Science.gov

Sample records for jet-cooled molecular ions

  1. The molecular structure and a Renner-Teller analysis of the ground and first excited electronic states of the jet-cooled CS2+ molecular ion

    NASA Astrophysics Data System (ADS)

    He, Sheng-Gui; Clouthier, Dennis J.

    2006-02-01

    The ÃΠu2-X˜Πg2 electronic band system of the jet-cooled CS2+ ion has been studied by laser-induced fluorescence and wavelength-resolved emission techniques. The ions were produced in a pulsed electric discharge jet using a precursor mixture of carbon disulfide vapor in high-pressure argon. Rotational analysis of the high-resolution spectrum of the Π3/22 component of the 000 band gave linear-molecule molecular structures of r0″=1.5554(10)Å and r0'=1.6172(12)Å. Renner-Teller analyses of the vibronic structure in the spectra showed that the ground-state spin-orbit splitting (A =-447.0cm-1) is much larger than that of the excited state (A=-177.5cm-1), but that the Renner-Teller parameters are of similar magnitude and that a strong ν1-2ν2 Fermi resonance occurs in both states. Previous analyses of the vibronic structure in the ground and excited states of the ion from pulsed field-ionization-photoelectron data are shown to be substantially correct.

  2. 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(+).

  3. 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.

  4. 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.

  5. 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.

  6. Spectroscopy of jet-cooled Bi3.

    PubMed

    Arrington, Caleb A; Morse, Michael D

    2008-12-18

    A resonant two-photon ionization spectroscopic study of jet-cooled Bi3 has identified two band systems in the molecule in the 9600-10 600 and 15 250-16 050 cm(-1) range. The latter of these has been previously observed in matrix isolation spectroscopy and tentatively attributed to Bi4; the mass-resolved work presented here reassigns it to Bi3. A review of all previously observed electronic states is presented, and it is argued that the new band system lying in the range 9600-10 600 cm(-1) corresponds to the spin-forbidden A' 4A1" <-- X1 2E" (E1/2 component) band system.

  7. 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.

  8. Electronic Spectra of the Jet-Cooled Acetaminophen

    NASA Astrophysics Data System (ADS)

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

    2010-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-08-01

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

  10. 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).

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Jet-Cooled Chlorofluorobenzyl Radicals: Spectroscopy and Mechanism

    NASA Astrophysics Data System (ADS)

    Yoon, Young; Lee, Sang

    2016-06-01

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

  17. 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.

  18. Laser Induced Fluorescence Spectroscopy of Jet-Cooled MgOMg

    NASA Astrophysics Data System (ADS)

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

    2017-06-01

    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}← ^{1}Σ^{+}_{g}}) of BeOBe. Preliminary data for the first electronic transition of the isovalent species, CaOCa, was presented previously (71^{st} ISMS, talk RI10). We now report the first electronic spectrum of MgOMg. Jet-cooled laser induced fluorescence spectra were recorded for multiple bands that occurred within the 21,000 - 24,000 cm^{-1} range. 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 (^{24Mg} has zero nuclear spin). 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.

  19. 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.

  20. 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/

  1. Spectroscopic study of jet-cooled deuterated porphycenes: unusual isotopic effects on proton tunneling.

    PubMed

    Mengesha, Ephriem T; Zehnacker-Rentien, Anne; Sepioł, J; Kijak, M; Waluk, J

    2015-02-12

    Porphycene (Pc) is a well-known model for studying double hydrogen transfer, which shows vibrational-mode-specific tunneling splitting when isolated in supersonic jets or helium nanodroplets. The effect of deuteration on tunneling splitting is reported for jet-cooled heterogeneous, deuterated Pc samples (Pc-d(mix)) with the prevailing contribution of Pc-d12 isotopologue. The sample introduced into the gas phase using laser desorption is studied by means of laser-induced fluorescence (LIF) and single vibronic level fluorescence (SVLF) measurements, in combination with quantum chemical calculations. The influence of molecular symmetry is studied by comparing Pc, Pc-d12, and Pc-d11. The spectra of Pc-d12 show strong similarity to those of the parent undeuterated porphycene (Pc). Comparable tunneling splitting is observed in the two isotopologues, both for the 0-0 transition and the most efficient promoting 2Ag mode. In contrast, an unusual isotopic effect is observed for the totally symmetrical 4Ag mode. While this vibration behaves as a neutral mode in Pc, neither enhancing nor decreasing the tunneling efficiency, it strongly promotes hydrogen transfer in Pc-d12. This observation is explained in terms of modification of the displacement vectors of the 4Ag mode upon deuteration. It demonstrates that isotope substitution affects hydrogen transfer even when the weak structural modifications are far from the reaction center, emphasizing the strongly multidimensional nature of the tunneling process.

  2. Jet-cooled infrared spectra of molecules and complexes with a cw mode-hop-free external-cavity QCL and a distributed-feedback QCL

    NASA Astrophysics Data System (ADS)

    Liu, X.; Xu, Y.; Su, Z.; Tam, W. S.; Leonov, I.

    2011-03-01

    The coupling of quantum cascade lasers (QCLs) with an off-axis cavity enhanced absorption (CEA) spectrometer and an astigmatic multiple pass absorption (MPA) spectrometer are described in this paper. A continuous wave (cw) liquid nitrogen cooled distributed-feedback QCL at 5.7 μm and a cw room temperature mode-hop-free external-cavity QCL at 6.1 μm were employed as the light source. For the CEA spectrometer, the effects of mirror size and laser scan rate were evaluated. For the MPA spectrometer, a pair of astigmatic mirrors with a 55 cm mirror distance was aligned to the 366-pass configuration. The jet-cooled samples were generated using a homemade pulsed slit jet nozzle assembly. Two LabVIEW programs were written to automate and synchronize the timing of the laser scan, the pulsed slit jet molecular expansion, and the data acquisition. Infrared spectra of jet-cooled methyl lactate and the Ar-H2O complex and room temperature N2O and NH3 samples were measured using both the rapid scan and the wavelength modulation methods to evaluate the sensitivity and resolution of the CEA and MPA spectrometers. The combination of the MPA spectrometer with the external-cavity QCL using the rapid scan method was found to be the best suited combination to measure high resolution jet-cooled infrared spectra.

  3. 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.

  4. Jet-cooled infrared spectra and investigation of the Torsion-rotation energy levels of methanol in the C-H stretch region

    SciTech Connect

    Hu, Li-Hong; Wang, X.; Perry, D.S.

    1996-12-31

    Jet-cooled absorption spectra of the C-H stretching bands of methanol have been recorded between 2965 and 3027 cm{sup -1} on two different molecular beam machines. In both cases, a color-center laser pumped by {approximately}1.6 W from a krypton ion laser at 647 nm was used to generate 8-9 mW of tunable IR radiation. The first spectrum between 2977-3027 cm{sup -1} was recorded in direct absorption with a 2 x 0.01 cm slit nozzle. The molecular rotational temperature was {approximately}17 K, and the linewidth was {approximately}75 MHz due to residual Doppler spread. Baseline subtraction was employed to suppress laser intensity fluctuations. Frequency calibration was accomplished by simultaneously recording absorption lines of ethylene and the transmission fringes of a vacuum-spaced 150 MHz-marker etalon. The second spectrum between 2965-3627 cm{sup -1} was recorded on a molecular-beam optothermal spectrometer. A mixture of a few percent methanol in He carrier was introduced to the beam chamber through a 60-{mu}m pinhole nozzle with {approximately}1atm backing pressure, giving a rotational temperature of {approximately}10 K. The beam was focused onto a He-cooled bolometer using quadrupole focusing in the flight chamber between the skimmer and the detector. In a few pathological regions, H{sub 2}O absorption completely obscured the methanol spectrum and spoiled control of the laser scan. Calibration traces were recorded to minimize errors due to gaps and drifts. On a given day the calibration interferometer drift was typically less than {approximately}10 MHz, defining the overall precision. Separations of close lines in a single scan should have precision better than 1 MHz. The two spectra were combined for analysis, with the straight absorption spectrum giving particularly nice and easily recognizable spectral patterns.

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

    SciTech Connect

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

    2015-01-22

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

  6. 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.

  7. 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)

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Lif Spectroscopy of Jet Cooled MgOH

    NASA Astrophysics Data System (ADS)

    Fukushima, Masaru; Ishiwata, Takashi

    2014-06-01

    We have generated MgOH in supersonic free jet expansions, and observed the laser induced fluorescence ( LIF ) of the tilde{A} ^2Π - tilde{X} ^2Σ^+ transition. We have reported rotational analyses of the bending vibronic bands, 2_0^n, n = 0, 2, and 4, and it has been found that the spin-orbit constant of the bending vibronic levels, tilde{A} ^2Π (0n^00) μ ^2Π, increases with increasing the bending vibrational quantum number, n. This observation is interpreted as the lower level possessing primarily bent character and the higher level possessing linear character. The bending potential surface of the tilde{A} ^2Π state is thought to be the reason for the present observation and interpretation. This potential surface is thought to be fairly flat and anharmonic with bent and linear geometries at the r_e and r_0 structures, respectively. We also observed the other two vibronic bands at almost the middle between the 2_0^2 and 2_0^4 bands. One of the two has a similar rotational structure with that of the origin band, 0_0^0, and is assigned to be the Mg-OH stretching vibronic band, tilde{A} ^2Π (00^01) - tilde{X} ^2Σ^+ (00^00). The rotational structure of another vibronic band is very complex, and it seems to overlap, at least, two vibronic bands, ^2Π - and ^2Σ(+) - ^2Σ^+. More precise analysis is underway. M. Fukushima and T. Ishiwata, The 21st Colloquium on High-Resolution Molecular Spectroscopy, F8 (2009).

  13. Supersonic jet cooled rotational spectrum of 2,4-difluorophenol

    NASA Astrophysics Data System (ADS)

    Nair, K. P. Rajappan; Dewald, David; Wachsmuth, Dennis; Grabow, Jens-Uwe

    2017-05-01

    The microwave spectrum of the cis form of aromatic 2,4-difluorophenol (DFP) has been recorded and analyzed in the frequency range of 5-25 GHz using a pulsed-jet Fourier transform microwave spectrometer. Rotational transitions were measured for the parent and all unique single 13C substituted isotopologues and 18O in natural abundance and on enriched deuterium species on the hydroxyl group. The rotational (MHz), centrifugal distortion (kHz), and quadrupole coupling constants (MHz) in deuterium species were determined. The rotational constants for the parent species are obtained as A = 3125.04158(43) MHz, B = 1290.154481(54) MHz, C = 913.197424(36) MHz, DJ = 0.020899(162) kHz, DK = 0.9456(100) kHz, DJK = 0.09273(65) kHz, d1 = -0.00794(14) kHz, d2 = -0.002356(93) kHz and for the deuterated species A = 3125.38579(44) MHz, B = 1261.749784(48) MHz, C = 898.927184(27) MHz, DJ = 0.02096(19) kHz, DK = 0.379(74) kHz, DJK = 0.0880(11) kHz, d1 = -0.00691(11) kHz, d2 = -0.00183(11) kHz. The deuterium quadrupole coupling constants are χaa = -0.0109(33) MHz, and (χbb - χcc) = 0.2985(59) MHz. The rs substitution structure was determined using the measured rotational constants of the isotopologues, a nonlinear least squares fit was performed to obtain the best fit gas phase r0 effective structure. Supporting ab initio (MP2) and density functional calculations provided consistent values for the rotational parameters, and molecular structure.

  14. 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

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

    DTIC Science & Technology

    2016-06-06

    chamber is the...system. Molecular and/or atomic ions that have been produced by laser ablation of a solid target are trapped in the middle chamber of... clouds of Ba+ ions and Ca atoms. Due to the strong Coulomb interaction, the Ba+ ions quickly cool the molecular ion translation motion, while

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

    SciTech Connect

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

    1986-10-23

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

  17. 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.

  18. 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

  19. 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.

  20. Mechanisms of Multiphoton Dissociation of Molecular Ions.

    DTIC Science & Technology

    1981-04-30

    dissociation energy and are thus re- Thus, some small fraction of all ions produced in our moved from the beam by unimolecular decomposition. source probably...AD-A099 121 SRI INTERNATIONAL MENLO PARK CA F/6 7/5 MECHANISMS OF MULTIPHOTON DISSOCIATION OF MOLECULAR IONS, U) APR 81 M J COGGIOLA. J R PETERSON, P...Final Report MECHANISMS OF MULTIPHOTON DISSOCIATION OF MOLECULAR IONS By: Michael J. Coggiola, Project Leader James R. Peterson, Project Supervisor

  1. Peltier Refrigerators for Molecular Ion Sources

    NASA Astrophysics Data System (ADS)

    Hershcovitch, Ady

    2008-11-01

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

  2. 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.

  3. Secondary ion mass spectrometry: Polyatomic and molecular ion emission

    NASA Astrophysics Data System (ADS)

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

    1986-03-01

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

  4. Molecular ions in the F2 layer.

    NASA Technical Reports Server (NTRS)

    Rishbeth, H.; Bauer, P.; Hanson, W. B.

    1972-01-01

    Data on ion concentrations at heights of 400-500 km, obtained by the OGO VI satellite, suggest that the O(+) and molecular ion concentrations are sometimes anticorrelated. To assist in explaining this phenomenon, a table of the chemical reactions most likely to control the molecular ion concentrations is drawn up, and its validity tested with the aid of data from rocket-borne mass spectrometers at heights of 220-400 km. The anticorrelation of O(+) and NO(+) ions by day is thought to be due to the importance of a reaction between N2(+) ions and O atoms; the main source of N2(+) above 300 km is probably charge-exchange between N2 and O(+), the latter being produced by photoionization. However, at night another source of NO(+) ions is required, which may be N(+) ions that are either stored in the magnetosphere or are produced from He(+) and N2.

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

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

    PubMed

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

    2011-12-15

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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. The Jet-Cooled High-Resolution IR Spectrum of Formic Acid Cyclic Dimer

    NASA Astrophysics Data System (ADS)

    Goubet, Manuel; Bteich, Sabath; Huet, Therese R.; Pirali, Olivier; Asselin, Pierre; Soulard, Pascale; Jabri, Atef; Roy, P.; Georges, Robert

    2017-06-01

    As the simplest carboxylic acid, formic acid (FA) is an excellent model molecule to investigate the general properties of carboxylic acids. FA is also an atmospherically and astrophysically relevant molecule. It is well known that its dimeric form is predominant in the gas phase at temperatures below 423 K. The cyclic conformation of the dimer (FACD) is an elementary system to be understood for the concerted hydrogen transfer through equivalent hydrogen bonds, an essential process within biomolecules. The IR range is a crucial spectral region, particularly the far-IR, as it gives a direct access to the intermolecular vibrational modes involved in this process. Moreover, due to its centrosymmetric conformation, the FACD exhibits no pure rotation spectrum and, due to spectral line congestion and Doppler broadening, IR bands cannot be rotationally resolved at room temperature. So far, only parts of the ν_{5}-GS band (C-O stretch) have been observed under jet-cooled conditions using laser techniques. We present here six rotationally resolved IR bands of FACD recorded under jet-cooled conditions using the Jet-AILES apparatus and the QCL spectrometer at MONARIS, including the far-IR ν_{24}-GS band (intermolecular in-plane bending). Splitting due to vibration-rotation-tunneling motions are clearly observed. A full spectral analysis is in progress starting from the GS constants obtained by Goroya et al. and with the support of electronic structure calculations. T. Miyazawa and K. S. Pitzer, J. Am. Chem. Soc. 81, 74, 1959 R. Georges, M. Freytes, D. Hurtmans, I. Kleiner, J. Vander Auwera, M. Herman, Chem. Phys. 305, 187, 2004 M. Ortlieb and M. Havenith, J. Phys. Chem. A 111, 7355, 2007; K. G. Goroya, Y. Zhu, P. Sun and C. Duan, J. Chem. Phys. 140, 164311, 2014 This work is supported by the CaPPA project (Chemical and Physical Properties of the Atmosphere) ANR-11-LABX-0005-01

  13. 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.

  14. 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.

  15. Carbon-based ion and molecular channels

    NASA Astrophysics Data System (ADS)

    Sint, Kyaw; Wang, Boyang; Kral, Petr

    2008-03-01

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

  16. 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.

  17. 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.

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

    NASA Astrophysics Data System (ADS)

    Jawad, Khadija M.; Zwier, Timothy S.

    2016-06-01

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

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

    NASA Astrophysics Data System (ADS)

    Yoon, Young; Lee, Sang

    2015-06-01

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

  20. The high-resolution infrared spectrum of the ν3 +ν5 combination band of jet-cooled propyne

    NASA Astrophysics Data System (ADS)

    Doney, K. D.; Zhao, D.; Bouwman, J.; Linnartz, H.

    2017-09-01

    We present the first detection of the high-resolution ro-vibrational spectrum of the ν3 +ν5 combination band of propyne around 3070 cm-1. The fully resolved spectrum is recorded for supersonically jet-cooled propyne using continuous wave cavity ring-down spectroscopy (cw-CRDS). The assignments are supported with the help of accurate ab initio vibration-rotation interaction constants (αi) and anharmonic frequencies. A detailed analysis of the rotationally cold spectrum is given.

  1. 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

  2. Towards quantum control of molecular ions

    NASA Astrophysics Data System (ADS)

    Hanneke, David; Kleiner, Edward; Frenett, Alexander

    2016-05-01

    Many atoms and molecules possess interesting spectroscopic transitions, but lack dissipative transitions useful for control and detection of internal states. In particular, molecules are candidates for quantum memories, low-temperature chemistry studies, tests of fundamental symmetries, and searches for time-variation of fundamental constants, but most lack a convenient cycling transition. By co-trapping a molecular ion with an atomic ion, the atom can provide all dissipation and detection. We present a system capable of such quantum control and report progress towards its use. We also present candidate molecules with analysis of potentially interesting transitions and systematic effects. This work is supported by the NSF and Amherst College.

  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. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

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

    SciTech Connect

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

    2015-01-22

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

  10. Modeling ion sensing in molecular electronics

    SciTech Connect

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

    2014-02-07

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

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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).

  16. 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.

  17. 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

  18. 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

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

    PubMed

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

    2016-10-07

    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 (1)ππ(∗) 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 ⋅ 10(9) s(-1) near the S1(v = 0) level to 1 ⋅ 10(11) s(-1) at Eexc = 516 cm(-1). The (1)ππ(∗) state of 1MCyt also relaxes into the lower-lying triplet T1 ((3)ππ(∗)) 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 ⋅ 10(8) s(-1) near S1(v = 0) to kISC = 2 ⋅ 10(9) 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 ((3)nπ(∗)) 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

  20. 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.

  1. 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.

  2. Molecular ion emission from alkanethiol-SAMs by HCI bombardment

    NASA Astrophysics Data System (ADS)

    Flores, Marcos; Esaulov, Vladimir; Yamazaki, Yasunori

    2011-06-01

    In this work, we employ highly charged ions to study the sputtering of positive molecular fragments from two different alkanethiol self-assembled monolayers (SAMs) on gold surfaces: undecanethiol and dodecanethiol. The SAMs are bombarded with a pulsed Arq+ beam (3molecular ions were detected and analyzed from time-of-flight spectra, and thereby the masses and yields of secondary ions were obtained. The proton yields are dependent on the charge state of the incident ion. On the other hand, the positive molecular ion yields, such as CnHm+, are charge state independent. The positive molecular ion yields decay with the molecular size n.

  3. Electronic spectra of jet-cooled 3- and 4-chlorotropolones: Influence of asymmetric substitution on the intramolecular hydrogen bonding

    NASA Astrophysics Data System (ADS)

    Tsuji, Takashi; Sekiya, Hiroshi; Ito, Sayaka; Ujita, Hiroki; Habu, Mariko; Mori, Akira; Takeshita, Hitoshi; Nishimura, Tukio

    1993-09-01

    The fluorescence excitation and fluorescence spectra of jet-cooled 3-chlorotropolone (3CTR-h) and 4-chlorotropolone (4CTR-h) were measured in the S(sub 1) - S(sub 0) region. Several transitions of 3CTR-h were identified in the region of 26,403 - 26,694 kayser, whereas only the origin band was detected at 26338 kayser in 4CTR-h. No tunneling splitting was observed in the spectra, suggesting that the hydroxylic proton is localized almost completely in one well of an asymmetric double-minimum potential function along the proton transfer coordinate. The vibronic structure in the fluorescence excitation spectrum of 4CTR-h is extremely different from that of 3CTR-h, which is ascribed to the change of the geometry in S(sub 1) of 4CTR-h.

  4. 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%.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

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

    NASA Astrophysics Data System (ADS)

    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.

  10. 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.

  11. 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.

  12. 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.

  13. Calculations of some weakly bound diatomic molecular negative ions

    SciTech Connect

    Li, Y.; Lin, C.D. )

    1999-09-01

    We examine the existence of stable bound states of some diatomic molecular ions where the neutral molecule itself is either unbound or barely bound. Two bound states have been found for the HeH[sup [minus

  14. 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).

  15. Molecular dynamics simulations of ion range profiles for heavy ions in light targets

    SciTech Connect

    Lan, Chune; Xue, Jianming; Zhang, Yanwen; Morris, James R.; Zhu, Zihua; Gao, Yuan; Wang, Yugang; Yan, Sha; Weber, William J.

    2012-09-01

    The determination of stopping powers for slow heavy ions in targets containing light elements is important to accurately describe ion-solid interactions, evaluate ion irradiation effects and predict ion ranges for device fabrication and nuclear applications. Recently, discrepancies of up to 40% between the experimental results and SRIM (Stopping and Range of Ions in Matter) predictions of ion ranges for heavy ions with medium and low energies (<25 keV/nucleon) in light elemental targets have been reported. The longer experimental ion ranges indicate that the stopping powers used in the SRIM code are overestimated. Here, a molecular dynamics simulation scheme is developed to calculate the ion ranges of heavy ions in light elemental targets. Electronic stopping powers generated from both a reciprocity approach and the SRIM code are used to investigate the influence of electronic stopping on ion range profiles. The ion range profiles for Au and Pb ions in SiC and Er ions in Si, with energies between 20 and 5250 keV, are simulated. The simulation results show that the depth profiles of implanted ions are deeper and in better agreement with the experiments when using the electronic stopping power values derived from the reciprocity approach. These results indicate that the origin of the discrepancy in ion ranges between experimental results and SRIM predictions in the low energy region may be an overestimation of the electronic stopping powers used in SRIM.

  16. Molecular dynamics simulations of ion range profiles for heavy ions in light targets

    SciTech Connect

    Lan, Chune; Xue, Jianming; Zhang, Yanwen; Morris, James R; Zhu, Zihua; Gao, Yuan; Wang, Yugang; Yan, Sha; Weber, William J

    2012-01-01

    The determination of stopping powers for slow heavy ions in targets containing light elements is important to accurately describe ion-solid interactions, evaluate ion irradiation effects and predict ion ranges for device fabrication and nuclear applications. Recently, discrepancies of up to 40% between the experimental results and SRIM (Stopping and Range of Ions in Matter) predictions of ion ranges for heavy ions with medium and low energies (< {approx} 25 keV/nucleon) in light elemental targets have been reported. The longer experimental ion ranges indicate that the stopping powers used in the SRIM code are overestimated. Here, a molecular dynamics simulation scheme is developed to calculate the ion ranges of heavy ions in light elemental targets. Electronic stopping powers generated from both a reciprocity approach and the SRIM code are used to investigate the influence of electronic stopping on ion range profiles. The ion range profiles for Au and Pb ions in SiC and Er ions in Si, with energies between 20 and 5250 keV, are simulated. The simulation results show that the depth profiles of implanted ions are deeper and in better agreement with the experiments when using the electronic stopping power values derived from the reciprocity approach. These results indicate that the origin of the discrepancy in ion ranges between experimental results and SRIM predictions in the low energy region may be an overestimation of the electronic stopping powers used in SRIM.

  17. 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

  18. 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).

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Identification of crystalline structures in jet-cooled acetylene large clusters studied by two-dimensional correlation infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Matsumoto, Yoshiteru; Yoshiura, Ryuto; Honma, Kenji

    2017-07-01

    We investigated the crystalline structures of jet-cooled acetylene (C2H2) large clusters by laser spectroscopy and chemometrics. The CH stretching vibrations of the C2H2 large clusters were observed by infrared (IR) cavity ringdown spectroscopy. The IR spectra of C2H2 clusters were measured under the conditions of various concentrations of C2H2/He mixture gas for supersonic jets. Upon increasing the gas concentration from 1% to 10%, we observed a rapid intensity enhancement for a band in the IR spectra. The strong dependence of the intensity on the gas concentration indicates that the band was assigned to CH stretching vibrations of the large clusters. An analysis of the IR spectra by two-dimensional correlation spectroscopy revealed that the IR absorption due to the C2H2 large cluster is decomposed into two CH stretching vibrations. The vibrational frequencies of the two bands are almost equivalent to the IR absorption of the pure- and poly-crystalline orthorhombic structures in the aerosol particles. The characteristic temperature behavior of the IR spectra implies the existence of the other large cluster, which is discussed in terms of the phase transition of a bulk crystal.

  6. 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.

  7. Ion pairing in molecular simulations of aqueous alkali halide solutions

    PubMed Central

    Fennell, Christopher J.; Bizjak, Alan; Vlachy, Vojko; Dill, Ken A.

    2009-01-01

    Using classical molecular dynamics simulations, we study ion-ion interactions in water. We study the potentials of mean force (PMF) for the full set of alkali halide ion pairs, and in each case, we test different parameter sets for modeling both the water and the ions. Altogether, we compared 300 different PMFs. We also calculate association equilibrium constants (KA) and compare them to two types of experiments. Of additional interest here was the proposition of Collins called the ‘law of matching water affinities’, where the relative affinity of ions in solution depends on the matching of cation and anion sizes. From observations on the relative depths of the free energies of the contact ion pair (CIP) and the solvent-shared ion pair (SIP), along with related solvent structure analyses, we find a good correlation with this proposition: small-small and large-large should associate in water and small-large should be more dissociated. PMID:19206510

  8. Ion pairing in molecular simulations of aqueous alkali halide solutions.

    PubMed

    Fennell, Christopher J; Bizjak, Alan; Vlachy, Vojko; Dill, Ken A

    2009-05-14

    Using classical molecular dynamics simulations, we study ion-ion interactions in water. We study the potentials of mean force (PMF) for the full set of alkali halide ion pairs, and in each case, we test different parameter sets for modeling both the water and the ions. Altogether, we compared 300 different PMFs. We also calculate association equilibrium constants (KA) and compare them to two types of experiments. Of additional interest here was the proposition of Collins called the "law of matching water affinities", where the relative affinity of ions in solution depends on the matching of cation and anion sizes. From observations on the relative depths of the free energies of the contact ion pair (CIP) and the solvent-shared ion pair (SIP), along with related solvent structure analyses, we find a good correlation with this proposition: small-small and large-large should associate in water, and small-large should be more dissociated.

  9. Dissociative processes in electron-molecular ion collisions

    NASA Astrophysics Data System (ADS)

    Djuric, Nada; Dunn, Gordon H.

    1998-10-01

    There is renewed interest in dissociation of molecular ions, primarily due to needs for modeling plasma generators for etching and deposition and for modeling edge plasmas for fusion reactors. At the same time, there are improvements in experimental techniques; e.g. use of heavy-ion storage rings has opened possibilities in dissociation studies of vibrationally relaxed molecular ions. At electron energies below the dissociation energy (D_e) of a molecular ion, the most importanat process is dissociative recombination (DR). Once the energy is above D_e, dissociative excitation (DE) is allowed, and at even higher energies dissociative ionization (DI) is energetically possible. In JILA we set up an apparatus wherein light fragment ions from DE of heteronuclear molecular ions are detected. In the heavy-ion storage ring at Stockholm (CRYRING) detection of neutral fragments was used for DE and DR studies. We will discuss the techniques and give examples of DE and DI obtainet at JILA and CRYRING [1,2,3]. Work supported in part by the Office of Fusion Energy of the U. S. DOE under Contract No. DE-A105-86ER53237 with NIST and in part by the Swedish Natural Science Research Council. 1. N. Djuric et al., Phys. Rev. A 56, 2887 (1997). 2. J. Semaniak et al., Ap. J. 498, 886 (1998). 3. J. R. Peterson et al., J. Chem. Phys. 108, 1978 (1998)

  10. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1985-01-01

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

  12. 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

  13. Optimised surface-electrode ion-trap junctions for experiments with cold molecular ions

    NASA Astrophysics Data System (ADS)

    Mokhberi, A.; Schmied, R.; Willitsch, S.

    2017-04-01

    We discuss the design and optimisation of two types of junctions between surface-electrode radiofrequency ion-trap arrays that enable the integration of experiments with sympathetically cooled molecular ions on a monolithic chip device. A detailed description of a multi-objective optimisation procedure applicable to an arbitrary planar junction is presented, and the results for a cross junction between four quadrupoles as well as a quadrupole-to-octupole junction are discussed. Based on these optimised functional elements, we propose a multi-functional ion-trap chip for experiments with translationally cold molecular ions at temperatures in the millikelvin range. This study extends complex chip-based trapping techniques to Coulomb-crystallised molecular ions with potential applications in mass spectrometry, spectroscopy, controlled chemistry and quantum technology.

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

    NASA Astrophysics Data System (ADS)

    Yoon, Young Wook; Lee, Sang Kuk

    2013-06-01

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

  15. 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

  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. Infrared and ultraviolet spectral signatures and conformational preferences of jet-cooled serotonin.

    PubMed

    LeGreve, Tracy A; Baquero, Esteban E; Zwier, Timothy S

    2007-04-04

    The ultraviolet and infrared spectroscopy of single conformations of neutral serotonin (5-hydroxytryptamine) have been studied in the gas phase using a combination of methods including laser-induced fluorescence, resonance-enhanced two-photon ionization, UV-UV hole-burning spectroscopy, and resonant ion-dip infrared spectroscopy. By comparison to its close analogue tryptamine, for which firm assignments to seven low-energy conformations have been made, UV and IR transitions due to eight conformations of serotonin are observed and assigned. The ultraviolet spectrum divides into two subsets of transitions separated from one another by approximately 230 cm-1 ascribable to syn and anti conformations of the 5-OH group. These two subsets are also distinguishable via their 5-OH stretch fundamentals, with the anti-OH subset shifted by approximately 4-5 cm-1 to lower frequency than those due to syn-OH conformers. The existing firm assignments for tryptamine play a decisive role in assignments in serotonin, where the alkyl CH stretch infrared spectrum is diagnostic of the conformation of the ethylamine side chain. Conformer A of serotonin (SERO(A)), with S1 <-- S0 origin transition at 32584 cm-1, is assigned to Gpy(out)/anti-OH, SERO(B) at 32548 cm-1 to Gpy(up)/anti, SERO(C) at 32545 cm-1 to Gph(out)/anti, SERO(D) at 32560 cm-1 to Anti(py)/anti, SERO(E) at 32537 cm-1 to Anti(up)/anti, SERO(F) at 32353 cm-1 to Gpy(out)/syn, SERO(G) at 32313 cm-1 to Gpy(up)/syn, and SERO(H) at 32282 cm-1 to Gph(out)/syn. The conformational preferences of serotonin differ from those of tryptamine most notably in the selective stabilization observed for the Gph(out)/anti-OH conformer SERO(C), which makes it the second-most intense transition in the ultraviolet spectrum, surpassed only by the Gpy(out)/anti-OH conformer SERO(A).

  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. Towards the Precision Spectroscopy of a Single Molecular Ion

    NASA Astrophysics Data System (ADS)

    Lin, Yen-Wei

    This dissertation presents some development of the single molecular ion precision spectroscopy experiment including construction of the project, spectroscopy state readout, and production of ultracold molecules. Such molecular ion spectroscopy aims at testing fundamental physics such as probing the time variation of electron-proton mass ratio. The theories and characterization of ion traps are first discussed along with information regarding building the ion trapping systems. Then, routines in this project such as loading ions, Doppler laser cooling, excessive micromotion compensation, secular motion detection, and fluorescence imaging are deliberated. In the state readout experiment, the coherent motion of a single trapped barium ion resonantly driving by a radiation pressure is studied. By scattering of order only one hundred photons, the radiation pressure is able to seed a laser-cooled ion with a secular oscillation that is detectable by the Doppler velocimetry technique after proper motional amplification. This seeding method provides a mapping between the ion's internal configuration and its secular motion and can be used to read out the spectroscopy results from a single non-fluorescing ion with a partially-closed cycling transition. The work of ultracold molecule production is done with silicon monoxide ions, which has a strong vibration-conserved spontaneous decay branching. Therefore, by optically pumping the rotational cooling transitions in silicon monoxide ions with a broadband radiation, the population can be efficiently driven into the ground rotational state before falling into other manifolds. To avoid the rotational heating transition, the broadband source, derived from a femtosecond pulsed laser, is spectrally filtered using an ultrashort pulse shaper.

  20. 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.

  1. Calculating Conductance of Ion Channels - Linking Molecular Dynamics and Electrophysiology

    NASA Astrophysics Data System (ADS)

    Wilson, Michael A.; Pohorille, Andrew

    2015-01-01

    Molecular dynamics computer simulations were combined with an electrodiffusion model to compute conduction of simple ion channels. The main assumptions of the model, and the consistency, efficiency and accuracy of the ion current calculations were tested and found satisfactory. The calculated current-voltage dependence for a synthetic peptide channel is in agreement with experiments and correctly captures the asymmetry of current with respect to applied field.

  2. 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.

  3. 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 !}.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

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

    ERIC Educational Resources Information Center

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

    2008-01-01

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

  9. 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…

  10. Unraveling the Structure of Ultracold Mesoscopic Collinear Molecular Ions

    NASA Astrophysics Data System (ADS)

    Schurer, J. M.; Negretti, A.; Schmelcher, P.

    2017-08-01

    We present an in-depth many-body investigation of the so-called mesoscopic molecular ions that can buildup when an ion is immersed into an atomic Bose-Einstein condensate in one dimension. To this end, we employ the multilayer multiconfiguration time-dependent Hartree method for mixtures of ultracold bosonic species for solving the underlying many-body Schrödinger equation. This enables us to unravel the actual structure of such massive charged molecules from a microscopic perspective. Laying out their phase diagram with respect to atom number and interatomic interaction strength, we determine the maximal number of atoms bound to the ion and reveal spatial densities and molecular properties. Interestingly, we observe a strong interaction-induced localization, especially for the ion, that we explain by the generation of a large effective mass, similarly to ions in liquid Helium. Finally, we predict the dynamical response of the ion to small perturbations. Our results provide clear evidence for the importance of quantum correlations, as we demonstrate by benchmarking them with wave function ansatz classes employed in the literature.

  11. 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.

  12. Molecular Dynamics of a Protein Surface: Ion-Residues Interactions

    PubMed Central

    Friedman, Ran; Nachliel, Esther; Gutman, Menachem

    2005-01-01

    Time-resolved measurements indicated that protons could propagate on the surface of a protein or a membrane by a special mechanism that enhanced the shuttle of the proton toward a specific site. It was proposed that a suitable location of residues on the surface contributes to the proton shuttling function. In this study, this notion was further investigated by the use of molecular dynamics simulations, where Na+ and Cl− are the ions under study, thus avoiding the necessity for quantum mechanical calculations. Molecular dynamics simulations were carried out using as a model a few Na+ and Cl− ions enclosed in a fully hydrated simulation box with a small globular protein (the S6 of the bacterial ribosome). Three independent 10-ns-long simulations indicated that the ions and the protein's surface were in equilibrium, with rapid passage of the ions between the protein's surface and the bulk. However, it was noted that close to some domains the ions extended their duration near the surface, thus suggesting that the local electrostatic potential hindered their diffusion to the bulk. During the time frame in which the ions were detained next to the surface, they could rapidly shuttle between various attractor sites located under the electrostatic umbrella. Statistical analysis of the molecular dynamics and electrostatic potential/entropy consideration indicated that the detainment state is an energetic compromise between attractive forces and entropy of dilution. The similarity between the motion of free ions next to a protein and the proton transfer on the protein's surface are discussed. PMID:15894639

  13. Jet-cooled fluorescence excitation spectra and carbonyl wagging potential energy functions of several cyclic ketones in their S 1(n, π*) electronic excited states

    NASA Astrophysics Data System (ADS)

    Zhang, J.; Chiang, W. Y.; Sagear, P.; Laane, J.

    1992-08-01

    The jet-cooled fluorescence excitation spectra of the n→π* transitions of cyclopentanone, 3-cyclopenten-1-one, and cyclobutanone have been analyzed to determine the vibrational energy spacings in the S 1(n, π*) electronic excited states for the out-of-plane carbonyl wagging motions. A double-minimum potential energy function was determined for each and the barriers were found to be 680, 926, and 1940 cm -1, respectively. The carbonyl wagging angles were determined to be 22°, 26°, and 41°, respectively.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

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

    NASA Astrophysics Data System (ADS)

    Süle, P.; Heinig, K.-H.

    2009-11-01

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

  20. Micro structure processing on plastics by accelerated hydrogen molecular ions

    NASA Astrophysics Data System (ADS)

    Hayashi, H.; Hayakawa, S.; Nishikawa, H.

    2017-08-01

    A proton has 1836 times the mass of an electron and is the lightest nucleus to be used for accelerator in material modification. We can setup accelerator with the lowest acceleration voltage. It is preferable characteristics of Proton Beam Writer (PBW) for industrial applications. On the contrary ;proton; has the lowest charge among all nuclei and the potential impact to material is lowest. The object of this research is to improve productivity of the PBW for industry application focusing on hydrogen molecular ions. These ions are generated in the same ion source by ionizing hydrogen molecule. There is no specific ion source requested and it is suitable for industrial use. We demonstrated three dimensional (3D) multilevel micro structures on polyester base FPC (Flexible Printed Circuits) using proton, H2+ and H3+. The reactivity of hydrogen molecular ions is much higher than that of proton and coincident with the level of expectation. We can apply this result to make micro devices of 3D multilevel structures on FPC.

  1. 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

  2. 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

  3. 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

  4. 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.

  5. Molecular dynamics simulation of ion flows around microparticles

    NASA Astrophysics Data System (ADS)

    Piel, Alexander

    2017-03-01

    The interaction of an ion flow with charged microparticles is studied by simulations with the molecular asymmetric dynamics (MAD) code. This code treats positive ions as "Yukawa particles" that are shielded by thermal electrons while the microparticle is assumed unshielded. The code is described and critically compared with results from published particle-in-cell simulations of other authors. As an application, the MAD code is used for a systematic study of the repulsive and ion-wake induced attractive forces in a particle pair. It is shown that the combined wake charges of a vertically, flow-aligned particle pair do not lead to a net attractive force. When the lower particle is shifted sidewards, a horizontal restoring force is found, which gives harmonic confinement for small displacements and a decreasing attraction force for a large distance.

  6. 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

  7. On the amount of heavy molecular ions in Titan's ionosphere

    NASA Astrophysics Data System (ADS)

    Wahlund, J.-E.; Galand, M.; Müller-Wodarg, I.; Cui, J.; Yelle, R. V.; Crary, F. J.; Mandt, K.; Magee, B.; Waite, J. H.; Young, D. T.; Coates, A. J.; Garnier, P.; Ågren, K.; André, M.; Eriksson, A. I.; Cravens, T. E.; Vuitton, V.; Gurnett, D. A.; Kurth, W. S.

    2009-12-01

    We present observational evidence that the ionosphere of Titan below an altitude of 1150 km is a significant source of heavy (>100 amu) molecular organic species. This study is based on measurements by five instruments (RPWS/LP, RPWS/E, INMS, CAPS/ELS, CAPS/IBS) onboard the Cassini spacecraft during three flybys (T17, T18, T32) of Titan. The ionospheric peaks encountered at altitudes of 950-1300 km had densities in the range 900-3000 cm -3. Below these peaks the number densities of heavy positively charged ions reached 100-2000 cm -3 and approached 50-70% of the total ionospheric density with an increasing trend toward lowest measured altitudes. Simultaneously measured negatively charged ion densities were in the range 50-150 cm -3. These results imply that ~10 5-10 6 heavy positively charged ions/m 3/s are continuously recombining into heavy neutrals and supply the atmosphere of Titan. The ionosphere may in this way produce 0.1-1 Mt/yr of heavy organic compounds and is therefore a sizable source for aerosol formation. We also predict that Titan's ionosphere is dominated by heavy (>100 amu) molecular ions below 950 km.

  8. 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.

  9. 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.

  10. 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.

  11. Saturated absorption and crossover resonances in a high-finesse cavity: Formalism and application to the hyperfine structure of jet-cooled NO2 by saturated-absorption cavity-ring-down spectroscopy

    NASA Astrophysics Data System (ADS)

    Dupré, Patrick

    2012-04-01

    The qR0(0) rotational transition in the Ã2B2←X˜2A1 system of jet-cooled NO2 located around 12536cm-1 is analyzed using a nonlinear-susceptibility formalism designed to describe the saturated absorption due to two identical counter-propagating radiations in an n-level system. An analytical solution of the equations of motion is obtained in the frequency space by considering the pertinent experimental conditions, mainly a high-finesse cavity and a slit-shaped supersonic expansion. Calculation of the nonlinear absorption coefficient requires the summing of all Zeeman-component contributions and a final numerical integration over the frequency detuning assuming a Maxwell-Boltzmann speed distribution. Determination of the experimental absorption coefficients is obtained by converting the shape of the temporal decay of the electromagnetic field amplitude initially captured inside the cavity. The molecular Hamiltonian includes both spin-rotation and hyperfine interactions. Molecular constants relative to the upper level are derived by exploiting Doppler-broadening-free so-called saturated-absorption cavity-ring-down spectroscopy. The dipole moment of the partially assigned hot band is obtained [μband=0.0047(12) D] together with the number density and the effective population relaxation rates. The model is validated by varying the intracavity power from 0 to 230 W (i.e., up to a maximum peak irradiance of 240×103W/cm2), representing saturation coefficients up to 120. The experimental position, shape, and width of the Lamb and crossover dips are well reproduced. The spatial shape and modulation of the electromagnetic field are discussed.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. Small Ion Channel Linking Molecular Simulations and Electrophysiology

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrzej

    2017-01-01

    Ion channels are pore-forming protein assemblies that mediate the transport of small ions across cell membranes. Otherwise, membrane bilayers would be almost impermeable to ions incapable to traverse the low dielectric constant, hydrophobic membrane core. Ion channels are ubiquitous to all life forms. In humans and other higher organisms they play the central role in conducting nerve impulses, cardiac functions, muscle contraction and apoptosis. On the other extreme of biological complexity, viral ion channels (viroporins) influence many stages of the virus infection cycle either through regulating virus replication, such as entry, assembly and release or modulating the electrochemical balance in the subcellular compartments of host cells. Ion channels were crucial components of protocells. Their emergence facilitated adaptation of nascent life to different environmental conditions. The earliest ion channels must have been much simpler than most of their modern ancestors. Viral channels are among only a few naturally occurring models to study the structure, function and evolution of primordial channels. Experimental studies of these properties are difficult and often unreliable. In principle, computational methods, and molecular dynamics (MD) simulations in particular, can aid in providing information about both the structure and the function of ion channels. However, MD suffers from its own problems, such as inability to access sufficiently long time scales or limited accuracy of force fields. It is, therefore, essential to determine the reliability of MD simulations. We propose to do so on the basis of two criteria. One is channel stability on time scales that extend for several microseconds or longer. The other is the ability to reproduce the measured ionic conductance as a function of applied voltage. If both the stability and the calculated ionic conductance are satisfactory it will greatly increase our confidence that the structure and the function of a

  20. Low molecular weight fluorescent organogel for fluoride ion detection.

    PubMed

    Rajamalli, P; Prasad, Edamana

    2011-07-15

    The design, synthesis, and the photophysical properties of a Low Molecular Weight Gel (LMWG) based on AB(3) and AB(2) type poly(aryl ether) dendrons with an anthracene chromophore attached through an acylhydrazone linkage are described. The gel is utilized for an efficient 'naked eye' detection of fluoride ions (as low as 0.1 equiv with respect to the gelator concentration), through a reversible gel-sol transition, which is associated with a color change from deep yellow to bright red. © 2011 American Chemical Society

  1. Rotational symmetry control of electronic relaxation in ultracold gaseous molecules: Optical-optical double resonance probe of the forbidden T{sub 1}{yields}S{sub 0} intersystem crossing in jet-cooled thiophosgene, Cl{sub 2}CS

    SciTech Connect

    Moule, David C.; Judge, Richard H.; Liu, Haisheng; Lim, Edward C.

    2000-09-08

    Two-color optical-optical double resonance studies of the T{sub 1}{yields}S{sub 0} intersystem crossing in jet-cooled thiophosgene indicate that rotational symmetry strongly influences the efficiency of an intersystem crossing in symmetric molecules with low degrees of rotational excitation. (c) 2000 American Institute of Physics.

  2. 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.

  3. He2+ molecular ion and the He- atomic ion in strong magnetic fields

    NASA Astrophysics Data System (ADS)

    Vieyra, J. C. Lopez; Turbiner, A. V.

    2017-08-01

    We study the question of existence, i.e., stability with respect to dissociation of the spin-quartet permutation- and reflection-symmetric 4(-3) +g (Sz=-3 /2 ,M =-3 ) state of the (α α e e e ) Coulomb system: the He2 + molecular ion, placed in a magnetic field 0 ≤B ≤10 000 a.u. We assume that the α particles are infinitely massive (Born-Oppenheimer approximation of zero order) and adopt the parallel configuration, when the molecular axis and the magnetic field direction coincide, as the optimal configuration. The study of the stability is performed variationally with a physically adequate trial function. To achieve this goal, we explore several helium-containing compounds in strong magnetic fields, in particular; we study the spin-quartet ground state of the He- ion and the ground (spin-triplet) state of the helium atom, both for a magnetic field in 100 ≤B ≤10 000 a.u. The main result is that the He2 + molecular ion in the state 4(-3) +g is stable towards all possible decay modes for magnetic fields B ≳120 a .u . and with the magnetic field increase the ion becomes more tightly bound and compact with a cigar-type form of electronic cloud. At B =1000 a .u . , the dissociation energy of He2 + into He-+α is ˜702 eV and the dissociation energy for the decay channel to He +α +e is ˜729 eV , and both energies are in the energy window for one of the observed absorption features of the isolated neutron star 1E1207.4-5209.

  4. Molecular Storage of Mg Ions with Vanadium Oxide Nanoclusters

    SciTech Connect

    Cheng, Yingwen; Shao, Yuyan; Raju, Vadivukarasi; Ji, Xiulei; Mehdi, B. Layla; Han, Kee Sung; Engelhard, Mark H.; Li, Guosheng; Browning, Nigel D.; Mueller, Karl T.; Liu, Jun

    2016-04-13

    Mg batteries have potential advantages in terms of safety, cost and reliability over existing battery chemistries, but their practical implementation is hindered substantially by the lack of amenable high voltage cathode materials. The development of cathode materials is complicated by a limited understanding of the unique divalent Mg ion electrochemistry. Here we show that highly dispersed vanadium oxide nanoclusters supported on porous carbon frameworks were able to react with Mg ions reversibly in electrolytes that are compatible with Mg metal, and exhibited high capacities and good reaction kinetics. Electrodes with the composite materials were able to deliver initial capacities exceeding 300 mAh/g at 40 mA/g in the voltage window of 0.5 to 2.8V. The combined electron microscope, spectroscopy and electrochemistry characterizations suggest the reaction is surface-controlled and may be best described as through a molecular reaction mechanism. This work could provide a new approach of using nanoclusters and the molecular energy storage mechanism to design electrode materials for Mg batteries.

  5. 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.

  6. 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.

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

    NASA Astrophysics Data System (ADS)

    Porambo, Michael W.

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

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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

  15. 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+.

  16. 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.

  17. 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.

  18. 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.

  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. 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.

  1. 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.

  2. 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

  3. 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

  4. Estimating electron affinity from the lifetime of negative molecular ions: Cycloheptatriene derivatives

    NASA Astrophysics Data System (ADS)

    Asfandiarov, N. L.; Pshenichnyuk, S. A.; Vorob'ev, A. S.; Nafikova, E. P.; Mavrodiev, V. K.; Furlei, I. I.; Dokichev, V. A.; Platonov, D. N.; Belyy, A. Yu.

    2017-05-01

    Cycloheptatriene derivatives are studied by means of resonance electron capture negative ion mass spectrometry (REC NIMS). The average lifetimes of molecular negative ions (NIs) are measured with respect to electron autodetachment. Using the Arrhenius approach, electron affinity EAa of the molecules under study is estimated, and the effective temperature of the resulting negative molecular ions is determined as a function of the electron energy. It is assumed that the dissociation of negative molecular ions in the ground electronic state is a process similar to that of the thermal degradation of molecules.

  5. 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.

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

    NASA Astrophysics Data System (ADS)

    Mouton, Thomas; Mercier, Xavier; Desgroux, Pascale

    2016-05-01

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

  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. The binding of metal ions to molecularly-imprinted polymers.

    PubMed

    Perera, Rukshan; Ashraf, Syed; Mueller, Anja

    2017-04-01

    Imprinting polymerization is a flexible method to make resins specific for different compounds. Imprinting polymerization involves the polymerization of the resin in the presence of a template, here cadmium ions or arsenate. The template is then removed by washing, leaving specific binding sites in the resin. In water treatment, the removal of toxic metal ions is difficult due to the limited affinity of these ions to ion exchange resins. Imprinting polymerization of ion-exchange resins is used to develop resins with high capacity and some selectivity for cadmium ions or arsenate for water treatment that still function as general ion-exchange resins. A minimum binding capacity of 325 meq/g was achieved for cadmium ions. Competition experiments elucidate the type of bonds present in the imprinting complex. The capacity and bond types for the cadmium ions and arsenate were contrasted. In the case of cadmium, metal-ligand bonds provide significant specificity of binding, although significant binding also occurs to non-specific surface sites. Arsenate ions are larger than cadmium ions and can only bind via ionic and hydrogen bonds, which are weaker than metal-ligand bonds. This results in lower specificity for arsenate. Additionally, diffusion into the resin is a limiting factor due to the larger size of the arsenate ion. These data elucidate the bonds formed between metal ions and the imprinting sites as well as other parameters that increase the capacity for heavy metals and arsenate.

  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. Molecular dynamics simulation of fluorine cluster ion impact

    NASA Astrophysics Data System (ADS)

    Aoki, Takaaki; Matsuo, Jiro; Yamada, Isao

    2000-04-01

    Molecular dynamics (MD) simulations of fluorine atoms, molecules and clusters impacting a silicon substrate were performed in order to investigate the impact process of a reactive cluster ion. This result shows that when the incident energy of the impacting fluorine atom or molecule is less than 10 eV/atom, the species are only adsorbed on the surface and sputtering of substrate atoms does not occur. On the other hand, a fluorine cluster consisting of 30 molecules produces sputtering even at a low incident energy of 1 eV/atom. At these conditions, the surface atoms are desorbed as fluorine-containing species, such as SiF or SiF 2, indicating that chemical desorption is enhanced by irradiation with fluorine clusters. As the incident energy of the cluster increases to values as high as 100 eV/atom, almost all the fluorine atoms penetrate the surface and a crater-shaped damage is formed. The incident F atoms reside at the bottom region of the crater. In this case, silicon atoms leave the surface as monomers, dimers or clusters without F atoms, i.e., in this regime physical sputtering through atomic collisions has a higher probability than chemical reactions, like in the case of Ne or Ar cluster impact.

  11. 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. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. 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.

  13. Laser-induced fluorescence spectroscopy of jet-cooled TiC: Observation of low-lying 1Σ+ states

    NASA Astrophysics Data System (ADS)

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

    2017-07-01

    The TiC has been investigated using laser-induced fluorescence spectroscopy. The a1Σ+, b1Σ+, and c1Σ+ states are found to lie respectively at T0 = 319.3, 786.0, and 1407.2 cm-1 and have internuclear distances respectively of r0 = 1.6607, 1.6906, and 1.6927 Å. Similar r0 values of the b1Σ+ and c1Σ+ states with that of the X3Σ+ state (1.6953 Å) indicate that either of these states could be isocofigurational to the ground state. Dispersed fluorescence suggests reassignment of the 3Π1 state to a mixed state with dominant 1Π character. Higher spectral resolution of the 1Π-X3Σ+ band provided improved molecular constants.

  14. 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

  15. Molecular simulations of ultra-low-energy nitrogen ion bombardment of A-DNA in vacuum.

    PubMed

    Ngaojampa, Chanisorn; Nimmanpipug, Piyarat; Yu, Liangdeng; Anuntalabhochai, Somboon; Lee, Vannajan Sanghiran

    2010-02-26

    For investigating mechanisms involved in low-energy ion beam induced mutation, besides experiments using low-energy and low-fluence ions to bombard naked DNA, molecular simulations were carried out as an effort towards the insight in molecular interactions between ions and DNA. In the current study, Monte Carlo (MC) and molecular dynamics (MD) simulations were applied. The results of MC simulations provide some clues about the interaction energies and sites of preference of N-ion bombardment on an A-DNA short duplex strand. MD simulations of a single N-ion moving towards the same DNA strand with different linear velocities corresponding to bombardment energies of 0.1, 1, 10 and 100 eV revealed information about changes in bond lengths and visibly distorted structures of bombarded nucleotides. The simulations demonstrated that ion-bombardment-induced DNA change in structure was not a random but preferential effect. Copyright 2009 Elsevier Inc. All rights reserved.

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  17. 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.

  18. 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.

  19. How enhanced molecular ions in Cold EI improve compound identification by the NIST library.

    PubMed

    Alon, Tal; Amirav, Aviv

    2015-12-15

    Library-based compound identification with electron ionization (EI) mass spectrometry (MS) is a well-established identification method which provides the names and structures of sample compounds up to the isomer level. The library (such as NIST) search algorithm compares different EI mass spectra in the library's database with the measured EI mass spectrum, assigning each of them a similarity score called 'Match' and an overall identification probability. Cold EI, electron ionization of vibrationally cold molecules in supersonic molecular beams, provides mass spectra with all the standard EI fragment ions combined with enhanced Molecular Ions and high-mass fragments. As a result, Cold EI mass spectra differ from those provided by standard EI and tend to yield lower matching scores. However, in most cases, library identification actually improves with Cold EI, as library identification probabilities for the correct library mass spectra increase, despite the lower matching factors. This research examined the way that enhanced molecular ion abundances affect library identification probability and the way that Cold EI mass spectra, which include enhanced molecular ions and high-mass fragment ions, typically improve library identification results. It involved several computer simulations, which incrementally modified the relative abundances of the various ions and analyzed the resulting mass spectra. The simulation results support previous measurements, showing that while enhanced molecular ion and high-mass fragment ions lower the matching factor of the correct library compound, the matching factors of the incorrect library candidates are lowered even more, resulting in a rise in the identification probability for the correct compound. This behavior which was previously observed by analyzing Cold EI mass spectra can be explained by the fact that high-mass ions, and especially the molecular ion, characterize a compound more than low-mass ions and therefore carries more

  20. Molecular design of the microbial cell surface toward the recovery of metal ions.

    PubMed

    Kuroda, Kouichi; Ueda, Mitsuyoshi

    2011-06-01

    The genetic engineering of microorganisms to adsorb metal ions is an attractive method to facilitate the environmental cleanup of metal pollution and to enrich the recovery of metal ions such as rare metal ions. For the recovery of metal ions by microorganisms, cell surface design is an effective strategy for the molecular breeding of bioadsorbents as an alternative to intracellular accumulation. The cell surface display of known metal-binding proteins/peptides and the molecular design of novel metal-binding proteins/peptides have been performed using a cell surface engineering approach. The adsorption of specific metal ions is the important challenge for the practical recovery of metal ions. In this paper, we discuss the recent progress in surface-engineered bioadsorbents for the recovery of metal ions. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

    PubMed

    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/.

  2. 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

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

    PubMed

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

    2012-09-13

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

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

    NASA Technical Reports Server (NTRS)

    Wilson, Michael A.; Pohorille, Andrew

    1991-01-01

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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

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

    PubMed

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

    2006-08-07

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

  11. High-resolution infrared studies in slit supersonic discharges: CH2 stretch excitation of jet-cooled CH2Cl radical.

    PubMed

    Whitney, Erin S; Haeber, Thomas; Schuder, Michael D; Blair, Andrew C; Nesbitt, David J

    2006-08-07

    First high-resolution infrared spectra are presented for jet-cooled CH2 35Cl and CH2 37Cl radicals in the symmetric (nu1) CH2 stretching mode. A detailed spectral assignment yields refined lower and upper state rotational constants, as well as fine structure spin-rotation parameters from least-squares fits to the sub-Doppler line shapes for individual transitions. The rotational constants are consistent with a nearly planar structure, but do not exclude substantial large amplitude bending motion over a small barrier to planarity accessible with zero-point excitation. High level coupled cluster (singles/doubles/triples) calculations, extrapolated to the complete basis set limit, predict a slightly nonplanar equilibrium structure (theta approximately 11 degrees), with a vibrationally adiabatic treatment of the bend coordinate yielding a v = 1<--0 anharmonic frequency (393 cm(-1)) in excellent agreement with matrix studies (nu(bend) approximately 400 cm(-1)). The antisymmetric CH2 stretch vibration is not observed despite high sensitivity detection (signal to noise ratio >20:1) in the symmetric stretch band. This is consistent with density functional theory intensity calculations indicating a >35-fold smaller antisymmetric stretch transition moment for CH2Cl, and yet contrasts dramatically with high-resolution infrared studies of CH2F radical, for which both symmetric and antisymmetric CH2 stretches are observed in a nearly 2:1 intensity ratio. A simple physical model is presented based on a competition between bond-dipole and "charge-sloshing" contributions to the transition moment, which nicely explains the trends in CH2X symmetric versus asymmetric stretch intensities as a function of electron withdrawing group (X = D,Br,Cl,F).

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

    NASA Astrophysics Data System (ADS)

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

    2010-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-08-01

    The combination of shot noise-limited direct absorption spectroscopy with long-path-length slit supersonic discharges has been used to obtain first high-resolution infrared spectra for jet-cooled CH2F radicals in the symmetric (ν1) and antisymmetric (ν5) CH2 stretching modes. Spectral assignment has yielded refined lower- and upper-state rotational constants and fine-structure parameters from least-squares fits to the sub-Doppler line shapes for individual transitions. The rotational constants provide indications of large amplitude vibrational averaging over a low-barrier double minimum inversion-bending potential. This behavior is confirmed by high-level coupled cluster singles/doubles/triples calculations extrapolated to the complete basis set limit and adiabatically corrected for zero point energy. The calculations predict a nonplanar equilibrium structure (θ ≈29°, where θ is defined to be 180° minus the angle between the C-F bond and the CH2 plane) with a 132cm-1 barrier to planarity and a vibrational bend frequency (νbend≈276cm-1), in good agreement with previous microwave estimates (νbend=300(30)cm-1) by Hirota and co-workers [Y. Endo et al., J. Chem. Phys. 79, 1605 (1983)]. The nearly 2:1 ratio of absorption intensities for the symmetric versus antisymmetric bands is in good agreement with density functional theory calculations, but in sixfold contrast with simple local mode CH2 bond dipole predictions of 1:3. This discrepancy arises from a surprisingly strong dependence of the symmetric stretch intensity on the inversion bend angle and provides further experimental support for a nonplanar equilibrium structure.

  14. 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.

  15. High resolution, jet-cooled infrared spectroscopy of (HCl)2: Analysis of ν1 and ν2 HCl stretching fundamentals, interconversion tunneling, and mode-specific predissociation lifetimes

    NASA Astrophysics Data System (ADS)

    Schuder, Michael D.; Lovejoy, Christopher M.; Lascola, Robert; Nesbitt, David J.

    1993-09-01

    An extensive series of near-infrared absorption spectra are recorded for jet-cooled (6-14 K) hydrogen chloride dimer (HCl)2. Both ΔKa=0 and ΔKa=±1 bands are observed for both the free (ν1) and bonded (ν2) HCl stretches; all three chlorine isotopomers (H 35Cl-H 35Cl, H 35Cl-H 37Cl, and H 37Cl-H 37Cl) are observed and analyzed for K`a ≤ 2. The slit jet spectrum extends significantly the previous cooled cell infrared study of this complex and provides a measure of tunneling splittings for Ka=0 and 1 for each of the HCl ground (v=0) and excited (v=1) states. Mode specific vibrational predissociation is observed via analysis of the absorption line shapes, with Lorentzian contributions to the line profiles of Δν1≲1.6 MHz and Δν2=5.1±1.2 (2σ) MHz full width at half-maximum for ν1 and ν2 excitation, respectively. Stronger coupling in (HCl)2 of the bonded (ν2) vs free (ν1) HCl vibration to the dissociation coordinate is consistent with the comparable trends observed in other hydrogen bonded dimers. Quantum mechanical variational calculations on an electrostatic angular potential energy surface are used to model the internal HCl rotor dynamics using a coupled rotor formalism; analysis of the internal rotor eigenfunctions provides direct evidence for large amplitude ``geared'' internal rotation of the HCl subunits.

  16. 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.

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

    PubMed

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

    2015-05-07

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

  18. Molecular Mechanism of Specific Ion Interactions Between Alkali Cations and Acetate Anion in Aqueous Solution: A Molecular Dynamics Study

    SciTech Connect

    Annapureddy, Harsha V.; Dang, Liem X.

    2012-06-28

    Specific ion interactions between the alkali cations (i.e., Li+, Na+ and K+) and an acetate anion in aqueous solution were studied using molecular dynamics simulation techniques and polarizable potential models. The ions-acetate systems were used as a model for understanding the interactions between ions and protein surfaces. We computed free energy profiles for different ion pairs using constrained mean force methods. Upon analyzing the computed free energy profiles for the Na+/K+-acetate ion-pairs, we observed a deeper contact ion minimum and also a larger association constant for the Na+-acetate pair compared to the corresponding K+-acetate pair. These observations help to demonstrate the preferential binding of Na+ over K+ to protein surfaces.

  19. Preparation and coherent manipulation of pure quantum states of a single molecular ion

    NASA Astrophysics Data System (ADS)

    Chou, Chin-Wen; Kurz, Christoph; Hume, David B.; Plessow, Philipp N.; Leibrandt, David R.; Leibfried, Dietrich

    2017-05-01

    Laser cooling and trapping of atoms and atomic ions has led to advances including the observation of exotic phases of matter, the development of precision sensors and state-of-the-art atomic clocks. The same level of control in molecules could also lead to important developments such as controlled chemical reactions and sensitive probes of fundamental theories, but the vibrational and rotational degrees of freedom in molecules pose a challenge for controlling their quantum mechanical states. Here we use quantum-logic spectroscopy, which maps quantum information between two ion species, to prepare and non-destructively detect quantum mechanical states in molecular ions. We develop a general technique for optical pumping and preparation of the molecule into a pure initial state. This enables us to observe high-resolution spectra in a single ion (CaH+) and coherent phenomena such as Rabi flopping and Ramsey fringes. The protocol requires a single, far-off-resonant laser that is not specific to the molecule, so many other molecular ions, including polyatomic species, could be treated using the same methods in the same apparatus by changing the molecular source. Combined with the long interrogation times afforded by ion traps, a broad range of molecular ions could be studied with unprecedented control and precision. Our technique thus represents a critical step towards applications such as precision molecular spectroscopy, stringent tests of fundamental physics, quantum computing and precision control of molecular dynamics.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Trapping molecular ions formed via photo-associative ionization of ultracold atoms.

    PubMed

    Sullivan, Scott T; Rellergert, Wade G; Kotochigova, Svetlana; Chen, Kuang; Schowalter, Steven J; Hudson, Eric R

    2011-11-14

    The formation of (40)Ca(2)(+) molecular ions is observed in a hybrid (40)Ca magneto-optical and ion trap system. The molecular ion formation process is determined to be photo-associative ionization of ultracold (40)Ca atoms. A lower bound for the two-body rate constant is found to be beta ≥ 2 ± 1 × 10(-15) cm(3) Hz. Ab initio molecular potential curves are calculated for the neutral Ca(2) and ionic Ca(2)(+) molecules and used in a model that identifies the photo-associative ionization pathway. As this technique does not require a separate photo-association laser, it could find use as a simple, robust method for producing ultracold molecular ions.

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

    PubMed

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

    2014-04-03

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

  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. 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.

  10. 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.

  11. 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.

  12. 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.

  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. 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.

  16. 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.

  17. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2002-05-01

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

  20. 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.

  1. 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.

  2. 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.

  3. 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

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

    SciTech Connect

    Gemmell, D.S.

    1987-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Gemmell, D. S.

    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, was termed a Coulomb explosion.

  6. Reduced fragmentation in liquid injection field desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry by use of helium for the thermalization of molecular ions.

    PubMed

    Bernhard Linden, H; Gross, Jürgen H

    2012-02-15

    To exploit the softness of liquid injection field desorption/ionization (LIFDI), the molecular ions, M(+•), need to be transferred from their origin at the field emitter through the mass analyzer without disrupting their integrity. To preserve the molecular ions, ion-activating events like collisions must therefore be avoided. In hybrid quadrupole Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers, however, multiple ion-guiding and ion-trapping events occur prior to mass analysis. The effects thereof compromised initial spectra from a LIFDI and electrospray ionization (ESI) combination (LIFDI-ESI) ion source and, thus, called for refined experimental conditions. A hybrid quadrupole FT-ICR instrument equipped with a new LIFDI-ESI combination ion source was used to obtain LIFDI spectra of polystyrene 1050, of 2,3,4-tridodecyloxybenzaldehyde, and of sewing machine oil as well as a field ionization (FI) spectrum of pentafluoroiodobenzene. The abundance of molecular ions, M(+•), was optimized, in particular by variation of the trapping conditions inside the instrument's accumulation RF-hexapole ion trap. Ion-buffer gas collisions in the instrument's accumulation RF-hexapole ion trap were detrimental to the easy-to-fragment molecular ions of hydrocarbon species, whereas more robust even-electron ions were not affected. Exchanging the instrument's standard supply of argon buffer gas for helium resulted in a remarkable improvement. Together with further adjustments of potentials applied along the ion transfer path, hydrocarbon species could be analyzed. The use of helium buffer gas remarkably improved LIFDI spectra, because the loss of molecular ions by dissociation during transfer from the LIFDI source into the ICR cell was significantly reduced. Hydrocarbon species could be analyzed while fragmentation of ions was avoided for the most part. Copyright © 2012 John Wiley & Sons, Ltd.

  7. Electronic spectra of jet-cooled calix[4]arene and its van der Waals clusters: encapsulation of a neutral atom in a molecular bowl.

    PubMed

    Ebata, Takayuki; Hodono, Yuki; Ito, Takafumi; Inokuchi, Yoshiya

    2007-04-14

    The encapsulation of neutral guest has been studied for calix[4]arene (C4A) by forming van der Waals clusters with Ar and Ne in supersonic jets. The electronic transitions of these clusters suggest that the first Ar (Ne) is encapsulated inside the C4A cavity, while the next atoms are bound outside.

  8. Molecular depth-profiling of polycarbonate with low-energy Cs+ ions.

    PubMed

    Mine, Nicolas; Douhard, Bastien; Brison, Jeremy; Houssiau, Laurent

    2007-01-01

    In this work, we explored the possibility of performing molecular depth-profiling by using very low-energy (about 200 eV) monoatomic Cs(+) ions. We show, for the first time, that this simple approach is successful on polymer layers of polycarbonate (PC). Under 200 eV Cs(+) irradiation of PC, a fast decrease of all characteristic negatively charged molecular ion signals is first observed but, rather surprisingly, these signals reach a minimum before rising again. A steady state is reached at which time most specific PC fragments are detected, some with even higher signal intensity (e.g. C(6)H(5)O(-)) than before irradiation. It is believed that the implanted Cs plays a major role in enhancing the negative ionisation of molecular fragments, leading to their easy detection for all the profile, although some material degradation obviously occurs. In the positive ion mode, all molecular fragments of the polymer disappear very rapidly, but clusters combining two Cs atoms and one molecular fragment (e.g. Cs(2)C(6)H(5)O(+)) are detected during the profile, proving that some molecular identification remains possible. In conclusion, this work presents a simple approach to molecular depth-profiling, complementary to cluster ion beam sputtering. Copyright (c) 2007 John Wiley & Sons, Ltd.

  9. Charge-state shifting of individual multiply-charged ions of bovine albumin dimer and molecular weight determination using an individual-ion approach

    SciTech Connect

    Cheng, X.; Bakhtiar, R.; Van Orden, S.; Smith, R.D. )

    1994-07-01

    Ion-molecule reactions of individual multiply-protonated ions of bovine albumin dimer, formed from electrospray ionization, have been studied using a Fourier transform ion cyclotron resonance mass spectrometer. Upon reaction of ammonia with a group of individual ions, charge-state shifting was observed due to proton transfer. Repeated additions of ammonia during remeasurements of the same ion population were observed to induce multiple-step charge-state shifts. Charge-state-dependent reactivity, as well as nonstatistical behavior in reactivity, was observed due to the small ion population. The molecular weights of individual ions whose charge state shifted during reaction were determined with an accuracy of 67 ppm, the first example of using an individual-ion approach to the determination of molecular weight for a large biopolymer. The molecular weight distribution of a group of ions can be determined with a precision related to the number of ions examined and the weight heterogeneity of the sample. We obtained the molecular weight for eight individual ions from which a molecular weight of 133 320 [+-] 210 Da was calculated for bovine albumin dimer. 17 refs., 3 figs., 1 tab.

  10. 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.

  11. 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.

  12. 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.

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

    EPA Science Inventory

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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

  20. 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.

  1. 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.

  2. Photodetachment cross section of a negative molecular ion near a nanospherical surface

    NASA Astrophysics Data System (ADS)

    Haroon, Uzma; Haneef, Muhammad; Bakhtawar; Khan, Humayun; Amin, Bin; Ullah Jan, Saeed

    2017-09-01

    The photodetachment of a diatomic negative molecular ion (H{\\hspace{0pt}}2- ) near a nanospherical surface is investigated. Analytical results for the flux of detached electron waves and photodetachment cross section are derived. It is demonstrated that the flux of the detached electron waves and photodetachment cross section of H{\\hspace{0pt}}2- near a nanospherical surface are directly related to the radius of curvature, inter-ion-surface distance, and bond length or separation of the atomic centers. These parameters strongly influence the oscillating structure of the detached electron spectra of the molecular ions. Fine control over these parameters can be used to determine structural information of negative ions, curvature and roughness in the surface at the nanoscale, and dissociation of molecules near surfaces and fields.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

    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.

  13. Properties of the Excited States of Molecular Ions.

    DTIC Science & Technology

    1981-04-13

    parent ion beam energy is typicalty 3000 A / eV, and W, for the work reported here, is on the range 0-100 meV. Thus the maximum angle in the center-of...niicant. j. Sec. 7, U. S. Goves nent Printing Office, Washington, D. C. (1976). Measurement of the kinetic energy of photofragrnents toP. Brix and G...entirely different manner by Tadjed- value for DO(O2, X) compares with the determination of dineM led her to the value Brix and Herzberg34 of 41260± 15 cm

  14. 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.

  15. Controlling surfaces in plasma processing: role of ions via molecular dynamics simulations of surface chemistry

    NASA Astrophysics Data System (ADS)

    Humbird, David; Graves, David B.

    2002-08-01

    A study of the interactions of energetic ions with various surfaces using molecular dynamics simulations is reported. Silicon atoms in the amorphous region are readily mixed by argon ions. Limited mixing in the crystalline layer is observed. Fluorine adsorbed on the silicon surface does not mix into the layer with argon ion impact. When an energetic F+ impacts a silicon surface, the uptake and apparent sub-surface mixing of F is much greater than Ar+-induced mixing. However, a closer examination shows that the F impacts have primarily increased the Si surface area by creating crevices and cracks, and that the F remains mainly on the surface of this layer.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Molecular dynamics and dynamic Monte-Carlo simulation of irradiation damage with focused ion beams

    NASA Astrophysics Data System (ADS)

    Ohya, Kaoru

    2017-03-01

    The focused ion beam (FIB) has become an important tool for micro- and nanostructuring of samples such as milling, deposition and imaging. However, this leads to damage of the surface on the nanometer scale from implanted projectile ions and recoiled material atoms. It is therefore important to investigate each kind of damage quantitatively. We present a dynamic Monte-Carlo (MC) simulation code to simulate the morphological and compositional changes of a multilayered sample under ion irradiation and a molecular dynamics (MD) simulation code to simulate dose-dependent changes in the backscattering-ion (BSI)/secondary-electron (SE) yields of a crystalline sample. Recent progress in the codes for research to simulate the surface morphology and Mo/Si layers intermixing in an EUV lithography mask irradiated with FIBs, and the crystalline orientation effect on BSI and SE yields relating to the channeling contrast in scanning ion microscopes, is also presented.

  1. Affinity of molecular ions for DNA structures is determined by solvent-accessible surface area.

    PubMed

    Nakano, Miki; Tateishi-Karimata, Hisae; Tanaka, Shigenori; Sugimoto, Naoki

    2014-08-14

    It is considered that Hoogsteen base pairs and DNA triplex structures play important roles in cellular processes even though these structures are less than duplexes of Watson-Crick base pairs. Molecular ions clearly affect the stability of DNA structures in vivo; however, the mechanisms are unknown. Here, we investigated the effects of sodium ions, choline ions, and tetramethylammonium ions on DNA triplexes using molecular dynamics simulations. We found that nonpolar interactions, which are associated with van der Waals interactions, and solvent-accessible surface area were more important than polar or electrostatic interactions in determining the affinity of a molecular cation for the DNA groove areas. The free energy gain due to a cation that fit optimally within a DNA groove was larger than the free energy loss due to the effect of dehydration. Cations with shapes complementary to that of a particular DNA groove configuration stabilized triplex formation, but cations that disturbed hydrogen bonds between DNA bases were destabilizing. These stabilizing and destabilizing mechanisms of molecular cations were also applicable to a DNA duplex composed of Watson-Crick base pairs. The molecular-level view of cation interactions with DNA structures will guide the design of DNA devices, DNA-based drugs, and genetic therapies.

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

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

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

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Nonlinear optical molecular switches for alkali ion identification.

    PubMed

    Plaquet, Aurélie; Champagne, Benoît; Castet, Frédéric

    2014-07-21

    This work demonstrates by means of DFT and ab initio calculations that recognition of alkali cations can be achieved by probing the variations of the second-order nonlinear optical properties along the commutation process in spiropyran/merocyanine systems. Due to the ability of the merocyanine isomer to complex metal cations, the switching between the two forms is accompanied by large contrasts in the quadratic hyperpolarizability that strongly depend on the size of the cation in presence. Exploiting the nonlinear optical responses of molecular switches should therefore provide powerful analytical tools for detecting and identifying metal cations in solution.

  11. Lithium Ion Solvation and Diffusion in Bulk Organic Battery Electrolytes from First Principles Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Ong, Mitchell; Lordi, Vincenzo; Draeger, Erik; Pask, John

    2014-03-01

    Lithium-ion batteries are commonly used to power many consumer devices. One of the key properties that influence the performance of lithium-ion batteries is the ionic conductivity of the electrolyte. This is dependent on the speed at which Li ions diffuse across the cell and related to the solvation structure of the Li ions. The choice of the electrolyte can greatly impact both solvation and diffusivity of Li ions. In this work, we use first principles molecular dynamics to examine the solvation and diffusion of Li ions in several bulk organic electrolytes. We find that differences in the local environment throughout the liquid can lead to solvation of Li ions by either carbonyl or ether oxygen atoms. In addition, we examine the differences in solvation of associated and dissociated Li(PF6) salts, showing that the bulky PF6 group blocks complete solvation of Li+ by solvent oxygen atoms. Finally, we calculate Li diffusion coefficients in each electrolyte, finding slightly larger diffusivities in a linear carbonate such as ethyl methyl carbonate (EMC) compared to a cyclic carbonate like ethylene carbonate (EC). Results from this work can be used to design new bulk electrolytes that will improve the performance of current Li-ion batteries.

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

    NASA Astrophysics Data System (ADS)

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

    2009-06-01

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

  13. 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.

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

    SciTech Connect

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

    1983-10-01

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

  15. 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.

  16. 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

  17. Analysis of Molecular Clusters in Simulations of Lithium-Ion Battery Electrolytes

    SciTech Connect

    Tenney, Craig M.; Cygan, Randall T.

    2013-11-27

    Graph theoretic tools were used to identify and classify clusters of ions and solvent molecules in molecular dynamics simulations of lithium-ion battery electrolytes. Electrolytes composed of various concentrations of LiPF6 dissolved in ethylene carbonate (EC), dimethylene carbonate (DMC), or a 1:1 EC/DMC mixture were simulated at multiple temperatures using classical molecular dynamics. Contrary to Nernst–Einstein theory but consistent with experiment, pure DMC systems had the greatest diffusivity but the lowest conductivity. This disagreement with Nernst–Einstein theory is explained by the observed clustering behavior, which found that systems with pure EC as a solvent formed ion clusters with nonzero charge, whereas systems with pure DMC as a solvent formed primarily neutral clusters.

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

    PubMed

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

    2015-04-01

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

  20. 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

  1. Next Generation Molecular Histology Using Highly Multiplexed Ion Beam Imaging (MIBI) of Breast Cancer Tissue Specimens for Enhanced Clinical Guidance

    DTIC Science & Technology

    2016-07-01

    AWARD NUMBER: W81XWH- 14-1-0192 TITLE: Next-Generation Molecular Histology Using Highly Multiplexed Ion Beam Imaging (MIBI) of Breast Cancer ...DATES COVERED 4. TITLE AND SUBTITLE Next-Generation Molecular Histology Using Highly Multiplexed Ion Beam Imaging (MIBI) of Breast Cancer Tissue

  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. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. Dansyl-naphthalimide dyads as molecular probes: effect of spacer group on metal ion binding properties.

    PubMed

    Shankar, Balaraman H; Ramaiah, Danaboyina

    2011-11-17

    Interaction of a few dansyl-naphthalimide conjugates 1a-e linked through polymethylene spacer groups with various metal ions was investigated through absorption, fluorescence, NMR, isothermal calorimetric (ITC), and laser flash photolysis techniques. The characteristic feature of these dyads is that they exhibit competing singlet-singlet energy transfer (SSET) and photoinduced electron transfer (PET) processes, both of which decrease with the increase in spacer length. Depending on the spacer group, these dyads interact selectively with divalent Cu(2+) and Zn(2+) ions, as compared to other mono- and divalent metal ions. Jobs plot analysis showed that these dyads form 2:3 complexes with Cu(2+) ions, while 1:1 complexes were observed with Zn(2+) ions. The association constants for the Zn(2+) and Cu(2+) complexes were determined and are found to be in the order 10(3)-10(5) M(-1). Irrespective of the length of the spacer group, these dyads interestingly act as fluorescence ratiometric molecular probes for Cu(2+) ions by altering the emission intensity of both dansyl and naphthalimide chromophores. In contrast, only the fluorescence intensity of the naphthalimide chromophore of the lower homologues (n = 1-3) was altered by Zn(2+) ions. (1)H NMR and ITC measurements confirmed the involvement of both sulfonamide and dimethylamine groups in the complexation with Cu(2+) ions, while only the latter group was involved with Zn(2+) ions. Laser excitation of the dyads 1a-e showed formation of a transient absorption which can be attributed to the radical cation of the naphthalimide chromophore, whereas only the triplet excited state of the dyads 1a-e was observed in the presence of Cu(2+) ions. Uniquely, the complexation of 1a-e with Cu(2+) ions affects both PET and SSET processes, while only the PET process was partially inhibited by Zn(2+) ions in the lower homologues (n = 1-3) and the higher homologues exhibited negligible changes in their emission properties. Our results

  10. 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

  11. 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

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

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

    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.

  13. 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.

  14. 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

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

    PubMed

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

    2015-05-01

    Ion mobility spectrometry experiments allow the mass spectrometrist to determine an ion's rotationally averaged collision cross section Ω(EXP). 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 Ω(CALC) 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 Ω(EXP) 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.

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

    PubMed

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

    2014-12-14

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

  17. First simultaneous detection of terrestrial ionospheric molecular ions in the Earth's inner magnetosphere and at the Moon

    NASA Astrophysics Data System (ADS)

    Dandouras, Iannis; Poppe, Andrew R.; Fillingim, Matt O.; Kistler, Lynn M.; Mouikis, Christopher G.; Rème, Henri

    2017-04-01

    Heavy molecular ions escaping from a planetary atmosphere can contribute to the long-term evolution of its composition. The ARTEMIS (Acceleration, Reconnection, Turbulence, and Electrodynamics of the Moon's Interaction with the Sun) spacecraft has recently observed outflowing molecular ions at lunar distances in the terrestrial magnetotail (Poppe et al., 2016). Backward particle tracing indicated that these ions should originate from the terrestrial inner magnetosphere. Here we have examined Cluster data acquired by the CIS-CODIF (Cluster Ion Spectrometry-Composition Distribution Function) ion mass spectrometer, obtained in the terrestrial magnetosphere. An event was selected where the orbital conditions were favourable and the Cluster spacecraft were in the high-latitude inner magnetosphere a few hours before the ARTEMIS molecular ion detection. Analysis shows that the CIS-CODIF instrument detected a series of energetic ion species, including not only O+ but also a group of molecular ions around 30 amu. Given the 5-7 m/Δm mass resolution of the instrument, these could include N2+, NO+, or O2+. These ions were detected by Cluster about 14 hours before the ARTEMIS observation in the lunar environment, a time which is compatible with the transfer to lunar distances. The event was during an active period followed by a northward rotation of the IMF. Although energetic heavy molecular ions have been detected in the storm time magnetosphere in the past (e.g. Klecker et al., 1986; Christon et al., 1994), this event constitutes the first coordinated observation in the Earth's inner magnetosphere and at the Moon. Additional events of coordinated outflowing molecular ion observations are currently under analysis. Future missions, as the proposed ESCAPE mission, should investigate in detail the mechanisms of molecular ion acceleration and escape, their link to the solar and magnetospheric activity, and their role in the magnetospheric dynamics and in the long-term evolution

  18. 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.

  19. 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.

  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. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

  3. 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.

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

    PubMed

    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.

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

    PubMed

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

    2016-08-26

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

  6. 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.

  7. 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.

  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. 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

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

    NASA Astrophysics Data System (ADS)

    Li, Xiong; Li, Hang; Yang, Gang

    2015-09-01

    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.

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

    PubMed

    Li, Xiong; Li, Hang; Yang, Gang

    2015-09-25

    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 Pb(2+) 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 Pb(2+) 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.

  12. 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.

  13. 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+.

  14. 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.

  15. Molecular dynamics simulation of ion bombardment on hydrogen terminated Si(001)2×1 surface

    NASA Astrophysics Data System (ADS)

    Satake, Koji; Graves, David B.

    2003-03-01

    Molecular dynamics simulations were performed to investigate H2+ and SiH3+ ion bombardment of hydrogen terminated Si(001)2×1 surfaces. Normal incidence ion bombardment effects on dangling bond generation, adatom diffusion, and nucleation were studied as a function of incident energy between 10 and 40 eV. The dangling bond generation rate due to H2+ impacts at 20 and 40 eV was about twice that of SiH3+. However these effects appeared to be insignificant compared to probable neutral radical effects under typical plasma-enhanced chemical vapor deposition conditions. The enhanced diffusion of Si adatoms due to ion bombardment was observed to be minor in comparison with thermal diffusion and the disruption of ledge sites due to SiH3+ ion bombardment is not significant, with ion incident energies up to 40 eV. Ion bombardment in the incident energy range between 10 and 20 eV can contribute the modification of surface kinetics without bulk damage.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. A differential ICT based molecular probe for multi-ions and multifunction logic circuits.

    PubMed

    Luxami, Vijay; Kumar, Subodh

    2012-04-21

    This paper presents anthraquinone and benzimidazole based hybrid molecular architect as the state of the art for multifunctional molecular logic circuits. The moleculator exhibits differential output behavior towards F(-), Zn(2+) and Cu(2+) ions to provide opportunities for elaboration of XOR, INHIBIT, XNOR, AND, OR, NOR, logic functions and their integrated logic functions half-adder, half-subtractor and comparator within a single molecule. These integral logic functions can be reprogrammed by self-annihilation or by another additional input in the same cell. This single molecule behaves uniquely where different logic functions can be operated and reset by using different inputs and outputs.

  1. 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.

  2. Copper ion implanted aluminum nitride dilute magnetic semiconductors (DMS) prepared by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Shah, A.; Ahmad, Jamil; Ahmad, Ishaq; Mehmood, Mazhar; Mahmood, Arshad; Rasheed, Muhammad Asim

    2014-10-01

    Diluted magnetic semiconductor (DMS) AlN:Cu films were fabricated by implanting Cu+ ions into AlN thin films at various ion fluxes. AlN films were deposited on c-plane sapphire by molecular beam epitaxy followed by Cu+ ion implantation. The structural and magnetic characterization of the samples was performed through Rutherford backscattering and channeling spectrometry (RBS/C), X-ray diffraction (XRD), Raman spectroscopy, vibrating sample magnetometer (VSM) and SQUID. Incorporation of copper into the AlN lattice was confirmed by RBS, while XRD revealed that no new phase was formed as a result of ion implantation. RBS also indicated formation of defects as a result of implantation process and the depth and degree of damage increased with an increase in ion fluence. Raman spectra showed only E2 (high) and A1 (LO) modes of wurtzite AlN crystal structure and confirmed that no secondary phases were formed. It was found that both Raman modes shift with Cu+ fluences, indicating that Cu ion may go to interstitial or substitutional sites resulting in distortion or damage of lattice. Although as implanted samples showed no magnetization, annealing of the samples resulted in appearance of room temperature ferromagnetism. The saturation magnetization increased with both the annealing temperature as well as with ion fluence. FC/ZFC measurements indicated that the ferromagnetic effect was not related with superparamagnetic phase formation. In spite, it was due to the formation of AlN based DMS material. The Curie temperature (TC) of the sample prepared at an ion fluence of 5 × 1015 cm-2 and an annealing temperature of 950 °C was found to lie above 340 K.

  3. Molecular Simulations of Disulfide-Rich Venom Peptides with Ion Channels and Membranes.

    PubMed

    Deplazes, Evelyne

    2017-02-27

    Disulfide-rich peptides isolated from the venom of arthropods and marine animals are a rich source of potent and selective modulators of ion channels. This makes these peptides valuable lead molecules for the development of new drugs to treat neurological disorders. Consequently, much effort goes into understanding their mechanism of action. This paper presents an overview of how molecular simulations have been used to study the interactions of disulfide-rich venom peptides with ion channels and membranes. The review is focused on the use of docking, molecular dynamics simulations, and free energy calculations to (i) predict the structure of peptide-channel complexes; (ii) calculate binding free energies including the effect of peptide modifications; and (iii) study the membrane-binding properties of disulfide-rich venom peptides. The review concludes with a summary and outlook.

  4. 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.

  5. 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.

  6. 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.

  7. Mixed quantum-classical molecular dynamics simulation of vibrational relaxation of ions in an electrostatic field.

    PubMed

    Koutselos, Andreas D

    2006-12-28

    The vibrational relaxation of ions in low-density gases under the action of an electrostatic field is reproduced through a molecular dynamics simulation method. The vibration is treated though quantum mechanics and the remaining degrees of freedom are considered classical. The procedure is tested through comparison against analytic results for a two-dimensional quantum model and by studying energy exchange during binary ion-atom collisions. Finally, the method has been applied successfully to the calculation of the mobility and the vibrational relaxation rate of O2+ in Kr as a function of the mean collision energy using a model interaction potential that reproduces the potential minimum of a previously known ab initio potential surface. The calculation of the steady mean vibrational motion of the ions in (flow) drift tubes seems straightforward, though at the expense of large amounts of computer time.

  8. 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 +}.

  9. 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.}

  10. 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.

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

    PubMed

    Erban, Radek

    2016-02-01

    Molecular dynamics (MD) simulations of ions (K(+), Na(+), Ca(2+) and Cl(-)) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.

  12. Toxic effects of zinc ions on kinesin - Potential molecular cause of impaired intracellular transport.

    PubMed

    Böhm, Konrad J

    2017-02-15

    In healthy organisms the metabolism of the trace element zinc is well balanced. If this balance becomes destroyed the free zinc level might increase and cause toxic effects. The present study demonstrates that under definite conditions zinc ions are able to inhibit the ATPase activity of neuron-specific KIF5A (kinesin-1). Correspondingly, the motility activity of KIF5A also decreased. The inhibition rates have been found to depend on the magnesium ion concentration. Lowering the magnesium concentration weakens the inhibition. In addition, also decreases of temperature or increasing the ATP concentration result in reduced inhibition. Zinc ion-mediated inhibition of KIF5A activity might be one molecular cause contributing to impaired transport processes within brain and other organs in cases of zinc dyshomeostasis. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

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

    NASA Astrophysics Data System (ADS)

    Smith, Winthrop; Wells, James

    2009-05-01

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

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

    PubMed

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

    2013-09-21

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

  1. Multi-ion detection and molecular switching behaviour of reversible dual fluorescent sensor.

    PubMed

    Basheer, Sabeel M; Muralisankar, M; Anjana, T V; Aneesrahman, K N; Sreekanth, Anandaram

    2017-07-05

    The selective chemosensing behaviour of imidazole bisthiocarbohydrazone (IBTC) towards F(-) and Cu(2+) are studied via colorimetric, UV-Visible, fluorescence spectra studies, and binding constants were calculated. The (1)H NMR titration study strongly support that the deprotonation of IBTC followed by the hydrogen bond formation via N1H1 and N2H2 protons with fluoride ion. The fluorescence inactive IBTC-Cu complex became fluorescence active in the presence of perchlorate (ClO4(-)) ion. The selective detection of perchlorate ion was also explained. The F(-) sensing mechanism of IBTC has been investigated by Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TDDFT) methods. The theoretical outcomes well reproduce the experimental results. And it concluded the NH protons, nearby the imine group was first captured by the added F(-) ion and then deprotonation happened followed by the formation of hydrogen bond. The IBTC found good reversibility character with the alternative addition of Ca(2+) and F(-). The multi-ion detection of IBTC was used to construct the NOR, OR and INHIBITION molecular logic gates. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. 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.

  3. 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.

  4. Multi-ion detection and molecular switching behaviour of reversible dual fluorescent sensor

    NASA Astrophysics Data System (ADS)

    Basheer, Sabeel M.; Muralisankar, M.; Anjana, T. V.; Aneesrahman, K. N.; Sreekanth, Anandaram

    2017-07-01

    The selective chemosensing behaviour of imidazole bisthiocarbohydrazone (IBTC) towards F- and Cu2 + are studied via colorimetric, UV-Visible, fluorescence spectra studies, and binding constants were calculated. The 1H NMR titration study strongly support that the deprotonation of IBTC followed by the hydrogen bond formation via N1sbnd H1 and N2sbnd H2 protons with fluoride ion. The fluorescence inactive IBTC-Cu complex became fluorescence active in the presence of perchlorate (ClO4-) ion. The selective detection of perchlorate ion was also explained. The F- sensing mechanism of IBTC has been investigated by Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TDDFT) methods. The theoretical outcomes well reproduce the experimental results. And it concluded the Nsbnd H protons, nearby the imine group was first captured by the added F- ion and then deprotonation happened followed by the formation of hydrogen bond. The IBTC found good reversibility character with the alternative addition of Ca2 + and F-. The multi-ion detection of IBTC was used to construct the NOR, OR and INHIBITION molecular logic gates.

  5. 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.

  6. 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.

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

    NASA Astrophysics Data System (ADS)

    Timachova, Ksenia; Balsara, Nitash

    2015-03-01

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

  8. 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.

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

    NASA Astrophysics Data System (ADS)

    Zettergren, Henning

    2015-07-01

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

  13. 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.

  14. 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.

  15. 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

  16. 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.

  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. Ion Transport and Structural Properties of Polymeric Electrolytes and Ionic Liquids from Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Borodin, Oleg

    2010-03-01

    Molecular dynamics simulations are well suited for exploring electrolyte structure and ion transport mechanisms on the nanometer length scale and the nanosecond time scales. In this presentation we will describe how MD simulations assist in answering fundamental questions about the lithium transport mechanisms in polymeric electrolytes and ionic liquids. In particular, in the first part of the presentation the extent of ion aggregation, the structure of ion aggregates and the lithium cation diffusion in binary polymeric electrolytes will be compared with that of single-ion conducting polymers. In the second part of the talk, the lithium transport in polymeric electrolytes will be compared with that of three ionic liquids ( [emim][FSI] doped with LiFSI , [pyr13][FSI] doped with LiFSI, [emim][BF4] doped with LiBF4). The relation between ionic liquid self-diffusion, conductivity and thermodynamic properties will be discussed in details. A number of correlations between heat of vaporization Hvap, cation-anion binding energy (E+/-), molar volume (Vm), self-diffusion coefficient (D) and ionic conductivity for 29 ionic liquids have been investigated using MD simulations. A significant correlation between D and Hvap has been found, while best correlation was found for -log((D Vm)) vs. Hvap+0.28E+/-. A combination of enthalpy of vaporization and a fraction of the cation-anion binding energy was suggested as a measure of the effective cohesive energy for ionic liquids.

  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 simulations of the structure and thermodynamics of carrier-assisted uranyl ion extraction.

    PubMed

    Jayasinghe, Manori; Beck, Thomas L

    2009-08-27

    We present molecular dynamics simulations of interfaces relevant to the selective chemical extraction of uranyl ions from aqueous solution. These molecular-level simulations model ion transfer in the PUREX process and in synthetic, selective membranes. We first present simulations of water/oil interfaces modified by incorporation of tributyl phosphate (TBP) into the oil phase (hexane). A range of concentrations is examined, from a single TBP molecule to values close to those utilized in the PUREX process. The TBP molecules exhibit strong interfacial activity, and the interface broadens relative to the water/oil case with increasing TBP concentrations. Additional structural features, including radial distribution functions and orientational distributions, are examined to elucidate the molecular ordering at the interface; the interface structure changes substantially with increasing TBP concentration. Finally, free-energy profiles are computed for (1) a single TBP molecule and a single uranyl nitrate complex [UO2(NO3)2] across the water/oil interface and (2) a UO2(NO3)2.TBP2 complex across both water/oil and water/(oil+TBP) interfaces. The UO2(NO3)2 complex is strongly repelled from the water/oil interface, while the UO2(NO3)2.TBP2 complex exhibits interfacial activity that decreases with increasing TBP concentration. The UO2(NO3)2.TBP2 complex displays a net free-energy driving force for partitioning into the oil phase that increases with increasing TBP concentration.

  1. 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.

  2. 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.

  3. 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.

  4. Initial Binding of Ions to the Interhelical Loops of Divalent Ion Transporter CorA: Replica Exchange Molecular Dynamics Simulation Study

    PubMed Central

    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 Mg2+ 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 Mg2+ 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 Mg2+ ions on the extracellular interhelical loops of CorA and the detailed inhibition mechanism of Co(III) Hexamine ions on CorA ions transportation. PMID:22952795

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

    PubMed Central

    2009-01-01

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

  6. 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.

  7. Gd-Based Single-Ion Magnets with Tunable Magnetic Anisotropy: Molecular Design of Spin Qubits

    NASA Astrophysics Data System (ADS)

    Martínez-Pérez, M. J.; Cardona-Serra, S.; Schlegel, C.; Moro, F.; Alonso, P. J.; Prima-García, H.; Clemente-Juan, J. M.; Evangelisti, M.; Gaita-Ariño, A.; Sesé, J.; van Slageren, J.; Coronado, E.; Luis, F.

    2012-06-01

    We report ac susceptibility and continuous wave and pulsed EPR experiments performed on GdW10 and GdW30 polyoxometalate clusters, in which a Gd3+ ion is coordinated to different polyoxometalate moieties. Despite the isotropic character of gadolinium as a free ion, these molecules show slow magnetic relaxation at very low temperatures, characteristic of single molecule magnets. For T≲200mK, the spin-lattice relaxation becomes dominated by pure quantum tunneling events, with rates that agree quantitatively with those predicted by the Prokof’ev and Stamp model [Phys. Rev. Lett. 80, 5794 (1998)PRLTAO0031-900710.1103/PhysRevLett.80.5794]. The sign of the magnetic anisotropy, the energy level splittings, and the tunneling rates strongly depend on the molecular structure. We argue that GdW30 molecules are also promising spin qubits with a coherence figure of merit QM≳50.

  8. 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.

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

    NASA Technical Reports Server (NTRS)

    Green, S.

    1984-01-01

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

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

    We present a theoretical analysis of optical pathways for the formation of cold Ca(1S)Na+(1S) molecular ions, based on accurate potential energy curves and transition dipole moments calculated using effective-core-potential methods of quantum chemistry. In the proposed approach, starting from a mixture of trapped laser-cooled Ca+ ions immersed into an ultracold gas of Na atoms, the (NaCa)+ are photoassociated in the excited E1Σ+ electronic state, followed by spontaneous radiative charge transfer and emission through an intermediate state. We find the optimal formation pathway and report radiative charge-exchange cross sections and vibrational distributions of participating electronic states. This work is partially supported by ARO.

  12. 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.

  13. 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.

  14. 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

  15. Molecular mechanism of the inhibitory effect of cobalt ion on thermolysin activity and the suppressive effect of calcium ion on the cobalt ion-dependent inactivation of thermolysin.

    PubMed

    Hashida, Yasuhiko; Inouye, Kuniyo

    2007-06-01

    Thermolysin activity in the hydrolysis of N-[3-(2-furyl)acryloyl]-glycyl-l-leucine amide (FAGLA) and FA-l-leucyl-l-alanine amide (FALAA) was examined at various Co(2+) and Ca(2+) concentrations. It decreased to 28% with increasing [Co(2+)] up to 18 mM. The Co(2+)-dependent inactivation was in part suppressed by adding Ca(2+) ion up to 0.5 mM, but 33% of the activity remained to be inactivated even with a sufficient concentration of Ca(2+) (>0.5 mM). The Co(2+)-dependent inactivation was shown to be composed of Ca(2+)-sensitive and Ca(2+)-insensitive parts. In the latter part which is observed at [Ca(2+)] >0.5 mM, Co(2+) plays as a competitive inhibitor. On the other hand, the Co(2+)-dependent inactivation in the Ca(2+)-sensitive part observed at [Ca(2+)] <0.5 mM proceeds time-dependently following second-order kinetics, and the time-course is in good agreement with that of decrease in the thermolysin band due to autolysis in SDS-PAGE. This indicates that Co(2+) accelerates the autolysis. Here, we describe the co-regulation of thermolysin activity by Co(2+) and Ca(2+) ions and propose a molecular mechanism for the inhibition of thermolysin by Co(2+) and suppressive effect of Ca(2+) on the Co(2+)-dependent inhibition. Co(2+) ion inhibits thermolysin activity not only as a competitive inhibitor but also promoting the autolysis.

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

    PubMed Central

    Cash, Derek J.; Hess, George P.

    1980-01-01

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

  17. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  19. 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

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

    SciTech Connect

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

    2014-03-10

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

  1. Fundamental Transitions and Ionization Energies of the Hydrogen Molecular Ions with Few ppt Uncertainty

    NASA Astrophysics Data System (ADS)

    Korobov, Vladimir I.; Hilico, L.; Karr, J.-Ph.

    2017-06-01

    We calculate ionization energies and fundamental vibrational transitions for H2 + , D2 + , and HD+ molecular ions. The nonrelativistic quantum electrodynamics expansion for the energy in terms of the fine structure constant α is used. Previous calculations of orders m α6 and m α7 are improved by including second-order contributions due to the vibrational motion of nuclei. Furthermore, we evaluate the largest corrections at the order m α8. That allows us to reduce the fractional uncertainty to the level of 7.6 ×10-12 for fundamental transitions and to 4.5 ×10-12 for the ionization energies.

  2. Fundamental Transitions and Ionization Energies of the Hydrogen Molecular Ions with Few ppt Uncertainty.

    PubMed

    Korobov, Vladimir I; Hilico, L; Karr, J-Ph

    2017-06-09

    We calculate ionization energies and fundamental vibrational transitions for H_{2}^{+}, D_{2}^{+}, and HD^{+} molecular ions. The nonrelativistic quantum electrodynamics expansion for the energy in terms of the fine structure constant α is used. Previous calculations of orders mα^{6} and mα^{7} are improved by including second-order contributions due to the vibrational motion of nuclei. Furthermore, we evaluate the largest corrections at the order mα^{8}. That allows us to reduce the fractional uncertainty to the level of 7.6×10^{-12} for fundamental transitions and to 4.5×10^{-12} for the ionization energies.

  3. 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.

  4. 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.

  5. 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.

  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. Jet-cooled fluorescence excitation spectrum, carbonyl wagging, and ring-puckering potential energy functions of 3-cyclopenten-1-one in its S1(n,π*) electronic excited state

    NASA Astrophysics Data System (ADS)

    Sagear, Paul; Laane, Jaan

    1995-05-01

    The jet-cooled fluorescence excitation spectrum of 3-cyclopenten-1-one has been recorded in the 308-330 nm region, and the electronic origin for the S1(n,π*) state of A2 symmetry was observed at 30 229 cm-1. The observed spectrum consists of more than 80 bands involving primarily ν3 (carbonyl stretch), ν29 (carbonyl out-of-plane wagging), and ν30 (ring puckering). Bands were also assigned to combinations with seven other vibrational modes. The energies for the v=0 to 11 quantum states of ν29 were measured and used to determine a one-dimensional potential energy function. This function has energy minima at wagging angles of ±24° and a barrier to inversion of 939 cm-1. Four bands associated with ν30 were observed and were used to determine an asymmetric single-minimum one-dimensional ring-puckering potential energy function for the S1(n,π*) state. The ring-puckering energy levels in the ν29 vibrational excited states are little changed from the v=0 state indicating that there is little interaction between the carbonyl wagging and the ring-puckering motions.

  8. Formation of diclofenac molecular ions as the effect of Cu(2+)-π interaction under electrospray ionization mass spectrometry conditions.

    PubMed

    Ostrowski, Wojciech; Linko, Katarzyna; Frański, Rafał

    2012-01-01

    Solutions containing diclofenac (M) and a copper salt [CuCl2, Cu(ClO4)2, Cu(NO3)2, CuSO4) were analysed by electrospray ionisation mass spectrometry (ESI-MS). Because of the cation-pi interactions in diclofenac-Cu(II) complexes, the diclofenac molecular ion M+* at m/z 295 was formed. It was found that the solvent composition (methanol versus water/methanol) and counter ion strongly affect the M+* ion formation. Formation pathways of ion M+* are discussed.

  9. 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.

  10. Observation of the infrared spectrum of the triatomic molecular ion H/sub 2/D/sup +/

    SciTech Connect

    Shy, J.; Farley, J.W.; Wing, W.H.

    1981-08-01

    The infrared vibrational-rotational spectrum of the H/sub 2/D/sup +/ molecular ion has been observed. Nine resonances between 1800 and 2000 cm/sup -1/ have been measured to a precision of 0.0005 cm/sup -1/ or 0.3 ppm (at 68% confidence level). This triatomic molecular ion is the simplest asymmetric top in nature. The quantum numbers of the observed transitions have not yet been unambiguously identified. This species is of great astrophysical interest in view of its important role in the chemistry of molecular clouds in the interstellar medium.

  11. Probing dynamic interference in high-order harmonic generation from long-range molecular ion: Bohmian trajectory investigation

    NASA Astrophysics Data System (ADS)

    Wang, Jun; Wang, Bing-Bing; Guo, Fu-Ming; Li, Su-Yu; Ding, Da-Jun; Chen, Ji-Gen; Zeng, Si-Liang; Yang, Yu-Jun

    2014-05-01

    Using Bohmian trajectory (BT) method, we investigate the dynamic interference in high-order harmonic generation from diatomic molecular ions. It is demonstrated that the main characteristics of the molecular harmonic spectrum can be well reproduced by only two BTs which are located at the two ions. This happens because these two localized trajectories can receive and store the whole collision information coming from all of the other re-collision trajectories. Therefore, the amplitudes and frequencies of these two trajectories represent the intensity and frequency distribution of the harmonic generation. Moreover, the interference between these two trajectories shows a dip in the harmonic spectrum, which reveals the molecular structure information.

  12. 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.

  13. 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

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

    PubMed

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

    2016-04-21

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

  15. 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.

  16. Measurement of charge exchange cross sections for highly charged xenon and thorium ions with molecular hydrogen in a Penning Ion Trap

    SciTech Connect

    Weinberg, G.M.

    1995-12-01

    Highly charged xenon (35+ to 46+) and thorium (72+ to 79+) ions were produced in an Electron Beam Ion Trap (EBIT). The ions were extracted from EBIT in a short pulse. Ions of one charge state were selected using an electromagnet. The ions were recaptured at low energy in a cryogenic Penning trap (RETRAP). As the ions captured electrons from molecular hydrogen, populations of the various charge states were obtained by measuring the image currents induced by the ions on the electrodes of the trap. Data on the number of ions in each charge state vs. time were compared to theoretical rate equations in order to determine the average charge exchange rates. These rates were compared to charge exchange rates of an ion with a known charge exchange cross section (Ar{sup 11+}) measured in a similar manner in order to determine the average charge exchange cross sections for the highly charged ions. The energy of interaction between the highly charged ions and hydrogen was estimated to be 4 eV in the center of mass frame. The mean charge exchange cross sections were 9 {times} 10{sup {minus}14} cm{sup 2} for Xe{sup 43+} to Xe{sup 46+} and 2 {times} 10{sup {minus}13} cm{sup 2} for Th{sup 73+} to Th{sup 79+}. Double capture was approximately 20--25% of the total for both xenon and thorium. A fit indicated that the cross sections were approximately proportional to q. This is consistent with a linear dependence of cross section on q within the measurement uncertainties.

  17. 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.

  18. 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.

  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. 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.

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

    PubMed Central

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

    2014-01-01

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

  2. 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.

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

    PubMed

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

    2014-03-24

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

  4. 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.

  5. 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

  6. 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.

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

    PubMed Central

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

    2011-01-01

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

  8. Molecular dynamics study of ion transport through an open model of voltage-gated sodium channel.

    PubMed

    Li, Yang; Sun, Ruining; Liu, Huihui; Gong, Haipeng

    2017-05-01

    Voltage-gated sodium (NaV) channels are critical in the signal transduction of excitable cells. In this work, we modeled the open conformation for the pore domain of a prokaryotic NaV channel (NaVRh), and used molecular dynamics simulations to track the translocation of dozens of Na(+) ions through the channel in the presence of a physiological transmembrane ion concentration gradient and a transmembrane electrical field that was closer to the physiological one than previous studies. Channel conductance was then estimated from simulations on the wide-type and DEKA mutant of NaVRh. Interestingly, the conductivity predicted from the DEKA mutant agrees well with experimental measurement on eukaryotic NaV1.4 channel. Moreover, the wide-type and DEKA mutant of NaVRh exhibited markedly distinct ion permeation patterns, which thus implies the mechanistic difference between prokaryotic and eukaryotic NaV channels. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. 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.

  10. Molecular dynamics simulation study of the "stay or leave" problem for two magnesium ions in gene transcription.

    PubMed

    Wu, Shaogui

    2017-06-01

    Two magnesium ions play important roles in nucleotide addition cycle (NAC) of gene transcription. However, at the end of each NAC, why does one ion stay in the active site while the other ion leaves with product pyrophosphate (PPi )? This problem still remains obscure. In this work, we studied the problem using all-atom molecular dynamics simulation combined with steered molecular dynamics and umbrella sampling simulation methods. Our simulations reveal that although both ions are located in the active site after chemistry, their detailed positions are not symmetrical, leading to their different forces from surrounding groups. One ion makes weaker contacts with PPi than the whole protein. Hence, PPi release is less likely to take it away. The other one forms tighter contacts with PPi relative to the protein. The formed (Mg(2+) -PPi )(2-) complex is found to break the contacts with surrounding protein residues one by one so as to dissociate from the active site. This effectively avoids the coexistence of two ions in the active site after PPi release and guarantees a reasonable Mg(2+) ion number in the active site for the next NAC. The observations from this work can provide valuable information for comprehensively understanding the molecular mechanism of transcription. Proteins 2017; 85:1002-1007. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

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

    PubMed Central

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

    2013-01-01

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

  12. The rise of 3-d single-ion magnets in molecular magnetism: towards materials from molecules?

    PubMed Central

    Frost, Jamie M.; Harriman, Katie L. M.

    2016-01-01

    Single-molecule magnets (SMMs) that contain one spin centre (so-called single-ion magnets) theoretically represent the smallest possible unit for spin-based electronic devices. The realisation of this and related technologies, depends on first being able to design systems with sufficiently large energy barriers to magnetisation reversal, U eff, and secondly, on being able to organise these molecules into addressable arrays. In recent years, significant progress has been made towards the former goal – principally as a result of efforts which have been directed towards studying complexes based on highly anisotropic lanthanide ions, such as Tb(iii) and Dy(iii). Since 2013 however, and the remarkable report by Long and co-workers of a linear Fe(i) system exhibiting U eff = 325 K, single-ion systems of transition metals have undergone something of a renaissance in the literature. Not only do they have important lessons to teach us about anisotropy and relaxation dynamics in the quest to enhance U eff, the ability to create strongly coupled spin systems potentially offers access to a whole of host of 1, 2 and 3-dimensional materials with interesting structural and physical properties. This perspective summarises recent progress in this rapidly expanding sub-genre of molecular magnetism from the viewpoint of the synthetic chemist, with a particular focus on the lessons that have so far been learned from single-ion magnets of the d-block, and, the future research directions which we feel are likely to emerge in the coming years. PMID:28660017

  13. 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.

  14. Validation of the Ion Torrent PGM sequencing for the prospective routine molecular diagnostic of colorectal cancer.

    PubMed

    Belardinilli, Francesca; Capalbo, Carlo; Buffone, Amelia; Petroni, Marialaura; Colicchia, Valeria; Ferraro, Sergio; Zani, Massimo; Nicolussi, Arianna; D'Inzeo, Sonia; Coppa, Anna; Screpanti, Isabella; Gulino, Alberto; Giannini, Giuseppe

    2015-09-01

    Treatment individualization based on specific molecular biomarkers is becoming increasingly important in oncology. In colorectal cancer (CRC), the molecular characterization of RAS and BRAF mutation status for prognostic and predictive purposes is commonly performed by different validated methods. However, as the number of clinically relevant mutations to be analyzed increases, the definition of new approaches for more sensitive, rapid and economic patient selection urges. To this aim, we evaluated the Ion Semiconductor sequencing using the Ion Torrent Personal Genome Machine (IT-PGM) in our routine molecular diagnostics for CRC in comparison with the gold standard direct Sanger sequencing. Formalin-fixed and paraffin-embedded tumor tissues obtained by surgery or biopsy of 66 CRCs were collected. DNA was extracted and sequenced by IT-PGM and Sanger method. The proposed IT-PGM sequencing strategy exceeded the 500 reads of coverage for all clinically relevant RAS/BRAF amplicons in most samples and thus guaranteed optimal determination. Indeed, the frequencies and the mutational spectrum of RAS and BRAF mutations were in agreement with literature data and revealed 100% concordance between the IT-PGM and routine Sanger sequencing approaches. Turnaround time and cost evaluation indicate that the IT-PGM sequencing permits the characterization of the clinically relevant mutational spots at lower cost and turnaround time compared to Sanger sequencing and allows inclusion of additional amplicons whose characterization may acquire significance in the very next future. The IT-PGM is a valid, flexible, sensitive and economical method alternative to the Sanger sequencing in routine diagnostics to select patients for anti-epidermal growth factor receptor therapy for metastatic CRC. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

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

    NASA Astrophysics Data System (ADS)

    Larriba, Carlos; Hogan, Christopher J.

    2013-10-01

    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

  16. 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

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

    SciTech Connect

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

    2009-10-15

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

  18. Generation of “bastard” molecular ions from van der Waals clusters: Arn(C2Cl4)m+ ions, suspected interlopers in collection of solar neutrinos

    PubMed Central

    Buelow, S. J.; Worsnop, D. R.; Herschbach, D. R.

    1981-01-01

    Gaseous molecular ions containing argon and perchlorethylene, Arn(C2Cl4)m+ in which n ≥ 1-29 and m ≥ 1-4, are produced by electron bombardment of van der Waals clusters formed by expanding an Ar/C2Cl4 mixture through a supersonic nozzle. Previous attempts to observe such ions in a high-pressure mass spectrometer were not successful, as with many other (“bastard”) ions that similarly lack a stable chemically bound neutral parent molecule. This is probably due to dissociation induced by the large exoergicity from charge transfer between species that differ greatly in ionization potential. Use of van der Waals clusters as parent species avoids entirely the exoergicity problem and thus offers a general method to generate bastard ions. The Ar(C2Cl4)m+ ions have been suspected of interfering with collection of 37Ar+ ions produced by the 37Cl(v,e-)37Ar+ reaction in the solar neutrino observatory. Although, as shown by our results, these ions are stable, they are unlikely to inhibit collection on the long time scale of the solar neutrino experiment. PMID:16593130

  19. Heavy-ion beam induced effects in enriched gadolinium target films prepared by molecular plating

    NASA Astrophysics Data System (ADS)

    Mayorov, D. A.; Tereshatov, E. E.; Werke, T. A.; Frey, M. M.; Folden, C. M.

    2017-09-01

    A series of enriched gadolinium (Gd, Z = 64) targets was prepared using the molecular plating process for nuclear physics experiments at the Cyclotron Institute at Texas A&M University. After irradiation with 48Ca and 45Sc projectiles at center-of-target energies of Ecot = 3.8-4.7 MeV/u, the molecular films displayed visible discoloration. The morphology of the films was examined and compared to the intact target surface. The thin films underwent a heavy-ion beam-induced density change as identified by scanning electron microscopy and α-particle energy loss measurements. The films became thinner and more homogenous, with the transformation occurring early on in the irradiation. This transformation is best described as a crystalline-to-amorphous phase transition induced by atomic displacement and destruction of structural order of the original film. The chemical composition of the thin films was surveyed using energy dispersive spectroscopy and X-ray diffraction, with the results confirming the complex chemistry of the molecular films previously noted in other publications.

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

    PubMed Central

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

    2014-01-01

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

  1. Origin of CH+ in diffuse molecular clouds. Warm H2 and ion-neutral drift

    NASA Astrophysics Data System (ADS)

    Valdivia, Valeska; Godard, Benjamin; Hennebelle, Patrick; Gerin, Maryvonne; Lesaffre, Pierre; Le Bourlot, Jacques

    2017-04-01

    Context. Molecular clouds are known to be magnetised and to display a turbulent and complex structure where warm and cold phases are interwoven. The turbulent motions within molecular clouds transport molecules, and the presence of magnetic fields induces a relative velocity between neutrals and ions known as the ion-neutral drift (vd). These effects all together can influence the chemical evolution of the clouds. Aims: This paper assesses the roles of two physical phenomena which have previously been invoked to boost the production of CH+ under realistic physical conditions: the presence of warm H2 and the increased formation rate due to the ion-neutral drift. Methods: We performed ideal magnetohydrodynamical (MHD) simulations that include the heating and cooling of the multiphase interstellar medium (ISM), and where we treat dynamically the formation of the H2 molecule. In a post-processing step we compute the abundances of species at chemical equilibrium using a solver that we developed. The solver uses the physical conditions of the gas as input parameters, and can also prescribe the H2 fraction if needed. We validate our approach by showing that the H2 molecule generally has a much longer chemical evolution timescale compared to the other species. Results: We show that CH+ is efficiently formed at the edge of clumps, in regions where the H2 fraction is low (0.3-30%) but nevertheless higher than its equilibrium value, and where the gas temperature is high (≳ 300 K). We show that warm and out of equilibrium H2 increases the integrated column densities of CH+ by one order of magnitude up to values still 3-10 times lower than those observed in the diffuse ISM. We balance the Lorentz force with the ion-neutral drag to estimate the ion-drift velocities from our ideal MHD simulations. We find that the ion-neutral drift velocity distribution peaks around 0.04 km s-1, and that high drift velocities are too rare to have a significant statistical impact on the

  2. 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

  3. Vibronic Emission Spectroscopy of Jet-Cooled Benzyl-Type Radicals from Corona Discharge of Chloro-Substituted O-Xylene Molecules

    NASA Astrophysics Data System (ADS)

    Yoon, Young; Lee, Sang

    2017-06-01

    Whereas benzyl radical, a prototypic aromatic free radical, has been the subject of numerous spectroscopic studies, chloro-substituted benzyl radicals have received less attention, due to the difficulties associated with production of radicals from precursors. The weak C-Cl bond can be easily dissociated in corona discharge of high voltage, leading to the formation of other benzyl-type radicals. During past years, we have concentrated the spectroscopy of chloro-substituted methylbenzyl radicals produced from corona discharge of precursor seeded in a large amount of helium carrier gas using a pinhole-type glass nozzle in a technique of corona excited supersonic expansion. From the analysis of the spectrum observed, we can easily distinguish the origin bands in the D_1 → D_0 transition of the isomeric chloro-substituted methylbenzyl radicals with the additivity rule, discovered from the analysis of a series of benzyl-type radicals. Also, the displacement of phenylic Cl by benzylic H was confirmed to be dependent on the distance between Cl and H atoms. The benzyl-type radicals produced in corona discharge from precursor were determined based on the bond dissociation energies and molecular structure of precursor molecules as well as the agreement of the observed with the calculated ones from Gaussian program, from which the 2-methyl-3-chlorobenzyl, 2-methyl-4-chlorobenzyl, 2-methyl-5-chlorobenzyl, and 2-methyl-6-chlorobenzyl radicals were newly identified. Y. W. Yoon, C. S. Huh, and S. K. Lee, Chem. Phys. Lett. 525-526, 44-48 (2012). Y. W. Yoon and S. K. Lee, J. Phys. Chem. A 117, 2485-2491 (2013).

  4. In situ characterization of a cold and short pulsed molecular beam by femtosecond ion imaging.

    PubMed

    Irimia, Daniel; Kortekaas, Rob; Janssen, Maurice H M

    2009-05-28

    In this paper we report on the in situ characterization of the cold velocity distribution of a pulsed molecular beam produced by a novel cantilever piezo valve. The velocity distribution is measured at various temporal positions within the pulsed expansion using femtosecond velocity map ion imaging. It is shown that the universal detection of molecules by multi-photon femtosecond velocity map ion imaging can provide directly the velocity distribution with excellent velocity resolution. The novel cantilever piezo valve can operate both in continuous (DC) and pulsed mode without any modification using the same drive electronics. Pulsed operation was tested at repetition rates of 20 Hz, 1 kHz and 5 kHz and a conical nozzle 200 mum in diameter. The cantilever valve produces a pulsed molecular beam of translationally cold molecules at modest backing pressures of about 6 bar. At low to medium repetition rates (20-1000 Hz) the pulsed piezo valve produces pulses of 12-40 mus duration of translationally cold seeded beams of helium and neon with speed ratios up to S = 135 (20 Hz, 0.1% CD(3)I in neon) and S = 55 (1 kHz). At the highest tested repetition rate of 5 kHz, the speed ratio obtained for the same seeded beam is reduced to about S = 45. This is still more than a factor of two better than the speed ratio S = 21 measured for a continuous beam produced with the same nozzle at 0.5 bar backing pressure. The cold velocity distribution of the pulsed beam expansion as compared to a continuous beam expansion is beneficial for improved spatial resolution in velocity map ion imaging experiments at high repetition rates of 1-5 kHz. The cantilever piezo valve has a simple design and may find broad applicability in areas where short gas pulses are warranted because of limited pumping speed, the effective use of (expensive) samples or the production of translationally and internally cold molecular beams at high repetition rate. When operating the piezo valve at high backing

  5. 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.

  6. Jet-cooled fluorescence excitation spectra and carbonyl wagging and ring-puckering potential energy functions of cyclobutanone and its 2,2,4,4-d4 isotopomer in the S1(n,π*) electronic excited state

    NASA Astrophysics Data System (ADS)

    Zhang, Jian; Chiang, Whe-Yi; Laane, Jaan

    1994-03-01

    The jet-cooled fluorescence excitation spectra of cyclobutanone and its 2,2,4,4-d4 isotopomer have been recorded in the 305-335 nm region. The electronic band origin of the d0 molecule for the S1(n,π*) state of A2 symmetry occurs at 30 292 cm-1 (30 265 cm-1 for the d4 molecule). The observed spectra consisting of more than 50 bands for each isotopomer involve ν7, ν8, and ν9 (the three A1 ring vibrations) as well as ν20(C=O in-plane wag), ν26 (C=O out-of-plane wag), and ν27 (ring puckering). Five bands associated with the excited vibrational states of ν26 in the S1(n,π*) electronic state were observed for each isotopic species, and these were used to determine the one-dimensional potential energy functions for the C=O out-of-plane wagging. The C=O wagging angle was determined to be 39° and the barrier to inversion is 2149 cm-1 (2188 cm-1 for the deuteride). For the ring-puckering in the S1 state the lowest three vibrational energy spacings were found to be 106, 166, and 185 cm-1 as compared to values of 35, 57, and 65 cm-1 in the S0 ground state. Several ring-puckering potential energy functions with varying degrees of asymmetry are capable of reproducing the observed results. In all cases, however, the v=0 puckering state lies above any barrier to planarity. A two-dimensional potential function which fits the observed data was also determined in terms of the wagging and puckering coordinates.

  7. 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.

  8. 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.

  9. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

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

    SciTech Connect

    Wasielewski, M.R.

    1997-01-01

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

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. Prediction of drift time in ion mobility-mass spectrometry based on Peptide molecular weight.

    PubMed

    Wang, Bing; Valentine, Steve; Plasencia, Manolo; Zhang, Xiang

    2010-09-01

    A computational model is introduced for predicting peptide drift time in ion mobility-mass spectrometry (IMMS). Each peptide was represented using a numeric descriptor: molecular weight. A simple linear regression predictor was constructed for peptides drift time prediction. Three datasets with different charge state assignments were used for the model training and testing. The dataset one contains 212 singly charged peptides, dataset two has 306 doubly charged peptides, and dataset three contains 77 triply charged peptides. Our proposed method achieved a prediction accuracy of 86.3%, 72.6%, and 59.7% for the dataset one, two and three, respectively. Peptide drift time prediction in IMMS will improve the confidence of peptide identifications by limiting the peptide search space during MS/MS database searching and therefore, reducing false discovery rate (FDR) of protein identification.

  19. 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.

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

    NASA Astrophysics Data System (ADS)

    Mafé, Salvador; Ramírez, Patricio; Alcaraz, Antonio

    2003-10-01

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

  2. 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.

  3. Molecular Architecture and Subunit Organization of TRPA1 Ion Channel Revealed by Electron Microscopy*

    PubMed Central

    Cvetkov, Teresa L.; Huynh, Kevin W.; Cohen, Matthew R.; Moiseenkova-Bell, Vera Y.

    2011-01-01

    Transient receptor potential ankyrin 1 (TRPA1) is a non-selective ion channel, which is expressed in nociceptor sensory neurons and transduces chemical, inflammatory, and neuropathic pain signals. Numerous non-reactive compounds and electrophilic compounds, such as endogenous inflammatory mediators and exogenous pungent chemicals, can activate TRPA1. Here we report a 16-Å resolution structure of purified, functional, amphipol-stabilized TRPA1 analyzed by single-particle EM. Molecular models of the N and C termini of the channel were generated using the I-TASSER protein structure prediction server and docked into the EM density to provide insight into the TRPA1 subunit organization. This structural analysis suggests a location for critical N-terminal cysteine residues involved in electrophilic activation at the interface between neighboring subunits. Our results indicate that covalent modifications within this pocket may alter interactions between subunits and promote conformational changes that lead to channel activation. PMID:21908607

  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. 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).

  6. 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.

  7. 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.

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

    PubMed Central

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

    2016-01-01

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

  9. 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).

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

    USGS Publications Warehouse

    Lee, M.W.; Meuwly, M.

    2013-01-01

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

  12. 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.

  13. 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.

  14. 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).

  15. 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.

  16. 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.

  17. 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).

  18. Ambient low temperature plasma etching of polymer films for secondary ion mass spectrometry molecular depth profiling.

    PubMed

    Muramoto, Shin; Staymates, Matthew E; Brewer, Tim M; Gillen, Greg

    2012-12-18

    The feasibility of a low temperature plasma (LTP) probe as a way to prepare polymer bevel cross sections for secondary ion mass spectrometry (SIMS) applications was investigated. Poly(lactic acid) and poly(methyl methacrylate) films were etched using He LTP, and the resulting crater walls were depth profiled using time-of-flight secondary ion mass spectrometry (ToF-SIMS) to examine changes in chemistry over the depth of the film. ToF-SIMS results showed that while exposure to even 1 s of plasma resulted in integration of atmospheric nitrogen and contaminants to the newly exposed surface, the actual chemical modification to the polymer backbone was found to be chemistry-dependent. For PLA, sample modification was confined to the top 15 nm of the PLA surface regardless of plasma exposure dose, while measurable change was not seen for PMMA. The confinement of chemical modification to 15 nm or less of the top surface suggests that LTP can be used as a simple method to prepare cross sections or bevels of polymer thin films for subsequent analysis by surface-sensitive molecular depth profiling techniques such as SIMS, X-ray photoelectron spectroscopy (XPS), and other spatially resolved mass spectrometric techniques.

  19. 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.

  20. Towards understanding the molecular basis of ion channel modulation by lipids: Mechanistic models and current paradigms.

    PubMed

    Poveda, José A; Marcela Giudici, A; Lourdes Renart, M; Morales, Andrés; González-Ros, José M

    2017-09-01

    Research on ion channel modulation has become a hot topic because of the key roles these membrane proteins play in both prokaryotic and eukaryotic organisms. In this respect, lipid modulation adds to the overall modulatory mechanisms as a potential via to find new pharmacological targets for drug design based on interfering with lipid/channel interactions. However, our knowledge in this field is scarce and often circumscribed to the sites where lipids bind and/or its final functional consequences. To fully understand this process it is necessary to improve our knowledge on its molecular basis, from the binding sites to the signalling pathways that derive in structural and functional effects on the ion channel. In this review, we have compiled information about such mechanisms and established a classification into four different modes of action. Afterwards, we have revised in more detail the lipid modulation of Cys-loop receptors and of the potassium channel KcsA, which were chosen as model channels modulated by specific lipids. This article is part of a Special Issue entitled: Membrane Lipid Therapy: Drugs Targeting Biomembranes edited by Pablo V. Escribá. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. 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.

  2. Sites of metabolic substitution: investigating metabolite structures utilising ion mobility and molecular modelling.

    PubMed

    Dear, Gordon J; Munoz-Muriedas, Jordi; Beaumont, Claire; Roberts, Andrew; Kirk, Jayne; Williams, Jonathan P; Campuzano, Iain

    2010-11-15

    Drug metabolism is an integral part of the drug development and drug discovery process. It is required to validate the toxicity of metabolites in support of safety testing and in particular provide information on the potential to form pharmacologically active or toxic metabolites. The current methodologies of choice for metabolite structural elucidation are liquid chromatography/tandem mass spectrometry (LC/MS/MS) and nuclear magnetic resonance (NMR) spectroscopy. There are, in certain cases, examples of metabolites whose sites of metabolism cannot be unequivocally identified by MS/MS alone. Utilising commercially available molecular dynamics packages and known quantum chemistry basis sets, an ensemble of lowest energy structures were generated for a group of aromatic hydroxylated metabolites of the model compound ondansetron. Theoretical collision cross-sections were calculated for each structure. Travelling-wave ion mobility (IMS) measurements were also performed on the compounds, thus enabling experimentally derived collision cross-sections to be calculated. A comparison of the theoretical and experimentally derived collision cross-sections were utilised for the accurate assignment of isomeric drug metabolites. The UPLC/IMS-MS method, described herein, demonstrates the ability to measure reproducibly by ion mobility, metabolite structural isomers, which differ in collision cross-section, both theoretical and experimentally derived, by less than 1 Å(2). This application has the potential to supplement and/or complement current methods of metabolite structural characterisation. Copyright © 2010 John Wiley & Sons, Ltd.

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

    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.

  4. 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.

  5. 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.

  6. 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.

  7. 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).

  8. Photophysical processes of triplet states and radical ions in pure and molecularly doped polymers. Final report

    SciTech Connect

    Burkhart, R.D.

    1998-01-01

    Both the past and current objectives are to learn how to control the rate and direction of triplet exciton migration in both pure and molecularly doped polymer systems. Since triplet excimers are efficient traps for migrating excitons, a secondary objective has been to characterize these excimers with a view toward their use as rate modifiers or excited state quenchers. Further objectives included those stated above as past and current objectives but with an additional goal. The authors learned that fluid solutions of many of the nitrogen containing chromophores with which they work produce both radical cations and anions upon excimer laser excitation. They also learned that a phosphorus analogue behaves similarly. At this time the mechanism of charge generation in these systems is not well established but they do know that the electronically excited states and radical ions can potentially interconvert. They wanted to find out whether or not the pure or molecularly doped polymer systems could be used in a step-wise sequence involving light absorption followed by charge generation. All of their activities are oriented toward the potential end use of polymeric systems in the conversion of light energy to perform various types of useful work.

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

    SciTech Connect

    Khan, Arnab; Tribedi, Lokesh C.; Misra, Deepankar

    2015-04-15

    We report the development and performance studies of a newly built recoil ion momentum spectrometer for the study of atomic and molecular fragmentation dynamics in gas phase upon the impact of charged particles and photons. The present design is a two-stage Wiley-McLaren type spectrometer which satisfies both time and velocity focusing conditions and is capable of measuring singly charged ionic fragments up-to 13 eV in all directions. An electrostatic lens has been introduced in order to achieve velocity imaging. Effects of the lens on time-of-flight as well as on the position have been investigated in detail, both, by simulation and in experiment. We have used 120 keV proton beam on molecular nitrogen gas target. Complete momentum distributions and kinetic energy release distributions have been derived from the measured position and time-of-flight spectra. Along with this, the kinetic energy release spectra of fragmentation of doubly ionized nitrogen molecule upon various projectile impacts are presented.

  10. 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.

  11. Molecular harmonic extension and enhancement from H2 + ions in the presence of spatially inhomogeneous fields