provides an introductory framework to further investigate the multimeric organization of the DEG/ENaC ion channel complex. PMID:20877470

  16. Molecular modeling of mechanosensory ion channel structural and functional features.

    PubMed

    Gessmann, Renate; Kourtis, Nikos; Petratos, Kyriacos; Tavernarakis, Nektarios

    2010-09-16

    The DEG/ENaC (Degenerin/Epithelial Sodium Channel) protein family comprises related ion channel subunits from all metazoans, including humans. Members of this protein family play roles in several important biological processes such as transduction of mechanical stimuli, sodium re-absorption and blood pressure regulation. Several blocks of amino acid sequence are conserved in DEG/ENaC proteins, but structure/function relations in this channel class are poorly understood. Given the considerable experimental limitations associated with the crystallization of integral membrane proteins, knowledge-based modeling is often the only route towards obtaining reliable structural information. To gain insight into the structural characteristics of DEG/ENaC ion channels, we derived three-dimensional models of MEC-4 and UNC-8, based on the available crystal structures of ASIC1 (Acid Sensing Ion Channel 1). MEC-4 and UNC-8 are two DEG/ENaC family members involved in mechanosensation and proprioception respectively, in the nematode Caenorhabditis elegans. We used these models to examine the structural effects of specific mutations that alter channel function in vivo. The trimeric MEC-4 model provides insight into the mechanism by which gain-of-function mutations cause structural alterations that result in increased channel permeability, which trigger cell degeneration. Our analysis provides an introductory framework to further investigate the multimeric organization of the DEG/ENaC ion channel complex.

  17. Thermodynamics and kinetics of ion speciation in supercritical aqueous solutions: A molecular based study

    SciTech Connect

    Chialvo, A.A.; Cummings, P.T. |; Simonson, J.M.; Mesmer, R.E.

    1997-05-01

    Molecular simulation of infinitely dilute NaCl aqueous solutions are performed to study the Na{sup +}/Cl{sup -} ion pairing in a polarizable and a nonpolarizable solvent at supercritical conditions. The Simple Point Charge, Pettitt-Rossky, and Fumi-Tosi models for the water-water, ion-water, and ion-ion interactions are used in determining the degree of dissociation, its temperature and density dependence, and the kinetics of the interconversion between ion-pair configurations in a nonpolarizable medium. To assess the effect of the solvent polarizability on the stability of the ion-pair configurations, we replace the Simple Point Charge by the Polarizable Point Charge water model and determine the anion-cation potential of mean force at T{sub r}=1.20 and {rho}{sub r}=1.5.

  18. 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.

  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. 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.

  1. 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

  2. Ion Channels as Single Molecular Sensors: Extracting Information from Noise

    NASA Astrophysics Data System (ADS)

    Goychuk, Igor

    2001-03-01

    Ion channels are the evolution's solution to participate in electrical signaling. A question that has been haunting the Stochastic Resonance (SR) community ever since its first evidence in biological systems in the early nineties is whether -- and how -- SR occurs in single and/or coupled ion channels. Up to this very date, there exists no convincing experimental proof that SR actually takes place in a realistic ion channel such as the Shaker IR potassium-selective channel. The idea, however, that the environmental noise assists in a beneficial manner the transduction of electric encoded information is appealing; i.e. the occurrence of SR on this most fundamental level of biological complexity should not come as too big a surprise. In order to elucidate this prominent challenge we theoretically have investigated SR for a simple, yet realistic enough model of a voltage-gated ion channel. In doing so, we model the process of successive opening and closing events by a continuous time, two-state random point process with experimentally determined residence time distributions. Using measures of information theory such as the rate of information gain we have shown that SR indeed occurs when the closed state of the channel is predominantly dwelled. With increasing opening probability noise deteriorates the rate of information transfer that eventually assumes a robust behavior, which is essentially insensitive to noise. (I. Goychuk and P. Hänggi, Phys. Rev. E 61), 4272 (2000); Eur. Biophys. J. 29, 345 (2000). Moreover, we study additional SR measures such as the spectral amplification and the signal-to-noise ratio. In a next step, we generalize this investigation to account also for non-Markovian conductance fluctuations with nonexponential residence time distributions and study their consequences for the likelihood for SR to persist.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Effect of initial ion positions on the interactions of monovalent and divalent ions with a DNA duplex as revealed with atomistic molecular dynamics simulations.

    PubMed

    Robbins, Timothy J; Wang, Yongmei

    2013-01-01

    Monovalent (Na(+)) and divalent (Mg(2+)) ion distributions around the Dickerson-Drew dodecamer were studied by atomistic molecular dynamics (MD) simulations with AMBER molecular modeling software. Different initial placements of ions were tried and the resulting effects on the ion distributions around DNA were investigated. For monovalent ions, results were found to be nearly independent of initial cation coordinates. However, Mg(2+) ions demonstrated a strong initial coordinate dependent behavior. While some divalent ions initially placed near the DNA formed essentially permanent direct coordination complexes with electronegative DNA atoms, Mg(2+) ions initially placed further away from the duplex formed a full, nonexchanging, octahedral first solvation shell. These fully solvated cations were still capable of binding with DNA with events lasting up to 20 ns, and in comparison were bound much longer than Na(+) ions. Force field parameters were also investigated with modest and little differences arising from ion (ions94 and ions08) and nucleic acid description (ff99, ff99bsc0, and ff10), respectively. Based on known Mg(2+) ion solvation structure, we conclude that in most cases Mg(2+) ions retain their first solvation shell, making only solvent-mediated contacts with DNA duplex. The proper way to simulate Mg(2+) ions around DNA duplex, therefore, should begin with ions placed in the bulk water.

  8. Comparative mass spectrometric analyses of Photofrin oligomers by fast atom bombardment mass spectrometry, UV and IR matrix-assisted laser desorption/ionization mass spectrometry, electrospray ionization mass spectrometry and laser desorption/jet-cooling photoionization mass spectrometry.

    PubMed

    Siegel, M M; Tabei, K; Tsao, R; Pastel, M J; Pandey, R K; Berkenkamp, S; Hillenkamp, F; de Vries, M S

    1999-06-01

    Photofrin (porfimer sodium) is a porphyrin derivative used in the treatment of a variety of cancers by photodynamic therapy. This oligomer complex and a variety of porphyrin monomers, dimers and trimers were analyzed with five different mass spectral ionization techniques: fast atom bombardment, UV and IR matrix-assisted laser desorption/ionization, electrospray ionization, and laser desorption/jet-cooling photoionization. All five approaches resulted in very similar oligomer distributions with an average oligomer length of 2.7 +/- 0.1 porphyrin units. In addition to the Photofrin analysis, this study provides a side-by-side comparison of the spectra for the five different mass spectrometric techniques.

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

    PubMed

    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 ~2 × 10(-11) cm(-1) Hz(-1/2) has been used to observe several transitions of the Meinel 1-0 band of N(2) (+) with linewidths of ~120 MHz. An optical frequency comb has been used for absolute frequency calibration of transition frequencies to within ~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. PMID:22168687

  10. 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.

  11. 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.

  12. Improving the Molecular Ion Signal Intensity for In Situ Liquid SIMS Analysis

    NASA Astrophysics Data System (ADS)

    Zhou, Yufan; Yao, Juan; Ding, Yuanzhao; Yu, Jiachao; Hua, Xin; Evans, James E.; Yu, Xiaofei; Lao, David B.; Heldebrant, David J.; Nune, Satish K.; Cao, Bin; Bowden, Mark E.; Yu, Xiao-Ying; Wang, Xue-Lin; Zhu, Zihua

    2016-09-01

    In situ liquid secondary ion mass spectrometry (SIMS) enabled by system for analysis at the liquid vacuum interface (SALVI) has proven to be a promising new tool to provide molecular information at solid-liquid and liquid-vacuum interfaces. However, the initial data showed that useful signals in positive ion spectra are too weak to be meaningful in most cases. In addition, it is difficult to obtain strong negative molecular ion signals when m/z>200. These two drawbacks have been the biggest obstacle towards practical use of this new analytical approach. In this study, we report that strong and reliable positive and negative molecular signals are achievable after optimizing the SIMS experimental conditions. Four model systems, including a 1,8-diazabicycloundec-7-ene (DBU)-base switchable ionic liquid, a live Shewanella oneidensis biofilm, a hydrated mammalian epithelia cell, and an electrolyte popularly used in Li ion batteries were studied. A signal enhancement of about two orders of magnitude was obtained in comparison with non-optimized conditions. Therefore, molecular ion signal intensity has become very acceptable for use of in situ liquid SIMS to study solid-liquid and liquid-vacuum interfaces.

  13. 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.

  14. 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

  15. 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.

  16. Thermal Behaviour of W+C Ion Implanted Ultra High Molecular Weight Polyethylene (UHMWPE)

    SciTech Connect

    Urkac, E. Sokullu; Oztarhan, A.; Tihminlioglu, F.; Ila, D.; Chhay, B.; Muntele, C.; Budak, S.; Oks, E.; Nikolaev, A.

    2009-03-10

    The aim of this work was to examine thermal behavior of the surface modified Ultra High Molecular Weight Poly Ethylene (UHMWPE ) in order to understand the effect of ion implantation on the properties of this polymer which is widely used especially for biomedical applications. UHMWPE samples were Tungsten and Carbon (W+C) hybrid ion implanted by using Metal Vapour Vacuum Arc (MEVVA) ion implantation technique with a fluence of 10 17 ions/cm2 and extraction voltage of 30 kV. Untreated and surface-treated samples were investigated by Rutherford Back Scattering (RBS) Analysis, Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) Spectrometry, Thermo Gravimetric Analysis (TGA) and Differential Scanning Calorimetry (DSC). This study has shown that ion implantation represents a powerful tool on modifying thermal properties of UHMWPE surfaces. This combination of properties can make implanted UHMWPE a preferred material for biomedical applications.

  17. Test particle comparison of heavy atomic and molecular ion distributions at Mars

    NASA Astrophysics Data System (ADS)

    Curry, S. M.; Liemohn, M.; Fang, X.; Ma, Y.; Slavin, J.; Espley, J.; Bougher, S.; Dong, C. F.

    2014-03-01

    This study uses the Mars Test Particle simulation to create virtual detections of O+, O2+, and CO2+ in an orbital configuration in the Mars space environment. These atomic and molecular planetary pickup ions are formed when the solar wind directly interacts with the neutral atmosphere, causing the ions to be accelerated by the background convective electric field. The subsequent ion escape is the subject of great interest, specifically with respect to which species dominates ion loss from Mars. O+ is found to be the dominant escaping ion because of the large sources of transported ions in the low-energy (<10 eV) and high-energy (>1 keV) range. O2+ and CO2+ are observed at these energy ranges but with much lower fluxes and are generally only found in the tail between 10 eV and 1 keV. Using individual particle traces, we reveal the origin and trajectories of the low-energy downtail O+ populations and high-energy polar O+ populations that contribute to the total escape. Comparing them against O2+ and CO2+ reveals that the extended hot oxygen corona contributes to source regions of high- and low-energy escaping ions. Additionally, we present results for solar minimum and maximum conditions with respect to ion fluxes and energies in order to robustly describe the physical processes controlling planetary ion distributions and atmospheric escape.

  18. Ion transport through membrane-spanning nanopores studied by molecular dynamics simulations and continuum electrostatics calculations.

    PubMed

    Peter, Christine; Hummer, Gerhard

    2005-10-01

    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 approximately 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.

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. 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.

  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. Molecular dynamics and brownian dynamics investigation of ion permeation and anesthetic halothane effects on a proton-gated ion channel.

    PubMed

    Cheng, Mary Hongying; Coalson, Rob D; Tang, Pei

    2010-11-24

    Bacterial Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) is activated to cation permeation upon lowering the solution pH. Its function can be modulated by anesthetic halothane. In the present work, we integrate molecular dynamics (MD) and Brownian dynamics (BD) simulations to elucidate the ion conduction, charge selectivity, and halothane modulation mechanisms in GLIC, based on recently resolved X-ray crystal structures of the open-channel GLIC. MD calculations of the potential of mean force (PMF) for a Na(+) revealed two energy barriers in the extracellular domain (R109 and K38) and at the hydrophobic gate of transmembrane domain (I233), respectively. An energy well for Na(+) was near the intracellular entrance: the depth of this energy well was modulated strongly by the protonation state of E222. The energy barrier for Cl(-) was found to be 3-4 times higher than that for Na(+). Ion permeation characteristics were determined through BD simulations using a hybrid MD/continuum electrostatics approach to evaluate the energy profiles governing the ion movement. The resultant channel conductance and a near-zero permeability ratio (P(Cl)/P(Na)) were comparable to experimental data. On the basis of these calculations, we suggest that a ring of five E222 residues may act as an electrostatic gate. In addition, the hydrophobic gate region may play a role in charge selectivity due to a higher dehydration energy barrier for Cl(-) ions. The effect of halothane on the Na(+) PMF was also evaluated. Halothane was found to perturb salt bridges in GLIC that may be crucial for channel gating and open-channel stability, but had no significant impact on the single ion PMF profiles.

  6. 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.

  7. 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

  8. 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.

  9. Molecular simulation studies of hydrophobic gating in nanopores and ion channels.

    PubMed

    Trick, Jemma L; Aryal, Prafulla; Tucker, Stephen J; Sansom, Mark S P

    2015-04-01

    Gating in channels and nanopores plays a key role in regulating flow of ions across membranes. Molecular simulations provide a 'computational microscope' which enables us to examine the physical nature of gating mechanisms at the level of the single channel molecule. Water enclosed within the confines of a nanoscale pore may exhibit unexpected behaviour. In particular, if the molecular surfaces lining the pore are hydrophobic this promotes de-wetting of the pore. De-wetting is observed as stochastic liquid-vapour transitions within a pore, and may lead to functional closure of a pore to the flow of ions and/or water. Such behaviour was first observed in simulations of simple model nanopores and referred to as 'hydrophobic gating'. Simulations of both the nicotinic acetylcholine receptor and of TWIK-1 potassium channels (the latter alongside experimental studies) suggest hydrophobic gating may occur in some biological ion channels. Current studies are focused on designing hydrophobic gates into biomimetic nanopores.

  10. 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

  11. Ion Flux Measurements in Electron Beam Produced Plasmas in Atomic and Molecular Gases

    NASA Astrophysics Data System (ADS)

    Walton, S. G.; Leonhardt, D.; Blackwell, D. D.; Murphy, D. P.; Fernsler, R. F.; Meger, R. A.

    2001-10-01

    In this presentation, mass- and time-resolved measurements of ion fluxes sampled from pulsed, electron beam-generated plasmas will be discussed. Previous works have shown that energetic electron beams are efficient at producing high-density plasmas (10^10-10^12 cm-3) with low electron temperatures (Te < 1.0 eV) over the volume of the beam. Outside the beam, the plasma density and electron temperature vary due, in part, to ion-neutral and electron-ion interactions. In molecular gases, electron-ion recombination plays a significant role while in atomic gases, ion-neutral interactions are important. These interactions also determine the temporal variations in the electron temperature and plasma density when the electron beam is pulsed. Temporally resolved ion flux and energy distributions at a grounded electrode surface located adjacent to pulsed plasmas in pure Ar, N_2, O_2, and their mixtures are discussed. Measurements are presented as a function of operating pressure, mixture ratio, and electron beam-electrode separation. The differences in the results for atomic and molecular gases will also be discussed and related to their respective gas-phase kinetics.

  12. Double Coincidence Studies of Molecular Dissociation Induced by Heavy Ion Impact.

    NASA Astrophysics Data System (ADS)

    Sampoll Ramirez, Gabriel

    Multielectron removal from an atom or molecule may be accomplished with high efficiency by the impact of a fast, highly-charged, heavy ion. When a diatomic molecule suffers the loss of electrons, it will generally dissociate into ions having considerable amounts of kinetic energy as a result of their mutual Coulomb repulsion. In the present work, experiments designed to examine the yield and kinetic energy distributions associated with different charge division pathways for the dissociation of multicharged CO, N_2 and O_2 molecular ions were performed. A beam of 96 MeV Ar ^{14+} ions was directed through a differentially pumped gas cell containing the molecules of interest into a microchannel plate detector. Dissociation products produced in ionizing collisions were accelerated out of the gas cell by an electric field into a time-of -flight (TOF) spectrometer. Upon reaching the end of the flight tube, the ions were detected by another set of microchannel plates. An acceptable binary dissociation event was one for which both dissociation-product ions were detected. The TOF of the first ion to reach the detector and the time difference between the arrival of the first ion and its partner were recorded on magnetic tape event-by-event so as to maintain their correlation. Separation of the time-difference (Delta t) distributions into sets correlated with the charge of the first ion was accomplished by off-line sorting of the event-by-event data. Transformation of the Deltat distributions into total kinetic energy distributions (TKED) required a detailed simulation of the ion trajectories in order to construct the response matrix of the spectrometer system. The average total kinetic energies were determined for all the observed dissociation channels and used to calculate the average excitation energies of the parent molecular ions. The TKED of CO^{2+} was in very good agreement with previous measurements obtained in a photoionization study using synchroton radiation. The

  13. Mobility and molecular ions of dimethyl methyl phosphonate, methyl salicylate and acetone

    NASA Astrophysics Data System (ADS)

    Nowak, D. M.

    1983-06-01

    The mobilities of positive and negative reactant ions are reported for (H2O)nH(+); (H2O)2O2 and (H2O)2CO3(-) ion clusters. The formation of positive DMMP monomer and dimer is reported, and equilbria molecular reactions are reported. Acetone is reported as forming a dimer at 81 ppb with a reduced mobility (K sub o) of 1.82, Methyl salicylate is shown to form a protonated and hydrated positive monomer. Mixtures of DMMP and methyl salicylate with acetone showed a substantial change in DMMP ion clustering and little or no change in the methyl salicylate mobility spectra. Negative ions were not observed for DMMP, methyl salicylate, acetone and the mixtures under the conditions reported.

  14. 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.

  15. Molecular dynamics simulations of electron-ion temperature equilibration in an SF6 plasma

    NASA Astrophysics Data System (ADS)

    Benedict, Lorin X.; Glosli, James N.; Richards, David F.; Streitz, Frederick H.; Hau-Riege, Stefan P.; London, Richard A.; Graziani, Frank R.; Murillo, Michael S.; Benage, John F.

    2009-11-01

    We describe classical non-equilibrium molecular dynamics simulations aimed at studying electron-ion temperature equilibration in a two-temperature SF6 plasma. We choose a density of 1.0 x10^6 (dissociated) SF6 molecules per cm^3 and initial temperatures of Te= 100 eV and TS= TF= 15 eV, in accordance with experiments currently underway at Los Alamos National Lab. Our computed relaxation time lies between two oft-used variants of the Landau-Spitzer relaxation formula. Discrepancies are also found when comparing to the predictions of more recent theoretical approaches. These differences should be large enough to be measured in the upcoming experiments. We highlight one particular source of discrepancy arising from the strong ion-ion coupling: the time-dependent specific heat of the screened ion subsystem.

  16. A Molecular Dynamics Investigation of the Titration of a Trivalent Aqueous Ion

    SciTech Connect

    Rustad, James R; Casey, William H

    2006-03-01

    We carried out a series of molecular dynamics simulations of the hydrolysis of a model trivalent metal ion in aqueous solution. We use a dissociative model for water and examine the spontaneous speciation of M3+ into M(OH)n(3-n)+(n = 1, 4) both in neutral solution and as a function of added protons and hydroxide ions. The species distributions in neutral solution correspond reasonably well with those expected for real trivalent metal ions at neutral pH. However, the change in the species distributions as a function of either added protons or hydroxide ions is much less than expected with very large concentrations of protons or hydroxide ions required to shift the species equilibria in either direction. The influence of added protons and hydroxide ions on the species distributions appears to be proportional to the average charge of the hydrolysis couples, being highest for the 3+/2+ couple and lowest for the 1+/0 and 0/1- couples. Proton exchange rates varywith proton/hydroxide ion concentration giving a minimum at intermediate values ([H+]≈ 0.166) with increasing rates at both lower and higher pH

  17. Energetic atomic and molecular ions of ionospheric origin observed in distant magnetotail flow-reversal events

    SciTech Connect

    Christon, S.P.; Gloeckler, G.; Williams, D.J.; McEntire, R.W.; Jacquey, C.; Angelopoulos, V.; Lui, A.T.Y.; Mukai, T.; Kokubun, S.; Fairfield, D.H.

    1994-12-15

    Energetic atomic (O{sup +1} and N{sup +1}) and molecular (O{sub 2}{sup +1}, NO{sup +1}, and N{sub 2}{sup +1}) ions of ionospheric origin were observed in Earth`s magnetotail at X {approximately} {minus}146 R{sub E} during two plasma sheet sunward/tailward flow-reversal events measured by instruments on the GEOTAIL spacecraft. These events were associated with concurrent ground-measured geomagnetic disturbance intensification at auroral- and mid-latitudes (Kp = 7{sup {minus}}). Energetic ions in the sunward-component and tailward flows were from both the solar wind and ionosphere. Plasma and energetic ions participated in the flows. During tailward flow, ionospheric origin ion abundance ratios at {approximately} 200-900 km/s in the rest frame were N{sup +1}/O{sup +1} = {approximately} 25-30% and (O{sub 2}{sup +1}, NO{sup +1}, and N{sub 2}{sup +1})/O{sup +1} = {approximately} 1-2%. The authors argue that tailward flow most likely initiated {approximately} 80-100 R{sub E} tailward of Earth and molecular ions were in the plasma sheet prior to geomagnetic intensification onset. 13 refs., 4 figs.

  18. 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

  19. 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

  20. 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

  1. 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.

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

    PubMed Central

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

    2013-01-01

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

  3. Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics.

    PubMed

    Koca, Jaroslav; Zhan, Chang-Guo; Rittenhouse, Robert C; Ornstein, Rick L

    2003-02-01

    We have run several molecular dynamics (MD) simulations on zinc-containing phosphotriesterase (PTE) with two bound substrates, sarin and paraoxon, and with the substrate analog diethyl 4-methylbenzylphosphonate. A standard nonbonded model was employed to treat the zinc ions with the commonly used charge of +2. In all the trajectories, we observed a tightly bound water (TBW) molecule in the active site that was coordinated to the less buried zinc ion. The phosphoryl oxygen of the substrate/inhibitor was found to be coordinated to the same zinc ion so that, considering all ligands, the less buried zinc was hexa-coordinated. The hexa-coordination of this zinc ion was not seen in the deposited X-ray pdb files for PTE. Several additional MD simulations were then performed using different charges (+1, +1.5) on the zinc ions, along with ab initio and density functional theory (DFT) calculations, to evaluate the following possibilities: the crystal diffraction data were not correctly interpreted; the hexa-coordinated zinc ion in PTE is only present in solution and not in the crystal; and the hexa-coordinated zinc ion in PTE is an artifact of the force field used. A charge of +1.5 leads to a coordination number (CN) of 5 on both zinc ions, which is consistent with the results from ab initio and DFT calculations and with the latest high resolution X-ray crystal structure. The commonly used charge of +2 produces a CN of 6 on the less buried zinc. The CN on the more buried zinc ion is 5 when the substrate/inhibitor is present in the simulation, and increases to 6 when the substrate/inhibitor is removed prior to the simulation. The results of both of the MD and quantum mechanical calculations lead to the conclusion that the zinc ions in the PTE active site are both penta-coordinated, and that the MD simulations performed with the charge of +2 overestimate the CN of the zinc ions in the PTE active site. The overall protein structures in the simulations remain unaffected by the

  4. 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

  5. Multiple Ionization of Free Ubiquitin Molecular Ions in Extreme Ultraviolet Free-Electron Laser Pulses.

    PubMed

    Schlathölter, Thomas; Reitsma, Geert; Egorov, Dmitrii; Gonzalez-Magaña, Olmo; Bari, Sadia; Boschman, Leon; Bodewits, Erwin; Schnorr, Kirsten; Schmid, Georg; Schröter, Claus Dieter; Moshammer, Robert; Hoekstra, Ronnie

    2016-08-26

    The fragmentation of free tenfold protonated ubiquitin in intense 70 femtosecond pulses of 90 eV photons from the FLASH facility was investigated. Mass spectrometric investigation of the fragment cations produced after removal of many electrons revealed fragmentation predominantly into immonium ions and related ions, with yields increasing linearly with intensity. Ionization clearly triggers a localized molecular response that occurs before the excitation energy equilibrates. Consistent with this interpretation, the effect is almost unaffected by the charge state, as fragmentation of sixfold deprotonated ubiquitin leads to a very similar fragmentation pattern. Ubiquitin responds to EUV multiphoton ionization as an ensemble of small peptides. PMID:27453360

  6. 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.

  7. 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.

  8. Long-Range Embedding of Molecular Ions and Excitations in a Polarizable Molecular Environment.

    PubMed

    Poelking, Carl; Andrienko, Denis

    2016-09-13

    We present a method for evaluating electrostatic and polarization energies of a localized charge, charge transfer state, or exciton embedded in a neutral molecular environment. The approach extends the Ewald summation technique to polarization effects, rigorously accounts for the long-range nature of the charge-quadrupole interactions, and addresses aperiodic embedding of the charged molecular cluster and its polarization cloud in a periodic environment. We illustrate the method by evaluating the density of states and ionization energies in thin films and heterostructures of organic semiconductors. By accounting for long-range mesoscale fields, we obtain the ionization energies in both crystalline and mesoscopically amorphous systems with high accuracy.

  9. Long-Range Embedding of Molecular Ions and Excitations in a Polarizable Molecular Environment.

    PubMed

    Poelking, Carl; Andrienko, Denis

    2016-09-13

    We present a method for evaluating electrostatic and polarization energies of a localized charge, charge transfer state, or exciton embedded in a neutral molecular environment. The approach extends the Ewald summation technique to polarization effects, rigorously accounts for the long-range nature of the charge-quadrupole interactions, and addresses aperiodic embedding of the charged molecular cluster and its polarization cloud in a periodic environment. We illustrate the method by evaluating the density of states and ionization energies in thin films and heterostructures of organic semiconductors. By accounting for long-range mesoscale fields, we obtain the ionization energies in both crystalline and mesoscopically amorphous systems with high accuracy. PMID:27463038

  10. Molecular Simulations of Water and Ion Diffusion in Nanosized Mineral Fractures

    SciTech Connect

    Kerisit, Sebastien N.; Liu, Chongxuan

    2009-02-01

    Molecular dynamics simulations were carried out to investigate the effects of confinement and of the presence of the mineral surface on the diffusion of water and electrolyte ions in nano-sized mineral fractures. Feldspar was used as a representative mineral because recent studies found that it is an important mineral that hosts contaminants within its intragrain fractures at US Department of Energy Hanford site (1, 2). Several properties of the mineral-water interface were varied, such as the fracture width, the ionic strength of the contacting solution, and the surface charge, to provide atomic-level insights into the diffusion of ions and contaminants within intragrain regions. In each case, the self-diffusion coefficient of water and that of the electrolyte ions were computed as a function of distance from the mineral surface. Our calculations reveal a 2.0 to 2.5 nm interfacial region within which the self-diffusion coefficient of water and that of the electrolyte ions decrease as the diffusing species approach the surface. As a result of the extent of the interfacial region, water and electrolyte ions are predicted to never reach bulk-like diffusion in fractures narrower than approximately 5 nm. A density weighted, averaged diffusion coefficient was computed as a function of fracture width and indicated that the surface effects only become negligible for fractures several tens of nanometers wide. The calculations also showed that, within 1.2 nm from the surface, the diffusion of electrolyte ions is affected by the presence of the mineral surface to a greater extent than that of water. The molecular dynamics results improve our conceptual models of ion transport in nano-scale pore regions surrounded by mineral surfaces in porous media.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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 +}.

  17. 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.

  18. 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

  19. Simultaneous ion and neutral evaporation in aqueous nanodrops: experiment, theory, and molecular dynamics simulations.

    PubMed

    Higashi, Hidenori; Tokumi, Takuya; Hogan, Christopher J; Suda, Hiroshi; Seto, Takafumi; Otani, Yoshio

    2015-06-28

    We use a combination of tandem ion mobility spectrometry (IMS-IMS, with differential mobility analyzers), molecular dynamics (MD) simulations, and analytical models to examine both neutral solvent (H2O) and ion (solvated Na(+)) evaporation from aqueous sodium chloride nanodrops. For experiments, nanodrops were produced via electrospray ionization (ESI) of an aqueous sodium chloride solution. Two nanodrops were examined in MD simulations: a 2500 water molecule nanodrop with 68 Na(+) and 60 Cl(-) ions (an initial net charge of z = +8), and (2) a 1000 water molecule nanodrop with 65 Na(+) and 60 Cl(-) ions (an initial net charge of z = +5). Specifically, we used MD simulations to examine the validity of a model for the neutral evaporation rate incorporating both the Kelvin (surface curvature) and Thomson (electrostatic) influences, while both MD simulations and experimental measurements were compared to predictions of the ion evaporation rate equation of Labowsky et al. [Anal. Chim. Acta, 2000, 406, 105-118]. Within a single fit parameter, we find excellent agreement between simulated and modeled neutral evaporation rates for nanodrops with solute volume fractions below 0.30. Similarly, MD simulation inferred ion evaporation rates are in excellent agreement with predictions based on the Labowsky et al. equation. Measurements of the sizes and charge states of ESI generated NaCl clusters suggest that the charge states of these clusters are governed by ion evaporation, however, ion evaporation appears to have occurred with lower activation energies in experiments than was anticipated based on analytical calculations as well as MD simulations. Several possible reasons for this discrepancy are discussed. PMID:26013735

  20. Simultaneous ion and neutral evaporation in aqueous nanodrops: experiment, theory, and molecular dynamics simulations.

    PubMed

    Higashi, Hidenori; Tokumi, Takuya; Hogan, Christopher J; Suda, Hiroshi; Seto, Takafumi; Otani, Yoshio

    2015-06-28

    We use a combination of tandem ion mobility spectrometry (IMS-IMS, with differential mobility analyzers), molecular dynamics (MD) simulations, and analytical models to examine both neutral solvent (H2O) and ion (solvated Na(+)) evaporation from aqueous sodium chloride nanodrops. For experiments, nanodrops were produced via electrospray ionization (ESI) of an aqueous sodium chloride solution. Two nanodrops were examined in MD simulations: a 2500 water molecule nanodrop with 68 Na(+) and 60 Cl(-) ions (an initial net charge of z = +8), and (2) a 1000 water molecule nanodrop with 65 Na(+) and 60 Cl(-) ions (an initial net charge of z = +5). Specifically, we used MD simulations to examine the validity of a model for the neutral evaporation rate incorporating both the Kelvin (surface curvature) and Thomson (electrostatic) influences, while both MD simulations and experimental measurements were compared to predictions of the ion evaporation rate equation of Labowsky et al. [Anal. Chim. Acta, 2000, 406, 105-118]. Within a single fit parameter, we find excellent agreement between simulated and modeled neutral evaporation rates for nanodrops with solute volume fractions below 0.30. Similarly, MD simulation inferred ion evaporation rates are in excellent agreement with predictions based on the Labowsky et al. equation. Measurements of the sizes and charge states of ESI generated NaCl clusters suggest that the charge states of these clusters are governed by ion evaporation, however, ion evaporation appears to have occurred with lower activation energies in experiments than was anticipated based on analytical calculations as well as MD simulations. Several possible reasons for this discrepancy are discussed.

  1. 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.

  2. 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

  3. Molecular models of alginic acid: Interactions with calcium ions and calcite surfaces

    NASA Astrophysics Data System (ADS)

    Perry, Thomas D.; Cygan, Randall T.; Mitchell, Ralph

    2006-07-01

    Cation binding by polysaccharides is observed in many environments and is important for predictive environmental modeling, and numerous industrial and food technology applications. The complexities of these cation-organic interactions are well suited for predictive molecular modeling and the analysis of conformation and configuration of polysaccharides and their influence on cation binding. In this study, alginic acid was chosen as a model polymer system and representative disaccharide and polysaccharide subunits were developed. Molecular dynamics simulation of the torsion angles of the ether linkage between various monomeric subunits identified local and global energy minima for selected disaccharides. The simulations indicate stable disaccharide configurations and a common global energy minimum for all disaccharide models at Φ = 274 ± 7°, Ψ = 227 ± 5°, where Φ and Ψ are the torsion angles about the ether linkage. The ability of disaccharide subunits to bind calcium ions and to associate with the (101¯4) surface of calcite was also investigated. Molecular models of disaccharide interactions with calcite provide binding energy differences for conformations that are related to the proximity and residence densities of the electron-donating moieties with calcium ions on the calcite surface, which are controlled, in part, by the torsion of the ether linkage between monosaccharide units. Dynamically optimized configurations for polymer alginate models with calcium ions were also derived.

  4. 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.

  5. Correlation of product ion profiles with molecular structures of androgenic and anabolic steroids in ESI MS/MS.

    PubMed

    Guan, Fuyu; Uboh, Cornelius E; Soma, Lawrence R; You, Youwen; Liu, Ying; Li, Xiaoqing

    2010-11-01

    Androgenic and anabolic steroids (AASs) are a class of chemical substances closely related to testosterone in molecular structure. They can be abused to enhance performances in human and equine athletes, and are banned by the sports authorities. To assist with method development for doping analyses of AASs, investigations were conducted to correlate their product ion profiles with the molecular structures. Although very similar in chemical structure, AASs generated noticeably different product ion profiles from collision-induced dissociation (CID). On the basis of both outlines of the product ion profiles and molecular structures, AASs studied were classified into six subclasses. In each subclass, the product ion profiles were identical or similar. However, the product ion profiles in one subclass were remarkably different from those in another. The classification reveals that the position and number of double bond(s) in conjugation with the 3-carbonyl group in the molecular structure of an AAS have significant effects on product ion profile. The presence or absence of the 19-methyl group in an AAS also has a remarkable influence on its product ion profile. A substitution in the A-, B- or D-ring of an AAS may cause a shift in mass value of the product ions. The correlation of product ion profiles with molecular structures of AASs has the implication that each AAS can be characterized by a combination of its [M + H](+) ion and product ion profile and as a result be identified with specificity. The classified product ion pattern may be useful in the identification of unknown AASs.

  6. Molecular dynamics simulation of Cu and Ar ion sputtering of Cu (111) surfaces. [Cu

    SciTech Connect

    Kress, J.D.; Hanson, D.E.; Voter, A.F. ); Liu, C.L.; Liu, X. ); Coronell, D.G. )

    1999-09-01

    In ionized physical vapor deposition, used in Cu interconnect technology, the interaction of energetic ions with the growing Cu film is sensitive to both the impact angle and the energy. Detailed information, such as the angle and energy dependence of the sputter yield and sticking probability, is required for realistic feature scale modeling of film coverage in the metallization of micron-sized features (vias and trenches) in integrated circuits. Here we describe the results of molecular dynamics (MD) simulations of sputtering of Cu (111) surfaces by Cu and Ar ions suitable for incorporation into feature scale simulations. For each impact angle and energy considered (10[endash]100 eV for Cu ions and 50[endash]250 eV for Ar ions), the following averaged properties were calculated: sputter yield (number of Cu atoms sputtered per impact), sticking probability, thermal accommodation coefficient, average reflection angle of the impact ion, and average emission angle of the sputter products. The calculated sputter yields and energy threshold at normal incidence for both Ar and Cu sputtering of Cu are in good agreement with experiment and other MD simulations. Detailed comparisons are also made with previously reported sputter yields calculated with binary collision theory. [copyright] [ital 1999 American Vacuum Society.

  7. Estimates of Collisional Cooling and Quenching Rates for Atomic and Molecular Ion Collisions with Ultracold Atoms.

    NASA Astrophysics Data System (ADS)

    Smith, Winthrop; Wells, James

    2009-05-01

    Translational cross sections and rate coefficients for cold ion-neutral elastic and charge-exchange collisions (either atomic or molecular) are >> larger (˜10^6 a.u.) than neutral-neutral collisions at the same CM energy. This is due to the long range polarization potential V(R) = -C4/R^4, where C4 is proportional to the polarizability of the neutral partner. Thus collisions between ultracold alkali atoms (trapped in a magneto-optic trap or MOT) and low-energy ions can be used for sympathetic cooling experiments. We are building a prototype hybrid-trap apparatus [1] that applies these principles to collisions of Ca^+ ions (which can be laser pre-cooled) with MOT-trapped ultracold Na atoms. Some calculations on this system and other related ion-neutral systems have been published [2] and some initial experiments on other ion-neutral species have begun [3]. Estimates of cooling and quenching rates in the low K-mK CM energy range for Ca+ on Na and other cases will be presented and possible experiments described. [1] Winthrop W. Smith, Oleg P. Makarov and Jian Lin, J. Modern Optics 52, 2253 (2005). [2] R. Côt'e and A. Dalgarno, Phys. Rev. A 62, 012709 (2000); R. Côt'e, Phys. Rev. Lett. 85, 5316 (2000). [3] A. Grier, M. Cetina, F.Orucevic, and V. Vuletic, ArXiv atom-ph/0808.3620.

  8. 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.

  9. A reversible fluorescent logic gate for sensing mercury and iodide ions based on a molecular beacon.

    PubMed

    Wu, Xu; Chen, Jiao; Zhao, Julia Xiaojun

    2013-09-21

    A simple, rapid, and reversible fluorescent DNA INHIBIT logic gate has been developed for sensing mercury (Hg(2+)) and iodide (I(-)) ions based on a molecular beacon (MB). In this logic gate, a mercury ion was introduced as the first input into the MB logic gate system to assist in the hybridization of the MB with an assistant DNA probe through the thymine-Hg(2+)-thymine interaction, which eventually restored the fluorescence of MB as the output. With this signal-on process, mercury ions can be detected with a limit of detection as low as 7.9 nM. Furthermore, when iodide ions were added to the Hg(2+)/MB system as the second input, the fluorescence intensity decreased because Hg(2+) in the thymine-Hg(2+)-thymine complex was grabbed by I(-) due to a stronger binding force. Iodide ions can be detected with a limit of detection of 42 nM. Meanwhile, we studied the feasibility and basic performance of the DNA INHIBIT logic gate, optimized the logic gate conditions, and investigated its sensitivity and selectivity. The results showed that the MB based logic gate is highly selective and sensitive for the detection of Hg(2+) and I(-) over other interfering cations and anions.

  10. 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.

  11. Lifetimes and stabilities of familiar explosive molecular adduct complexes during ion mobility measurements.

    PubMed

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

    2015-08-21

    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 tailor the stability of the molecular adduct complex. The flexibility of TIMS 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 high confidence levels.

  12. 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.

  13. Reactive ion etching of Si by Cl and Cl{sub 2} ions: Molecular dynamics simulations with comparisons to experiment

    SciTech Connect

    Hanson, D.E.; Kress, J.D.; Voter, A.F.

    1999-07-01

    We present results of molecular dynamics simulations of reactive ion etching (RIE) of a reconstructed Si(100)(2{times}1) surface. The existing Stillinger{endash}Weber interatomic potential for Si/Cl of Feil {ital et al.} has been modified by correcting the Si{endash}Si bond strength for a SiCl{sub n} moiety bound to a Si surface and the Si{endash}Cl bond strength in SiCl{sub m} molecules. This potential has been used to study RIE of Si by Cl and Cl{sub 2} ions. The calculated properties such as the Si yield, product stoichiometry, stoichiometry of the chlorosilyl surface, and Cl content of the chlorosilyl layer are in reasonable agreement with experiment. The dissociative chemisorption probability of Cl{sub 2} on Si(100)(2{times}1) as a function of energy has been simulated and the results are in reasonable agreement with experiment. {copyright} {ital 1999 American Vacuum Society.}

  14. Simulation of the energy spectra of original versus recombined H{sub 2}{sup +} molecular ions transmitted through thin foils

    SciTech Connect

    Barriga-Carrasco, Manuel D.; Garcia-Molina, Rafael

    2004-09-01

    This work presents the results of computer simulations for the energy spectra of original versus recombined H{sub 2}{sup +} molecular ions transmitted through thin amorphous carbon foils, for a broad range of incident energies. A detailed description of the projectile motion through the target has been done, including nuclear scattering and Coulomb repulsion as well as electronic self-retarding and wake forces; the two latter are calculated in the dielectric formalism framework. Differences in the energy spectra of recombined and original transmitted H{sub 2}{sup +} molecular ions clearly appear in the simulations, in agreement with the available experimental data. Our simulation code also differentiates the contributions due to original and to recombined H{sub 2}{sup +} molecular ions when the energy spectra contain both contributions, a feature that could be used for experimental purposes in estimating the ratio between the number of original and recombined H{sub 2}{sup +} molecular ions transmitted through thin foils.

  15. Development of a molecularly imprinted polymer for pyridoxine using an ion-pair as template.

    PubMed

    Alizadeh, Taher

    2008-08-01

    One of the main challenges in the molecularly imprinted polymers (MIP) field is the proper MIP design for water-soluble compounds because of appearance of serious drawbacks in polar solvents and insolubility of those compounds in non-polar solvents which are commonly used for MIP synthesis. In this work a novel and simple method for synthesis of molecularly imprinted polymers for a water-soluble compound was introduced. Pyridoxine was chosen as a target molecule and the ion-pair complex formed between pyridoxine ion (Py(+)) and dodecyl sulfate ion (DS(-)) was transferred into the chloroform via liquid-liquid extraction. Then polymerization was carried out in chloroform. The molecular mechanics and density functional theory were proposed to screen proper monomer. Binding energy, DeltaE, of a template and a monomer as a measure of their interaction was considered. Ion-pair [Py(+)-DS(-)] was supposed as a template molecule and acrylic acid, methacrylic acid, allyamine, vinylpridine and 2-hydroxy ethyl methacrylate were as tested monomers. The MIP synthesized using acrylic acid showed the highest selectivity to pyridoxine as predicted from the DeltaE calculation. The obtained MIP showed very high affinity against vitamin B6 in comparison to non-imprinted polymers (NIP). It was proved that the obtained MIP with introduced method was much better than that prepared in methanol as porogen. It was showed that the MIP prepared by this new method could be used as an adsorber for extraction and determination of pyridoxine in real and synthetic samples.

  16. Spectroscopic study of photon, ion and electron stimulated molecular synthesis in astrophysical ices

    NASA Astrophysics Data System (ADS)

    Dawes, Anita

    The universe is a vast chemical and physical factory consisting of large collections of stars, gas and dust. Energetic processing of ices and subsequent molecular synthesis in astrophysical environments, including icy Solar System bodies and grain mantles in the interstellar medium, are responsible for the observation of some of the molecular species found in space. Gas phase processes alone cannot explain the reaction mechanisms and the observed abundances of some of these molecules. This thesis reviews the current state of knowledge on solid state molecular synthesis in astrophysical ices and highlights the relevance of this work to understanding the chemical origins of life. The nature and origin of astrophysical ices and their environments is discussed to provide a background for the design and implementation of a new apparatus built to simulate astrophysical environments. An outline is given of the relevant collisional and chemical processes associated with interactions between radiation and matter pertinent to astrochemistry, e.g. ion, photon and electron processing of ices. A detailed description of the design and construction of the new apparatus is given and the theory and instrumentation in the spectroscopic techniques used are discussed. This is followed by a detailed explanation of the experimental procedures implemented at both ion and synchrotron radiation sources. The first results of ion and photon irradiation of H2O and CO2 ices (both pure and binary) using this apparatus are presented and discussed in detail. Ion irradiation is carried out using both reactive and unreactive ions. Reactive carbon ion implantation in pure H2O is investigated and the production of CO and CO2 monitored. Experiments involving both high (100 keV) and low (1-5 keV) energy ion irradiation of mixed H2O:CO2 ices are described and the production of H2CO3 (carbonic acid) and CO investigated. The production of CO and CO3 is described in UV irradiation experiments of mixed H2O

  17. Molecular modeling studies suggest that zinc ions inhibit HIV-1 protease by binding at catalytic aspartates.

    PubMed Central

    York, D M; Darden, T A; Pedersen, L G; Anderson, M W

    1993-01-01

    Human immunodeficiency virus type 1 protease is inhibited in vitro by zinc ions at neutral pH. The binding site of these ions is not known; however, experimental data suggest that binding may occur in the active site. To examine the possibility of zinc binding in the active site, molecular dynamics simulations in the presence and absence of zinc have been carried out to 200 psec. The results are compared with the 2.8-A crystallographic structures of a synthetic HIV-1 protease, and a zinc binding site at the catalytic aspartate residues (Asp-25, Asp-25') is proposed. Molecular dynamics simulations show that the zinc ion remains stably bound in this region, coordinating the carboxylate side chains of both aspartate residues. Interaction with zinc does not disrupt the dimeric structure of the protein or significantly alter the structure of the active site. These data are consistent with experimental studies of HIV-1 protease inhibition by zinc and give strong evidence that this is the binding site that leads to inactivation. Images p246-a Figure 1. Figure 2. Figure 3. PMID:8404763

  18. 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

  19. Structure of DPPC-hyaluronan interfacial layers - effects of molecular weight and ion composition.

    PubMed

    Wieland, D C Florian; Degen, Patrick; Zander, Thomas; Gayer, Sören; Raj, Akanksha; An, Junxue; Dėdinaitė, Andra; Claesson, Per; Willumeit-Römer, Regine

    2016-01-21

    Hyaluronan and phospholipids play an important role in lubrication in articular joints and provide in combination with glycoproteins exceptionally low friction coefficients. We have investigated the structural organization of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) Langmuir layers at the solution-air interface at different length scales with respect to the adsorption of hyaluronan (HA). This allows us to assemble a comprehensive picture of the adsorption and the resulting structures, and how they are affected by the molecular weight of HA and the presence of calcium ions. Brewster angle microscopy and grazing incident diffraction were used to determine the lateral structure at the micro- and macro scale. The data reveals an influence of HA on both the macro and micro structure of the DPPC Langmuir layer, and that the strength of this effect increases with decreasing molecular weight of HA and in presence of calcium ions. Furthermore, from X-ray reflectivity measurements we conclude that HA adsorbs to the hydrophilic part of DPPC, but data also suggest that two types of interfacial structures are formed at the interface. We argue that hydrophobic forces and electrostatic interactions play important rules for the association between DPPC and HA. Surface pressure area isotherms were used to determine the influence of HA on the phase behavior of DPPC while electrophoretic mobility measurements were used to gain insight into the binding of calcium ions to DPPC vesicles and hyaluronan.

  20. Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters.

    PubMed

    Joung, In Suk; Cheatham, Thomas E

    2009-10-01

    The dynamic and energetic properties of the alkali and halide ions were calculated using molecular dynamics (MD) and free energy simulations with various different water and ion force fields including our recently developed water-model-specific ion parameters. The properties calculated were activity coefficients, diffusion coefficients, residence times of atomic pairs, association constants, and solubility. Through calculation of these properties, we can assess the validity and range of applicability of the simple pair potential models and better understand their limitations. Due to extreme computational demands, the activity coefficients were only calculated for a subset of the models. The results qualitatively agree with experiment. Calculated diffusion coefficients and residence times between cation-anion, water-cation, and water-anion showed differences depending on the choice of water and ion force field used. The calculated solubilities of the alkali-halide salts were generally lower than the true solubility of the salts. However, for both the TIP4P(EW) and SPC/E water-model-specific ion parameters, solubility was reasonably well-reproduced. Finally, the correlations among the various properties led to the following conclusions: (1) The reliability of the ion force fields is significantly affected by the specific choice of water model. (2) Ion-ion interactions are very important to accurately simulate the properties, especially solubility. (3) The SPC/E and TIP4P(EW) water-model-specific ion force fields are preferred for simulation in high salt environments compared to the other ion force fields.

  1. 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.

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

    PubMed

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

    1999-08-01

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

  3. Molecular structure and mechanisms of action of cyclic and linear ion transport antibiotics.

    PubMed

    Duax, W L; Griffin, J F; Langs, D A; Smith, G D; Grochulski, P; Pletnev, V; Ivanov, V

    1996-01-01

    Ionophores are antibiotics that induce ion transport across natural and artificial membranes. The specific function of a given ionophore depends upon its selectivity and the kinetics of ion capture, transport, and release. Systematic studies of complexed and uncomplexed forms of linear and cyclic ionophores provide insight into molecular mechanisms of ion capture and release and the basis for ion selectivity. The cyclic dodecadepsipeptide valinomycin, cyclo[(-L-Val-D-Hyi-D-Val-L-Lac)3-], transports potassium ions across cellular membrane bilayers selectively. The x-ray crystallographic and nmr spectroscopic data concerning the structures of Na+, K+, and Ba+2 complexes are consistent and provide a rationale for the K+ selectivity of valinomycin. Three significantly different conformations of valinomycin are observed in anhydrous crystals, in hydrated crystals grown from dimethylsulfoxide, and in crystals grown from dioxane. Each of these conformations suggests a different mechanism of ion capture. One of the observed conformations has an elliptical structure stabilized by four 4<--1 intramolecular hydrogen bonds and two 5<--1 hydrogen bonds. Ion capture could be readily achieved by disruption of the 5<--1 hydrogen bonds to permit coordination to a potassium ion entering the cavity. The conformation found in crystals obtained from dimethyl sulfoxide is an open flower shape having three petals and three 4<--1 hydrogen bonds. Complexation could proceed by a closing up of the three petals of the flower around the desolvating ion. In the third form, water molecules reside in the central cavity of a bracelet structure having six 4<--1 hydrogen bonds. Two of these bracelets stack over one another with their valine-rich faces surrounding a dioxane molecule. The stacked molecules form a channel approximately 20 A in length, suggesting that under certain circumstances valinomycin might function as a channel. A series of analogues of valinomycin differing in ring composition

  4. Metal ion mediated molecularly imprinted polymer for selective capturing antibiotics containing beta-diketone structure.

    PubMed

    Qu, Shanshan; Wang, Xiaobo; Tong, Changlun; Wu, Jianmin

    2010-12-24

    A new molecularly imprinted polymer (MIP) targeting to quinolones (Qs) and tetracyclines (TCs) was synthesized using itaconic acid (ITA) and ciprofloxacin (CIP) as a functional monomer and template molecule, respectively. Factors affecting the overall performance of MIP were investigated, and the results showed that Fe(3+) ion play a vital role in the formation of MIP with high molecular imprinting effect. Meanwhile, the chelating ability of monomer, species of template molecule, as well as the molar ratio of monomer and template also contribute to the performance of the obtained MIP. Cyclic voltammetry verified that, with the participation of Fe(3+) ions, a ternary complex of ITA-Fe(3+)-CIP could be formed before polymerization. Compared with conventional MIP prepared from commonly used monomer, methacrylic acid (MAA), the new MIP show significantly enhanced molecular imprinting effect and higher capacity for specific adsorption of target compounds as revealed by static and dynamic binding experiments. The MIP was successfully used as solid-phase extraction (SPE) adsorbent for enriching a broad spectrum of antibiotics containing beta-diketone structure from surface water sample. HPLC detection showed that high recovery rate (78.6-113.6%) was found in these spiked antibiotics, whereas recovery rate for the non structurally related drugs, epinephrine (EP) and dopamine (DOPA), was very low (4.7-7.6%) on the MIP cartridges. The results demonstrate that the MIP prepared by the strategy proposed in this work, could specifically target to a series of structurally related antibiotics containing beta-diketone structure.

  5. Catalytic and molecular beacons for amplified detection of metal ions and organic molecules with high sensitivity.

    PubMed

    Zhang, Xiao-Bing; Wang, Zidong; Xing, Hang; Xiang, Yu; Lu, Yi

    2010-06-15

    The catalytic beacon has emerged as a general platform for sensing metal ions and organic molecules. However, few reports have taken advantage of the true potential of catalytic beacons in signal amplification through multiple enzymatic turnovers, as existing designs require either equal concentrations of substrate and DNAzyme or an excess of DNAzyme in order to maintain efficient quenching, eliminating the excess of substrate necessary for multiple turnovers. On the basis of the large difference in the melting temperatures between the intramolecular molecular beacon stem and intermolecular products of identical sequences, we here report a general strategy of catalytic and molecular beacon (CAMB) that combines the advantages of the molecular beacon for highly efficient quenching with the catalytic beacon for amplified sensing through enzymatic turnovers. Such a CAMB design allows detection of metal ions such as Pb(2+) with a high sensitivity (LOD = 600 pM). Furthermore, the aptamer sequence has been introduced into DNAzyme to use the modified CAMB for amplified sensing of adenosine with similar high sensitivity. These results together demonstrate that CAMB provides a general platform for amplified detection of a wide range of targets.

  6. 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.

  7. UV photodissociation of proline-containing peptide ions: insights from molecular dynamics.

    PubMed

    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, S(2) and S(3), lie close to 213 nm. Non-adiabatic MD simulation starting from S(2) and S(3) 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.

  8. 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

  9. Investigations into the role of oxacarbenium ions in glycosylation reactions by ab initio molecular dynamics.

    PubMed

    Ionescu, Andrei R; Whitfield, Dennis M; Zgierski, Marek Z; Nukada, Tomoo

    2006-12-29

    We present a constrained ab initio molecular dynamics method that allows the modeling of the conformational interconversions of glycopyranosyl oxacarbenium ions. The model was successfully tested by estimating the barriers to ring inversion for two 4-substituted tetrahydropyranosyl oxacarbenium ions. The model was further extended to predict the pathways that connect the (4)H(3) half-chair conformation of 2,3,4,6-tetra-O-methyl-d-glucopyranosyl cation to its inverted (5)S(1) conformation and the (4)H(3) half-chair conformation of 2,3,4,6-tetra-O-methyl-d-mannopyranosyl cation to its inverted (3)E conformation. The modeled interconversion pathways reconcile a large body of experimental work on the acid-catalyzed hydrolysis of glycosides and the mechanisms of a number of glucosidases and mannosidases.

  10. 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.

  11. Molecular dynamics study of accelerated ion-induced shock waves in biological media

    NASA Astrophysics Data System (ADS)

    de Vera, Pablo; Mason, Nigel J.; Currell, Fred J.; Solov'yov, Andrey V.

    2016-09-01

    We present a molecular dynamics study of the effects of carbon- and iron-ion induced shock waves in DNA duplexes in liquid water. We use the CHARMM force field implemented within the MBN Explorer simulation package to optimize and equilibrate DNA duplexes in liquid water boxes of different sizes and shapes. The translational and vibrational degrees of freedom of water molecules are excited according to the energy deposited by the ions and the subsequent shock waves in liquid water are simulated. The pressure waves generated are studied and compared with an analytical hydrodynamics model which serves as a benchmark for evaluating the suitability of the simulation boxes. The energy deposition in the DNA backbone bonds is also monitored as an estimation of biological damage, something which is not possible with the analytical model. Contribution to the Topical Issue "Atomic Cluster Collisions (7th International Symposium)", edited by Gerardo Delgado Barrio, Andrey V. Solov'yov, Pablo Villarreal, Rita Prosmiti.

  12. Towards producing ultracold CaNa+ molecular ions in the ground electronic state

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

    We present a theoretical analysis of optical pathways for the formation of cold Ca(1S)Na+(1S) molecular ions, based on accurate 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 trapped laser-cooled Ca+ ions immersed into an ultracold gas of Na atoms, the (NaCa)+ are photoassociated in the excited E1Σ+ electronic state, followed by spontaneous radiative charge transfer and emission through an intermediate state. We find the optimal formation pathway and report radiative charge-exchange cross sections and vibrational distributions of participating electronic states. This work is partially supported by ARO.

  13. Molecular dynamics study of accelerated ion-induced shock waves in biological media

    NASA Astrophysics Data System (ADS)

    de Vera, Pablo; Mason, Nigel J.; Currell, Fred J.; Solov'yov, Andrey V.

    2016-09-01

    We present a molecular dynamics study of the effects of carbon- and iron-ion induced shock waves in DNA duplexes in liquid water. We use the CHARMM force field implemented within the MBN Explorer simulation package to optimize and equilibrate DNA duplexes in liquid water boxes of different sizes and shapes. The translational and vibrational degrees of freedom of water molecules are excited according to the energy deposited by the ions and the subsequent shock waves in liquid water are simulated. The pressure waves generated are studied and compared with an analytical hydrodynamics model which serves as a benchmark for evaluating the suitability of the simulation boxes. The energy deposition in the DNA backbone bonds is also monitored as an estimation of biological damage, something which is not possible with the analytical model.

  14. Metastability of isoformyl ions in collisions with helium and hydrogen. [in interstellar molecular clouds

    NASA Technical Reports Server (NTRS)

    Green, S.

    1984-01-01

    The stability of HOC(+) ions under conditions in interstellar molecular clouds is considered. In particular, the possibility that collisions with helium or hydrogen will induce isomerization to the stable HCO(+) form is examined theoretically. Portions of the electronic potential energy surfaces for interaction with He and H atoms are obtained from standard quantum mechanical calculations. Collisions with He atoms are found to be totally ineffective for inducing isomerization. Collisions with H atoms are found to be ineffective at low interstellar temperatures owing to a small (about 500 K) barrier in the entrance channel; at higher temperatures where this barrier can be overcome, however, collisions with hydrogen atoms do result in conversion to the stable HCO(+) form. Although detailed calculations are not presented, it is argued that low-energy collisions with H2 molecules are also ineffective in destroying the metastable ion.

  15. Electron and Ion Reactions in Molecular Solids: from water ice to DNA

    NASA Astrophysics Data System (ADS)

    Huels, Michael A.

    2002-05-01

    Wherever ionizing radiation interacts with matter, it initiates reaction cascades involving non-thermal ions, radicals, and ballistic secondary electrons, which in turn may lead to substantial physical and chemical modifications of a medium. The detailed study of the fundamental reaction mechanisms which occur on a molecular level aids our general understanding of radiation induced processes in a variety of contexts, ranging from radiobiology to astrochemistry. Here I present measurements of electron (1 - 80 eV) and some ion (1 - 8 eV) mediated reactions in molecular films that resemble biological model systems. These consist of cryogenic films (pure or mixed) of rare gases, oxygen, water, methane, or aromatic hydrocarbons of increasing complexity, including bases, sugars, single and double stranded DNA. Although the basic nature of the electron or ion reaction mechanisms are found to be similar to those in the gas phase, they are often modulated by the physico-chemical characteristics of the medium. Depending on the latter, some reaction channels may be strongly enhanced, some may be quenched, and new reaction pathways, unavailable in the gas phase, may open. Thus, a given reaction cascade may lead to different end-points even in the same target. Although the goal of these studies is to unravel some of the nascent secondary-electron and reactive-ion induced events that contribute to radiation damage in living tissue, the basic observed reactions relate to other areas of application which will be briefly discussed. This research is supported by the Canadian Institutes of Health Research (CIHR), the National Cancer Institutes of Canada, the Natural Science and Engineering Research Council, and NATO.

  16. Surface Modification and Chemical Sputtering of Graphite Induced by Low Energy Atomic and Molecular Deuterium Ions

    SciTech Connect

    Zhang, Hengda; Meyer, Fred W; Meyer III, Harry M; Lance, Michael J

    2008-01-01

    The surface morphology, and chemical/structural modifications induced during chemical sputtering of ATJ graphite by low-energy (<200 eV/D) deuterium atomic and molecular ions are explored by Scanning Electron Microscopy (SEM), Raman and Auger Electron Spectroscopy (AES) diagnostics. At the lowest impact energies, the ion range may become less than the probe depth of Raman and AES spectroscopy diagnostics. We show that such diagnostics are still useful probes at these energies. As demonstration, we used these surface diagnostics to confirm the characteristic changes of surface texture, increased amorphization, enhanced surface reactivity to impurity species, and increased sp{sup 3} content that low-energy deuterium ion bombardment to steady-state chemical sputtering conditions produces. To put these studies into proper context, we also present new chemical sputtering yields for methane production of ATJ graphite at room temperature by impact of D{sub 2}{sup +} in the energy range 10-250 eV/D, and by impact of D{sup +} and D{sub 3}{sup +} at 30 eV/D and 125 eV/D, obtained using a Quadrupole Mass Spectroscopy (QMS) approach. Below 100 eV/D, the methane production in ATJ graphite is larger than that in HOPG by a factor of {approx} 2. In the energy range 10-60 eV/D, the methane production yield is almost independent of energy and then decreases with increasing ion energies. The results are in good agreement with recent molecular dynamics simulations.

  17. 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

  18. Improved Spectroscopy of Molecular Ions in the Mid-Infrared with Up-Conversion Detection

    NASA Astrophysics Data System (ADS)

    Markus, Charles R.; Perry, Adam J.; Hodges, James N.; McCall, Benjamin J.

    2016-06-01

    Heterodyne detection, velocity modulation, and cavity enhancement are useful tools for observing rovibrational transitions of important molecular ions. We have utilized these methods to investigate a number of molecular ions, such as H_3^+, CH_5^+, HeH^+, and OH^+. In the past, parasitic etalons and the lack of fast and sensitive detectors in the mid-infrared have limited the number of transitions we could measure with MHz-level precision. Recently, we have significantly reduced the amplitude of unwanted interference fringes with a Brewster-plate spoiler. We have also developed a detection scheme which up-converts the mid-infrared light with difference frequency generation which allows the use of a faster and more sensitive avalanche photodetector. The higher detection bandwidth allows for optimized heterodyne detection at higher modulation frequencies. The overall gain in signal-to-noise from both improvements will enable extensive high-precision line lists of molecular ions and searches for previously unobserved transitions. K.N. Crabtree, J.N. Hodges, B.M. Siller, A.J. Perry, J.E. Kelly, P.A. Jenkins II, and B.J. McCall, Chem. Phys. Lett. 551 (2012) 1-6. A.J. Perry, J.N. Hodges, C.R. Markus, G.S. Kocheril, and B.J. McCall, J. Mol. Spec. 317 (2015) 71-73. J.N. Hodges, A.J. Perry, P.A. Jenkins II, B.M. Siller, and B.J. McCall, J. Chem. Phys. 139 (2013) 164291. A.J. Perry, J.N. Hodges, C.R. Markus, G.S. Kocheril, and B.J. McCall. 2014, J. Chem. Phys. 141, 101101 C.R. Markus, J.N. Hodges, A.J. Perry, G.S. Kocheril, H.S.P. Muller, and B.J. McCall, Astrophys. J. 817 (2016) 138.

  19. 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.

  20. 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.

  1. Formation of antihydrogen atoms and ions in a strongly magnetized plasma: A molecular dynamics simulation

    SciTech Connect

    Vrinceanu, D.; Hu, S.X.; Mazevet, S.; Collins, L.A.

    2005-10-15

    Formation of antihydrogen atoms in a magnetized plasma of positrons and antiprotons is explicitly demonstrated in a molecular dynamics simulation. The parameters chosen are compatible with the experimental setup. We employ a special, adaptive time step symplectic integrator to perform full dynamics simulation, without using the guiding center approximation, for very long times (of the order of {mu}s). The large number of antihydrogen atoms formed allows detailed statistical analysis and distributions for the binding energy, pseudomomentum, sizes, and other quantities that characterize these atoms. We also find that a significantly smaller number of antihydrogen positive ions form during the free expansion of the plasma.

  2. Enhancement of molecular ions in mass spectrometry using an ultrashort optical pulse in multiphoton ionization.

    PubMed

    Shimizu, Takashi; Watanabe-Ezoe, Yuka; Yamaguchi, Satoshi; Tsukatani, Hiroko; Imasaka, Tomoko; Zaitsu, Shin-Ichi; Uchimura, Tomohiro; Imasaka, Totaro

    2010-05-01

    The spectral domain of an ultraviolet femtosecond laser was expanded by stimulated Raman scattering/four-wave Raman mixing, and the resulting laser pulse was compressed using a pair of gratings. The pulse width was then measured using an autocorrelator comprised of a Michelson interferometer equipped with a multiphoton ionization/mass spectrometer which was used as a two-photon detector. A gas chromatograph/mass spectrometer was employed to analyze triacetone triperoxide (TATP), and the molecular ion induced by multiphoton ionization was substantially enhanced by decreasing the laser pulse width. PMID:20364824

  3. Young-type interference in collisions between hydrogen molecular ions and helium.

    PubMed

    Schmidt, L Ph H; Schössler, S; Afaneh, F; Schöffler, M; Stiebing, K E; Schmidt-Böcking, H; Dörner, R

    2008-10-24

    The dissociative electron transfer from He into 10 keV H2+ was measured in a kinematically complete experiment by using the cold target recoil ion momentum spectroscopy imaging technique in combination with a highly resolving molecular fragment imaging technique. The electron transfer into the dissociative b(3)Sigma+_(u) state of H2 could be selected by kinematic conditions. We find a striking double slit interference pattern in the transverse momentum transfer which we can modify by selecting different internuclear distances. Compared to an optical double slit, interference minima and maxima are interchanged. The latter is the result of a phase shift in the electronic part of the wave function.

  4. 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.

  5. 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

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

    PubMed

    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

  7. Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters

    PubMed Central

    2009-01-01

    The dynamic and energetic properties of the alkali and halide ions were calculated using molecular dynamics (MD) and free energy simulations with various different water and ion force fields including our recently developed water-model-specific ion parameters. The properties calculated were activity coefficients, diffusion coefficients, residence times of atomic pairs, association constants, and solubility. Through calculation of these properties, we can assess the validity and range of applicability of the simple pair potential models and better understand their limitations. Due to extreme computational demands, the activity coefficients were only calculated for a subset of the models. The results qualitatively agree with experiment. Calculated diffusion coefficients and residence times between cation−anion, water−cation, and water−anion showed differences depending on the choice of water and ion force field used. The calculated solubilities of the alkali−halide salts were generally lower than the true solubility of the salts. However, for both the TIP4PEW and SPC/E water-model-specific ion parameters, solubility was reasonably well-reproduced. Finally, the correlations among the various properties led to the following conclusions: (1) The reliability of the ion force fields is significantly affected by the specific choice of water model. (2) Ion−ion interactions are very important to accurately simulate the properties, especially solubility. (3) The SPC/E and TIP4PEW water-model-specific ion force fields are preferred for simulation in high salt environments compared to the other ion force fields. PMID:19757835

  8. Parallelization of a Molecular Dynamics Simulation of AN Ion-Surface Collision System:

    NASA Astrophysics Data System (ADS)

    Atiş, Murat; Özdoğan, Cem; Güvenç, Ziya B.

    Parallel molecular dynamics simulation study of the ion-surface collision system is reported. A sequential molecular dynamics simulation program is converted into a parallel code utilizing the concept of parallel virtual machine (PVM). An effective and favorable algorithm is developed. Our parallelization of the algorithm shows that it is more efficient because of the optimal pair listing, linear scaling, and constant behavior of the internode communications. The code is tested in a distributed memory system consisting of a cluster of eight PCs that run under Linux (Debian 2.4.20 kernel). Our results on the collision system are discussed based on the speed up, efficiency and the system size. Furthermore, the code is used for a full simulation of the Ar-Ni(100) collision system and calculated physical quantities are presented.

  9. Molecular Magnets from Stable Organic Free Radicals: AN Ion-Binding Approach

    NASA Astrophysics Data System (ADS)

    Jang, Sei-Hum

    Structural studies of the propeller-shaped radical 1 and related triaryl-X species show pairs of binding sites comprising tripods of ether oxygens. The preorganized nucleophilic pockets have enough flexibility to accept a range of metal ion sizes. By coordination with small alkali metal cations the radicals may stack to make extended chains of interacting electron spins as shown below. In fact, mixtures of tris(2,6-dimethoxyphenyl)methyl 1 and LiBF_4 form solids with weak ferromagnetic behavior and solids from 1 and CdCl_2 show clear antiferromagnetic behavior. NMR, pulsed EPR, UV-Vis, and electrochemical studies of radicals and diamagnetic analogs show behavior consistent with ion binding to form complexes. In addition, by varying substituents on the aryl rings of 1, it is possible to adjust redox and binding properties and thus the radical's electronic and structural nature. Such adjustments are significant tools for fine tuning radicals for effective ion binding and electron coupling. Potential chain-coupling di- and tri-radical building blocks were devised by utilizing m-phenylene as a high spin coupling unit. Magnetic measurements with a Superconducting Quantum Interference Device (SQUID) magnetometer show that, unlike 1cdotLiX, some of monomeric complexes show simple paramagnetism, with independent electron spins. Control over magnetic properties can be achieved by varying the metal cation, thus complex 1cdotLiX shows weak ferromagnetism while complex 1cdot CdCl_2 shows antiferromagnetic coupling. Electron Spin Echo Envelope Modulation (ESEEM) studies of complexes in the radical ionophoric system 28 in frozen matrices yield the number of metal ions bound and their distances to the radical center. Molecular mechanics and semiempirical molecular orbital (MO) calculations coincide remarkably well with the spectroscopic findings. Complexation studies in solution support these ideas while Ab Initio calculations on a linear rm H_3C{ cdot}Li^+{cdot}CH_3 model show

  10. Molecular desorption of stainless steel vacuum chambers irradiated with 4.2 MeV/u lead ions

    NASA Astrophysics Data System (ADS)

    Mahner, E.; Hansen, J.; Laurent, J.-M.; Madsen, N.

    2003-01-01

    In preparation for the heavy ion program of the Large Hadron Collider at CERN, accumulation and cooling tests with lead ion beams have been performed in the Low Energy Antiproton Ring. These tests have revealed that due to the unexpected large outgassing of the vacuum system, the dynamic pressure of the ring could not be maintained low enough to reach the required beam intensities. To determine the actions necessary to lower the dynamic pressure rise, an experimental program has been initiated for measuring the molecular desorption yields of stainless steel vacuum chambers by the impact of 4.2 MeV/u lead ions with the charge states +27 and +53. The test chambers were exposed either at grazing or at perpendicular incidence. Different surface treatments (glow discharges, nonevaporable getter coating) are reported in terms of the molecular desorption yields for H2, CH4, CO, Ar, and CO2. Unexpected large values of molecular yields per incident ion up to 2×104 molecules/ion have been observed. The reduction of the ion-induced desorption yield due to continuous bombardment with lead ions (beam cleaning) has been investigated for five different stainless steel vacuum chambers. The implications of these results for the vacuum system of the future Low Energy Ion Ring and possible remedies to reduce the vacuum degradation are discussed.

  11. 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.

  12. 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

  13. Surface behavior of hydrated guanidinium and ammonium ions: a comparative study by photoelectron spectroscopy and molecular dynamics.

    PubMed

    Werner, Josephina; Wernersson, Erik; Ekholm, Victor; Ottosson, Niklas; Ohrwall, Gunnar; Heyda, Jan; Persson, Ingmar; Söderström, Johan; Jungwirth, Pavel; Björneholm, Olle

    2014-06-26

    Through the combination of surface sensitive photoelectron spectroscopy and molecular dynamics simulation, the relative surface propensities of guanidinium and ammonium ions in aqueous solution are characterized. The fact that the N 1s binding energies differ between these two species was exploited to monitor their relative surface concentration through their respective photoemission intensities. Aqueous solutions of ammonium and guanidinium chloride, and mixtures of these salts, have been studied in a wide concentration range, and it is found that the guanidinium ion has a greater propensity to reside at the aqueous surface than the ammonium ion. A large portion of the relative excess of guanidinium ions in the surface region of the mixed solutions can be explained by replacement of ammonium ions by guanidinium ions in the surface region in combination with a strong salting-out effect of guanidinium by ammonium ions at increased concentrations. This interpretation is supported by molecular dynamics simulations, which reproduce the experimental trends very well. The simulations suggest that the relatively higher surface propensity of guanidinium compared with ammonium ions is due to the ease of dehydration of the faces of the almost planar guanidinium ion, which allows it to approach the water-vapor interface oriented parallel to it.

  14. Explicit water molecular dynamics study of the mobility of halide ions in presence of ionene oligocations

    NASA Astrophysics Data System (ADS)

    Druchok, Maksym; Lukšič, Miha; Vlachy, Vojko

    2012-07-01

    We present explicit water molecular dynamics simulations of solutions of aliphatic 3,3- and 6,6-ionene oligocations neutralized with (i) fluoride, chloride, bromide, or iodide counterions, respectively, or (ii) with a 1:1 mixture of chloride and bromide anions in presence of a low molecular weight salt at 298 K. The SPC/E model was used to describe water molecules. Results of the simulation are presented in form of the pair distribution functions between various atoms on the ionene oligoion and counterions in solution. In addition, we were interested in the dynamics of counterions around model ionenes. We showed that counterions residing in the vicinity of the oligoion exchange rapidly with those in the bulk solution, with the frequency depending on the nature of the counterion and on the charge density of the oligoion. We calculated the average residence times of the various counterion species to the oligoions and proposed the model which divides the counterions into "free" and "bound" and calculated the fraction of "free" counterions. In the second part of the study, we investigated interaction of the sodium chloride and sodium bromide, being simultaneously present in the solution, with differently charged ionenes in water. The selectivity effect was clearly observed: bromide ions tend to replace chloride ions in the immediate vicinity of the ionene oligoions. Simulation results are discussed in light of our recent measurements of thermodynamic and transport properties of aqueous ionene solutions.

  15. Molecular Motions in Ion Channels: a Possible Link to Noise in Single Channels

    NASA Astrophysics Data System (ADS)

    Tieleman, D. Peter

    2003-05-01

    Molecular dynamics simulations of proteins and lipid bilayers give detailed information on molecular motions on a timescale of up to a microsecond. Collective motions of proteins are thought to play a functionally important role in many water-soluble proteins and simulations of potassium channel structures show that ion transport might be linked to structural fluctuations in key areas of the protein. I describe simulations of two model channels —a channel consisting of parallel alpha-helices formed by the antimicrobial peptide alamethicin, and the bacterial porin OmpF, a large beta-barrel protein that forms three water-filled pores that allow transport of small molecules. Structural fluctuations in alamethicin during ion transport are hypothesized to be a possible source of high-frequency noise observed in single-channel conductance measurements. In a model of the alamethicin channel on a 100 ns time scale almost all the structural fluctuations are in individual helices with no evidence for collective motions of the channel as a whole. In porins, single channel measurements can obtain information on the interaction between permeating molecules and the protein. I present recent simulations that study the interactions between glucose and alanine with OmpF.

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

    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.

  17. 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

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

    PubMed

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

    2014-03-24

    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.

  19. 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

  20. 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.

  1. 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

  2. Cellular and molecular portrait of eleven human glioblastoma cell lines under photon and carbon ion irradiation.

    PubMed

    Ferrandon, S; Magné, N; Battiston-Montagne, P; Hau-Desbat, N-H; Diaz, O; Beuve, M; Constanzo, J; Chargari, C; Poncet, D; Chautard, E; Ardail, D; Alphonse, G; Rodriguez-Lafrasse, C

    2015-04-28

    This study aimed to examine the cellular and molecular long-term responses of glioblastomas to radiotherapy and hadrontherapy in order to better understand the biological effects of carbon beams in cancer treatment. Eleven human glioblastoma cell lines, displaying gradual radiosensitivity, were irradiated with photons or carbon ions. Independently of p53 or O(6)-methylguanine-DNA methyltransferase(1) status, all cell lines responded to irradiation by a G2/M phase arrest followed by the appearance of mitotic catastrophe, which was concluded by a ceramide-dependent-apoptotic cell death. Statistical analysis demonstrated that: (i) the SF2(2) and the D10(3) values for photon are correlated with that obtained in response to carbon ions; (ii) regardless of the p53, MGMT status, and radiosensitivity, the release of ceramide is associated with the induction of late apoptosis; and (iii) the appearance of polyploid cells after photon irradiation could predict the Relative Biological Efficiency(4) to carbon ions. This large collection of data should increase our knowledge in glioblastoma radiobiology in order to better understand, and to later individualize, appropriate radiotherapy treatment for patients who are good candidates.

  3. Activation of protonated peptides and molecular ions of small molecules using heated filaments in Fourier-transform ion cyclotron resonance mass spectrometry

    NASA Astrophysics Data System (ADS)

    Wong, Richard L.; Robinson, Errol W.; Williams, Evan R.

    2004-05-01

    A new apparatus that uses heated filaments to dissociate ions in Fourier-transform ion cyclotron resonance mass spectrometry is described. With this apparatus, molecular ions of both acetophenone and n-butylbenzene can be dissociated very rapidly. A plot of the natural log of the dissociation rate constant versus inverse radiant temperature yields a straight line from which an Arrhenius activation energy is obtained. From this value, the threshold dissociation energy can be estimated. For acetophenone, we find a value that is within the range of previously measured values. However, for n-butylbenzene, the calculated threshold dissociation energy value is too high. We attribute this result, and the appearance of a higher energy dissociation product, to the absorption of visible photons produced at the high filament temperatures used, a factor not currently included in our modeling. In contrast to the small ions, larger peptide ions do not undergo significant dissociation with the current apparatus. The "effective" internal temperature of the larger ions can be measured by using the heated filaments in combination with blackbody infrared radiative dissociation. The "effective" temperature of the peptide ions is increased substantially less than that for the smaller ions.

  4. Structure, hydrolysis, and diffusion of aqueous vanadium ions from Car-Parrinello molecular dynamics

    NASA Astrophysics Data System (ADS)

    Jiang, Zhen; Klyukin, Konstantin; Alexandrov, Vitaly

    2016-09-01

    A molecular level understanding of the properties of electroactive vanadium species in aqueous solution is crucial for enhancing the performance of vanadium redox flow batteries. Here, we employ Car-Parrinello molecular dynamics simulations based on density functional theory to investigate the hydration structures, first hydrolysis reaction, and diffusion of aqueous V2+, V3+, VO2+, and VO 2+ ions at 300 K. The results indicate that the first hydration shell of both V2+ and V3+ contains six water molecules, while VO2+ is coordinated to five and VO 2+ to three water ligands. The first acidity constants (pKa) estimated using metadynamics simulations are 2.47, 3.06, and 5.38 for aqueous V3+, VO 2+ , and VO2+, respectively, while V2+ is predicted to be a fairly weak acid in aqueous solution with a pKa value of 6.22. We also show that the presence of chloride ions in the first coordination sphere of the aqueous VO 2+ ion has a significant impact on water hydrolysis leading to a much higher pKa value of 4.8. This should result in a lower propensity of aqueous VO 2+ for oxide precipitation reaction in agreement with experimental observations for chloride-based electrolyte solutions. The computed diffusion coefficients of vanadium species in water at room temperature are found to increase as V 3 + < VO 2 + < V O 2 + < V 2 + and thus correlate with the simulated hydrolysis constants, namely, the higher the pKa value, the greater the diffusion coefficient.

  5. Structural and Thermal Characterization of Ti+O Ion Implanted UltraHigh Molecular Weight Polyethylene (UHMWPE)

    SciTech Connect

    Oztarhan, A.; Urkac, E. Sokullu; Kaya, N.; Tihminlioglu, F.; Ila, D.; Chhay, B.; Muntele, C.; Budak, S.; Oks, E.; Nikolaev, A.

    2009-03-10

    In this work, Metal-Gas Hybrid Ion Implantation technique was used as a tool for the surface modification of Ultra High Molecular Weight Polyethylene (UHMWPE). Samples were Ti+O ion implanted by using Metal-Vapour Vacuum Arc (MEVVA) ion implanter to a fluence of 5x10{sup 16} ion/cm{sup 2} for each species and extraction voltage of 30 kV. Untreated and surface treated samples were investigated by Rutherford Back Scattering (RBS) Spectrometry, Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) Spectroscopy, Thermo Gravimetric Analysis (TGA) and Differential Scanning Calorimetry (DSC). Results indicate that Ti+O ion implantation can be applied on UHMWPE surfaces successfully. ATR-FTIR spectra indicate that the C-H concentration on the surface decreased after Ti+O implantation. Thermal characterization with TGA and DSC shows that polymeric decomposition temperature is shifted after ion implantation.

  6. Free molecular collision cross section calculation methods for nanoparticles and complex ions with energy accommodation

    SciTech Connect

    Larriba, Carlos Hogan, Christopher J.

    2013-10-15

    The structures of nanoparticles, macromolecules, and molecular clusters in gas phase environments are often studied via measurement of collision cross sections. To directly compare structure models to measurements, it is hence necessary to have computational techniques available to calculate the collision cross sections of structural models under conditions matching measurements. However, presently available collision cross section methods contain the underlying assumption that collision between gas molecules and structures are completely elastic (gas molecule translational energy conserving) and specular, while experimental evidence suggests that in the most commonly used background gases for measurements, air and molecular nitrogen, gas molecule reemission is largely inelastic (with exchange of energy between vibrational, rotational, and translational modes) and should be treated as diffuse in computations with fixed structural models. In this work, we describe computational techniques to predict the free molecular collision cross sections for fixed structural models of gas phase entities where inelastic and non-specular gas molecule reemission rules can be invoked, and the long range ion-induced dipole (polarization) potential between gas molecules and a charged entity can be considered. Specifically, two calculation procedures are described detail: a diffuse hard sphere scattering (DHSS) method, in which structures are modeled as hard spheres and collision cross sections are calculated for rectilinear trajectories of gas molecules, and a diffuse trajectory method (DTM), in which the assumption of rectilinear trajectories is relaxed and the ion-induced dipole potential is considered. Collision cross section calculations using the DHSS and DTM methods are performed on spheres, models of quasifractal aggregates of varying fractal dimension, and fullerene like structures. Techniques to accelerate DTM calculations by assessing the contribution of grazing gas

  7. 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.

  8. Quasidiatomic Approach to the Collisions of Low KEV Molecular Ions with Atoms

    NASA Astrophysics Data System (ADS)

    Yenen, Orhan

    The polarization of L(,(alpha)) radiation is measured in coincidence with a charged particle scattered at specific laboratory angles, resulting from the collision induced dissociation of low keV H(,2)('+) and H(,3)('+) incident on target gases. Coincidence measurements of the polarization pattern are made for a variety of scattering angles for 3.22 keV H(,2)('+) incident on He and Ne, and for 4.83 keV H(,3)('+) incident on He. The molecular states excited during the collision are determined from the alignment of the observed polarization patterns. A quasidiatomic collision model, which is an extension of the electron promotion model of ion-atom collisions at low keV energies to molecule-atom collisional systems, is developed to interpret the experimental results. The rules of building simple quasidiatomic correlation diagrams, to qualitatively estimate the dynamical behavior of molecular collisions, are presented. The general idea of treating the molecule as an atom under certain circumstances, is applied to a molecular two-state calculation of the differential charge-transfer probabilities in H('+)-H(,2) collisions. This calculation reproduces the essential features of previous experiments.

  9. 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

  10. 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.

  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 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.

  13. High Resolution Jet Cooled Cavity Ringdown Spectroscopy of the tilde{A} State 31_0 Band of the NO_3 Radical

    NASA Astrophysics Data System (ADS)

    Codd, Terrance J.; Roudjane, Mourad; Miller, Terry A.

    2012-06-01

    The 2E''tilde{A} state of NO_3 is doubly degenerate and is therefore subject to Jahn-Teller (JT) distortion. In the tilde{A} state there are two JT active modes, ν_3 and ν_4 (e' stretch and in plane bend respectively). Theoretical work has predicted that the JT effect in the tilde{A} state should be quite strong and approach the static case (D≥1) where the molecule is permanently distorted to a lower symmetry geometry. A moderate resolution spectrum of the tilde{A} state showed a feature that we tentatively assigned as the 31_0 band based on position and band contour. Using high resolution cavity ringdown spectroscopy we have now obtained a rotationally resolved spectrum of this band. The analysis of this band has been commenced using an oblate symmetric top Hamiltonian with spin-rotation terms. This analysis supports the assignment of this band to the a_1'' vibronic component of the 31_0 band. So far, the spectrum shows no evidence of a large geometric distortion of the molecule. Some lines appear to be split, as was previously observed in the 41_0 and 42_0 bands, and the possible sources of this splitting are being investigated. J.F. Stanton, 66th OSU International Symposium on Molecular Spectroscopy, The Ohio State University, Columbus Ohio, 2011, TJ-03 W. Eisfeld, K. Morokuma, J. Chem. Phys. 114, 9430 (2001) S. Faraji, H. Köppel, W. Eisfeld, S. Mahapatra, J. Chem. Phys. 347, 110 (2008) T.J. Codd, M.W. Chen, T.A. Miller, 66th OSU International Symposium on Molecular Spectroscopy, The Ohio State University, Columbus Ohio, 2011, TD-06 M.W. Chen, T.J. Codd, G. Just, T.A. Miller, OSU International Symposium on Molecular Spectroscopy, The Ohio State University, Columbus Ohio, 2011, TD-07

  14. 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.

  15. Intra- and Inter-Molecular Cross-Linking of Peptide Ions in the Gas Phase: Reagents and Conditions

    NASA Astrophysics Data System (ADS)

    Mentinova, Marija; McLuckey, Scott A.

    2011-05-01

    Intra-molecular and inter-molecular cross-linking of protonated polypeptide ions in the gas phase via ion/ion reactions have been demonstrated using N-hydroxysulfosuccinimide (sulfo-NHS)- based reagent anions. The initial step in the ion/ion reaction involves the formation of a long-lived complex between the peptide and reagent, which is a prerequisite for the covalent bioconjugation chemistry. The sulfonate groups on the NHS rings of the homo-bifunctional cross-linking reagents have high affinity for the protonated sites in the peptide and, therefore, facilitate the long-lived complex formation. In addition to the formation of a long-lived chemical complex, intra-molecular cross-linking also requires two unprotonated primary amine sites within a molecule where the covalent modification takes place. Alternatively, inter-molecular cross-linking demands the availability of one neutral primary amine site in each of the two peptides that are being cross-linked. Nucleophilic displacement of two sulfo-NHS groups by the amine functionalities in the peptide is a signature of the covalent cross-linking chemistry in the gas phase. Upon removal of the two sulfo-NHS groups, two amide bonds are formed between an unprotonated, primary amine group of a lysine side chain in the peptide and the carboxyl group in the reagent.

  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. 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

  18. 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.

  19. Hydration of Y3+ ion: A Car-Parrinello molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Ikeda, Takashi; Hirata, Masaru; Kimura, Takaumi

    2005-01-01

    The solvation shell structure of Y3+ and the dynamics of the hydrated ion in an aqueous solution of 0.8M YCl3 are studied in two conditions with and without an excess proton by using first principles molecular dynamics method. We find that the first solvation shell around Y3+ contains eight water molecules forming a square antiprism as expected from x-ray absorption near edge structure in both the conditions we examined. A detailed analysis relying upon localized orbitals reveals that the complexation of water molecules with yttrium cation leads to a substantial amount of charge redistribution particularly on the oxygen atoms, giving rise to the chemical shifts of ˜-20 ppm in 17O nuclear magnetic resonance relative to the computed nuclear shieldings of the bulk water.

  20. Simple molecular model for the binding of antibiotic molecules to bacterial ion channels

    NASA Astrophysics Data System (ADS)

    Mafé, Salvador; Ramírez, Patricio; Alcaraz, Antonio

    2003-10-01

    A molecular model aimed at explaining recent experimental data by Nestorovich et al. [Proc. Natl. Acad. Sci. USA 99, 9789 (2002)] on the interaction of ampicillin molecules with the constriction zone in a channel of the general bacterial porin, OmpF (outer membrane protein F), is presented. The model extends T. L. Hill's theory for intermolecular interactions in a pair of binding sites [J. Am. Chem. Soc. 78, 3330 (1956)] by incorporating two binding ions and two pairs of interacting sites. The results provide new physical insights on the role of the complementary pattern of the charge distributions in the ampicillin molecule and the narrowest part of the channel pore. Charge matching of interacting sites facilitates drug binding. The dependence of the number of ampicillin binding events per second with the solution pH and salt concentration is explained qualitatively using a reduced number of fundamental concepts.

  1. Molecular Dynamics Simulations of Electron-Ion Temperature Equilibration in an SF6 Plasma

    NASA Astrophysics Data System (ADS)

    Benedict, Lorin X.; Glosli, James N.; Richards, David F.; Streitz, Frederick H.; Hau-Riege, Stefan P.; London, Richard A.; Graziani, Frank R.; Murillo, Michael S.; Benage, John F.

    2009-05-01

    We use classical molecular dynamics to investigate electron-ion temperature equilibration in a two-temperature SF6 plasma. We choose a density of 1.0×1019SF6 molecules per cm3 and initial temperatures of Te=100eV and TS=TF=15eV, in accordance with experiments currently underway at Los Alamos National Laboratory. Our computed relaxation time lies between two oft-used variants of the Landau-Spitzer relaxation formula which invoke static screening. Discrepancies are also found when comparing to the predictions made by more recent theoretical approaches. These differences should be large enough to be measured in the upcoming experiments.

  2. Molecular dynamics simulations of electron-ion temperature equilibration in an SF6 plasma.

    PubMed

    Benedict, Lorin X; Glosli, James N; Richards, David F; Streitz, Frederick H; Hau-Riege, Stefan P; London, Richard A; Graziani, Frank R; Murillo, Michael S; Benage, John F

    2009-05-22

    We use classical molecular dynamics to investigate electron-ion temperature equilibration in a two-temperature SF6 plasma. We choose a density of 1.0 x 10;{19}SF_{6} molecules per cm;{3} and initial temperatures of T_{e} = 100 eV and T_{S} = T_{F} = 15 eV, in accordance with experiments currently underway at Los Alamos National Laboratory. Our computed relaxation time lies between two oft-used variants of the Landau-Spitzer relaxation formula which invoke static screening. Discrepancies are also found when comparing to the predictions made by more recent theoretical approaches. These differences should be large enough to be measured in the upcoming experiments.

  3. 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.

  4. Ion-induced molecular emission of polymers: analytical potentialities of FTIR and mass spectroscopy

    NASA Astrophysics Data System (ADS)

    Picq, V.; Balanzat, E.

    1999-05-01

    The release of small gaseous molecules is a general phenomenon of irradiated polymers. Polyethylene (PE), polypropylene (PP) and polybutene (PB) were irradiated with ions of different electronic stopping power. We show that the gas emission can provide important information on the damage process if a reliable chemical identification of the molecules released and accurate yield values are obtained. The outgassing products were analysed by two techniques: (1) by a novel set-up using a Fourier Transform Infrared (FTIR) analysis of the gas mixture released from the polymer film and (2) by residual gas analysis (RGA) with a quadrupole mass spectrometer. Comparing the analytical potentialities of both methods we come to the conclusion that the FTIR method gives a more straightforward and accurate determination of the chemical nature and of the yield of most of the released molecules. However, RGA provides complementary information on the gas release kinetics and also on the release of heavy hydrocarbon molecules and symmetric molecules like molecular hydrogen.

  5. 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.

  6. 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.

  7. 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.'

  8. 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).

  9. 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

  10. 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).

  11. 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.

  12. 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).

  13. 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.

  14. 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.

  15. Molecular ions and protonated molecules observed in the atmospheric solids analysis probe analysis of steroids.

    PubMed

    Ray, Andrew D; Hammond, Janet; Major, Hilary

    2010-01-01

    Atmospheric pressure chemical ionisation (APCI) has often been used to ionise steroids in mass spectrometry, usually when interfaced to high-performance liquid chromatography (HPLC). However, in positive ion mode, a dehydrated protonated molecule is often observed with a loss of structural information. The recently introduced technique of atmospheric solids analysis probe (ASAP) has the advantage that the sample can be analysed directly and does not need to be interfaced to HPLC. Existing ionisation sources such as direct analysis in real time (DART) and desorption electrospray ionisation (DESI) have shown the advantage of direct analysis techniques in a variety of applications. ASAP can be performed on commercial atmospheric pressure ionisation (API) mass spectrometers with only simple modifications to API sources. The samples are vaporised by hot nitrogen gas from the electrospray desolvation heater and ionised by a corona discharge. A range of commercially available steroids were analysed by ASAP to investigate the mechanism of ionisation. ASAP analysis of steroids generally results in the formation of the parent molecular ion as either the radical cation M+* or the protonated molecule MH+. The formation of the protonated molecule is a result of proton transfer from ionised water clusters in the source. However, if the source is dry, then formation of the radical cation is the primary ionisation mechanism.

  16. Sub-Doppler Spectroscopy of Molecular Ions in the Mid-Infrared

    NASA Astrophysics Data System (ADS)

    Hodges, James N.; Crabtree, Kyle N.; McCall, Benjamin J.

    2012-06-01

    High precision, high accuracy spectroscopy in the mid-IR plays an important role in many areas of study. It provides benchmarks for {ab initio} calculations, acts as a reference for astronomical searches, and enables the study of highly fluxional ions, such as CH_5^+ and H_5^+. In an effort to advance these interests, we built an instrument that uses Noise Immune Cavity Enhanced Optical Heterodyne Velocity Modulation Spectroscopy to achieve sensitive, high signal-to-noise spectra of molecular ions with sub-Doppler features. There are four main components of the instrument: a tunable cw-OPO, an optical cavity with a finesse of ˜200, a liquid nitrogen cooled AC positive column cell, and an optical frequency comb for absolute frequency calibration. The OPO is pumped by a fiber laser at 1064 nm with a signal cavity resonant between 1.5 and 1.6 μm, which corresponds to an idler wavelength tunable between 3.2 and 3.9 μm. The idler is actively locked to the cavity via a Pound-Drever-Hall locking scheme responsible for maintaining the resonance condition of the cavity. Inside the cavity is a AC driven positive column plasma, which produces a high ion density and modulates their velocity providing neutral discrimination. Since the cell can be cooled by liquid nitrogen, the instrument has an extra advantage due to signal enhancement of low J transitions. Saturation spectroscopy is possible because of enhancement of laser power in the cavity, which leads to improved precision with respect to line center determination due to narrow Lamb dips. To achieve sub-MHz accuracy, the signal and pump are roughly calibrated with a near-IR wavemeter and then referenced to a frequency comb. To demonstrate the advantages of this technique, measurements of the ν2 fundamental band of H3+ will be presented.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. Progress of a New Instrument to Study Molecular Dynamics of Interstellar Ion-Neutral Reactions

    NASA Astrophysics Data System (ADS)

    Roenitz, Kevin; Lamm, Ben; Rudd, Lydia; Justl, Andy; Landeweer, Steven; Roadman, Danny; Koscielniak, Justyna; Sonnenberger, Andrew; Perera, Manori

    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 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 astrochemical needs that motivated my research, how the new instrument will meet those needs, and the present status of the instrument and measurements in my lab.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. Cationic conjugated polyelectrolytes-triggered conformational change of molecular beacon aptamer for highly sensitive and selective potassium ion detection.

    PubMed

    Kim, Boram; Jung, In Hwan; Kang, Mijeong; Shim, Hong-Ku; Woo, Han Young

    2012-02-15

    We demonstrate highly sensitive and selective potassium ion detection against excess sodium ions in water, by modulating the interaction between the G-quadruplex-forming molecular beacon aptamer (MBA) and cationic conjugated polyelectrolyte (CPE). The K(+)-specific aptamer sequence in MBA is used as the molecular recognition element, and the high binding specificity of MBA for potassium ions offers selectivity against a range of metal ions. The hairpin-type MBA labeled with a fluorophore and quencher at both termini undergoes a conformational change (by complexation with CPEs) to either an open-chain form or a G-quadruplex in the absence or presence of K(+) ions. Conformational changes of MBA as well as fluorescence (of the fluorophore in MBA) quenching or amplification via fluorescence resonance energy transfer from CPEs provide clear signal turn-off and -on in the presence or absence of K(+). The detection limit of the K(+) assays is determined to be ~1.5 nM in the presence of 100 mM Na(+) ions, which is ~3 orders of magnitude lower than those reported previously. The successful detection of 5'-adenosine triphosphate (ATP) with the MBA containing an ATP-specific aptamer sequence is also demonstrated using the same sensor scheme. The scheme reported herein is applicable to the detection of other kinds of G-rich aptamer-binding chemicals and biomolecules.

  9. Metal Ion Coordination Essential for Specific Molecular Interactions of Butea monosperma Lectin: ITC and MD Simulation Studies.

    PubMed

    Abhilash, J; Haridas, M

    2015-05-01

    Crystal structure of Butea monosperma seed lectin (BML) was analyzed and the metal ion geometry identified. In order to understand the role of metal ions for the structural stability and ligand binding, studies of demetallized protein were carried out. Binding of different ligands like GalNAc, lactose, and galactose onto native and demetallized protein was studied by isothermal titration calorimetry as well as molecular simulation methods. Molecular dynamics was applied to the structure after removing the coordinates of metal ions, to identify the effect of demetallization in silico. Docking studies of different sugar molecules as well as the fungal α-amylase was carried out and compared the interactions in the native and apo states. It was found that metal ions are important for the ligand binding with increased affinity. However, their absence did not make any alteration to the secondary structure. Though the metal ions were not coordinated to the loops contacting the α-amylase, the absence of metal ions reduced the protein-protein binding strength due to long-range changes in irregular structures of the lectin.

  10. Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel.

    PubMed

    Ulmschneider, Martin B; Bagnéris, Claire; McCusker, Emily C; Decaen, Paul G; Delling, Markus; Clapham, David E; Ulmschneider, Jakob P; Wallace, B A

    2013-04-16

    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.

  11. Reversible molecular switching of molecular beacon: controlling DNA hybridization kinetics and thermodynamics using mercury(ii) ions.

    PubMed

    Yang, Ronghua; Jin, Jianyu; Long, Liping; Wang, Yongxiang; Wang, Hao; Tan, Weihong

    2009-01-21

    We report that the hydrogen-bonding pattern in a molecular beacon can be replaced by metal-dependent pairs of Hg(2+) and DNA thymine (T) bases. A molecular beacon based on T-Hg(2+)-T exhibits a lower background signal and higher thermostability than regular molecular beacons.

  12. Charge exchange of metastable 2D oxygen ions with molecular oxygen - A new source of thermospheric O2/+/ ions

    NASA Technical Reports Server (NTRS)

    Torr, D. G.; Torr, M. R.; Rusch, D. W.; Nier, A. O.; Kayser, D.; Hanson, W. B.; Hoffman, J. H.; Donahue, K.

    1979-01-01

    Reactions involving metastable ions are difficult to study in the laboratory. Much new information on these reactions has been derived from satellite measurements of aeronomic parameters. In this paper, Atmosphere Explorer D data are used to study charge exchange of metastable O(+)(2D) ions with O2. Using direct measurements of the O2 at 200 km to compute O2 densities at 300 km and supporting ionic concentrations and temperature observations, we find the rate coefficient for this reaction to be 1 + or - 0.6 times 10 to the minus 9th cu cm/sec. The process constitutes a significant source of O2(+) ions in the F2 layer at times when the N2 and O2 densities are enhanced. This finding leads to the conclusion that charge exchange with O2 must be a major sink for O(+)(2D) and an important source of O2(+) ions in the E region, because of the increase in the O2 concentration/N2 concentration ratio with decreasing altitude. The results imply that 80% of all O(+) ions formed in the E region are converted to O2(+) and that only about 20% of the metastable O(+) ions are converted into N2(+) through charge exchange with N2.

  13. 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.

  14. Sub-10-fs control of dissociation pathways in the hydrogen molecular ion with a few-pulse attosecond pulse train

    NASA Astrophysics Data System (ADS)

    Nabekawa, Yasuo; Furukawa, Yusuke; Okino, Tomoya; Amani Eilanlou, A.; Takahashi, Eiji J.; Yamanouchi, Kaoru; Midorikawa, Katsumi

    2016-09-01

    The control of the electronic states of a hydrogen molecular ion by photoexcitation is considerably difficult because it requires multiple sub-10 fs light pulses in the extreme ultraviolet (XUV) wavelength region with a sufficiently high intensity. Here, we demonstrate the control of the dissociation pathway originating from the 2pσu electronic state against that originating from the 2pπu electronic state in a hydrogen molecular ion by using a pair of attosecond pulse trains in the XUV wavelength region with a train-envelope duration of ~4 fs. The switching time from the peak to the valley in the oscillation caused by the vibrational wavepacket motion in the 1sσg ground electronic state is only 8 fs. This result can be classified as the fastest control, to the best of our knowledge, of a molecular reaction in the simplest molecule on the basis of the XUV-pump and XUV-probe scheme.

  15. Measurements of mobilities and longitudinal diffusion coefficients for Li + ions in some molecular gases

    NASA Astrophysics Data System (ADS)

    Satoh, Y.; Takebe, M.; Iinuma, K.

    1987-12-01

    The transport coefficients for Li+ ions in some moleculars gases have been measured over a wide range of E/N with a conventional drift tube at temperatures close to 300 K. The zero-field reduced mobilities are found to be 3.91±0.11, 4.44±0.12, 3.64±0.10, 2.46±0.07, and 3.44±0.10 cm2/V s in N2, O2, CO, CO2, and CH4 gas, respectively, and these values except in O2 gas significantly deviate from the Langevin limit. In N2, CO, and CO2 gas, the resulting mobility curves show clear minima at intermediate E/N, but the depressions in O2 and CH4 gas are slight. The drop of the zero-field values in N2, CO, and CO2 gas is explained in terms of an effective ion-quadrupole interaction which provides the r-6 attractive behavior. From the mobility calculations with using n-4-6(γ) potential, it is suggested that the depression of the mobility curve is developed by the addition of a sufficient r-6 term and is partly attributed to inelastic collisions as expected even at intermediate E/N. The experimental diffusion data are compared with the values derived from the generalized Einstein relation. For all systems, the agreement is quite good at intermediate E/N, but there are large discrepancies at other E/N. The sources of the deviation are considered to be clustering reactions and inelastic collisions at low and high field, respectively.

  16. 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

  17. 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.

  18. 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).

  19. Theoretical study of the low-lying electronic states of the RbCs+ molecular ion

    NASA Astrophysics Data System (ADS)

    Korek, M.; Allouche, A. R.

    2001-09-01

    The potential energy has been calculated over a wide range of internuclear distance for the 64 lowest molecular states of symmetry 2Σ+, 2Π, 2Δ, and Ω = ½, 3/2, 3/2 of the molecular ion RbCs+. This calculation has been done by using an ab initio method based on non-empirical pseudopotentials and parametrized l-dependent polarization potentials. We used Gaussian basis sets for both atoms and the spin-orbit effect has been taken into account through a non-empirical spin-orbit pseudopotential. For the four bound states (1) 2Σ+, (1) 2Π, (1) Ω = ½ and (1) Ω = 3/2 the main spectroscopic constants ωe, Be, and De have been derived. By replacing the rovibrational differential Schrödinger equation by a Volterra integral equation the wavefunction is given by Ψ = ∑i = 01{aifi}, where the coefficients ai are obtained from the boundary conditions of the wavefunction and fi are two well defined canonical functions. Using these functions the eigenvalues Ev, the rotational constants Bv and the centrifugal distortion constants Dv have been calculated for the four considered bound states up to v = 121 as well as the dipole moment functions and oscillator strengths for transitions between (1) 2Σ+ and (1) 2Π. No comparison of these values with other results is yet possible because they are given here for the first time. Extensive tables of energy values versus internuclear distance and the values of Ev, Bv and Dv are displayed at the following address: http://lasim.univ-lyon1.fr/allouche/rbcsplus

  20. 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. PMID:26922337

  1. 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.

  2. 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.

  3. Molecular dynamics simulations of aqueous ions at the liquid-vapor interface accelerated using graphics processors.

    PubMed

    Bauer, Brad A; Davis, Joseph E; Taufer, Michela; Patel, Sandeep

    2011-02-01

    Molecular dynamics (MD) simulations are a vital tool in chemical research, as they are able to provide an atomistic view of chemical systems and processes that is not obtainable through experiment. However, large-scale MD simulations require access to multicore clusters or supercomputers that are not always available to all researchers. Recently, scientists have returned to exploring the power of graphics processing units (GPUs) for various applications, such as MD, enabled by the recent advances in hardware and integrated programming interfaces such as NVIDIA's CUDA platform. One area of particular interest within the context of chemical applications is that of aqueous interfaces, the salt solutions of which have found application as model systems for studying atmospheric process as well as physical behaviors such as the Hoffmeister effect. Here, we present results of GPU-accelerated simulations of the liquid-vapor interface of aqueous sodium iodide solutions. Analysis of various properties, such as density and surface tension, demonstrates that our model is consistent with previous studies of similar systems. In particular, we find that the current combination of water and ion force fields coupled with the ability to simulate surfaces of differing area enabled by GPU hardware is able to reproduce the experimental trend of increasing salt solution surface tension relative to pure water. In terms of performance, our GPU implementation performs equivalent to CHARMM running on 21 CPUs. Finally, we address possible issues with the accuracy of MD simulaions caused by nonstandard single-precision arithmetic implemented on current GPUs. PMID:20862755

  4. 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+.

  5. 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.

  6. Molecular mechanism for 3:1 subunit stoichiometry of rod cyclic nucleotide-gated ion channels

    PubMed Central

    Shuart, Noah G.; Haitin, Yoni; Camp, Stacey S.; Black, Kevin D.; Zagotta, William N.

    2011-01-01

    Molecular determinants of ion channel tetramerization are well characterized, but those involved in heteromeric channel assembly are less clearly understood. The heteromeric composition of native channels is often precisely controlled. Cyclic nucleotide-gated (CNG) channels from rod photoreceptors exhibit a 3:1 stoichiometry of CNGA1 and CNGB1 subunits that tunes the channels for their specialized role in phototransduction. Here we show, using electrophysiology, fluorescence, biochemistry, and X-ray crystallography, that the mechanism for this controlled assembly is the formation of a parallel 3-helix coiled-coil domain of the carboxy-terminal leucine zipper region of CNGA1 subunits, constraining the channel to contain three CNGA1 subunits, followed by preferential incorporation of a single CNGB1 subunit. Deletion of the carboxy-terminal leucine zipper domain relaxed the constraint and permitted multiple CNGB1 subunits in the channel. The X-ray crystal structures of the parallel 3-helix coiled-coil domains of CNGA1 and CNGA3 subunits were similar, suggesting that a similar mechanism controls the stoichiometry of cone CNG channels. PMID:21878911

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. 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

  12. Communication: Hydration structure and polarization of heavy alkali ions: A first principles molecular dynamics study of Rb+ and Cs+

    NASA Astrophysics Data System (ADS)

    Ikeda, Takashi; Boero, Mauro

    2012-07-01

    Hydration structure and polarization of Rb+ and Cs+ in liquid water at ambient conditions were studied by first principles molecular dynamics. Our systematic analysis of the relevant electronic structures, based on maximally localized Wannier functions, revealed that the dipole moment of H2O molecules in the first solvation shell of the ions slightly increases with increasing the atomic number. We also found that the polarization of heavy alkali ions, particularly Cs+, tends to stabilize a peculiar asymmetric hydration structure with relevant consequences in the extraction of the harmful 137Cs resulting from nuclear wastes.

  13. Single-crystal cubic boron nitride thin films grown by ion-beam-assisted molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Hirama, Kazuyuki; Taniyasu, Yoshitaka; Karimoto, Shin-ichi; Krockenberger, Yoshiharu; Yamamoto, Hideki

    2014-03-01

    We investigated the formation of cubic boron nitride (c-BN) thin films on diamond (001) and (111) substrates by ion-beam-assisted molecular beam epitaxy (MBE). The metastable c-BN (sp3-bonded BN) phase can be epitaxially grown as a result of the interplay between competitive phase formation and selective etching. We show that a proper adjustment of acceleration voltage for N2+ and Ar+ ions is a key to selectively discriminate non-sp3 BN phases. At low acceleration voltage values, the sp2-bonded BN is dominantly formed, while at high acceleration voltages, etching dominates irrespective of the bonding characteristics of BN.

  14. 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.

  15. 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

  16. 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

  17. Molecular dynamics simulation study on substrate temperature dependence of sputtering yields for an organic polymer under ion bombardment

    SciTech Connect

    Yamashiro, Masashi; Yamada, Hideaki; Hamaguchi, Satoshi

    2007-02-15

    Substrate temperature dependence of sputtering yields in organic polymer etching processes has been examined with the use of molecular dynamics (MD) simulations. The simulation results indicate that structural weakness arising from high substrate temperatures alone is not sufficient to account for the experimentally observed strong dependence of sputtering yields on substrate temperatures. In other words, thermal desorption is likely to increase significantly at high substrate temperatures in reactive ion etching processes of organic polymers.

  18. Comparative study of the ab initio potential curves for Be2+, Mg2+, Ca2+ and Sr2+ molecular ions

    NASA Astrophysics Data System (ADS)

    Banerjee, Sandipan; Montgomery, John; Côté, Robin

    2013-05-01

    We perform a comparative study of the X 2Σu+, A 2Πu and B 2Σg+ states in the homonuclear alkaline-earth family of molecular ions -- Be2+, Mg2+, Ca2+ and Sr2++. A qualitative comparison of the ``double-well'' in the B 2Σg+ state and interaction with the excited 2 2Σg+ state is made for all the molecular ions. Multireference configuration interaction (MRCI) calculations are performed with a complete active space (CAS) wavefunction as reference. Spectroscopic constants, bound vibrational levels, transition moments and radiative lifetimes are calculated. The static dipole and quadrupole polarizabilities, and the leading order van der Waals coefficients are also reported. We also show preliminary results for corrections to the Born-Oppenheimer Hamiltonian -- non-adiabatic couplings and and hyperfine structure due to nuclear spins and electric quadrupoles. We perform a comparative study of the X 2Σu+ , A 2Πu and B 2Σg+ states in the homonuclear alkaline-earth family of molecular ions -- Be2+, Mg2+, Ca2+ and Sr2+. A qualitative comparison of the ``double-well'' in the B 2Σg+ state and interaction with the excited 2 2Σg+ state is made for all the molecular ions. Multireference configuration interaction (MRCI) calculations are performed with a complete active space (CAS) wavefunction as reference. Spectroscopic constants, bound vibrational levels, transition moments and radiative lifetimes are calculated. The static dipole and quadrupole polarizabilities, and the leading order van der Waals coefficients are also reported. We also show preliminary results for corrections to the Born-Oppenheimer Hamiltonian -- non-adiabatic couplings and and hyperfine structure due to nuclear spins and electric quadrupoles. This work was funded in part by the Air Force Office for Scientific Research MURI and the Department of Energy Office of Basic Sciences.

  19. 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

  20. 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

  1. Effect of Gallium ion damage on poly-crystalline Zirconium: Direct experimental observations and molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Revelly, A. K.; Monpara, G.; Samajdar, I.; Krishna, K. V. Mani; Tewari, R.; Srivastava, D.; Dey, G. K.; Panwar, A. S.

    2015-12-01

    This study involved controlled focused ion beam (FIB) damage of high purity poly-crystalline Zirconium (Zr) and EBSD (electron backscattered diffraction) observations on the same region/microstructure. Direct experimental observations were augmented by molecular dynamics (MD) simulations: the latter demonstrating a hierarchy of microstructural features enabling/retarding relative ion damage. Experimental results clearly established a non-monotonic dependence of damage kinetics with average grain size. Damage increased with grain size, till an average grain size of 12 micron, and then dropped. This was explained from combined effects of grain size and in-grain misorientations. For lower than 12 micron average grain size, noticeable in-grain misorientations enabled lower damage kinetics. For greater than 17 micron grain size, with insignificant in-grain misorientations, reduced presence of high angle grain boundaries were shown to retard relative ion damage.

  2. Molecular nature of mutations induced by high-LET irradiation with argon and carbon ions in Arabidopsis thaliana.

    PubMed

    Hirano, Tomonari; Kazama, Yusuke; Ohbu, Sumie; Shirakawa, Yuki; Liu, Yang; Kambara, Tadashi; Fukunishi, Nobuhisa; Abe, Tomoko

    2012-07-01

    Linear energy transfer (LET) is an important parameter to be considered in heavy-ion mutagenesis. However, in plants, no quantitative data are available on the molecular nature of the mutations induced with high-LET radiation above 101-124keVμm(-1). In this study, we irradiated dry seeds of Arabidopsis thaliana with Ar and C ions with an LET of 290keVμm(-1). We analyzed the DNA alterations caused by the higher-LET radiation. Mutants were identified from the M(2) pools. In total, 14 and 13 mutated genes, including bin2, egy1, gl1, gl2, hy1, hy3-5, ttg1, and var2, were identified in the plants derived from Ar- and C-ions irradiation, respectively. In the mutants from both irradiations, deletion was the most frequent type of mutation; 13 of the 14 mutated genes from the Ar ion-irradiated plants and 11 of the 13 mutated genes from the C ion-irradiated plants harbored deletions. Analysis of junction regions generated by the 2 types of irradiation suggested that alternative non-homologous end-joining was the predominant pathway of repair of break points. Among the deletions, the proportion of large deletions (>100bp) was about 54% for Ar-ion irradiation and about 64% for C-ion irradiation. Both current results and previously reported data revealed that the proportions of the large deletions induced by 290-keVμm(-1) radiations were higher than those of the large deletions induced by lower-LET radiations (6% for 22.5-30.0keVμm(-1) and 27% for 101-124keVμm(-1)). Therefore, the 290keVμm(-1) heavy-ion beams can effectively induce large deletions and will prove useful as novel mutagens for plant breeding and analysis of gene functions, particularly tandemly arrayed genes.

  3. Accurate static and dynamic properties of liquid electrolytes for Li-ion batteries from ab initio molecular dynamics.

    PubMed

    Ganesh, P; Jiang, De-en; Kent, P R C

    2011-03-31

    Lithium-ion batteries have the potential to revolutionize the transportation industry, as they did for wireless communication. A judicious choice of the liquid electrolytes used in these systems is required to achieve a good balance among high-energy storage, long cycle life and stability, and fast charging. Ethylene-carbonate (EC) and propylene-carbonate (PC) are popular electrolytes. However, to date, almost all molecular-dynamics simulations of these fluids rely on classical force fields, while a complete description of the functionality of Li-ion batteries will eventually require quantum mechanics. We perform accurate ab initio molecular-dynamics simulations of ethylene- and propylene-carbonate with LiPF(6) at experimental concentrations to build solvation models which explain available neutron scattering and nuclear magnetic resonance (NMR) results and to compute Li-ion solvation energies and diffusion constants. Our results suggest some similarities between the two liquids as well as some important differences. Simulations also provide useful insights into formation of solid-electrolyte interphases in the presence of electrodes in conventional Li-ion batteries.

  4. A hydrogen ion beam method of molecular density measurement inside a 4.2-K beam tube

    SciTech Connect

    Alinovsky, N.; Anashin, V.; Beschasny, P.

    1994-06-01

    In our first experiments on synchrotron radiation-induced photodesorption in a 4.2-K beam tube, the moleculm density was measured by room temperature ion gauges and RGAs outside the beam tube. The molecular density inside the 4.2-K beam tube was therefore unknown, since the mean molecular speed of photodesorbed molecules had not been measured. To determine the density inside the 4.2-K beam tube we have developed a direct method of measurement utilizing the neutralization of H{sup +} beams, which are proportional to gas density. The hydrogen ion beams (up to 20 keV, {approximately}1 {mu}A) are extracted from an rf ion source and guided into the cold beam tube by a bending magnet. The H{sup 0} and H{sup {minus}} produced in the beam tube are magnetically separated from H{sup {minus}} and detected with secondary electron multipliers (SEMs). Small superconducting dipole magnets located near the center of the beam tube allow a {approximately}20-cm segment of the injected ion beam to be offset a few mm from the injection axis; detection of H{sup 0} and H{sup {minus}} produced along this offset segment provides a localized density measurement. If necessary, detector background due to synchrotron radiation photons can be discriminated against by gating the detector on between the bursts of synchrotron radiation. The experimental setup and initial data will be presented.

  5. An insight to conserved water molecular dynamics of catalytic and structural Zn(+2) ions in matrix metalloproteinase 13 of human.

    PubMed

    Chakrabarti, Bornali; Bairagya, Hridoy R; Mallik, Payel; Mukhopadhyay, Bishnu P; Bera, Asim K

    2011-02-01

    Matrix Metalloproteinase (MMP)--13 or Collagenase--3 plays a significant role in the formation and remodeling of bone, tumor invasion and causes osteoarthritis. Water molecular dynamic studies of the five (1XUC, 1XUD, 1XUR, 456C, 830C) PDB and solvated structures of MMP-13 in human have been carried out upto 5 ns on assigning the differential charges (+2, +1, +0.5 e) to both the Zinc ions. The MM and MD-studies have revealed the coordination of three water molecules (W(H), W(I) and W(S)) to Zn(c) and one water to Zn(s). The transition of geometry around the Znc from tetrahedral to octahedral via trigonal bipyramidal, and for Zn(s) from tetrahedral to trigonal bipyramidal are seem interesting. Recognition of two zinc ions through water molecular bridging (Zn(c) - W(H) (W(1))...W(2)....W(3)....H(187) Zn(s)) and the stabilization of variable coordination geometries around metal ions may indicate the possible involvement of Zn(c) ...Zn(s) coupled mechanism in the catalytic process. So the hydrophilic topology and stereochemistry of water mediated coupling between Zn-ions may provide some plausible hope towards the design of some bidentate/polydentate bridging ligands or inhibitors for MMP-13.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. Pairing preferences of the model mono-valence mono-atomic ions investigated by molecular simulation.

    PubMed

    Zhang, Qiang; Zhang, Ruiting; Zhao, Ying; Li, HuanHuan; Gao, Yi Qin; Zhuang, Wei

    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.

  12. ATOMIC AND MOLECULAR PHYSICS: Guided transmission of oxygen ions through Al2O3 nanocapillaries

    NASA Astrophysics Data System (ADS)

    Chen, Yi-Feng; Chen, Xi-Meng; Lou, Feng-Jun; Xu, Jin-Zhang; Shao, Jian-Xiong; Sun, Guang-Zhi; Wang, Jun; Xi, Fa-Yuan; Yin, Young-Zhi; Wang, Xing-An; Xu, Jun-Kui; Cui, Ying; Ding, Bao-Wei

    2009-07-01

    The transmissions of oxygen ions through Al2O3 nanocapillaries each 50 nm in diameter and 10 μm in length at a series of different tilt angles are measured, where the ions with energies ranging from 10 to 60 keV and charge states from 1 up to 6 are involved. The angular distribution and the transmission yields of transported ions are investigated. Our results indicate both the existence of a guiding effect when ions pass through the capillary and a significant dependence of the ion transmission on the energy and the charge state of the ions. The guiding effects are observed to be enhanced at lower projectile energies and higher charge states. Meanwhile, the results also exhibit that the transmission yields increase as the tilt angle decreases at a given energy and charge state.

  13. Molecular dynamics study of the foam stability of a mixed surfactant/water system with and without calcium ions.

    PubMed

    Yang, Wenhong; Yang, Xiaozhen

    2011-04-28

    The foam stability performance of a mixture surfactant system with and without calcium ions, including linear alkylbenzenesulfonate (LAS) and sodium dodecyl sulfate (SDS), has been studied by molecular dynamics. Microscopic interaction analysis reveals that the average binding number (ABN) indicates the population of interaction configurations at short distance (∼0.23 nm), ABN = 0.88 for the mixture system that is larger than that of SDS (0.08) and smaller than that of LAS (1.00). ABN of the mixture 0.88 in between is consistent with experimental observations; the performance of the mixture becomes worse than that of LAS and better than that of SDS on the foam stability influenced by calcium ions. In the present anionic system, the fraction of free calcium ions, X(f), in the film system was obtained. If X(f) is in the high calcium ion zone (X(f) > 0.5), the foam stability performance appears to be considerably impacted by calcium ions. In the present study, we validated the variable of tail mass out of water film, W, is an indicator of foam stability in a system without Ca(2+). LAS+SDS mixture system has lower W value than the LAS single system, corresponding to its experimental observation on more stable foam film. Results show that a maximum of W value occurs before reaching the critical thickness for each investigated system. This was probably due to structural transition of the surfactant film system.

  14. 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.

  15. Treatise on the Measurement of Molecular Masses with Ion Mobility Spectrometry

    PubMed Central

    Valentine, Stephen J.; Clemmer, David E.

    2009-01-01

    The ability to separate isotopes by high-resolution ion mobility spectrometry techniques is considered as a direct means for determining mass at ambient pressures. Calculations of peak shapes from the transport equation show that it should be possible to separate isotopes for low mass ions (<200) by utilizing heavy collision gasses and high resolution ion mobility analyzers. The mass accuracy associated with this isotopic separation approach based on ion mobility separation is considered. Finally, we predict several isotopes that should be separable. PMID:19548697

  16. Treatise on the measurement of molecular masses with ion mobility spectrometry.

    PubMed

    Valentine, Stephen J; Clemmer, David E

    2009-07-15

    The ability to separate isotopes by high-resolution ion mobility spectrometry techniques is considered as a direct means for determining mass at ambient pressures. Calculations of peak shapes from the transport equation show that it should be possible to separate isotopes for low-mass ions (<200) by utilizing heavy collision gases and high-resolution ion mobility analyzers. The mass accuracy associated with this isotopic separation approach based on ion mobility separation is considered. Finally, we predict several isotopes that should be separable.

  17. Infrared Photodiodes Made by Low Energy Ion Etching of Molecular Beam Epitaxy Grown Mercury-Cadmium Alloy

    NASA Astrophysics Data System (ADS)

    Yoo, Sung-Shik

    Ion etching was used to form junctions on the p-type (111)B Hg_{1-x}Cd_ {x}Te grown by Molecular Beam Epitaxy(MBE). When Hg_{1-x}Cd_{x}Te layers are etched by Ar ions at energies ranging between 300 and 450eV, the top Hg_{1 -x}Cd_{x}Te layer is converted to n-type. The converted region is electrically characterized as a defective n^+-region near the surface, and a low doped n^--region exist below the damaged region. The total thickness of the converted n-type layer was found to be considerable. These results suggest that the creation of the n-type layer is due to the filling of mercury vacancies by mercury atoms displaced by the Ar ion irradiation on the surface. For the performance of the resulting photodiodes on MBE grown (111)B Hg_{1-x}Cd _{x}Te using this technique, the dynamic resistances at 80K are one order of magnitude less than those of junctions made on Liquid Phase Epitaxially and Bulk grown Hg_{1 -x}Cd_{x}Te. The ion etching technique was compared with ion implantation technique by fabricating diodes on the same MBE grown (111)B Hg _{1-x}Cd_{x}Te layers. The result of the comparison illustrates that ion etching technique is as good as ion implantation technique for the fabrication of Hg_{1-x}Cd _{x}Te photodiodes. Also it is believed that the performance of the diodes is limited by a relatively large density of twin defects usually found in MBE grown (111)B Hg_{1-x}Cd _{x}Te.

  18. Emergent ion-gated binding of cationic host-guest complexes within cationic M12L24 molecular flasks.

    PubMed

    Bruns, Carson J; Fujita, Daishi; Hoshino, Manabu; Sato, Sota; Stoddart, J Fraser; Fujita, Makoto

    2014-08-27

    "Molecular flasks" are well-defined supramolecular cages that can encapsulate one or more molecular guests within their cavities and, in so doing, change the physical properties and reactivities of the guests. Although molecular flasks are powerful tools for manipulating matter on the nanoscale, most of them are limited in their scope because of size restrictions. Recently, however, increasingly large and diverse supramolecular cages have become available with enough space in their cavities for larger chemical systems such as polymers, nanoparticles, and biomolecules. Here we report how a class of metallosupramolecular cages known as M12L24 polyhedra have been adapted to serve as nanometer-scale containers for solutions of a pseudorotaxane host-guest complex based on a tetracationic cyclophane host, cyclobis(paraquat-p-phenylene) (CBPQT(4+)), and a 1,5-dioxynaphthalene (DNP) guest. Remarkably, the hierarchical integration of pseudorotaxanes and M12L24 superhosts causes the system to express stimulus-responsive behavior, a property which can be described as emergent because neither the DNP⊂CBPQT(4+) nor the M12L24 assemblies exhibit this behavior independently. The DNP-containing M12L24 molecular flasks are effectively "sealed off" to CBPQT(4+) until ions are added as a stimulus to "open" them. The electrolyte stimulus reduces the electrostatic screening distance in solution, allowing favorable DNP⊂CBPQT(4+) host-guest interactions to overcome repulsive Coulombic interactions between the cationic M12L24 cages and CBPQT(4+) rings. This unusual example of ion-gated transport into chemical nanocontainers is reminiscent of transmembrane ion channels which act as gates to the cell, with the important difference that this system is reversible and operates at equilibrium.

  19. 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

  20. 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

  1. 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

  2. What have we learnt about the mechanisms of rapid water transport, ion rejection and selectivity in nanopores from molecular simulation?

    PubMed

    Thomas, Michael; Corry, Ben; Hilder, Tamsyn A

    2014-04-24

    Nanopores have demonstrated an extraordinary ability to allow water molecules to pass through their interiors at rates far exceeding expectations based on continuum theory. Moreover, simulation studies suggest that particular nanoscale pores have the potential to discriminate between water and salts as well as to distinguish between a range of different ion types. Some of the unusual features of transport in these nanopores have been elucidated with molecular dynamics simulation, specifically the spontaneous filling and rapid transport of water, the rejection of ions and the selection between ions. The main focus of this review, however, is the physical mechanisms which act to produce such remarkable behaviour at this scale, drawing on the many studies that have been conducted in the last decade. Since molecular dynamics simulations allow the motion of individual atoms to be followed over time, they have the potential to provide fundamental insight into the reasons why transport in nanoscale pores differs from expectations based on macroscopic theory. Gaining an understanding of the mechanisms of transport in these tiny pores should guide future experiments in this area aimed at developing novel technologies and improving existing membrane separation techniques.

  3. Molecular diagnostics of the HBB gene in an Omani cohort using bench-top DNA Ion Torrent PGM technology.

    PubMed

    Hassan, S M; Vossen, R H A M; Chessa, R; den Dunnen, J T; Bakker, E; Giordano, P C; Harteveld, C L

    2014-09-01

    Hemoglobinopathies, such as sickle cell disease (SCD) and beta-thalassemia major (TM), are severe diseases and the most common autosomal recessive condition worldwide and in particular in Oman. Early screening and diagnosis of carriers are the key for primary prevention. Once a country-wide population screening program is mandated by law, a sequencing technology that can rapidly confirm or identify disease-causing mutations for a large number of patients in a short period of time will be necessary. While Sanger sequencing is the standard protocol for molecular diagnosis, next generation sequencing starts to become available to reference laboratories. Using the Ion Torrent PGM sequencer, we have analyzed a cohort of 297 unrelated Omani cases and reliably identified mutations in the beta-globin (HBB) gene. Our model study has shown that Ion Torrent PGM can rapidly sequence such a small gene in a large number of samples using a barcoded uni-directional or bi-directional sequence methodology, reducing cost, workload and providing accurate diagnosis. Based on our results we believe that the Ion Torrent PGM sequencing platform, able to analyze hundreds of patients simultaneously for a single disease gene can be a valid molecular screening alternative to ABI sequencing in the diagnosis of hemoglobinopathies and other genetic disorders in the near future.

  4. 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.

  5. 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.

  6. 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.

  7. Sub-10-fs control of dissociation pathways in the hydrogen molecular ion with a few-pulse attosecond pulse train.

    PubMed

    Nabekawa, Yasuo; Furukawa, Yusuke; Okino, Tomoya; Amani Eilanlou, A; Takahashi, Eiji J; Yamanouchi, Kaoru; Midorikawa, Katsumi

    2016-01-01

    The control of the electronic states of a hydrogen molecular ion by photoexcitation is considerably difficult because it requires multiple sub-10 fs light pulses in the extreme ultraviolet (XUV) wavelength region with a sufficiently high intensity. Here, we demonstrate the control of the dissociation pathway originating from the 2pσu electronic state against that originating from the 2pπu electronic state in a hydrogen molecular ion by using a pair of attosecond pulse trains in the XUV wavelength region with a train-envelope duration of ∼4 fs. The switching time from the peak to the valley in the oscillation caused by the vibrational wavepacket motion in the 1sσg ground electronic state is only 8 fs. This result can be classified as the fastest control, to the best of our knowledge, of a molecular reaction in the simplest molecule on the basis of the XUV-pump and XUV-probe scheme. PMID:27647423

  8. 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.

  9. 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.

  10. Single-crystal cubic boron nitride thin films grown by ion-beam-assisted molecular beam epitaxy

    SciTech Connect

    Hirama, Kazuyuki Taniyasu, Yoshitaka; Karimoto, Shin-ichi; Krockenberger, Yoshiharu; Yamamoto, Hideki

    2014-03-03

    We investigated the formation of cubic boron nitride (c-BN) thin films on diamond (001) and (111) substrates by ion-beam-assisted molecular beam epitaxy (MBE). The metastable c-BN (sp{sup 3}-bonded BN) phase can be epitaxially grown as a result of the interplay between competitive phase formation and selective etching. We show that a proper adjustment of acceleration voltage for N{sub 2}{sup +} and Ar{sup +} ions is a key to selectively discriminate non-sp{sup 3} BN phases. At low acceleration voltage values, the sp{sup 2}-bonded BN is dominantly formed, while at high acceleration voltages, etching dominates irrespective of the bonding characteristics of BN.

  11. Molecular dynamics-based ion-surface interaction models for ionized physical vapor deposition feature scale simulations

    SciTech Connect

    Coronell, D.G.; Hansen, D.E.; Voter, A.F.; Liu, C.; Liu, X.; Kress, J.D.

    1998-12-01

    A procedure is presented for incorporating the results of atomistic simulations of ion{endash}surface interactions into integrated circuit topographic simulations of ionized physical vapor deposition (PVD). Energy and angular dependent sticking probabilities for energetic Cu atoms impacting a {l_brace}111{r_brace} Cu surface, obtained from molecular dynamics simulations, were implemented in a simple Monte Carlo flux model. The resulting flux-averaged Cu sticking probability was found to vary significantly with position within submicron features and with the feature geometry. This illustrates the shortcomings of a constant (energy and angle independent) sticking probability model for ionized PVD. {copyright} {ital 1998 American Institute of Physics.}

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. Interaction of MeV ions and VUV photons with polymers and high molecular hydrocarbons

    NASA Astrophysics Data System (ADS)

    Mahfouz, R. M.; Sauer, M.; Atwa, S. T.; Kaiser, R. I.; Roessler, K.

    1992-03-01

    Organic solids such as polymethylene, polyethylene, polyoxymethylene, aliphatic and cyclic paraffins, naphthalene, anthracene and kerogen were irradiated at 77 K with 10-20 MeV cyclotron ions (p, 3He) and up to 10 eV photons. The products were analysed by quadrupole mass spectrometry (QMS). Fourier transform infrared spectroscopy (FT-IR), Raman spectroscopy and gas chromatography (GC). Besides radiolytic fragmentation, also synthesis of new and complex compounds was observed as a consequence of hot carbon chemistry. Vacuum ultraviolet (VUV) irradiation proved to be less effective in the buildup of new structures than MeV ions, due to its lower linear energy transfer.

  18. Brownian dynamics simulations of ions channels: A general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry

    NASA Astrophysics Data System (ADS)

    Im, Wonpil; Roux, Benoît

    2001-09-01

    A general method has been developed to include the electrostatic reaction field in Brownian dynamics (BD) simulations of ions diffusing through complex molecular channels of arbitrary geometry. Assuming that the solvent is represented as a featureless continuum dielectric medium, a multipolar basis-set expansion is developed to express the reaction field Green's function. A reaction field matrix, which provides the coupling between generalized multipoles, is calculated only once and stored before the BD simulations. The electrostatic energy and forces are calculated at each time step by updating the generalized multipole moments. The method is closely related to the generalized solvent boundary potential [Im et al., J. Chem. Phys. 114, 2924 (2001)] which was recently developed to include the influence of distant atoms on a small region part of a large macromolecular system in molecular dynamics simulations. It is shown that the basis-set expansion is accurate and computationally inexpensive for three simple models such as a spherical ionic system, an impermeable membrane system, and a cylindrical pore system as well as a realistic system such as OmpF porin with all atomic details. The influence of the static field and the reaction field on the ion distribution and conductance in the OmpF channel is studied and discussed.

  19. 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.

  20. Atomic/molecular depth profiling of nanometric-metallized polymer thin films by secondary ion mass spectrometry.

    PubMed

    Téllez, Helena; Vadillo, José Miguel; Laserna, José Javier

    2010-02-01

    The capability of secondary ion mass spectrometry (SIMS) to perform atomic and molecular in-depth analysis in complex nanometric-metallized thin polymer films used to manufacture capacitors is demonstrated through three different case studies related to failure analysis. The excellent repeatability and sensitivity of the technique allow us to study the degradation process of the nanometric-metallized layer in the capacitor films and the accurate location of the metal-polymer interface. The analysis of the sample is challenging due to the extreme difference in conductivity between layers, and the reduced thickness of the metallization grown on top of a rough polymeric base. However, SIMS has provided reliable and reproducible results with relative standard deviation (RSD) values better than 1.5% in the metallic layer thickness estimation. The detailed information of atomic and molecular ion in-depth distributions provided by SIMS depth profiling has allowed the identification of different factors (demetallization, generation of interstitial oxide regions, and diffusion processes or modification in the metallization thickness) that can be directly related to the origin of the lack of performance of the mounted devices.

  1. 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.

  2. Molecular basis of the interaction between gating modifier spider toxins and the voltage sensor of voltage-gated ion channels

    PubMed Central

    Lau, Carus H. Y.; King, Glenn F.; Mobli, Mehdi

    2016-01-01

    Voltage-sensor domains (VSDs) are modular transmembrane domains of voltage-gated ion channels that respond to changes in membrane potential by undergoing conformational changes that are coupled to gating of the ion-conducting pore. Most spider-venom peptides function as gating modifiers by binding to the VSDs of voltage-gated channels and trapping them in a closed or open state. To understand the molecular basis underlying this mode of action, we used nuclear magnetic resonance to delineate the atomic details of the interaction between the VSD of the voltage-gated potassium channel KvAP and the spider-venom peptide VSTx1. Our data reveal that the toxin interacts with residues in an aqueous cleft formed between the extracellular S1-S2 and S3-S4 loops of the VSD whilst maintaining lipid interactions in the gaps formed between the S1-S4 and S2-S3 helices. The resulting network of interactions increases the energetic barrier to the conformational changes required for channel gating, and we propose that this is the mechanism by which gating modifier toxins inhibit voltage-gated ion channels. PMID:27677715

  3. Molecular dynamics study of water and Na+ ions in models of the pore region of the nicotinic acetylcholine receptor.

    PubMed Central

    Smith, G R; Sansom, M S

    1997-01-01

    The nicotinic acetylcholine receptor (nAChR) is an integral membrane protein that forms ligand-gated and cation-selective channels. The central pore is lined by a bundle of five approximately parallel M2 helices, one from each subunit. Candidate model structures of the solvated pore region of a homopentameric (alpha7)5 nAChR channel in the open state, and in two possible forms of the closed state, have been studied using molecular dynamics simulations with restraining potentials. It is found that the mobility of the water is substantially lower within the pore than in bulk, and the water molecules become aligned with the M2 helix dipoles. Hydrogen-bonding patterns in the pore, especially around pore-lining charged and hydrophilic residues, and around exposed regions of the helix backbone, have been determined. Initial studies of systems containing both water and sodium ions together within the pore region have also been conducted. A sodium ion has been introduced into the solvated models at various points along the pore axis and its energy profile evaluated. It is found that the ion causes only a local perturbation of the water structure. The results of these calculations have been used to examine the effectiveness of the central ring of leucines as a component of a gate in the closed-channel model. Images FIGURE 1 PMID:9284304

  4. 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.

  5. 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

  6. 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.

  7. Role of Auger-type emission from diatomic molecular targets interacting with fast multicharged ions

    SciTech Connect

    Tachino, Carmen A.; Galassi, Mariel E.; Rivarola, Roberto D.

    2009-07-15

    Multiple electron emission in collisions between bare multiply charged ions and diatomic molecules is studied. The role played by Auger-type emission in cross sections for fixed number of ejected electrons is investigated. It is shown that this postcollisional reaction gives the main contribution to these cross sections at high enough impact velocities. This behavior is accentuated as the ionization degree increases.

  8. 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

  9. Cellular and molecular effects for mutation induction in normal human cells irradiated with accelerated neon ions.

    PubMed

    Suzuki, Masao; Tsuruoka, Chizuru; Kanai, Tatsuaki; Kato, Takeshi; Yatagai, Fumio; Watanabe, Masami

    2006-02-22

    We investigated the linear energy transfer (LET) dependence of mutation induction on the hypoxanthine-guanine phosphoribosyl transferase (HPRT) locus in normal human fibroblast-like cells irradiated with accelerated neon-ion beams. The cells were irradiated with neon-ion beams at various LETs ranging from 63 to 335 keV/microm. Neon-ion beams were accelerated by the Riken Ring Cyclotron at the Institute of Physical and Chemical Research in Japan. Mutation induction at the HPRT locus was detected to measure 6-thioguanine-resistant clones. The mutation spectrum of the deletion pattern of exons of mutants was analyzed using the multiplex polymerase chain reaction (PCR). The dose-response curves increased steeply up to 0.5 Gy and leveled off or decreased between 0.5 and 1.0 Gy, compared to the response to (137)Cs gamma-rays. The mutation frequency increased up to 105 keV/microm and then there was a downward trend with increasing LET values. The deletion pattern of exons was non-specific. About 75-100% of the mutants produced using LETs ranging from 63 to 335 keV/mum showed all or partial deletions of exons, while among gamma-ray-induced mutants 30% showed no deletions, 30% partial deletions and 40% complete deletions. These results suggested that the dose-response curves of neon-ion-induced mutations were dependent upon LET values, but the deletion pattern of DNA was not.

  10. Recombination and relaxation of molecular ions in size-selected clusters: Monte Carlo and molecular dynamics simulations of I - 2 (CO2)n

    NASA Astrophysics Data System (ADS)

    Papanikolas, John M.; Maslen, Paul E.; Parson, Robert

    1995-02-01

    The equilibrium structures and the recombination dynamics of I-2 molecular ions embedded in clusters of 3-17 CO2 molecules are studied by Monte Carlo and molecular dynamics simulations. The potential model incorporates, in a self-consistent manner, a description of the I-2 electronic structure that depends on both the I-2 bond length and the solvent degrees of freedom. The influence of the solvent upon the I-2 electronic structure is treated by means of a single effective solvent coordinate, in a manner reminiscent of the theory of electron transfer reactions. This causes the electronic charge to localize on a single I atom when the I-I bond is long or when the solvent cage has become highly asymmetric. The primary focus is the I-2 vibrational relaxation that follows recombination. Simulations of I-2(CO2)16 and I-2(CO2)9 yield vibrational relaxation times of less than 3 ps, even faster than the experimentally observed absorption recovery time of 10-40 ps. It is suggested that the latter time scale is determined by electronic as well as vibrational relaxation mechanisms.

  11. 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.

  12. 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

  13. High Resolution Laboratory Spectroscopy in Support of Herschel and SOFIA: From Small Molecular Ions to PAHs and Fullerenes

    NASA Astrophysics Data System (ADS)

    McCall, Benjamin

    The spectral lines of molecules serve as essential tools for astronomers, allowing them to probe the physical and chemical conditions of diverse environments, ranging from the diffuse interstellar medium to quiescent molecular clouds to star- and planet-forming regions to nebulae and circumstellar shells. This use of molecules as astronomical probes is only possible because of decades of work by laboratory spectroscopists, who have measured the frequencies of molecular spectral lines and determined the energy levels from which they originate. Ground-based astronomical spectroscopy has been mostly limited to frequencies below ~1 THz or above ~60 THz (below ~5 1/4m) due to the opacity of Earth s atmosphere, but new NASA missions (Herschel and SOFIA) are enabling high resolution spectroscopy in the no-man s land between 1-60 THz. However, comparatively little laboratory spectroscopy has been performed in this region, jeopardizing the scientific return from these missions. There is therefore a critical need to measure THz/far-IR spectral line frequencies of astrophysically important molecules. Two particularly important classes of such molecules are molecular ions and large neutral molecules. The objective of this particular proposal is to perform spectroscopy of astrophysically important molecular cations and large molecules with unprecedented precision and accuracy, to determine their transition frequencies in the THz/far-IR region. The rationale for the proposed research is that it will enable the study of these species with Herschel and SOFIA, thereby improving our understanding of interstellar clouds, star- forming regions, and other astronomical environments. The specific objectives of the proposed research is to measure high-precision infrared spectra of astrophysically important molecular cations, and determine their THz/far-IR frequencies to support Herschel and SOFIA. Using our newly discovered technique NICE-OHVMS (noise-immune cavity-enhanced optical

  14. Molecular effect on equilibrium charge-state distributions. [of nitrogen ions injected through carbon foil

    NASA Technical Reports Server (NTRS)

    Wickholm, D.; Bickel, W. S.

    1976-01-01

    The paper describes an experiment consisting of the acceleration of N(+) and N2(+) ions to energies between 0.25 and 1.75 MeV and their injection through a thin carbon foil, whereupon they were charge-state analyzed with an electrostatic analyzer. A foil-covered electrically suppressed Faraday cup, connected to a stepping motor, moved in the plane of the dispersed beams. The Faraday cup current, which was proportional to the number of incident ions, was sent to a current digitizer and computer programmed as a multiscaler. The energy-dependent charge-state fractions, the mean charge and the distribution width were calculated. It was shown that for incident atoms, the charge state distribution appeared to be spread over more charge states, while for the incident molecules, there was a greater fraction of charge states near the mean charge.

  15. 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

  16. Molecular dynamics simulations of electron-ion temperature equilibration in an SF6 plasma

    NASA Astrophysics Data System (ADS)

    Benedict, Lorin X.; Glosli, James N.; Richards, David F.; Streitz, Frederick H.; Hau-Riege, Stefan P.; Graziani, Frank R.; Murillo, Michael S.; Benage, John F.

    2009-03-01

    We use classical MD to investigate electron-ion temperature equilibration in a two- temperature SF6 plasma. We choose a density of 1.0x10^19 (dissociated) SF6 molecules per cm^3 and initial temperatures of Te˜100 eV and TS˜TF˜15 eV in accordance with experiments currently underway at Los Alamos National Laboratory. Our computed relaxation time is significantly longer than that predicted by the classic theory of Landau and Spitzer. Similar discrepancies are found when comparing to predictions made be more recent theories of electron-ion equilibration. These differences should be large enough to be measured in the upcoming experiments.

  17. 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.

  18. 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.

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

    USGS Publications Warehouse

    Evans, H.T.

    1966-01-01

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

  20. Electron elastic back-scattering from aligned CO_2^+ molecular ions in the 15-30 eV energy range

    NASA Astrophysics Data System (ADS)

    Cornaggia, C.

    2013-10-01

    Angular distributions of electrons elastically back-scattered from aligned CO_2^+ ions are extracted in the 15-30 eV energy range from electron spectra recorded in field-free-aligned CO2 molecules using a femtosecond pump-probe scheme. The angular distributions are found to exhibit a steeper increase as the scattering angle goes from 150° to 180° for molecular ions aligned with the incident electron momentum.

  1. 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.

  2. 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

  3. Functional layers for Zn(II) ion detection: from molecular design to optical fiber sensors.

    PubMed

    Liu, Zhihong; Tonnelé, Claire; Battagliarin, Glauco; Li, Chen; Gropeanu, Radu A; Weil, Tanja; Surin, Mathieu; Beljonne, David; Lazzaroni, Roberto; Debliquy, Marc; Renoirt, Jean-Michel; Müllen, Klaus

    2014-01-01

    We report on the synthesis of a novel perylene monoimide derivative that shows high response and selectivity for zinc ion detection. The complexation of Zn(2+) by the dye is followed by FD-MS, (1)H NMR, UV-vis spectroscopy, and isothermal titration calorimetry. Quantum chemical calculations are performed to gain further insight into the electronic processes responsible for the spectroscopic changes observed upon complexation. Finally, the perylene dye is incorporated in a sol-gel silica layer coated on optical fibers that are then used for Zn(2+) detection in aqueous solution.

  4. Ratiometric and near-infrared molecular probes for the detection and imaging of zinc ions.

    PubMed

    Carol, Priya; Sreejith, Sivaramapanicker; Ajayaghosh, Ayyappanpillai

    2007-03-01

    The detection and imaging of Zn2+ in biological samples are of paramount interest owing to the role of this cation in physiological functions. This is possible only with molecular probes that specifically bind to Zn2+ and result in changes in emission properties. A "turn-on" emission or shift in the emission color upon binding to Zn2+ should be ideal for in vivo imaging. In this context, ratiometric and near-IR probes are of particular interest. Therefore, in the area of chemosensors or molecular probes, the design of fluorophores that allow ratiometric sensing or imaging in the near-IR region is attracting the attention of chemists. The purpose of this Focus Review is to highlight recent developments in this area and stress the importance of further research for future applications.

  5. 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

  6. Electronic states and wavefunctions of diatomic donor molecular ions in silicon: multi-valley envelope function theory.

    PubMed

    Klymenko, M V; Remacle, F

    2014-02-12

    Using the Burt-Foreman envelope function theory and effective mass approximation, we develop a theoretical model for an arbitrary number of interacting donor atoms embedded in silicon which reproduces the electronic energy spectrum with high computational efficiency, taking into account the effective mass anisotropy and the valley-orbit coupling. We show that the variation of the relative magnitudes of the electronic coupling between the donor atoms with respect to the valley-orbit coupling as a function of the internuclear distance leads to different kinds of spatial interference patterns of the wavefunction. We also report on the impact of the orientation of the diatomic phosphorus donor molecular ion in the crystal lattice on the ionization energy and on the energy separation between the ground state and the lowest excited state. PMID:24451236

  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. 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.

  9. Is a pyrene-like molecular ion the cause of the 4,430-A diffuse interstellar absorption band?

    NASA Technical Reports Server (NTRS)

    Salama, F.; Allamandola, L. J.

    1992-01-01

    The diffuse interstellar band (DIB) absorption features of astronomical spectra are suggested by recent results to be separable from the grains that cause visual extinction. Attention is presently given to laboratory measurements of the optical spectrum of the pyrene cation C16H10(+), which is one of the polycyclic aromatic hydrocarbon (PAH) molecular candidates proposed as carriers for DIBs. This ion exhibits an intense but strangely broad continuum similar to that of the naphthalene cation, so that this may be a common feature of all PAH cations and the basis of an explanation for PAHs' converting of an interstellar radiation fraction as large as that from the UV and visible range down to the IR.

  10. Electron thermalization distances and free ion yields in dense gases and liquids: Effect of molecular dipole moment

    NASA Astrophysics Data System (ADS)

    Gee, Norman; Freeman, Gordon R.

    1989-11-01

    The effect of a molecular dipole moment on electron thermalization in X-irradiated fluids was examined by determining the effect of density on the density-normalized electron thermalization distance bGPd in dimethyl ether. Free ion yields were measured as a function of electric field strength at 0.06≤d/dc<2.7 (critical fluid density dc =271 kg m-3), and bGP values were obtained using an extended Onsager model. The permanent dipole increases the thermalizing ability of the fluid at all densities. However, the effect is smaller in the dense fluids and the transition from low-density gas behavior occurs at d/dc≊0.2.

  11. Ion Association in Hydrothermal Sodium Sulfate Solutions Studied by Modulated FT-IR-Raman Spectroscopy and Molecular Dynamics.

    PubMed

    Reimer, Joachim; Steele-MacInnis, Matthew; Wambach, Jörg M; Vogel, Frédéric

    2015-07-30

    Saline aqueous solutions at elevated pressures and temperatures play an important role in processes such as supercritical water oxidation (SCWO) and supercritical water gasification (SCWG), as well as in natural geochemical processes in Earth and planetary interiors. Some solutions exhibit a negative temperature coefficient of solubility at high temperatures, thereby leading to salt precipitation with increasing temperature. Using modulated FT-IR Raman spectroscopy and classical molecular dynamics simulations (MD), we studied the solute speciation in solutions of 10 wt % Na2SO4, at conditions close to the saturation limit. Our experiments reveal that ion pairing and cluster formation are favored as solid saturation is approached, and ionic clusters form prior to the precipitation of solid sulfate. The proportion of such clusters increases as the phase boundary is approached either by decreasing pressure or by increasing temperature in the vicinity of the three-phase (vapor-liquid-solid) curve.

  12. 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.

  13. Electronic states and wavefunctions of diatomic donor molecular ions in silicon: multi-valley envelope function theory.

    PubMed

    Klymenko, M V; Remacle, F

    2014-02-12

    Using the Burt-Foreman envelope function theory and effective mass approximation, we develop a theoretical model for an arbitrary number of interacting donor atoms embedded in silicon which reproduces the electronic energy spectrum with high computational efficiency, taking into account the effective mass anisotropy and the valley-orbit coupling. We show that the variation of the relative magnitudes of the electronic coupling between the donor atoms with respect to the valley-orbit coupling as a function of the internuclear distance leads to different kinds of spatial interference patterns of the wavefunction. We also report on the impact of the orientation of the diatomic phosphorus donor molecular ion in the crystal lattice on the ionization energy and on the energy separation between the ground state and the lowest excited state.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. Strategy to improve the quantitative LC-MS analysis of molecular ions resistant to gas-phase collision induced dissociation: application to disulfide-rich cyclic peptides.

    PubMed

    Ciccimaro, Eugene; Ranasinghe, Asoka; D'Arienzo, Celia; Xu, Carrie; Onorato, Joelle; Drexler, Dieter M; Josephs, Jonathan L; Poss, Michael; Olah, Timothy

    2014-12-01

    Due to observed collision induced dissociation (CID) fragmentation inefficiency, developing sensitive liquid chromatography tandem mass spectrometry (LC-MS/MS) assays for CID resistant compounds is especially challenging. As an alternative to traditional LC-MS/MS, we present here a methodology that preserves the intact analyte ion for quantification by selectively filtering ions while reducing chemical noise. Utilizing a quadrupole-Orbitrap MS, the target ion is selectively isolated while interfering matrix components undergo MS/MS fragmentation by CID, allowing noise-free detection of the analyte's surviving molecular ion. In this manner, CID affords additional selectivity during high resolution accurate mass analysis by elimination of isobaric interferences, a fundamentally different concept than the traditional approach of monitoring a target analyte's unique fragment following CID. This survivor-selected ion monitoring (survivor-SIM) approach has allowed sensitive and specific detection of disulfide-rich cyclic peptides extracted from plasma.

  19. Ion-selective electrodes based on molecular tweezer-type neutral carriers.

    PubMed

    Shim, Jun Ho; Jeong, In Seok; Lee, Min Hyung; Hong, Hun Pyo; On, Jeung Hoon; Kim, Ki Soo; Kim, Hong-Seok; Kim, Byeong Hyo; Cha, Geun Sig; Nam, Hakhyun

    2004-05-10

    Potentiometric properties of cholic and deoxycholic acid derivatives substituted with various ion-recognizing moieties, such as dithiocarbamate, bipyridyl, glycolic and malonic diamides, urea and thiourea, and trifluoroacetophenons (TFAP), have been studied using solvent polymeric membranes. The dithiocarbamate and bipyridyl group containing ionophores exhibit high silver ion selectivity. The cholic acid derivatized with glycolic diamides exhibited high calcium selectivity, but its complex formulation constant was 10(5) times smaller than that of ETH 1001. The reduced calcium binding ability of the glycolic diamide-substituted ionophore was advantageous for eliminating anionic interference. The bi- or tripodal malonic diamide-substituted ionophores exhibited substantially increased magnesium selectivity. Anion-selective ionophores have been designed by substituting urea and thiourea group containing chains to the hydroxyl linkers of chenodeoxycholic acid frames; their selectivity closely followed the sequence of Hoffmeister series, except the unusually large response of the thiourea-substituted ionophore to sulfate. The most successful examples of cholic or deoxycholic acid frame-based ionophores are those functionalized with two carbonate-selective TFAP groups: bipodal TFAP groups behaves like a tweezers for the incoming carbonate, and exhibit analytically interference free and quantitative responses to the carbonate in serum and seawater samples. PMID:18969404

  20. 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.

  1. 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

  2. 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.

  3. Antibiotic assisted molecular ion transport across a membrane in real time.

    PubMed

    Liu, Jian; Shang, Xiaoming; Pompano, Rebecca; Eisenthal, Kenneth B

    2005-01-01

    The transport of an organic cation across a 4-5 nm liposome bilayer is observed in real time using second harmonic generation. It is proposed that an electrostatic barrier between the inside and outside of the liposome develops as the cation crosses the bilayer. This would explain why the SHG signal does not approach zero at long times. To test this mechanism, the antibiotic valinomycin, which can transport alkali ions across a phospholipid bilayer, is introduced into the system. It is found that the transport time is reduced by a factor of three from 90+/-2 s to 30+/-1 s with 1.25 x 10(-8) M valinomycin concentration, and a factor of fifteen to 6.2+/-0.2 s with 1.25 x 10(-8) M valinomycin concentration. In addition, the SHG signal approaches zero, which further supports the presence of an electrostatic barrier that can be eliminated by the alkali ion transporter valinomycin.

  4. 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

  5. He 2++ molecular ion in a strong time-dependent magnetic field: a current-density functional study.

    PubMed

    Vikas

    2011-08-01

    The He 2++ molecular ion exposed to a strong ultrashort time-dependent (TD) magnetic field of the order of 10(9) G is investigated through a quantum fluid dynamics (QFD) and current-density functional theory (CDFT) based approach using vector exchange-correlation (XC) potential and energy density functional that depend not only on the electronic charge-density but also on the current density. The TD-QFD-CDFT computations are performed in a parallel internuclear-axis and magnetic field-axis configuration at the field-free equilibrium internuclear separation R = 1.3 au with the field-strength varying between 0 and 10(11) G. The TD behavior of the exchange- and correlation energy of the He 2++ is analyzed and compared with that obtained using a [B-TD-QFD-density functional theory (DFT)] approach based on the conventional TD-DFT under similar computational constraints but using only scalar XC potential and energy density functional dependent on the electronic charge-density alone. The CDFT based approach yields TD exchange- and correlation energy and TD electronic charge-density significantly different from that obtained using the conventional TD-DFT based approach, particularly, at typical magnetic field strengths and during a typical time period of the TD field. This peculiar behavior of the CDFT-based approach is traced to the TD current-density dependent vector XC potential, which can induce nonadiabatic effects causing retardation of the oscillating electronic charge density. Such dissipative electron dynamics of the He 2++ molecular ion is elucidated by treating electronic charge density as an electron-"fluid" in the terminology of QFD. PMID:21598275

  6. 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.

  7. New concepts in molecular and energy transport within carbon nanotubes: thermopower waves and stochastically resonant ion channels

    NASA Astrophysics Data System (ADS)

    Strano, Michael

    2012-02-01

    Our laboratory has been interested in how carbon nanotubes can be utilized to illustrate new concepts in molecular and energy transfer. In the first example, we predict and demonstrate the concept of thermopower waves for energy generation [1]. Coupling an exothermic chemical reaction with a thermally conductive CNT creates a self-propagating reactive wave driven along its length. We realize such waves in MWNT and show that they produce concomitant electrical pulses of high specific power >7 kW/kg. Such waves of high power density may find uses as unique energy sources. In the second system, we fabricate and study SWNT ion channels for the first time [2] and show that the longest, highest aspect ratio, and smallest diameter synthetic nanopore examined to date, a 500 μm SWNT, demonstrates oscillations in electro-osmotic current at specific ranges of electric field, that are the signatures of coherence resonance, yielding self-generated rhythmic and frequency locked transport. The observed oscillations in the current occur due to a coupling between stochastic pore blocking and a diffusion limitation that develops at the pore mouth during proton transport. [4pt] [1] Choi W, Hong S, Abrahamson JT, Han JH, Song C, Nair N, Baik S, Strano MS: Chemically driven carbon-nanotube-guided thermopower waves. NATURE MATERIALS, 9 (2010) 423-429.[0pt] [2] Lee, CY, Choi W, Han, JH, Strano MS: Coherence Resonance in a Single-Walled Carbon Nanotube Ion Channel. SCIENCE, 239

  8. 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.

  9. Ab initio molecular dynamics study of proton transfer in a polyglycine analog of the ion channel gramicidin A.

    PubMed Central

    Sagnella, D E; Laasonen, K; Klein, M L

    1996-01-01

    Proton transfer in biological systems is thought to often proceed through hydrogen-bonded chains of water molecules. The ion channel, gramicidin A (gA), houses within its helical structure just such a chain. Using the density functional theory based ab initio molecular dynamics Car-Parrinello method, the structure and dynamics of proton diffusion through a polyglycine analog of the gA ion channel has been investigated. In the channel, a proton, which is initially present as hydronium (H3O+), rapidly forms a strong hydrogen bond with a nearest neighbor water, yielding a transient H5O2+ complex. As in bulk water, strong hydrogen bonding of this complex to a second neighbor solvation shell is required for proton transfer to occur. Within gA, this second neighbor shell included not only a channel water molecule but also a carbonyl of the channel backbone. The present calculations suggest a transport mechanism in which a priori carbonyl solvation is a requirement for proton transfer. Images FIGURE 1 FIGURE 3 PMID:8873991

  10. Molecular-dynamics simulations of hillocks induced by highly-charged Arq+, Xeq+ ions impact on HOPG surface

    NASA Astrophysics Data System (ADS)

    Zhang, Zhengrong; Cheng, Xinlu; Li, Huifang; Song, Ting; Guo, Fen; Liu, Zijiang; Chen, Jianhong

    2015-11-01

    The hillocks on highly oriented pyrolytic graphite (HOPG) surface induced by highly charged Arq+, Xeq+ ions are studied by using molecular-dynamics (MD) simulations. And a hybrid potential created by combining the ReaxFF potential with the repulsive ZBL potential is used to describe the interatomic interactions. The effects of incident highly charged ion (HCI)'s kinetic energy and the energy gain due to the interaction of HCI with its own image on the formation of the hillocks are considered in the present simulations. Our results show that both potential and kinetic energy of HCI may affect the hillock size. However, the potential energy of HCI increases dramatically with charge state, which is more important than kinetic energy in the formation of the hillock in extremely high charge states. And it is found that both the height and width of the hillock agree well with experimental data. In addition, the bond breaking and bond formation during the formation of the hillock are also investigated, and the results show that there are many σ bonds breaking and interlayer bonds formation in one layer or between two layers during this process. Furthermore, most of the interlayer bonds in HOPG surface induced by HCI impact are sp2 bond, although some interlayer sp3 bonds are also observed in the present work.

  11. 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.

  12. Velocity correlation functions, Fickian and higher order diffusion coefficients for ions in electrostatic fields via molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Koutselos, Andreas D.

    1996-06-01

    The dynamic and transport properties of swarms of ions in a uniform electrostatic field are studied by using a molecular dynamics method. For a representative system, K+ in Ar, using a universal interaction model potential, second and third order ion-velocity correlation functions are determined at various field strengths. From them, Fickian diffusion coefficients parallel and perpendicular to the field, as well as higher order diffusion coefficients, Qzzz, are obtained within estimated overall accuracy 5% and 7%, respectively. Comparisons of the Fickian diffusion coefficients against results of the moment solution of Boltzmann kinetic equation and a Monte Carlo simulation method using the same interaction potential as well as against experimental data, reveal consistency among all calculation procedures and in addition agreement with drift tube measurements. These comparisons provide new tests for the accuracy of the employed interaction potential. The method has been applied for up to third order velocity correlations and diffusion coefficients but it is extendible to higher order dynamic and transport properties.

  13. Weathering trend characterization of medium-molecular weight polycyclic aromatic disulfur heterocycles by Fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Hegazi, Abdelrahman H; Fathalla, Eiman M; Andersson, Jan T

    2014-09-01

    Different weathering factors act to change petroleum composition once it is spilled into the environment. n-Alkanes, biomarkers, low-molecular weight polyaromatic hydrocarbons and sulfur heterocycles compositional changing in the environment have been extensively studied by different researchers and many parameters have been used for oil source identification and monitoring of weathering and biological degradation processes. In this work, we studied the fate of medium-molecular weight polycyclic aromatic disulfur heterocycles (PAS2Hs), up to ca. 900Da, of artificially weathered Flotta North Sea crude oil by ultra high-resolution Fourier transform ion cyclotron resonance mass spectrometry. It was found that PAS2Hs in studied crude oil having double bond equivalents (DBE) from 5 to 8 with a mass range from ca 316 to 582Da were less influenced even after six months artificial weathering experiment. However, compounds having DBEs 12, 11 and 10 were depleted after two, four and six months weathering, respectively. In addition, DBE 9 series was more susceptible to weathering than those of DBE 7 and 8.

  14. Development of AN External Cavity Quantum Cascade Laser Spectrometer for High-Resolution Spectroscopy of Molecular Ions

    NASA Astrophysics Data System (ADS)

    Stewart, Jacob T.; Gibson, Bradley M.; McCall, Benjamin J.

    2013-06-01

    Quantum cascade lasers (QCLs) have proven to be valuable tools for performing high-resolution infrared spectroscopy because of their high output powers and availability throughout the mid-infrared region of the electromagnetic spectrum. Despite their usefulness, typical QCLs can only be frequency tuned within a narrow window, requiring a specific laser to be used for measuring a specific molecular target. Recent advances in QCL technology have improved the tuning range of QCLs by creating lasers with broader gain profiles which can be used in an external cavity setup to produce widely-tunable, single-mode infrared radiation. In collaboration with the Wysocki research group at Princeton, we are developing a high-resolution infrared spectrometer based on an external cavity QCL (EC-QCL) system, which will allow us to perform spectroscopy from ˜1120 - 1250 cm^{-1}. We will present details of the development of the instrument, as well as preliminary spectroscopic results using the EC-QCL system. We will also outline future work we plan to perform with this spectrometer, particularly high-resolution spectroscopy of molecular ions.

  15. 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

  16. 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.

  17. 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

  18. 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...

  19. Ion association characteristics in MgCl2 and CaCl2 aqueous solutions: a density functional theory and molecular dynamics investigation

    NASA Astrophysics Data System (ADS)

    Dai, Qian; Xu, Jia-Jia; Li, Hui-Ji; Yi, Hai-Bo

    2015-11-01

    In this work, ion association characteristics in MgCl2 and CaCl2 aqueous solutions have been investigated using density functional theory (DFT) and molecular dynamics (MD) simulation at various temperatures and pressures. Results all indicate that the ion association is more obvious in MgCl2 solution than in CaCl2 solution, due to the hydration characteristics of Mg2+ and Ca2+. Although ion association can occur in concentrated MgCl2 solution, contact ion pair (CIP) structures and solvent-shared ion pair (SSIP) with single Cl- dissociated (SSIP/s) ([MgCl(H2O)6Cl]0) are quite unstable. CIP and SSIP/s conformers are almost iso-energetic even in CaCl2 solution, and the lifetime of CIP conformer is much longer than that of SSIP/s conformer in concentrated CaCl2 solution. However, the possibility of CIP conformer found in concentrated CaCl2 solution is obviously lower than its SSIP/s isomers. MD simulations exhibit that ion association characteristics do not change as pressure ranges from 0.5 to 20.0 bar in MgCl2 solution while ion association in CaCl2 solution does change as pressure rises. Moreover, ion association decreases with temperature increasing in MgCl2 solution, but the situation is reversed in CaCl2 solution.

  20. Interactions of lipids and detergents with a viral ion channel protein: molecular dynamics simulation studies.

    PubMed

    Rouse, Sarah L; Sansom, Mark S P

    2015-01-22

    Structural studies of membrane proteins have highlighted the likely influence of membrane mimetic environments (i.e., lipid bilayers versus detergent micelles) on the conformation and dynamics of small α-helical membrane proteins. We have used molecular dynamics simulations to compare the conformational dynamics of BM2 (a small α-helical protein from the membrane of influenza B) in a model phospholipid bilayer environment with its behavior in protein-detergent complexes with either the zwitterionic detergent dihexanoylphosphatidylcholine (DHPC) or the nonionic detergent dodecylmaltoside (DDM). We find that DDM more closely resembles the lipid bilayer in terms of its interaction with the protein, while the short-tailed DHPC molecule forms "nonphysiological" interactions with the protein termini. We find that the intrinsic micelle properties of each detergent are conserved upon formation of the protein-detergent complex. This implies that simulations of detergent micelles may be used to help select optimal conditions for experimental studies of membrane proteins.

  1. Improved Re-Crystallization of p+ Poly-Si Gates with Molecular Ion Implantation

    NASA Astrophysics Data System (ADS)

    Lee, Jin-Ku; Ju, Min-Ae; Oh, Jae-Geun; Hwang, Sun-Hwan; Jeon, Seung-Joon; Ku, Ja-Chun; Park, Sungki; Lee, Kyung-Won; Kim, Steve; Ra, Geum-Joo; Reece, Ron; Rubin, Leonard M.; Krull, W. A.; Cho, H. T.

    2008-11-01

    Implantation of B18H22 molecules at 80 keV and doses up to 4×1016 cm-2 were evaluated for the application of p-type counterdoping of in situ n-type doped polysilicon gates. Compared to conventional B implants, molecular implantation provides greatly improved throughput without the risk of energy contamination. Implants at these high doses resulted in poor re-crystallization of the polysilicon layer due to the formation of excessive cluster-type defects. Subjecting the polysilicon to either UV-curing or low temperature soak annealing prior to dopant activation was not effective in improving the re-crystallization process. However, breaking the dose into two portions at two different energies was shown to significantly improve re-crystallization of the polysilicon layer. Improved dopant activation was confirmed by a >90% reduction in ring oscillator delay time on a 60 nm PMOSFET.

  2. 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.

  3. 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

  4. 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.

  5. Collision cross sectional areas from analysis of Fourier transform ion cyclotron resonance line width: a new method for characterizing molecular structure.

    PubMed

    Yang, Fan; Voelkel, Jacob E; Dearden, David V

    2012-06-01

    We demonstrate a technique for determining molecular collision cross sections via measuring the variation of Fourier transform ion cyclotron resonance (FTICR) line width with background damping gas pressure, under conditions where the length of the FTICR transient is pressure limited. Key features of our method include monoisotopic isolation of ions, the pulsed introduction of damping gas to a constant pressure using a pulsed leak valve, short excitation events to minimize collisions during the excitation, and proper choice of damping gas (Xe is superior to He). The measurements are reproducible within a few percent, which is sufficient for distinguishing between many structural possibilities and is comparable to the uncertainty in cross sections calculated from computed molecular structures. These techniques complement drift ion mobility measurements obtained on dedicated instruments. They do not require a specialized instrument, but should be easily performed on any FTICR mass spectrometer equipped with a pulsed leak valve.

  6. Molecular and functional profiling of histamine receptor-mediated calcium ion signals in different cell lines.

    PubMed

    Meisenberg, Annika; Kaschuba, Dagmar; Balfanz, Sabine; Jordan, Nadine; Baumann, Arnd

    2015-10-01

    Calcium ions (Ca(2+)) play a pivotal role in cellular physiology. Often Ca(2+)-dependent processes are studied in commonly available cell lines. To induce Ca(2+) signals on demand, cells may need to be equipped with additional proteins. A prominent group of membrane proteins evoking Ca(2+) signals are G-protein coupled receptors (GPCRs). These proteins register external signals such as photons, odorants, and neurotransmitters and convey ligand recognition into cellular responses, one of which is Ca(2+) signaling. To avoid receptor cross-talk or cross-activation with introduced proteins, the repertoire of cell-endogenous receptors must be known. Here we examined the presence of histamine receptors in six cell lines frequently used as hosts to study cellular signaling processes. In a concentration-dependent manner, histamine caused a rise in intracellular Ca(2+) in HeLa, HEK 293, and COS-1 cells. The concentration for half-maximal activation (EC50) was in the low micromolar range. In individual cells, transient Ca(2+) signals and Ca(2+) oscillations were uncovered. The results show that (i) HeLa, HEK 293, and COS-1 cells express sufficient amounts of endogenous receptors to study cellular Ca(2+) signaling processes directly and (ii) these cell lines are suitable for calibrating Ca(2+) biosensors in situ based on histamine receptor evoked responses.

  7. Spatial correlation of confocal Raman scattering and secondary ion mass spectrometric molecular images of lignocellulosic materials.

    PubMed

    Li, Zhen; Chu, Li-Qiang; Sweedler, Jonathan V; Bohn, Paul W

    2010-04-01

    A detailed chemical and structural understanding of pre-enzymatic processing of lignocellulosic materials (LCMs) is a key objective in the development of renewable energy. Efficient rendering of biomass components into fermentable substrates for conversion into biofuel feedstocks would benefit greatly from the development of new technologies to provide high-quality, spatially resolved chemical information about LCMs during the various processing states. In an effort to realize this important goal, spatially correlated confocal Raman and mass spectrometric images allow the extraction of three-dimensional information from the perennial grass, Miscanthus x giganteus. An optical microscopy-based landmark registry scheme was developed that allows samples to be transferred between laboratories at different institutions, while retaining the capability to access the same physical regions of the samples. Subsequent to higher resolution imaging via confocal Raman microscopy and secondary ion mass spectrometry (SIMS), laser desorption-ionization mass spectrometry was used to place these regions within the overall sample architecture. Excellent sample registry was evident in the highly correlated Raman and SIMS images. In addition, the correlation of vibrational Raman scattering with mass spectra from specific spatial locations allowed confirmation of the assignment of intracellular globular structures to hemicellulose-rich lignin complexes, an assignment which could only be made tentatively from either image alone. PMID:20205411

  8. [MOLECULAR EVOLUTION OF ION CHANNELS: AMINO ACID SEQUENCES AND 3D STRUCTURES].

    PubMed

    Korkosh, V S; Zhorov, B S; Tikhonov, D B

    2016-01-01

    An integral part of modern evolutionary biology is comparative analysis of structure and function of macromolecules such as proteins. The first and critical step to understand evolution of homologous proteins is their amino acid sequence alignment. However, standard algorithms fop not provide unambiguous sequence alignments for proteins of poor homology. More reliable results can be obtained by comparing experimental 3D structures obtained at atomic resolution, for instance, with the aid of X-ray structural analysis. If such structures are lacking, homology modeling is used, which may take into account indirect experimental data on functional roles of individual amino-acid residues. An important problem is that the sequence alignment, which reflects genetic modifications, does not necessarily correspond to the functional homology. The latter depends on three-dimensional structures which are critical for natural selection. Since alignment techniques relying only on the analysis of primary structures carry no information on the functional properties of proteins, including 3D structures into consideration is very important. Here we consider several examples involving ion channels and demonstrate that alignment of their three-dimensional structures can significantly improve sequence alignments obtained by traditional methods.

  9. Structural characterization of saturated branched chain fatty acid methyl esters by collisional dissociation of molecular ions generated by electron ionization[S

    PubMed Central

    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

  10. Magnetic exchange between metal ions with unquenched orbital angular momenta: basic concepts and relevance to molecular magnetism

    NASA Astrophysics Data System (ADS)

    Palii, Andrei; Tsukerblat, Boris; Clemente-Juan, Juan Modesto; Coronado, Eugenio

    This review article is a first attempt to give a systematic and comprehensive description (in the framework of the unified theoretical approach) of the exchange interactions in polynuclear systems based on orbitally degenerate metal ions in the context of their relevance to the modern molecular magnetism. Interest in these systems is related to the fundamental problems of magnetism and at the same time steered by a number of impressive potential applications of molecular magnets, like high-density memory storage units, nanoscale qubits, spintronics and photoswitchable devices. In the presence of orbital degeneracy, the conventional spin Hamiltonian (Heisenberg-Dirac-van Vleck model) becomes inapplicable even as an approximation. The central component of this review article constitutes the concept of orbitally-dependent exchange interaction between metal ions possessing unquenched orbital angular momenta. We present a rigorous procedure of derivation of the kinetic exchange Hamiltonian for a pair of orbitally degenerate transition metal ions that is expressed in terms of the orbital matrices and spin operators. The microscopic background reveals the interrelations between the parameters of the Hamiltonian and the internal parameters of the system including all relevant transfer integrals and fundamental intracenter interactions. The developed formalism integrated with the irreducible tensor operator (ITO) technique makes it possible to describe the exchange coupling and all relevant interactions (crystal fields, spin-orbit (SO) and Zeeman couplings) in terms of the ITOs of the full spherical group, and in this way to develop anunified and efficient computational tool. The orbitally-dependent exchange was shown to lead to an anomalously strong magnetic anisotropy that can be considered as a main physical manifestation of the unquenched orbital angular momentum in metal clusters of orbitally-degenerate ions. The theoretical background is illustrated by the following

  11. Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies

    PubMed Central

    Bardhan, Jaydeep P.; Jungwirth, Pavel; Makowski, Lee

    2012-01-01

    Two mechanisms have been proposed to drive asymmetric solvent response to a solute charge: a static potential contribution similar to the liquid-vapor potential, and a steric contribution associated with a water molecule's structure and charge distribution. In this work, we use free-energy perturbation molecular-dynamics calculations in explicit water to show that these mechanisms act in complementary regimes; the large static potential (∼44 kJ/mol/e) dominates asymmetric response for deeply buried charges, and the steric contribution dominates for charges near the solute-solvent interface. Therefore, both mechanisms must be included in order to fully account for asymmetric solvation in general. Our calculations suggest that the steric contribution leads to a remarkable deviation from the popular “linear response” model in which the reaction potential changes linearly as a function of charge. In fact, the potential varies in a piecewise-linear fashion, i.e., with different proportionality constants depending on the sign of the charge. This discrepancy is significant even when the charge is completely buried, and holds for solutes larger than single atoms. Together, these mechanisms suggest that implicit-solvent models can be improved using a combination of affine response (an offset due to the static potential) and piecewise-linear response (due to the steric contribution). PMID:23020318

  12. 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.

  13. Detection and Quantitation of Heavy Metal Ions on Bona Fide DVDs Using DNA Molecular Beacon Probes.

    PubMed

    Zhang, Lingling; Wong, Jessica X H; Li, Xiaochun; Li, Yunchao; Yu, Hua-Zhong

    2015-01-01

    A sensitive and cost-effective method for the simultaneous quantitation of trace amounts of Hg(2+) and Pb(2+) in real-world samples has been developed using DNA molecular beacon probes bound to bona fide digital video discs (DVDs). With specially designed T-rich or G-rich loop sequences, the detection is based on the strong T-Hg(2+)-T coordination chemistry of Hg(2+) and the formation of G-quadruplexes induced by Pb(2+), respectively. In particular, the presence of metal cations leads to hairpin opening and exposure of the terminal biotin moiety for binding nanogold-streptavidin conjugates. The recognition signal was subsequently enhanced by gold nanoparticle-promoted silver deposition, which leads to quantifiable digital signals upon reading with a standard computer drive. This method exhibits a wide response range and low detection limits for both Hg(2+) and Pb(2+). In addition, the quantitative determination of heavy metals in food products (e.g., rice samples) has been demonstrated and the method compares favorably with other optical sensors developed recently.

  14. Analytical Formulae of Molecular Ion Abundances and the N2H+ Ring in Protoplanetary Disks

    NASA Astrophysics Data System (ADS)

    Aikawa, Yuri; Furuya, Kenji; Nomura, Hideko; Qi, Chunhua

    2015-07-01

    We investigate the chemistry of ion molecules in protoplanetary disks, motivated by the detection of the N2H+ ring around TW Hya. While the ring inner radius coincides with the CO snow line, it is not apparent why N2H+ is abundant outside the CO snow line in spite of the similar sublimation temperatures of CO and N2. Using the full gas-grain network model, we reproduced the N2H+ ring in a disk model with millimeter grains. The chemical conversion of CO and N2 to less volatile species (sink effect hereinafter) is found to affect the N2H+ distribution. Since the efficiency of the sink depends on various parameters such as activation barriers of grain-surface reactions, which are not well constrained, we also constructed the no-sink model; the total (gas and ice) CO and N2 abundances are set constant, and their gaseous abundances are given by the balance between adsorption and desorption. Abundances of molecular ions in the no-sink model are calculated by analytical formulae, which are derived by analyzing the full-network model. The N2H+ ring is reproduced by the no-sink model, as well. The 2D (R-Z) distribution of N2H+, however, is different among the full-network model and no-sink model. The column density of N2H+ in the no-sink model depends sensitively on the desorption rate of CO and N2 and the cosmic-ray flux. We also found that N2H+ abundance can peak at the temperature slightly below the CO sublimation, even if the desorption energies of CO and N2 are the same.

  15. Fragment profiling of low molecular weight heparins using reversed phase ion pair liquid chromatography-electrospray mass spectrometry.

    PubMed

    Xu, Xiaohui; Li, Daoyuan; Chi, Lequan; Du, Xuzhao; Bai, Xue; Chi, Lianli

    2015-04-30

    Low molecular weight heparins (LMWHs) are linear and highly charged carbohydrate polymers prepared by chemical or enzymatic depolymerization of heparin. Compared to unfractionated heparin (UFH), LMWHs are prevalently used as clinical anticoagulant drugs due to their lower side effects and better bioavailability. The work presented herein provides a rapid and powerful fragment mapping method for structural characterization of LMWHs. The chain fragments of two types of LMWHs, enoxaparin and nadroparin, were generated by controlled enzymatic digestion with each of heparinase I (Hep I, Enzyme Commission (EC) # 4.2.2.7), heparinase II (Hep II, no EC # assigned) and heparinase III (Hep III, EC # 4.2.2.8). Reversed phase ion pair high performance liquid chromatography (RPIP-HPLC) coupled with electrospray ion trap time-of-flight mass spectrometry (ESI-IT-TOF-MS) was used to profile the oligosaccharide chains ranging from disaccharides to decasaccharides. A database containing all theoretical structural compositions was established to assist the mass spectra interpretation. The six digests derived by three enzymes from two types of LMWHs exhibited distinguishable fingerprinting patterns. And a total of 94 enoxaparin fragments and 109 nadroparin fragments were detected and identified. Besides the common LMWH oligosaccharides, many components containing characteristic LMWH structures such as saturated L-idopyranosuronic acid, 2,5-anhydro-D-mannitol, 1,6-anhydro-D-aminopyranose, as well as odd number oligosaccharides were also revealed. Quantitative comparison of major components derived from innovator and generic nadroparin products was presented. This approach to profile LMWHs' fragments offers a highly reproducible, high resolution and information-rich tool for evaluating the quality of this category of anticoagulant drugs or comparing structural similarities among samples from various sources.

  16. 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

  17. 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

  18. 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

  19. Phycodnavirus Potassium Ion Channel Proteins Question the Virus Molecular Piracy Hypothesis

    PubMed Central

    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

  20. [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