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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 spectroscopy of jet-cooled HCP+: molecular structure, phosphorus hyperfine structure, and Renner-Teller analysis.

    PubMed

    Sunahori, Fumie X; Zhang, Xiaopeng; Clouthier, Dennis J

    2007-09-14

    Laser-induced fluorescence spectra of jet-cooled HCP(+) and DCP(+) have been obtained with the pulsed discharge technique using HCPDCP and argon precursor mixtures. Transitions involving all of the excited state vibrations have been observed and a set of vibrational constants has been obtained. High-resolution spectra of the (2)Pi(32) components of the 0(0) (0) bands of both isotopomers have been recorded, and these spectra show resolved phosphorus hyperfine structure which allowed the determination of the excited state Fermi contact parameter. The B values were used to obtain the ground and excited state effective geometric parameters as r(0) (")(CH)=1.077(2) A, r(0) (")(CP)=1.6013(3) A, r(0) (')(CH)=1.082(2) A, and r(0) (')(CP)=1.5331(3) A. A Renner-Teller analysis of the ground state vibrational energy levels obtained from the literature was attempted. All of the observed levels of DCP(+) and the majority of those of HCP(+) were satisfactorily fitted with a standard Renner-Teller model, but three HCP(+) levels showed large systematic deviations which could not be accommodated by reassignments or improvements in the Fermi resonance Hamiltonian. Further improvements in the theory or in the experimental data will be needed to resolve this discrepancy.

  3. Competition between inter- and intra-molecular hydrogen bonding: An infrared spectroscopic study of jet-cooled amino-ethanol and its dimer

    NASA Astrophysics Data System (ADS)

    Asselin, Pierre; Madebène, Bruno; Soulard, Pascale; Georges, Robert; Goubet, Manuel; Huet, Thérèse R.; Pirali, Olivier; Zehnacker-Rentien, Anne

    2016-12-01

    The Fourier transform IR vibrational spectra of amino-ethanol (AE) and its dimer have been recorded at room temperature and under jet-cooled conditions over the far and mid infrared ranges (50-4000 cm-1) using the White-type cell and the supersonic jet of the Jet-AILES apparatus at the synchrotron facility SOLEIL. Assignment of the monomer experimental frequencies has been derived from anharmonic frequencies calculated at a hybrid CCSD(T)-F12/MP2 level. Various thermodynamical effects in the supersonic expansion conditions including molar dilution of AE and nature of carrier gas have been used to promote or not the formation of dimers. Four vibrational modes of the observed dimer have been unambiguously assigned using mode-specific scaling factors deduced from the ratio between experimental and computed frequencies for the monomer. The most stable g'Gg' monomer undergoes strong deformation upon dimerization, leading to a homochiral head to head dimer involving two strong hydrogen bonds.

  4. Spectroscopy of jet-cooled tyrosine derivatives

    NASA Astrophysics Data System (ADS)

    Teh, Chin Khuan; Sulkes, Mark

    1991-05-01

    Using fluorescence-based techniques (excitation and emission spectra lifetimes), we have studied the jet-cooled tyrosine derivatives tyramine and 3-(4-hydroxyphenyl) propionic acid (HPA). For solvent addition resulting in small, mainly one adduct complexes, there is a high degree of analogy with the results for the corresponding analogs of the amino acid tryptophan. In particular, for tyramine, as had been the case with its tryptophan analog tryptamine, addition of one -OH bearing solvent molecule at the α-amine apparently results in a complex in a single conformation.

  5. Thermal Management Using Pulsating Jet Cooling Technology

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

  6. 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).

  7. 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.

  8. Simulation of jet cooling effects on Czochralski crystal growth

    NASA Technical Reports Server (NTRS)

    Srivastava, R. K.; Ramachandran, P. A.; Dudukovic, M. P.

    1986-01-01

    The effects of cooling the crystal side surface by blowing a jet of an inert gas are examined in detail for Czochralski crystal growth. A combined model of the crystal + melt, which incorporates the detailed radiation calculations, the shape of the melt-gas meniscus, predicts the growth rate and the crystal-melt interface shape, is used for this study. The convective heat transfer coefficient for the jet is estimated from the correlation available in the literature. The effect of the jet cooling on the interface shape and the pulling rate is significant. The crystal diameter as well as the interface shape tend to be more stable in the environment of the rapid cooling of the crystal by the jet. The crystal diameter or the interface shape can be easily controlled by adjusting the gas flow rate through the jet. This gives the Czochralski pulling an additional degree of freedom facilitating the control of crystal diameter and interface shape.

  9. 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.

  10. 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.

  11. Electronic spectra of jet-cooled isoindoline: Spectroscopic determination of energy difference between conformational isomers

    NASA Astrophysics Data System (ADS)

    Tanaka, Sei'ichi; Okuyama, Katsuhiko

    2010-04-01

    The electronic spectra of jet-cooled isoindoline between the electronic ground (S0) state and the ππ ∗ lowest-excited singlet state (S1) were observed by the fluorescence excitation and single-vibronic-level dispersed fluorescence methods. The low-frequency progression due to the puckering vibration appeared in both spectra. Analysis of dispersed spectra together with geometry optimization at the level of B3LYP/6-311+G(d) indicated the presence of conformational isomers possessing axial and equatorial N-H bonds with respect to the molecular plane. The 0-0 bands of the axial and equatorial conformers were measured at 37 022 and 36 761 cm-1, respectively. Three common levels in the S1 state accessible from the respective S0-state zero levels were observed. From their transition frequencies, the S0-state energy difference between the isomers was determined to be 47.7±0.2 cm-1, where the axial conformer was more stable. In the S1 state, the energy difference was 213.7±0.2 cm-1, and the equatorial conformer was more stable. The cause of switching from a stable conformation upon excitation is discussed in terms of the electron conjugation between the π∗ orbital in benzene and the lone pair orbital of nitrogen.

  12. Laser Induced Fluorescence Spectroscopy of Jet-Cooled CaOCa

    NASA Astrophysics Data System (ADS)

    Sullivan, Michael N.; Frohman, Daniel J.; Heaven, Michael; Fawzy, Wafaa M.

    2016-06-01

    The group IIA metals have stable hypermetallic oxides of the general form MOM. Theoretical interest in these species is associated with the multi-reference character of the ground states. It is now established that the ground states can be formally assigned to the M+O^{2-M+} configuration, which leaves two electrons in orbitals that are primarily metal-centered ns orbitals. Hence the MOM species are diradicals with very small energy spacings between the lowest energy singlet and triplet states. Previously, we have characterized the lowest energy singlet transition (1Σ^{+u← X1Σ+g}) of BeOBe. In this study we obtained the first electronic spectrum of CaOCa. Jet-cooled laser induced fluorescence spectra were recorded for multiple bands that occured within the 14,800 - 15,900 cm-1 region. Most of the bands exhibited simple P/R branch rotational line patterns that were blue-shaded. Only even rotational levels were observed, consistent with the expected X 1Σ^{+g} symmetry of the ground state (40Ca has zero nuclear spin). A progression of excited bending modes was evident in the spectrum, indicating that the transition is to an upper state that has a bent equilibrium geometry. Molecular constants were extracted from the rovibronic bands using PGOPHER. The experimental results and interpretation of the spectrum, which was guided by the predictions of electronic structure calculation, will be presented.

  13. 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/

  14. Jet-Cooled Broad Range Near-Ir Scan of Reactive Intermediates Using Cavity Ringdown Spectroscopy

    NASA Astrophysics Data System (ADS)

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

    2012-06-01

    A technique has been developed for obtaining broad range scans of jet-cooled radicals using cavity ringdown spectroscopy. The talk will describe a method that uses a slit jet expansion in tandem with an electrical discharge to produce the reactive intermediates and obtain rotational temperatures of 15-30 K and effective vibrational temperatures of 0 K. The spectrum can be recorded by scanning the second stokes of an H_2 Raman shifted YAG-pumped dye laser with bandwidth of ≈ 0.1 cm-1. This technique has been used to obtain the jet-cooled widetilde{A} - widetilde{X} spectra of the NO_3 radical and the 2,1-hydroxypropyl peroxy radical (2,1-HPP). Obtaining the jet-cooled spectra helped to identify hot bands present in the room temperature spectrum of NO_3 and also helped to identify cold, low-frequency fundamental bands present in the 2,1-HPP spectrum.

  15. Surface modification by molecular ions

    SciTech Connect

    Hanley, L.; Schultz, D. G.; Ada, E. T.

    1999-06-10

    There are several advantages in using molecular ions for surface modification. The modification can be confined to the uppermost layer of the surface, the molecular character of the ion can be imparted to the surface, and sputter yields are often higher. These effects are demonstrated by the use of mass selected ion beams incident on well characterized surfaces. Energy transfer is examined by detecting the masses and energies of ions scattered off surfaces and performing molecular dynamics simulations. Surface modification is followed by chemical analysis with x-ray photoelectron spectroscopy and surface mass spectrometry. TRIDYN monte carlo simulations are used to support some of the modification experiments. Energy transfer is examined for Si(CD{sub 3}){sub 3}{sup +} scattered off clean and hexanethiolate covered Au(111). Adsorbate desorption cross sections and substrate damage depths for NH{sub 3}/CO/Ni(111) are compared for 10-1000 eV isobaric atomic and polyatomic ions, Xe{sup +} and SF{sub 5}{sup +}. The surface chemical modification of polystyrene thin films by 10-100 eV SF{sub 5}{sup +} and C{sub 3}F{sub 5}{sup +} ions is also examined.

  16. 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)

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  18. Molecular 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.

  19. Spectroscopic evidence of jet-cooled o-chloro-alpha-methylbenzyl radical in corona excitation.

    PubMed

    Ahn, Hyeon Geun; Lee, Gi Woo; Lee, Sang Kuk

    2008-12-25

    We report the first spectroscopic evidence of the o-chloro-alpha-methylbenzyl radical. The electronically hot but jet-cooled o-chloro-alpha-methylbenzyl radical was formed from precursor o-chloro-ethylbenzene seeded in a large amount of inert carrier gas helium, by employing the technique of corona excited supersonic expansion with a pinhole-type glass nozzle. The vibronic emission spectrum was recorded with a long path monochromator in the D(1) --> D(0) electronic transition in the visible region. By comparing the observed spectrum with that of the o-chlorobenzyl radical reported previously, we could easily identify the spectroscopic evidence of the jet-cooled o-chloro-alpha-methylbenzyl radical generated in the corona discharge of o-chloro-ethylbenzene, from which the electronic transition energy and several vibrational mode frequencies in the ground electronic state were accurately determined.

  20. Spectroscopic evidence of jet-cooled p-methyl-α-methylbenzyl radical

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

    We report spectroscopic evidence of the jet-cooled p-methyl-α-methylbenzyl radical in corona discharge. The visible vibronic emission spectra were recorded from the corona discharge of three precursors, p-xylene, p-ethyltoluene, and p-isopropyltoluene seeded in a large amount of carrier gas helium using a pinhole-type glass nozzle. From the analysis of the vibronic spectra observed from each precursor and the bond dissociation energies of precursor molecules, we are able to confirm the formation of the jet-cooled p-methyl-α-methylbenzyl radical in corona discharge, and determine the energy of the D1 → D0 transition and a few vibrational mode frequencies in the D0 state.

  1. High resolution infrared spectroscopy of slit-jet cooled transient molecules: From van der Waals clusters, to hydrogen bound dimers, to small organic radicals

    NASA Astrophysics Data System (ADS)

    Davis, Scott Robert

    2000-10-01

    This dissertation describes high resolution (<0.0005 cm-1 ), high sensitivity (absorbance sensitivity ~2 × 10 -6 per root Hz), direct absorption, infrared laser spectroscopy of transient molecules formed in a slit supersonic expansion. A series of molecular species, ranging from weakly bound van der Waals clusters, through hydrogen bound dimers, to a group of small organic free radicals are investigated. The advantages provided by the combination of a high optical resolution and the rotational and translational cooling of a slit supersonic expansion are exploited to probe an array of spectroscopic and dynamic phenomena. Investigations which probe the v = 1 <-- 0 vibrational transition for the hydrogen halides DF and HCl sequentially clustered with one through three Ar atoms are presented. Vibrational redshifts and rotational constants are compared with theoretical calculations on accurate pairwise additive potentials, providing insight into the importance of many body terms. Near-ir spectroscopic investigations of the hydrogen bond prototype (HF) 2 and it isotopomer (DF)2 are also presented. For both isotopomers, all four, large amplitude intermolecular vibrations are observed as combination bands built on top of intramolecular excitation. In addition to vibrational energies, mode specific vibrational predissociation rates, interconversion tunneling rates, and rotational constants are reported. Comparison with full 6-D quantum calculations provide an unprecedented test of trial hydrogen bonding potential energy surfaces. A novel high-intensity source of jet-cooled molecular radicals and ions is also described based on the combination of (i)slit supersonic expansions with (ii)electric discharges. Confinement of the discharge to a region just prior to supersonic expansion results in efficient rotational cooling of molecular radicals. Infrared studies of methyl, ethyl, allyl, and cyclopropyl are presented. Resolution of fine and hyperfine structure provides

  2. 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.

  3. Spectroscopic identification of dichlorobenzyl radicals: Jet-cooled 2,3-dichlorobenzyl radical

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

    The vibronically excited but jet-cooled 2,3-dichlorobenzyl radical was generated from the corona discharge of precursor 2,3-dichlorotoluene seeded in a large amount of carrier gas He using a pinhole-type glass nozzle. From an analysis of the visible vibronic emission spectrum observed, we obtained the electronic energy of the D1 → D0 transition and vibrational mode frequencies in the D0 state of the 2,3-dichlorobenzyl radical by comparing the observation with the results of ab initio calculations. In addition, we discussed substituent effect of Cls on electronic transition energy in terms of substituent orientation for the first time.

  4. Peltier Refrigerators for Molecular Ion Sources

    NASA Astrophysics Data System (ADS)

    Hershcovitch, Ady

    2008-11-01

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

  5. 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

  6. 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.

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

    SciTech Connect

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

    2016-02-15

    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 (C{sub 4}H{sub 12}B{sub 10}O{sub 4}) 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 4PH{sub 3} = P{sub 4} + 6H{sub 2}; generated molecular phosphorous in a pure gaseous process was then injected into the HCEI Calutron-Bernas ion source, from which P{sub 4}{sup +} ion beams were extracted. Results from devices and some additional concepts are described.

  8. Understanding Molecular Ion-Neutral Atom Collisions for the Production of Ultracold Molecular Ions

    DTIC Science & Technology

    2016-06-06

    molecular ions has emerged as a new discipline within AMO to bring molecules under control. It is now clear that a trapped sample of ultracold molecular...Angeles Office of Contract and Grant Administration 11000 Kinross Avenue, Suite 211 Los Angeles, CA 90095 -1406 ABSTRACT Final Report: Understanding...ions has emerged as a new discipline within AMO to bring molecules under control. It is now clear that a trapped sample of ultracold molecular ions

  9. 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.

  10. 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.

  11. Vibronic spectrum of jet-cooled 2-chloro-5-fluorobenzyl radical: Assignments and substituent effect

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

    We report spectroscopic constants of the jet-cooled 2-chloro-5-fluorobenzyl radical which was generated by corona discharge of precursor 2-chloro-5-fluorotoluene seeded in a large amount of helium carrier gas using a pinhole-type glass nozzle. The visible vibronic emission spectrum was recorded with a long-path monochromator. From an analysis of the spectrum observed, the electronic energy of the D1 → D0 transition and vibrational mode frequencies in the D0 state were determined for the first time by comparing its vibronic data with those of a precursor and ab initio calculation. In addition, the substituent effect on electronic transition energy has been discussed.

  12. Vibronic emission spectroscopy of benzyl-type radicals: Jet-cooled 2-fluoro-5-chlorobenzyl radical

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

    We produced the vibronically excited but jet-cooled 2-fluoro-5-chlorobenzyl radical by corona discharge of precursor 2-fluoro-5-chlorotoluene with a large amount of carrier gas He using a pinhole-type glass nozzle in a technique of corona excited supersonic jet expansion. The vibronic emission spectrum was recorded using a long-path double monochromator in the visible region. From an analysis of the spectrum, we determined the electronic energy of the D1 → D0 transition and vibrational mode frequencies in the ground electronic state of the 2-fluoro-5-chlorobenzyl radical for the first time. In addition, substituent effect on electronic transition energy was discussed for substituents on the benzene ring.

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

  14. Jet-cooled infrared absorption spectrum of the v4 fundamental band of HCOOH and HCOOD

    NASA Astrophysics Data System (ADS)

    Luo, Wei; Zhang, Yulan; Li, Wenguang; Duan, Chuanxi

    2017-04-01

    The jet-cooled absorption spectrum of the v4 fundamental band of normal formic acid (HCOOH) and deuterated formic acid (HCOOD) was recorded in the frequency range of 1370-1392 cm-1 with distributed-feedback quantum cascade lasers (DFB-QCLs) as the tunable infrared radiations. A segmented rapid-scan data acquisition scheme was developed for pulsed supersonic jet infrared laser absorption spectroscopy based on DFB-QCLs with a moderate vacuum pumping capacity. The unperturbed band-origin and rotational constants in the excited vibrational state were determined for both HCOOH and HCOOD. The unperturbed band-origin locates at 1379.05447(11) cm-1 for HCOOH, and 1366.48430(39) cm-1 for HCOOD, respectively.

  15. 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.

  16. Mean excitation energies for molecular ions

    NASA Astrophysics Data System (ADS)

    Jensen, Phillip W. K.; Sauer, Stephan P. A.; Oddershede, Jens; Sabin, John R.

    2017-03-01

    The essential material constant that determines the bulk of the stopping power of high energy projectiles, the mean excitation energy, is calculated for a range of smaller molecular ions using the RPA method. It is demonstrated that the mean excitation energy of both molecules and atoms increase with ionic charge. However, while the mean excitation energies of atoms also increase with atomic number, the opposite is the case for mean excitation energies for molecules and molecular ions. The origin of these effects is explained by considering the spectral representation of the excited state contributing to the mean excitation energy.

  17. High Resolution Infrared Spectroscopy of Slit-Jet Cooled Radicals and Ions

    NASA Astrophysics Data System (ADS)

    Roberts, Melanie A.

    This thesis presents high-resolution spectra of supersonically-cooled organic radicals in the mid-infrared, the details and design of the instruments necessary to obtain the spectra, and the theory to understand the spectra and the larger context of the results. Specifically, four organic radicals are studied: singly-deuterated methyl radical (CH2D), phenyl radical (C6H5), hydroxymethyl radical (CH2OH), and ethynyl radical (C2H). All of the spectroscopic studies presented use an existing mid-infrared high-resolution spectrometer with a frequency precision of better than 10 MHz. The radicals are generated using a discharge to dissociate a neutral precursor and form the radicals. The discharge is localized at the orifice of a slit supersonic expansion, which cools the radicals to around 20 K and allows for sub-Doppler spectral resolution. In addition to the description of the existing spectrometer, the design, construction, and successful testing of a new, automated mid-infrared spectrometer is presented. The new spectrometer is based upon difference frequency generation of a scanning Ti:Sapphire laser and a single-frequency Nd:YAG laser to create high-resolution mid-infrared radiation. The new system speeds up data-taking by fully automating the scanning process. The four radicals studied in this thesis are all intermediates in combustion processes of hydrocarbon fuels. First, the out-of-phase symmetric stretch of phenyl radical is presented. As the first high-resolution infrared study of phenyl, it paves the way for future studies of this and other aromatic radicals. Second, the two fundamental CH stretches in CH2D are studied with full rotational resolution. The narrow linewidth of the transitions reveals resolved fine structure and partially resolved hyperfine structure. This resolution yields additional information regarding the distribution of electrons in the radical. With this study of CH2D, a nearly complete set of vibrational frequencies is present in the literature. This inspired us to develop a comprehensive model that is capable of simultaneously fitting the CH and CD stretches of all the hydrogenic isotopomers of methyl radical. Third, while ethynyl absorbs in the mid-infrared, the transition studied are low-lying electronic states. The combination of a cold source of C2H and high frequency precision allows us to clarify line assignments and find new transitions. Additionally, localized shifting of transition frequencies allows for identification and partial characterization of the dark perturber states. Fourth, the symmetric CH stretch of hydroxymethyl radical is studied at high-resolution. The high-resolution spectra improve upon band origin and structural information in the radical as well as set the stage for further experimental studies into potential large amplitude dynamics in the radical.

  18. 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

  19. Ion channels: molecular targets of neuroactive insecticides.

    PubMed

    Raymond-Delpech, Valérie; Matsuda, Kazuhiko; Sattelle, Benedict M; Rauh, James J; Sattelle, David B

    2005-11-01

    Many of the insecticides in current use act on molecular targets in the insect nervous system. Recently, our understanding of these targets has improved as a result of the complete sequencing of an insect genome, i.e., Drosophila melanogaster. Here we examine the recent work, drawing on genetics, genomics and physiology, which has provided evidence that specific receptors and ion channels are targeted by distinct chemical classes of insect control agents. The examples discussed include, sodium channels (pyrethroids, p,p'-dichlorodiphenyl-trichloroethane (DDT), dihydropyrazoles and oxadiazines); nicotinic acetylcholine receptors (cartap, spinosad, imidacloprid and related nitromethylenes/nitroguanidines); gamma-aminobutyric acid (GABA) receptors (cyclodienes, gamma-BHC and fipronil) and L-glutamate receptors (avermectins). Finally, we have examined the molecular basis of resistance to these molecules, which in some cases involves mutations in the molecular target, and we also consider the future impact of molecular genetic technologies in our understanding of the actions of neuroactive insecticides.

  20. Ion mobility analysis of molecular dynamics.

    PubMed

    Wyttenbach, Thomas; Pierson, Nicholas A; Clemmer, David E; Bowers, Michael T

    2014-01-01

    The combination of mass spectrometry and ion mobility spectrometry (IMS) employing a temperature-variable drift cell or a drift tube divided into sections to make IMS-IMS experiments possible allows information to be obtained about the molecular dynamics of polyatomic ions in the absence of a solvent. The experiments allow the investigation of structural changes of both activated and native ion populations on a timescale of 1-100 ms. Five different systems representing small and large, polar and nonpolar molecules, as well as noncovalent assemblies, are discussed in detail: a dinucleotide, a sodiated polyethylene glycol chain, the peptide bradykinin, the protein ubiquitin, and two types of peptide oligomers. Barriers to conformational interconversion can be obtained in favorable cases. In other cases, solution-like native structures can be observed, but care must be taken in the experimental protocols. The power of theoretical modeling is demonstrated.

  1. F 3 - molecular ions in fluoride crystals

    NASA Astrophysics Data System (ADS)

    Radzhabov, E. A.

    2016-02-01

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

  2. 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.

  3. 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.

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

    PubMed

    Liu, Jinjun; Miller, Terry A

    2014-12-26

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

  5. 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

  6. 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.

  7. 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.

  8. Understanding Molecular-Ion Neutral Atom Collisions for the Production of Ultracold Molecular Ions

    DTIC Science & Technology

    2014-02-03

    Schowalter, Svetlana Kotochigova, Kuang Chen, Eric R. Hudson. Evidence for sympathetic vibrational cooling of translationally cold molecules, Nature...03 2013): 0. doi: 10.1038/nature11937 Wade G. Rellergert, Scott T. Sullivan, Svetlana Kotochigova, Eric R. Hudson. Role of Electronic Excitations...109.223002 Kuang Chen, Steven Schowalter, Svetlana Kotochigova, Alexander Petrov, Wade Rellergert, Scott Sullivan, Eric Hudson. Molecular-ion trap

  9. Laser induced fluorescence of trapped molecular ions

    SciTech Connect

    Winn, J.S.

    1980-10-01

    Laser induced fluoresence (LIF) spectra (laser excitation spectra) are conceptually among the most simple spectra to obtain. One need only confine a gaseous sample in a suitable container, direct a laser along one axis of the container, and monitor the sample's fluorescence at a right angle to the laser beam. As the laser wavelength is changed, the changes in fluorescence intensity map the absorption spectrum of the sample. (More precisely, only absorption to states which have a significant radiative decay component are monitored.) For ion spectroscopy, one could benefit in many ways by such an experiment. Most optical ion spectra have been observed by emission techniques, and, aside from the problems of spectral analysis, discharge emission methods often produce the spectra of many species, some of which may be unknown or uncertain. Implicit in the description of LIF given above is certainty as to the chemical identity of the carrier of the spectrum. This article describes a method by which the simplifying aspects of LIF can be extended to molecular ions (albeit with a considerable increase in experimental complexity over that necessary for stable neutral molecules).

  10. 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.

  11. 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.

  12. Production of molecular ion beams using an electron cyclotron resonance ion source

    SciTech Connect

    Draganić, I. N.; Bannister, M. E.; Meyer, F. W.; Vane, C. R.; Havener, C. C.

    2011-06-01

    An all-permanent magnet electron cyclotron resonance (ECR) ion source is tuned to create a variety of intense molecular ion beams for basic energy research. Based on simultaneous injection of several gases with spectroscopic high purity or enriched isotope content (e.g., H2, D2, N2, O2, or CO) and lower power microwave heating, the ECR ion source produces diatomic molecular ion beams of H2+, D2+, HD+, HO+, DO+, NH+, ND+, and more complex polyatomic molecular ions such as H3+, D3+, HD2+, H2O+, D2O+, H3O+, D3O+, and NHn+, NDn+ with n=2,3,4 and possibly higher. Molecular ion beams have been produced with very high current intensities compared to other molecular beam sources. The recorded molecular ion beam spectra are discussed.

  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. Relative stopping powers for atomic and molecular ions in carbon

    NASA Astrophysics Data System (ADS)

    Steuer, Malcolm F.

    1986-03-01

    Electronic stopping powers of carbon for atomic and molecular nitrogen ions have been calculated using semi-classical free electron scattering from Herman-Skillman potentials, parametrized to include an adjustable exponential screening factor F( tv, Z), representing atomic ions. For molecular ions, aligned along the beam direction and having velocity 1.2 a.u., the stopping powers for individual atomic components were calculated as a function of internuclear separation. Screening factors for the two centers of force were assumed to decrease linearly from the value at zero internuclear separation, equivalent to that of a silicon ion, to that for nitrogen ions at large separations. Results are consistent with the diminishment of average stopping power per atomic ion which has been observed for beam-aligned nitrogen molecular ions. Similar calculations for molecular hydrogen in carbon agree with the enhancement of stopping power which has been observed. Evidence of nonlinear effects is indicated.

  16. 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.

  17. 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%.

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

    PubMed

    Rácz, R; Biri, S; Juhász, Z; Sulik, B; Pálinkás, J

    2012-02-01

    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(-), O(-), OH(-), O(2)(-), C(-), C(60)(-) negative ions and H(2)(+), H(3)(+), OH(+), H(2)O(+), H(3)O(+), O(2)(+) 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 μA and positive molecular ion beams in the mA range were successfully obtained.

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

    SciTech Connect

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

    2012-02-15

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

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

    PubMed

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

    2014-12-01

    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.

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

    SciTech Connect

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

    2014-12-15

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

  3. The electric quadrupole moment of molecular hydrogen ions and their potential for a molecular ion clock

    NASA Astrophysics Data System (ADS)

    Bakalov, D.; Schiller, S.

    2014-01-01

    The systematic shifts of the transition frequencies in the molecular hydrogen ions are of relevance to ultra-high-resolution radio-frequency, microwave and optical spectroscopy of these systems, performed in ion traps. We develop the ab initio description of the interaction of the electric quadrupole moment of this class of molecules with the static electric field gradients present in ion traps. In good approximation, it is described in terms of an effective perturbation Hamiltonian. An approximate treatment is then performed in the Born-Oppenheimer approximation. We give an expression of the electric quadrupole coupling parameter valid for all hydrogen molecular ion species and evaluate it for a large number of states of H{2/+}, HD+, and D{2/+}. The systematic shifts can be evaluated as simple expectation values of the perturbation Hamiltonian. Results on radio-frequency, one-photon electric dipole (E1), and two-photon E1 transitions between hyperfine states in HD+ are reported. For two-photon E1 transitions between rotationless states, the shifts vanish. For a large subset of rovibrational one-photon transitions, the absolute values of the quadrupole shifts range from 0.3 to 10 Hz for an electric field gradient of 108 V/m2. We point out an experimental procedure for determining the quadrupole shift which will allow reducing its contribution to the uncertainty of unperturbed rovibrational transition frequencies to the 1 × 10-15 fractional level and, for selected transitions, even below it. The combined contributions of black-body radiation, Zeeman, Stark and quadrupole effects are considered for a large set of transitions, and it is estimated that the total transition frequency uncertainty of selected transitions can be reduced below the 1 × 10-15 level.

  4. 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).

  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. Ion beam sculpting molecular scale devices

    NASA Astrophysics Data System (ADS)

    Stein, Derek Martin

    We envision solid-state nanopores at the heart of a device capable of detecting, manipulating, and ultimately sequencing individual DNA molecules. To reliably fabricate holes whose diameter is commensurate with that of the DNA molecule (˜2nm), low energy ion beams are employed to tailor the size of holes in solid-state membranes by a new technique we call "ion beam sculpting". The transmission rate of ions through the hole is monitored to provide a direct, real-time measure of the hole area that is used as a feedback signal to trigger the termination of the ion irradiation process when the desired hole size is obtained. The sensitivity of the transmitted ion count rate to atomic-scale material rearrangements at the perimeter of a hole led to a surprising discovery: Low-energy ion beams stimulate the lateral transport of matter when incident on a surface, resulting in the growth of a thin film from the boundary of a hole that closes the hole. The net flow of matter is determined by a competition between sputter erosion, which opens the hole, and a hole closing process that dominates at high temperature and low flux. The timescale for lateral matter transport under ion irradiation is surprisingly long---on the order of a second. Two physical models are proposed to account for the surprising ion-stimulated transport of matter. One model is based on the viscous flow of a stressed surface layer, while the other is based on the diffusion of mobile, ion-stimulated species at the surface of the material into the hole. The predictions of the latter are compared to ion beam sculpting experiments. We exploit ion beam sculpting to fabricate solid-state nanopores used as electronic detectors of individual DNA molecules. In ionic solution, negatively charged DNA molecules are drawn to the nanopore by an applied electrochemical potential, resulting in a detectable characteristic ionic current blockade when a molecules occludes the nanopore. The applicability of the ion sculpting

  9. Anomalous Decline of Molecular Ion Mobility in Cooled Helium Gas

    NASA Astrophysics Data System (ADS)

    Ohtsuki, Kazumasa; Hananoe, Masatoshi; Matsuzawa, Michio

    2005-11-01

    We present a first successful theoretical account of the ion mobilities of N2+ and O2+ in helium gas at 4.3 K. Measured mobilities of various molecular ions at low effective temperatures reportedly tend to values smaller than their polarization limits, with the exception of N2+ [J. Sanderson , J. Phys. BJPAPEH0953-4075 26, L465 (1993)10.1088/0953-4075/26/15/006; J. SandersonJ. Phys. BJPAPEH0953-407527, L433 (1994)10.1088/0953-4075/27/14/021]. The present theoretical results obtained by the classical trajectory calculations agree with the experimental ones very well, and make it definitive that the anomalous decline of molecular ion mobility is caused by a Feshbach-like resonance due to the anisotropic interaction potential between a molecular ion and a helium atom. The mechanism thus revealed is supported by quantitative quantum mechanical calculations. The process appears very similar to that of laser cooling.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

    Masser, Hanqing

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

  12. 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.

  13. Spectroscopy and decay dynamics of jet-cooled carbazole and N-ethylcarbazole and their homocyclic analogues

    NASA Astrophysics Data System (ADS)

    Auty, A. R.; Jones, A. C.; Phillips, D.

    1986-03-01

    Fluorescence excitation spectra of supersonic jet-cooled carbazole (C) and N-ethylcarbazole (EC) are reported together with those of their homocyclic analogues fluorene (F) and 9-ethylfluorene (EF). Fluorescence spectra of C and EC have been measured following excitation at energies up to ≈ 1300 cm -1 above the S 1 origin and reveal that the onset of intramolecular vibrational redistribution occurs at around 900 cm -1 for both molecules, with redistribution being more extensive in the ethylated molecule. In C and EC, a number of modes are active in vibronically coupling the S 1 and S 2 states and Duschinsky mixing of these modes is apparent in the spectra. The fluorescence lifetimes of both C and EC show a slowly decreasing trend with increasing excitation energy in the range 0-1500 cm -1 excess vibrational energy; vibrational redistribution does not appear to enhance the rate of non-radiative decay in either molecule. Comparison of lifetime values under supersonic jet conditions with solution phase results indicates that solvation produces a considerable increase in the rate of intersystem crossing in these molecules.

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

    SciTech Connect

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

    1996-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1996-04-01

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

  16. 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.

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

    PubMed

    Chang, Chih-Hsuan; Nesbitt, David J

    2015-07-16

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

  18. 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.

  19. 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.

  20. Spectroscopy of atomic and molecular ions using quantum logic

    NASA Astrophysics Data System (ADS)

    Schmidt, P. O.; Rosenband, T.; Koelemeij, J. C. J.; Hume, D. B.; Itano, W. M.; Bergquist, J. C.; Wineland, D. J.

    2006-10-01

    Recently developed techniques for quantum computation using trapped ions allow precise coherent control of the internal and external states of single atoms. Here we report how these techniques can be employed to perform precision spectroscopy of atomic and molecular ions that lack accessible transitions for laser cooling and detection. Furthermore, we discuss how quantum logic can be used to laser-cool molecules to near their rotational and vibrational ground state by avoiding detrimental spontaneous emission of photons from the molecule.

  1. 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 !}.

  2. Predicting Molecular Crowding Effects in Ion-RNA Interactions.

    PubMed

    Yu, Tao; Zhu, Yuhong; He, Zhaojian; Chen, Shi-Jie

    2016-09-01

    We develop a new statistical mechanical model to predict the molecular crowding effects in ion-RNA interactions. By considering discrete distributions of the crowders, the model can treat the main crowder-induced effects, such as the competition with ions for RNA binding, changes of electrostatic interaction due to crowder-induced changes in the dielectric environment, and changes in the nonpolar hydration state of the crowder-RNA system. To enhance the computational efficiency, we sample the crowder distribution using a hybrid approach: For crowders in the close vicinity of RNA surface, we sample their discrete distributions; for crowders in the bulk solvent away from the RNA surface, we use a continuous mean-field distribution for the crowders. Moreover, using the tightly bound ion (TBI) model, we account for ion fluctuation and correlation effects in the calculation for ion-RNA interactions. Applications of the model to a variety of simple RNA structures such as RNA helices show a crowder-induced increase in free energy and decrease in ion binding. Such crowding effects tend to contribute to the destabilization of RNA structure. Further analysis indicates that these effects are associated with the crowder-ion competition in RNA binding and the effective decrease in the dielectric constant. This simple ion effect model may serve as a useful framework for modeling more realistic crowders with larger, more complex RNA structures.

  3. 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.

  4. 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.

  5. 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…

  6. 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.

  7. 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.

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

    NASA Astrophysics Data System (ADS)

    Sunahori, Fumie X.; Xu, Yunjie

    2012-06-01

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

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. State-selective generation of molecular ions via Rydberg states

    NASA Astrophysics Data System (ADS)

    Grimes, David; Zhou, Yan; Barnum, Timothy; Coy, Stephen; Kay, Jeffrey; Field, Robert

    2014-05-01

    Autoionizing Rydberg states of molecules in the range n = 30-50 have the potential to enable the production of single quantum state selected ensembles of molecular ions, which have uses from spectroscopy to high precision measurements of fundamental constants. Multichannel Quantum Defect Theory (MQDT) fully describes the Rydberg states of molecules and the dynamics of autoionization. We have used our full MQDT description of CaF to determine optimal autoionizing resonances for producing a variety of selected rotation-vibration states of the ion. Progress towards experimental demonstrations in BaF will also be discussed. This work was supported by the NSF and an NDSEG Fellowship

  14. 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

  15. Ion-Pair States in Triplet Molecular Hydrogen

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  16. 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

  17. 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.

  18. 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.

  19. High-resolution infrared spectroscopy: Jet-cooled halogenated methyl radicals and reactive scattering dynamics in an atom + polyatom system

    NASA Astrophysics Data System (ADS)

    Whitney, Erin Sue

    This thesis describes a series of projects whose common theme comprises the structure and internal energy distribution of gas-phase radicals. In the first two projects, shot noise-limited direct absorption spectroscopy is combined with long path-length slit supersonic discharges to obtain first high-resolution infrared spectra for jet-cooled CH2F and CH2Cl in the symmetric and antisymmetric CH2 stretching modes. Drawing motivation from the question of the equilibrium structures of halogen-substituted methyl radicals, spectral assignment yields refined lower and upper state rotational constants, as well as fine-structure parameters from least-square fits to the sub-Doppler lineshapes for individual transitions. High-level CCSD(T) calculations extrapolated to the complete basis set (CBS) limit confirm the existence of a non-planar (theta=29°) CH2F equilibrium structure with a 132 cm-1 barrier to planarity and a vibrational bend frequency of 276 cm-1. Similar calculations for CH 2Cl predict a slightly nonplanar equilibrium structure (theta=11°) with a vibrationally adiabatic one-dimensional treatment of the bend coordinate yielding a fundamental anharmonic frequency (393 cm-1). Both sets of calculations are in excellent agreement with previous studies. More interesting, however, are the unexpected intensity ratios of the symmetric vs. antisymmetric bands for CH2F and the absence of an antisymmetric band for CH2Cl. While a simple bond-dipole picture predicts a ratio of 1:3 for the symmetric vs. antisymmetric intensities, the experimentally observed value for CH2F is ˜2:1. This ratio is confirmed by DFT [B3LYP/aug-cc-pVTZ] calculations in a novel albeit indirect probe of the effective non-planarity for CH2F. For CH2Cl, similar DFT calculations predict a 30-fold decrease between the intensity of the symmetric and antisymmetric CH2 stretches, leading to the postulation of a nearly perfect cancellation of antisymmetric stretch intensity transition moment with

  20. Molecular orbital predictions of the vibrational frequencies of some molecular ions

    NASA Technical Reports Server (NTRS)

    Defrees, D. J.; Mclean, A. D.

    1985-01-01

    The initial detections of IR vibration-rotation bands in polyatomic molecular ions by recent spectroscopic advances were guided by ab initio prediction of vibrational frequencies. The present calculations predict the vibrational frequencies of additional ions which are candidates for laboratory analysis. Neutral molecule vibrational frequencies were computed at three levels of theory and then compared with experimental data; the effect of scaling was also investigated, in order to determine how accurately vibrational frequencies could be predicted. For 92 percent of the frequencies examined, the relatively simple HF/6-31G theory's vibrational frequencies were within 100/cm of experimental values, with a mean absolute error of 49/cm. On this basis, the frequencies of 30 molecular ions (many possessing astrophysical significance) were computed.

  1. Cryogenic molecular separation system for radioactive (11)C ion acceleration.

    PubMed

    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 (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 (11)C ion beams. In the ISOL system, (11)CH4 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 (12)CH4 gases, which can simulate the chemical characteristics of (11)CH4 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. The Torsion-Inversion Energy Levels in the S1( n, π*) Electronic State of Acetaldehyde from High-Resolution Jet-Cooled Fluorescence Excitation Spectroscopy

    NASA Astrophysics Data System (ADS)

    Liu, H.; Lim, E. C.; Muñoz-Caro, C.; Niño, A.; Judge, R. H.; Moule, D. C.

    1996-01-01

    The laser-induced fluorescence excitation spectrum (LIF) of acetaldehyde that results from the emission from theS1(n, π*) electronic state has been observed under very high resolution with a CW pulse-amplified laser under jet-cooled conditions. The origins of seven bands were determined by rotational analyses with a rigid-rotor Hamiltonian. The origins were fitted to a set of levels that were obtained from a Hamiltonian that employed flexible torsion-wagging large amplitude coordinates. The potential surface derived from the fitting procedure yielded barriers to torsion and inversion of 721.43 and 585.13 cm-1, respectively. Minima in the potential hypersurface at θ = 58.6° and α = 35.7° defined the corresponding equilibrium positions for the torsion and wagging coordinates.

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

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

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

  8. Soft-x-ray fragmentation studies of molecular ions

    NASA Astrophysics Data System (ADS)

    Wolf, Andreas; Pedersen, Henrik B.; Lammich, Lutz; Jordon-Thaden, Brandon; Altevogt, Simon; Domesle, Christian; Hergenhahn, Uwe; Förstel, Marko; Heber, Oded

    2010-10-01

    Imaging of photofragments from molecular ions after irradiation by soft x-ray photons has been realized at the ion beam infrastructure TIFF set up at the FLASH facility. Photodissociation of the two-electron system HeH+ at 38.7 eV revealed the electronic excitations and the charge-state ratios for the products of this process, reflecting the non-adiabatic dissociation dynamics through multiple avoided crossings among the HeH+ Rydberg potential curves. Dissociative ionization of the protonated water molecules H3O+ and H5O+2 at 90 eV revealed the main fragmentation pathways after the production of valence vacancies in these ionic species, which include a strong three-body channel with a neutral fragment (OH + H+ + H+) in H3O+ photolysis and a significant two-body fragmentation channel (H3O++ H2O+) in H5O+2 photolysis. The measurements yield absolute cross sections and fragment angular distributions. Increased precision and sensitivity of the technique were realized in recent developments, creating a tool for exploring x-ray excited molecular states under highly controlled target conditions challenging detailed theoretical understanding.

  9. 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.

  10. Molecular simulations of ion exchange in NaA zeolite membranes

    NASA Astrophysics Data System (ADS)

    Murad, S.; Jia, W.; Krishnamurthy, M.

    2003-02-01

    Molecular simulations using the method of molecular dynamics have been carried out to determine the possibility of studying ion exchanges between electrolyte solutions (here an aqueous LiCl solution) and an ion-exchange membrane (NaA zeolite) using direct simulations of upto a nanosecond. Our results show that with appropriate driving forces, such ion-exchange processes can be clearly witnessed and investigated using molecular simulations. We have also attempted to understand the phenomenon at the molecular level. Our results have shown that the ion-exchange process is energetically driven and entropic forces are not playing any significant role in the exchanges observed.

  11. Water Exchange Rates and Molecular Mechanism around Aqueous Halide Ions

    SciTech Connect

    Annapureddy, Harsha V.; Dang, Liem X.

    2014-07-17

    Molecular dynamics simulations were performed to systematically study the water-exchange mechanism around aqueous chloride, bromide, and iodide ions. Transition state theory, Grote-Hynes theory, and the reactive flux method were employed to compute water exchange rates. We computed the pressure dependence of rate constants and the corresponding activation volumes to investigate the mechanism of the solvent exchange event. The activation volumes obtained using the transition state theory rate constants are negative for all the three anions, thus indicating an associative mechanism. Contrary to the transition state theory results, activation volumes obtained using rate constants from Grote-Hynes theory and the reactive flux method are positive, thus indicating a dissociative mechanism. The Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences (BES), of the U.S. Department of Energy (DOE) funded this work. Battelle operates Pacific Northwest National Laboratory for DOE. The calculations were carried out using computer resources provided by BES.

  12. 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

  13. 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

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

    PubMed

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

    2015-03-01

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

  15. Lipid specific molecular ion emission as a function of the primary ion characteristics in TOF-SIMS.

    PubMed

    Adams, Kendra J; DeBord, John Daniel; Fernandez-Lima, Francisco

    2016-09-01

    In the present work, the emission characteristics of lipids as a function of the primary ion cluster size and energy were studied using time-of-flight secondary ion mass spectrometry (TOF-SIMS). Characteristic fragmentation patterns for common lipids are described, and changes in secondary ion (SI) yields using various primary ion beams are reported. In particular, emission characteristics were studied for pairs of small polyatomic and nanoparticle primary ion beams (e.g., Bi3(+) versus Ar1000(+) and Au3(+) versus Au400(+4)) based on the secondary ion yield of characteristic fragment and intact molecular ions as a function of the lipid class. Detailed descriptions of the fragmentation patterns are shown for positive and negative mode TOF-SIMS. Results demonstrate that the lipid structure largely dictates the spectral presence of molecular and/or fragment ions in each ionization mode due to the localization of the charge carrier (head group or fatty acid chain). Our results suggest that the larger the energy per atom for small polyatomic projectiles (Bi3(+) and Au3(+)), the larger the SI yield; in the case of nanoparticle projectiles, the SI increase with primary ion energy (200-500 keV range) for Au400(+4) and with the decrease of the energy per atom (10-40 eV/atom range) for Arn=500-2000(+) clusters. The secondary ion yield of the molecular ion of lipids from a single standard or from a mixture of lipids does not significantly change with the primary ion identity in the positive ion mode TOF-SIMS and slightly decreases in the negative ion mode TOF-SIMS.

  16. 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

  17. Theoretical studies on dissociative recombination of molecular ions

    NASA Astrophysics Data System (ADS)

    Larson, Åsa

    2016-09-01

    In dissociative recombination a molecular ion captures an electron forming a neutral state that dissociates into fragment. Due to the Coulomb attraction between the reactants, the cross section is typically large at low collision energies and the process is important for different types of plasmas. Here, it will be described how the reaction can be studied theoretically. The goal is to compute reaction cross sections and to determine what fragments are formed. The calculations are done in close collaboration with experiments. In the process, the electron may be captured directly into an electronic resonant state that then is dissociated into fragments. An alternative mechanism is driven by an electron capture into a ro-vibrationally excited Rydberg state that then is predissociated. The two mechanisms are competing and should be considered coherently. The study of dissociative recombination requires both the accurate treatment of the electron scattering processes, but must also include an accurate representation of the potential energy curves, both for electronically bound states and the resonant states. In addition, the couplings between these states, both the coupling between the resonant states and the scattering continuum (the autoionization width) and the non-adiabatic coupling between all states are needed to complete describe the cross section including the branching ratios into final states. These are obtained using structure calculations as well as scattering calculations, using the complex Kohn variational method. The electronic states are diabatized before the nuclear dynamics is studied quantum mechanically. The theoretical method will be illustrated with examples on dissociative recombination of small molecular ions such as HF+, BeH+, H2O+ and N2H+.

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

    PubMed

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

    1996-04-01

    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.

  19. 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.

  20. 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.

  1. Molecular dynamics simulation of graphene bombardment with Si ion

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    PubMed

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

    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(+), Cl(-), and Ag(+) 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 (DeltaG(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(+)/Cl(-) and Ag(+)/Cl(-) AIMD DeltaG(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(+)+Ni(+)-->Ag+Ni(2+) in water. The predictions for this reaction suggest that existing estimates of DeltaG(hyd) for unstable radiolysis intermediates such as Ni(+) may need to be extensively revised.

  3. 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.

  4. Molecular Designs for Controlling the Local Environments around Metal Ions

    PubMed Central

    Cook, Sarah A.; Borovik, A.S.

    2015-01-01

    CONSPECTUS 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. Non-covalent 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 FeIII–oxo species directly from the activation of O2 that was subsequently oxidized to form a monomeric FeIV–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 MnIII–oxo center that was prepared from water could be converted to a high spin MnV–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 MnIV–oxyl species rather than the isoelectronic MnV–oxo system as the key oxidant based on computational studies. However, there is no experimental information to support the existence

  5. Quantum State Control of Trapped Atomic and Molecular Ions

    NASA Astrophysics Data System (ADS)

    Seck, Christopher M.

    Full quantum control of a molecule would have a significant impact in molecular coherent control (alignment and orientation) and ultracold and quantum chemistry, quantum computing and simulation as well as hybrid quantum devices, and precision spectroscopy of importance to fundamental physics research. Precision spectroscopy of even simple diatomic molecules offers the possibility of uncovering physics beyond the standard model, specifically time variation of the proton-to-electron mass ratio, which is currently constrained by astronomical molecular observations at the 10-16 1/yr level and laboratory atomic measurements at the 10-17 1/yr level. To achieve this level of measurement and to avoid the complications of diatomic structure on traditional spectroscopy methods, molecular quantum logic spectroscopy (mQLS) will be the spectroscopy technique of choice. We discuss development of in-house external-cavity diode laser (ECDL) systems and improvements to the Libbrecht-Hall circuit, which is a well-known, low-noise current driver for narrow-linewidth diode lasers. However, as the current approaches the maximum set limit, the noise in the laser current increases dramatically. This behavior is documented and simple circuit modifications to alleviate this issue are explored. We cool trapped AlH+ molecules to their ground rotational-vibrational quantum state using an electronically-exciting broadband laser to simultaneously drive cooling resonances from many different rotational levels. We demonstrate rotational cooling on the 140(20) ms timescale from room temperature to 3.8 K, with the ground state population increasing from 3% to 95.4%. Since QLS does not require the high gate fidelities usually associated with quantum computation and quantum simulation, it is possible to make simplifying choices in ion species and quantum protocols at the expense of some fidelity. We demonstrate sideband cooling and motional state detection protocols for 138Ba+ of sufficient fidelity

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  7. High Resolution Jet-Cooled Infrared Absorption Spectra of Formic Acid Dimer: a Reinvestigation of the Fermi-Triad System in the C-O Stretching Region

    NASA Astrophysics Data System (ADS)

    Duan, Chuanxi

    2014-06-01

    High resolution jet-cooled absorption spectra of the formic acid dimer (HCOOH)2 have been measured in the C-O stretching region at 1215-1240 wn using a rapid-scan tunable diode laser spectrometer. Three vibrational bands of (HCOOH)2 have been assigned unambiguously. They were interpreted as the Fermi-triad system consisting of the νb{22} fundamental band and two combination bands in a previous low-resolution study [F. Ito, Chem. Phys. Lett. 447, 202(2007)]. The spectral coverage in the high-resolution study of the middle band [M. Ortlieb and M. Havenith, J. Phys. Chem. A. 111, 7355(2007)] were extended. These three vibrational bands were analyzed together using a standard rigid rotor Watson A-reduced Hamiltonian without explicit consideration of the perturbation among three vibrationally excited states. The perturbed energies for three vibrationally excited states are 1219.71637(20), 1225.34666(15), and 1233.95863(17) wn, respectively.

  8. Strong parallel magnetic field effects on the hydrogen molecular ion

    NASA Astrophysics Data System (ADS)

    Guan, Xiaoxu; Li, Baiwen; Taylor, K. T.

    2003-09-01

    Equilibrium distances, binding energies and dissociation energies for the ground and low-lying states of the hydrogen molecular ion in a strong magnetic field parallel to the internuclear axis are calculated and refined, by using the two-dimensional pseudospectral method. High-precision results are presented for the binding energies over a wider field regime than already given in the literature (Kravchenko and Liberman 1997 Phys. Rev. A 55 2701). The present work removes a long-standing discrepancy for the Req value in the 1sigmau state at a field strength of 1.0 × 106 T. The dissociation energies of the antibonding 1pig state induced by magnetic fields are determined accurately. We have also observed that the antibonding 1pig potential energy curve develops a minimum if the field is sufficiently strong. Some unreliable results in the literature are pointed out and discussed. A way to efficiently treat vibrational processes and coupling between the nuclear and the electronic motions in magnetic fields is also suggested within a three-dimensional pseudospectral scheme.

  9. 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.

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

    PubMed

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

    2017-01-20

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

  11. 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

  12. 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.

  13. Ab-initio method for X-ray absorption spectra simulation of hydride molecular ions

    NASA Astrophysics Data System (ADS)

    Puglisi, Alessandra; Sisourat, Nicolas; Carniato, Stéphane

    2017-03-01

    Soft X-ray absorption spectra of molecular ions are important data for the modeling and understanding of laboratory and astrophysical plasma. In this work, we present an ab-initio method, based on the Configuration Interaction (CI) approach, for the calculations of energy positions and oscillator strengths of X-ray absorption spectra. Furthermore, we investigate the effects of the choice of the nature and number of spin-orbitals used in the CI expansion on the spectra. The method is applied on three hydride molecular ions, namely CH+, OH+ and SiH+. However, the approach proposed here is general and may thus be applied to any kind of molecular ions.

  14. 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.

  15. IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion Channels

    PubMed Central

    Kasahara, Kota; Kinoshita, Kengo

    2016-01-01

    Ion conduction mechanisms of ion channels are a long-standing conundrum. Although the molecular dynamics (MD) method has been extensively used to simulate ion conduction dynamics at the atomic level, analysis and interpretation of MD results are not straightforward due to complexity of the dynamics. In our previous reports, we proposed an analytical method called ion-binding state analysis to scrutinize and summarize ion conduction mechanisms by taking advantage of a variety of analytical protocols, e.g., the complex network analysis, sequence alignment, and hierarchical clustering. This approach effectively revealed the ion conduction mechanisms and their dependence on the conditions, i.e., ion concentration and membrane voltage. Here, we present an easy-to-use computational toolkit for ion-binding state analysis, called IBiSA_tools. This toolkit consists of a C++ program and a series of Python and R scripts. From the trajectory file of MD simulations and a structure file, users can generate several images and statistics of ion conduction processes. A complex network named ion-binding state graph is generated in a standard graph format (graph modeling language; GML), which can be visualized by standard network analyzers such as Cytoscape. As a tutorial, a trajectory of a 50 ns MD simulation of the Kv1.2 channel is also distributed with the toolkit. Users can trace the entire process of ion-binding state analysis step by step. The novel method for analysis of ion conduction mechanisms of ion channels can be easily used by means of IBiSA_tools. This software is distributed under an open source license at the following URL: http://www.ritsumei.ac.jp/~ktkshr/ibisa_tools/ PMID:27907142

  16. 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.

  17. 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.

  18. Conformers of β-aminoisobutyric acid probed by jet-cooled microwave and matrix isolation infrared spectroscopic techniques.

    PubMed

    Kuş, N; Sharma, A; Peña, I; Bermúdez, M C; Cabezas, C; Alonso, J L; Fausto, R

    2013-04-14

    β-aminoisobutyric acid (BAIBA) has been studied in isolation conditions: in the gas phase and trapped into a cryogenic N2 matrix. A solid sample of the compound was vaporized by laser ablation and investigated through their rotational spectra in a supersonic expansion using two different spectroscopic techniques: broadband chirped pulse Fourier transform microwave spectroscopy and conventional molecular beam Fourier transform microwave spectroscopy. Four conformers with structures of two types could be successfully identified by comparison of the experimental rotational and (14)N nuclear quadruple coupling constants with those predicted theoretically: type A, bearing an OH⋯N intramolecular hydrogen bond and its carboxylic group in the trans geometry (H-O-C=O dihedral ∼180°), and type B, having an NH⋯O bond and the cis arrangement of the carboxylic group. These two types of conformers could also be trapped from the gas phase into a cryogenic N2 matrix and probed by Fourier transform infrared (IR) spectroscopy. In situ irradiation of BAIBA isolated in N2 matrix of type B conformers using near-IR radiation tuned at the frequency of the O-H stretching 1st overtone (∼6930 cm(-1)) of these forms allowed to selectively convert them into type A conformers and into a new type of conformers of higher energy (type D) bearing an NH⋯O=C bond and a O-H "free" trans carboxylic group.

  19. Conformers of β-aminoisobutyric acid probed by jet-cooled microwave and matrix isolation infrared spectroscopic techniques

    NASA Astrophysics Data System (ADS)

    Kuş, N.; Sharma, A.; Peña, I.; Bermúdez, M. C.; Cabezas, C.; Alonso, J. L.; Fausto, R.

    2013-04-01

    β-aminoisobutyric acid (BAIBA) has been studied in isolation conditions: in the gas phase and trapped into a cryogenic N2 matrix. A solid sample of the compound was vaporized by laser ablation and investigated through their rotational spectra in a supersonic expansion using two different spectroscopic techniques: broadband chirped pulse Fourier transform microwave spectroscopy and conventional molecular beam Fourier transform microwave spectroscopy. Four conformers with structures of two types could be successfully identified by comparison of the experimental rotational and 14N nuclear quadruple coupling constants with those predicted theoretically: type A, bearing an OH⋯N intramolecular hydrogen bond and its carboxylic group in the trans geometry (H-O-C=O dihedral ˜180°), and type B, having an NH⋯O bond and the cis arrangement of the carboxylic group. These two types of conformers could also be trapped from the gas phase into a cryogenic N2 matrix and probed by Fourier transform infrared (IR) spectroscopy. In situ irradiation of BAIBA isolated in N2 matrix of type B conformers using near-IR radiation tuned at the frequency of the O-H stretching 1st overtone (˜6930 cm-1) of these forms allowed to selectively convert them into type A conformers and into a new type of conformers of higher energy (type D) bearing an NH⋯O=C bond and a O-H "free" trans carboxylic group.

  20. Molecular mechanism of ion-ion and ion-substrate coupling in the Na+-dependent leucine transporter LeuT.

    PubMed

    Caplan, David A; Subbotina, Julia O; Noskov, Sergei Yu

    2008-11-15

    Ion-coupled transport of neurotransmitter molecules by neurotransmitter:sodium symporters (NSS) play an important role in the regulation of neuronal signaling. One of the major events in the transport cycle is ion-substrate coupling and formation of the high-affinity occluded state with bound ions and substrate. Molecular mechanisms of ion-substrate coupling and the corresponding ion-substrate stoichiometry in NSS transporters has yet to be understood. The recent determination of a high-resolution structure for a bacterial homolog of Na(+)/Cl(-)-dependent neurotransmitter transporters, LeuT, offers a unique opportunity to analyze the functional roles of the multi-ion binding sites within the binding pocket. The binding pocket of LeuT contains two metal binding sites. The first ion in site NA1 is directly coupled to the bound substrate (Leu) with the second ion in the neighboring site (NA2) only approximately 7 A away. Extensive, fully atomistic, molecular dynamics, and free energy simulations of LeuT in an explicit lipid bilayer are performed to evaluate substrate-binding affinity as a function of the ion load (single versus double occupancy) and occupancy by specific monovalent cations. It was shown that double ion occupancy of the binding pocket is required to ensure substrate coupling to Na(+) and not to Li(+) or K(+) cations. Furthermore, it was found that presence of the ion in site NA2 is required for structural stability of the binding pocket as well as amplified selectivity for Na(+) in the case of double ion occupancy.

  1. Photodissociation of Trapped Rb2+: Implications for Simultaneous Trapping of Atoms and Molecular Ions

    NASA Astrophysics Data System (ADS)

    Jyothi, S.; Ray, Tridib; Dutta, Sourav; Allouche, A. R.; Vexiau, Romain; Dulieu, Olivier; Rangwala, S. A.

    2016-11-01

    The direct photodissociation of trapped 85Rb2+ (rubidium) molecular ions by the cooling light for the 85Rb magneto-optical trap (MOT) is studied, both experimentally and theoretically. Vibrationally excited Rb2+ ions are created by photoionization of Rb2 molecules formed photoassociatively in the Rb MOT and are trapped in a modified spherical Paul trap. The decay rate of the trapped Rb2+ ion signal in the presence of the MOT cooling light is measured and agreement with our calculated rates for molecular ion photodissociation is observed. The photodissociation mechanism due to the MOT light is expected to be active and therefore universal for all homonuclear diatomic alkali metal molecular ions.

  2. Photodissociation of Trapped Rb_{2}^{+}: Implications for Simultaneous Trapping of Atoms and Molecular Ions.

    PubMed

    Jyothi, S; Ray, Tridib; Dutta, Sourav; Allouche, A R; Vexiau, Romain; Dulieu, Olivier; Rangwala, S A

    2016-11-18

    The direct photodissociation of trapped ^{85}Rb_{2}^{+} (rubidium) molecular ions by the cooling light for the ^{85}Rb magneto-optical trap (MOT) is studied, both experimentally and theoretically. Vibrationally excited Rb_{2}^{+} ions are created by photoionization of Rb_{2} molecules formed photoassociatively in the Rb MOT and are trapped in a modified spherical Paul trap. The decay rate of the trapped Rb_{2}^{+} ion signal in the presence of the MOT cooling light is measured and agreement with our calculated rates for molecular ion photodissociation is observed. The photodissociation mechanism due to the MOT light is expected to be active and therefore universal for all homonuclear diatomic alkali metal molecular ions.

  3. 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

    2013-10-03

    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.

  4. Buoyancy and cross flow effects on heat transfer of multiple impinging slot air jets cooling a flat plate at different orientations

    NASA Astrophysics Data System (ADS)

    Nada, S. A.

    2009-06-01

    The present article reports on heat transfer characteristics associated with multiple laminar impinging air jet cooling a hot flat plat at different orientations. The work aims to study the interactions of the effects of cross flow, buoyancy induced flow, orientation of the hot surface with respect to gravity, Reynolds numbers and Rayleigh numbers on heat transfer characteristics. Experiments have been carried out for different values of jet Reynolds number, Rayleigh number and cross flow strength and at different orientations of the air jet with respect to the target hot plate. In general, the effective cooling of the plate has been observed to be increased with increasing Reynolds number and Rayleigh number. The results concluded that the hot surface orientation is important for optimum performance in practical applications. It was found that for Re ≥ 400 and Ra ≥ 10,000 (these ranges give 0.0142 ≤ Ri ≤ 1.59 the Nusselt number is independent on the hot surface orientation. However, for Re ≤ 300 and Ra ≥ 100,000 (these ranges give 1.59 ≤ Ri ≤ 42.85): (i) the Nusselt number for horizontal orientation with hot surface facing down is less that that of vertical orientation and that of horizontal orientation with hot surface facing up, and (ii) the Nusselt number of vertical orientation is approximately the same as that of horizontal orientation with hot surface facing up. For all surfaces orientations and for the entire ranges of Re and Ra, it was found that increasing the cross flow strength decreases the effective cooling of the surface.

  5. 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.

  6. 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.

  7. Radii broadening due to molecular collision in focused ion beams

    NASA Astrophysics Data System (ADS)

    Komuro, Masanori

    1988-01-01

    Point exposures of poly(methyl methacrylate) resist are carried out with focused ion beams of Si++ and Au++ from a liquid AuSi ion source in order to obtain a current density distribution in the probe. All the distributions are composed of a main Gaussian distribution and a long tail dependent on r-3.3 (r means radial distance). The magnitude of this tail increases with the increase in ambient pressure of the ion-drifting space. When the probe is steered at the corner of deflection field, two types of clear ghost patterns appear: (1) circular patterns and (2) lines trailing from the main spot toward the deflection center. It is revealed that they are produced by exposures to ions or energetic neutrals generated with charge transfer collision of the primary ions with residual gas molecules. It is shown that the long tail in the current density distribution is also due to scattering with the residual gas molecules.

  8. 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.

  9. Toward the Use of Rydberg States for State-Selective Production of Molecular Ions

    NASA Astrophysics Data System (ADS)

    Grimes, David; Barnum, Timothy J.; Coy, Stephen; Field, Robert W.

    2014-06-01

    The usual simplified view of Rydberg states of molecules as consisting of a single Rydberg electron loosely bound to a molecular ion core in a well-defined rotation-vibration state suggests an attractive possibility for state-selective production of molecular ions. A Rydberg electron excited above the energy of the ground state of the ion core will spontaneously autoionize, leaving behind a molecular ion. The autoionizing states are of strongly mixed character due to the ubiquitous nonadiabatic interactions between Rydberg series associated with different states of the ion core. Using our complete Multichannel Quantum Defect Theory (MQDT) fit model for CaF, we have predicted the locations and strengths of special autoionizing resonances that decay into a single rotation-vibration state of a molecular ion. Few molecules are as well characterized as CaF, nor as elegantly simple. We additionally describe the use of core nonpenetrating states as a general method to produce an ensemble of molecular ions in a single, selectable quantum state.

  10. Molecular Layer Deposition for Surface Modification of Lithium-Ion Battery Electrodes

    SciTech Connect

    Ban, Chunmei; George, Steven M.

    2016-10-21

    Inspired by recent successes in applying molecular layer deposition (MLD) to stabilize lithium-ion (Li-ion) electrodes, this review presents the MLD process and its outstanding attributes for electrochemical applications. The review discusses various MLD materials and their implementation in Li-ion electrodes. The rationale behind these emerging uses of MLD is examined to motivate future efforts on the fundamental understanding of interphase chemistry and the development of new materials for enhanced electrochemical performance.

  11. Observation of Ions Emitted from Hot Graphite, including Excited Molecular Ions

    NASA Astrophysics Data System (ADS)

    Gee, Philip; Ehrenrich, Thomas; Kessel, Quentin; Pollack, Edward; Smith, Winthrop

    2002-10-01

    Thermal desorption of K ions from positively biased graphite (grafoil) containing K impurities has been investigated by measuring the energies of the emitted ions with a hemispherical electrostatic analyzer and the masses with a residual gas analyzer under ultra-high vacuum conditions. Potassium ions are seen to be emitted at temperatures above 800*C. The present data provide evidence for the emission of K+ ions for sample bias voltages from 1V to 6V and the emission of K2+ ions for biases above 10V. The emission of excited K2+ ions are inferred from the measurement of the K+ ion energies which for sample biases above 10 volts with energies which correspond to approximately half of the bias (accelerating) voltage. From this it is deduced that the K2+ ions are produced and disassociate after leaving the surface. The K ion emission can be greatly enhanced by prior bombardment with an ion beam (not K ions) and quenched by ion beam doses that amorphize the graphite surface. This would appear to indicate the emission phenomenon depends upon the degree and crystallinity nature of the graphite surface.

  12. Observation of Ions Emitted from Hot Graphite, Including Excited Molecular Ions

    NASA Astrophysics Data System (ADS)

    Gee, P.; Ehrenrich, T.; Kessel, Q. C.; Pollack, E.; Smith, W. W.

    2003-08-01

    Thermal desorption of K ions from positively biased graphite (grafoil) containing K impurities has been investigated by measuring the energies of the emitted ions with a hemispherical electrostatic analyzer and the masses with a residual gas analyzer under ultra-high vacuum conditions. Potassium ions are seen to be emitted at temperatures above 800°C. The present data provide evidence for the emission of K+ ions for sample bias voltages from 1V to 6V and the emission of K2+ ions for biases above 10V. The emission of excited K2+ ions are inferred from the measurement of the K+ ion energies which for sample biases above 10 volts with energies which correspond to approximately half of the bias (accelerating) voltage. From this it is deduced that the K2+ ions are produced and disassociate after leaving the surface. The K ion emission can be greatly enhanced by prior bombardment with an ion beam (not K ions) and quenched by ion beam doses that amorphize the graphite surface. This would appear to indicate the emission phenomenon depends upon the degree and crystallinity nature of the graphite surface.

  13. 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.

  14. Fabrication of nanopores in a graphene sheet with heavy ions: A molecular dynamics study

    SciTech Connect

    Li, Weisen; Liang, Li; Zhang, Shuo; Zhao, Shijun; Xue, Jianming

    2013-12-21

    Molecular dynamics simulations were performed to study the formation process of nanopores in a suspended graphene sheet irradiated by using energetic ions though a mask. By controlling the ion parameters including mass, energy, and incident angle, different kinds of topography were observed in the graphene sheet. Net-like defective structures with carbon atom chains can be formed at low ion fluences, which provide the possibility to functionalize the irradiated sample with subsequent chemical methods; finally a perfect nanopore with smooth edge appears when the ion fluence is high enough. We found that the dependence of ion damage efficiency on ion fluence, energy, and incident angle are different from that predicted by the semi-empirical model based on the binary-collision approximation, which results from the special structure of graphene. Our results demonstrate that it is feasible to fabricate controlled nanopores/nanostructures in graphene via heavy ion irradiation.

  15. 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

  16. Simultaneous ejection of two molecular ions from keV gold atomic and polyatomic projectile impacts.

    PubMed

    Rickman, R D; Verkhoturov, S V; Parilis, E S; Schweikert, E A

    2004-01-30

    We present the first experimental data on the simultaneous ejection of two molecular ions from the impact of Au(+)(n) (1< or =n< or =4) with energies ranging between 17 and 56 keV. The yields from single phenylalanine (Ph) emission, coemission of two Ph ions, and emission of the Ph dimer were measured. Large increases (1 to 2 orders of magnitude) in coemitted ion yields were observed with increasing projectile energy and complexity. Correlation coefficients were calculated for the coemission of two Ph ions; their behavior suggests differences in emission pathways for bombardment by atomic and polyatomic projectiles.

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

    NASA Technical Reports Server (NTRS)

    Macelroy, R. D.; Pohorille, A.

    1986-01-01

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

  18. Parallel helix bundles and ion channels: molecular modeling via simulated annealing and restrained molecular dynamics.

    PubMed Central

    Kerr, I D; Sankararamakrishnan, R; Smart, O S; Sansom, M S

    1994-01-01

    A parallel bundle of transmembrane (TM) alpha-helices surrounding a central pore is present in several classes of ion channel, including the nicotinic acetylcholine receptor (nAChR). We have modeled bundles of hydrophobic and of amphipathic helices using simulated annealing via restrained molecular dynamics. Bundles of Ala20 helices, with N = 4, 5, or 6 helices/bundle were generated. For all three N values the helices formed left-handed coiled coils, with pitches ranging from 160 A (N = 4) to 240 A (N = 6). Pore radius profiles revealed constrictions at residues 3, 6, 10, 13, and 17. A left-handed coiled coil and a similar pattern of pore constrictions were observed for N = 5 bundles of Leu20. In contrast, N = 5 bundles of Ile20 formed right-handed coiled coils, reflecting loosened packing of helices containing beta-branched side chains. Bundles formed by each of two classes of amphipathic helices were examined: (a) M2a, M2b, and M2c derived from sequences of M2 helices of nAChR; and (b) (LSSLLSL)3, a synthetic channel-forming peptide. Both classes of amphipathic helix formed left-handed coiled coils. For (LSSLLSL)3 the pitch of the coil increased as N increased from 4 to 6. The M2c N = 5 helix bundle is discussed in the context of possible models of the pore domain of nAChR. Images FIGURE 1 FIGURE 3 PMID:7529585

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

    SciTech Connect

    Gemmell, D.S.

    1987-01-01

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

  20. 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.

  1. 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.

  2. 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.

  3. Mechanism of beta-purothionin antimicrobial peptide inhibition by metal ions: molecular dynamics simulation study.

    PubMed

    Oard, Svetlana; Karki, Bijaya

    2006-04-20

    Wheat beta-purothionin is a highly potent antimicrobial peptide which, however, is inactivated by metal ions. The key structural properties and mechanisms of inhibition of beta-purothionin were investigated for the first time using unconstrained molecular dynamics simulations in explicit water. A series of simulations were performed to determine effects of temperature and the metal ions. Analyses of the unconstrained simulations allowed the experimentally unavailable structural and dynamic details to be unambiguously examined. The global fold and the alpha1 helix of beta-purothionin are thermally stable and not affected by metal ions. In contrast, the alpha2 helix unfolds with shift of temperature from 300 K and in the presence of metal ions. The network of conserved residues including Arg30 and Lys5 is sensitive to environmental changes and triggers unfolding. Loop regions display high flexibility and elevated dynamics, but are affected by metal ions. Our study provides insights into the mechanism of metal ion-based inhibition.

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

    NASA Astrophysics Data System (ADS)

    Drewsen, Michael

    2016-05-01

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

  5. Millimeter-wave Velocity Modulation Spectroscopy as a Technique to Selectively Detect Molecular Ions

    NASA Astrophysics Data System (ADS)

    Halfen, Dewayne; Ziurys, Lucy

    2009-05-01

    Molecular ions are usually very unstable and reactive species. As a result, their spectroscopic features can be difficult to identify and distinguish from those of neutral species, which tend to be more stable and thus have stronger signals. The technique of velocity modulation allows this disadvantage to be removed. This method uses the alternating plus and minus polarity of an electric field created by an AC discharge, which also produces the molecular ions, to selectively detect the molecular ions, while eliminating the neutral features. This technique has been applied at infrared and optical wavelengths for many years with much success. Recently, we designed and built a millimeter-wave velocity modulation spectrometer, the first ever constructed. This instrument has been used to create and study multiple molecular ions, including metal-bearing molecular ions. The rotational spectrum of these species, such as TiCl^+, VCl^+, TiF^+, FeO^+, FeCO^+, and SiCl^+, has been investigated with this new machine in our laboratory. Results of these studies along with a description of the velocity modulation technique and instrument will be presented.

  6. 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.

  7. Investigation of the silicon ion density during molecular beam epitaxy growth

    NASA Astrophysics Data System (ADS)

    Eifler, G.; Kasper, E.; Ashurov, Kh.; Morozov, S.

    2002-05-01

    Ions impinging on a surface during molecular beam epitaxy influence the growth and the properties of the growing layer, for example, suppression of dopant segregation and the generation of crystal defects. The silicon electron gun in the molecular beam epitaxy (MBE) equipment is used as a source for silicon ions. To use the effect of ion bombardment the mechanism of generation and distribution of ions was investigated. A monitoring system was developed and attached at the substrate position in the MBE growth chamber to measure the ion and electron densities towards the substrate. A negative voltage was applied to the substrate to modify the ion energy and density. Furthermore the current caused by charge carriers impinging on the substrate was measured and compared with the results of the monitoring system. The electron and ion densities were measured by varying the emission current of the e-gun achieving silicon growth rates between 0.07 and 0.45 nm/s and by changing the voltage applied to the substrate between 0 to -1000 V. The dependencies of ion and electron densities were shown and discussed within the framework of a simple model. The charged carrier densities measured with the monitoring system enable to separate the ion part of the substrate current and show its correlation to the generation rate. Comparing the ion density on the whole substrate and in the center gives a hint to the ion beam focusing effect. The maximum ion and electron current densities obtained were 0.40 and 0.61 μA/cm2, respectively.

  8. 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

    2016-03-07

    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.

  9. 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.

  10. Properties of the Excited States of Molecular Ions.

    DTIC Science & Technology

    1981-04-13

    constants of Albritton, Schmeltekopf. Harrop, that a population of ions with an energy spread AE which Zara , and Czarny. " as previously described. A de...J. T. Moseley, J. -B. Ozencs. F. V. Kowalski. R.. T. Hawkins, and A. L. Schseme. J. Opt. C. Paent. end M. Tadjedine. Chain . Ph,.. 17, 81 (1976). Soc...Mass Spectrometry, Houston. Texas (1975); tin and Dispersion on High-Alttoade Ideasrnents of Atino- U. L. Vestal and G. H. Mauclalrs. J. Chain . Ph

  11. Hydration Free Energies of Molecular Ions from Theory and Simulation.

    PubMed

    Misin, Maksim; Fedorov, Maxim V; Palmer, David S

    2016-02-11

    We present a theoretical/computational framework for accurate calculation of hydration free energies of ionized molecular species. The method is based on a molecular theory, 3D-RISM, combined with a recently developed pressure correction (PC+). The 3D-RISM/PC+ model can provide ∼3 kcal/mol hydration free energy accuracy for a large variety of ionic compounds, provided that the Galvani potential of water is taken into account. The results are compared with direct atomistic simulations. Several methodological aspects of hydration free energy calculations for charged species are discussed.

  12. 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.

  13. Li ion diffusion mechanisms in LiFePO4: an ab initio molecular dynamics study.

    PubMed

    Yang, Jianjun; Tse, John S

    2011-11-17

    The mechanisms for thermal (self) diffusion of Li ions in fully lithiated LiFePO(4) have been investigated with spin polarized ab initio molecular dynamics calculations. The effect of electron correlation is taken into account with the GGA+U formalism. It was found that Li ion diffusion is not a continuous process but through a series of jumps from one site to another. A dominant process is the hopping between neighboring Li sites around the PO(4) groups, which results in a zigzag pathway along the crystallographic b-axis. This observation is in agreement with a recent neutron diffraction experiment. A second process involves the collaborative movements of the Fe ions leading to the formation of antisite defects and promotes Li diffusion across the Li ion channels. The finding of the second mechanism demonstrates the benefit of ab initio molecular dynamics simulation in sampling diffusion pathways that may not be anticipated.

  14. 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.

  15. Molecular Growth Inside of Polycyclic Aromatic Hydrocarbon Clusters Induced by Ion Collisions.

    PubMed

    Delaunay, Rudy; Gatchell, Michael; Rousseau, Patrick; Domaracka, Alicja; Maclot, Sylvain; Wang, Yang; Stockett, Mark H; Chen, Tao; Adoui, Lamri; Alcamí, Manuel; Martín, Fernando; Zettergren, Henning; Cederquist, Henrik; Huber, Bernd A

    2015-05-07

    The present work combines experimental and theoretical studies of the collision between keV ion projectiles and clusters of pyrene, one of the simplest polycyclic aromatic hydrocarbons (PAHs). Intracluster growth processes induced by ion collisions lead to the formation of a wide range of new molecules with masses larger than that of the pyrene molecule. The efficiency of these processes is found to strongly depend on the mass and velocity of the incoming projectile. Classical molecular dynamics simulations of the entire collision process-from the ion impact (nuclear scattering) to the formation of new molecular species-reproduce the essential features of the measured molecular growth process and also yield estimates of the related absolute cross sections. More elaborate density functional tight binding calculations yield the same growth products as the classical simulations. The present results could be relevant to understand the physical chemistry of the PAH-rich upper atmosphere of Saturn's moon Titan.

  16. Observation of a rotational transition of trapped and sympathetically cooled molecular ions

    NASA Astrophysics Data System (ADS)

    Shen, J.; Borodin, A.; Hansen, M.; Schiller, S.

    2012-03-01

    We demonstrate rotational excitation of molecular ions that are sympathetically cooled by laser-cooled atomic ions to a temperature as low as approximately 10 mK. The molecular hydrogen ions HD+ and the fundamental rotational transition (v=0,N=0)→(v'=0,N'=1) at 1.3 THz, the most fundamental dipole-allowed rotational transition of any molecule, are used as a test case. This transition has not been observed before. Rotational laser cooling was employed in order to increase the signal, and resonance-enhanced multiphoton dissociation was used as detection method. The black-body-radiation-induced rotational excitation is also observed. The extension of the method to other molecular species is briefly discussed.

  17. 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.

  18. 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.

  19. A Molecular Mechanics Study of Monensin B Ion Selectivity.

    DTIC Science & Technology

    well known knot theorist working with Jon Simon under the math part of the ONR stereochemical topology project. 2) The 5-rung THYME diol-ditosylate has...trefoil knot, which will posses 100 atoms in the ring. 3) The first molecular mechanics studies on the THYME system have been accomplished. 4) Preliminary

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

    PubMed

    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

    2016-12-01

    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. Graphical Abstract ᅟ.

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

    SciTech Connect

    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

    2016-09-06

    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 to use for in situ liquid SIMS to study solid–liquid and liquid–vacuum interfaces.

  2. 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

    2016-12-01

    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.

  3. Evolutions of Molecular Oxygen Formation and Sodium Migration in Xe Ion Irradiated Borosilicate Glasses

    SciTech Connect

    Chen, Liang; Zhang, Duofei F.; Lv, Peng; Zhang, Jiandong; Du, Xing; Yuan, Wei; Nan, Shuai; Zhu, Zihua; Wang, Tieshan

    2016-07-23

    The modifications of a commercial borosilicate glass induced by Xe ion irradiation have been studied by Raman spectroscopy and ToF-SIMS depth profiling. A decrease in the average Si–O–Si angle, an increase in the population of three-membered rings and an increase of the glass polymerization are evidenced. The molecular oxygen appears in the irradiated glasses after the irradiation fluence reaches approximately 1015 ions/cm2. The O2 concentration decreaseswith the depth of irradiated glass at the ion fluence of 2 × 1016 ions/cm2. A sodiumdepleted layer at the surface and a depleted zone at around the penetration depth of 5 MeV Xe ions are observed. The thickness of the sodium depleted layer increases with the irradiation fluence. Moreover, comparing with previous results after electron and Ar ion irradiation, it can be concluded that the nuclear energy deposition can partially inhibit the formation of molecular oxygen and increase the threshold value of electron energy deposition for the molecular oxygen formation.

  4. Leading-order relativistic corrections to the dipole polarizability of hydrogen molecular ions

    NASA Astrophysics Data System (ADS)

    Aznabayev, D. T.; Bekbaev, A. K.; Zhaugasheva, S. A.; Korobov, V. I.

    2017-01-01

    The static dipole polarizability for the hydrogen molecular ions {{{H}}}2+, HD+, and {{{D}}}2+ are calculated. These new data for polarizability take into account the leading-order relativistic corrections to the wave function of the three-body system resulting from the Breit-Pauli Hamiltonian of m{α }4 order. Our study covers a wide range of rotational (J=0-5) and vibrational (v=0-10) states, which are of practical interest for precision spectroscopy of the hydrogen molecular ions.

  5. Molecular Dynamics Simulation of Multivalent-Ion Mediated Attraction between DNA Molecules

    NASA Astrophysics Data System (ADS)

    Dai, Liang; Mu, Yuguang; Nordenskiöld, Lars; van der Maarel, Johan R. C.

    2008-03-01

    All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+) and cobalt hexamine (3+). The inter-DNA interaction potential is obtained with the umbrella sampling technique. The attractive force is rationalized in terms of the formation of ion bridges, i.e., multivalent ions which are simultaneously bound to the two opposing DNA molecules. The lifetime of the ion bridges is short on the order of a few nanoseconds.

  6. Optimization of the molecular dynamics method for simulations of DNA and ion transport through biological nanopores.

    PubMed

    Wells, David B; Bhattacharya, Swati; Carr, Rogan; Maffeo, Christopher; Ho, Anthony; Comer, Jeffrey; Aksimentiev, Aleksei

    2012-01-01

    Molecular dynamics (MD) simulations have become a standard method for the rational design and interpretation of experimental studies of DNA translocation through nanopores. The MD method, however, offers a multitude of algorithms, parameters, and other protocol choices that can affect the accuracy of the resulting data as well as computational efficiency. In this chapter, we examine the most popular choices offered by the MD method, seeking an optimal set of parameters that enable the most computationally efficient and accurate simulations of DNA and ion transport through biological nanopores. In particular, we examine the influence of short-range cutoff, integration timestep and force field parameters on the temperature and concentration dependence of bulk ion conductivity, ion pairing, ion solvation energy, DNA structure, DNA-ion interactions, and the ionic current through a nanopore.

  7. 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.

  8. 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.

  9. 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.

  10. The role of ion electrophoresis in electroporation-mediated molecular delivery

    NASA Astrophysics Data System (ADS)

    Li, Jianbo; Lin, Hao

    2009-11-01

    Electroporation is a widely applied technique to deliver active molecules into the cellular compartment, to perform a variety of tasks such as gene therapy and directed stem cell differentiation. In this technique, an electric field transiently permeabilizes the cellular membrane to facilitate molecular exchange. While the permeabilization process is relatively well-understood, the transport mechanisms for molecular delivery are still under debate. In this work, the role of ion electrophoresis in electroporation-mediated molecular delivery is investigated using numerical simulations. The result indicates that ion electrophoresis is the dominant mode of transport in the delivery of small charged molecules. Furthermore, the achievable intracellular concentration is strongly influenced by the conductivity difference between the cytoplasm and the buffer, a phenomenon known as ``field-amplified sample stacking''. The result agrees well with the fluorescence measurement by Gabriel and Teissi'e (1999), and suggests a new possibility to simultaneously improve cell viability and efficiency in electroporation-mediated molecular delivery.

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

    NASA Astrophysics Data System (ADS)

    Tudryn, Gregory J.

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

  12. Molecular depth profiling of multilayer polymer films using time-of-flight secondary ion mass spectrometry.

    PubMed

    Wagner, M S

    2005-02-01

    The low penetration depth and high sputter rates obtained using polyatomic primary ions have facilitated their use for the molecular depth profiling of some spin-cast polymer films by secondary ion mass spectrometry (SIMS). In this study, dual-beam time-of-flight (TOF) SIMS (sputter ion, 5 keV SF(5)(+); analysis ion, 10 keV Ar(+)) was used to depth profile spin-cast multilayers of poly(methyl methacrylate) (PMMA), poly(2-hydroxyethyl methacrylate) (PHEMA), and trifluoroacetic anhydride-derivatized poly(2-hydroxyethyl methacrylate) (TFAA-PHEMA) on silicon substrates. Characteristic positive and negative secondary ions were monitored as a function of depth using SF(5)(+) primary ion doses necessary to sputter through the polymer layer and uncover the silicon substrate (>5 x10(14) ions/cm(2)). The sputter rates of the polymers in the multilayers were typically less than for corresponding single-layer films, and the order of the polymers in the multilayer affected the sputter rates of the polymers. Multilayer samples with PHEMA as the outermost layer resulted in lowered sputter rates for the underlying polymer layer due to increased ion-induced damage accumulation rates in PHEMA. Additionally, the presence of a PMMA or PHEMA overlayer significantly decreased the sputter rate of TFAA-PHEMA underlayers due to ion-induced damage accumulation in the overlayer. Typical interface widths between adjacent polymer layers were 10-15 nm for bilayer films and increased with depth to approximately 35 nm for the trilayer films. The increase in interface width and observations using optical microscopy showed the formation of sputter-induced surface roughness during the depth profiles of the trilayer polymer films. This study shows that polyatomic primary ions can be used for the molecular depth profiling of some multilayer polymer films and presents new opportunities for the analysis of thin organic films using TOF-SIMS.

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  14. 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.

  15. Molecular biology and biophysical properties of ion channel gating pores.

    PubMed

    Moreau, Adrien; Gosselin-Badaroudine, Pascal; Chahine, Mohamed

    2014-11-01

    The voltage sensitive domain (VSD) is a pivotal structure of voltage-gated ion channels (VGICs) and plays an essential role in the generation of electrochemical signals by neurons, striated muscle cells, and endocrine cells. The VSD is not unique to VGICs. Recent studies have shown that a VSD regulates a phosphatase. Similarly, Hv1, a voltage-sensitive protein that lacks an apparent pore domain, is a self-contained voltage sensor that operates as an H⁺ channel. VSDs are formed by four transmembrane helices (S1-S4). The S4 helix is positively charged due to the presence of arginine and lysine residues. It is surrounded by two water crevices that extend into the membrane from both the extracellular and intracellular milieus. A hydrophobic septum disrupts communication between these water crevices thus preventing the permeation of ions. The septum is maintained by interactions between the charged residues of the S4 segment and the gating charge transfer center. Mutating the charged residue of the S4 segment allows the water crevices to communicate and generate gating pore or omega pore. Gating pore currents have been reported to underlie several neuronal and striated muscle channelopathies. Depending on which charged residue on the S4 segment is mutated, gating pores are permeant either at depolarized or hyperpolarized voltages. Gating pores are cation selective and seem to converge toward Eisenmann's first or second selectivity sequences. Most gating pores are blocked by guanidine derivatives as well as trivalent and quadrivalent cations. Gating pores can be used to study the movement of the voltage sensor and could serve as targets for novel small therapeutic molecules.

  16. A molecular dynamics analysis of ion irradiation of ultrathin amorphous carbon films

    NASA Astrophysics Data System (ADS)

    Qi, J.; Komvopoulos, K.

    2016-09-01

    Molecular dynamics (MD) simulations provide insight into nanoscale problems where continuum description breaks down, such as the modeling of ultrathin films. Amorphous carbon (a-C) films are commonly used as protective overcoats in various contemporary technologies, including microelectromechanical systems, bio-implantable devices, optical lenses, and hard-disk drives. In all of these technologies, the protective a-C film must be continuous and very thin. For example, to achieve high storage densities (e.g., on the order of 1 Tb/in.2) in magnetic recording, the thickness of the a-C film used to protect the magnetic media and the recording head against mechanical wear and corrosion must be 2-3 nm. Inert ion irradiation is an effective post-deposition method for reducing the film thickness, while preserving the mechanical and chemical characteristics. In this study, MD simulations of Ar+ ion irradiated a-C films were performed to elucidate the effects of the ion incidence angle and ion kinetic energy on the film thickness and structure. The MD results reveal that the film etching rate exhibits a strong dependence on the ion kinetic energy and ion incidence angle, with a maximum etching rate corresponding to an ion incidence angle of ˜20°. It is also shown that Ar+ ion irradiation mainly affects the structure of the upper half of the ultrathin a-C film and that carbon atom hybridization is a strong function of the ion kinetic energy and ion incidence angle. The results of this study elucidate the effects of important ion irradiation parameters on the structure and thickness of ultrathin films and provide fundamental insight into the physics of dry etching.

  17. 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

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

    NASA Technical Reports Server (NTRS)

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

    1974-01-01

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

  19. 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

  20. Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods.

    PubMed

    Chakravorty, Dhruva K; Wang, Bing; Lee, Chul Won; Guerra, Alfredo J; Giedroc, David P; Merz, Kenneth M

    2013-06-01

    Correctly calculating the structure of metal coordination sites in a protein during the process of nuclear magnetic resonance (NMR) structure determination and refinement continues to be a challenging task. In this study, we present an accurate and convenient means by which to include metal ions in the NMR structure determination process using molecular dynamics (MD) simulations constrained by NMR-derived data to obtain a realistic and physically viable description of the metal binding site(s). This method provides the framework to accurately portray the metal ions and its binding residues in a pseudo-bond or dummy-cation like approach, and is validated by quantum mechanical/molecular mechanical (QM/MM) MD calculations constrained by NMR-derived data. To illustrate this approach, we refine the zinc coordination complex structure of the zinc sensing transcriptional repressor protein Staphylococcus aureus CzrA, generating over 130 ns of MD and QM/MM MD NMR-data compliant sampling. In addition to refining the first coordination shell structure of the Zn(II) ion, this protocol benefits from being performed in a periodically replicated solvation environment including long-range electrostatics. We determine that unrestrained (not based on NMR data) MD simulations correlated to the NMR data in a time-averaged ensemble. The accurate solution structure ensemble of the metal-bound protein accurately describes the role of conformational sampling in allosteric regulation of DNA binding by zinc and serves to validate our previous unrestrained MD simulations of CzrA. This methodology has potentially broad applicability in the structure determination of metal ion bound proteins, protein folding and metal template protein-design studies.

  1. 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.

  2. Studies of the Temperature Dependence of Electron Dissociative Recombination for a Series of Molecular Ions

    NASA Astrophysics Data System (ADS)

    McLain, Jason; Plasil, Radek; Molek, Chris; Adams, Nigel

    2003-04-01

    A temperature variable flowing afterglow is being used with an electrostatic Langmuir probe to determine the rate coefficients for the recombination of a series of molecular ions with electrons. Recombination rate coefficients for ions such as CH_5^+, C_2H_5^+, and C_6H_7^+, have been determined at temperatures ranging from 80 to 600 K, and this is being extended to other hydrocarbon ions. The data available at present indicate recombination rate coefficients are large and exhibit only slight dependencies on temperature. Techniques are also being developed for measuring recombination rate coefficients for several simultaneously recombining ionic species. The dissociative recombination of many of these ions is significant to the atmosphere of Titan, which is to be probed by the NASA Huygens-Cassini spacecraft that is presently approaching the Saturnian system.

  3. Molecular dynamics study on ion diffusion in LiFePO4 olivine materials.

    PubMed

    Zhang, Peixin; Wu, Yanpeng; Zhang, Dongyun; Xu, Qiming; Liu, Jianhong; Ren, Xiangzhong; Luo, Zhongkuan; Wang, Mingliang; Hong, Weiliang

    2008-06-19

    Molecular dynamics (MD) simulations have been employed to investigate the ionic diffusion and the structure of LiFePO 4 cathode material. The results correspond well with the published experimental observations. The simulation results indicated that the diffusion of lithium ions was thermally activated and more significant than those of other ions. Compared with other cathode materials, the shifts of ions were less significant in LiFePO 4. This suggested that LiFePO 4 was more thermally stable. The snapshots of the positions of lithium atoms over a range of the steps provided a microscopic picture and the picture showed the lithium ions migrated through one-dimension channels.

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

    PubMed Central

    Jordan, P C

    1990-01-01

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

  5. Understanding the rates and molecular mechanism of water-exchange around aqueous ions using molecular simulations.

    PubMed

    Annapureddy, Harsha V R; Dang, Liem X

    2014-07-31

    Solvation processes occurring around aqueous ions are of fundamental importance in physics, chemistry, and biology. Over the past few decades, several experimental and theoretical studies were devoted to understanding ion solvation and the processes involved in it. In this article, we present a summary of our recent efforts that, through computer simulations, focused on providing a comprehensive understanding of solvent-exchange processes around aqueous ions. To accomplish these activities, we have looked at the mechanistic properties associated with the water-exchange process, such as potentials of mean force, time-dependent transmission coefficients, and the corresponding rate constants using transition state theory, the reactive flux method, and Grote-Hynes treatments of the dynamic response of the solvent.

  6. Molecular dynamics simulation analysis of ion irradiation effects on plasma-liquid interface

    NASA Astrophysics Data System (ADS)

    Minagawa, Yudai; Shirai, Naoki; Uchida, Satoshi; Tochikubo, Fumiyoshi

    2013-09-01

    Nonthermal atmospheric plasmas are used in a wide range of fields because the high-density plasma can be easily irradiated to various substances such as solid, liquid, biological object and so on. On the other hand, the mechanisms of physical and chemical phenomena at the plasma-liquid interface are not well understood yet. To investigate the effects of ion impact from plasma on water surface, we analyzed behavior of liquid water by classical molecular dynamics simulation. Simulation system consists of an irradiation particle in gas phase and 2000 water molecules in liquid phase. O+ ion with 10 eV or 100 eV was impinged on the water surface. Ion impact induced increasing water temperature and ejection of water molecules. The averaged number of evaporated water molecules by ion impact is 0.6 molecules at 10 eV and 7.0 molecules at 100 eV. The maximum ion penetration depth was 1.14 nm at 10 eV and 2.75 nm at 100 eV. Ion entering into water disturbs the stable hydrogen bonding configurations between water molecules and gives energy to water molecules. Some water molecules rotated and moved by ion interaction impact on other water molecules one after another. When the water molecule near the surface received strongly repulsive force, it released into gas phase. This work was supported financially in part by a Grant-in-Aid for Scientific Research on Innovation Areas (No21110007) from MEXT, Japan.

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

    PubMed

    Wineman-Fisher, Vered; Miller, Yifat

    2016-08-03

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

  8. An ion gating mechanism of gastric H,K-ATPase based on molecular dynamics simulations.

    PubMed

    Law, Richard J; Munson, Keith; Sachs, George; Lightstone, Felice C

    2008-09-15

    Gastric H,K-ATPase is an electroneutral transmembrane pump that moves protons from the cytoplasm of the parietal cell into the gastric lumen in exchange for potassium ions. The mechanism of transport against the established electrochemical gradients includes intermediate conformations in which the transferred ions are trapped (occluded) within the membrane domain of the pump. The pump cycle involves switching between the E1 and E2P states. Molecular dynamics simulations on homology models of the E2P and E1 states were performed to investigate the mechanism of K(+) movement in this enzyme. We performed separate E2P simulations with one K(+) in the luminal channel, one K(+) ion in the occlusion site, two K(+) ions in the occlusion site, and targeted molecular dynamics from E2P to E1 with two K(+) ions in the occlusion site. The models were inserted into a lipid bilayer system and were stable over the time course of the simulations, and K(+) ions in the channel moved to a consistent location near the center of the membrane domain, thus defining the occlusion site. The backbone carbonyl oxygen from residues 337 through 342 on the nonhelical turn of M4, as well as side-chain oxygen from E343, E795, and E820, participated in the ion occlusion. A single water molecule was stably bound between the two K(+) ions in the occlusion site, providing an additional ligand and partial shielding the positive charges from one another. Targeted molecular dynamics was used to transform the protein from the E2P to the E1 state (two K(+) ions to the cytoplasm). This simulation identified the separation of the water column in the entry channel as the likely gating mechanism on the luminal side. A hydrated exit channel also formed on the cytoplasmic side of the occlusion site during this simulation. Hence, water molecules became available to hydrate the ions. The movement of the M1M2 transmembrane segments, and the displacement of residues Q159, E160, Q110, and T152 during the

  9. Biomimetic supercontainers for size-selective electrochemical sensing of molecular ions

    PubMed Central

    Netzer, Nathan L.; Must, Indrek; Qiao, Yupu; Zhang, Shi-Li; Wang, Zhenqiang; Zhang, Zhen

    2017-01-01

    New ionophores are essential for advancing the art of selective ion sensing. Metal-organic supercontainers (MOSCs), a new family of biomimetic coordination capsules designed using sulfonylcalix[4]arenes as container precursors, are known for their tunable molecular recognition capabilities towards an array of guests. Herein, we demonstrate the use of MOSCs as a new class of size-selective ionophores dedicated to electrochemical sensing of molecular ions. Specifically, a MOSC molecule with its cavities matching the size of methylene blue (MB+), a versatile organic molecule used for bio-recognition, was incorporated into a polymeric mixed-matrix membrane and used as an ion-selective electrode. This MOSC-incorporated electrode showed a near-Nernstian potentiometric response to MB+ in the nano- to micro-molar range. The exceptional size-selectivity was also evident through contrast studies. To demonstrate the practical utility of our approach, a simulated wastewater experiment was conducted using water from the Fyris River (Sweden). It not only showed a near-Nernstian response to MB+ but also revealed a possible method for potentiometric titration of the redox indicator. Our study thus represents a new paradigm for the rational design of ionophores that can rapidly and precisely monitor molecular ions relevant to environmental, biomedical, and other related areas. PMID:28393841

  10. Predicting molecular formulas of fragment ions with isotope patterns in tandem mass spectra.

    PubMed

    Zhang, Jingfen; Gao, Wen; Cai, Jinjin; He, Simin; Zeng, Rong; Chen, Runsheng

    2005-01-01

    A number of different approaches have been proposed to predict elemental component formulas (or molecular formulas) of molecular ions in low and medium resolution mass spectra. Most of them rely on isotope patterns, enumerate all possible formulas for an ion, and exclude certain formulas violating chemical constraints. However, these methods cannot be well generalized to the component prediction of fragment ions in tandem mass spectra. In this paper, a new method, FFP (Fragment ion Formula Prediction), is presented to predict elemental component formulas of fragment ions. In the FFP method, the prediction of the best formulas is converted into the minimization of the distance between theoretical and observed isotope patterns. And, then, a novel local search model is proposed to generate a set of candidate formulas efficiently. After the search, FFP applies a new multiconstraint filtering to exclude as many invalid and improbable formulas as possible. FFP is experimentally compared with the previous enumeration methods, and shown to outperform them significantly. The results of this paper can help to improve the reliability of de novo in the identification of peptide sequences.

  11. 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

  12. Time slicing in 3D momentum imaging of the hydrogen molecular ion photo-fragmentation

    NASA Astrophysics Data System (ADS)

    Kaya, N.; Kaya, G.; Pham, F. V.; Strohaber, J.; Kolomenskii, A. A.; Schuessler, H. A.

    2017-02-01

    Photo-fragmentation of the hydrogen molecular ion was investigated with 800 nm, 50 fs laser pulses by employing a time slicing 3D imaging technique that enables the simultaneous measurement of all three momentum components which are linearly related with the pixel position and slicing time. This is done for each individual product particle arriving at the detector. This mode of detection allows us to directly measure the three-dimensional fragment momentum vector distribution without having to rely on mathematical reconstruction methods, which additionally require the investigated system to be cylindrically symmetric. We experimentally reconstruct the laser-induced photo-fragmentation of the hydrogen molecular ion. In previous experiments, neutral molecules were used as a target, but in this work, performed with molecular ions, the initial vibrational level populations are well-defined after electron bombardment, which facilitates the interpretation. We show that the employed time-slicing technique allows us to register the fragment momentum distribution that reflects the initial molecular states with greater detail, revealing features that were concealed in the full time-integrated distribution on the detector.

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

    PubMed Central

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

    2013-01-01

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

  14. 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.

  15. 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.

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

    SciTech Connect

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

    2009-01-01

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

  17. 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.

  18. Energy distributions of atomic and molecular ions sputtered by C 60+ projectiles

    NASA Astrophysics Data System (ADS)

    Delcorte, A.; Poleunis, C.; Bertrand, P.

    2006-07-01

    In the process of investigating the interaction of fullerene projectiles with adsorbed organic layers, we measured the kinetic energy distributions (KEDs) of fragment and parent ions sputtered from an overlayer of polystyrene (PS) oligomers cast on silver under 15 keV C 60+ bombardment. These measurements have been conducted using our TRIFT™ spectrometer, recently equipped with the C 60+ source developed by Ionoptika, Ltd. For atomic ions, the intensity corresponding to the high energy tail decreases in the following order: C +( E-0.4) > H +( E-1.5) > Ag +( E-3.5). In particular, the distribution of Ag + is not broader than those of Ag 2+ and Ag 3+ clusters, in sharp contrast with 15 keV Ga + bombardment. On the other hand, molecular ions (fragments and parent-like species) exhibit a significantly wider distribution using C 60+ instead of Ga + as primary ions. For instance, the KED of Ag-cationized PS oligomers resembles that of Ag + and Ag n+ clusters. A specific feature of fullerene projectiles is that they induce the direct desorption of positively charged oligomers, without the need of a cationizing metal atom. The energy spectrum of these PS + ions is significantly narrower then that of Ag-cationized oligomers. For characteristic fragments of PS, such as C 7H 7+ and C 15H 13+ and polycyclic fragments, such as C 9H 7+ and C 14H 10+, the high energy decay is steep ( E-4 - E-8). In addition, reorganized ions generally show more pronounced high energy tails than characteristic ions, similar to the case of monoatomic ion bombardment. This observation is consistent with the higher excitation energy needed for their formation. Finally, the fraction of hydrocarbon ions formed in the gas phase via unimolecular dissociation of larger species is slightly larger with gallium than with fullerene projectiles.

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

    NASA Astrophysics Data System (ADS)

    Glosli, James N.; Philpott, Michael R.

    1993-04-01

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

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

    PubMed

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

    2016-07-01

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

  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. Photoelectron momentum distributions of the hydrogen molecular ion driven by multicycle near-infrared laser pulses

    NASA Astrophysics Data System (ADS)

    Murakami, Mitsuko; Chu, Shih-I.

    2016-10-01

    The photoelectron momentum distributions (PMDs) of the hydrogen molecular ion H2+ driven by strong near-infrared laser pulses are studied based on the ab initio numerical solution of the time-dependent Schrödinger equation and the Volkov wave propagation. Both linear and circular polarization are considered, in accordance with the recent experiment by M. Odenweller et al. [Phys. Rev. A 89, 013424 (2014), 10.1103/PhysRevA.89.013424]. We will discuss the difference between the molecular (diatomic) and the atomic PMDs and the effect of molecular potential to the photoelectron energy. In particular, we demonstrate that the above-threshold ionization spectra of H2+ could upshift their energy when driven by a linearly polarized laser field parallel to the molecular axis.

  3. Understanding the Rates and Molecular Mechanism of Water-Exchange around Aqueous Ions Using Molecular Simulations

    SciTech Connect

    Annapureddy, Harsha V.; Dang, Liem X.

    2014-07-31

    Solvation processes occurring around aqueous ions are of fundamental importance in physics, chemistry, and biology. Over the past few decades, several experimental and theoretical studies were devoted to understanding ion solvation and the processes involved in it. In this article, we present a summary of our recent efforts that, through computer simulations, focused on providing a comprehensive understanding of solvent-exchange processes around aqueous ions. To accomplish these activities, we have looked at the mechanistic properties associated with the water-exchange process, such as potentials of mean force, time-dependent transmission coefficients, and the corresponding rate constants using transition rate theory, the reactive flux method, and Grote-Hynes treatments of the dynamic response of the solvent. The Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences (BES), of the U.S. Department of Energy (DOE) funded this work. Battelle operates Pacific Northwest National Laboratory for DOE. The calculations were carried out using computer resources provided by BES.

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

    NASA Astrophysics Data System (ADS)

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

    2007-01-01

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

  5. Ion channels or aquaporins as novel molecular targets in gastric cancer.

    PubMed

    Xia, Jianling; Wang, Hongqiang; Li, Shi; Wu, Qinghui; Sun, Li; Huang, Hongxiang; Zeng, Ming

    2017-03-06

    Gastric cancer (GC) is a common disease with few effective treatment choices and poor prognosis, and has the second-highest mortality rates among all cancers worldwide. Dysregulation and/or malfunction of ion channels or aquaporins (AQPs) are common in various human cancers. Furthermore, ion channels are involved in numerous important aspects of the tumor aggressive phonotype, such as proliferation, cell cycle, apoptosis, motility, migration, and invasion. Indeed, by localizing in the plasma membrane, ion channels or AQPs can sense and respond to extracellular environment changes; thus, they play a crucial role in cell signaling and cancer progression. These findings have expanded a new area of pharmaceutical exploration for various types of cancer, including GC. The involvement of multiple ion channels, such as voltage-gated potassium and sodium channels, intracellular chloride channels, 'transient receptor potential' channels, and AQPs, which have been shown to facilitate the pathogenesis of other tumors, also plays a role in GC. In this review, an overview of ion channel and aquaporin expression and function in carcinogenesis of GC is presented. Studies of ion channels or AQPs will advance our understanding of the molecular genesis of GC and may identify novel and effective targets for the clinical application of GC.

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  7. 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

  8. 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.

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

    PubMed Central

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

    1995-01-01

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

  10. Organic surfaces excited by low-energy ions: atomic collisions, molecular desorption and buckminsterfullerenes.

    PubMed

    Delcorte, Arnaud

    2005-10-07

    This article reviews the recent progress in the understanding of kiloelectronvolt particle interactions with organic solids, including atomic displacements in a light organic medium, vibrational excitation and desorption of fragments and entire molecules. This new insight is the result of a combination of theoretical and experimental approaches, essentially molecular dynamics (MD) simulations and secondary ion mass spectrometry (SIMS). Classical MD simulations provide us with a detailed microscopic view of the processes occurring in the bombarded target, from the collision cascade specifics to the scenarios of molecular emission. Time-of-flight SIMS measures the mass and energy distributions of sputtered ionized fragments and molecular species, a precious source of information concerning their formation, desorption, ionization and delayed unimolecular dissociation in the gas phase. The mechanisms of energy transfer and sputtering are compared for bulk molecular solids, organic overlayers on metal and large molecules embedded in a low-molecular weight matrix. These comparisons help understand some of the beneficial effects of metal substrates and matrices for the analysis of molecules by SIMS. In parallel, I briefly describe the distinct ionization channels of molecules sputtered from organic solids and overlayers. The specific processes induced by polyatomic projectile bombardment, especially fullerenes, are discussed on the basis of new measurements and calculations. Finally, the perspective addresses the state-of-the-art and potential developments in the fields of surface modification and analysis of organic materials by kiloelectronvolt ion beams.

  11. 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.

  12. 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.

  13. Dose effects on amorphous silicon sputtering by argon ions: A molecular dynamics simulation

    SciTech Connect

    Marques, L.A.; Rubio, J.E.; Jaraiz, M.; Bailon, L.A.; Barbolla, J.J.

    1997-02-01

    We have investigated, using molecular dynamics techniques, the sputtering yield enhancement of amorphous silicon produced by argon ion accumulation within the target. Several amorphous silicon samples, with different argon contents, were bombarded with 1 keV argon ions at normal incidence. To study the influence of the target structure, we considered samples with different argon arrangements, either uniformly distributed or within solid bubbles. We have observed that silicon sputtering yield increases linearly with dose until steady state conditions are reached. This enhancement is produced by the shallow argon atoms through the weakening of Si{endash}Si bonds. We have also observed that argon release takes place even long after the end of the collisional phase, and it is produced by ion-induced desorption and bubble destabilization. This enhanced argon yield determines the dose where target saturation and steady state conditions are reached. {copyright} {ital 1997 American Institute of Physics.}

  14. 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 +}.

  15. Field-enhanced ion transport in solids: Reexamination with molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Genreith-Schriever, A. R.; De Souza, R. A.

    2016-12-01

    Classical molecular-dynamics simulations were used to examine the effect of an electric field on the mobility of oxygen ions in the model crystalline oxide CeO2. Simulation cells containing oxygen vacancies were subjected at temperatures 1000 ≤T /K ≤1600 to electric field strengths 0.1 ≤E /MV cm-1≤40 to obtain the oxygen-ion mobility ui(E ,T ) . In addition, static nudged-elastic-band calculations were performed to obtain directly the forward/reverse barriers for oxygen-ion migration, Δ Hmigf /r . Qualitatively, ui behaves as expected: independent of E at low values of E and exponentially dependent on E at high values. The quantitative (standard) Mott-Gurney treatment, however, underestimates Δ Hmigf at high E and thus overestimates ui. A new, superior analytical expression for ui(E ,T ) is consequently derived.

  16. Molecular mechanisms of decomposition of hydrated Na+Cl- ion pairs under planar nanopore conditions

    NASA Astrophysics Data System (ADS)

    Shevkunov, S. V.

    2017-02-01

    The decomposition of Na+Cl- ion pairs under the conditions of a nanoscopic planar pore with structureless walls in a material contact with water vapor at 298 K is simulated by Monte Carlo method. The transition from the state of a contact ion pair (CIP) to the state of solvent-separated ion pair (SSIP) is shown to occur as a result of an increase in the vapor pressure over a pore after exceeding the threshold number of molecules in a hydrate shell. It is found that the planar form of a molecular cluster under the conditions of a narrow pore does not level an abrupt structural transition and the formation of hydrogen bonds in the hydrate shell starts after three molecules are added. The hydrogen bond length under pore conditions is found to be resistant to variations in the hydrate shell size and coincides with that in water under normal conditions.

  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. Ion regulation in fish gills: recent progress in the cellular and molecular mechanisms.

    PubMed

    Hwang, Pung-Pung; Lee, Tsung-Han; Lin, Li-Yih

    2011-07-01

    Fish encounter harsh ionic/osmotic gradients on their aquatic environments, and the mechanisms through which they maintain internal homeostasis are more challenging compared with those of terrestrial vertebrates. Gills are one of the major organs conducting the internal ionic and acid-base regulation, with specialized ionocytes as the major cells carrying out active transport of ions. Exploring the iono/osmoregulatory mechanisms in fish gills, extensive literature proposed several models, with many conflicting or unsolved issues. Recent studies emerged, shedding light on these issues with new opened windows on other aspects, on account of available advanced molecular/cellular physiological approaches and animal models. Respective types of ionocytes and ion transporters, and the relevant regulators for the mechanisms of NaCl secretion, Na(+) uptake/acid secretion/NH(4)(+) excretion, Ca(2+) uptake, and Cl(-) uptake/base secretion, were identified and functionally characterized. These new ideas broadened our understanding of the molecular/cellular mechanisms behind the functional modification/regulation of fish gill ion transport during acute and long-term acclimation to environmental challenges. Moreover, a model for the systematic and local carbohydrate energy supply to gill ionocytes during these acclimation processes was also proposed. These provide powerful platforms to precisely study transport pathways and functional regulation of specific ions, transporters, and ionocytes; however, very few model species were established so far, whereas more efforts are needed in other species.

  19. 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

  20. 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.

  1. The Solvation Structure of Lithium Ions in an Ether Based Electrolyte Solution from First-Principles Molecular Dynamics.

    PubMed

    Callsen, Martin; Sodeyama, Keitaro; Futera, Zdeněk; Tateyama, Yoshitaka; Hamada, Ikutaro

    2017-01-12

    The solvation and desolvation of the Li ion play a crucial role in the electrolytes of Li based secondary batteries, and their understanding at the microscopic level is of great importance. Oligoether (glyme) based electrolytes have attracted much attention as electrolytes used in Li based secondary batteries, such as Li-ion, Li-S, and Li-O2 batteries. However, the solvation structure of the Li ion in glyme based electrolytes has not been fully clarified yet. We present a computational study on the solvation structure of lithium ions in the mixture of triglyme and lithium bis(trifluoromethylsulfonyl)-amide (LiTFSA) by means of molecular orbital and molecular dynamics calculations based on density functional theory. We found that, in the electrolyte solution composed of the equimolar mixture of triglyme and LiTFSA, lithium ions are solvated mainly by crown-ether-like curled triglyme molecules and in direct contact with an TFSA anion. We also found the aggregate formed with Li ion and TFSA anions and/or triglyme molecule(s) is equally stable, which has not been reported in the previous classical molecular dynamics simulations, suggesting that in reality a small fraction of Li ions form aggregates and they might have a significant impact on the Li ion transport. Our results demonstrate the importance of performing electronic structure based molecular dynamics of electrolyte solution to clarify the detailed solvation structure of the Li ion.

  2. Effect of uranyl ion concentration on structure and dynamics of aqueous uranyl solution: a molecular dynamics simulation study.

    PubMed

    Chopra, Manish; Choudhury, Niharendu

    2014-12-11

    The effect of uranyl ion concentration on structure and dynamics of aqueous solutions of uranyl ions is investigated by molecular dynamics simulations. In order to get an idea about the effect of concentration of uranyl ions on local structural arrangements of water molecules around the uranyl ion, radial distribution functions of water molecules around the uranyl ion are analyzed for aqueous uranyl solutions of various concentrations. The concentration effect on translational dynamics has also been analyzed by calculating diffusion coefficients of uranyl ion, water, and nitrate ions in solution from their respective mean squared displacements. Mobility of water as well as uranyl ions has been found to decrease with increasing concentration of the uranyl ions. Orientational dynamics of water about different molecular axes of water have also been analyzed and decreasing orientational mobility of water with increasing uranyl concentration has been found. In order to get further insight into origin of slowing down of the translational mobility of water molecules with increasing uranyl ion concentration, two separate effects namely long-range effect of uranyl ions on the dynamics of water molecules beyond the solvation shell and short-range effect involving dynamics of solvation shell water have been analyzed. It is found that long-range effect is responsible for the slowing down of translational dynamics of water molecules in the presence of uranyl ions.

  3. The influence of mineral ions on the microbial production and molecular weight of hyaluronic acid.

    PubMed

    Pires, Aline Mara B; Eguchi, Silvia Y; Santana, Maria Helena Andrade

    2010-12-01

    This study aimed to evaluate the influence of the culture medium supplementation with mineral ions, focusing on the growth of Streptococcus zooepidemicus as well as on the production and average molecular weight (MW) of hyaluronic acid (HA). The ions were investigated in terms of individual absence from the totally supplemented medium (C+) or individual presence in the non-supplemented medium (C-), where C+ and C- were used as controls. Differences between the effects were analyzed using the Tukey's test at p < 0.05. The adopted criteria considered required the ions, whose individual absence attained at 80% or less of the C+ and their individual presence was 20% or more than the C-. The supplementation was either inhibitory or acted in synergy with other ions, when the individual absence or presence was 20% higher than C+ or 20% lower than C-, respectively. Results showed that the effects of C+ or C- were equal for both the production of HA and its yield from glucose. However, C+ showed to be beneficial to cell growth while the individual absence of Na+ was beneficial to the production of HA. The highest MW of HA (7.4 x 10⁷ Da) was observed in the individual presence of Na+ in spite of the lowest HA concentration (0.65 g x L⁻¹). These results suggest that the quality of HA can be modulated through the mineral ion supplementation.

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

    NASA Astrophysics Data System (ADS)

    Mogurampelly, Santosh; Ganesan, Venkat

    2015-03-01

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

  5. A molecular framework for temperature-dependent gating of ion channels

    PubMed Central

    Chowdhury, Sandipan; Jarecki, Brian W.; Chanda, Baron

    2014-01-01

    Summary Perception of heat or cold in higher organisms is mediated by specialized ion channels whose gating is exquisitely sensitive to temperature. The physicochemical underpinnings of this temperature-sensitive gating have proven difficult to parse. Here, we took a bottom-up protein design approach, and rationally engineered ion channels to activate in response to thermal stimuli. By varying amino acid polarities at sites undergoing state-dependent changes in solvation, we were able to systematically confer temperature-sensitivity to a canonical voltage-gated ion channel. Our results imply that the specific heat capacity change during channel gating is a major determinant of thermo-sensitive gating. We also show that reduction of gating charges amplifies temperature-sensitivity of designer channels which accounts for low voltage-sensitivity in all known temperature-gated ion channels. These emerging principles suggest a plausible molecular mechanism for temperature-dependent gating that reconcile how ion channels with an overall conserved transmembrane architecture may exhibit a wide range of temperature-sensing phenotypes. PMID:25156949

  6. 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.

  7. Rotation of cold molecular ions inside a Bose-Einstein condensate

    NASA Astrophysics Data System (ADS)

    Midya, Bikashkali; Tomza, Michał; Schmidt, Richard; Lemeshko, Mikhail

    2016-10-01

    We use recently developed angulon theory [R. Schmidt and M. Lemeshko, Phys. Rev. Lett. 114, 203001 (2015), 10.1103/PhysRevLett.114.203001] to study the rotational spectrum of a cyanide molecular anion immersed into Bose-Einstein condensates of rubidium and strontium. Based on ab initio potential energy surfaces, we provide a detailed study of the rotational Lamb shift and many-body-induced fine structure which arise due to dressing of molecular rotation by a field of phonon excitations. We demonstrate that the magnitude of these effects is large enough in order to be observed in modern experiments on cold molecular ions. Furthermore, we introduce a novel method to construct pseudopotentials starting from the ab initio potential energy surfaces, which provides a means to obtain effective coupling constants for low-energy polaron models.

  8. Ion Association in AlCl3 Aqueous Solutions from Constrained First-Principles Molecular Dynamics

    SciTech Connect

    Cauet, Emilie L.; Bogatko, Stuart A.; Bylaska, Eric J.; Weare, John H.

    2012-10-15

    Ab initio molecular dynamics was used to investigate the ion pairing behavior between Cl- and the Al3+ ion in an aqueous AlCl3 solution containing 63 water molecules. A series of constrained simulations was carried out at 300 K for up to 16 ps each, by fixing the inter-nuclear separation (rAl-Cl) between the Al3+ ion and one of the Cl- ions. The calculated potential of mean force of the Al3+-Cl- ion pair shows a pronounced minimum at rAl-Cl = 2.3 Å corresponding to a contact ion pair (CIP). Two local minima assigned to solvent separated ion pairs (SSIP) are identified at rAl-Cl= 4.4 and 6.0 Å. The positions of the free energy minima coincide with the hydration shell intervals of the Al3+ cation suggesting that the Cl- ion is inclined to reside in regions of low concentration of waters, i.e. between the 1st and 2nd shells of Al3+ and between the 2nd shell and bulk. A detailed analysis of solvent structure around the Al3+ and Cl- ions as a function of rAl-Cl is presented. The results are compared to structure data from X-ray measurements and unconstrained AIMD simulations of single ions Al3+ and Cl- and AlCl3 solutions. The dipole moment of the water molecules inside the 1st and 2nd hydration shells of Al3+ and in the bulk region and those of the Clion were calculated as a function of rAl-Cl. Major changes in the electronic structure of the system result from the removal of Cl- from the 1st hydration shell of the Al3+ cation. Finally, two unconstrained AIMD simulations of aqueous AlCl3 solutions corresponding to CIP and SSIP configurations were performed (17 ps, 300 K). Only minor structural changes are observed in these systems, confirming their stability.

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

    NASA Astrophysics Data System (ADS)

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

    2012-08-01

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

  10. 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

    2009-10-08

    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.

  11. Detection of Fatty Acids from Intact Microorganisms by Molecular Beam Static Secondary Ion Mass Spectrometry

    SciTech Connect

    Ingram, Jani Cheri; Lehman, Richard Michael; Bauer, William Francis; O'Connell, Sean Patrick; Colwell, Frederick Scott; Shaw, Andrew D.

    2003-06-01

    We report the use of a surface analysis approach, static secondary ion mass spectrometry (SIMS) equipped with a molecular (ReO4-) ion primary beam, to analyze the surface of intact microbial cells. SIMS spectra of 28 microorganisms were compared to fatty acid profiles determined by gas chromatographic analysis of transesterfied fatty acids extracted from the same organisms. The results indicate that surface bombardment using the molecular primary beam cleaved the ester linkage characteristic of bacteria at the glycerophosphate backbone of the phospholipid components of the cell membrane. This cleavage enables direct detection of the fatty acid conjugate base of intact microorganisms by static SIMS. The limit of detection for this approach is approximately 107 bacterial cells/cm2. Multivariate statistical methods were applied in a graded approach to the SIMS microbial data. The results showed that the full data set could initially be statistically grouped based upon major differences in biochemical composition of the cell wall. The gram-positive bacteria were further statistically analyzed, followed by final analysis of a specific bacterial genus that was successfully grouped by species. Additionally, the use of SIMS to detect microbes on mineral surfaces is demonstrated by an analysis of Shewanella oneidensis on crushed hematite. The results of this study provide evidence for the potential of static SIMS to rapidly detect bacterial species based on ion fragments originating from cell membrane lipids directly from sample surfaces.

  12. 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.

  13. 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.

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

    PubMed Central

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

    1999-01-01

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

  15. 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.

  16. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  19. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

  3. Molecular dynamics simulations of ion conductance in field-stabilized nanoscale lipid electropores.

    PubMed

    Ho, Ming-Chak; Casciola, Maura; Levine, Zachary A; Vernier, P Thomas

    2013-10-03

    Molecular dynamics (MD) simulations of electrophoretic transport of monovalent ions through field-stabilized electropores in POPC lipid bilayers permit systematic characterization of the conductive properties of lipid nanopores. The radius of the electropore can be controlled by the magnitude of the applied sustaining external electric field, which also drives the transport of ions through the pore. We examined pore conductances for two monovalent salts, NaCl and KCl, at physiological concentrations. Na(+) conductance is significantly less than K(+) and Cl(-) conductance and is a nonlinear function of pore radius over the range of pore radii investigated. The single pore electrical conductance of KCl obtained from MD simulation is comparable to experimental values measured by chronopotentiometry.

  4. Geometric isotope effects on small chloride ion water clusters with path integral molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Wang, Qi; Suzuki, Kimichi; Nagashima, Umpei; Tachikawa, Masanori; Yan, Shiwei

    2013-11-01

    The geometric isotope effects on the structures of hydrated chloride ionic hydrogen bonded clusters are explored by carrying out path integral molecular dynamics simulations. First, an outer shell coordinate is selected to display the rearrangement of single and multi hydration shell cluster structures. Next, to show the competition of intramolecular and intermolecular nuclear quantum effects, the intramolecular OH∗ stretching and intermolecular ion-water wagging motions are studied for single and multi shell structures, respectively. The results indicate that the intermolecular nuclear quantum effects stabilize the ionic hydrogen bonds in single shell structures, while they are destabilized through the competition with intramolecular nuclear quantum effects in multi shell structures. In addition, the correlations between ion-water stretching motion and other cluster vibrational coordinates are discussed. The results indicate that the intermolecular nuclear quantum effects on the cluster structures are strongly related to the cooperation of the water-water hydrogen bond interactions.

  5. Initial binding of ions to the interhelical loops of divalent ion transporter CorA: replica exchange molecular dynamics simulation study.

    PubMed

    Zhang, Tong; Mu, Yuguang

    2012-01-01

    Crystal structures of Thermotoga maritima magnesium transporter CorA, reported in 2006, revealed its homo-pentameric constructions. However, the structure of the highly conserved extracellular interhelical loops remains unsolved, due to its high flexibility. We have explored the configurations of the loops through extensive replica exchange molecular dynamics simulations in explicit solvent model with the presence of either Co(III) Hexamine ions or Mg(2+) ions. We found that there are multiple binding sites available on the interhelical loops in which the negatively charged residues, E316 and E320, are located notably close to the positively charged ions during the simulations. Our simulations resolved the distinct binding patterns of the two kinds of ions: Co(III) Hexamine ions were found to bind stronger with the loop than Mg(2+) ions with binding free energy -7.3 kJ/mol lower, which is nicely consistent with the previous data. Our study provides an atomic basis description of the initial binding process of Mg(2+) ions on the extracellular interhelical loops of CorA and the detailed inhibition mechanism of Co(III) Hexamine ions on CorA ions transportation.

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

    NASA Astrophysics Data System (ADS)

    Glosli, James N.; Philpott, Michael R.

    1993-06-01

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

  7. 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.

  8. 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.

  9. Dependence of the rate of LiF ion pairing on the description of molecular interaction

    SciTech Connect

    Pluharova, Eva; Baer, Marcel D.; Schenter, Gregory K.; Jungwirth, Pavel; Mundy, Christopher J.

    2016-03-03

    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 Gener- alized 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 parameterization. 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 straight forward application of variational transition state the- ory 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. CJM and GKS are supported by the U.S. Department of Energy‘s (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest Na- tional Laboratory (PNNL) is operated for the Department of Energy by Battelle. MDB is grateful for the support of Laboratory Directed Research and Development funding under the auspices of PNNL’s Laboratory Initiative Materials Synthesis and Simulation across Scales (MS3). Additional computing resources were generously allocated by PNNL’s Institutional Computing program. EP acknowledges support from PNNL’s Alternate Sponsored

  10. 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.

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

    SciTech Connect

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

    1986-07-01

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

  12. Car–Parrinello molecular dynamics in the DFT + U formalism: Structure and energetics of solvated ferrous and ferric ions

    SciTech Connect

    Sit, P H L.; Cococcioni, Matteo; Marzari, Nicola N.

    2007-09-01

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. We implemented a rotationally-invariant Hubbard U extension to density-functional theory in the Car–Parrinello molecular dynamics framework, with the goal of bringing the accuracy of the DFT + U approach to finite-temperature simulations, especially for liquids or solids containing transition-metal ions. First, we studied the effects on the Hubbard U on the static equilibrium structure of the hexaaqua ferrous and ferric ions, and the inner-sphere reorganization energy for the electron-transfer reaction between aqueous ferrous and ferric ions. It is found that the reorganization energy is increased, mostly as a result of the Fe–O distance elongation in the hexa-aqua ferrous ion. Second, we performed a first-principles molecular dynamics study of the solvation structure of the two aqueous ferrous and ferric ions. The Hubbard term is found to change the Fe–O radial distribution function for the ferrous ion, while having a negligible effect on the aqueous ferric ion. Moreover, the frequencies of vibrations between Fe and oxygen atoms in the first-solvation shell are shown to be unaffected by the Hubbard corrections for both ferrous and ferric ions.

  13. Lifetime of negative molecular ions of tetracene and pentacene with respect to the autodetachment of an electron

    NASA Astrophysics Data System (ADS)

    Khatymov, R. V.; Tuktarov, R. F.; Muftakhov, M. V.

    2011-06-01

    The processes of nondissociative resonant attachment and autodetachment of electrons in a number of poly-cyclic aromatic hydrocarbon molecules have been investigated by mass spectrometry. Long-lived negative molecular ions of phenanthrene and triphenylene have not been observed. Such ions have been detected for anthracene, pyrene, and benzo[e]pyrene capturing thermal electrons. Negative molecular ions of tetracene and pentacene have also been observed up to 2.5-3 eV. The lifetimes of these ions with respect to the auto-detachment of an electron have been measured throughout the energy range where they are observed. This lifetime for tetracene and pentacene is more than 10 ms, which is two or three orders of magnitude larger than that for remaining compounds. Correlation between the lifetime of ions and the electron affinity of the molecules has been revealed.

  14. A new crossed molecular beam apparatus using time-sliced ion velocity imaging technique

    SciTech Connect

    Wu Guorong; Zhang Weiqing; Pan Huilin; Shuai Quan; Jiang Bo; Dai Dongxu; Yang Xueming

    2008-09-15

    A new crossed molecular beam apparatus has been constructed for investigating polyatomic chemical reactions using the time-sliced ion velocity map imaging technique. A unique design is adopted for one of the two beam sources and allows us to set up the molecular beam source either horizontally or vertically. This can be conveniently used to produce versatile atomic or radical beams from photodissociation and as well as electric discharge. Intensive H-atom beam source with high speed ratio was produced by photodissociation of the HI molecule and was reacted with the CD{sub 4} molecule. Vibrational-state resolved HD product distribution was measured by detecting the CD{sub 3} product. Preliminary results were also reported on the F+SiH{sub 4} reaction using the discharged F atom beam. These results demonstrate that this new instrument is a powerful tool for investigating chemical dynamics of polyatomic reactions.

  15. Static dielectric properties of polarizable ion models: molecular dynamics study of molten AgI and NaI.

    PubMed

    Bitrián, Vicente; Alcaraz, Olga; Trullàs, Joaquim

    2009-06-21

    The fluctuation-dissipation theorem for the static dielectric response function of systems of ions with inducible point dipoles is derived. It is shown that the static longitudinal dielectric function is determined by spatial correlations of both charge and dipole-moment density fluctuations. Moreover, it is deduced that the long-wavelength behavior of the charge structure factor for polarizable ion systems is different from that for systems of rigid ions. Molecular dynamics simulation results of rigid and polarizable ion models for molten AgI and NaI are reported.

  16. Ion-exchange of monovalent and bivalent cations with NaA zeolite membranes : a molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Murad, S.; Jia, W.; Krishnamurthy, M.

    2004-01-01

    Molecular simulations using the method of molecular dynamics have been carried out to study the dynamics and energetics of ion exchanges between monovalent and bivalent cations in supercritical and subcritical (liquid) electrolyte solutions (here Li+, and Ca++ in aqueous solutions of LiCl and CaCl2) and an ion exchange membrane (NaA zeolite) using direct simulations of up to a nanosecond or more. NaA zeolites are widely used in many commercial ion-exchange processes including detergents. Results show that with appropriate driving forces, such ion exchange processes can be clearly witnessed and investigated using molecular simulations at these timescales, especially for supercritical solutions. An attempt is made to understand the phenomenon of ion exchange at the molecular level. Results have shown that the ion-exchange process is primarily energetically driven and entropic forces do not appear to be playing a significant role in the exchanges observed. For supercritical LiCl solutions, small differences were found between the energy of the Li+ inside and outside the membrane. In contrast, for Na+ there was a considerable energetic advantage in being outside the membrane, making the overall exchange process energetically favourable. In subcritical (liquid) LiCl solutions an exchange was found to be more favourable energetically than supercritical solutions. For Ca++ similar trends were observed, except the differences in the energies were much larger (compared to the corresponding Li+ exchanges), making them more energetically efficient, as has also been observed experimentally. In addition to clarifying the molecular basis for these exchanges, simulations can also potentially be very useful to determine the behaviour (e.g. state dependence, etc.) of hydrodynamic parameters commonly used to characterize ion-exchange processes at a fundamental molecular level, and to determine if the hydrodynamic equations used for ion-exchange processes are applicable to nano

  17. 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.

  18. Molecular dynamics simulations of triflic acid and triflate ion/water mixtures: a proton conducting electrolytic component in fuel cells.

    PubMed

    Sunda, Anurag Prakash; Venkatnathan, Arun

    2011-11-30

    Triflic acid is a functional group of perflourosulfonated polymer electrolyte membranes where the sulfonate group is responsible for proton conduction. However, even at extremely low hydration, triflic acid exists as a triflate ion. In this work, we have developed a force-field for triflic acid and triflate ion by deriving force-field parameters using ab initio calculations and incorporated these parameters with the Optimized Potentials for Liquid Simulations - All Atom (OPLS-AA) force-field. We have employed classical molecular dynamics (MD) simulations with the developed force field to characterize structural and dynamical properties of triflic acid (270-450 K) and triflate ion/water mixtures (300 K). The radial distribution functions (RDFs) show the hydrophobic nature of CF(3) group and presence of strong hydrogen bonding in triflic acid and temperature has an insignificant effect. Results from our MD simulations show that the diffusion of triflic acid increases with temperature. The RDFs from triflate ion/water mixtures shows that increasing hydration causes water molecules to orient around the SO(3)(-) group of triflate ions, solvate the hydronium ions, and other water molecules. The diffusion of triflate ions, hydronium ion, and water molecules shows an increase with hydration. At λ = 1, the diffusion of triflate ion is 30 times lower than the diffusion of triflic acid due to the formation of stable triflate ion-hydronium ion complex. With increasing hydration, water molecules break the stability of triflate ion-hydronium ion complex leading to enhanced diffusion. The RDFs and diffusion coefficients of triflate ions, hydronium ions and water molecules resemble qualitatively the previous findings using per-fluorosulfonated membranes.

  19. Molecular Dynamics Simulation of Electron-Ion Temperature Relaxation in Dense Hydrogen: Electronic Quantum Effects

    NASA Astrophysics Data System (ADS)

    Ma, Qian; Dai, Jiayu; Zhao, Zengxiu

    2016-10-01

    The electron-ion temperature relaxation is an important non-equilibrium process in the generation of dense plasmas, particularly in Inertial Confinement Fusion. Classical molecular dynamics considers electrons as point charges, ignoring important quantum processes. We use an Electron Force Field (EFF) method to study the temperature relaxation processes, considering the nuclei as semi-classical point charges and assume electrons as Gaussian wave packets which includes the influences of the size and the radial motion of electrons. At the same time, a Pauli potential is used to describe the electronic exchange effect. At this stage, quantum effects such as exchange, tunneling can be included in this model. We compare the results from EFF and classical molecular dynamics, and find that the relaxation time is much longer with including quantum effects, which can be explained directly by the deference of collision cross sections between quantum particles and classical particles. Further, the final thermal temperature of electron and ion is different compared with classical results that the electron quantum effects cannot be neglected.

  20. 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.

  1. TaO+ as a candidate molecular ion for searches of physics beyond the standard model

    NASA Astrophysics Data System (ADS)

    Fleig, Timo

    2017-02-01

    The TaO+ molecular ion is proposed as a candidate system for detecting signatures of charge-parity-violating physics beyond the standard model of elementary particles. The electron electric dipole moment (EDM) effective electric field Eeff=20.2 GV/cm, the nucleon-electron scalar-pseudoscalar (SPS) interaction constant WS=17.7 kHz, and the nuclear magnetic quadrupole interaction constant WM=0.45 ×1033 Hz/(e cm2) are found to be sizable P ,T -odd enhancements. The ratio of the leptonic and semileptonic enhancements differs strongly from the one for the ThO system which may provide improved limits on the electron EDM, de, and the SPS coupling constant, CS. TaO+ is found to have a 3Δ1 electronic ground state like the previously proposed ThF+ molecular ion, but an order of magnitude smaller parallel G -tensor component which makes it less vulnerable to systematic errors in experiment.

  2. Conformational evolution of ubiquitin ions in electrospray mass spectrometry: molecular dynamics simulations at gradually increasing temperatures.

    PubMed

    Segev, Elad; Wyttenbach, Thomas; Bowers, Michael T; Gerber, R Benny

    2008-06-07

    Evidence from cross section data indicates that ubiquitin +13 ions lose their secondary and tertiary structure in mass spectrometric experiments. These transitions from the folded state into the near linear final structure occur at the experimental temperatures on time scales that are far too long for conventional molecular dynamics simulations. In this study, an approach to mass spectrometric unfolding processes is developed and a detailed application to an ubiquitin +13 ion system is presented. The approach involves a sequence of molecular dynamics simulations at gradually increasing temperatures leading to identification of major intermediate states, and the unfolding pathway. The unfolding rate at any temperature can then be calculated by a Rice-Ramsperger-Kassel (RRK) approach. For ubiquitin +13, three interesting intermediate states were found and the final near linear geometry was computed. The several relevant energy barriers calculated for the process are in the range of 7 to 15 kcal mol(-1). The unfolding time scale at 300 K was computed to be 2 ms. Cross section calculations using a hard sphere scattering model were carried out for the final structure and found to be in good accord with the results of electrospray experiments supporting the theoretical model used. The approach employed here should be applicable to any other solvent-free protein system.

  3. 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.

  4. 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

  5. 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.

  6. The Torsion-Inversion-Bending Energy Levels in the S1( n, π*) Electronic State of Acetaldehyde . A High-Resolution Study of the Bands #7 to #20 in the Jet-Cooled Fluorescence Excitation Spectrum

    NASA Astrophysics Data System (ADS)

    Liu, Haisheng; Lim, Edward C.; Niño, Alfonso; Muñoz-Caro, Camelia; Judge, Richard H.; Moule, David C.

    1998-07-01

    The band assignments and analyses of the jet-cooled high-resolution laser-induced fluorescence excitation spectrum of acetaldehyde that results from theS1(n, π*) electronic state have been extended to +600 cm-1from the 000system origin. The new assignments start at Band #7 and finish at Band #21. Bands #8 and #9, originally assigned to 1420, have now been assigned to 1530. The assignments of the lower energy bands remain unaltered. The origins of the bands that involve the torsional modes ν15(v= 1 to 4) in combination with the wagging mode ν14(v= 1 and 2) and the ν10(v= 1) were determined by analyses with a rigid rotational Hamiltonian. These origins were fitted to a set of levels that were derived from a torsion-wagging-bending Hamiltonian that employed flexible large amplitude coordinates. The resulting potential surface was found to have barriers to torsion and inversion of 712.5 and 638.6 cm-1, respectively, with minima in the potential hypersurface at θ = 59.9° and α = 33.5° for the torsion and wagging coordinates.

  7. 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.

  8. 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.

  9. 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

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

    PubMed

    Rodríguez-Jeangros, Nicolás; Seminario, Jorge M

    2014-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Abate, Yohannes

    Ion-molecule interactions in isolated molecular clusters and proteins are studied in this work using experimental and theoretical methods. Photodissociation spectroscopy and chemical dynamics of several metal ion-molecule clusters are studied. The experimental tool used for these studies is an Angular Reflectron Time Of Flight Mass Spectrometer (ARTOFMS). The experimental work is supported by ab initio electronic structure calculations on the Gaussian and GAMESS platforms. This work also describes a computational study of the interaction of protonated histidine with other aromatic residues in proteins. We have studied the photodissociation spectroscopy of weakly bound Zn +(H2O) and Zn+(D2O) bimolecular complexes. We assign two molecular absorption bands in the near UV correlating to Zn+ (4s-4p)-metal centered transitions, and identify vibrational progressions associated with both intermolecular and intramolecular vibrational modes of the cluster. Partially resolved rotational structure is consistent with a C2 V equilibrium complex geometry. The photodissociation spectroscopy and chemical dynamics of Zn +-formaldehyde and Zn+-acetaldehyde clusters are investigated in the near UV spectral range. The work is also supported by ab initio electronic structure calculations to study the ground-state bonding and interactions in the low-lying doublet excited states. We identify absorption bands corresponding to photoinduced charge transfer, Zn+(4s-4p)-based transitions, and aldehyde-based excitations. We propose a reaction mechanism for the reactive dissociation that proceeds via H-atom abstraction on the charge-transfer surface. This work shows important differences with results from earlier experiments on Mg+- and Ca+-aldehyde complexes despite the similar valence character for these metal ions. In the study of Mg+-acetic acid we observe three distinct absorption bands, two red-shifted and one blue-shifted from the Mg +(3s ← 3p) resonance at 280 nm (35714 cm-1). We

  12. Reduction of the energy loss of swift molecular ions in solids due to vicinage effects in the charge state

    SciTech Connect

    Heredia-Avalos, Santiago; Garcia-Molina, Rafael

    2007-09-15

    We have calculated the energy loss of swift O{sub 2}{sup +}, N{sub 2}{sup +}, and C{sub n}{sup +} (n=2-60) molecular ions moving through an amorphous carbon target. The dielectric formalism is used to evaluate the vicinage effects in the energy loss of the atomic ions that form the molecular projectile, but we take into account that the charge state of these atomic ions is affected by their correlated motion through the target and by the screened Coulomb potential between them. When vicinage effects in the charge state are taken into account, the Coulomb repulsion is weakened, leading to a reduction in the interatomic separations ({approx}3% for N{sub 2}{sup +} and {approx}9% for C{sub 60}{sup +}, both having similar velocities). These charge state effects can be neglected for diatomic molecular ions, but they give rise to a reduction of {approx}8% in the vicinage effects in the energy loss of larger molecular ions with cage like geometrical structures, like C{sub n}{sup +} (n=20,60) projectiles.

  13. 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

  14. A new spectral emission source of rotationally cooled molecular ions. Application to supersonic expansions of CO and CO 2 gases

    NASA Astrophysics Data System (ADS)

    Cossart, Daniel; Cossart-Magos, Claudina

    1996-02-01

    A new emission source for the spectroscopy of rotationally cooled molecular ions has been developed in which a Penning-type electric discharge is established through a supersonic free jet. CO and CO 2 gases were used to test its working conditions. Several previously unobserved emission bands were identified, among them one that probably originates from the CO 2+ ion. Moreover, anomalous rotational intensity distributions in the CO + B-X emission observed from the excitation of rotationally cooled CO 2 suggest the existence of a dissociative bent electronic state in the CO 2+ ion.

  15. Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels.

    PubMed

    Allen, Toby W; Andersen, Olaf S; Roux, Benoit

    2006-12-01

    Ion channels catalyze the permeation of charged molecules across cell membranes and are essential for many vital physiological functions, including nerve and muscle activity. To understand better the mechanisms underlying ion conduction and valence selectivity of narrow ion channels, we have employed free energy techniques to calculate the potential of mean force (PMF) for ion movement through the prototypical gramicidin A channel. Employing modern all-atom molecular dynamics (MD) force fields with umbrella sampling methods that incorporate one hundred 1-2 ns trajectories, we find that it is possible to achieve semi-quantitative agreement with experimental binding and conductance measurements. We also examine the sensitivity of the MD-PMF results to the choice of MD force field and compare PMFs for potassium, calcium and chloride ions to explore the basis for the valence selectivity of this narrow and uncharged ion channel. A large central barrier is observed for both anions and divalent ions, consistent with lack of experimental conductance. Neither anion or divalent cation is seen to be stabilized inside the channel relative to the bulk electrolyte and each leads to large disruptions to the protein and membrane structure when held deep inside the channel. Weak binding of calcium ions outside the channel corresponds to a free energy well that is too shallow to demonstrate channel blocking. Our findings emphasize the success of the MD-PMF approach and the sensitivity of ion energetics to the choice of biomolecular force field.

  16. Marked influence of the nature of the chemical bond on CP-violating signature in molecular ions HBr(+) and HI(+).

    PubMed

    Ravaine, Boris; Porsev, Sergey G; Derevianko, Andrei

    2005-01-14

    Heavy polar molecules offer a great sensitivity to the electron electric dipole moment (EDM). To guide emerging searches for EDMs with molecular ions, we estimate the EDM-induced energy corrections for hydrogen halide ions HBr(+) and HI(+) in their respective ground X (2)Pi(3/2) states. We find that the energy corrections due to EDM for the two ions differ by an unexpectedly large factor of 15. We demonstrate that a major part of this enhancement is due to a dissimilarity in the nature of the chemical bond for the two ions: the bond that is nearly of ionic character in HBr(+) exhibits predominantly a covalent nature in HI(+). We conclude that because of this enhancement the HI(+) ion may be a potentially competitive candidate for the EDM search.

  17. 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.

  18. Water and ions in clays: Unraveling the interlayer/micropore exchange using molecular dynamics

    NASA Astrophysics Data System (ADS)

    Rotenberg, Benjamin; Marry, Virginie; Vuilleumier, Rodolphe; Malikova, Natalie; Simon, Christian; Turq, Pierre

    2007-11-01

    We present the first microscopic description of the exchange of water and ions between clay interlayers and microporosity. A force field based on ab-initio calculations is developed and used in classical molecular dynamics simulations. The latter allow to compute the potential of mean force for the interlayer/micropore exchange for water, Na + and Cs + cations and Cl - anions. For the simulated water content (water bilayer, with interlayer spacing 15.4 Å) and salt concentration in the micropore (0.52 mol dm -3) the exchange is found to be almost not activated for water and cations, whereas the entrance of an anion into the interlayer is strongly unfavorable ( ΔF˜9kT). Calculations of the diffusion tensor in the interlayer and in the micropore complete the study of the exchange dynamics.

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

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

    SciTech Connect

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

    2016-06-07

    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, 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.

  1. 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.

  2. Tethering metal ions to photocatalyst particulate surfaces by bifunctional molecular linkers for efficient hydrogen evolution.

    PubMed

    Yu, Weili; Isimjan, Tayirjan; Del Gobbo, Silvano; Anjum, Dalaver H; Abdel-Azeim, Safwat; Cavallo, Luigi; Garcia-Esparza, Angel T; Domen, Kazunari; Xu, Wei; Takanabe, Kazuhiro

    2014-09-01

    A simple and versatile method for the preparation of photocatalyst particulates modified with effective cocatalysts is presented; the method involves the sequential soaking of photocatalyst particulates in solutions containing bifunctional organic linkers and metal ions. The modification of the particulate surfaces is a universal and reproducible method because the molecular linkers utilize strong covalent bonds, which in turn result in modified monolayer with a small but controlled quantity of metals. The photocatalysis results indicated that the CdS with likely photochemically reduced Pd and Ni, which were initially immobilized via ethanedithiol (EDT) as a linker, were highly efficient for photocatalytic hydrogen evolution from Na2S-Na2SO3-containing aqueous solutions. The method developed in this study opens a new synthesis route for the preparation of effective photocatalysts with various combinations of bifunctional linkers, metals, and photocatalyst particulate materials.

  3. Electrochemically driven formation of a molecular capsule around the ferrocenium ion.

    PubMed

    Philip, Ivy E; Kaifer, Angel E

    2002-10-30

    Electrochemical experiments were used to show that the oxidation of ferrocene triggers the self-assembly of six molecules of the resocin[4]arene 2 to form a molecular capsule around the oxidized, ferrocenium (+1) form. The nature of the supporting electrolyte anion is crucial for this process of electrochemically driven self-assembly. 1H NMR spectroscopic data obtained with cobaltocenium, a diamagnetic analogue of the paramagnetic ferrocenium ion, verify its encapsulation by six molecules of 2. The encapsulation of cobaltocenium was also observed in voltammetric experiments. Encapsulation of ferrocenium (or cobaltocenium) inside the large 26 capsule led to a dramatic slowing of its usually fast, one-electron electrochemical reduction to ferrocene (or cobaltocene).

  4. Molecular dynamics study on low-energy sputtering of carbon material by Xe ion bombardment

    NASA Astrophysics Data System (ADS)

    Muramoto, T.; Hyakutake, T.

    2013-05-01

    The low-energy sputtering of carbon material under Xe ion bombardment is studied through the molecular dynamics (MD) simulation. For the normal incidence of Xe, the MD result of sputtering yield almost agrees with the experimental result by Williams et al. (AIAA-2004-3788). However, the experimental result shows a less incident angle dependence than the MD result because the experiment performed on a rough surface. It is found that the sputtered particles have memory of the projectile because the sputtered particles by the low-energy projectile undergo only a few collisions before the ejection. Low density of an amorphous carbon surface brings the decrease of the sputtering yield and the increase of high-energy sputtered atoms.

  5. 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).

  6. A molecular dynamics investigation of the influence of water structure on ion conduction through a carbon nanotube.

    PubMed

    Liu, L; Patey, G N

    2017-02-21

    Molecular dynamics simulations are employed to investigate pressure-driven water and ion transport through a (9,9) carbon nanotube (CNT). We consider NaCl solutions modeled with both the TIP3P and TIP4P/2005 water models. Concentrations range from 0.25 to 2.8 mol l(-1) and temperatures from 260 to 320 K are considered. We discuss the influences on flow rates of continuum hydrodynamic considerations and molecular structural effects. We show that the flow rate of water, sodium, and chloride ions through the CNT is strongly model dependent, consistent with earlier simulations of pure water conduction. To remove the effects of different water flow rates, and clearly expose the influence of other factors on ion flow, we calculate ion transport efficiencies. Ion transport efficiencies are much smaller for TIP4P/2005 solutions than for those using the TIP3P model. Particularly at lower temperatures, the ion transport efficiencies for the TIP4P/2005 model are small, despite the fact that the nanotube conducts water at a significant rate. We trace the origin of small ion transport efficiencies to the presence of ring-like water structures within the CNT. Such structures occur commonly for the TIP4P/2005 model, but less frequently for TIP3P. The water structure acts to reduce ion "solvation" within the CNT, posing an additional barrier to ion entry and transport. Our results demonstrate that increasing the water structure within the CNT by decreasing the temperature strongly inhibits ion conduction, while still permitting significant water transport.

  7. A molecular dynamics investigation of the influence of water structure on ion conduction through a carbon nanotube

    NASA Astrophysics Data System (ADS)

    Liu, L.; Patey, G. N.

    2017-02-01

    Molecular dynamics simulations are employed to investigate pressure-driven water and ion transport through a (9,9) carbon nanotube (CNT). We consider NaCl solutions modeled with both the TIP3P and TIP4P/2005 water models. Concentrations range from 0.25 to 2.8 mol l-1 and temperatures from 260 to 320 K are considered. We discuss the influences on flow rates of continuum hydrodynamic considerations and molecular structural effects. We show that the flow rate of water, sodium, and chloride ions through the CNT is strongly model dependent, consistent with earlier simulations of pure water conduction. To remove the effects of different water flow rates, and clearly expose the influence of other factors on ion flow, we calculate ion transport efficiencies. Ion transport efficiencies are much smaller for TIP4P/2005 solutions than for those using the TIP3P model. Particularly at lower temperatures, the ion transport efficiencies for the TIP4P/2005 model are small, despite the fact that the nanotube conducts water at a significant rate. We trace the origin of small ion transport efficiencies to the presence of ring-like water structures within the CNT. Such structures occur commonly for the TIP4P/2005 model, but less frequently for TIP3P. The water structure acts to reduce ion "solvation" within the CNT, posing an additional barrier to ion entry and transport. Our results demonstrate that increasing the water structure within the CNT by decreasing the temperature strongly inhibits ion conduction, while still permitting significant water transport.

  8. Practical Aspects of Molecular Spectroscopy in Plasmas 4. The Role of Molecular Spectroscopy in the Vacuum Ultraviolet Region for the Development of a Negative Ion Source

    NASA Astrophysics Data System (ADS)

    Nishiura, Masaki

    Fundamental plasma processes of negative ions in a low pressure region (a gas pressure Pg < 1.5 Pa) have been studied using the photodetachment technique and vacuum ultraviolet (VUV) spectroscopic measurements in the spectral range from 100 to 180 nm. Understanding the behavior of a plasma with negative ions, in particular, the correlation between H- density and vibrationally excited H2 density, is of great interest in the field of atomic-molecular physics and ion source developments. The volume and the surface effects of negative ions are discussed taking into account the e-V, the E-V, and the RD processes, and the measured VUV spectrum is compared with the synthetic one. The cascade transition to the B1Σ+u state by the electron excitation contributes to the production of the highly vibrationally excited levels of the X1Σ+g ground electronic state.

  9. 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.

  10. Doubly excited states of molecular nitrogen by scattered electron-ion coincidence measurements

    NASA Astrophysics Data System (ADS)

    Takahashi, Karin; Hasegawa, Toru; Sakai, Yasuhiro

    2017-03-01

    Scattered electron-ion coincidence measurements were performed on molecular nitrogen (N2) to study the relaxation dynamics of doubly excited states. Doubly excited states are typically so unstable that they result in either auto-ionization or a neutral dissociation. In auto-ionization, ionization and dissociation typically occur. Using a mixed-gas method, we determined the absolute values of the generalized oscillator strength (GOS) distributions using an incident electron energy of 200 eV and a scattering angle of 6°. The GOS distributions of N2+ and N+ were determined by combining the coincidence ion signals, which revealed some doubly excited states of N2. Since electron impact experiments can provide information on optically forbidden transitions, the contribution of optically forbidden states appears in the GOS distributions of both N2+ and N+. We observed auto-ionization and dissociative auto-ionization induced by excitation to the optically forbidden doubly excited states in the range of 30-40 eV.

  11. 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).

  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

    2016-04-05

    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. Coherent manipulation of three-qubit states in a molecular single-ion magnet

    NASA Astrophysics Data System (ADS)

    Jenkins, M. D.; Duan, Y.; Diosdado, B.; García-Ripoll, J. J.; Gaita-Ariño, A.; Giménez-Saiz, C.; Alonso, P. J.; Coronado, E.; Luis, F.

    2017-02-01

    We study the quantum spin dynamics of nearly isotropic Gd3 + ions entrapped in polyoxometalate molecules and diluted in crystals of a diamagnetic Y3 + derivative. The full energy-level spectrum and the orientations of the magnetic anisotropy axes have been determined by means of continuous-wave electron paramagnetic resonance experiments, using X-band (9-10 GHz) cavities and on-chip superconducting waveguides and 1.5-GHz resonators. The results show that seven allowed transitions between the 2 S +1 spin states can be separately addressed. Spin coherence T2 and spin-lattice relaxation T1 rates have been measured for each of these transitions in properly oriented single crystals. The results suggest that quantum spin coherence is limited by residual dipolar interactions with neighbor electronic spins. Coherent Rabi oscillations have been observed for all transitions. The Rabi frequencies increase with microwave power and agree quantitatively with predictions based on the spin Hamiltonian of the molecular spin. We argue that the spin states of each Gd3 + ion can be mapped onto the states of three addressable qubits (or, alternatively, of a d =8 -level "qudit"), for which the seven allowed transitions form a universal set of operations. Within this scheme, one of the coherent oscillations observed experimentally provides an implementation of a controlled-controlled-NOT (or Toffoli) three-qubit gate.

  14. Molecular ion implantation technique for obtaining the same depth profile for the component atoms

    SciTech Connect

    Ishikawa, Junzo; Tsuji, Hiroshi; Mimura, Masakazu; Gotoh, Yasuhito

    1996-12-31

    The molecular ion implantation, in which the ions of polyatomic molecule are used as an implantation particle, is expected to have two main advantages: (1) obtaining the similar depth profiles of implanted component atoms of different elements at a single implantation, and (2) achieving simultaneous implantation of different atoms at the same position. In this paper, we have showed these advantages by an analytical estimation of the projected ranges for each implanted atoms of a polyatomic molecule, and then, by the computer simulation by TRIM. In addition, the experimental results obtained by SIMS were also presented. As for the evaluation of depth profiles, the overlap areas between two depth distributions were calculated by a numerical integration as a degree of the similarity between two depth profiles of different atoms. As a result, the projected ranges and overlap areas showed that depth profiles are almost the same in a usual implantation energy range, except of hydrogen due to the lack of neutron in the nucleus. For the simple evaluation for the similarity of two depth profiles, a factor S was proposed instead of the overlap area.

  15. 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.

  16. Solvation of Mg2+ ions in methanol-water mixtures: Molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Rybicki, Marcin; Hawlicka, Ewa

    2012-05-01

    Molecular dynamics simulations of MgCl2 solutions in methanol-water mixtures, over the whole range of the methanol mole fraction at room temperature have been performed. The methanol and water molecules have been modeled as flexible three-site bodies. Solvation of the magnesium ions has been discussed on the basis of the radial and angular distribution functions, the orientation of the solvent molecules and their geometrical arrangement in the coordination shells. Analysis of the H-bonds of the solvent molecules coordinated by Mg2+ has been based on a geometric criterion of the H-bond. Persistence of the primary and secondary shell has been estimated. In all studied solutions Mg2+ is six-coordinated and the solvent molecules form an octahedron. The antidipole orientation of the molecules favours the water molecules as H-donors in the first shell and the methanol molecules as H-acceptor in the second shell. Thus an excess of water and an excess of methanol has been observed in the first and the second shells of Mg2+. An exchange of the solvent molecules between the primary and secondary shells occur. The persistence of the second shell is longer than the shells of monovalent ions.

  17. Molecular spectroscopy by stepwise two-photon ion-pair production at 71 nm

    SciTech Connect

    Kung, A.H.; Page, R.H.; Larkin, R.J.; Shen, Y.R.; Lee, Y.T.

    1985-06-01

    The Rydberg states of H/sub 2/ have been a continuing subject of intensive study by various research groups. However, understanding of the high lying electronic states of this molecule has been inhibited by the lack of spectroscopic data in the region <75 nm. Experimental studies have been difficult because spectroscopic features are generally buried under an intense absorption or photoionization continuum. Intense, high-resolution excitation sources are not easily available. Recent developments on tunable, narrowband, coherent xuv sources provide new means of studying the spectroscopy in this region with high resolution (+- .0005 nm). We have applied the technique of stepwise two-photon excitation to study photoionization of H/sub 2/ in a molecular beam using the two lowest excited states of H/sub 2/ as the intermediate level. This excitation, coupled with the detection of background-free H/sup -/ ions has enabled us to uncover, for the first time, spectroscopic features that are difficult to observe in positive ion detection. These features have been successfully assigned to new Rydberg series converging to the high vibrations of the H/sub 2//sup +/ ground electronic state.

  18. 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.

  19. Hydration of the cyanide ion: an ab initio quantum mechanical charge field molecular dynamics study.

    PubMed

    Moin, Syed Tarique; Hofer, Thomas S

    2014-12-21

    This paper presents an ab initio quantum mechanical charge field molecular dynamics simulation study of the cyanide anion (CN(-)) in aqueous solution where hydrogen bond formation plays a dominant role in the hydration process. Preferential orientation of water hydrogens compared to oxygen atoms was quantified in terms of radial, angular as well as coordination number distributions. All structural results indicate that the water hydrogens are attracted towards CN(-) atoms, thus contributing to the formation of the hydration layer. Moreover, a clear picture of the local arrangement of water molecules around the ellipsoidal CN(-) ion is provided via angular-radial distribution and spatial distribution functions. Apart from the structural analysis, the evaluation of water dynamics in terms of ligand mean residence times and H-bond correlation functions indicates the weak structure making capacity of the CN(-) ion. The similar values of H-bond lifetimes obtained for the NHwat and CHwat bonds indicate an isokinetic behaviour of these H-bonds, since there is a very small difference in the magnitude of the lifetimes. On the other hand, the H-bond lifetimes between water molecules of the hydration shell, and between solute and solvent evidence the slightly stable hydration of the CN(-). Overall, the H-bonding dominates in the hydration process of the cyanide anion enabling it to become soluble in the aqueous environment associated to chemical and biological processes.

  20. Vibronic spectra of jet-cooled 2-aminopurine·H2O clusters studied by UV resonant two-photon ionization spectroscopy and quantum chemical calculations.

    PubMed

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

    2011-06-16

    For understanding the major- and minor-groove hydration patterns of DNAs and RNAs, it is important to understand the local solvation of individual nucleobases at the molecular level. We have investigated the 2-aminopurine·H(2)O monohydrate by two-color resonant two-photon ionization and UV/UV hole-burning spectroscopies, which reveal two isomers, denoted A and B. The electronic spectral shift δν of the S(1) ← S(0) transition relative to bare 9H-2-aminopurine (9H-2AP) is small for isomer A (-70 cm(-1)), while that of isomer B is much larger (δν = -889 cm(-1)). B3LYP geometry optimizations with the TZVP basis set predict four cluster isomers, of which three are doubly H-bonded, with H(2)O acting as an acceptor to a N-H or -NH2 group and as a donor to either of the pyrimidine N sites. The "sugar-edge" isomer A is calculated to be the most stable form with binding energy D(e) = 56.4 kJ/mol. Isomers B and C are H-bonded between the -NH2 group and pyrimidine moieties and are 2.5 and 6.9 kJ/mol less stable, respectively. Time-dependent (TD) B3LYP/TZVP calculations predict the adiabatic energies of the lowest (1)ππ* states of A and B in excellent agreement with the observed 0(0)(0) bands; also, the relative intensities of the A and B origin bands agree well with the calculated S(0) state relative energies. This allows unequivocal identification of the isomers. The R2PI spectra of 9H-2AP and of isomer A exhibit intense low-frequency out-of-plane overtone and combination bands, which is interpreted as a coupling of the optically excited (1)ππ* state to the lower-lying (1)nπ* dark state. In contrast, these overtone and combination bands are much weaker for isomer B, implying that the (1)ππ* state of B is planar and decoupled from the (1)nπ* state. These observations agree with the calculations, which predict the (1)nπ* above the (1)ππ* state for isomer B but below the (1)ππ* for both 9H-2AP and isomer A.

  1. Impact ionization of molecular oxygen by 3.5-MeV/u bare carbon ions

    NASA Astrophysics Data System (ADS)

    Nandi, Saikat; Agnihotri, Aditya N.; Kasthurirangan, S.; Kumar, Ajay; Tachino, Carmen A.; Rivarola, Roberto D.; Martín, F.; Tribedi, Lokesh C.

    2012-06-01

    We have measured the absolute double-differential cross sections (DDCSs) for electron emission in ionization of O2 molecules under the impact of 3.5-MeV/u C6+ ions. The data were collected between 10 and 600 eV, in an angular range of 30∘ to 150∘. The single-differential cross sections (SDCSs) in emission angle and electron energy are deduced from the electron DDCS spectra. Also, the total cross section has been obtained from the SDCS spectra. The DDCS spectra as well as the SDCS spectra are compared with continuum distorted-wave eikonal initial-state calculations which employ molecular wave functions built as linear combinations of atomic orbitals. The DDCS ratio i.e. σO2/2σO, derived by dividing the experimental DDCS for molecular oxygen with the theoretical DDCS for atomic oxygen, does not show any primary or secondary oscillations arising from Young-type interference, which is apparently in contrast to what has been observed earlier for H2 and in agreement with the model calculation. Similarly, the forward-backward angular asymmetry increases monotonically with the velocity of the emitted electrons. However, the results on the DDCSs, SDCSs, the asymmetry parameter, and the nonexistence of oscillations are in qualitative agreement with the predictions of the model used.

  2. 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.

  3. 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.

  4. Rotational Spectra of the Molecular Ions H_2NCO^+ and NCO^-

    NASA Astrophysics Data System (ADS)

    Lattanzi, Valerio; Gottlieb, Carl A.; Thaddeus, Patrick; McCarthy, Michael C.; Thorwirth, Sven

    2010-06-01

    We report the first high resolution spectroscopic detection of H_2NCO^+, the protonated cation of isocyanic acid, in a discharge through HNCO heavily diluted in hydrogen in the throat of a supersonic nozzle. Spectroscopic constants derived from the two lowest rotational transitions agree very well with theoretical structure calculations of the ground state isomer, in which protonation occurs at the nitrogen atom, yielding an isomer of C2v symmetry. In the same molecular beam, the fundamental rotational transition of NCO^- was observed with well-resolved nitrogen quadrupole hyperfine structure. Detection of NCO^- in our beam was subsequently confirmed by observation of several millimeter-wave transitions in a low pressure discharge through cyanogen and water. The spectroscopic constants of NCO^- obtained earlier by infrared laser spectroscopy are in good agreement with the highly accurate constants derived here. Owing to the high abundance of HNCO in many galactic molecular sources, both ions are excellent candidates for astronomical detection in the radio band. Structure calculated at the CCSD(T)/cc-pwCV5Z level of theory and zero-point vibrational effects at CCSD(T)/cc-pVQZ. M. Gruebele, M. Polak, and R. J. Saykally, J. Chem. Phys., 86, 6631, (1987).

  5. A recoil ion momentum spectrometer for molecular and atomic fragmentation studies

    NASA Astrophysics Data System (ADS)

    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.

  6. Molecular dynamics studies of electron-ion temperature equilibration in the coupled-mode regime

    NASA Astrophysics Data System (ADS)

    Benedict, Lorin X.; Surh, Michael P.; Scullard, Christian R.; Stanton, Liam G.; Correa, Alfredo A.; Castor, John I.; Graziani, Frank R.; Collins, Lee A.; Kress, Joel D.; Cimarron Collaboration; T-1 Collaboration

    2016-10-01

    We use classical molecular dynamics (MD) to study electron-ion temperature equilibration in two-component plasmas in regimes in which the presence of coupled collective modes substantively impacts the equilibration rate. Guided by previous kinetic theory work in which predictions were made of both the regimes and the sizes of this effect, we examine hydrogen plasmas at a density of n =102 6 1/cm3, Ti =105 K, and 107 K molecular dynamics simulations. This work is performed under the auspices of the U. S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 and by Los Alamos National Laboratory under Contract DE-AC52-06NA25396.

  7. 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

  8. Molecular dynamics simulations of the first charge of a Li-ion-Si-anode nanobattery.

    PubMed

    Galvez-Aranda, Diego E; Ponce, Victor; Seminario, Jorge M

    2017-04-01

    Rechargeable lithium-ion batteries are the most popular devices for energy storage but still a lot of research needs to be done to improve their cycling and storage capacity. Silicon has been proposed as an anode material because of its large theoretical capacity of ∼3600 mAh/g. Therefore, focus is needed on the lithiation process of silicon anodes where it is known that the anode increases its volume more than 300%, producing cracking and other damages. We performed molecular dynamics atomistic simulations to study the swelling, alloying, and amorphization of a silicon nanocrystal anode in a full nanobattery model during the first charging cycle. A dissolved salt of lithium hexafluorophosphate in ethylene carbonate was chosen as the electrolyte solution and lithium cobalt oxide as cathode. External electric fields are applied to emulate the charging, causing the migration of the Li-ions from the cathode to the anode, by drifting through the electrolyte solution, thus converting pristine Si gradually into Li14Si5 when fully lithiated. When the electric field is applied to the nanobattery, the temperature never exceeds 360 K due to a temperature control imposed resembling a cooling mechanism. The volume of the anode increases with the amorphization of the silicon as the external field is applied by creating a layer of LiSi alloy between the electrolyte and the silicon nanocrystal and then, at the arrival of more Li-ions changing to an alloy, where the drift velocity of Li-ions is greater than the velocity in the initial nanocrystal structure. Charge neutrality is maintained by concerted complementary reduction-oxidation reactions at the anode and cathode, respectively. In addition, the nanobattery model developed here can be used to study charge mobility, current density, conductance and resistivity, among several other properties of several candidate materials for rechargeable batteries and constitutes the initial point for further studies on the formation of the

  9. Diffusion of water and sodium counter-ions in nanopores of a β-lactoglobulin crystal: a molecular dynamics study.

    PubMed

    Malek, Kourosh; Odijk, Theo; Coppens, Marc-Olivier

    2005-07-01

    The dynamics of water and sodium counter-ions (Na(+)) in a C222(1) orthorhombic β-lactoglobulin crystal is investigated by means of 5 ns molecular dynamics simulations. The effect of the fluctuation of the protein atoms on the motion of water and sodium ions is studied by comparing simulations in a rigid and in a flexible lattice. The electrostatic interactions of sodium ions with the positively charged LYS residues inside the crystal channels significantly influence the ionic motion. According to our results, water molecules close to the protein surface undergo an anomalous diffusive motion. On the other hand, the motion of water molecules further away from the protein surface is normal diffusive. Protein fluctuations affect the diffusion constant of water, which increases from 0.646 ± 0.108 to 0.887 ± 0.41 nm(2) ns(-1), when protein fluctuations are taken into account. The pore size (0.63-1.05 nm) and the water diffusivities are in good agreement with previous experimental results. The dynamics of sodium ions is disordered. LYS residues inside the pore are the main obstacles to the motion of sodium ions. However, the simulation time is still too short for providing a precise description of anomalous diffusion of sodium ions. The results are not only of interest for studying ion and water transport through biological nanopores, but may also elucidate water-protein and ion-protein interactions in protein crystals.

  10. Molecular Dynamics Simulation of Na(+)-Cl(-) Ion-Pair in Water-Methanol Mixtures under Supercritical and Ambient Conditions.

    PubMed

    Keshri, Sonanki; Sarkar, Atanu; Tembe, B L

    2015-12-17

    Constrained molecular dynamics simulations have been performed to investigate the structure and thermodynamics of Na(+)-Cl(-) ion-pair association in water-methanol mixtures under supercritical and ambient conditions in dilute solutions. From the computed potentials of mean force (PMFs) we find that contact ion pairs (CIPs) are more stable than all other associated states of the ion pairs in both ambient and supercritical conditions. Stabilities of CIPs increase with increase in the mole fraction of methanol. In supercritical conditions, major changes in PMFs occur as we go from x(methanol) = 0.00 to x(methanol) = 0.50. The stable solvent shared ion pair (SShIP) which occurs in x(methanol) = 0.00 and 0.25, vanishes when x(methanol) is 0.50 or greater. The stabilities of these ion pairs increase with increasing temperature. Local structures around the ions are studied using the radial distribution functions, density profiles, angular distribution functions, running coordination numbers and excess coordination numbers. Preferential solvation analysis shows that both Na(+) and Cl(-) ions are preferentially solvated by water. From the calculation of enthalpies and entropies, we find that Na(+)-Cl(-) ion-pair association in water-methanol binary mixtures is endothermic and driven by entropy both in ambient as well as under supercritical conditions.

  11. Molecular characteristics of a fluorescent chemosensor for the recognition of ferric ion based on photoresponsive azobenzene derivative

    NASA Astrophysics Data System (ADS)

    Chi, Zhen; Ran, Xia; Shi, Lili; Lou, Jie; Kuang, Yanmin; Guo, Lijun

    2017-01-01

    Metal ion recognition is of great significance in biological and environmental detection. So far, there is very few research related to the ferric ion sensing based on photoresponsive azobenzene derivatives. In this work, we report a highly selective fluorescent ;turn-off; sensor for Fe3 + ions and the molecular sensing characteristics based on an azobenzene derivative, N-(3,4,5-octanoxyphenyl)-N‧-4-[(4-hydroxyphenyl)azophenyl]1,3,4-oxadiazole (AOB-t8). The binding association constant was determined to be 6.07 × 103 M- 1 in ethanol and the stoichiometry ratio of 2:2 was obtained from Job's plot and MS spectra. The AOB-t8 might be likely to form the dimer structure through the chelation of ferric ion with the azobenzene moiety. Meanwhile, it was found that the photoisomerization property of AOB-t8 was regulated by the binding with Fe3 +. With the chelation of Fe3 +, the regulated molecular rigidity and the perturbed of electronic state and molecular geometry was suggested to be responsible for the accelerated isomerization of AOB-t8 to UV irradiation and the increased fluorescence lifetime of both trans- and cis-AOB-t8-Fe(III). Moreover, the reversible sensing of AOB-t8 was successfully observed by releasing the iron ion from AOB-t8-Fe(III) with the addition of citric acid.

  12. Nanojets, Electrospray, and Ion Field Evaporation: Molecular Dynamics Simulations and Laboratory Experiments

    DTIC Science & Technology

    2008-07-22

    fragmented ions of FC-43 were measured for all investigated quadrupole transmission energies ...observed ions that are produced with internal energies above the dissociation limit, and to substantiate the present interpretation that ion field... ions with internal energies exceeding the binding energy , we determine the unimolecular dissociation rate using a RRKM approach, following

  13. Molecular dynamics study of linear and comb-like polyelectrolytes in aqueous solution: effect of Ca2+ ions

    NASA Astrophysics Data System (ADS)

    Tong, Kefeng; Song, Xingfu; Sun, Shuying; Xu, Yanxia; Yu, Jianguo

    2014-08-01

    All-atom molecular dynamics simulations were employed to provide microscopic mechanism for the salt tolerance of polyelectrolytes dispersants. The conformational variation of polyelectrolytes and interactions between COO- groups and counterions/water molecules were also studied via radius of gyration and pair correlations functions. Sodium polyacrylate (NaPA) and sodium salts of poly(acrylic acid)-poly(ethylene oxide) (NaPA-PEO) were selected as the representative linear and comb-like polyelectrolyte, respectively. The results show that Ca2+ ions interact with COO- groups much stronger than Na+ ions and can bring ion-bridging interaction between intermolecular COO- groups in the NaPA systems. While in the NaPA-PEO systems, the introduced PEO side chains can prevent backbone chains from ion-bridging interactions and weaken the conformational changes. The present results can help in selecting and designing new-type efficient polyelectrolyte dispersants with good salt tolerance.

  14. Is there a difference in metal ion-based inhibition between members of thionin family: Molecular dynamics simulation study.

    PubMed

    Oard, Svetlana; Karki, Bijaya; Enright, Frederick

    2007-10-01

    Thionins have a considerable potential as antimicrobial compounds although their application may be restricted by metal ion-based inhibition of membrane permeabilizing activity. We previously reported the properties associated with the proposed mechanism of metal ion-based inhibition of beta-purothionin. In this study, we investigated the effects of metal ions on alpha-hordothionin which differs from beta-purothionin by eight out of 45 residues. Three of the differing residues are thought to be involved in the mechanism of metal ion-based inhibition in beta-purothionin. The structure and dynamics of alpha-hordothionin were explored using unconstrained molecular dynamics (MD) simulations in explicit water as a function of metal ions. Although the global fold is almost identical to that of beta-purothionin, alpha-hordothionin displays reduced fluctuating motions. Moreover, alpha-hordothionin is more resistant to the presence of metal ions than beta-purothionin. Mg(+2) ions do not affect alpha-hordothionin, whereas K(+) ions induce perturbations in the alpha2 helix, modify dynamics and electrostatic properties. Nevertheless, these changes are considerably smaller than those in beta-purothionin. The proposed mechanism of metal ion-based inhibition involves the hydrogen bonding network of Arg5-Arg30-Gly27, which regulates dynamic unfolding of the alpha2 C-end which is similar to beta-purothionin response. The key residues responsible for the increased resistance for alpha-hordothionin are Gly27 and Gly42 which replace Asn27 and Asp42 involved into the mechanism of metal ion-based inhibition in beta-purothionin. Comparison of MD simulations of alpha-hordothionin with beta-purothionin reveals dynamic properties which we believe are intrinsic properties of thionins with four disulphide bonds.

  15. Modelling of ion permeation in K+ channels by nonequilibrium molecular dynamics simulations: I. Permeation energetics and structure stability.

    PubMed

    Neamţu, A; Suciu, Daniela

    2004-01-01

    Because of the great importance of physiological and pathophysiological processes in which ion channels are involved and because their operation is described by physicochemical laws, there have been many attempts to develop physical models able to describe the membrane permeability and also the structural and functional properties of the channel protein structures. In this study (in two parts) we present a series of simulations on a K+ channel model (KcsA) using Nonequilibrium Molecular Dynamics simulations (NEMD), in order to follow structure stability, permeation energetics and the possibility of obtaining quantitative information about the permeation process using the Linear Response Theory (LRT). On K+ ions were applied external forces to determine them to pass through the channel in a relatively small amount of time, accessible computationally. We ascertained a high resistance of the protein to deformation even in conditions when great forces were applied on ions (the system was far from equilibrium). The estimation of energy profiles in the course of ions passage through the channel demonstrates that these proteins create a conductivity pathway with no energetic barriers for ions movement across the channel (which could be present due to ions dehydration). The dynamic model used demonstrates (as proposed before in the literature after the examination of the static KcsA structure obtained by X-Ray crystallography) that this is due to the interaction of ions with the negatively charged carbonyl oxygens of the main polypeptide chain in the selectivity filter region.

  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.

  17. 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

  18. Molecular dynamics simulation of polymerlike thin films irradiated by fast ions: A comparison between FENE and Lennard-Jones potentials

    NASA Astrophysics Data System (ADS)

    Lima, N. W.; Gutierres, L. I.; Gonzalez, R. I.; Müller, S.; Thomaz, R. S.; Bringa, E. M.; Papaléo, R. M.

    2016-11-01

    In this paper, the surface effects of individual heavy ions impacting thin polymerlike films were investigated, using molecular dynamics simulations with the finite extensible nonlinear elastic (FENE) potential to describe the molecular chains. The perturbation introduced by the ions in the lattice was modeled assuming that the initial excitation energy in the ion track is converted into an effective temperature, as in a thermal spike. The track was heated only within the film thickness h , leaving a nonexcited substrate below. The effect of decreasing thickness on cratering and sputtering was evaluated. The results were compared to experimental data of thin polymer films bombarded by MeV-GeV ions and to simulations performed with the Lennard-Jones potential. While several qualitative results observed in the experiments were also seen in the simulations, irrespective of the potential used, there are important differences observed on FENE films. Crater dimensions, rim volume, and sputtering yields are substantially reduced, and a threshold thickness for molecular ejection appears in FENE simulations. This is attributed to the additional restrictions on mass transport out of the excited track region imposed by interchain interactions (entanglements) and by the low mobility of the molten phase induced by the spike.

  19. Aromaticity of Heterofullerenes C18BxNy (x + y = 2) and Their Molecular Ions

    NASA Astrophysics Data System (ADS)

    Chen, Jia-li; Kerim, Ablikim

    2008-04-01

    The aromaticity of all possible substituted fullerene isomers of C18N2, C18B2, C18BN, and their molecular ions which originate from the C20 (Ih) cage were studied by the topological resonance energy (TRE) and the percentage topological resonance energy methods. The relationship between the aromaticity of C18BxNy isomers and the sites where the heteroatoms dope at the C20 (Ih) cage is discussed. Calculation results show that at the neutral and cationic states all the isomers are predicted to be antiaromatic with negative TREs, but their polyvalent anions are predicted to be aromatic with positive TREs. The most stable isomer is formed by heteroatom doping at the 1, 11-sites in C18N2, C18B2, and C18BN. Heterofullerenes are more aromatic than C20. The stability order in the neutral states is C18N2 > C18 BN > C18 B2 > C20. The stability order in closed-shell is C18B28- > C206- > C18BN6- > C18N24-. This predicts theoretically that their polyvalent anions have high aromaticity.

  20. Molecular mapping of general anesthetic sites in a voltage-gated ion channel.

    PubMed

    Barber, Annika F; Liang, Qiansheng; Amaral, Cristiano; Treptow, Werner; Covarrubias, Manuel

    2011-10-05

    Several voltage-gated ion channels are modulated by clinically relevant doses of general anesthetics. However, the structural basis of this modulation is not well understood. Previous work suggested that n-alcohols and inhaled anesthetics stabilize the closed state of the Shaw2 voltage-gated (Kv) channel (K-Shaw2) by directly interacting with a discrete channel site. We hypothesize that the inhibition of K-Shaw2 channels by general anesthetics is governed by interactions between binding and effector sites involving components of the channel's activation gate. To investigate this hypothesis, we applied Ala/Val scanning mutagenesis to the S4-S5 linker and the post-PVP S6 segment, and conducted electrophysiological analysis to evaluate the energetic impact of the mutations on the inhibition of the K-Shaw2 channel by 1-butanol and halothane. These analyses identified residues that determine an apparent binding cooperativity and residue pairs that act in concert to modulate gating upon anesthetic binding. In some instances, due to their critical location, key residues also influence channel gating. Complementing these results, molecular dynamics simulations and in silico docking experiments helped us visualize possible anesthetic sites and interactions. We conclude that the inhibition of K-Shaw2 by general anesthetics results from allosteric interactions between distinct but contiguous binding and effector sites involving inter- and intrasubunit interfaces.

  1. 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.

  2. Three-body fragmentation of triatomic molecular ions in a strong laser field

    NASA Astrophysics Data System (ADS)

    Ablikim, U.; Zohrabi, M.; Jochim, Bethany; Berry, Ben; Carnes, K. D.; Ben-Itzhak, I.

    2014-05-01

    Coincidence three-dimensional momentum imaging measurements of three-body fragmentation of transient triply-charged CO2 molecules reveal competing fragmentation paths involving bending, symmetric and asymmetric stretching, as well as the more complex sequential breakup (i.e. one bond at a time). We have extended these studies using a CO2+molecular-ion-beam target, providing similar results for the breakup of the transient CO23+ --> O+ + C+ + O+. The detection of neutral fragments also enables kinematically complete measurements of the three-body breakup of the transient CO22+ . Our results, for CO2+in ultrashort (~26 fs) intense (1015 to 1016 W/cm2) laser pulses at 790 nm, suggest significant bending in the C+ + O+ + O+ channel as well as sequential breakup. In contrast, sequential breakup is suppressed in the O+ + C+ + O and O+ + C +O+ channels. Supported by the Chemical Sciences, Geosciences, and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U.S.

  3. Mapping of low molecular weight heparins using reversed phase ion pair liquid chromatography-mass spectrometry.

    PubMed

    Li, Daoyuan; Chi, Lequan; Jin, Lan; Xu, Xiaohui; Du, Xuzhao; Ji, Shengli; Chi, Lianli

    2014-01-01

    Low molecular weight heparins (LMWHs) are structurally complex, highly sulfated and negatively charged, linear carbohydrate polymers prepared by chemical or enzymatic depolymerization of heparin. They are widely used as anticoagulant drugs possessing better bioavailability, longer half-life, and lower side effects than heparin. Comprehensive structure characterization of LMWHs is important for drug quality assurance, generic drug application, and new drug research and development. However, fully characterization of all oligosaccharide chains in LMWHs is not feasible for current available analytical technologies due to their structure complexity and heterogeneity. Fingerprinting profiling is an efficient way for LMWHs' characterization and comparison. In this work, we present a simple, sensitive, and powerful analytical approach for structural characterization of LMWHs. Two different LMWHs, enoxaparin and nadroparin, were analyzed using reversed phase ion pair electrospray ionization mass spectrometry (RPIP-ESI-MS). More than 200 components were identified, including major structures, minor structures, and process related impurities. This approach is robust for high resolution and complementary fingerprinting analysis of LMWHs.

  4. Volatile single-source molecular precursor for the lithium ion battery cathode.

    PubMed

    Navulla, Anantharamulu; Huynh, Lan; Wei, Zheng; Filatov, Alexander S; Dikarev, Evgeny V

    2012-04-04

    The first single-source molecular precursor for a lithium-manganese cathode material is reported. Heterometallic β-diketonate LiMn(2)(thd)(5) (1, thd = 2,2,6,6-tetramethyl-3,5-heptanedionate) was obtained in high yield by simple one-step solid-state reactions employing commercially available reagents. Substantial scale-up preparation of 1 was achieved using a solution approach. The crystal structure of the precursor contains discrete Li:Mn = 1:2 trinuclear molecules held together by bridging diketonate ligands. The complex is relatively stable in open air, highly volatile, and soluble in all common solvents. It was confirmed to retain its heterometallic structure in solutions of non-coordinating solvents. The heterometallic diketonate 1 was shown to exhibit clean, low-temperature decomposition in air/oxygen that results in nanosized particles of spinel-type oxide LiMn(2)O(4), one of the leading cathode materials for lithium ion batteries.

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

    DOE PAGES

    Fan, Fei; Wang, Weiyu; Holt, Adam P.; ...

    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

  6. 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.

  7. 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.

  8. Important role of pedestal ion temperature in the ELM mitigation by supersonic molecular beam injection

    NASA Astrophysics Data System (ADS)

    Ma, Q.; Yu, D. L.; Chen, C. Y.; Wei, Y. L.; Zhong, W. L.; Zou, X. L.; Zuo, H. Y.; Du, J. L.; Liu, L.; Dong, C. F.; Shi, Z. B.; Zhao, K. J.; Feng, B. B.; Zhou, Y.; Wang, Z. H.; Xu, M.; Liu, Yi; Yan, L. W.; Yang, Q. W.; Yao, L. H.; Ding, X. T.; Dong, J. Q.; Duan, X. R.; Liu, Yong; HL-2A Team

    2016-12-01

    Edge localized mode (ELM) is successfully mitigated by helium and deuterium supersonic molecular beam injections (SMBIs) on HL-2A. During the ELM mitigation by SMBIs, gradients of ion temperature (T i) and electron density are softened in the pedestal. It has been observed that the averaged gradient of the T i decreases around 44% and the well depth of radial electric field (E r) is reduced by the SMBI during ELM mitigation. Furthermore, at least 20% decrements of T i have to be attained to achieve a noticeable increase (decrease) of the ELM frequency (amplitude). In addition, the duration of ELM mitigation with helium SMBI is much longer than that with deuterium, likely due to the higher level of recycling neutral gas compared to that of deuterium; in the case of ELM mitigation by helium SMBI, the recovery duration of the density gradient is much shorter (10-20 ms) than that of T i (up to 40 ms or longer), indicating the importance of the T i in the ELM mitigation by SMBI. Finally, it has been observed that the T i is reduced before the beginning of the ELM mitigation, suggesting that the mechanism of the ELM mitigation by SMBI is closely related to the cooling effect.

  9. 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.

  10. 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.

  11. Potassium ion surrounded by aromatic rings: molecular dynamics of the first solvation shell

    NASA Astrophysics Data System (ADS)

    Albertí, Margarita; Aguilar, Antonio; Marques, Jorge M. C.

    2014-12-01

    We study the potassium ion in non-polar environments due to the interaction with aromatic rings, which is relevant to get insight on the selectivity of several biochemical processes. In concrete, we performed molecular dynamics simulations of the first solvation shell of K+ surrounded by either benzene (Bz) or hexafluorobenzene (HFBz) molecules. The global intermolecular interaction for these clusters has been decomposed in Bz-Bz (or HFBz-HFBz) and in K+-Bz (or K+-HFBz) contributions, using a potential model based on different decompositions of the molecular polarizability of the solvent molecule (Bz or HFBz). For the molecular dynamics simulations, we used as starting geometries the low-energy structures of the K+-(Bz) n ( n = 3,4) and K+-(HFBz) n ( n = 8,9) clusters that were obtained in our previous global optimization studies [J.M.C. Marques, J.L. Llanio-Trujillo, M. Albertí, A. Aguilar, F. Pirani, J. Phys. Chem. A 116, 4947 (2012); J.M.C. Marques, J.L. Llanio-Trujillo, M. Albertí, A. Aguilar, F. Pirani, J. Phys. Chem. A 117, 8043 (2013)]; a total of 11 starting geometries were employed (including the 4 global minima): 4 (4) for K+-(Bz)3 (K+-(Bz)4) and 2 (1) for K+-(HFBz)8 (K+-(HFBz)9). We have found that all the K+-(Bz)3 local minimum structures isomerise to form the lowest-energy aggregate at T< 20 K. As for K+-(Bz)4, such kind of isomerisation is only observed at T> 90 K for two of the local minima; the highest-energy minimum, that corresponds to a K+-(Bz)4 structure with a Bz molecule placed in the second solvation shell, tends to dissociate before it can isomerise. In the case of K+-(HFBz)8 (or K+-(HFBz)9), the dissociation only occurs at higher temperatures, i.e., T = 260 K (or T = 210 K). By lowering the temperature of the simulation after the dissociation of K+-(HFBz)9, one observes the formation of the global minimum structure of K+-(HFBz)8.

  12. Molecular dynamics investigation into the electric charge effect on the operation of ion-based carbon nanotube oscillators

    NASA Astrophysics Data System (ADS)

    Ansari, R.; Ajori, S.; Sadeghi, F.

    2015-10-01

    The fabrication of nanoscale oscillators working in the gigahertz (GHz) range and beyond has now become the focal center of interest to many researchers. Motivated by this issue, this paper proposes a new type of nano-oscillators with enhanced operating frequency in which both the inner core and outer shell are electrically charged. To this end, molecular dynamics (MD) simulations are performed to investigate the mechanical oscillatory behavior of ions, and in particular chloride ion, tunneling through electrically charged carbon nanotubes (CNTs). It is assumed that the electric charges with similar sign and magnitude are evenly distributed on two ends of nanotube. The interatomic interactions between carbon atoms and van der Waals (vdW) interactions between ion and nanotube are respectively modeled by Tersoff-Brenner and Lennard-Jones (LJ) potential functions, whereas the electrostatic interactions between ion and electric charges are modeled by Coulomb potential function. A comprehensive study is conducted to get an insight into the effects of different parameters such as sign and magnitude of electric charges, nanotube radius, nanotube length and initial conditions (initial separation distance and velocity) on the oscillatory behavior of chloride ion-charged CNT oscillators. It is shown that, the chloride ion frequency inside negatively charged CNTs is lower than that inside positively charged ones with the same magnitude of electric charge, while it is higher than that inside uncharged CNTs. It is further observed that, higher frequencies are generated at higher magnitudes of electric charges distributed on the nanotube.

  13. Lithium Ion Solvation and Diffusion in Bulk Organic Electrolytes from First-Principles and Classical Reactive Molecular Dynamics

    SciTech Connect

    Ong, Mitchell T.; Verners, Osvalds; Draeger, Erik W.; van Duin, Adri C. T.; Lordi, Vincenzo; Pask, John E.

    2014-12-19

    We report that 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 PF $\\bar{6}$ 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 PF $\\bar{6}$ anion shows greater diffusivity associated with a weakly bound, poorly defined first solvation shell. In conclusion, these results can be used to aid in the design of new electrolytes to improve Li-ion battery performance.

  14. Lithium Ion Solvation and Diffusion in Bulk Organic Electrolytes from First-Principles and Classical Reactive Molecular Dynamics

    DOE PAGES

    Ong, Mitchell T.; Verners, Osvalds; Draeger, Erik W.; ...

    2014-12-19

    We report that 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 PF more » $$\\bar{6}$$ 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 PF $$\\bar{6}$$ anion shows greater diffusivity associated with a weakly bound, poorly defined first solvation shell. In conclusion, these results can be used to aid in the design of new electrolytes to improve Li-ion battery performance.« less

  15. Developments in molecular SIMS depth profiling and 3D imaging of biological systems using polyatomic primary ions.

    PubMed

    Fletcher, John S; Lockyer, Nicholas P; Vickerman, John C

    2011-01-01

    In principle mass spectral imaging has enormous potential for discovery applications in biology. The chemical specificity of mass spectrometry combined with spatial analysis capabilities of liquid metal cluster beams and the high yields of polyatomic ion beams should present unprecedented ability to spatially locate molecular chemistry in the 100 nm range. However, although metal cluster ion beams have greatly increased yields in the m/z range up to 1000, they still have to be operated under the static limit and even in most favorable cases maximum yields for molecular species from 1 µm pixels are frequently below 20 counts. However, some very impressive molecular imaging analysis has been accomplished under these conditions. Nevertheless although molecular ions of lipids have been detected and correlation with biology is obtained, signal levels are such that lateral resolution must be sacrificed to provide a sufficient signal to image. To obtain useful spatial resolution detection below 1 µm is almost impossible. Too few ions are generated! The review shows that the application of polyatomic primary ions with their low damage cross-sections offers hope of a new approach to molecular SIMS imaging by accessing voxels rather than pixels to thereby increase the dynamic signal range in 2D imaging and to extend the analysis to depth profiling and 3D imaging. Recent data on cells and tissue analysis suggest that there is, in consequence, the prospect that a wider chemistry might be accessible within a sub-micron area and as a function of depth. However, these advances are compromised by the pulsed nature of current ToF-SIMS instruments. The duty cycle is very low and results in excessive analysis times, and maximum mass resolution is incompatible with maximum spatial resolution. New instrumental directions are described that enable a dc primary beam to be used that promises to be able to take full advantage of all the capabilities of the polyatomic ion beam. Some new

  16. Molecular dynamic-secondary ion mass spectrometry (D-SIMS) ionized by co-sputtering with C60+ and Ar+.

    PubMed

    You, Yun-Wen; Chang, Hsun-Yun; Lin, Wei-Chun; Kuo, Che-Hung; Lee, Szu-Hsian; Kao, Wei-Lun; Yen, Guo-Ji; Chang, Chi-Jen; Liu, Chi-Ping; Huang, Chih-Chieh; Liao, Hua-Yang; Shyue, Jing-Jong

    2011-10-15

    Dynamic secondary ion mass spectrometry (D-SIMS) analysis of poly(ethylene terephthalate) (PET) and poly(methyl methacrylate) (PMMA) was conducted using a quadrupole mass analyzer with various combinations of continuous C(60)(+) and Ar(+) ion sputtering. Individually, the Ar(+) beam failed to generate fragments above m/z 200, and the C(60)(+) beam generated molecular fragments of m/z ~1000. By combining the two beams, the auxiliary Ar(+) beam, which is proposed to suppress carbon deposition due to C(60)(+) bombardment and/or remove graphitized polymer, the sputtering range of the C(60)(+) beam is extended. Another advantage of this technique is that the high sputtering rate and associated high molecular ion intensity of the C(60)(+) beam generate adequate high-mass fragments that mask the damage from the Ar(+) beam. As a result, fragments at m/z ~900 can be clearly observed. As a depth-profiling tool, the single C(60)(+) beam cannot reach a steady state for either PET or PMMA at high ion fluence, and the intensity of the molecular fragments produced by the beam decreases with increasing C(60)(+) fluence. As a result, the single C(60)(+) beam is suitable for profiling surface layers with limited thickness. With C(60)(+)-Ar(+) co-sputtering, although the initial drop in intensity is more significant than with single C(60)(+) ionization because of the damage introduced by the auxiliary Ar(+), the intensity levels indicate that a more steady-state process can be achieved. In addition, the secondary ion intensity at high fluence is higher with co-sputtering. As a result, the sputtered depth is enhanced with co-sputtering and the technique is suitable for profiling thick layers. Furthermore, co-sputtering yields a smoother surface than single C(60)(+) sputtering.

  17. Probing the Electron Capture Dissociation Mass Spectrometry of Phosphopeptides with Traveling Wave Ion Mobility Spectrometry and Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Kim, Doyong; Pai, Pei-Jing; Creese, Andrew J.; Jones, Andrew W.; Russell, David H.; Cooper, Helen J.

    2015-06-01

    Electron capture dissociation mass spectrometry offers several advantages for the analysis of peptides, most notably that backbone c and z fragments typically retain labile modifications such as phosphorylation. We have shown previously that, in some cases, the presence of phosphorylation has a deleterious effect on peptide sequence coverage, and hypothesized that intramolecular interactions involving the phosphate group were preventing separation of backbone fragments. In the present work, we seek to rationalize the observed ECD behavior through a combination of ECD of model peptides, traveling wave ion mobility mass spectrometry and molecular dynamics simulations. The results suggest that for doubly protonated ions of phosphopeptide APLpSFRGSLPKSYVK a salt-bridge structure is favored, whereas for the doubly-protonated ions of APLSFRGSLPKpSYVK ionic hydrogen bonds predominate.

  18. Effect of swift-ion irradiation on DNA molecules: A molecular dynamics study using the REAX force field

    NASA Astrophysics Data System (ADS)

    Bottländer, Dominik; Mücksch, Christian; Urbassek, Herbert M.

    2015-12-01

    Modern REAX potentials allow to use molecular dynamics simulation to study bond breaking and reformation in biomolecules. We use this technique to simulate the effects of a swift-ion track on a B-DNA fragment in water. We monitor the number of single- and double-strand breaks as a function of the deposited energy. In addition we compare the results of direct DNA heating with the effect of hydrolysis which we model by heating only the water environment.

  19. Computation of the hindrance factor for the diffusion for nanoconfined ions: molecular dynamics simulations versus continuum-based models

    NASA Astrophysics Data System (ADS)

    Zhu, Haochen; Ghoufi, Aziz; Szymczyk, Anthony; Balannec, Béatrice; Morineau, Denis

    2012-06-01

    We report the self-diffusion coefficients and hindrance factor for the diffusion of ions into cylindrical hydrophilic silica nanopores (hydrated silica) determined from molecular dynamics (MD) simulations. We make a comparison with the hindered diffusion coefficients used in continuum-based models of nanofiltration (NF). Hindrance factors for diffusion estimated from the macroscopic hydrodynamic theory were found to be in fair quantitative agreement with MD simulations for a protonated pore, but they strongly overestimate diffusion inside a deprotonated pore.

  20. Electric potential invariants and ions-in-molecules effective potentials for molecular Rydberg states

    NASA Astrophysics Data System (ADS)

    Coy, Stephen L.; Grimes, David D.; Zhou, Yan; Field, Robert W.; Wong, Bryan M.

    2016-12-01

    The dependence of multipole moments and polarizabilities on external fields appears in many applications including biomolecular molecular mechanics, optical non-linearity, nanomaterial calculations, and the perturbation of spectroscopic signatures in atomic clocks. Over a wide range of distances, distributed multipole and polarizability potentials can be applied to obtain the variation of atom-centered atoms-in-molecules electric properties like bonding-quenched polarizability. For cylindrically symmetric charge distributions, we examine single-center and atom-centered effective polarization potentials in a non-relativistic approximation for Rydberg states. For ions, the multipole expansion is strongly origin-dependent, but we note that origin-independent invariants can be defined. The several families of invariants correspond to optimized representations differing by origin and number of terms. Among them, a representation at the center of dipole polarizability optimizes the accuracy of the potential with terms through 1/r4. We formulate the single-center expansion in terms of polarization-modified effective multipole moments, defining a form related to the source-multipole expansion of Brink and Satchler. Atom-centered potentials are an origin independent alternative but are limited both by the properties allowed at each center and by the neglected effects like bond polarizability and charge flow. To enable comparisons between single-center effective potentials in Cartesian or spherical form and two-center effective potentials with differing levels of mutual induction between atomic centers, we give analytical expressions for the bond-length and origin-dependence of multipole and polarizability terms projected in the multipole and polarizability expansion of Buckingham. The atom-centered potentials can then be used with experimental data and ab initio calculations to estimate atoms-in-molecules properties. Some results are given for BaF+ and HF showing the

  1. 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.

  2. Electric potential invariants and ions-in-molecules effective potentials for molecular Rydberg states.

    PubMed

    Coy, Stephen L; Grimes, David D; Zhou, Yan; Field, Robert W; Wong, Bryan M

    2016-12-21

    The dependence of multipole moments and polarizabilities on external fields appears in many applications including biomolecular molecular mechanics, optical non-linearity, nanomaterial calculations, and the perturbation of spectroscopic signatures in atomic clocks. Over a wide range of distances, distributed multipole and polarizability potentials can be applied to obtain the variation of atom-centered atoms-in-molecules electric properties like bonding-quenched polarizability. For cylindrically symmetric charge distributions, we examine single-center and atom-centered effective polarization potentials in a non-relativistic approximation for Rydberg states. For ions, the multipole expansion is strongly origin-dependent, but we note that origin-independent invariants can be defined. The several families of invariants correspond to optimized representations differing by origin and number of terms. Among them, a representation at the center of dipole polarizability optimizes the accuracy of the potential with terms through 1/r(4). We formulate the single-center expansion in terms of polarization-modified effective multipole moments, defining a form related to the source-multipole expansion of Brink and Satchler. Atom-centered potentials are an origin independent alternative but are limited both by the properties allowed at each center and by the neglected effects like bond polarizability and charge flow. To enable comparisons between single-center effective potentials in Cartesian or spherical form and two-center effective potentials with differing levels of mutual induction between atomic centers, we give analytical expressions for the bond-length and origin-dependence of multipole and polarizability terms projected in the multipole and polarizability expansion of Buckingham. The atom-centered potentials can then be used with experimental data and ab initio calculations to estimate atoms-in-molecules properties. Some results are given for BaF(+) and HF showing the

  3. 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.

  4. 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.

  5. Detection and investigation of the molecular nature of low-molecular-mass copper ions in isolated rheumatoid knee-joint synovial fluid.

    PubMed

    Naughton, D P; Knappitt, J; Fairburn, K; Gaffney, K; Blake, D R; Grootveld, M

    1995-03-20

    Low-molecular-mass copper(II) species have been detected and quantified in ultrafiltrates (n = 7) of rheumatoid synovial fluid (SF) by a highly-sensitive HPLC-based assay system with the ability to determine Cu(II) concentrations of < 10(-7) mol.dm-3. High field 1H NMR spectroscopy demonstrated that addition of Cu(II)(aq.) to isolated samples of RA SF ultrafiltrates resulted in complexation by histidine > alanine > formate > threonine > lactate > tyrosine > phenylalanine, their effectiveness in this context being in the given order. CD spectra of Cu(II)-treated samples of intact SF exhibited absorption bands typical of copper(II)-albumin complexes, in addition to a band attributable to a low-molecular-mass histidinate complex (lambda min 610 nm). Since both albumin and histidine are potent radical scavengers, these results indicate that any .OH radical generated from bound copper ions will be 'site-specifically' scavenged. Hence, low-molecular-mass copper complexes with the ability to promote the generation of .OH radical which can then escape from the metal ion co-ordination sphere (and in turn, cause damage to critical biomolecules) appear to be absent from inflammatory SF.

  6. 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.

  7. Molecular dynamics study of nano-porous materials—Enhancement of mobility of Li ions in lithium disilicate

    NASA Astrophysics Data System (ADS)

    Habasaki, Junko

    2016-11-01

    In several nano-porous materials and their composites, enhancement of ionic conductivity has been reported and several mechanisms having different origins have been proposed so far. In the present work, ionic motion of Li ions in porous lithium disilicates is examined by molecular dynamics simulation in the constant volume conditions and the enhancement of the dynamics is predicted. Structures and dynamics of ions in a nano-porous system were characterized and visualized to clarify the mechanism of the enhancement. The diffusion coefficient of Li ions has shown the maximum in the medium density (and porosity) region, and near the maximum, shortening of the nearly constant loss region in the mean squared displacement of ions as well as changes of the structures of the coordination polyhedra, LiOx is found. It suggests that the loosening of the cage, which increases the jump rate of ions, is an origin of the enhancement. When larger (but still in a nano-scale) voids are formed with a further decrease of density, more tight cages are reconstructed and the diffusion coefficient decreases again. These behaviors are closely related to the residual stress in the system. It is noteworthy that the explanation is not based on the percolation of the path only or formation of boundaries, although the former also affects the dynamics.

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

    NASA Astrophysics Data System (ADS)

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

    2002-09-01

    The rumpled surface structure and thermal lattice vibrations of KI(001) were studied by high-resolution medium-energy ion scattering (MEIS) and molecular dynamics (MD) simulation. The relaxation of the interlayer distance between the top and second layer and the rumpling of the top and second layers were measured directly by MEIS with an accuracy of 0.01 Å. From the displaced lattice positions determined above, we derived the dipole moments of the top- and second-layer K+ and I- ions self-consistently using the polalizabilities estimated from the optical refractive index combined with the Clausius-Mossotti relation. The balance between a short-range force and a long-range Coulombic one made it possible to judge the applicability of the short-range pair potentials proposed so far. We also determined the root-mean-square thermal vibration amplitudes of the bulk and top-layer ions together with the correlations between the top- and second-layer ions by means of the ion shadowing effect applied to various kinds of scattering geometries. The results obtained were compared with those calculated from the MD simulations based on a semiclassical model using the dipole moments determined above and a Born-Mayer- or Hellmann-type pair potential. The present results are in overall agreement with the MD simulations employing the pair potential proposed by Catlow et al. [J. Phys. C 10, 1395 (1977)].

  9. Molecular dynamics study of nano-porous materials-Enhancement of mobility of Li ions in lithium disilicate.

    PubMed

    Habasaki, Junko

    2016-11-28

    In several nano-porous materials and their composites, enhancement of ionic conductivity has been reported and several mechanisms having different origins have been proposed so far. In the present work, ionic motion of Li ions in porous lithium disilicates is examined by molecular dynamics simulation in the constant volume conditions and the enhancement of the dynamics is predicted. Structures and dynamics of ions in a nano-porous system were characterized and visualized to clarify the mechanism of the enhancement. The diffusion coefficient of Li ions has shown the maximum in the medium density (and porosity) region, and near the maximum, shortening of the nearly constant loss region in the mean squared displacement of ions as well as changes of the structures of the coordination polyhedra, LiOx is found. It suggests that the loosening of the cage, which increases the jump rate of ions, is an origin of the enhancement. When larger (but still in a nano-scale) voids are formed with a further decrease of density, more tight cages are reconstructed and the diffusion coefficient decreases again. These behaviors are closely related to the residual stress in the system. It is noteworthy that the explanation is not based on the percolation of the path only or formation of boundaries, although the former also affects the dynamics.

  10. Fragmentation of peptide negative molecular ions induced by resonance electron capture

    PubMed Central

    Vasil’ev, Yury V.; Figard, Benjamin J.; Morré, Jeff; Deinzer, Max L.

    2009-01-01

    A simple robust method to study resonance gas-phase reactions between neutral peptides of low volatility and free electrons has been designed and implemented. Resonance electron capture (REC) experiments were performed by several neutral model peptides and two naturally occurring peptides. The assignment of negative ions (NIs) formed in these gas-phase reactions was based on high mass-resolving power experiments. From these accurate mass measurements, it was concluded that fragment NIs formed by low (1–2 eV) energy REC are of the same types as those observed in electron capture∕transfer dissociation, where the positive charge is a factor. The main feature resulting from these REC experiments by peptides is the occurrence of zn−1 ions, which are invariably of the highest abundances in the negative ion mass spectra of larger peptides. [M–H]− NIs presumably the carboxylate anion structure dominate the REC spectra of smaller peptides. There was no evidence for the occurrence of the complementary reaction, i.e., the formations of cn+1 ions. Instead, cn ions arose without hydrogen∕proton transfer albeit with lower abundances than that observed for zn−1 ions. Only the amide forms of small peptides showed more abundant ion peaks for the cn ions than for the zn−1 ions. The mechanisms for the N–Cα bond cleavage are discussed. PMID:19655877

  11. Fragmentation of peptide negative molecular ions induced by resonance electron capture

    SciTech Connect

    Vasil'ev, Yury V.; Figard, Benjamin J.; Morre, Jeff; Deinzer, Max L.

    2009-07-28

    A simple robust method to study resonance gas-phase reactions between neutral peptides of low volatility and free electrons has been designed and implemented. Resonance electron capture (REC) experiments were performed by several neutral model peptides and two naturally occurring peptides. The assignment of negative ions (NIs) formed in these gas-phase reactions was based on high mass-resolving power experiments. From these accurate mass measurements, it was concluded that fragment NIs formed by low (1-2 eV) energy REC are of the same types as those observed in electron capture/transfer dissociation, where the positive charge is a factor. The main feature resulting from these REC experiments by peptides is the occurrence of z{sub n}-1 ions, which are invariably of the highest abundances in the negative ion mass spectra of larger peptides. [M-H]{sup -} NIs presumably the carboxylate anion structure dominate the REC spectra of smaller peptides. There was no evidence for the occurrence of the complementary reaction, i.e., the formations of c{sub n}+1 ions. Instead, c{sub n} ions arose without hydrogen/proton transfer albeit with lower abundances than that observed for z{sub n}-1 ions. Only the amide forms of small peptides showed more abundant ion peaks for the c{sub n} ions than for the z{sub n}-1 ions. The mechanisms for the N-C{sub {alpha}} bond cleavage are discussed.

  12. Infrared spectroscopy of molecular ions in selected rotational and spin-orbit states

    NASA Astrophysics Data System (ADS)

    Jacovella, U.; Agner, J. A.; Schmutz, H.; Deiglmayr, J.; Merkt, F.

    2016-07-01

    First results are presented obtained with an experimental setup developed to record IR spectra of rotationally state-selected ions. The method we use is a state-selective version of a method developed by Schlemmer et al. [Int. J. Mass Spectrom. 185, 589 (1999); J. Chem. Phys. 117, 2068 (2002)] to record IR spectra of ions. Ions are produced in specific rotational levels using mass-analyzed-threshold-ionization spectroscopy. The state-selected ions generated by pulsed-field ionization of Rydberg states of high principal quantum number (n ≈ 200) are extracted toward an octupole ion guide containing a neutral target gas. Prior to entering the octupole, the ions are excited by an IR laser. The target gas is chosen so that only excited ions react to form product ions. These product ions are detected mass selectively as a function of the IR laser wavenumber. To illustrate this method, we present IR spectra of C 2 H2 + in selected rotational levels of the 2Πu,3/2 and 2Πu,1/2 spin-orbit components of the vibronic ground state.

  13. Solar wind ion impacts into ice surfaces: A molecular-dynamics study using the REAX force field

    NASA Astrophysics Data System (ADS)

    Anders, Christian; Urbassek, Herbert M.

    2017-01-01

    Molecular dynamics simulation is used to study the effects of solar-wind ion irradiation on an ice target, focusing on the effects of nuclear energy deposition. A reactive force field (REAX) interatomic interaction potential is employed that allows us to model the breaking and formation of molecular bonds and hence to follow the chemistry occurring in the target. As ions we study H and He ions as typical constituents of the solar wind, and Ne as an example of a heavier ion; they impact at the speed of maximum flux in the solar wind, 400 km/s. The ice consists of a mixture of H2O, CO2, CH3OH and NH3. We find that molecular dissociations occur within 0.2 ps after ion impact and new products are formed up to a time of 1 ps; only water has a slower dynamics, due to highly mobile H atoms allowing for late recombinations. The number of dissociations, and hence also of product molecules increases from H over He to Ne ion projectiles and can be quantified by the amount of energy deposited in the target by these ions. The most abundant products formed include CO, OH and NH2. Reaction products are most complex for Ne impact, and include H3O, formaldehyde (H2CO), HO2, and NO. Formaldehyde is important as it is formed relatively frequently and is known as a precursor in the formation of sugars. In addition, molecules containing all CHON elements are formed, among which are CH2NO, CONH, methanolamine (CH5NO), and ethyne (C2H2). Repeated impacts generate novel, and more complex product species; we found CN, CH4, CH3NO, methylamine (CH3NH2), and acetamide (CH3CONH2), among others; the complex species are formed less frequently than the simple fragments. Sputtering occurs for all projectiles, even H. The ejecta are either original molecules - in particular CO2 - or simple fragments; only few product molecules are emitted.

  14. In vitro neurotoxicity of magnetic resonance imaging (MRI) contrast agents: influence of the molecular structure and paramagnetic ion.

    PubMed

    Bertin, Annabelle; Michou-Gallani, Anne-Isabelle; Gallani, Jean-Louis; Felder-Flesch, Delphine

    2010-08-01

    Interest in contrast agent's (CA) neurotoxicity has greatly increased due to the growing need of new compounds dedicated to brain imaging. Magnetic resonance imaging (MRI) CA have been evaluated by means of different toxicological assays with cultured rat primary neurons (evaluation of neurite specific parameters via immunostaining of the cells and LDH leakage). To determine the potential neurotoxicity of a precise paramagnetic ion in a defined structure (architecture and molecular weight), novel hydrosoluble dendritic Manganese (II) and Gadolinium (III) complexes derived from diethylenetriamine pentaacetic acid (DTPA) have been studied and compared to a linear homologue (same molecular weight) and commercially available low molecular weight MRI CA like Mn-DPDP (Teslascan, GE Healthcare) and Gd-DTPA (Magnevist, Schering). The range of CA concentrations studied was 0.1-10mM, suitable for MRI examinations. This set of experiments allows a toxicity ranking of these reagents as a function of molecular structure and nature of the paramagnetic ion. We could determine that the architecture (linear vs. dendritic) does not play an important role in the in vitro neurotoxicity, whereas the structure of the chelating cage is of greater importance.

  15. Ambient Ionization and FAIMS Mass Spectrometry for Enhanced Imaging of Multiply Charged Molecular Ions in Biological Tissues

    PubMed Central

    Feider, Clara L.; Elizondo, Natalia

    2017-01-01

    Ambient ionization mass spectrometry imaging (MSI) has been increasingly used to investigate the molecular distribution of biological tissue samples. Here, we report the integration and optimization of desorption electrospray ionization (DESI) and liquid-microjunction surface sampling probe (LMJ-SSP) with a chip-based high-field asymmetric waveform ion mobility spectrometry (FAIMS) device to image metabolites, lipids, and proteins in biological tissue samples. Optimized FAIMS parameters for specific molecular classes enabled semitargeted detection of multiply charged molecular species at enhanced signal-to-noise ratios (S/N), improved visualization of spatial distributions, and, most importantly, allowed detection of species which were unseen by ambient ionization MSI alone. Under static DESI-FAIMS conditions selected for transmission of doubly charged cardiolipins (CL), for example, detection of 71 different CL species was achieved in rat brain, 23 of which were not observed by DESI alone. Diagnostic CL were imaged in a human thyroid tumor sample with reduced interference of isobaric species. LMJ-SSP-FAIMS enabled detection of 84 multiply charged protein ions in rat brain tissue, 66 of which were exclusive to this approach. Spatial visualization of proteins in substructures of rat brain, and in human ovarian cancerous, necrotic, and normal tissues was achieved. Our results indicate that integration of FAIMS with ambient ionization MS allows improved detection and imaging of selected molecular species. We show that this methodology is valuable in biomedical applications of MSI for detection of multiply charged lipids and proteins from biological tissues. PMID:27782388

  16. Specific ion effects on the self-assembly of ionic surfactants: a molecular thermodynamic theory of micellization with dispersion forces.

    PubMed

    Lukanov, Boris; Firoozabadi, Abbas

    2014-06-10

    The self-assembly of amphiphilic molecules is a key process in numerous biological and chemical systems. When salts are present, the formation and properties of molecular aggregates can be altered dramatically by the specific types of ions in the electrolyte solution. We present a molecular thermodynamic model for the micellization of ionic surfactants that incorporates quantum dispersion forces to account for specific ion effects explicitly through ionic polarizabilities and sizes. We assume that counterions are distributed in the diffuse region according to a modified Poisson-Boltzmann equation and can reach all the way to the micelle surface of charge. Stern layers of steric exclusion or distances of closest approach are not imposed externally; these are accounted for through the counterion radial distribution profiles due to the incorporation of dispersion potentials, resulting in a simple and straightforward treatment. There are no adjustable or fitted parameters in the model, which allows for a priori quantitative prediction of surfactant aggregation behavior based only on the initial composition of the system and the surfactant molecular structure. The theory is validated by accurately predicting the critical micelle concentration (CMC) for the well-studied sodium dodecyl sulfate (SDS) surfactant and its alkaline-counterion derivatives in mono- and divalent salts, as well as the molecular structure parameters of SDS micelles such as aggregation numbers and micelle surface potential.

  17. The influence of silver ion exchange on the formation and luminescent properties of lead sulfide molecular clusters and quantum dots

    NASA Astrophysics Data System (ADS)

    Abdrshin, A. N.; Lipatova, Zh. O.; Kolobkova, E. V.; Sgibnev, E. M.; Nikonorov, N. V.

    2016-12-01

    PbS molecular clusters and quantum dots are formed by heat treatment in fluorophosphate glasses of the Na2O3-P2O5-Ga2O3-AlF3-ZnO(S)-PbF2 system with different lead concentrations. PbS molecular clusters are characterized by optical absorption in the range of 300-800 nm and low quantum yields, which decrease from 8.9 to 2.7% with a semiconductor component concentration. It is shown that the parameters of formation of quantum dots luminescing in the wavelength range of 1000-1500 nm are considerably different at different semiconductor component concentrations. The influence of silver ion exchange on the formation of PbS nanoparticles is studied. Introduction of silver stimulates the growth of molecular clusters, which is seen in the absorption spectra. A possible mechanism of interaction of silver nanoparticles with PbS quantum dots is presented.

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

    SciTech Connect

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

    1990-09-01

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

  19. Effect of valence of lanthanide ion and molecular symmetry in polyoxotungstoborate on the molecular structure and spectrochemical properties

    NASA Astrophysics Data System (ADS)

    Iijima, Jun; Naruke, Haruo

    2017-01-01

    The compound K9(NH4)H[CeIV(α-BW11O39)(W5O18)]·16H2O (1) was successfully isolated and structurally characterized. The structural investigation revealed that 1 displayed a less molecular distortion, whereas Ln3+-analogs exhibited a large molecular distortion. IR spectroscopy demonstrated that the spectral patterns of 1 and Ce3+-analog were depending on each valence of Ce (IV/III). 11B-NMR spectroscopy showed that a decrease in site symmetry of B atom in the polyoxotungstoborate was related with an increase in a half width of NMR peak. There is a difference in molecular distortion between 1 and Ce3+-analog, but they have similar large half widths because of the same site symmetry of B atom. The 4f electron in Ce atom exhibited less effect on the chemical shift.

  20. 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.

  1. Rotational state-dependent attachment of He atoms to cold molecular ions: An action spectroscopic scheme for rotational spectroscopy

    NASA Astrophysics Data System (ADS)

    Brünken, Sandra; Kluge, Lars; Stoffels, Alexander; Pérez-Ríos, Jesús; Schlemmer, Stephan

    2017-02-01

    We present a kinetics model description of a newly developed action spectroscopic method for rotational spectroscopy based on rotational state-dependent three-body attachment of He atoms to cold molecular ions stored in a cryogenic 22-pole ion trap. The model results from numerical simulations and an approximate analytical expression are compared to measurements of the J = 1- 0 rotational transition of CD+, for which we obtain a refined transition frequency of 453.5218509(7) GHz. From the analysis of the spectroscopic data recorded at varying experimental conditions, e.g. over a wide range of He number densities and excitation powers, we deduce that the ternary rate coefficient in the first excited rotational state of CD+ is reduced to (55 ± 5) % of the rotational ground state value. This decrease in the rate coefficient can be rationalized as an increase of the redissociation probability in the ternary collision process. A summary of rotational spectroscopy measurements of other molecular ions using the new method will be given, and its general applicability is discussed.

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

    PubMed

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

    2015-09-09

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

  3. 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.

  4. 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.

  5. Molecular dynamics simulation study of distribution and dynamics of aqueous solutions of uranyl ions: the effect of varying temperature and concentration.

    PubMed

    Chopra, Manish; Choudhury, Niharendu

    2015-11-07

    Investigating the characteristics of actinyl ions has been of great interest due to their direct relevance in the nuclear fuel cycle. All-atom molecular dynamics simulations have been employed to study the orientational structure and dynamics of aqueous solutions of uranyl ions of various concentrations. The orientational structure of water around a uranyl ion has been thoroughly investigated by calculating different orientational probability distributions corresponding to different molecular axes of water. The orientational distribution of water molecules in the first coordination shell of a uranyl ion is found to be markedly different from that in bulk water. Analysis of counterion distribution around the uranyl ion reveals the presence of nitrate ions along with water molecules in the first solvation shell. From the comparison of the number of coordinated water and nitrate ions at various uranyl nitrate concentrations, it is evident that these two species compete for occupying the first solvation shell of the uranyl ion. Orientational dynamics of water molecules about different molecular axes of water in the vicinity of uranyl ions have also been investigated and decreasing orientational mobility of water with increasing uranyl concentration has been found. However, it is observed that the orientational dynamics remains more or less the same whether we consider all the water molecules in the aqueous solution or only the solvation shell water molecules. The effect of temperature on the translational and orientational characteristics of the aqueous uranyl solutions has also been studied in detail.

  6. 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.

  7. Coupling mechanical forces to electrical signaling: molecular motors and the intracellular transport of ion channels.

    PubMed

    Barry, Joshua; Gu, Chen

    2013-04-01

    Proper localization of various ion channels is fundamental to neuronal functions, including postsynaptic potential plasticity, dendritic integration, action potential initiation and propagation, and neurotransmitter release. Microtubule-based forward transport mediated by kinesin motors plays a key role in placing ion channel proteins to correct subcellular compartments. PDZ- and coiled-coil-domain proteins function as adaptor proteins linking ionotropic glutamate and GABA receptors to various kinesin motors, respectively. Recent studies show that several voltage-gated ion channel/transporter proteins directly bind to kinesins during forward transport. Three major regulatory mechanisms underlying intracellular transport of ion channels are also revealed. These studies contribute to understanding how mechanical forces are coupled to electrical signaling and illuminating pathogenic mechanisms in neurodegenerative diseases.

  8. Molecular alteration and carbonization of aspartic acid upon N + ion irradiation

    NASA Astrophysics Data System (ADS)

    Cui, F. Z.; Sun, S. Q.; Zhang, D. M.; Ma, Z. L.; Chen, G. Q.

    2000-06-01

    Structural changes of aspartic acid (Asp) irradiated by nitrogen ions of 30 keV were studied using Fourier transform infrared (FTIR) spectroscopy. Significant decreases of the intensities of COO -, NH 3+, COOH and CH 2 vibrations in the FTIR spectra, compared with those of unirradiated Asp, were observed for the sample irradiated at the fluence of 1×10 16 ions/cm 2. The decrease rates of the intensities of COO -, NH 3+, COOH and CH 2 vibrations with respect to the increasing irradiation fluences up to 4×10 16 ions/cm 2 were different. The results were attributable to the nonstoichiometrical desorption of corresponding volatile species such as H 2, NH 3+ and CO 2. The radiolysis residue of Asp after irradiation at a high fluence of 1×10 17 ions/cm 2 was analyzed and fatty acid was detected.

  9. 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.

  10. Size dependence of the folding of multiply charged sodium cationized polylactides revealed by ion mobility mass spectrometry and molecular modelling.

    PubMed

    De Winter, Julien; Lemaur, Vincent; Ballivian, Renaud; Chirot, Fabien; Coulembier, Olivier; Antoine, Rodolphe; Lemoine, Jérôme; Cornil, Jérôme; Dubois, Philippe; Dugourd, Philippe; Gerbaux, Pascal

    2011-08-22

    Ion mobility spectrometry coupled with mass spectrometry was used to experimentally determine the three-dimensional structure of multiply charged sodium cationized polylactides (PLA). In particular, the experiments were conducted to evaluate the influence of the charge state and the size on the gas-phase conformation of cationized PLA. The measured collision cross sections were then compared to calculated values obtained by computational chemistry methods. The most striking feature was the experimental and theoretical observation of a breaking point in the quasilinear relationship between the average collision cross sections and the number of monomer units for the triply charged cations. This breaking point was theoretically demonstrated, for the doubly and triply charged cations, to be associated with a significant folding of the polymer chains around the cationizing agents. The occurrence of such breaking points could be exploited to correlate the charge state of the most intense ion series observed upon electrospray ionization with the number-average molecular mass of a polymer.

  11. Ion association in concentrated NaCI brines from ambient to supercritical conditions: results from classical molecular dynamics simulations

    PubMed Central

    Sherman, David M; Collings, Matthew D

    2002-01-01

    Highly concentrated NaCl brines are important geothermal fluids; chloride complexation of metals in such brines increases the solubility of minerals and plays a fundamental role in the genesis of hydrothermal ore deposits. There is experimental evidence that the molecular nature of the NaCl–water system changes over the pressure–temperature range of the Earth's crust. A transition of concentrated NaCl–H2O brines to a "hydrous molten salt" at high P and T has been argued to stabilize an aqueous fluid phase in the deep crust. In this work, we have done molecular dynamic simulations using classical potentials to determine the nature of concentrated (0.5–16 m) NaCl–water mixtures under ambient (25°C, 1 bar), hydrothermal (325°C, 1 kbar) and deep crustal (625°C, 15 kbar) conditions. We used the well-established SPCE model for water together with the Smith and Dang Lennard-Jones potentials for the ions (J. Chem. Phys., 1994, 100, 3757). With increasing temperature at 1 kbar, the dielectric constant of water decreases to give extensive ion-association and the formation of polyatomic (NanClm)n-m clusters in addition to simple NaCl ion pairs. Large polyatomic (NanClm)n-m clusters resemble what would be expected in a hydrous NaCl melt in which water and NaCl were completely miscible. Although ion association decreases with pressure, temperatures of 625°C are not enough to overcome pressures of 15 kbar; consequently, there is still enhanced Na–Cl association in brines under deep crustal conditions.

  12. Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 1. An Advanced Protocol for Molecular Dynamics Simulations and Collision Cross-Section Calculation

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

    Collision cross-section (CCS) measurements with a linear drift tube have been utilized to study the gas-phase conformers of a model peptide (acetyl-PAAAAKAAAAKAAAAKAAAAK). Extensive molecular dynamics (MD) simulations have been conducted to derive an advanced protocol for the generation of a comprehensive pool of in-silico structures; both higher energy and more thermodynamically stable structures are included to provide an unbiased sampling of conformational space. MD simulations at 300 K are applied to the in-silico structures to more accurately describe the gas-phase transport properties of the ion conformers including their dynamics. Different methods used previously for trajectory method (TM) CCS calculation employing the Mobcal software [1] are evaluated. A new method for accurate CCS calculation is proposed based on clustering and data mining techniques. CCS values are calculated for all in-silico structures, and those with matching CCS values are chosen as candidate structures. With this approach, more than 300 candidate structures with significant structural variation are produced; although no final gas-phase structure is proposed here, in a second installment of this work, gas-phase hydrogen deuterium exchange data will be utilized as a second criterion to select among these structures as well as to propose relative populations for these ion conformers. Here the need to increase conformer diversity and accurate CCS calculation is demonstrated and the advanced methods are discussed.

  13. Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 1. An Advanced Protocol for Molecular Dynamics Simulations and Collision Cross-Section Calculation.

    PubMed

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

    2017-02-16

    Collision cross-section (CCS) measurements with a linear drift tube have been utilized to study the gas-phase conformers of a model peptide (acetyl-PAAAAKAAAAKAAAAKAAAAK). Extensive molecular dynamics (MD) simulations have been conducted to derive an advanced protocol for the generation of a comprehensive pool of in-silico structures; both higher energy and more thermodynamically stable structures are included to provide an unbiased sampling of conformational space. MD simulations at 300 K are applied to the in-silico structures to more accurately describe the gas-phase transport properties of the ion conformers including their dynamics. Different methods used previously for trajectory method (TM) CCS calculation employing the Mobcal software [1] are evaluated. A new method for accurate CCS calculation is proposed based on clustering and data mining techniques. CCS values are calculated for all in-silico structures, and those with matching CCS values are chosen as candidate structures. With this approach, more than 300 candidate structures with significant structural variation are produced; although no final gas-phase structure is proposed here, in a second installment of this work, gas-phase hydrogen deuterium exchange data will be utilized as a second criterion to select among these structures as well as to propose relative populations for these ion conformers. Here the need to increase conformer diversity and accurate CCS calculation is demonstrated and the advanced methods are discussed. Graphical Abstract ᅟ.

  14. 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.

  15. Electron-capture collisions at keV energies of multiply charged ions of carbon and argon with molecular deuterium

    SciTech Connect

    Bliman, S.; Aubert, J.; Geller, R.; Jacquot, B.; Van Houtte, D.

    1981-04-01

    Single- and double-electron-capture cross sections have been measured for C/sup q/+ with initial charges 2 < or = q < or = 6 and for Ar/sup q/+ with initial charges 2 < or = q < or = 12 incident on molecular deuterium gas targets. The cross sections show little dependence on the incident-ion energy for the range studied 2q to 10q keV. The single-electron-capture cross sections do not vary monotonically with the initial charge, but show an oscillation about a mean curve, reflecting the projectile electronic structure.

  16. ORF8a of SARS-CoV forms an ion channel: experiments and molecular dynamics simulations.

    PubMed

    Chen, Cheng-Chang; Krüger, Jens; Sramala, Issara; Hsu, Hao-Jen; Henklein, Peter; Chen, Yi-Ming Arthur; Fischer, Wolfgang B

    2011-02-01

    ORF8a protein is 39 residues long and contains a single transmembrane domain. The protein is synthesized using solid phase peptide synthesis and reconstituted into artificial lipid bilayers that forms cation-selective ion channels with a main conductance level of 8.9±0.8pS at elevated temperature (38.5°C). Computational modeling studies including multi nanosecond molecular dynamics simulations in a hydrated POPC lipid bilayer are done with a 22 amino acid transmembrane helix to predict a putative homooligomeric helical bundle model. A structural model of a pentameric bundle is proposed with cysteines, serines and threonines facing the pore.

  17. 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

  18. The molecular mechanism of ion-dependent gating in secondary transporters.

    PubMed

    Zhao, Chunfeng; Noskov, Sergei Yu

    2013-10-01

    LeuT-like fold Na-dependent secondary active transporters form a large family of integral membrane proteins that transport various substrates against their concentration gradient across lipid membranes, using the free energy stored in the downhill concentration gradient of sodium ions. These transporters play an active role in synaptic transmission, the delivery of key nutrients, and the maintenance of osmotic pressure inside the cell. It is generally believed that binding of an ion and/or a substrate drives the conformational dynamics of the transporter. However, the exact mechanism for converting ion binding into useful work has yet to be established. Using a multi-dimensional path sampling (string-method) followed by all-atom free energy simulations, we established the principal thermodynamic and kinetic components governing the ion-dependent conformational dynamics of a LeuT-like fold transporter, the sodium/benzyl-hydantoin symporter Mhp1, for an entire conformational cycle. We found that inward-facing and outward-facing states of Mhp1 display nearly the same free energies with an ion absent from the Na2 site conserved across the LeuT-like fold transporters. The barrier separating an apo-state from inward-facing or outward-facing states of the transporter is very low, suggesting stochastic gating in the absence of ion/substrate bound. In contrast, the binding of a Na2 ion shifts the free energy stabilizing the outward-facing state and promoting substrate binding. Our results indicate that ion binding to the Na2 site may also play a key role in the intracellular thin gate dynamics modulation by altering its interactions with the transmembrane helix 5 (TM5). The Potential of Mean Force (PMF) computations for a substrate entrance displays two energy minima that correspond to the locations of the main binding site S1 and proposed allosteric S2 binding site. However, it was found that substrate's binds to the site S1 ∼5 kcal/mol more favorable than that to the

  19. Development of a High Resolution Analyzing Magnet System for Heavy Molecular Ions

    NASA Astrophysics Data System (ADS)

    Ghazaly, Mohamed O. A. El; Dehnel, Morgan; Defrance, Pierre

    At the King Abdulaziz City for Science and Technology (KACST, Saudi Arabia), a versatile ion-beam injector was constructed to provide the electrostatic storage ring with the required high-quality ion beams. In order to remove the ambiguity over the ion mass due to the exclusive application of electric fields in the set-up, the injector is being equipped with a high resolution mass analyzing magnet. A high resolution Analyzing Magnet System has been designed to provide a singly-charged ion beam of kinetic energy up to 50 keV, mass up to 1500 Amu, and with the mass resolution fixed to Δm/m =1:1500. The system includes specific entrance and exit slits, designed to sustain the required mass resolution. Furthermore, specific focusing and shaping optics have been added upstream and downstream the system, in order to monitor and adapt the shape of the ion beam at the entrance and exit of the system, respectively. The present paper gives an overview on the design of this mass analyzing magnet system together with the upstream/downstream adapting optics.

  20. 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.

  1. Complete Molecular Weight Profiling of Low-Molecular Weight Heparins Using Size Exclusion Chromatography-Ion Suppressor-High-Resolution Mass Spectrometry.

    PubMed

    Zaia, Joseph; Khatri, Kshitij; Klein, Joshua; Shao, Chun; Sheng, Yuewei; Viner, Rosa

    2016-11-01

    Low-molecular weight heparins (LMWH) prepared by partial depolymerization of unfractionated heparin are used globally to treat coagulation disorders on an outpatient basis. Patent protection for several LMWH has expired and abbreviated new drug applications have been approved by the Food and Drug Administration. As a result, reverse engineering of LMWH for biosimilar LMWH has become an active global endeavor. Traditionally, the molecular weight distributions of LMWH preparations have been determined using size exclusion chromatography (SEC) with optical detection. Recent advances in liquid chromatography-mass spectrometry methods have enabled exact mass measurements of heparin saccharides roughly up to degree-of-polymerization 20, leaving the high molecular weight half of the LMWH preparation unassigned. We demonstrate a new LC-MS system capable of determining the exact masses of complete LMWH preparations, up to dp30. This system employed an ion suppressor cell to desalt the chromatographic effluent online prior to the electrospray mass spectrometry source. We expect this new capability will impact the ability to define LMWH mixtures favorably.

  2. [Molecular dynamics simulations of migration of ions and molecules through the acetylcholine receptor channel].

    PubMed

    Shaĭtan, K V; Li, A; Tershkina, K B; Kirpichnikov, M P

    2007-01-01

    A dynamic model of the channel of an acetylcholine receptor in a closed state has been proposed. The channel is formed by five a-helices of subunit M2 and stabilized by the cyclic hydrocarbon (CH2)105. The migration of charged and unchanged van der Waals particles with a diameter of 7.72 A equivalent to the diameter of a hydrated sodium ion has been studied. The migration occurred by the action of external force applied to the complex along the channel axis. In the closed state, the inhibition of ions is due to two components: electrostatic interaction and steric constraints. The van der Waals channel gate is formed by residues 13'-A-Val255, B-Val261, C-Val269, D-Val255, and E-Ile264, and the negatively changed residues occurring in the upper part of the channel have a great effect on ion selectivity.

  3. Analysis and modification of surfaces using molecular ions in the ambient environment.

    PubMed

    Espy, Ryan D; Badu-Tawiah, Abraham; Cooks, R Graham

    2011-10-01

    The analysis and modification of surfaces in their native conditions can be performed using new mass spectrometric methods. Ambient ionization sources, including desorption electrospray ionization (DESI), have been implemented for the rapid analysis of unmodified biological surfaces including whole plant material, tissue sections, algae, and bacterial colonies. Recent advances have shown promise for in vivo and high-throughput clinical analysis. Additionally, the recent development of ambient ion soft landing (SL) allows polyatomic ions to be deposited onto surfaces in open air. Ambient SL offers speed, control, and flexibility for surface reactions and modification.

  4. Ion Content of Moist Atmospheric Air and the Molecular Structure of Water Vapor Thus Inferred

    DTIC Science & Technology

    1988-07-01

    Nucleation 04 02 Water VaporP Hydrogen~bonding, Evaporation. 20 05 I Ions , Eletrical Conductivity Infrared.(-R) ASTRACT (Continue on reverse If necessary... eletrical charges are liberated by evaporating water. Fard a! . :;44 that jets of escaping wet steam can produce strong Inc t w n jO 1:o92, Lenard 22...I to the right as the ions are swept away in the vapor, forcing neutral clusters to be dissociated at a faster rate in an attempt to maintain the

  5. Sensitivity of ion-induced sputtering to the radial distribution of energy transfers: A molecular dynamics study

    SciTech Connect

    Mookerjee, S.; Khan, S. A.; Roy, A.; Beuve, M.; Toulemonde, M.

    2008-07-15

    Using different models for the deposition of energy on the lattice and a classical molecular dynamics approach to the subsequent transport, we evaluate how the details of the energy deposition model influence sputtering yield from a Lennard-Jones target irradiated with a MeV/u ion beam. Two energy deposition models are considered: a uniform, instantaneous deposition into a cylinder of fixed radius around the projectile ion track, used in earlier molecular dynamics and fluid dynamics simulations of sputtering yields; and an energy deposition distributed in time and space based on the formalism developed in the thermal spike model. The dependence of the sputtering yield on the total energy deposited on the target atoms is very sensitive to the energy deposition model. To clarify the origin of this strong dependence, we explore the role of the radial expansion of the electronic system prior to the transfer of its energy to the lattice. The results imply that observables such as the sputtering yield may be used as signatures of the fast electron-lattice energy transfer in the electronic energy-loss regime, and indicate the need for more experimental and theoretical investigations of these processes.

  6. 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

    2016-02-02

    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.

  7. Superdressed H+2 and H2+3 molecular ions in intense, high-frequency laser fields

    NASA Astrophysics Data System (ADS)

    Zuo, T.; Bandrauk, A. D.

    1995-01-01

    We study the radiative distortion of the lowest two potential surfaces of H+2 and H2+3 molecular ions in a superintense (I>~1016 W/cm2), high-frequency, linearly polarized laser field, using the space-translation or acceleration representation of laser-matter interaction. The electron clouds undergo field-induced redistribution in the molecular ions due to the presence of field-induced ``dichotomous'' dressed Coulomb potentials. Such super-field-dressed systems have a greater tendency to transfer electronic charge into the region between the nuclei and hence become more ``stable'' than the field-free ones. For example, at the equilibrium nuclear separation the dissociation energy of the superdressed H+2 is found to increase by about 20% compared with the field-free H+2. More dramatically, the lowest two surfaces of H2+3 that are repulsive in zero field become attractive (bonding) in the presence of an intense, high-frequency field. The possibility of molecules becoming stabilized against both ionization and dissociation in superintense fields is discussed.

  8. Refolding of denatured/reduced lysozyme at high concentrations by artificial molecular chaperone-ion exchange chromatography.

    PubMed

    Wang, Chaozhan; Zhang, Qinming; Cheng, Yan; Wang, Lili

    2010-01-01

    Development of high efficiency and low cost protein refolding methods is a highlighted research focus in biotechnology. Artificial molecular chaperone (AMC) and protein folding liquid chromatography (PFLC) are two attractive refolding methods developed in recent years. In the present work, AMC and one branch of PFLC, ion exchange chromatography (IEC), are integrated to form a new refolding method, artificial molecular chaperone-ion exchange chromatography (AMC-IEC). This new method is applied to the refolding of a widely used model protein, urea-denatured/dithiothreitol-reduced lysozyme. Many factors influencing the refolding of lysozyme, such as urea concentration, beta-cyclodextrin concentration, molar ratio of detergent to protein, mobile phase flow rate, and type of detergent, were investigated, respectively, to optimize the conditions for lysozyme refolding by AMC-IEC. Compared with normal IEC refolding method, the activity recoveries of lysozyme obtained by AMC-IEC were much higher in the investigated range of initial protein concentrations. Moreover, the activity recoveries obtained by using this newly developed refolding method were still quite high for denatured/reduced lysozyme at high initial concentrations. When the initial protein concentration was 200 mg mL(-1), the activity recovery was over 60%. In addition, the lifetime of the chromatographic column during AMC-IEC was much longer than that during protein refolding by normal IEC. Therefore, AMC-IEC is a high efficient and low cost protein refolding method.

  9. Electron spin resonance and electron spin echo modulation studies of ion-exchanged NiH-SAPO-17 and NiH-SAPO-35 molecular sieves: Comparison with ion-exchanged NiH-SAPO-34 molecular sieve

    SciTech Connect

    Djieugoue, M.A.; Prakash, A.M.; Zhu, Z.; Kevan, L.

    1999-08-26

    Erionite-like silicoaluminophosphate molecular sieve SAPO-17 and levyne-like SAPO-35, in which Ni ions were incorporated via solid-state ion-exchange into known extra framework sites, have been studied by electron spin resonance (ESR) and electron spin echo modulation (ESEM). The Ni ion reducibility, location, and interaction with several adsorbates have been investigated. Among these adsorbates, the interaction with nitric oxide was emphasized and compared to that of Ni ion with NO in the previously studied chabazite-like SAPO-34. Room-temperature adsorption of C{sub 2}D{sub 4} on NiH-SAPO-17 after dehydration at 573 K, oxygen treatment at 823 K, evacuation, and subsequent hydrogen treatment at 573 K produces two Ni-ethylene complexes. Carbon monoxide adsorption gives rise to a Ni(I)-(CO){sub n} complex with unresolved {sup 13}C hyperfine lines. Following the kinetics of nitric oxide adsorption on NiH-SAPO-17 shows that initially, a Ni(I)-(NO){sup +} complex, a NO radical, and a new species which appears to be another NO species are generated. After a reaction time of 24 h, NO{sub 2} is observed. As the adsorption time further increases, NO{sub 2} becomes stronger while Ni(I)-(NO){sup +} decays, and after 5 days only NO{sub 2} remains. NO adsorption on NiH-SAPO-35 shows different features. Initially, two Ni(I)-(NO){sup +} complexes along with a NO radical are seen. As the adsorption time increases, one of the Ni(I)-(NO){sup +} complexes decreases in intensity while the other one increases, and after a few days only one Ni(I)-(NO){sup +} complex remains. Simulation of the {sup 31}P ESEM spectrum, supplemented by {sup 27}Al modulation, suggests that, upon dehydration, Ni ions in NiH-SAPO-17 migrate from the erioinite supercage to the smaller cancrinite cage. In dehydrated NiH-SAPO-17 migrate from the erionite supercage to the smaller cancrinite cage. In dehydrated NiH-SAPO-34 and NiH-SAPO-35, Ni ions remain in the large chabazite and levyne cages, respectively. As a

  10. Electron spin resonance and electron spin echo modulation studies of ion-exchanged NiH-SAPO-17 and NiH-SAPO-35 molecular sieves: Comparison with ion-exchanged NiH-SAPO-34 molecular sieve

    SciTech Connect

    Djieugoue, M.A.; Prakash, A.M.; Zhu, Z.; Kevan, L. . Dept. of Chemistry)

    1999-08-26

    Erionite-like silicoaluminophosphate molecular sieve SAPO-17 and levyne-like SAPO-35, in which Ni ions were incorporated via solid-state ion-exchange into known extra framework sites, have been studied by electron spin resonance (ESR) and electron spin echo modulation (ESEM). The Ni ion reducibility, location, and interaction with several adsorbates have been investigated. Among these adsorbates, the interaction with nitric oxide was emphasized and compared to that of Ni ion with NO in the previously studied chabazite-like SAPO-34. Room-temperature adsorption of C[sub 2]D[sub 4] on NiH-SAPO-17 after dehydration at 573 K, oxygen treatment at 823 K, evacuation, and subsequent hydrogen treatment at 573 K produces two Ni-ethylene complexes. Carbon monoxide adsorption gives rise to a Ni(I)-(CO)[sub n] complex with unresolved [sup 13]C hyperfine lines. Following the kinetics of nitric oxide adsorption on NiH-SAPO-17 shows that initially, a Ni(I)-(NO)[sup +] complex, a NO radical, and a new species which appears to be another NO species are generated. After a reaction time of 24 h, NO[sub 2] is observed. As the adsorption time further increases, NO[sub 2] becomes stronger while Ni(I)-(NO)[sup +] decays, and after 5 days only NO[sub 2] remains. NO adsorption on NiH-SAPO-35 shows different features. Initially, two Ni(I)-(NO)[sup +] complexes along with a NO radical are seen. As the adsorption time increases, one of the Ni(I)-(NO)[sup +] complexes decreases in intensity while the other one increases, and after a few days only one Ni(I)-(NO)[sup +] complex remains. Simulation of the [sup 31]P ESEM spectrum, supplemented by [sup 27]Al modulation, suggests that, upon dehydration, Ni ions in NiH-SAPO-17 migrate from the erioinite supercage to the smaller cancrinite cage. In dehydrated NiH-SAPO-17 migrate from the erionite supercage to the smaller cancrinite cage. In dehydrated NiH-SAPO-34 and NiH-SAPO-35, Ni ions remain in the large chabazite and levyne cages, respectively. As a

  11. 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.

  12. 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.

  13. Effects of molecular model, ionic strength, divalent ions, and hydrophobic interaction on human neurofilament conformation.

    PubMed

    Lee, Joonseong; Kim, Seonghoon; Chang, Rakwoo; Jayanthi, Lakshmi; Gebremichael, Yeshitila

    2013-01-07

    The present study examines the effects of the model dependence, ionic strength, divalent ions, and hydrophobic interaction on the structural organization of the human neurofilament (NF) brush, using canonical ensemble Monte Carlo (MC) simulations of a coarse-grained model with the amino-acid resolution. The model simplifies the interactions between the NF core and the sidearm or between the sidearms by the sum of excluded volume, electrostatic, and hydrophobic interactions, where both monovalent salt ions and solvents are implicitly incorporated into the electrostatic interaction potential. Several important observations are made from the MC simulations of the coarse-grained model NF systems. First, the mean-field type description of monovalent salt ions works reasonably well in the NF system. Second, the manner by which the NF sidearms are arranged on the surface of the NF backbone core has little influence on the lateral extension of NF sidearms. Third, the lateral extension of the NF sidearms is highly affected by the ionic strength of the system: at low ionic strength, NF-M is most extended but at high ionic strength, NF-H is more stretched out because of the effective screening of the electrostatic interaction. Fourth, the presence of Ca(2+) ions induces the attraction between negatively charged residues, which leads to the contraction of the overall NF extension. Finally, the introduction of hydrophobic interaction does not change the general structural organization of the NF sidearms except that the overall extension is contracted.

  14. Coordination and hydrolysis of plutonium ions in aqueous solution using Car-Parrinello molecular dynamics free energy simulations.

    PubMed

    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 Pu(3+), Pu(4+), PuO2(+), and PuO2(2+) 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 PuO2(2+) species is coordinated to five aquo ligands while the pentavalent PuO2(+) complex is coordinated to four aquo ligands. The Pu(3+) and Pu(4+) ions are both coordinated to eight water molecules. The first hydrolysis constants obtained for Pu(3+) and PuO2(2+) are 6.65 and 5.70, respectively, all within 0.3 pH unit of the experimental values (6.90 and 5.50, respectively). The hydrolysis constant of Pu(4+), 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. Acta 1992, 56, 15]. A correlation between the pKa of the first hydrolysis reaction and the effective charge of the plutonium center was found.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

    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.

  16. 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.

  17. 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

  18. Control of morphology and nanostructure of copper and cobalt oxalates: Effect of complexing ions, polymeric additives and molecular weight

    NASA Astrophysics Data System (ADS)

    Bowen, Paul; Pujol, Ollivier; Jongen, Nathalie; Lemaître, Jacques; Fink, Alke; Stadleman, Pierre; Hofmann, Heinrich

    2010-11-01

    Precipitated oxalates are often nanostructured and can be used as precursors for nanostructured oxides for different applications. The modification of the particle shape and nanostructures of both copper and cobalt oxalates has been demonstrated using polymeric additives or complexing counter-ions. In the case of cobalt oxalate the characteristic elongated rod particle shape (axial ratio of 10) can be modified by using polymethymethacrylate (PMMA) to produce particles with lower axial ratios of 2, through cubes all the way to platelets (axial ratio 0.2). The PMMA inhibits the growth of the particles along the [101] direction more and more strongly as the concentration of the polymer increases. The crystallite size from XRD line broadening is not modified by the PMMA indicating that the PMMA does not influence the nucleation and growth but modifies the aggregation kinetics. Copper oxalates precipitated in the presence of different cellulose derived polymers with different molecular weights and functional groups (methyl and propyl) showed sensitivity to both molecular weight and functional group. Higher molecular weights did not influence the copper oxalate particle shape, whereas methyl cellulose gave elongated particles and propyl celluloses gave platelet like particles. Copper oxalate precipitated in the presence of acetate counter ions gave platelets with an axial ratio of 0.15 compared to the cushion-like morphology (axial ratio 0.5). The primary crystallites were more elongated along the [001] direction in the presence of acetate, modifying the proportion of the hydrophobic and hydrophilic surfaces and hence influencing the aggregation kinetics and particle shape. The copper and cobalt oxalate particle formation seems to be dominated by the primary particle aggregation with the different additives interacting specifically with different crystallographic faces of the primary particles. By tuning this interaction particles with different shapes and substructures

  19. Molecular dynamics investigation of desorption and ion separation following picosecond infrared laser (PIRL) ablation of an ionic aqueous protein solution.

    PubMed

    Zou, J; Wu, C; Robertson, W D; Zhigilei, L V; Miller, R J D

    2016-11-28

    Molecular dynamics simulations were performed to characterize the ablation process induced by a picosecond infrared laser (PIRL) operating in the regime of desorption by impulsive vibrational excitation (DIVE) of a model peptide (lysozyme)/counter-ion system in aqueous solution. The simulations were performed for ablation under typical experimental conditions found within a time-of-flight mass spectrometer (TOF-MS), that is in vacuum with an applied electric field (E = ± 10(7) V/m), for up to 2 ns post-ablation and compared to the standard PIRL-DIVE ablation condition (E = 0 V/m). Further, a simulation of ablation under an extreme field condition (E = 10(10) V/m) was performed for comparison to extend the effective dynamic range of the effect of the field on charge separation. The results show that the plume dynamics were retained under a typical TOF-MS condition within the first 1 ns of ablation. Efficient desorption was observed with more than 90% of water molecules interacting with lysozyme stripped off within 1 ns post-ablation. The processes of ablation and desolvation of analytes were shown to be independent of the applied electric field and thus decoupled from the ion separation process. Unlike under the extreme field conditions, the electric field inside a typical TOF-MS was shown to modify the ions' motion over a longer time and in a soft manner with no enhancement to fragmentation observed as compared to the standard PIRL-DIVE. The study indicates that the PIRL-DIVE ablation mechanism could be used as a new, intrinsically versatile, and highly sensitive ion source for quantitative mass spectrometry.

  20. Molecular dynamics investigation of desorption and ion separation following picosecond infrared laser (PIRL) ablation of an ionic aqueous protein solution

    NASA Astrophysics Data System (ADS)

    Zou, J.; Wu, C.; Robertson, W. D.; Zhigilei, L. V.; Miller, R. J. D.

    2016-11-01

    Molecular dynamics simulations were performed to characterize the ablation process induced by a picosecond infrared laser (PIRL) operating in the regime of desorption by impulsive vibrational excitation (DIVE) of a model peptide (lysozyme)/counter-ion system in aqueous solution. The simulations were performed for ablation under typical experimental conditions found within a time-of-flight mass spectrometer (TOF-MS), that is in vacuum with an applied electric field (E = ± 107 V/m), for up to 2 ns post-ablation and compared to the standard PIRL-DIVE ablation condition (E = 0 V/m). Further, a simulation of ablation under an extreme field condition (E = 1010 V/m) was performed for comparison to extend the effective dynamic range of the effect of the field on charge separation. The results show that the plume dynamics were retained under a typical TOF-MS condition within the first 1 ns of ablation. Efficient desorption was observed with more than 90% of water molecules interacting with lysozyme stripped off within 1 ns post-ablation. The processes of ablation and desolvation of analytes were shown to be independent of the applied electric field and thus decoupled from the ion separation process. Unlike under the extreme field conditions, the electric field inside a typical TOF-MS was shown to modify the ions' motion over a longer time and in a soft manner with no enhancement to fragmentation observed as compared to the standard PIRL-DIVE. The study indicates that the PIRL-DIVE ablation mechanism could be used as a new, intrinsically versatile, and highly sensitive ion source for quantitative mass spectrometry.

  1. Recombination of simple molecular ions studied in storage ring: dissociative recombination of H2O+

    PubMed

    Rosen; Derkatch; Semaniak; Neau; al-Khalili; Le Padellec A; Vikor; Thomas; Danared; af Ugglas M; Larsson

    2000-01-01

    Dissociative recombination of vibrationally relaxed H2O+ ions with electrons has been studied in the heavy-ion storage ring CRYRING. Absolute cross-sections have been measured for collision energies between 0 eV and 30 eV. The energy dependence of the cross-section below 0.1 eV is found to be much steeper than the E-1 behaviour associated with the dominance of the direct recombination mechanism. Resonant structures found at 4 eV and 11 eV have been attributed to the electron capture to Rydberg states converging to electronically excited ionic states. Complete branching fractions for all dissociation channels have been measured at a collision energy of 0 eV. The dissociation process is dominated by three-body H + H + O breakup that occurs with a branching ratio of 0.71.

  2. Single-ion hydration thermodynamics from clusters to bulk solutions: Recent insights from molecular modeling

    SciTech Connect

    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 accuracy of ion–water interaction models and our views on possible ways to fill this substantial knowledge gap in aqueous physical chemistry.

  3. Single-ion hydration thermodynamics from clusters to bulk solutions: Recent insights from molecular modeling

    DOE PAGES

    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

  4. 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.

  5. Influence of ions on genome packaging and ejection: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Ali, I.; Marenduzzo, D.

    2011-09-01

    We, theoretically, investigate the effect of ions on the packing and ejection dynamics of flexible and semiflexible polymers from spherical viral capsids. We find that when the polymer charge is less screened, or the Debye length increases (corresponding to a buffer with low concentration of a monovalent salt, such as Na+), the packing becomes more difficult and it may stop midway. Ejection, instead, proceeds more easily if the electrostatic screening is small. On the other hand, more screening (corresponding, for example, to the addition of divalent ions such as Mg2 +) results in easier packing and slower ejection. We interpret this as resulting from electrostatic forces among the various polymer sections, which can be tuned with the type of salt present in the solution. We also discuss how the DNA structure inside the capsid changes due to screened electrostatic interactions.

  6. [Preliminary study on molecular mechanism of lotus mutants induced by ion implantation].

    PubMed

    Deng, Chuan-Liang; Jia, Yan-Yan; Ren, Ying-Xue; Gao, Wu-Jun; Zhang, Tao; Li, Peng-Fei; Lu, Long-Dou

    2011-01-01

    Ion implantation, as a new biophysically mutagenic technique, has shown a great potential for horticultural plant breeding. Up to date, little is known about the mutation mechanism of ion implantation at the DNA level. To reveal the mutation effect of Fe+ ion implantation on Baiyangdian red lotus, the random amplified polymorphic DNA (RAPD) was used, and then the bands of mutants and the control in the radiation-sensitive sites were cloned to be sequenced for comparing their DNA sequences. The results indicated that the total base mutation rate of mutants was 0.87%, and there was different in the six mutants. The types of base changes included base transition, transversion, deletion, and insertion. Among the 159 base changes detected, the frequency of single base substitutions (61.01%) was higher than that of base deletions and insertions (38.99%), and the frequency of base transitions (44.65%) was 2.7 times of that of the base transversions (16.35%). The transitions between C and T accounted for largest proportion, A→G transitions and A→T transversions were also present at high frequency. Adenine, thymine, guanine or cytosine could be replaced by any of other three bases, except that there was no C → G substitution. However, thymine was more sensitive to the irradiation than other bases. In our study, we found many purine bases around the purine mutational sites, and many pyrimidine bases around the pyrimidine mutational sites. These will further help us to understand the mechanism of mutagenesis by ion implantation.

  7. Structural Investigation of Fluoridated POSS Cages Using Ion Mobility Mass Spectrometry and Molecular Mechanics (Preprint)

    DTIC Science & Technology

    2008-01-09

    organic polymer. For example, the low surface energy properties of fluorinated POSS compounds have been used to augment both fluorinated and non... fluorinated polymers.10-13 Many POSS monomers have been successfully characterized using MALDI techniques14-16 in conjunction with ion mobility mass...nucleophilic attack, are shown in blue. Negative contours, showing susceptibility to electrophilic attack, are shown in red. The positive contour of

  8. 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.

  9. 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

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

    USGS Publications Warehouse

    Evans, H.T.

    1966-01-01

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

  11. 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.

  12. YIP - Ultrasensitive Infrared Spectroscopy of Molecular Ions of Importance in Atmospheric Chemistry and Propulsion

    DTIC Science & Technology

    2010-08-23

    State University, the University of Wisconsin at Madison, the Massachusetts Institute of Technology, the Harvard-Smithsonian Center for Astrophysics ...awarded the 2009 Coblentz Award at the 64th International Symposium on Molecular Spectroscopy. Prior to this effort, I was selected for a Presidential Early Career Award for Scientists and Engineers (PECASE) by the White House.

  13. 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

  14. Direct detection of atomic ions from molecular photofragmentation during nonresonant multiphoton ionization of sputtered species

    SciTech Connect

    Coon, S.R.; Calaway, W.F.; Pellin, M.J.; Burnett, J.W.; White, J.M.

    1993-09-01

    The photoionization of sputtered Cu, Al, and Ru atoms and dimers was investigated by measuring velocity distributions using both resonant and nonresonant photoionization. Nonresonant ionization produced an atomic distribution that peaked at the same velocity as the respective dimer distribution, indicating that virtually all the nonresonant atomic ion signal is from photofragmented dimers. Various mechanisms of dimer photofragmentation are discussed. Domination of the atomic photoion channel by molecule fragmentation appears to be a general phenomenon that must be accounted for in all gas-phase multiphoton nonresonant ionization experiments at easily achievable laser power densities ({le} 10{sup 9} W/cm{sup 2}).

  15. Fireball as the result of self-organization of an ensemble of diamagnetic electron-ion nanoparticles in molecular gas

    SciTech Connect

    Lopasov, V. P.

    2011-12-15

    The conditions for dissipative self-organization of a fireball (FB) is a molecular gas by means of a regular correction of an elastic collision of water and nitrogen molecules by the field of a coherent bi-harmonic light wave (BLW) are presented. The BWL field is generated due to conversion of energy of a linear lightning discharge into light energy. A FB consists of two components: an ensemble of optically active diamagnetic electron-ion nanoparticles and a standing wave of elliptical polarization (SWEP). It is shown that the FB lifetime depends on the energies accumulated by nanoparticles and the SWEP field and on the stability of self-oscillations of the energy between nanoparticles and SWEP.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Single-particle detection of products from atomic and molecular reactions in a cryogenic ion storage ring

    NASA Astrophysics Data System (ADS)

    Krantz, C.; Novotný, O.; Becker, A.; George, S.; Grieser, M.; Hahn, R. von; Meyer, C.; Schippers, S.; Spruck, K.; Vogel, S.; Wolf, A.

    2017-04-01

    We have used a single-particle detector system, based on secondary electron emission, for counting low-energetic (∼keV/u) massive products originating from atomic and molecular ion reactions in the electrostatic Cryogenic Storage Ring (CSR). The detector is movable within the cryogenic vacuum chamber of CSR, and was used to measure production rates of a variety of charged and neutral daughter particles. In operation at a temperature of ∼ 6 K , the detector is characterised by a high dynamic range, combining a low dark event rate with good high-rate particle counting capability. On-line measurement of the pulse height distributions proved to be an important monitor of the detector response at low temperature. Statistical pulse-height analysis allows to infer the particle detection efficiency of the detector, which has been found to be close to unity also in cryogenic operation at 6 K.

  1. A comprehensive molecular dynamics approach to protein retention modeling in ion exchange chromatography.

    PubMed

    Lang, Katharina M H; Kittelmann, Jörg; Dürr, Cathrin; Osberghaus, Anna; Hubbuch, Jürgen

    2015-02-13

    In downstream processing, the underlying adsorption mechanism of biomolecules to adsorbent material are still subject of extensive research. One approach to more mechanistic understanding is simulating this adsorption process and hereby the possibility to identify the parameters with strongest impact. So far this method was applied with all-atom molecular dynamics simulations of two model proteins on one cation exchanger. In this work we developed a molecular dynamics tool to simulate protein-adsorber interaction for various proteins on an anion exchanger and ran gradient elution experiments to relate the simulation results to experimental data. We were able to show that simulation results yield similar results as experimental data regarding retention behavior as well as binding orientation. We could identify arginines in case of cation exchangers and aspartic acids in case of anion exchangers as major contributors to binding.

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

    PubMed

    Carol, Priya; Sreejith, Sivaramapanicker; Ajayaghosh, Ayyappanpillai

    2007-03-05

    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.

  3. 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.

  4. 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.

  5. 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

  6. 5-Fluorouracil delivery from metal-ion mediated molecularly imprinted cryogel discs.

    PubMed

    Çetin, Kemal; Denizli, Adil

    2015-02-01

    The objective of this study is to prepare imprinted cryogel discs for delivery of 5-fluorouracil. The coordinate bond interactions are utilized to accomplish a coordination complex between metal-chelate monomer N-methacryloyl-L-histidine and 5-FU with the assistance of Cu(2+) ion. The complex is copolymerized with hydroxyethyl methacrylate to produce poly(hydroxyethyl methacrylate-N-methacryloyl-(L)-histidine methyl ester) cryogel discs. The cryogel discs are characterized thoroughly by performing swelling tests, scanning electron microscopy, differential scanning calorimetry and X-ray diffraction studies. In vitro delivery studies are performed to investigate the effects of cross-linker ratio, medium pH and drug concentration. 5-FU imprinted cryogel discs have highly macroporous structures. Drug molecules are homogeneously dispersed in the 5-FU imprinted cryogel matrix. The cumulative release of 5-FU decreased by increasing the cross-linker density in the polymer matrix. Delivery rate of 5-FU varied with different pH values in a coordination complex since metal ion acts as a Lewis acid, and the ligand, i.e. 5-FU acts as a Lewis base. The cumulative release of 5-FU increased with increasing drug concentration in polymer matrix. The nature of the 5-FU transport mechanism is non-Fickian.

  7. Direct Correlation between Ionic Liquid Transport Properties and Ion Pair Lifetimes: A Molecular Dynamics Study.

    PubMed

    Zhang, Yong; Maginn, Edward J

    2015-02-19

    Self-diffusivities as a function of temperature were computed for 29 different ionic liquids (ILs) covering a wide variety of cation and anion classes. Ideal ionic conductivities (σNE) were estimated from the self-diffusivities via the Nernst-Einstein relation. The ion pair (IP) lifetimes (τIP) and ion cage (IC) lifetimes (τIC) of each IL were also computed. A linear relationship between the calculated self-diffusivities and the inverse of IP or IC lifetimes was observed. A similar inverse linear relationship was also observed for ideal ionic conductivity. These relationships were found to be independent of temperature and the nature of the IL. These observations connect macroscopic dynamic properties with local atomic-level motions and strongly suggest that the dynamics of ILs are governed by a universal IP or IC forming and breaking mechanism. Thus, in order to design an ionic liquid with enhanced dynamics, one should consider how to minimize IP or IC lifetimes.

  8. 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.

  9. 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.

  10. 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.

  11. Free energies of absorption of alkali ions onto beidellite and montmorillonite surfaces from constrained molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Suter, James L.; Sprik, Michiel; Boek, Edo S.

    2012-08-01

    Ab initio Molecular dynamics have been performed to study the free energy of adsorption of alkali atoms onto smectite clay surfaces and to identify the most favourable region in the interlayer for the cations. This is achieved by potential of mean force calculations using a constraint method to determine the lowest free energy configurations of lithium, potassium and sodium beidellite and sodium montmorillonite clays with a monolayer and bilayer of water present in the interlayer region. The constraint method has allowed us to examine the changes in the lowest free energy configuration for each ion with increasing hydration. From this, we can interpret the likelihood of clay swelling from the monolayer to bilayer coverage and compare with experimental observations. We find, that with a bilayer of water present, both lithium beidellite and sodium montmorillonite have their free energy minimum in the centre of the interlayer. For monolayer coverage, the free energy minimum for lithium, sodium and potassium beidellite is approximately the mid-point of the interlayer. Na-beidellite has a lowest free energy region at 6.1 Å from the centre of the clay layer for both mono- and bi-layer coverage, while for the potassium counter-ion, commonly used as swelling inhibitor, the free energy profile for K-beidellite shows peaks close to both surfaces at approximately 6.2 and 8.6 Å. We find that for systems where the free energy minimum remains in the middle of the interlayer when the hydration levels increase from monolayer to bilayer, it is known experimentally that these systems will swell in contact with water. The move to the middle of the interlayer with increasing hydration is associated with the full hydration sphere of the ion being composed purely of water oxygen atoms, and no clay surface oxygen atoms.

  12. A hydrated ion model of [UO2] 2 + in water: Structure, dynamics, and spectroscopy from classical molecular dynamics

    NASA Astrophysics Data System (ADS)

    Pérez-Conesa, Sergio; Torrico, Francisco; Martínez, José M.; Pappalardo, Rafael R.; Sánchez Marcos, Enrique

    2016-12-01

    A new ab initio interaction potential based on the hydrated ion concept has been developed to obtain the structure, energetics, and dynamics of the hydration of uranyl in aqueous solution. It is the first force field that explicitly parameterizes the interaction of the uranyl hydrate with bulk water molecules to accurately define the second-shell behavior. The [UO2(H2O)5 ] 2 + presents a first hydration shell U-O average distance of 2.46 Å and a second hydration shell peak at 4.61 Å corresponding to 22 molecules using a coordination number definition based on a multisite solute cavity. The second shell solvent molecules have longer mean residence times than those corresponding to the divalent monatomic cations. The axial regions are relatively de-populated, lacking direct hydrogen bonding to apical oxygens. Angle-solved radial distribution functions as well as the spatial distribution functions show a strong anisotropy in the ion hydration. The [UO2(H2O)5 ] 2 + solvent structure may be regarded as a combination of a conventional second hydration shell in the equatorial and bridge regions, and a clathrate-like low density region in the axial region. Translational diffusion coefficient, hydration enthalpy, power spectra of the main vibrational modes, and the EXAFS spectrum simulated from molecular dynamics trajectories agree fairly well with the experiment.

  13. 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.

  14. Electron Capture Processes Following Collisions of He^2+ Ions with Molecular Targets

    NASA Astrophysics Data System (ADS)

    Abu-Haija, O.

    2005-05-01

    Energy-gain spectra, absolute state-selective and total cross sections have been measured for single-electron capture processes in collisions of He^2+ ions with O2, H2O, CO2, N2, and NH3 at impact energies between 100 eV and 1600 eV and scattering angles between 0^o and 6^o using the translational energy-gain spectroscopy (TES) technique. As apparent from the translational energy-gain measurements, single-electron capture (SEC) from O2 and H2O proceeds by both dissociative and non-dissociative channels, whereas for N2 and CO2 only dissociative SEC has been observed. However, for NH3 the non-dissociative SEC channel is found to be predominantly populated. Total cross sections have also been compared with available measurements and theoretical calculations based on Landua-Zener model and Demkov model.

  15. The sodium pump. Its molecular properties and mechanics of ion transport.

    PubMed

    Scheiner-Bobis, Georgios

    2002-05-01

    The sodium pump (Na(+)/K(+)-ATPase; sodium- and potassium-activated adenosine 5'-triphosphatase; EC 3.6.1.37) has been under investigation for more than four decades. During this time, the knowledge about the structure and properties of the enzyme has increased to such an extent that specialized groups have formed within this field that focus on specific aspects of the active ion transport catalyzed by this enzyme. Taking this into account, this review, while somewhat speculative, is an attempt to summarize the information regarding the enzymology of the sodium pump with the hope of providing to interested readers from outside the field a concentrated overview and to readers from related fields a guide in their search for gathering specific information concerning the structure, function, and enzymology of this enzyme.

  16. Molecular dynamics study of ion capture from water by a model ionophore, tetraprotonated cryptand SC24

    NASA Technical Reports Server (NTRS)

    Owenson, Brian; Macelroy, Robert D.; Pohorille, Andrew

    1988-01-01

    The molecular dynamics of chloride capture from water by the tetraprotonated cryptand SC24 has been studied for the cases of 19 distances between the criptand and the chloride. The chloride capture is found to be characterized by a rapid cooperative change in the conformation of the cryptand when the Cl(-) begins to enter the ligand and just as it encounters the energy barrier. The conformational transition is associated with a shift of three N-H bonds from the pure endo orientation, such that they point toward the chloride.

  17. 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.

  18. Charged dendrimers under the action of AC electric fields: Breathing characteristics of molecular size, polarizations, and ion distributions

    NASA Astrophysics Data System (ADS)

    Das, Ashok K.; Hsiao, Pai-Yi

    2015-02-01

    Langevin dynamics simulations are performed to study the response of charged dendrimers in alternating current electric fields in 3:1 salt solutions. Time evolutions of molecular size show breathing characteristics which take saw-tooth-like patterns in square-wave electric fields and undulated sine-function ones in sine-wave fields. Detailed study reveals how the dendrimer and condensed ions oscillate in the electric fields, which result in polarization of the molecule. To effect a significant deformation of the dendrimer, the applied field amplitude must be larger than some critical strength Ecrit and the field frequency smaller than a threshold fcrit. The response behavior is characterized by two relaxation times in square-wave fields, both of which decrease linearly with the strong field strength larger than Ecrit. In sine-wave fields, the molecular size exhibits interesting hysteretic behavior in plotting the curves with the field variation. A Maxwell-Wagner type polarization theory is derived and proved by simulations, which connects fcrit with the strength of the applied electric field.

  19. Molecular determinants for binding of ammonium ion in the ammonia transporter AmtB-A quantum chemical analysis.

    PubMed

    Liu, Yuemin; Hu, Xiche

    2006-02-02

    The transport of ammonium across the cell membrane represents an important biological process in all living organisms. The mechanisms for ammonium translocation were analyzed by computer simulations based on first principles. Intermolecular interaction energies between the differentially methylated ammonium and the ammonium channel protein AmtB were calculated by means of the supermolecular approach at the MP2/6-311+G* level based on the high-resolution crystal structures of ligand-bound protein complexes. Our analysis attributes the molecular determinants for protein-ligand recognition in ammonium transporter AmtB to the aromatic cage formed by three aromatic residues Phe103, Phe107, and Trp148, as well as Ser219. The former residues are involved in cation-pi interactions with the positively charged methylated ammoniums. The latter residue acts as a hydrogen bond acceptor to ammonium. Thus, this work provides directly the missing evidence for the hypothesized role played by the wider vestibule site of AmtB at the periplasmic side of the membrane in "recruiting" NH(4)(+) or methylammonium ions as proposed by Khademi et al. (Science 2004, 305, 1587). In addition, a hybrid quantum mechanics/molecular mechanics scheme was applied to optimize the structures of differentially methylated ammoniums in the AmtB protein, which generated structural and energetic data that provide a satisfactory explanation to the experimental observation that tetramethylammonium is not inhibitory to conducting ammonium and methylammonium in the ammonium transport channel.

  20. Ab initio molecular dynamics simulations of ion-solid interactions in zirconate pyrochlores

    DOE PAGES

    Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen; ...

    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

  1. 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.

  2. 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...

  3. Spectral-luminescent properties of silver molecular clusters and nanoparticles formed by ion exchange in antimony-doped photo-thermo-refractive glasses

    NASA Astrophysics Data System (ADS)

    Sgibnev, E. M.; Nikonorov, N. V.; Ignat'ev, A. I.

    2017-01-01

    The formation of silver molecular clusters and nanoparticles in photo-thermo-refractive (PTR) glasses with different antimony contents has been investigated using ion exchange with subsequent thermal treatment. The influence of the antimony oxide (Sb2O3) concentration and treatment temperature on the spectral-luminescent properties of silver molecular clusters and nanoparticles in glass has been investigated. It is shown that silver molecular clusters in PTR glasses are characterized by strong broadband luminescence in the visible and near-IR ranges and that the formation of silver nanoparticles leads to luminescence quenching.

  4. 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.

  5. Hydration properties of magnesium and calcium ions from constrained first principles molecular dynamics

    NASA Astrophysics Data System (ADS)

    Ikeda, Takashi; Boero, Mauro; Terakura, Kiyoyuki

    2007-08-01

    We studied the solvation structures of the divalent metal cations Mg2+ and Ca2+ in ambient water by applying a Car-Parrinello-based constrained molecular dynamics method. By employing the metal-water oxygen coordination number as a reaction coordinate, we could identify distinct aqua complexes characterized by structural variations of the first coordination shell. In particular, our estimated free-energy profile clearly shows that the global minimum for Mg2+ is represented by a rather stable sixfold coordination in the octahedral arrangement, in agreement with experiments. Conversely, for Ca2+ the free-energy curve shows several shallow local minima, suggesting that the hydration structure of Ca2+ is highly variable. Implications for water exchange reactions are also discussed.

  6. 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.

  7. Photofragmentation and vibrational relaxation of size-selected clusters ions : Non-adiabatic molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Douady, J.; Gervais, B.; Jacquet, E.; Zanuttini, D.; Giglio, E.

    2009-11-01

    We present non-adiabatic molecular dynamics simulations of size-selected Na2+ Arn (n=6-11-17) cluster. Their electronic structure is obtained from an accurate 1-electron model using core polarization pseudopotentials. We follow the dynamics of two specific photoexcitation processes (X2 Σ+g → A2Σ+u) and (X2 Σ+g → B2 Πu) during the first 10 ps. We identify a variety of processes in these clusters, such as dissociation of the Na2+ chromophore, solvation of the Na+ fragment as Na+ Arp and the recombination to the ground state of the Na2+ Arp with an important solvent evaporation. These processes depend significantly on the transition and on the isomer. We discuss these processes as a function of the cluster size.

  8. 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.

  9. A molecular dynamics study on slow ion interactions with the polycyclic aromatic hydrocarbon molecule anthracene

    SciTech Connect

    Postma, J.; Hoekstra, R.; Schlathölter, T.; Tielens, A. G. G. M.

    2014-03-01

    Atomic collisions with polycyclic aromatic hydrocarbon (PAH) molecules are astrophysically particularly relevant for collision energies of less than 1 keV. In this regime, the interaction dynamics are dominated by elastic interactions. We have employed a molecular dynamics simulation based on analytical interaction potentials to model the interaction of low energy hydrogen and helium projectiles with isolated anthracene (C{sub 14}H{sub 10}) molecules. This approach allows for a very detailed investigation of the elastic interaction dynamics on an event by event basis. From the simulation data the threshold projectile kinetic energies above which direct C atom knock out sets in were determined. Anthracene differential energy transfer cross sections and total (dissociation) cross sections were computed for a wide range of projectile kinetic energies. The obtained results are interpreted in the context of PAH destruction in astrophysical environments.

  10. Multifunctional molecular design as an efficient polymeric binder for silicon anodes in lithium-ion batteries.

    PubMed

    Jeena, M T; Lee, Jung-In; Kim, Si Hoon; Kim, Chanhoon; Kim, Ju-Young; Park, Soojin; Ryu, Ja-Hyoung

    2014-10-22

    This work demonstrates the design, synthesis, characterization, and study of the electrochemical performance of a novel binder for silicon (Si) anodes in lithium-ion batteries (LIBs). Polymeric binders with three different functional groups, namely, carboxylic acid (COOH), carboxylate (COO(-)), and hydroxyl (OH), in a single polymer backbone have been synthesized and characterized via (1)H NMR and FTIR spectroscopies. A systematic study that involved varying the ratio of the functional groups indicated that a material with an acid-to-alcohol molar ratio of 60:40 showed promise as an efficient binder with an initial columbic efficiency of 89%. This exceptional performance is attributed to the strong adhesion of the binder to the silicon surface and to cross-linking between carboxyl and hydroxyl functional groups, which minimize the disintegration of the Si anode structure during the large volume expansion of the lithiated Si nanoparticle. Polymers with multiple functional groups can serve as practical alternative binders for the Si anodes of LIBs, resulting in higher capacities with less capacity fade.

  11. [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.

  12. Molecular approach to protein-polymer interactions in ion-exchange chromatography.

    PubMed

    Noinville, V; Craescu, C T; Vidal-Madjar, C; Sebille, B

    1995-02-03

    A model was developed and implemented to aid in understanding and predicting the retention behaviour of proteins in ion-exchange chromatography. The model structures chosen were calcium-loaded and -depleted alpha-lactalbumin (ALC) and hen egg white lysozyme (HEWL) and a comparison was made with chromatographic measurements. A characteristic charge of -3.4 was found under the experimental conditions applied for both forms of ALC, and HEWL was not retained. The model explicitly considers all of the atoms, each being assigned a set of force field parameters. Because of the computational time necessary to include them, water molecules were not taken into account, but a sigmoidal function of the dielectric permittivity was introduced in the calculations. Interaction potential energies from bulk down to the contact were evaluated for each protein. The results were in qualitative agreement with those of the chromatographic experiments. It was possible to reproduce the difference in retention between both forms of ALC and also the behaviour of HEWL.

  13. Molecular dynamics study of the effect of titanium ion energy on surface structure during the amorphous TiO2 films deposition

    NASA Astrophysics Data System (ADS)

    Chen, Xian; Wang, Yan-Wu; Liu, Xin; Wang, Xiao-Yan; Wang, Xiao-Bo; An, Shu-Dong; Zhao, Yu-Qing

    2015-08-01

    This paper has investigated the impact of the incident titanium ion energy on the surface structure formation mechanism and the film properties during the amorphous TiO2 thin film deposition process with the molecular dynamics simulation method. The results show that the increase of film density and the reduction of the surface roughness happen when the energy of incident titanium ions is increased. It is also found that the film growth mode is the Volmer-Weber (island) growth mode under the influence of the surface potential. The effect of surface potential is more significant if the incident ions energy becomes smaller. That will make the Volmer-Weber (island) growth mode promoted and the surface roughness of the deposited films become larger. Conversely, the Volmer-Weber growth mode is inhibited when the incident ion energy is higher. It will be conducive to the formation of more smooth film surface.

  14. 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.

  15. Using PFI-ZEKE spectroscopy to study excited states of molecular ions: implications for state selection through pulsed field ionization

    NASA Astrophysics Data System (ADS)

    Martin, James D.; Alcaraz, Christian; Mank, A.; Kong, Wei; Hepburn, John W.

    1995-09-01

    The introduction of the pulsed field ionization zero kinetic energy photoelectron spectroscopy technique (referred to as PFI-ZEKE spectroscopy) has resulted in a revolution in photoelectron spectroscopy, because of the tremendous improvement in resolution. This method of threshold photoelectron spectroscopy is based on field ionization of metastable high principal quantum number Rydberg states using a pulsed electric field, delayed from the laser excitation. The detailed mechanism for stabilization of the high principal quantum number Rydberg states has been the subject of a great deal of recent discussion in the literature, and is still somewhat controversial. It is well known that Rydberg state lifetimes scale as n-3, for fluorescence, autoionization, or predissociation, under ideal conditions. This means that for a Rydberg series that can decay by autoionization, if the lifetime of a 5p Rydberg state is 10-12 s, the lifetime of a 150p state will be 10-7 s, which is an order of magnitude shorter than typical delay times used in PFI-ZEKE. The 150p state will be field ionized by an electric field of 0.7 to 1.5 V/cm, which is typical of the pulsed fields used for Stark ionization. This question about Rydberg state lifetimes becomes quite important if one wishes to carry out PFI-ZEKE spectroscopy of ion states well above the lowest ionization threshold, as many decay channels will be available to the Rydberg states converging to the high energy states, resulting in shorter lifetimes for these high energy Rydberg states. Our work in this area has focused largely on PFI-ZEKE spectroscopy at excited state thresholds in molecular ions, where problems of autoionization will be most severe. To reach these high energy thresholds, we have usually used single photon excitation with coherent vacuum ultraviolet light. This excitation method has many advantages.

  16. Spin dynamics in HeH(2+) molecular ion in intense laser fields.

    PubMed

    Korani, Youssef; Sabzyan, Hassan

    2016-11-23

    A theoretical study is carried out on the effect of non-dipole interactions on the electron spin dynamics in the asymmetric diatomic HeH(2+) in its first excited state in intense linearly polarized laser fields. The Foldy-Wouthuysen transformation is used to solve the Dirac equation numerically without BOA. Effects of the phase of the laser pulse and alignment of the molecule on the relativistic characteristics, such as the pure spin and the pure spin-orbit current densities, spin-orbit force and spin torque, are investigated. The results of this study demonstrate that population oscillates between the two spin states during the course of interaction and its configuration depends on the molecular axis orientation and initial phase of the laser pulse. Also, a small polarization takes place in the spin states, even in the absence of the spin-orbit coupling. Furthermore, spin and spin-orbit current densities are phase-dependent and affected differently by the phase of the laser pulse.

  17. Screening effects on the electronic structure of the hydrogen molecular ion

    NASA Astrophysics Data System (ADS)

    Ordóñez-Lasso, Andrés Felipe; Martín, Fernando; Sanz-Vicario, José Luis

    2017-01-01

    We study the effect that a statically screened Coulomb potential represented by a Debye-Hückel-Yukawa potential has in the electronic structure of the simplest molecule H2 + within the Born-Oppenheimer approximation. The method of solution is based on a two-center partial-wave expansion expressed in confocal elliptic coordinates using B-spline polynomials. General algorithms for the computation of energies, wave functions, and dipole and nonadiabatic radial matrix elements are given in detail. As it occurs in atoms, screening in simple molecules shifts the energies of bound states upwards so that, as screening increases, every bound state eventually crosses the upper ionization threshold at a critical screening value. The loss of long-range Coulomb interactions has its effect in the structure of wave functions, and consequently in the dipole and nonadiabatic matrix elements at intermediate and long internuclear distances, which determine the dynamics in external electromagnetic fields and collisional processes. Other issues related to a practical solution of the arbitrary sign problem, as well as the assignment of angular and radial nodes to the variational eigenfunctions, and the appearance of molecular shape resonances and Borromean states in H2 + as screening increases, are also addressed in this work.

  18. Interactions of Lipids and Detergents with a Viral Ion Channel Protein: Molecular Dynamics Simulation Studies

    PubMed Central

    2014-01-01

    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. PMID:25286030

  19. Protostar Formation in Magnetic Molecular Clouds beyond Ion Detachment. II. Typical Axisymmetric Solution

    NASA Astrophysics Data System (ADS)

    Tassis, Konstantinos; Mouschovias, Telemachos Ch.

    2007-05-01

    We follow the ambipolar-diffusion-driven formation and evolution of a fragment in a magnetically supported molecular cloud, until a hydrostatic protostellar core forms at its center. This problem was formulated in Paper I. We determine the density, velocity, and magnetic field as functions of space and time, and the contribution of ambipolar diffusion and Ohmic dissipation to the resolution of the magnetic flux problem of star formation. The issue of whether the magnetic field ever decouples from the (neutral) matter is also addressed. We also find that the electrons do not decouple from the field lines before thermal ionization becomes important and recouples the magnetic field to the neutral matter. Ohmic dissipation becomes more effective than ambipolar diffusion as a flux reduction mechanism only at the highest densities (a few × 1012 cm-3). In the high-density central parts of the core, the magnetic field acquires an almost spatially uniform structure, with a value that, at the end of the calculation (nn~5×1014 cm-3), is found to be in excellent agreement with meteoritic measurements of magnetic fields in the protosolar nebula. Outside the hydrostatic protostellar core, a concentration of magnetic flux (a ``magnetic wall'') forms, which gives rise to a magnetic shock. This magnetic shock is the precursor of the repeated shocks previously found by Tassis & Mouschovias, which cause spasmodic accretion onto the hydrostatic core at later times.

  20. 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.

  1. 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

  2. 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

  3. Molecular Interactions of the Difluoro(oxalato)borate Anion and Its Application for Lithium Ion Battery Electrolytes

    NASA Astrophysics Data System (ADS)

    Allen, Joshua Lee

    Understanding the molecular interactions within electrolyte mixtures is essential for designing next generation electrolyte materials for high-voltage lithium ion (Li-ion) battery applications. Despite significant advancements in Li-ion battery electrode materials, which have theoretically enabled cell operation in excess of 5 V (vs. Li/Li+), the state-of-the-art electrolyte formulation has remained largely unchanged over two decades after its initial commercialization. To optimize the electrolyte properties, it is crucial to understand and relate the molecular-level interactions to the measured bulk properties. In the present study, these interactions have been explored through the use of the following techniques: phase diagrams (DSC analysis), X-ray single crystal structural determination, spectroscopic vibrational analysis (Raman) of the solvent and anion bands, and other techniques for determining electrolyte physical and electrochemical properties (density, viscosity and ionic conductivity). The primary focus of the present work is on the difluoro(oxalato)borate (DFOB--) anion and how the properties of this anion differ from other anions used in Li-ion battery electrolyte mixtures. The synthesis of highly pure LiDFOB is reported, along with the X-ray single crystal structural analysis of the neat salt and its dihydrate (LiDFOB·2H2O). The ion coordination behavior of the DFOB-- anion is compared with the structurally similar BF4 . and lithium bis(oxalato)borate (BOB --) anions. The decomposition mechanism and Raman vibrational band assignments for the LiDFOB salt are also compared with those for LiBF 4 and LiBOB. The carbonate-based solvents ethylene carbonate (EC) and propylene carbonate (PC) are of extraordinary importance due to their applications in state-of-the-art electrolytes. The Raman analysis of EC- and PC-based electrolyte mixtures to determine solvation numbers, without appropriate correction factors, is inherently flawed due to varying Raman

  4. 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

  5. Phycodnavirus potassium ion channel proteins question the virus molecular piracy hypothesis.

    PubMed

    Hamacher, Kay; Greiner, Timo; Ogata, Hiroyuki; Van Etten, James L; Gebhardt, Manuela; Villarreal, Luis P; Cosentino, Cristian; Moroni, Anna; Thiel, Gerhard

    2012-01-01

    Phycodnaviruses are large dsDNA, algal-infecting viruses that encode many genes with homologs in prokaryotes and eukaryotes. Among the viral gene products are the smallest proteins known to form functional K(+) channels. To determine if these viral K(+) channels are the product of molecular piracy from their hosts, we compared the sequences of the K(+) channel pore modules from seven phycodnaviruses to the K(+) channels from Chlorella variabilis and Ectocarpus siliculosus, whose genomes have recently been sequenced. C. variabilis is the host for two of the viruses PBCV-1 and NY-2A and E. siliculosus is the host for the virus EsV-1. Systematic phylogenetic analyses consistently indicate that the viral K(+) channels are not related to any lineage of the host channel homologs and that they are more closely related to each other than to their host homologs. A consensus sequence of the viral channels resembles a protein of unknown function from a proteobacterium. However, the bacterial protein lacks the consensus motif of all K(+) channels and it does not form a functional channel in yeast, suggesting that the viral channels did not come from a proteobacterium. Collectively, our results indicate that the viruses did not acquire their K(+) channel-encoding genes from their current algal hosts by gene transfer; thus alternative explanations are required. One possibility is that the viral genes arose from ancient organisms, which served as their hosts before the viruses developed their current host specificity. Alternatively the viral proteins could be the origin of K(+) channels in algae and perhaps even all cellular organisms.

  6. Collision cross section prediction of deprotonated phenolics in a travelling-wave ion mobility spectrometer using molecular descriptors and chemometrics.

    PubMed

    Gonzales, Gerard Bryan; Smagghe, Guy; Coelus, Sofie; Adriaenssens, Dieter; De Winter, Karel; Desmet, Tom; Raes, Katleen; Van Camp, John

    2016-06-14

    The combination of ion mobility and mass spectrometry (MS) affords significant improvements over conventional MS/MS, especially in the characterization of isomeric metabolites due to the differences in their collision cross sections (CCS). Experimentally obtained CCS values are typically matched with theoretical CCS values from Trajectory Method (TM) and/or Projection Approximation (PA) calculations. In this paper, predictive models for CCS of deprotonated phenolics were developed using molecular descriptors and chemometric tools, stepwise multiple linear regression (SMLR), principal components regression (PCR), and partial least squares regression (PLS). A total of 102 molecular descriptors were generated and reduced to 28 after employing a feature selection tool, composed of mass, topological descriptors, Jurs descriptors and shadow indices. Therefore, the generated models considered the effects of mass, 3D conformation and partial charge distribution on CCS, which are the main parameters for either TM or PA (only 3D conformation) calculations. All three techniques yielded highly predictive models for both the training (R(2)SMLR = 0.9911; R(2)PCR = 0.9917; R(2)PLS = 0.9918) and validation datasets (R(2)SMLR = 0.9489; R(2)PCR = 0.9761; R(2)PLS = 0.9760). Also, the high cross validated R(2) values indicate that the generated models are robust and highly predictive (Q(2)SMLR = 0.9859; Q(2)PCR = 0.9748; Q(2)PLS = 0.9760). The predictions were also very comparable to the results from TM calculations using modified mobcal (N2). Most importantly, this method offered a rapid (<10 min) alternative to TM calculations without compromising predictive ability. These methods could therefore be used in routine analysis and could be easily integrated to metabolite identification platforms.

  7. Identification and analysis of low molecular weight dissolved organic carbon in subglacial basal ice ecosystems by ion chromatography

    NASA Astrophysics Data System (ADS)

    Lawson, E. C.; Wadham, J. L.; Lis, G. P.; Tranter, M.; Pickard, A. E.; Stibal, M.; Dewsbury, P.; Fitzsimons, S.

    2015-08-01

    Glacial runoff is an important source of dissolved organic carbon (DOC) for downstream heterotrophic activity, despite the low overall DOC concentrations. This is because of the abundance of bioavailable, low molecular weight (LMW) DOC species. However, the provenance and character of LMW-DOC is not fully understood. We investigated the abundance and composition of DOC in subglacial environments via a molecular level DOC analysis of basal ice, which forms by water/sediment freeze-on to the glacier sole. Spectrofluorometry and a novel ion chromatographic method, which has been little utilised in glacial science for LMW-DOC determinations, were employed to identify and quantify the major LMW fractions (free amino acids, carbohydrates and carboxylic acids) in basal ice from four glaciers, each with a different basal debris type. Basal ice from Joyce Glacier (Antarctica) was unique in that 98 % of the LMW-DOC was derived from the extremely diverse FAA pool, comprising 14 FAAs. LMW-DOC concentrations in basal ice were dependent on the bioavailability of the overridden organic carbon (OC), which in turn, was influenced by the type of overridden material. Mean LMW-DOC concentrations in basal ice from Russell Glacier (Greenland), Finsterwalderbreen (Svalbard) and Engabreen (Norway) were low (0-417 nM C), attributed to the relatively refractory nature of the OC in the overridden paleosols and bedrock. In contrast, mean LMW-DOC concentrations were an order of magnitude higher (4430 nM C) in basal ice from Joyce Glacier, a reflection of the high bioavailability of the overridden lacustrine material (>17 % of the sediment OC comprised extractable carbohydrates, a proxy for bioavailable OC). We find that the overridden material may act as a direct (via abiotic leaching) and indirect (via microbial cycling) source of DOC to the subglacial environment and provides a range of LMW-DOC compounds that may stimulate microbial activity in wet sediments in current subglacial

  8. Potential curves and nonadiabatic matrix elements for collisions involving fragments of the HeN + molecular ion

    NASA Astrophysics Data System (ADS)

    Gu, Jian-ping; Buenker, Robert J.; Hirsch, Gerhard; Kimura, Mineo

    1995-05-01

    Ab initio multireference CI calculations have been carried out for the HeN+ molecular ion in order to describe collision processes between its constituent neutral and ionized atoms. The accuracy of these calculations is evaluated by means of a comparison of results obtained at large internuclear separations with the corresponding asymptotic energies deduced from atomic spectral data. Energy values are computed for the eleven lowest He++N and He+N+ atomic limits and average discrepancies relative to the experimental excitation energies up to 110 000 cm-1 are found to lie in the 1000-3000 cm-1 range, of which only 200 cm-1 appears to be the fault of the configuration interaction (CI) technique itself, with the main portion of the error stemming from the choice of atomic orbital (AO) basis instead. The HeN+ X 3Σ- ground state is calculated to have a De value of only 1414 cm-1, but the excited 2 3Π state has a much larger value of 22 133 cm-1 by virtue of an avoided crossing with the lower state of this symmetry. The corresponding radial nonadiabatic coupling is responsible for a large cross section for an excitation process between the N+(3Pg)+He and N+(3Du)+He channels which indirectly provides an efficient electron-capture mechanism leading to the N(4Su)+He+ exit channel. Additional nonadiabatic matrix elements for rotational and spin-orbit coupling have also been obtained and analyzed, as well as transition moments between the various HeN+ molecular states calculated.

  9. Coordination numbers of K(+) and Na(+) Ions inside the selectivity filter of the KcsA potassium channel: insights from first principles molecular dynamics.

    PubMed

    Bucher, Denis; Guidoni, Leonardo; Carloni, Paolo; Rothlisberger, Ursula

    2010-05-19

    Quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello simulations were performed to estimate the coordination numbers of K(+) and Na(+) ions in the selectivity filter of the KcsA channel, and in water. At the DFT/BLYP level, K(+) ions were found to display an average coordination number of 6.6 in the filter, and 6.2 in water. Na(+) ions displayed an average coordination number of 5.2 in the filter, and 5.0 in water. A comparison was made with the average coordination numbers obtained from using classical molecular dynamics (6.7 for K(+) in the filter, 6.6 for K(+) in water, 6.0 for Na(+) in the filter, and 5.2 for Na(+) in water). The observation that different coordination numbers were displayed by the ions in QM/MM simulations and in classical molecular dynamics is relevant to the discussion of selectivity in K-channels.

  10. Formation rate for Rb 2 + molecular ions created in collisions of Rb Rydberg and ground-state atoms

    NASA Astrophysics Data System (ADS)

    Stanojevic, Jovica; Côté, Robin

    2016-05-01

    We calculate the formation rate of the molecular Rb2+ion in its various bound states produced in the associative ionization of a Rydberg and a ground-state atom. Before the formation takes place, the colliding atoms are accelerated by an attractive force between the collision partners. In this way the ground-state atom is first captured by the Rydberg electron and then guided towards the positive ion-core where a molecular ion is subsequently formed. As recently demonstrated, this process results in giant collisional cross sections for the molecular ion formation, with the cross sections essentially determined by the size of the Rydberg atom. For sufficient high principal quantum numbers and atomic densities, many ground-state atoms are already located inside the Rydberg atom and ready to participate in the associative ionization. The same process can occur between a Rydberg and a ground-state atom that form a long-range Rydberg molecule, possibly contributing to the shortening of the lifetimes of Rydberg atoms and molecules. Partial support from the US Army Research Office (ARO-MURI W911NF-14-1-0378), and from NSF (Grant No. PHY-1415560).

  11. The coupling between stability and ion pair formation in magnesium electrolytes from first-principles quantum mechanics and classical molecular dynamics.

    PubMed

    Rajput, Nav Nidhi; Qu, Xiaohui; Sa, Niya; Burrell, Anthony K; Persson, Kristin A

    2015-03-11

    In this work we uncover a novel effect between concentration dependent ion pair formation and anion stability at reducing potentials, e.g., at the metal anode. Through comprehensive calculations using both first-principles as well as well-benchmarked classical molecular dynamics over a matrix of electrolytes, covering solvents and salt anions with a broad range in chemistry, we elucidate systematic correlations between molecular level interactions and composite electrolyte properties, such as electrochemical stability, solvation structure, and dynamics. We find that Mg electrolytes are highly prone to ion pair formation, even at modest concentrations, for a wide range of solvents with different dielectric constants, which have implications for dynamics as well as charge transfer. Specifically, we observe that, at Mg metal potentials, the ion pair undergoes partial reduction at the Mg cation center (Mg(2+) → Mg(+)), which competes with the charge transfer mechanism and can activate the anion to render it susceptible to decomposition. Specifically, TFSI(-) exhibits a significant bond weakening while paired with the transient, partially reduced Mg(+). In contrast, BH4(-) and BF4(-) are shown to be chemically stable in a reduced ion pair configuration. Furthermore, we observe that higher order glymes as well as DMSO improve the solubility of Mg salts, but only the longer glyme chains reduce the dynamics of the ions in solution. This information provides critical design metrics for future electrolytes as it elucidates a close connection between bulk solvation and cathodic stability as well as the dynamics of the salt.

  12. Comparison of the applicability of mass spectrometer ion sources using a polarity- molecular weight scattergram with a 600 sample in-house chemical library.

    PubMed

    Sugimura, Natsuhiko; Furuya, Asami; Yatsu, Takahiro; Shibue, Toshimichi

    2015-01-01

    To provide a practical guideline for the selection of a mass spectrometer ion source, we compared the applicability of three types of ion source: direct analysis in real time (DART), electrospray ionization (ESI) and fast atom bombardment (FAB), using an in-house high-resolution mass spectrometry sample library consisting of approximately 600 compounds. The great majority of the compounds (92%), whose molecular weights (MWs) were broadly distributed between 150 and 1000, were detected using all the ion sources. Nevertheless, some compounds were not detected using specific ion sources. The use of FAB resulted in the highest sample detection rate (>98%), whereas the detection rates obtained using DART and ESI were slightly lower (>96%). A scattergram constructed using MW and topological polar surface area (tPSA) as a substitute for molecular polarity showed that the performance of ESI was weak in the low-MW (<400), low-polarity (tPSA<60) area, whereas the performance of DART was weak in the high-MW (>800) area. These results might provide guidelines for the selection of ion sources for inexperienced mass spectrometry users.

  13. Rydberg and continuum states of the HeH+ molecular ion: Variational R -matrix and multichannel quantum defect theory calculations

    NASA Astrophysics Data System (ADS)

    Bouhali, I.; Bezzaouia, S.; Telmini, M.; Jungen, Ch.

    2016-08-01

    Variational ab initio R -matrix theory combined with generalized multichannel quantum defect theory is used to calculate singly excited Rydberg states of the hydrohelium molecular ion, HeH+, for Σ,3+1,Π,31,Δ,31,Φ,31, and Γ,31 symmetry. Bound levels are calculated for n values up to n ≈10 , and continuum states up to ≈3 eV above the HeH2 + threshold. The calculations span the range of internuclear distances R from 1 to 5 bohrs. The present work follows a preliminary study on the Δ,31 states of HeH+ [Bouhali, Bezzaouia, Telmini, and Jungen, EPJ Web Conf. 84, 04004 (2015), 10.1051/epjconf/20158404004] which was also based on R -matrix theory. Further—although limited to rather small R values—the present work extends the recent ab initio computations of Jungen and Jungen [Mol. Phys. 113, 2333 (2015), 10.1080/00268976.2015.1040094] to higher excitation energies which are not accessible to standard quantum-chemical methods. Where a comparison with the calculations of Jungen and Jungen and other older results can be made, namely for n ≤5 , very good agreement with previous ab initio results is obtained.

  14. Molecular Beam Epitaxy on Gas Cluster Ion Beam Prepared GaSb Substrates: Towards Improved Surfaces and Interfaces

    SciTech Connect

    Krishnaswami, Kannan; Shivashankar, Vangala; Dauplaise, Helen; Allen, Lisa; Dallas, Gordon; Bakken, Daniel; Bliss, David; Goodhue, William

    2008-04-01

    A key problem in producing mid-infrared optoelectronic and low-power electronic devices in the GaSb material system is the lack of substrates with appropriate surfaces for epitaxial growth. Chemical mechanical polishing (CMP) of GaSb results in surface damage accompanied by tenacious oxides that do not easily desorb. To overcome this, we have developed a process using gas cluster ion beams (GCIB) to remove surface damage and produce engineered surface oxides. In this paper, we present surface modification results on GaSb substrates using O2-, CF4/O2-, and HBr-GCIB processes. X-ray photoelectron spectroscopy of GCIB produced surface layers showed the presence of mixed Ga- and Sb-oxides, with mostly Ga-oxides at the interface, desorbing at temperatures ranging 530°C to 560°C. Cross-sectional transmission electron microscopy of molecular beam epitaxy grown GaSb/AlGaSb layers showed that GCIB surfaces yielded smooth defect free substrate to epi transitions as compared to CMP surfaces. Furthermore, HBr-GCIB surfaces exhibited neither dislocation layers nor discernable interfaces, indicating complete oxide desorbtion prior to epigrowth on a clean single crystal template. Atomic force microscopy of GCIB epilayers exhibited smooth surfaces with characteristic step-terrace formations comprising monatomic steps and wide terraces. The HBr-GCIB process can be easily adapted to a large scale manufacturing process for epi-ready GaSb.

  15. Effect of organic solvents on Li+ ion solvation and transport in ionic liquid electrolytes: a molecular dynamics simulation study.

    PubMed

    Li, Zhe; Borodin, Oleg; Smith, Grant D; Bedrov, Dmitry

    2015-02-19

    Molecular dynamics simulations of N-methyl-N-propylpyrrolidinium (pyr13) bis(trifluoromethanesulfonyl)imide (Ntf2) ionic liquid [pyr13][Ntf2] doped with [Li][Ntf2] salt and mixed with acetonitrile (AN) and ethylene carbonate (EC) organic solvents were conducted using polarizable force field. Structural and transport properties of ionic liquid electrolytes (ILEs) with 20 and 40 mol % of organic solvents have been investigated and compared to properties of neat ILEs. Addition of AN and EC solvents to ILEs resulted in the partial displacement of the Ntf2 anions from the Li(+) first coordination shell by EC and AN and shifting the Li-Ntf2 coordination from bidentate to monodentate. The presence of organic solvents in ILE has increased the ion mobility, with the largest effect observed for the Li(+) cation. The Li(+) conductivity has doubled with addition of 40 mol % of AN. The Li(+)-N(Ntf2) residence times were dramatically reduced with addition of solvents, indicating an increasing contribution from structural diffusion of the Li(+) cations.

  16. Time-of-Flight Secondary Ion Mass Spectrometry based Molecular Histology of Human Spinal Cord Tissue and Motor Neurons

    PubMed Central

    Hanrieder, Jörg; Malmberg, Per; Lindberg, Olle R.; Fletcher, John S.; Ewing, Andrew G.

    2013-01-01

    Secondary ion mass spectrometry is a powerful method for imaging biological samples with high spatial resolution. Whole section ToF SIMS scans and multivariate data analysis have been performed on human spinal cord in order to delineate anatomical regions of interest based on their chemical distribution pattern. ToF SIMS analysis of thoracic spinal cord sections was performed at 5µm resolution within 2 hours. Multivariate image analysis by means of principal component analysis and maximum auto correlation factor analysis resulted in detection of more than 400 m/z peaks that were found to be significantly changed. Here, the results show characteristic biochemical distributions that are well in line with major histological regions, including grey and white matter. As an approach for iterative segmentation, we further evaluated previously outlined regions of interest as identified by multivariate image analysis. Here, further discrimination of the grey matter into ventral, lateral and dorsal neuroanatomical regions was observed. TOF SIMS imaging has been carried out at submicron resolution obtaining localization and characterization of spinal motor neurons based on their chemical fingerprint, including neurotransmitter precursors that serve as molecular indicators for motor neuron integrity. Thus, TOF SIMS can be used as an approach for chemical histology and pathology. SIMS holds immense potential for investigating the subcellular mechanisms underlying spinal cord related diseases including chronic pain and amyotrophic lateral sclerosis. PMID:23947367

  17. Molecular dynamics studies unravel role of conserved residues responsible for movement of ions into active site of DHBPS

    PubMed Central

    Shinde, Ranajit Nivrutti; Karthikeyan, Subramanian; Singh, Balvinder

    2017-01-01

    3,4-dihydroxy-2-butanone-4-phosphate synthase (DHBPS) catalyzes the conversion of D-ribulose 5-phosphate (Ru5P) to L-3,4-dihydroxy-2-butanone-4-phosphate in the presence of Mg2+. Although crystal structures of DHBPS in complex with Ru5P and non-catalytic metal ions have been reported, structure with Ru5P along with Mg2+ is still elusive. Therefore, mechanistic role played by Mg2+ in the structure of DHBPS is poorly understood. In this study, molecular dynamics simulations of DHBPS-Ru5P complex along with Mg2+ have shown entry of Mg2+ from bulk solvent into active site. Presence of Mg2+ in active site has constrained conformations of Ru5P and has reduced flexibility of loop-2. Formation of hydrogen bonds among Thr-108 and residues - Gly-109, Val-110, Ser-111, and Asp-114 are found to be critical for entry of Mg2+ into active site. Subsequent in silico mutations of residues, Thr-108 and Asp-114 have substantiated the importance of these interactions. Loop-4 of one monomer is being proposed to act as a “lid” covering the active site of other monomer. Further, the conserved nature of residues taking part in the transfer of Mg2+ suggests the same mechanism being present in DHBPS of other microorganisms. Thus, this study provides insights into the functioning of DHBPS that can be used for the designing of inhibitors. PMID:28079168

  18. Molecular characterisation of murine acute myeloid leukaemia induced by 56Fe ion and 137Cs gamma ray irradiation

    PubMed Central

    Bacher, Jeffery W.

    2013-01-01

    Exposure to sparsely ionising gamma- or X-ray irradiation is known to increase the risk of leukaemia in humans. However, heavy ion radiotherapy and extended space exploration will expose humans to densely ionising high linear energy transfer (LET) radiation for which there is currently no understanding of leukaemia risk. Murine models have implicated chromosomal deletion that includes the hematopoietic transcription factor gene, PU.1 (Sfpi1), and point mutation of the second PU.1 allele as the primary cause of low-LET radiation-induced murine acute myeloid leukaemia (rAML). Using array comparative genomic hybridisation, fluorescence in situ hybridisation and high resolution melt analysis, we have confirmed that biallelic PU.1 mutations are common in low-LET rAML, occurring in 88% of samples. Biallelic PU.1 mutations were also detected in the majority of high-LET rAML samples. Microsatellite instability was identified in 42% of all rAML samples, and 89% of samples carried increased microsatellite mutant frequencies at the single-cell level, indicative of ongoing instability. Instability was also observed cytogenetically as a 2-fold increase in chromatid-type aberrations. These data highlight the similarities in molecular characteristics of high-LET and low-LET rAML and confirm the presence of ongoing chromosomal and microsatellite instability in murine rAML. PMID:22987027

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

    NASA Technical Reports Server (NTRS)

    Salama, F.; Allamandola, L. J.

    1992-01-01

    The diffuse interstellar bands (DIBs), ubiquitous absorption features in astronomical spectra, have been known since early this century and now number more than a hundred. Ranging from 4,400 angstroms to the near infrared, they differ markedly in depth, width and shape, making the concept of a single carrier unlikely. Whether they are due to gas or grains is not settled, but recent results suggest that the DIB carriers are quite separate from the grains that cause visual extinction. Among molecular candidates the polycyclic aromatic hydrocarbons (PAHs) have been proposed as the possible carriers of some of the DIBs, and we present here laboratory measurements of the optical spectrum of the pyrene cation C16H10+ in neon and argon matrices. The strongest absorption feature falls at 4,435 +/- 5 angstroms in the argon matrix and 4,395 +/- 5 angstroms in the neon matrix, both close to the strong 4,430-angstroms DIB. If this or a related pyrene-like species is responsible for this particular band, it must account for 0.2% of all cosmic carbon. The ion also shows an intense but puzzling broad continuum, extending from the ultraviolet to the visible, similar to what is seen in the naphthalene cation and perhaps therefore a common feature of all PAH cations. This may provide an explanation of how PAHs convert a large fraction of interstellar radiation from ultraviolet and visible wavelengths down to the infrared.

  20. Molecular dynamics simulations and generalized Lenard-Balescu calculations of electron-ion temperature equilibration in plasmas

    NASA Astrophysics Data System (ADS)

    Benedict, Lorin X.; Surh, Michael P.; Castor, John I.; Khairallah, Saad A.; Whitley, Heather D.; Richards, David F.; Glosli, James N.; Murillo, Michael S.; Scullard, Christian R.; Grabowski, Paul E.; Michta, David; Graziani, Frank R.

    2012-10-01

    We study the problem of electron-ion temperature equilibration in plasmas. We consider pure H at various densities and temperatures and Ar-doped H at temperatures high enough so that the Ar is fully ionized. Two theoretical approaches are used: classical molecular dynamics (MD) with statistical two-body potentials and a generalized Lenard-Balescu (GLB) theory capable of treating multicomponent weakly coupled plasmas. The GLB is used in two modes: (1) with the quantum dielectric response in the random-phase approximation (RPA) together with the pure Coulomb interaction and (2) with the classical (ℏ→0) dielectric response (both with and without local-field corrections) together with the statistical potentials. We find that the MD results are described very well by classical GLB including the statistical potentials and without local-field corrections (RPA only); worse agreement is found when static local-field effects are included, in contradiction to the classical pure-Coulomb case with like charges. The results of the various approaches are all in excellent agreement with pure-Coulomb quantum GLB when the temperature is high enough. In addition, we show that classical calculations with statistical potentials derived from the exact quantum two-body density matrix produce results in far better agreement with pure-Coulomb quantum GLB than classical calculations performed with older existing statistical potentials.