WorldWideScience

Sample records for warm molecular hydrogen

  1. Wave packet molecular dynamics simulations of warm dense hydrogen

    CERN Document Server

    Knaup, M; Toepffer, C; Zwicknagel, G

    2003-01-01

    Recent shock-wave experiments with deuterium in a regime where a plasma phase-transition has been predicted and their theoretical interpretation are the matter of a controversial discussion. In this paper, we apply 'wave packet molecular dynamics' (WPMD) simulations to investigate warm dense hydrogen. The WPMD method was originally used by Heller for a description of the scattering of composite particles such as simple atoms and molecules; later it was applied to Coulomb systems by Klakow et al. In the present version of our model the protons are treated as classical point-particles, whereas the electrons are represented by a completely anti-symmetrized Slater sum of periodic Gaussian wave packets. We present recent results for the equation of state of hydrogen at constant temperature T = 300 K and of deuterium at constant Hugoniot E - E sub 0 + 1/2(1/n - 1/n sub 0)(p + p sub 0) = 0, and compare them with the experiments and several theoretical approaches.

  2. Mapping warm molecular hydrogen with Spitzer's Infrared Array Camera (IRAC)

    CERN Document Server

    Neufeld, David

    2008-01-01

    Photometric maps, obtained with Spitzer's Infrared Array Camera (IRAC), can provide a valuable probe of warm molecular hydrogen within the interstellar medium. IRAC maps of the supernova remnant IC443, extracted from the Spitzer archive, are strikingly similar to spectral line maps of the H2 pure rotational transitions that we obtained with the Infrared Spectrograph (IRS) instrument on Spitzer. IRS spectroscopy indicates that IRAC Bands 3 and 4 are indeed dominated by the H2 v=0-0 S(5) and S(7) transitions, respectively. Modeling of the H2 excitation suggests that Bands 1 and 2 are dominated by H2 v=1-0 O(5) and v=0-0 S(9). Large maps of the H2 emission in IC433, obtained with IRAC, show band ratios that are inconsistent with the presence of gas at a single temperature. The relative strengths of IRAC Bands 2, 3, and 4 are consistent with pure H2 emission from shocked material with a power-law distribution of gas temperatures. CO vibrational emissions do not contribute significantly to the observed Band 2 inte...

  3. Warm Molecular Hydrogen in the Galactic Wind of M82

    CERN Document Server

    Veilleux, S; Swaters, R

    2009-01-01

    We report the detection of a complex of extraplanar warm H_2 knots and filaments extending more than ~3 kpc above and below the galactic plane of M82, roughly coincident with the well-known galactic wind in this system. Comparisons of these data with published results at other wavelengths provide quantitative constraints on the topology, excitation, heating, and stability against disruption of the wind-entrained molecular ISM in this prototypical galactic wind. Deep H_2 2.12 um observations such as these represent a promising new method to study the elusive but potentially important molecular component of galactic winds.

  4. Tracing Ram-Pressure Stripping with Warm Molecular Hydrogen Emission

    CERN Document Server

    Sivanandam, Suresh; Rieke, George H

    2014-01-01

    We use the Spitzer Infrared Spectrograph (IRS) to study four infalling cluster galaxies with signatures of on-going ram-pressure stripping. H$_2$ emission is detected in all four; two show extraplanar H$_2$ emission. The emission usually has a warm (T $\\sim$ $115 - 160$K) and a hot (T $\\sim$ 400 $-$ 600K) component that is approximately two orders of magnitude less massive than the warm one. The warm component column densities are typically $10^{19} - 10^{20}$ cm$^{-2}$ with masses of $10^6 - 10^8 M_\\odot$. The warm H$_2$ is anomalously bright compared with normal star-forming galaxies and therefore may be excited by ram-pressure. In the case of CGCG 97-073, the H$_2$ is offset from the majority of star formation along the direction of the galaxy's motion in the cluster, suggesting it is forming in the ram-pressure wake of the galaxy. Another galaxy, NGC 4522, exhibits a warm H$_2$ tail approximately 4 kpc in length. These results support the hypothesis that H$_2$ within these galaxies is shock-heated from th...

  5. Tracing ram-pressure stripping with warm molecular hydrogen emission

    Energy Technology Data Exchange (ETDEWEB)

    Sivanandam, Suresh [Dunlap Institute for Astronomy and Astrophysics, University of Toronto, Rm 101, 50 St. George Street, Toronto, ON M5S 3H4 (Canada); Rieke, Marcia J.; Rieke, George H., E-mail: sivanandam@dunlap.utoronto.ca [Steward Observatory, University of Arizona, 933 North Cherry Avenue, Tucson, AZ 85721 (United States)

    2014-12-01

    We use the Spitzer Infrared Spectrograph to study four infalling cluster galaxies with signatures of ongoing ram-pressure stripping. H{sub 2} emission is detected in all four, and two show extraplanar H{sub 2} emission. The emission usually has a warm (T ∼ 115-160 K) and a hot (T ∼ 400-600 K) component that is approximately two orders of magnitude less massive than the warm one. The warm component column densities are typically 10{sup 19} to 10{sup 20} cm{sup –2} with masses of 10{sup 6} to 10{sup 8} M {sub ☉}. The warm H{sub 2} is anomalously bright compared with normal star-forming galaxies and therefore may be excited by ram-pressure. In the case of CGCG 97-073, the H{sub 2} is offset from the majority of star formation along the direction of the galaxy's motion in the cluster, suggesting that it is forming in the ram-pressure wake of the galaxy. Another galaxy, NGC 4522, exhibits a warm H{sub 2} tail approximately 4 kpc in length. These results support the hypothesis that H{sub 2} within these galaxies is shock-heated from the interaction with the intracluster medium. Stripping of dust is also a common feature of the galaxies. For NGC 4522, where the distribution of dust at 8 μm is well resolved, knots and ripples demonstrate the turbulent nature of the stripping process. The Hα and 24 μm luminosities show that most of the galaxies have star-formation rates comparable to similar mass counterparts in the field. Finally, we suggest a possible evolutionary sequence primarily related to the strength of ram-pressure that a galaxy experiences to explain the varied results observed in our sample.

  6. Detection of warm molecular hydrogen in the circumstellar disk around the Herbig Ae star HD97048

    CERN Document Server

    Martin-Zaidi, C; Pantin, E; Habart, E

    2007-01-01

    We present high resolution spectroscopic mid-infrared observations of the circumstellar disk around the Herbig Ae star HD97048 with the VLT Imager and Spectrometer for the mid-InfraRed (VISIR). We detect the S(1) pure rotational line of molecular hydrogen (H2) at 17.035 microns arising from the disk around the star. This detection reinforces the claim that HD97048 is a young object surrounded by a flared disk at an early stage of evolution. The emitting warm gas is located within the inner 35 AU of the disk. The line-to-continuum flux ratio is much higher than expected from models of disks at local thermodynamics equilibrium. We investigate the possible physical conditions, such as a gas-to-dust mass ratio higher than 100 and different excitation mechanisms of molecular hydrogen (X-ray heating, shocks, ...) in order to explain the detection. We tentatively estimate the mass of warm gas to be in the range from 0.01 to nearly 1 Jupiter Mass. Further observations are needed to better constrain the excitation mec...

  7. A Warm Molecular Hydrogen Tail Due to Ram Pressure Stripping of a Cluster Galaxy

    CERN Document Server

    Sivanandam, Suresh; Rieke, George H

    2009-01-01

    We have discovered a remarkable warm (140 - 160 K) molecular hydrogen tail with a mass of approximately 2.5*10^7 M_sun extending 20 kpc from a cluster spiral galaxy, ESO 137-001, in Abell 3627. Some portion of this gas is lost permanently to the intracluster medium, as the tail extends beyond the tidal radius of the galaxy. We also detect a hot (580 - 680 K) component in the tail that is approximately 1% of the mass of the warm component. This discovery is direct evidence that the galaxy is currently undergoing ram-pressure stripping, as also indicated by its X-ray and H\\alpha tail found by other studies. We estimate the galaxy is losing its interstellar gas at a rate of at least ~ 1 - 2 M_sun yr^-1. If the galaxy persists to lose mass at this estimated rate, it will exhaust its gas reservoir in a single pass through the cluster core, which will take approximately 0.5 - 1 Gyr. The results produced from the modeling of the ram-pressure stripping timescale are consistent with our upper limit and suggest that th...

  8. Collisional excitation of sulfur dioxide by molecular hydrogen in warm molecular clouds

    Science.gov (United States)

    Balança, Christian; Spielfiedel, Annie; Feautrier, Nicole

    2016-08-01

    Interpretation of SO2 line emission in warm environments requires a detailed knowledge of collisional rate coefficients for a wide range of levels and temperatures. Using an accurate theoretical interaction potential for SO2-H2, rate coefficients for collisions of SO2 with para and ortho-H2 for the 31 first SO2, rotational levels are calculated for temperatures up to 500 K using the coupled states (CS) approximation. From a comparison with previously published close-coupling (CC) results, it was shown that the two sets of data agree within 20-30 per cent for both para- and ortho-H2 collisions. As previously found within the CC approach, the CS rate coefficients with ortho and para-H2 differ by a factor of 2 in average, the largest being mainly the rates for collisions with ortho-H2. For higher levels and temperatures, rate constants were computed within the infinite order sudden (IOS) approximation. Rate coefficients were obtained for the lowest 410 rotational levels of SO2 in the 100-1000 K temperature range. A comparison at 30, 100 and 300 K of the IOS data with the corresponding para-H2 CS results indicates that the IOS approximation systematically underestimates the CS results by a factor up to 2 at the lowest temperatures. As expected, IOS and CS rates are in a better agreement at higher temperatures. Considering that the IOS theory was developed for collisions with para-H2, this approach cannot describe with the same accuracy collisions with ortho-H2. So, our IOS data may be considered as quite reliable for collisions with para-H2 and less accurate for collisions with ortho-H2.

  9. Thermophysical properties of warm dense hydrogen

    CERN Document Server

    Holst, Bastian; Desjarlais, Michael P

    2007-01-01

    We study the thermophysical properties of warm dense hydrogen using quantum molecular dynamics simulations. New results are presented for the pair distribution functions, the equation of state, the Hugoniot curve, and the reflectivity. We compare with available experimental data and predictions of the chemical picture. Especially, we discuss the nonmetal-to-metal transition which occurs at about 40 GPa in the dense fluid.

  10. Molecular and Metallic Hydrogen

    Science.gov (United States)

    1977-05-01

    interaction between hydroge , molecules. Fortunately, theoretical calculation of the pair potential from first principles at small intermolecular...three- ,’ody effect is a general phenomenon for all highly condensed states of molecular hydroger The effect of t’ ,ree-body contribution to the...parameters of metallic hydroge -. have given more consis- tent results than those for the molecular hydrogen. For example, the r-sults of the earliest

  11. Equilibration dynamics and conductivity of warm dense hydrogen

    Science.gov (United States)

    Zastrau, U.; Sperling, P.; Becker, A.; Bornath, T.; Bredow, R.; Döppner, T.; Dziarzhytski, S.; Fennel, T.; Fletcher, L. B.; Förster, E.; Fortmann, C.; Glenzer, S. H.; Göde, S.; Gregori, G.; Harmand, M.; Hilbert, V.; Holst, B.; Laarmann, T.; Lee, H. J.; Ma, T.; Mithen, J. P.; Mitzner, R.; Murphy, C. D.; Nakatsutsumi, M.; Neumayer, P.; Przystawik, A.; Roling, S.; Schulz, M.; Siemer, B.; Skruszewicz, S.; Tiggesbäumker, J.; Toleikis, S.; Tschentscher, T.; White, T.; Wöstmann, M.; Zacharias, H.; Redmer, R.

    2014-07-01

    We investigate subpicosecond dynamics of warm dense hydrogen at the XUV free-electron laser facility (FLASH) at DESY (Hamburg). Ultrafast impulsive electron heating is initiated by a ≤300-fs short x-ray burst of 92-eV photon energy. A second pulse probes the sample via x-ray scattering at jitter-free variable time delay. We show that the initial molecular structure dissociates within (0.9±0.2) ps, allowing us to infer the energy transfer rate between electrons and ions. We evaluate Saha and Thomas-Fermi ionization models in radiation hydrodynamics simulations, predicting plasma parameters that are subsequently used to calculate the static structure factor. A conductivity model for partially ionized plasma is validated by two-temperature density-functional theory coupled to molecular dynamic simulations and agrees with the experimental data. Our results provide important insights and the needed experimental data on transport properties of dense plasmas.

  12. Indentifying the Molecular Origin of Global Warming

    Science.gov (United States)

    Bera, P. P.; Lee, T. J.; Francisco, J.

    2009-12-01

    Indentifying the Molecular Origin of Global Warming Partha P. Bera, Joseph S. Francisco and Timothy J. Lee NASA Ames Research Center, Space Science and Astrobiology Division, Moffett Field, California 94035, and Department of Chemistry and Department of Earth and Atmospheric Sciences, Purdue University, West Lafayette, Indiana 47907-1393 Abstract The physical characteristics of greenhouse gases (GHGs) have been investigated to assess which properties are most important in determining the radiative efficiency of a GHG. Chlorofluorcarbons (CFCs), hydrofluorocarbons (HFCs), perfluorocarbons (PFCs), hydrofluoroethers, fluoroethers, nitrogen fluorides, and various other known atmospheric trace molecules have been included in this study. Compounds containing the halogens F or Cl have in common very polar X-F or X-Cl bonds, particularly the X-F bonds. It is shown that as more F atoms bond to the same central atom, the bond dipoles become larger as a result of the central carbon atom becoming more positive. This leads to a linear increase in the total or integrated X-F bond dipole derivatives for the molecule, which leads to a non-linear (quadratic) increase in infrared (IR) intensity. Moreover, virtually all of the X-F bond stretches occur in the atmospheric IR window as opposed to X-H stretches, which do not occur in the atmospheric window. It is concluded that molecules possessing several F atoms will always have a large radiative forcing parameter in the calculation of their global warming potential. Some of the implications for global warming and climate change and a new design strategy for more environmentally friendly industrial materials from a molecular quantum chemistry perspective will be discussed.

  13. Warm Pressurant Gas Effects on the Liquid Hydrogen Bubble Point

    Science.gov (United States)

    Hartwig, Jason W.; McQuillen, John B.; Chato, David J.

    2013-01-01

    This paper presents experimental results for the liquid hydrogen bubble point tests using warm pressurant gases conducted at the Cryogenic Components Cell 7 facility at the NASA Glenn Research Center in Cleveland, Ohio. The purpose of the test series was to determine the effect of elevating the temperature of the pressurant gas on the performance of a liquid acquisition device. Three fine mesh screen samples (325 x 2300, 450 x 2750, 510 x 3600) were tested in liquid hydrogen using cold and warm noncondensible (gaseous helium) and condensable (gaseous hydrogen) pressurization schemes. Gases were conditioned from 0 to 90 K above the liquid temperature. Results clearly indicate a degradation in bubble point pressure using warm gas, with a greater reduction in performance using condensable over noncondensible pressurization. Degradation in the bubble point pressure is inversely proportional to screen porosity, as the coarsest mesh demonstrated the highest degradation. Results here have implication on both pressurization and LAD system design for all future cryogenic propulsion systems. A detailed review of historical heated gas tests is also presented for comparison to current results.

  14. Molecular Hydrogen in Infrared Cirrus

    CERN Document Server

    Gillmon, K; Gillmon, Kristen

    2006-01-01

    We combine data from our recent FUSE survey of interstellar molecular hydrogen absorption toward 50 high-latitude AGN with COBE-corrected IRAS 100 micron emission maps to study the correlation of infrared cirrus with H2. A plot of the H2 column density vs. IR cirrus intensity shows the same transition in molecular fraction, f_H2, as seen with total hydrogen column density, N_H. This transition is usually attributed to H2 self-shielding, and it suggests that many diffuse cirrus clouds contain H2 in significant fractions, f_H2 = 1-30%. These clouds cover approximately 50% of the northern sky at latitudes b > 30 degrees, at temperature-corrected 100 micron intensities D_100 > 1.5 MJy/sr. The sheetlike cirrus clouds, with hydrogen densities n_H > 30 cm^-3, may be compressed by dynamical processes at the disk-halo interface, and they are conducive to H2 formation on grain surfaces. Exploiting the correlation between N(H2) and 100 micron intensity, we estimate that cirrus clouds at b > 30 contain approximately 3000...

  15. Identifying the Molecular Origin of Global Warming

    Science.gov (United States)

    Bera, Partha P.; Francisco, Joseph S.; Lee, Timothy J.

    2009-01-01

    We have investigated the physical characteristics of greenhouse gases (GHGs) to assess which properties are most important in determining the efficiency of a GHG. Chlorofluorcarbons (CFCs), hydrofluorocarbons (HFCs), perfluorocarbons (PFCs), nitrogen fluorides, and various other known atmospheric trace molecules have been included in this study. Compounds containing the halogens F or Cl have in common very polar X-F or X-Cl bonds, particularly the X-F bonds. It is shown that as more F atoms bond to the same central atom, the bond dipoles become larger as a result of the central atom becoming more positive. This leads to a linear increase in the total or integrated XF bond dipole derivatives for the molecule, which leads to a non-linear (quadratic) increase in infrared (IR) intensity. Moreover, virtually all of the X-F bond stretches occur in the atmospheric IR window as opposed to X-H stretches, which do not occur in the atmospheric window. It is concluded that molecules possessing several F atoms will always have a large radiative forcing parameter in the calculation of their global warming potential. Some of the implications for global warming and climate change are discussed.

  16. Warm Molecular Gas in Luminous Infrared Galaxies

    CERN Document Server

    Lu, N; Xu, C K; Gao, Y; Armus, L; Mazzarella, J M; Isaak, K G; Petric, A O; Charmandaris, V; Diaz-Santos, T; Evans, A S; Howell, J; Appleton, P; Inami, H; Iwasawa, K; Leech, J; Lord, S; Sanders, D B; Schulz, B; Surace, J; van der Werf, P P

    2014-01-01

    We present our initial results on the CO rotational spectral line energy distribution (SLED) of the $J$ to $J$$-$1 transitions from $J=4$ up to $13$ from Herschel SPIRE spectroscopic observations of 65 luminous infrared galaxies (LIRGs) in the Great Observatories All-Sky LIRG Survey (GOALS). The observed SLEDs change on average from one peaking at $J \\le 4$ to a broad distribution peaking around $J \\sim\\,$6$-$7 as the IRAS 60-to-100 um color, $C(60/100)$, increases. However, the ratios of a CO line luminosity to the total infrared luminosity, $L_{\\rm IR}$, show the smallest variation for $J$ around 6 or 7. This suggests that, for most LIRGs, ongoing star formation (SF) is also responsible for a warm gas component that emits CO lines primarily in the mid-$J$ regime ($5 \\lesssim J \\lesssim 10$). As a result, the logarithmic ratios of the CO line luminosity summed over CO (5$-$4), (6$-$5), (7$-$6), (8$-$7) and (10$-$9) transitions to $L_{\\rm IR}$, $\\log R_{\\rm midCO}$, remain largely independent of $C(60/100)$, ...

  17. From the warm magnetized atomic medium to molecular clouds

    CERN Document Server

    Hennebelle, P; Vázquez-Semadeni, E; Klessen, R; Audit, E

    2008-01-01

    {It has recently been proposed that giant molecular complexes form at the sites where streams of diffuse warm atomic gas collide at transonic velocities.} {We study the global statistics of molecular clouds formed by large scale colliding flows of warm neutral atomic interstellar gas under ideal MHD conditions. The flows deliver material as well as kinetic energy and trigger thermal instability leading eventually to gravitational collapse.} {We perform adaptive mesh refinement MHD simulations which, for the first time in this context, treat self-consistently cooling and self-gravity.} {The clouds formed in the simulations develop a highly inhomogeneous density and temperature structure, with cold dense filaments and clumps condensing from converging flows of warm atomic gas. In the clouds, the column density probability density distribution (PDF) peaks at $\\sim 2 \\times 10^{21} \\psc$ and decays rapidly at higher values; the magnetic intensity correlates weakly with density from $n \\sim 0.1$ to $10^4 \\pcc$, an...

  18. Modeling the Hydrogen Bond within Molecular Dynamics

    Science.gov (United States)

    Lykos, Peter

    2004-01-01

    The structure of a hydrogen bond is elucidated within the framework of molecular dynamics based on the model of Rahman and Stillinger (R-S) liquid water treatment. Thus, undergraduates are exposed to the powerful but simple use of classical mechanics to solid objects from a molecular viewpoint.

  19. Antiproton collisions with molecular hydrogen

    DEFF Research Database (Denmark)

    Lühr, Armin Christian; Saenz, Alejandro

    2008-01-01

    Theoretical antiproton and proton cross sections for ionization and excitation of hydrogen molecules as well as energy spectra of the ionized electrons were calculated in the impact-energy range from 8  to  4000  keV. The cross sections were computed with the close-coupling formulation of the sem......Theoretical antiproton and proton cross sections for ionization and excitation of hydrogen molecules as well as energy spectra of the ionized electrons were calculated in the impact-energy range from 8  to  4000  keV. The cross sections were computed with the close-coupling formulation...

  20. Glitters of warm H2 in cold diffuse molecular gas

    NARCIS (Netherlands)

    Falgarone, Edith; Beichman, Chaz; Boulanger, Francois; Combes, Francoise; Gry, Cecile; Helou, Georges; Laureijs, Rene; Pineau Des Forets, Guillaume; Valentijn, Edwin; Verstraete, Laurent

    2004-01-01

    Cold molecular hydrogen, a possibly dominant gas fraction in galaxies, does not radiate due to the symmetry and small moment of inertia of the molecule. The only tracers of cold H2, the rotational lines of CO and dust thermal emission operate only in metal-rich environments. By detecting the lowest

  1. Upgradation of bauxite by molecular hydrogen and hydrogen plasma

    Science.gov (United States)

    Parhi, B. R.; Sahoo, S. K.; Mishra, S. C.; Bhoi, B.; Paramguru, R. K.; Satapathy, B. K.

    2016-10-01

    An approach was developed to upgrade the bauxite ore by molecular hydrogen and hydrogen plasma. A gibbsite-type bauxite sample was obtained from National Aluminium Company (NALCO), Odisha, India. The obtained sample was crushed and sieved (to 100 μm) prior to the chemical analysis and grain-size distribution study. The bauxite sample was calcined in the temperature range from 500 to 700°C for different time intervals to optimize the conditions for maximum moisture removal. This process was followed by the reduction of the calcined ore by molecular hydrogen and hydrogen plasma. Extraction of alumina from the reduced ore was carried out via acid leaching in chloride media for 2 h at 60°C. X-ray diffraction, scanning electron microscopy, thermogravimetry in conjunction with differential scanning calorimetry, and Fourier transform infrared spectroscopy were used to determine the physicochemical characteristics of the material before and after extraction. Alumina extracted from the reduced ore at the optimum calcination temperature of 700°C and the optimum calcination time of 4 h is found to be 90% pure.

  2. Water lubricates hydrogen-bonded molecular machines

    Science.gov (United States)

    Panman, Matthijs R.; Bakker, Bert H.; den Uyl, David; Kay, Euan R.; Leigh, David A.; Buma, Wybren Jan; Brouwer, Albert M.; Geenevasen, Jan A. J.; Woutersen, Sander

    2013-11-01

    The mechanical behaviour of molecular machines differs greatly from that of their macroscopic counterparts. This applies particularly when considering concepts such as friction and lubrication, which are key to optimizing the operation of macroscopic machinery. Here, using time-resolved vibrational spectroscopy and NMR-lineshape analysis, we show that for molecular machinery consisting of hydrogen-bonded components the relative motion of the components is accelerated strongly by adding small amounts of water. The translation of a macrocycle along a thread and the rotation of a molecular wheel around an axle both accelerate significantly on the addition of water, whereas other protic liquids have much weaker or opposite effects. We tentatively assign the superior accelerating effect of water to its ability to form a three-dimensional hydrogen-bond network between the moving parts of the molecular machine. These results may indicate a more general phenomenon that helps explain the function of water as the ‘lubricant of life’.

  3. Hydrogen-nitrogen greenhouse warming in Earth's early atmosphere.

    Science.gov (United States)

    Wordsworth, Robin; Pierrehumbert, Raymond

    2013-01-04

    Understanding how Earth has sustained surface liquid water throughout its history remains a key challenge, given that the Sun's luminosity was much lower in the past. Here we show that with an atmospheric composition consistent with the most recent constraints, the early Earth would have been significantly warmed by H(2)-N(2) collision-induced absorption. With two to three times the present-day atmospheric mass of N(2) and a H(2) mixing ratio of 0.1, H(2)-N(2) warming would be sufficient to raise global mean surface temperatures above 0°C under 75% of present-day solar flux, with CO(2) levels only 2 to 25 times the present-day values. Depending on their time of emergence and diversification, early methanogens may have caused global cooling via the conversion of H(2) and CO(2) to CH(4), with potentially observable consequences in the geological record.

  4. Molecular hydrogen attenuates neuropathic pain in mice.

    Directory of Open Access Journals (Sweden)

    Masanori Kawaguchi

    Full Text Available Neuropathic pain remains intractable and the development of new therapeutic strategies are urgently required. Accumulating evidence indicates that overproduction of oxidative stress is a key event in the pathogenesis of neuropathic pain. However, repeated intra-peritoneal or intrathecal injections of antioxidants are unsuitable for continuous use in therapy. Here we show a novel therapeutic method against neuropathic pain: drinking water containing molecular hydrogen (H2 as antioxidant. The effect of hydrogen on neuropathic pain was investigated using a partial sciatic nerve ligation model in mice. As indicators of neuropathic pain, temporal aspects of mechanical allodynia and thermal hyperalgesia were analysed for 3 weeks after ligation. Mechanical allodynia and thermal hyperalgesia were measured using the von Frey test and the plantar test, respectively. When mice were allowed to drink water containing hydrogen at a saturated level ad libitum after ligation, both allodynia and hyperalgesia were alleviated. These symptoms were also alleviated when hydrogen was administered only for the induction phase (from day 0 to 4 after ligation. When hydrogen was administered only for the maintenance phase (from day 4 to 21 after ligation, hyperalgesia but not allodynia was alleviated. Immunohistochemical staining for the oxidative stress marker, 4-hydroxy-2-nonenal and 8-hydroxydeoxyguanosine, showed that hydrogen administration suppressed oxidative stress induced by ligation in the spinal cord and the dorsal root ganglion. In conclusion, oral administration of hydrogen water may be useful for alleviating neuropathic pain in a clinical setting.

  5. Molecular Hydrogen Attenuates Neuropathic Pain in Mice

    Science.gov (United States)

    Kawaguchi, Masanori; Satoh, Yasushi; Otsubo, Yukiko; Kazama, Tomiei

    2014-01-01

    Neuropathic pain remains intractable and the development of new therapeutic strategies are urgently required. Accumulating evidence indicates that overproduction of oxidative stress is a key event in the pathogenesis of neuropathic pain. However, repeated intra-peritoneal or intrathecal injections of antioxidants are unsuitable for continuous use in therapy. Here we show a novel therapeutic method against neuropathic pain: drinking water containing molecular hydrogen (H2) as antioxidant. The effect of hydrogen on neuropathic pain was investigated using a partial sciatic nerve ligation model in mice. As indicators of neuropathic pain, temporal aspects of mechanical allodynia and thermal hyperalgesia were analysed for 3 weeks after ligation. Mechanical allodynia and thermal hyperalgesia were measured using the von Frey test and the plantar test, respectively. When mice were allowed to drink water containing hydrogen at a saturated level ad libitum after ligation, both allodynia and hyperalgesia were alleviated. These symptoms were also alleviated when hydrogen was administered only for the induction phase (from day 0 to 4 after ligation). When hydrogen was administered only for the maintenance phase (from day 4 to 21 after ligation), hyperalgesia but not allodynia was alleviated. Immunohistochemical staining for the oxidative stress marker, 4-hydroxy-2-nonenal and 8-hydroxydeoxyguanosine, showed that hydrogen administration suppressed oxidative stress induced by ligation in the spinal cord and the dorsal root ganglion. In conclusion, oral administration of hydrogen water may be useful for alleviating neuropathic pain in a clinical setting. PMID:24941001

  6. Modelling the global tropospheric molecular hydrogen cycle

    NARCIS (Netherlands)

    Pieterse, G.

    2013-01-01

    Would urban air quality and climate improve if we replaced the fossil fuels by molecular hydrogen (H2) as an energy carrier? A quantitative answer to this question requires a thorough understanding of the current role of H2 in the Earth’s atmosphere. On its own, H2 does not impact climate, as for ex

  7. Modelling the global tropospheric molecular hydrogen cycle

    NARCIS (Netherlands)

    Pieterse, G.

    2013-01-01

    Would urban air quality and climate improve if we replaced the fossil fuels by molecular hydrogen (H2) as an energy carrier? A quantitative answer to this question requires a thorough understanding of the current role of H2 in the Earth’s atmosphere. On its own, H2 does not impact climate, as for

  8. Collisions of antiprotons with hydrogen molecular ions

    DEFF Research Database (Denmark)

    Lühr, Armin Christian; Saenz, Alejandro

    2009-01-01

    Time-dependent close-coupling calculations of the ionization and excitation cross section for antiproton collisions with molecular hydrogen ions are performed in an impact energy range from 0.5 keV to 10 MeV. The Born-Oppenheimer and Franck-Condon approximations as well as the impact parameter...

  9. Rotation of the Warm Molecular Gas Surrounding Ultracompact HII Regions

    CERN Document Server

    Klaassen, P D; Keto, E R; Zhang, Q

    2009-01-01

    We present molecular line and 1.4 mm continuum observations towards five massive star forming regions at arcsecond resolution using the Submillimeter Array (SMA). We find that the warm molecular gas surrounding each HII region (as traced by SO_2 and OCS) appears to be undergoing bulk rotation. From the molecular line emission and thermal component of the continuum emission, we independently derived gas masses for each region which are consistent with each other. From the free-free component of the continuum emission we estimate the minimum stellar mass required to power the HII region and find that this mass, when added to the derived gas mass, is a significant fraction of the dynamical mass for that region.

  10. Analysis of laser shock experiments on precompressed samples using a quartz reference and application to warm dense hydrogen and helium

    CERN Document Server

    Brygoo, Stephanie; Loubeyre, Paul; Lazicki, Amy E; Hamel, Sebastien; Qi, Tingting; Celliers, Peter M; Coppari, Federica; Eggert, Jon H; Fratanduono, Dayne E; Hicks, Damien G; Rygg, J Ryan; Smith, Raymond F; Swift, Damian C; Collins, Gilbert W; Jeanloz, Raymond

    2015-01-01

    Megabar (1 Mbar = 100 GPa) laser shocks on precompressed samples allow reaching unprecedented high densities and moderately high 10000-100000K temperatures. We describe here a complete analysis framework for the velocimetry (VISAR) and pyrometry (SOP) data produced in these experiments. Since the precompression increases the initial density of both the sample of interest and the quartz reference for pressure-density, reflectivity and temperature measurements, we describe analytical corrections based on available experimental data on warm dense silica and density-functional-theory based molecular dynamics computer simulations. Using our improved analysis framework we report a re-analysis of previously published data on warm dense hydrogen and helium, compare the newly inferred pressure, density and temperature data with most advanced equation of state models and provide updated reflectivity values.

  11. Parameters of Warm Molecular Clouds from Methyl Acetylene Observations

    CERN Document Server

    Alakoz, A V; Promislov, V G; Johansson, L E B; Winnberg, A

    2002-01-01

    The results of a survey of 63 galactic star-forming regions in the 6_K-5_K and 5_K-4_K methyl acetylene lines at 102 and 85 GHz, respectively, are presented. Fourty-three sources were detected at 102 GHz, and twenty-five at 85 GHz. Emission was detected towards molecular clouds with kinetic temperatures 20-60 K (so-called ``warm clouds''). The CH3CCH abundances in these clouds appeared to be about several units X 10^(-9). Five mapped sources were analyzed using the maximum entropy method. The sizes of the mapped clouds fall within the range between 0.1 and 1.7 pc, virial masses - between 90-6200 Msun, and densities - between 6 X 10^4 and 6 X 10^5 cm^(-3). The CH3CCH sources spatially coincide with the CO and CS sources. Chemical evolution simulations showed that the typical methyl acetylene abundance in the observed clouds corresponds to an age of ~ 6 X 10^4 years.

  12. Crack growth behavior of warm-rolled 316L austenitic stainless steel in high-temperature hydrogenated water

    Science.gov (United States)

    Choi, Kyoung Joon; Yoo, Seung Chang; Jin, Hyung-Ha; Kwon, Junhyun; Choi, Min-Jae; Hwang, Seong Sik; Kim, Ji Hyun

    2016-08-01

    To investigate the effects of warm rolling on the crack growth of 316L austenitic stainless steel, the crack growth rate was measured and the oxide structure was characterized in high-temperature hydrogenated water. The warm-rolled specimens showed a higher crack growth rate compared to the as-received specimens because the slip bands and dislocations produced during warm rolling served as paths for corrosion and cracking. The crack growth rate increased with the dissolved hydrogen concentration. This may be attributed to the decrease in performance and stability of the protective oxide layer formed on the surface of stainless steel in high-temperature water.

  13. Molecular hydrogen formation in the interstellar medium

    CERN Document Server

    Cazaux, S

    2002-01-01

    We have developed a model for molecular hydrogen formation under astrophysically relevant conditions. This model takes fully into account the presence of both physisorbed and chemisorbed sites on the surface, allows quantum mechanical diffusion as well as thermal hopping for absorbed H-atoms, and has been benchmarked versus recent laboratory experiments on H2 formation on silicate surfaces. The results show that H2 formation on grain surface is efficient in the interstellar medium up to some 300K. At low temperatures (<100K), H2 formation is governed by the reaction of a physisorbed H with a chemisorbed H. At higher temperatures, H2 formation proceeds through reaction between two chemisorbed H atoms. We present simple analytical expressions for H2 formation which can be adopted to a wide variety of surfaces once their surfaces characteristics have been determined experimentally.

  14. Molecular Hydrogen Therapy Ameliorates Organ Damage Induced by Sepsis

    Directory of Open Access Journals (Sweden)

    Yijun Zheng

    2016-01-01

    Full Text Available Since it was proposed in 2007, molecular hydrogen therapy has been widely concerned and researched. Many animal experiments were carried out in a variety of disease fields, such as cerebral infarction, ischemia reperfusion injury, Parkinson syndrome, type 2 diabetes mellitus, metabolic syndrome, chronic kidney disease, radiation injury, chronic hepatitis, rheumatoid arthritis, stress ulcer, acute sports injuries, mitochondrial and inflammatory disease, and acute erythema skin disease and other pathological processes or diseases. Molecular hydrogen therapy is pointed out as there is protective effect for sepsis patients, too. The impact of molecular hydrogen therapy against sepsis is shown from the aspects of basic vital signs, organ functions (brain, lung, liver, kidney, small intestine, etc., survival rate, and so forth. Molecular hydrogen therapy is able to significantly reduce the release of inflammatory factors and oxidative stress injury. Thereby it can reduce damage of various organ functions from sepsis and improve survival rate. Molecular hydrogen therapy is a prospective method against sepsis.

  15. High excitation rovibrational molecular analysis in warm environments

    Science.gov (United States)

    Zhang, Ziwei; Stancil, Phillip C.; Cumbee, Renata; Ferland, Gary J.

    2017-06-01

    Inspired by advances in infrared observation (e.g., Spitzer, Herschel and ALMA), we investigate rovibrational emission CO and SiO in warm astrophysical environments. With recent innovation in collisional rate coefficients and rescaling methods, we are able to construct more comprehensive collisional data with high rovibrational states (vibration up to v=5 and rotation up to J=40) and multiple colliders (H2, H and He). These comprehensive data sets are used in spectral simulations with the radiative transfer codes RADEX and Cloudy. We obtained line ratio diagnostic plots and line spectra for both near- and far-infrared emission lines over a broad range of density and temperature for the case of a uniform medium. Considering the importance of both molecules in probing conditions and activities of UV-irradiated interstellar gas, we model rovibrational emission in photodissociation region (PDR) and AGB star envelopes (such as VY Canis Majoris, IK Tau and IRC +10216) with Cloudy. Rotational diagrams, energy distribution diagrams, and spectra are produced to examine relative state abundances, line emission intensity, and other properties. With these diverse models, we expect to have a better understanding of PDRs and expand our scope in the chemical architecture and evolution of AGB stars and other UV-irradiated regions. The soon to be launched James Webb Space Telescope (JWST) will provide high resolution observations at near- to mid-infrared wavelengths, which opens a new window to study molecular vibrational emission calling for more detailed chemical modeling and comprehensive laboratory astrophysics data on more molecules. This work was partially supported by NASA grants NNX12AF42G and NNX15AI61G. We thank Benhui Yang, Kyle Walker, Robert Forrey, and N. Balakrishnan for collaborating on the collisional data adopted in the current work.

  16. Cold and warm atomic gas around the Perseus molecular cloud I: Basic Properties

    CERN Document Server

    Stanimirovic, Snezana; Lee, Min-Young; Heiles, Carl; Miller, Jesse

    2014-01-01

    (Abridged) Using the Arecibo Observatory we have obtained neutral hydrogen (HI) absorption and emission spectral pairs in the direction of 26 background radio continuum sources in the vicinity of the Perseus molecular cloud. Strong absorption lines were detected in all cases allowing us to estimate spin temperature (T_s) and optical depth for 107 individual Gaussian components along these lines of sight. Basic properties of individual HI clouds (spin temperature, optical depth, and the column density of the cold and warm neutral medium, CNM and WNM) in and around Perseus are very similar to those found for random interstellar lines of sight sampled by the Millennium HI survey. This suggests that the neutral gas found in and around molecular clouds is not atypical. However, lines of sight in the vicinity of Perseus have on average a higher total HI column density and the CNM fraction, suggesting an enhanced amount of cold HI relative to an average interstellar field. Our estimated optical depth and spin temper...

  17. Molecular hydrogen absorption systems in SDSS

    CERN Document Server

    Balashev, S A; Ivanchik, A V; Varshalovich, D A; Petitjean, P; Noterdaeme, P

    2014-01-01

    We present a systematic search for molecular hydrogen absorption systems at high redshift in quasar spectra from the Sloan Digital Sky Survey (SDSS) II Data Release 7 and SDSS-III Data Release 9. We have selected candidates using a modified profile fitting technique taking into account that the Ly$\\alpha$ forest can effectively mimic H$_2$ absorption systems at the resolution of SDSS data. To estimate the confidence level of the detections, we use two methods: a Monte-Carlo sampling and an analysis of control samples. The analysis of control samples allows us to define regions of the spectral quality parameter space where H$_2$ absorption systems can be confidently identified. We find that H$_2$ absorption systems with column densities $\\log {\\rm N_{H_2}} > 19$ can be detected in only less than 3% of SDSS quasar spectra. We estimate the upper limit on the detection rate of saturated H$_2$ absorption systems ($\\log {\\rm N_{H_2}} > 19$) in Damped Ly-$\\alpha$ (DLA) systems to be about 7%. We provide a sample of ...

  18. Molecular hydrogen in Lyman Alpha Emitters

    CERN Document Server

    Vallini, Livia; Ferrara, Andrea

    2012-01-01

    We present a physically motivated model to estimate the molecular hydrogen (H2) content of high-redshift (z~5.7,6.6) Lyman Alpha Emitters (LAEs) extracted from a suite of cosmological simulations. We find that the H2 mass fraction, (f_H2), depends on three main LAE physical properties: (a) star formation rate, (b) dust mass, and (c) cold neutral gas mass. At z~5.7, the value of f_H2 peaks and ranges between 0.5-0.9 for intermediate mass LAEs with stellar mass M_* ~ 10^{9-10} solar mass, decreasing for both smaller and larger galaxies. However, the largest value of the H2 mass is found in the most luminous LAEs. These trends also hold at z\\sim6.6, although, due to a lower dust content, f_H2(z=6.6)\\sim0.5 f_H2(z=5.7) when averaged over all LAEs; they arise due to the interplay between the H2 formation/shielding controlled by dust and the intensity of the ultraviolet (UV) Lyman-Werner photo-dissociating radiation produced by stars. We then predict the carbon monoxide (CO) luminosities for such LAEs and check tha...

  19. The Catalytic Role of Coronene for Molecular Hydrogen Formation

    DEFF Research Database (Denmark)

    Mennella, Vito; Hornekær, Liv; Thrower, John

    2012-01-01

    We present the results of an experimental study on the interaction of atomic deuterium with coronene films. The effects of D atom irradiation have been analyzed with infrared spectroscopy. The spectral changes provide evidence for deuteration of the outer edge coronene C sites via a D addition...... showthat hydrogenated neutral polycyclic aromatic hydrocarbon molecules act as catalysts for the formation of molecular hydrogen....

  20. Warming-Induced Changes to the Molecular Composition of Soil Organic Matter

    Science.gov (United States)

    Feng, X.; Simpson, M. J.; Simpson, A. J.; Wilson, K. P.; Williams, D.

    2007-12-01

    Soil organic matter (SOM) contains two times more carbon than the atmosphere and the potential changes to SOM quantity and quality with global warming are a major concern. It is commonly believed that global warming will accelerate the decomposition of labile SOM compounds while refractory SOM constituents will remain stable. However, experimental evidence of molecular-level changes to SOM composition with global warming is currently lacking. Here we employ SOM biomarkers and nuclear magnetic resonance (NMR) spectroscopy to study SOM composition and degradation in a soil warming experiment in southern Ontario, Canada. The soil warming experiment consisted of a control and a treatment plot in a mixed forest that had a temperature difference of about 5 degrees C for 14 months. Before soil warming the control and treatment plots had the same organic carbon (OC) content and SOM composition. Soil warming significantly increased soil OC content and the abundance of cutin-derived carbon originating from leaf tissues and decreased carbohydrates that are regarded as easily degradable. Lignin components, which are believed to be part of the stable and slowly-cycling SOM, were observed to be in an advanced stage of degradation. This observation is corroborated by increases in fungal biomass in the warmed soil because fungi are considered the primary decomposer of lignin in the soil environment. An NMR study of SOM in the warmed and control plots indicates that alkyl carbon, mainly originating from plant cuticles in the soil, increased in the warmed soil while O-alkyl carbon, primarily occurring in carbohydrates, decreased. Aromatic and phenolic carbon regions, which include the main structures found in lignin, decreased in the warmed soil. These data collectively suggest that there is a great potential for lignin degradation with soil warming, and that the refractory (aromatic) soil carbon storage may be reduced as a result of increased fungal growth in a warmer climate.

  1. Soft X-Ray Thomson Scattering in Warm Dense Hydrogen at FLASH

    Energy Technology Data Exchange (ETDEWEB)

    Faustlin, R R; Toleikis, S; Bornath, T; Doppner, T; Dusterer, S; Forster, E; Fortmann, C; Glenzer, S H; Gode, S; Gregori, G; Irsig, R; Laarmann, T; Lee, H J; Li, B; Meiwes-Broer, K; Mithen, J; Przystawik, A; Redlin, H; Redmer, R; Reinholz, H; Ropke, G; Tavella, F; Thiele, R; Tiggesbaumker, J; Uschmann, I; Zastrau, U; Tschentscher, T

    2009-07-15

    We present collective Thomson scattering with soft x-ray free electron laser radiation as a method to track the evolution of warm dense matter plasmas with {approx}200 fs time resolution. In a pump-probe scheme an 800 nm laser heats a 20 {micro}m hydrogen droplet to the plasma state. After a variable time delay in the order of ps the plasma is probed by an x-ray ultra violet (XUV) pulse which scatters from the target and is recorded spectrally. Alternatively, in a self-Thomson scattering experiment, a single XUV pulse heats the target while a portion of its photons are being scattered probing the target. From such inelastic x-ray scattering spectra free electron temperature and density can be inferred giving insight on relaxation time scales in plasmas as well as the equation of state. We prove the feasibility of this method in the XUV range utilizing the free electron laser facility in Hamburg, FLASH. We recorded Thomson scattering spectra for hydrogen plasma, both in the self-scattering and in the pump-probe mode using optical laser heating.

  2. Path Integral Molecular Dynamics for Hydrogen with Orbital-Free Density Functional Theory

    Science.gov (United States)

    Runge, Keith; Karasiev, Valentin; Deymier, Pierre

    2014-03-01

    The computational bottleneck for performing path-integral molecular dynamics (PIMD) for nuclei on a first principles electronic potential energy surface has been the speed with which forces from the electrons can be generated. Recent advances in orbital-free density functional theory (OF-DFT) not only allow for faster generation of first principles forces but also include the effects of temperature on the electron density. We will present results of calculations on hydrogen in warm dense matter conditions where the protons are described by PIMD and the electrons by OF-DFT. Work supported by U.S. Dept. of Energy, grant DE-SC0002139.

  3. Conduction Mechanism in a Molecular Hydrogen Contact

    DEFF Research Database (Denmark)

    Thygesen, Kristian Sommer; Jacobsen, Karsten Wedel

    2005-01-01

    We present first principles calculations for the conductance of a hydrogen molecule bridging a pair of Pt electrodes. The transmission function has a wide plateau with Tapproximate to1 which extends across the Fermi level and indicates the existence of a single, robust conductance channel with ne...... allow us to derive a resonant-level model for the system with all parameters determined from the fully self-consistent Kohn-Sham Hamiltonian....

  4. Molecular hydrogen in the cosmic recombination epoch

    CERN Document Server

    Alizadeh, Esfandiar

    2010-01-01

    The advent of precise measurements of the cosmic microwave background (CMB) anisotropies has motivated correspondingly precise calculations of the cosmic recombination history. Cosmic recombination proceeds far out of equilibrium because of a "bottleneck" at the $n=2$ level of hydrogen: atoms can only reach the ground state via slow processes: two-photon decay or Lyman-$\\alpha$ resonance escape. However, even a small primordial abundance of molecules could have a large effect on the interline opacity in the recombination epoch and lead to an additional route for hydrogen recombination. Therefore, this paper computes the abundance of the H$_2$ molecule during the cosmic recombination epoch. Hydrogen molecules in the ground electronic levels X$^1\\Sigma^+_g$ can either form from the excited H$_2$ electronic levels B$^1\\Sigma^+_u$ and C$^1\\Pi_u$ or through the charged particles H$_2^+$, HeH$^+$ and H$^-$. We follow the transitions among all of these species, resolving the rotational and vibrational sub-levels. Si...

  5. Accretion-Inhibited Star Formation in the Warm Molecular Disk of the Green-valley Elliptical Galaxy NGC 3226

    CERN Document Server

    Appleton, P N; Bitsakis, T; Lacy, M; Alatalo, K; Armus, L; Charmandaris, V; Duc, P -A; Lisenfeld, U; Ogle, P

    2014-01-01

    We present archival Spitzer photometry and spectroscopy, and Herschel photometry, of the peculiar "Green Valley" elliptical galaxy NGC~3226. The galaxy, which contains a low-luminosity AGN, forms a pair with NGC~3227, and is shown to lie in a complex web of stellar and HI filaments. Imaging at 8 and 16$\\mu$m reveals a curved plume structure 3 kpc in extent, embedded within the core of the galaxy, and coincident with the termination of a 30 kpc-long HI tail. In-situ star formation associated with the IR plume is identified from narrow-band HST imaging. The end of the IR-plume coincides with a warm molecular hydrogen disk and dusty ring, containing 0.7-1.1 $\\times$ 10$^7$ M$_{\\odot}$ detected within the central kpc. Sensitive upper limits to the detection of cold molecular gas may indicate that a large fraction of the H$_2$ is in a warm state. Photometry, derived from the UV to the far-IR, shows evidence for a low star formation rate of $\\sim$0.04 M$_{\\odot}$ yr$^{-1}$ averaged over the last 100 Myrs. A mid-IR ...

  6. Modeling molecular hydrogen emission in M dwarf exoplanetary systems

    Science.gov (United States)

    Evonosky, William; France, Kevin; Kruczek, Nick E.; Youngblood, Allison; Measurements of the Ultraviolet Spectral Characteristics of Low-mass Exoplanet host Stars (MUSCLES)

    2017-01-01

    Exoplanets orbiting low-mass stars are prime candidates for atmospheric characterization due to their astronomical abundance and short orbital periods. These planets orbit stars that are often more active than main sequence solar-type stars. They are exposed to differing levels of ultraviolet radiation which can cause traditional “biosignature” gases to be generated abiotically, potentially causing false-positive identifications of life. We modeled the recently discovered molecular hydrogen emission in the ultraviolet spectra (1350 - 1650 Å) as arising from the stellar surface, excited by radiation generated in the upper chromosphere. The model was compared with observed hydrogen emission from the “Measurements of the Ultraviolet Spectral Characteristics of Low-mass Exoplanet host Stars” (MUSCLES) survey by conducting a grid search and implementing a chi-squared minimization routine. We considered only progressions from the [1, 4] and [1, 7] first excited electronic levels. Our modeling procedure varied the atomic hydrogen column density (in the chromosphere) as well as the photospheric molecular hydrogen column density and temperature. The model required as an input a reconstructed intrinsic Lyman α profile which served as the pumping radiation for the molecular hydrogen. We found that an atomic hydrogen column density of log10N(H I) = 14.13 ± 0.16 cm-2 represents a breaking point above which there is not enough Lyman α flux available to excite a significant molecular hydrogen population into the [1, 7] state. We also present H2 temperatures which may suggest that star spots on low mass stars persist longer, and encompass more area than star spots on solar-type stars.

  7. Silane plus molecular hydrogen as a possible pathway to metallic hydrogen.

    Science.gov (United States)

    Yao, Yansun; Klug, Dennis D

    2010-12-07

    The high-pressure behavior of silane, SiH(4), plus molecular hydrogen was investigated using a structural search method and ab initio molecular dynamics to predict the structures and examine the physical origin of the pressure-induced drop in hydrogen intramolecular vibrational (vibron) frequencies. A structural distortion is predicted at 15 GPa from a slightly strained fcc cell to a rhombohedral cell that involves a small volume change. The predicted equation of state and the pressure-induced drop in the hydrogen vibron frequencies reproduces well the experimental data (Strobel TA, Somayazulu M, Hemley RJ (2009) Phys Rev Lett 103:065701). The bond weakening in H(2) is induced by intermolecular interactions between the H(2) and SiH(4) molecules. A significant feature of the high-pressure structures of SiH(4)(H(2))(2) is the dynamical behavior of the H(2) molecules. It is found that H(2) molecules are rotating in this pressure range whereas the SiH(4) molecules remain rigid. The detailed nature of the interactions of molecular hydrogen with SiH(4) in SiH(4)(H(2))(2) is therefore strongly influenced by the dynamical behavior of the H(2) molecules in the high-pressure structure. The phase with the calculated structure is predicted to become metallic near 120 GPa, which is significantly lower than the currently suggested pressure for metallization of bulk molecular hydrogen.

  8. Molecular processes of transgenerational acclimation to a warming ocean

    Science.gov (United States)

    Veilleux, Heather D.; Ryu, Taewoo; Donelson, Jennifer M.; van Herwerden, Lynne; Seridi, Loqmane; Ghosheh, Yanal; Berumen, Michael L.; Leggat, William; Ravasi, Timothy; Munday, Philip L.

    2015-12-01

    Some animals have the remarkable capacity to acclimate across generations to projected future climate change; however, the underlying molecular processes are unknown. We sequenced and assembled de novo transcriptomes of adult tropical reef fish exposed developmentally or transgenerationally to projected future ocean temperatures and correlated the resulting expression profiles with acclimated metabolic traits from the same fish. We identified 69 contigs representing 53 key genes involved in thermal acclimation of aerobic capacity. Metabolic genes were among the most upregulated transgenerationally, suggesting shifts in energy production for maintaining performance at elevated temperatures. Furthermore, immune- and stress-responsive genes were upregulated transgenerationally, indicating a new complement of genes allowing the second generation of fish to better cope with elevated temperatures. Other differentially expressed genes were involved with tissue development and transcriptional regulation. Overall, we found a similar suite of differentially expressed genes among developmental and transgenerational treatments. Heat-shock protein genes were surprisingly unresponsive, indicating that short-term heat-stress responses may not be a good indicator of long-term acclimation capacity. Our results are the first to reveal the molecular processes that may enable marine fishes to adjust to a future warmer environment over multiple generations.

  9. Molecular processes of transgenerational acclimation to a warming ocean

    KAUST Repository

    Veilleux, Heather D.

    2015-07-20

    Some animals have the remarkable capacity to acclimate across generations to projected future climate change1, 2, 3, 4; however, the underlying molecular processes are unknown. We sequenced and assembled de novo transcriptomes of adult tropical reef fish exposed developmentally or transgenerationally to projected future ocean temperatures and correlated the resulting expression profiles with acclimated metabolic traits from the same fish. We identified 69 contigs representing 53 key genes involved in thermal acclimation of aerobic capacity. Metabolic genes were among the most upregulated transgenerationally, suggesting shifts in energy production for maintaining performance at elevated temperatures. Furthermore, immune- and stress-responsive genes were upregulated transgenerationally, indicating a new complement of genes allowing the second generation of fish to better cope with elevated temperatures. Other differentially expressed genes were involved with tissue development and transcriptional regulation. Overall, we found a similar suite of differentially expressed genes among developmental and transgenerational treatments. Heat-shock protein genes were surprisingly unresponsive, indicating that short-term heat-stress responses may not be a good indicator of long-term acclimation capacity. Our results are the first to reveal the molecular processes that may enable marine fishes to adjust to a future warmer environment over multiple generations.

  10. Water lubricates hydrogen-bonded molecular machines

    NARCIS (Netherlands)

    Panman, M.R.; Bakker, B.H.; den Uyl, D.; Kay, E.R.; Leigh, D.A.; Buma, W.J.; Brouwer, A.M.; Geenevasen, J.A.J.; Woutersen, S.

    2013-01-01

    The mechanical behaviour of molecular machines differs greatly from that of their macroscopic counterparts. This applies particularly when considering concepts such as friction and lubrication, which are key to optimizing the operation of macroscopic machinery. Here, using time-resolved vibrational

  11. Nuclear spin-rotation interaction in the hydrogen molecular ion

    CERN Document Server

    Babb, J F

    1995-01-01

    The nuclear spin--rotation interaction in the hyperfine structure of the hydrogen molecular ion is investigated. The interaction constants are determined and are found to differ in sign and magnitude compared to another theory, but they are in agreement with some values derived from experiment.

  12. Theoretical study of piezoelectrochemical reactions in molecular compression chambers: In-situ generation of molecular hydrogen

    Science.gov (United States)

    Pichierri, Fabio

    2016-09-01

    Nitrogen-containing molecular compression chambers (MCCs) undergo stepwise protonation followed by a 2-electron reduction step which affords molecular hydrogen in situ. This piezoelectrochemical reaction is favored by the high compression that characterizes the molecular skeleton of MCC and its fluorinated analogue. Besides H2, the MCCs are also capable of trapping molecular fluorine and the small monoatomic gases helium and neon. A topological analysis of the electronic charge density reveals the presence of closed-shell interactions between hosts and guests.

  13. Experimental and Observational Studies of Molecular Hydrogen in Interstellar and Circumstellar Environments

    Science.gov (United States)

    Hoadley, Keri

    2017-08-01

    Understanding the evolution of gas over the lifetime of protoplanetary disks provides us with important clues about how planet formation mechanisms drive the diversity of exoplanetary systems observed to date. In the first part of my thesis, I discuss how I use fluorescent emission observations of molecular hydrogen (H2) in the far-ultraviolet (far-UV) with the Hubble Space Telescope to study the warm molecular regions (a distributions of H 2 help provide important constraints on the radiation properties of gas left in the inner disk of protoplanetary disks as they evolve. Additionally, I analyzed the absorption component of these fluorescence features, embedded within the hydrogen Lyman-alpha emission line produced by the accretion of material onto the host protostar. I present column density and temperature estimates for the H2 populations in each disk sightline, and discuss the behavior and possible spatial origins of these hot molecules. As part of my thesis, I address some observational requirements needed to gain further insights into the behavior of the warm, gaseous protoplanetary disk, focusing specifically on a spectrograph concept for the next-generation LUVOIR Surveyor. I discuss a testbed instrument, the Colorado High-resolution Echelle Stellar Spectrograph (CHESS), built as a demonstration of one component of the LUVOIR spectrograph and new technological improvements to UV optical components for the next generation of near- to far-UV astrophysical observatories. CHESS is a far-UV sounding rocket experiment designed to probe the warm and cool atoms and molecules near sites of recent star formation in the local interstellar medium. I present the science goals, design, research and development components, and calibration of the CHESS instrument. I provide results on observations taken during both launches of CHESS, with detailed analysis of the epsilon Per sightline, as inferred from the flight data. I conclude by providing future works and simple

  14. Molecular hydrogen polarization images of OMC-1

    Science.gov (United States)

    Burton, Michael G.; Minchin, N. R.; Hough, J. H.; Aspin, C.; Axon, D. J.

    1991-01-01

    An image of the polarization of the shocked H2 v = 1-0 S(1) line emission in the core of OMC-1 has been obtained. Along the molecular outflow of the source, the line is dichroically polarized by a medium of aligned grains located between the earth and the shock fronts. The polarization pattern traces the magnetic field direction, which is parallel to the outflow axis and to the large-scale field direction determined from far-IR continuum measurements. Close to the IR source IRc2, the likely source of the outflow, the aligned vectors twist, indicating that the magnetic field direction changes. Modeling the line ratios of scattered H2 lines in the reflection nebula, it is concluded that the size distribution of grains there is typical of the small grains in the diffuse interstellar medium. By contrast, the scattered continuum radiation from the core region suggests that the grains there are larger than this.

  15. Molecular hydrogen polarization images of OMC-1

    Science.gov (United States)

    Burton, Michael G.; Minchin, N. R.; Hough, J. H.; Aspin, C.; Axon, D. J.

    1991-01-01

    An image of the polarization of the shocked H2 v = 1-0 S(1) line emission in the core of OMC-1 has been obtained. Along the molecular outflow of the source, the line is dichroically polarized by a medium of aligned grains located between the earth and the shock fronts. The polarization pattern traces the magnetic field direction, which is parallel to the outflow axis and to the large-scale field direction determined from far-IR continuum measurements. Close to the IR source IRc2, the likely source of the outflow, the aligned vectors twist, indicating that the magnetic field direction changes. Modeling the line ratios of scattered H2 lines in the reflection nebula, it is concluded that the size distribution of grains there is typical of the small grains in the diffuse interstellar medium. By contrast, the scattered continuum radiation from the core region suggests that the grains there are larger than this.

  16. Molecular absorption cryogenic cooler for liquid hydrogen propulsion systems

    Science.gov (United States)

    Klein, G. A.; Jones, J. A.

    1982-01-01

    A light weight, long life molecular absorption cryogenic cooler (MACC) system is described which can use low temperature waste heat to provide cooling for liquid hydrogen propellant tanks for interplanetary spacecraft. Detailed tradeoff studies were made to evaluate the refrigeration system component interactions in order to minimize the mass of the spacecraft cooler system. Based on this analysis a refrigerator system mass of 31 kg is required to provide the .48 watts of cooling required by a 2.3 meter diameter liquid hydrogen tank.

  17. Two-phase equilibrium and molecular hydrogen formation in damped Lyman-alpha systems

    CERN Document Server

    Liszt, H S

    2002-01-01

    Molecular hydrogen is quite underabundant in damped Lyman-alpha systems at high redshift, when compared to the interstellar medium near the Sun. This has been interpreted as implying that the gas in damped Lyman-alpha systems is warm. like the nearby neutral intercloud medium, rather than cool, as in the clouds which give rise to most H I absorption in the Milky Way. Other lines of evidence suggest that the gas in damped Lyman-alpha systems -- in whole or part -- is actually cool; spectroscopy of neutral and ionized carbon, discussed here, shows that the damped Lyman-alpha systems observed at lower redshift z $$ 2.8 are warm (though not devoid of H2). To interpret the observations of carbon and hydrogen we constructed detailed numerical models of H2 formation under the conditions of two-phase thermal equilibrium, like those which account for conditions near the Sun, but with varying metallicity, dust-gas ratio, $etc$. We find that the low metallicity of damped Lyman-alpha systems is enough to suppress H2 form...

  18. The warm molecular gas and dust of Seyfert galaxies: two different phases of accretion?

    CERN Document Server

    Mezcua, M; Fernández-Ontiveros, J A; Tristram, K; Neumayer, N

    2015-01-01

    The distribution of warm molecular gas (1000--3000 K), traced by the near-IR H$_2$ 2.12 $\\mu$m line, has been imaged with a resolution $<0.5$ arcsec in the central 1 kpc of seven nearby Seyfert galaxies. We find that this gas is highly concentrated towards the central 100 pc and that its morphology is often symmetrical. Lanes of warm H$_2$ gas are observed only in three cases (NGC\\,1068, NGC\\,1386 and Circinus) for which the morphology is much wider and extended than the dust filaments. We conclude that there is no one-to-one correlation between dust and warm gas. This indicates that, if the dust filaments and lanes of warm gas are radial streaming motions of fueling material, they must represent \\textit{two different phases of accretion}: the dust filaments represent a colder phase than the gas close to the nucleus (within $\\sim$100 pc). We predict that the morphology of the nuclear dust at these scales should resemble that of the cold molecular gas (e.g. CO at 10-40 K), as we show for CenA and NGC\\,1566 ...

  19. Electronic excitation of molecular hydrogen by low-energy electrons

    Science.gov (United States)

    Hargreaves, Leigh

    2016-09-01

    Molecular hydrogen is the most abundant element in the universe, particularly in interstellar plasmas such as atmospheres of gas giant planets and stars. Electron collision data for hydrogen is critical to interpreting the spectroscopy of interstellar objects, as well as being of applied value for modelling technological plasmas. Hydrogen is also fundamentally interesting, as while highly accurate wave functions for this simple molecule are available, providing an accurate, ab initio, treatment the collision dynamics has proven challenging, on account of the need to have a complete description of channel coupling and polarization effects. To date, no single theoretical approach has been able to replicate experimental results across all transitions and incident energies, while the experimental database that is available is far from complete and not all available measurements are in satisfactory agreement. In this talk, we present differential and integral cross section measurements for electronic excitation cross sections for molecular hydrogen by low-energy electron impact. The data were measured at incident energies below 20eV, using a well-tested crossed beam apparatus and employing a moveable gas source approach to ensure that background contributions to the scattering are accurately accounted for. These measurements are compared with new theoretical results employing the convergent close coupling approach.

  20. Evolution of dust and molecular hydrogen in the Magellanic System

    CERN Document Server

    Yozin, Cameron

    2014-01-01

    We investigate the evolution of the interstellar medium (ISM) in self-consistent, chemodynamical simulations of the Magellanic Clouds (MCs) during their recent (z<0.3) past. An explicit modelling of dust and molecular hydrogen lifecycles enables the comparison of our models against the observed properties of the ISM, including elemental depletion from the gas-phase. Combining this model with a tidal-dominated paradigm for the formation for the Magellanic Stream and Bridge, we reproduce the age-metallicity relations, long gas depletion timescales, and presently observed dust and molecular hydrogen masses of the MCs to within their respective uncertainties. We find that these models' enrichment depends sensitively on the processing of dust within the ISM and the dynamical influence of external tides/stellar bars. The ratio of characteristic dust destruction timescales in our SMC and LMC models, a governing parameter of our models' evolution, is consistent with estimates based on observed supernova (SN) rates...

  1. FUSE Team Project on Molecular Hydrogen in Translucent Clouds

    Science.gov (United States)

    Snow, Theodore P.

    This Cycle 2 program plans observations of 11 stars (in addition to the original list) as an add-on to our medium project to study molecular hydrogen in translucent clouds. The new stars have been selected on the basis of reddening, known extinction and interstellar line parameters, and inclusion in the comprehensive survey of diffuse interstellar bands being carried out by group member Don York and collaborators (e.g. Snow, Welty et al.).

  2. Warm Molecular Gas Traced with CO J=7->6 in the Galaxy's Central 2 Parsecs: Dynamical Heating of the Circumnuclear Disk

    CERN Document Server

    Bradford, C M; Nikola, T; Bolatto, A D; Jackson, J M; Savage, M L; Davidson, J A

    2005-01-01

    We present an 11 arcsec resolution map of the central two parsecs of the Galaxy in the CO J =7->6 rotational transition. The CO emission shows rotation about Sgr A*, but also evidence for non-circular turbulent motion and a clumpy morphology. We combine our dataset with available CO measurements to model the physical conditions in the disk. We find that the molecular gas in the region is both warm and dense, with T~200-300 K, n_H2~50,000-70,000 cm^-3. The mass of warm molecular gas we measure in the central two parsecs is at least 2000 M_solar, about 20 times the UV-excited atomic gas mass, ruling out an UV heating scenario for the molecular material. We compare the available spectral tracers with theoretical models and conclude that molecular gas is heated with magneto-hydrodynamic shocks with v~10-20 kms and B~0.3-0.5 mG. Using the conditions derived with the CO analysis, we include the other important coolants--neutral oxygen and molecular hydrogen--to estimate the total cooling budget of the molecular mat...

  3. ACCRETION-INHIBITED STAR FORMATION IN THE WARM MOLECULAR DISK OF THE GREEN-VALLEY ELLIPTICAL GALAXY NGC 3226?

    Energy Technology Data Exchange (ETDEWEB)

    Appleton, P. N.; Bitsakis, T.; Alatalo, K. [NASAHerschel Science Center, Infrared Processing and Analysis Center, Caltech, 770S Wilson Avenue, Pasadena, CA 91125 (United States); Mundell, C. [Astrophysics Research Institute, John Moores University, Liverpool Science Park, 146 Brownlow Hill, Liverpool L3 5RF (United Kingdom); Lacy, M. [NRAO, Charlottesville, VA (United States); Armus, L. [Spitzer NASAHerschel Science Center, 1200 East California Boulevard, Caltech, Pasadena, CA 91125 (United States); Charmandaris, V. [Department of Physics, University of Crete, GR-71003 Heraklion (Greece); Duc, P.-A. [Service d' Astrophysique, Laboratoire AIM, CEA-Saclay, Orme des Merisiers, Bat 709, F-91191 Gif sur Yvette (France); Lisenfeld, U. [Dept. Fisica Teorica y del Cosmos, University of Granada, Edifica Mecenas, Granada (Spain); Ogle, P., E-mail: apple@ipac.caltech.edu [NASA Extragalactic Database, IPAC, Caltech, 1200 East California Boulevard, Caltech, Pasadena, CA 91125 (United States)

    2014-12-20

    We present archival Spitzer photometry and spectroscopy and Herschel photometry of the peculiar ''Green Valley'' elliptical galaxy NGC 3226. The galaxy, which contains a low-luminosity active galactic nucleus (AGN), forms a pair with NGC 3227 and is shown to lie in a complex web of stellar and H I filaments. Imaging at 8 and 16 μm reveals a curved plume structure 3 kpc in extent, embedded within the core of the galaxy and coincident with the termination of a 30 kpc long H I tail. In situ star formation associated with the infrared (IR) plume is identified from narrowband Hubble Space Telescope (HST) imaging. The end of the IR plume coincides with a warm molecular hydrogen disk and dusty ring containing 0.7-1.1 × 10{sup 7} M {sub ☉} detected within the central kiloparsec. Sensitive upper limits to the detection of cold molecular gas may indicate that a large fraction of the H{sub 2} is in a warm state. Photometry derived from the ultraviolet (UV) to the far-IR shows evidence for a low star-formation rate of ∼0.04 M {sub ☉} yr{sup –1} averaged over the last 100 Myr. A mid-IR component to the spectral energy distribution (SED) contributes ∼20% of the IR luminosity of the galaxy, and is consistent with emission associated with the AGN. The current measured star formation rate is insufficient to explain NGC 3226's global UV-optical ''green'' colors via the resurgence of star formation in a ''red and dead'' galaxy. This form of ''cold accretion'' from a tidal stream would appear to be an inefficient way to rejuvenate early-type galaxies and may actually inhibit star formation.

  4. The Molecular Hydrogen Deficit in Gamma-Ray Burst Afterglows

    CERN Document Server

    Whalen, Daniel; Heger, Alexander; Tumlinson, Jason

    2008-01-01

    Recent analysis of five gamma-ray burst (GRB) afterglow spectra reveal the absence of molecular hydrogen absorption lines, a surprising result in light of their large neutral hydrogen column densities and the detection of H$_2$ in similar, more local star-forming regions like 30 Doradus in the LMC. Observational evidence further indicates that the bulk of the neutral hydrogen column in these sight lines lies 100 pc beyond the progenitor and that H$_2$ was absent prior to the burst, suggesting that direct flux from the star, FUV background fields, or both suppressed its formation. We present one-dimensional radiation hydrodynamical models of GRB host galaxy environments, including self-consistent radiative transfer of both ionizing and Lyman-Werner photons, nine-species primordial chemistry with dust formation of H$_2$, and dust extinction of UV photons. We find that a single GRB progenitor is sufficient to ionize neutral hydrogen to distances of 50 - 150 pc but that a galactic Lyman-Werner background is requi...

  5. Nuclear conversion theory: molecular hydrogen in non-magnetic insulators

    Science.gov (United States)

    Ilisca, Ernest; Ghiglieno, Filippo

    2016-09-01

    The hydrogen conversion patterns on non-magnetic solids sensitively depend upon the degree of singlet/triplet mixing in the intermediates of the catalytic reaction. Three main `symmetry-breaking' interactions are brought together. In a typical channel, the electron spin-orbit (SO) couplings introduce some magnetic excitations in the non-magnetic solid ground state. The electron spin is exchanged with a molecular one by the electric molecule-solid electron repulsion, mixing the bonding and antibonding states and affecting the molecule rotation. Finally, the magnetic hyperfine contact transfers the electron spin angular momentum to the nuclei. Two families of channels are considered and a simple criterion based on the SO coupling strength is proposed to select the most efficient one. The denoted `electronic' conversion path involves an emission of excitons that propagate and disintegrate in the bulk. In the other denoted `nuclear', the excited electron states are transients of a loop, and the electron system returns to its fundamental ground state. The described model enlarges previous studies by extending the electron basis to charge-transfer states and `continui' of band states, and focuses on the broadening of the antibonding molecular excited state by the solid conduction band that provides efficient tunnelling paths for the hydrogen conversion. After working out the general conversion algebra, the conversion rates of hydrogen on insulating and semiconductor solids are related to a few molecule-solid parameters (gap width, ionization and affinity potentials) and compared with experimental measures.

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

    Science.gov (United States)

    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.

  7. Molecular and ionic hydrogen bond formation in fluorous solvents.

    Science.gov (United States)

    O'Neal, Kristi L; Weber, Stephen G

    2009-01-08

    There are only a few studies of noncovalent association in fluorous solvents and even fewer that are quantitative. A full understanding, particularly of stoichiometry and binding strength of noncovalent interactions in fluorous solvents could be very useful in improved molecular-receptor-based extractions, advancements in sensor technologies, crystal engineering, and supramolecular chemistry. This work investigates hydrogen bonding between heterocyclic bases and a perfluoropolyether with a terminal carboxylic acid group (Krytox 157FSH (1)), chiefly in FC-72 (a mixture of perfluorohexanes). In particular, we were interested in whether or not proton transfer occurs, and if so, under what conditions in H-bonded complexes. Continuous variations experiments show that in FC-72 weaker bases (pyrazine, pyrimidine, and quinazoline) form 1:1 complexes with 1, whereas stronger bases (quinoline, pyridine, and isoquinoline) form 1:3 complexes. Ultraviolet and infrared spectral signatures reveal that the 1:1 complexes are molecular (B.HA) whereas the 1:3 complexes are ionic (BH+.A-HAHA). Infrared spectra of 1:3 ionic complexes are discussed in detail. Literature and experimental data on complexes between N-heterocyclic bases and carboxylic acids in a range of solvents are compiled to compare solvent effects on proton transfer. Polar solvents support ionic hydrogen bonds at a 1:1 mol ratio. In nonpolar organic solvents, ionic hydrogen bonds are only observed in complexes with 1:2 (base/acid) stoichiometries. In fluorous solvents, a larger excess of acid, 1:3, is necessary to facilitate proton transfer in hydrogen bonds between carboxylic acids and the bases studied.

  8. Spectropolarimetry of the molecular hydrogen line emission from OMC-1

    Science.gov (United States)

    Burton, Michael G.; Hough, J. H.; Axon, David J.; Hasegawa, T.; Tamura, M.

    1988-01-01

    Observations of the H2 v = 1-0 S(1) line at 35 km/s velocity resolution were obtained at several locations within OMC-1, including the molecular hydrogen reflection nebula. All line profiles are smooth and show no evidence for being composed of discrete components. The data are discussed with respect to a model for the H2 line formation in which the emission originates in discrete clumps moving at different velocities. It is suggested that the extended blue wing may come from fast-moving clumps embedded in a wind.

  9. Spectropolarimetry of the molecular hydrogen line emission from OMC-1

    Science.gov (United States)

    Burton, Michael G.; Hough, J. H.; Axon, David J.; Hasegawa, T.; Tamura, M.

    1988-01-01

    Observations of the H2 v = 1-0 S(1) line at 35 km/s velocity resolution were obtained at several locations within OMC-1, including the molecular hydrogen reflection nebula. All line profiles are smooth and show no evidence for being composed of discrete components. The data are discussed with respect to a model for the H2 line formation in which the emission originates in discrete clumps moving at different velocities. It is suggested that the extended blue wing may come from fast-moving clumps embedded in a wind.

  10. Equation of state and transport properties of warm dense helium via quantum molecular dynamics simulations

    Science.gov (United States)

    Li, Zhi-Guo; Cheng, Yan; Chen, Qi-Feng; Chen, Xiang-Rong

    2016-05-01

    The equation of state, self-diffusion, and viscosity coefficients of helium have been investigated by quantum molecular dynamics (QMD) simulations in the warm dense matter regime. Our simulations are validated through the comparison with the reliable experimental data. The calculated principal and reshock Hugoniots of liquid helium are in good agreement with the gas-gun data. On this basis, we revisit the issue for helium, i.e., the possibility of the instabilities predicted by chemical models at around 2000 GPa and 10 g/cm3 along the pressure isotherms of 6309, 15 849, and 31 623 K. Our calculations show no indications of instability in this pressure-temperature region, which reconfirm the predictions of previous QMD simulations. The self-diffusion and viscosity coefficients of warm dense helium have been systematically investigated by the QMD simulations. We carefully test the finite-size effects and convergences of statistics, and obtain numerically converged self-diffusion and viscosity coefficients by using the Kubo-Green formulas. The present results have been used to evaluate the existing one component plasma models. Finally, the validation of the Stokes-Einstein relationship for helium in the warm dense regime is discussed.

  11. Ion-Pair States in Triplet Molecular Hydrogen

    Science.gov (United States)

    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.

  12. Photodetachment of a Negative Hydrogen Molecular Ion near an Interface

    Institute of Scientific and Technical Information of China (English)

    WANG Pe-Hua

    2007-01-01

    Photodetachment of a negative hydrogen molecular ion near an interface is studied by using the two-centre model and the closed orbit theory. The calculation results show that the photodetachment cross section is related to the distance between the two centres in the H-2 and different molecular ion-interface distances. The comparison between the cross section of H-2 near an interface with the section of H- shows that at the equilibrium distance of two centres and at low photon energy, the photodetachment cross section of H-2 is about twice the cross section of H-, which shows that the interference of the two nuclei is very strong; when the distance between the two centres is large, the section of H-2 is almost the same as the cross section of H- near one interface, which indicates that the interference effect of the two centres vanishes.

  13. Reaction dynamics of molecular hydrogen on silicon surfaces

    DEFF Research Database (Denmark)

    Bratu, P.; Brenig, W.; Gross, A.

    1996-01-01

    between the two surfaces. These results indicate that tunneling, molecular vibrations, and the structural details of the surface play only a minor role for the adsorption dynamics. Instead, they appear to be governed by the localized H-Si bonding and Si-Si lattice vibrations. Theoretically, an effective...... of the preexponential factor by about one order of magnitude per lateral degree of freedom. Molecular vibrations have practically no effect on the adsorption/desorption dynamics itself, but lead to vibrational heating in desorption with a strong isotope effect. Ab initio calculations for the H-2 interaction......Experimental and theoretical results on the dynamics of dissociative adsorption and recombinative desorption of hydrogen on silicon are presented. Using optical second-harmonic generation, extremely small sticking probabilities in the range 10(-9)-10(-5) could be measured for H-2 and D-2 on Si(111...

  14. Kinetic modelling of molecular hydrogen transport in microporous carbon materials.

    Science.gov (United States)

    Hankel, Marlies; Zhang, Hong; Nguyen, Thanh X; Bhatia, Suresh K; Gray, Stephen K; Smith, Sean C

    2011-05-07

    The proposal of kinetic molecular sieving of hydrogen isotopes is explored by employing statistical rate theory methods to describe the kinetics of molecular hydrogen transport in model microporous carbon structures. A Lennard-Jones atom-atom interaction potential is utilized for the description of the interactions between H(2)/D(2) and the carbon framework, while the requisite partition functions describing the thermal flux of molecules through the transition state are calculated quantum mechanically in view of the low temperatures involved in the proposed kinetic molecular sieving application. Predicted kinetic isotope effects for initial passage from the gas phase into the first pore mouth are consistent with expectations from previous modeling studies, namely, that at sufficiently low temperatures and for sufficiently narrow pore mouths D(2) transport is dramatically favored over H(2). However, in contrast to expectations from previous modeling, the absence of any potential barrier along the minimum energy pathway from the gas phase into the first pore mouth yields a negative temperature dependence in the predicted absolute rate coefficients-implying a negative activation energy. In pursuit of the effective activation barrier, we find that the minimum potential in the cavity is significantly higher than in the pore mouth for nanotube-shaped models, throwing into question the common assumption that passage through the pore mouths should be the rate-determining step. Our results suggest a new mechanism that, depending on the size and shape of the cavity, the thermal activation barrier may lie in the cavity rather than at the pore mouth. As a consequence, design strategies for achieving quantum-mediated kinetic molecular sieving of H(2)/D(2) in a microporous membrane will need, at the very least, to take careful account of cavity shape and size in addition to pore-mouth size in order to ensure that the selective step, namely passage through the pore mouth, is also

  15. Molecular dynamics simulations of the hydration of poly(vinyl methyl ether): Hydrogen bonds and quasi-hydrogen bonds

    Institute of Scientific and Technical Information of China (English)

    WU RongLiang; JI Qing; KONG Bin; YANG XiaoZhen

    2008-01-01

    Atomistic detailed hydration structures of poly(vinyl methyl ether) (PVME) have been investigated by molecular dynamics simulations under 300 K at various concentrations. Both radial distribution func-tions and the distance distributions between donors and acceptors in hydrogen bonds show that the hydrogen bonds between the polymer and water are shorter by 0.005 nm than those between water molecules. The Quasi-hydrogen bonds take only 7.2% of the van der Waals interaction pairs. It was found the hydrogen bonds are not evenly distributed along the polymer chain, and there still exists a significant amount (10%) of ether oxygen atoms that are not hydrogen bonded to water at a concentra-tion as low as 3.3%. This shows that in polymer solutions close contacts occur not only between polymer chains but also between chain segments within the polymer, which leads to inefficient con-tacts between ether oxygen atoms and water molecules. Variation of the quasi-hydrogen bonds with the concentration is similar to that of hydrogen bonds, but the ratio of the repeat units forming quasi-hydrogen bonds to those forming hydrogen bonds approaches 0.2. A transition was found in the demixing enthalpy at around 30% measured by dynamic testing differential scanning calorimetry (DTDSC) for aqueous solutions of a mono-dispersed low molecular weight PVME, which can be related to the transition of the fractions of hydrogen bonds and quasi-hydrogen bonds at ~27%. The transition of the fractions of hydrogen bonds and quasi-hydrogen bonds at ~27% can be used to explain the demixing enthalpy transition at 30% at a molecular scale. In addition, at the concentration of 86%, each ether oxygen atom bonded with water is assigned 1.56 water molecules on average, and 'free' water molecules emerge at the concentration of around 54%.

  16. Molecular dynamics simulations of the hydration of poly(vinyl methyl ether):Hydrogen bonds and quasi-hydrogen bonds

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Atomistic detailed hydration structures of poly(vinyl methyl ether)(PVME) have been investigated by molecular dynamics simulations under 300 K at various concentrations. Both radial distribution functions and the distance distributions between donors and acceptors in hydrogen bonds show that the hydrogen bonds between the polymer and water are shorter by 0.005 nm than those between water molecules. The Quasi-hydrogen bonds take only 7.2% of the van der Waals interaction pairs. It was found the hydrogen bonds are not evenly distributed along the polymer chain,and there still exists a significant amount(10%) of ether oxygen atoms that are not hydrogen bonded to water at a concentration as low as 3.3%. This shows that in polymer solutions close contacts occur not only between polymer chains but also between chain segments within the polymer,which leads to inefficient contacts between ether oxygen atoms and water molecules. Variation of the quasi-hydrogen bonds with the concentration is similar to that of hydrogen bonds,but the ratio of the repeat units forming quasi-hydrogen bonds to those forming hydrogen bonds approaches 0.2. A transition was found in the demixing enthalpy at around 30% measured by dynamic testing differential scanning calorimetry(DTDSC) for aqueous solutions of a mono-dispersed low molecular weight PVME,which can be related to the transition of the fractions of hydrogen bonds and quasi-hydrogen bonds at ~27%. The transition of the fractions of hydrogen bonds and quasi-hydrogen bonds at ~27% can be used to explain the demixing enthalpy transition at 30% at a molecular scale. In addition,at the concentration of 86%,each ether oxygen atom bonded with water is assigned 1.56 water molecules on average,and ’free’ water molecules emerge at the concentration of around 54%.

  17. Symmetry-resolved spectroscopy by detection of a metastable hydrogen atom for investigating the doubly excited states of molecular hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Odagiri, Takeshi; Kumagai, Yoshiaki; Tanabe, Takehiko; Nakano, Motoyoshi; Kouchi, Noriyuki [Department of Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8551 (Japan); Suzuki, Isao H, E-mail: joe@chem.titech.ac.j [Photon Factory, IMSS, KEK, Tsukuba, Ibaraki 305-0801 (Japan)

    2009-11-01

    Symmetry-resolved spectroscopy for investigating the doubly excited states of molecular hydrogen has been newly developed, where a metastable hydrogen atom dissociating in a direction parallel and perpendicular to the electric vector of the linearly polarized incident light is detected.

  18. Modeling deuterium fractionation in cold and warm molecular environments with large chemical networks

    CERN Document Server

    Albertsson, T; Henning, Th

    2013-01-01

    Observations of deuterated species have long proven essential to probe properties and thermal history of various astrophysical environments. We present an elaborated chemical model that includes tens of thousands of reactions with multi-deuterated species, both gas-phase and surface, in which the most recent information on deuterium chemistry is implemented. A detailed study of the chemical evolution under wide range of temperatures and densities typical of cold molecular cores, warm protostellar envelopes, and hot cores/corinos is performed. We consider two cases of initial abundances, with 1) mainly atomic composition and all deuterium locked in HD, and 2) molecular abundances accumulated at 1 Myr of the evolution of a cold prestellar core. We indicate deuterated species that are particularly sensitive to temperature gradients and initial chemical composition. Many multiply-deuterated species produced at 10 K by exothermic ion-molecule chemistry retain large abundances even when temperature rises above 100 ...

  19. Warm neutral halos around molecular clouds. VI - Physical and chemical modeling

    Science.gov (United States)

    Andersson, B.-G.; Wannier, P. G.

    1993-01-01

    A combined physical and chemical modeling of the halos around molecular clouds is presented, with special emphasis on the H-to-H2 transition. On the basis of H I 21 cm observations, it is shown that the halos are extended. A physical model is employed in conjunction with a chemistry code to provide a self-consistent description of the gas. The radiative transfer code provides a check with H I, CO, and OH observations. It is concluded that the warm neutral halos are not gravitationally bound to the underlying molecular clouds and are isobaric. It is inferred from the observed extent of the H I envelopes and the large observed abundance of OH in them that the generally accepted rate for H2 information on grains is too large by a factor of two to three.

  20. Nuclear quantum effect on intramolecular hydrogen bond of hydrogen maleate anion: An ab initio path integral molecular dynamics study

    Science.gov (United States)

    Kawashima, Yukio; Tachikawa, Masanori

    2013-05-01

    Ab initio path integral molecular dynamics simulation was performed to understand the nuclear quantum effect on the hydrogen bond of hydrogen malonate anion. Static calculation predicted the proton transfer barrier as 0.12 kcal/mol. Conventional ab initio molecular dynamics simulation at 300 K found proton distribution with a double peak on the proton transfer coordinate. Inclusion of thermal effect alone elongates the hydrogen bond length, which increases the barrier height. Inclusion of nuclear quantum effect washes out this barrier, and distributes a single broad peak in the center. H/D isotope effect on the proton transfer is also discussed.

  1. Implementing Molecular Hydrogen in Hydrodynamic Simulations of Galaxy Formation

    CERN Document Server

    Christensen, Charlotte; Governato, Fabio; Stilp, Adrienne; Shen, Sijing; Wadsley, James

    2012-01-01

    Motivated by the observed connection between molecular hydrogen (H2) and star formation, we present a method for tracking the non-equilibrium abundance and cooling processes of H2 and H2-based star formation in Smoothed Particle Hydrodynamic simulations. The local abundances of H2 are calculated by integrating over the hydrogen chemical network. This calculation includes the gas-phase and dust grain formation of H2, shielding of HI and H2, and photodissociation of H2 by Lyman-Werner radiation from nearby stellar populations. Because this model does not assume equilibrium abundances, it is particularly well suited for simulations that model low-metallicity environments, such as dwarf galaxies and the early Universe. We further introduce an explicit link between star formation and local H2 abundance. This link limits star formation to "star-forming regions," represented by areas with abundant H2. With this implementation, we determine the effect of H2 on star formation in a cosmological simulation of a dwarf ga...

  2. Effects of Varying the Three-Body Molecular Hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Turk, Matthew J.; /San Diego, CASS; Clark, Paul; Glover, S.C.O.; /ZAH, Heidelberg; Greif, T.H.; /Garching, Max Planck Inst. Plasmaphys.; Abel, Tom; Klessen, Ralf; /KIPAC, Menlo Park /ZAH, Heidelberg /KIPAC, Menlo Park; Bromm, Volker; /Texas U., Astron. Dept.

    2011-03-03

    The transformation of atomic hydrogen to molecular hydrogen through three-body reactions is a crucial stage in the collapse of primordial, metal-free halos, where the first generation of stars (Population III stars) in the Universe are formed. However, in the published literature, the rate coefficient for this reaction is uncertain by nearly an order of magnitude. We report on the results of both adaptive mesh refinement (AMR) and smoothed particle hydrodynamics (SPH) simulations of the collapse of metal-free halos as a function of the value of this rate coefficient. For each simulation method, we have simulated a single halo three times, using three different values of the rate coefficient. We find that while variation between halo realizations may be greater than that caused by the three-body rate coefficient being used, both the accretion physics onto Population III protostars as well as the long-term stability of the disk and any potential fragmentation may depend strongly on this rate coefficient.

  3. Effects of Varying the Three-Body Molecular Hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Turk, Matthew J.; /San Diego, CASS; Clark, Paul; Glover, S.C.O.; /ZAH, Heidelberg; Greif, T.H.; /Garching, Max Planck Inst. Plasmaphys.; Abel, Tom; Klessen, Ralf; /KIPAC, Menlo Park /ZAH, Heidelberg /KIPAC, Menlo Park; Bromm, Volker; /Texas U., Astron. Dept.

    2011-03-03

    The transformation of atomic hydrogen to molecular hydrogen through three-body reactions is a crucial stage in the collapse of primordial, metal-free halos, where the first generation of stars (Population III stars) in the Universe are formed. However, in the published literature, the rate coefficient for this reaction is uncertain by nearly an order of magnitude. We report on the results of both adaptive mesh refinement (AMR) and smoothed particle hydrodynamics (SPH) simulations of the collapse of metal-free halos as a function of the value of this rate coefficient. For each simulation method, we have simulated a single halo three times, using three different values of the rate coefficient. We find that while variation between halo realizations may be greater than that caused by the three-body rate coefficient being used, both the accretion physics onto Population III protostars as well as the long-term stability of the disk and any potential fragmentation may depend strongly on this rate coefficient.

  4. Hydrogen molecular ions for improved determination of fundamental constants

    CERN Document Server

    Karr, J -Ph; Koelemeij, Jeroen; Korobov, Vladimir

    2016-01-01

    The possible use of high-resolution rovibrational spectroscopy of the hydrogen molecular ions H + 2 and HD + for an independent determination of several fundamental constants is analyzed. While these molecules had been proposed for metrology of nuclear-to-electron mass ratios, we show that they are also sensitive to the radii of the proton and deuteron and to the Rydberg constant at the level of the current discrepancies colloquially known as the proton size puzzle. The required level of accuracy, in the 10 --12 range, can be reached both by experiments, using Doppler-free two-photon spectroscopy schemes, and by theoretical predictions. It is shown how the measurement of several well-chosen rovibrational transitions may shed new light on the proton-radius puzzle, provide an alternative accurate determination of the Rydberg constant, and yield new values of the proton-to-electron and deuteron-to-proton mass ratios with one order of magnitude higher precision.

  5. Shocked molecular hydrogen in the bipolar outflow NGC 2071

    Energy Technology Data Exchange (ETDEWEB)

    Burton, M.G. (Edinburgh Univ. (UK). Dept. of Astronomy; National Aeronautics and Space Administration, Moffett Field, CA (USA). Ames Research Center); Geballe, T.R. (Joint Astronomy Centre, Hilo, Hawaii (USA); Foundation for Astronomical Research in the Netherlands (ASTRON)); Brand, P.W.J.L. (Edinburgh Univ. (UK). Dept. of Astronomy)

    1989-06-15

    Emission from the 4u = 1 - 0 S(1) line of molecular hydrogen has been mapped in the bipolar outflow NGC 2071. The line emission peaks at six positions distributed irregularly along the two lobes, which extend over a distance of {similar to} 1 pc. These lobes are parallel to, but offset {similar to} 20 arcsec from, the lobes of high-velocity CO line emission. Spectra from 2.1 to 2.45 {mu}m of the H{sub 2} emission lines are typical of shock-excited emission. The total H{sub 2} line luminosity is estimated to be {similar to} 4.5 time the solar luminosity. Profiles of the 1-0 S(1) line are relatively narrow (< 30 km s{sup -1} FWHM) for shocked gas. The peak velocity varies systematically across the source, in a manner consistent with the observed bipolarity of the millimetre-wave CO line emission. (author).

  6. Pahs, Ionized Gas, and Molecular Hydrogen in Brightest Cluster Galaxies of Cool Core Clusters of Galaxies

    CERN Document Server

    Donahue, Megan; O'Connell, Robert W; Voit, G Mark; Hoffer, Aaron; McNamara, Brian R; Nulsen, Paul E J

    2011-01-01

    We present measurements of 5-25 {\\mu}m emission features of brightest cluster galaxies (BCGs) with strong optical emission lines in a sample of 9 cool-core clusters of galaxies observed with the Infrared Spectrograph on board the Spitzer Space Telescope. These systems provide a view of dusty molecular gas and star formation, surrounded by dense, X-ray emitting intracluster gas. Past work has shown that BCGs in cool-core clusters may host powerful radio sources, luminous optical emission line systems, and excess UV, while BCGs in other clusters never show this activity. In this sample, we detect polycyclic aromatic hydrocarbons (PAHs), extremely luminous, rotationally-excited molecular hydrogen line emission, forbidden line emission from ionized gas ([Ne II] and [Ne III]), and infrared continuum emission from warm dust and cool stars. We show here that these BCGs exhibit more luminous forbidden neon and H2 rotational line emission than star-forming galaxies with similar total infrared luminosities, as well as ...

  7. Equations of state and transport properties of warm dense beryllium: a quantum molecular dynamics study.

    Science.gov (United States)

    Wang, Cong; Long, Yao; Tian, Ming-Feng; He, Xian-Tu; Zhang, Ping

    2013-04-01

    We have calculated the equations of state, the viscosity and self-diffusion coefficients, and electronic transport coefficients of beryllium in the warm dense regime for densities from 4.0 to 6.0 g/cm(3) and temperatures from 1.0 to 10.0 eV by using quantum molecular dynamics simulations. The principal Hugoniot curve is in agreement with underground nuclear explosive and high-power laser experimental results up to ~20 Mbar. The calculated viscosity and self-diffusion coefficients are compared with the one-component plasma model, using effective charges given by the average-atom model. The Stokes-Einstein relationship, which connects viscosity and self-diffusion coefficients, is found to hold fairly well in the strong coupling regime. The Lorenz number, which is the ratio between thermal and electrical conductivities, is computed via Kubo-Greenwood formula and compared to the well-known Wiedemann-Franz law in the warm dense region.

  8. Warm Molecular Gas Traced with CO J = 7 --> 6 in the Galaxy's Central 2 Parsecs: Dynamical Heating of the Circumnuclear Disks

    Science.gov (United States)

    Bradford, C. M.; Stacey, G. J.; Nikola, T.; Bolatto, A. D.; Jackson, J. M.; Savage, M. L.; Davidson, J. A.

    2005-01-01

    We present an 11" resolution map of the central 2 pc of the Galaxy in the CO J = 7 --> 6 rotational transition. The CO emission shows rotation about Sgr A* but also evidence for noncircular turbulent motion and a clumpy morphology. We combine our data set with available CO measurements to model the physical conditions in the disk. We find that the molecular gas in the region is both warm and dense, with T approx. 200-300 K and n(sub H2) approx. (5-7) x 10(exp 4) cm(exp -3). The mass of warm molecular gas we measure in the central 2 pc is at least 2000 M(solar), about 20 times the UV-excited atomic gas mass, ruling out a UV heating scenario for the molecular material. We compare the available spectral tracers with theoretical models and conclude that molecular gas is heated with magnetohydrodynamic shocks with v approx. 10-20 km s(exp -1) and B approx. 0.3- 0.5 mG. Using the conditions derived with the CO analysis, we include the other important coolants, neutral oxygen and molecular hydrogen, to estimate the total cooling budget of the molecular material. We derive a mass-to-luminosity ratio of approx. 2-3 M(solar)(L(solar)exp -1), which is consistent with the total power dissipated via turbulent decay in 0.1 pc cells with v(sub rms) approx. 15 kilometers per second. These size and velocity scales are comparable to the observed clumping scale and the velocity dispersion. At this rate, the material near Sgr A* is dissipating its orbital energy on an orbital timescale and cannot last for more than a few orbits. Our conclusions support a scenario in which the features near Sgr A* such as the circumnuclear disk and northern arm are generated by infalling clouds with low specific angular momentum.

  9. Path Integral Monte Carlo and Density Functional Molecular Dynamics Simulations of Warm Dense Matter

    Science.gov (United States)

    Militzer, Burkhard; Driver, Kevin

    2011-10-01

    We analyze the applicability of two first-principles simulation techniques, path integral Monte Carlo (PIMC) and density functional molecular dynamics (DFT-MD), to study the regime of warm dense matter. We discuss the advantages as well as the limitations of each method and propose directions for future development. Results for dense, liquid helium, where both methods have been applied, demonstrate the range of each method's applicability. Comparison of the equations of state from simulations with analytical theories and free energy models show that DFT is useful for temperatures below 100000 K and then PIMC provides accurate results for all higher temperatures. We characterize the structure of the liquid in terms of pair correlation functions and study the closure of the band gap with increasing density and temperature. Finally, we discuss simulations of heavier elements and demonstrate the reliability are both methods in such cases with preliminary results.

  10. Quantum molecular dynamics simulations of equation of state of warm dense ethane

    Science.gov (United States)

    Li, Chuan-Ying; Wang, Cong; Li, Yong-Sheng; Li, Da-Fang; Li, Zi; Zhang, Ping

    2016-09-01

    The equation of state of warm dense ethane is obtained using quantum molecular dynamics simulations based on finite-temperature density functional theory for densities from 0.1 g / cm 3 to 3.1 g / cm 3 and temperatures from 0.1 eV to 5.17 eV. The calculated pressure and internal energy are fitted with cubic polynomials in terms of density and temperature. Specific density-temperature-pressure tracks such as the principal and double shock Hugoniot curves along with release isentropes are predicted which are fundamental for the analysis and interpretation of high-pressure experiments. The principal and double shock Hugoniot curves are in agreement with the experimental data from the Sandia Z-Machine [Magyar et al., Phys. Rev. B 91, 134109 (2015)].

  11. Molecular simulation of adsorption and diffusion of hydrogen in metal-organic frameworks.

    Science.gov (United States)

    Yang, Qingyuan; Zhong, Chongli

    2005-06-23

    Metal-organic frameworks (MOFs) are thought to be a set of promising hydrogen storage materials; however, little is known about the interactions between hydrogen molecules and pore walls as well as the diffusivities of hydrogen in MOFs. In this work, we performed a systematic molecular simulation study on the adsorption and diffusion of hydrogen in MOFs to provide insight into molecular-level details of the underlying mechanisms. This work shows that metal-oxygen clusters are preferential adsorption sites for hydrogen in MOFs, and the effect of the organic linkers becomes evident with increasing pressure. The hydrogen storage capacity of MOFs is similar to carbon nanotubes, which is higher than zeolites. Diffusion of hydrogen in MOFs is an activated process that is similar to diffusion in zeolites. The information derived in this work is useful to guide the future rational design and synthesis of tailored MOF materials with improved hydrogen adsorption capability.

  12. The static dipole polarizabilities of helium and molecular hydrogen by differential diffusion Monte Carlo

    NARCIS (Netherlands)

    Huiszoon, C.; Briels, W.J.

    1993-01-01

    The differential diffusion Monte Carlo method, involving correlated random walks, is used to calculate the static polarizabilities of molecular hydrogen and helium by application of a finite electrostatic field. The results are for molecular hydrogen (alpha)=4.60(3) au; (alpha)|=6.38(5) au; for heli

  13. The stable isotopic signature of biologically produced molecular hydrogen (H2)

    NARCIS (Netherlands)

    Walter, S.; Laukenmann, S.; Stams, A.J.M.; Vollmer, M.K.; Gleixner, G.; Roeckmann, T.|info:eu-repo/dai/nl/304838233

    2011-01-01

    Biologically produced molecular hydrogen (H2) is characterized by a very strong depletion in deuterium. Although the biological source to the atmosphere is small compared to photochemical or combustion sources, it makes an important contribution to the global isotope budget of molecular hydrogen

  14. Photoproduction of molecular hydrogen by a plant-algal symbiotic system

    Energy Technology Data Exchange (ETDEWEB)

    Newton, J.W.

    1976-02-13

    The rapidly growing water fern Azolla, which contains a nitrogen-fixing blue-green algal symbiont, has been studied as a possible system for photoproduction of molecular hydrogen. When this plant is grown on a combined nitrogen supply, photochemically generated hydrogen can be diverted through the algal nitrogenase system, which serves as a source of molecular hydrogen generated from water. This symbiosis has several advantages as a possible biological energy conversion system. (auth)

  15. Cryogenic Adsorption of Low-concentration Hydrogen on 5A Molecular Sieve Bed

    Institute of Scientific and Technical Information of China (English)

    LIU; Zhen-xing; YANG; Hong-guang; XIA; Ti-rui; ZHAN; Qin; YANG; Li-ling

    2013-01-01

    The separation of low-concentration hydrogen isotopes from helium is a processing step that is required for ceramic lithium breeding blanket processing.In this study,the adsorption of low-concentration hydrogen from helium carrier was measured using 5A molecular sieve fixed bed in the cryogenic condition.The adsorption performances of hydrogen on 5A molecular sieve were discussed.The effect of the different

  16. Quantum molecular dynamics simulations of hydrogen production and solar cells

    Science.gov (United States)

    Mou, Weiwei

    The global energy crisis presents two major challenges for scientists around the world: Producing cleaner energy which is sustainable for the environment; And improving the efficiency of energy production as well as consumption. It is crucial and yet elusive to understand the atomistic mechanisms and electronic properties, which are needed in order to tackle those challenges. Quantum molecular dynamics simulations and nonadiabatic quantum molecular dynamics are two of the dominant methods used to address the atomistic and electronic properties in various energy studies. This dissertation is an ensemble of three studies in energy research: (1) Hydrogen production from the reaction of aluminum clusters with water to provide a renewable energy cycle; (2) The photo-excited charge transfer and recombination at a quaterthiophene/zinc oxide interface to improve the power conversion efficiency of hybrid poly(3-hexylthiophene) (P3HT) /ZnO solar cells; and (3) the charge transfer at a rubrene/C60 interface to understand why phenyl groups in rubrene improve the performance of rubrene/C60 solar cells.

  17. Restricted Path-Integral Molecular Dynamics for Simulating the Correlated Electron Plasma in Warm Dense Matter

    Science.gov (United States)

    Kapila, Vivek; Deymier, Pierre; Runge, Keith

    2011-10-01

    Several areas of study including heavy ion beam, large scale laser, and high pressure or Thomson scattering studies necessitate a fundamental understanding of warm dense matter (WDM) i.e. matter at high temperature and high density. The WDM regime, however, lacks any adequate highly developed class of simulation methods. Recent progress to address this deficit has been the development of orbital-free Density Functional Theory (ofDFT). However, scant benchmark information is available on temperature and pressure dependence of simple but realistic models in WDM regime. The present work aims to fill this critical gap using the restricted path-integral molecular dynamics (rPIMD) method. Within the discrete path integral representation, electrons are described as harmonic necklaces. Quantum exchange takes the form of cross linking between electron necklaces. The fermion sign problem is addressed by restricting the density matrix to positive values. The molecular dynamics algorithm is employed to sample phase space. Here, we focus on the behavior of strongly correlated electron plasmas under WDM conditions. We compute the kinetic and potential energies and compare them to those obtained with the ofDFT method. Several areas of study including heavy ion beam, large scale laser, and high pressure or Thomson scattering studies necessitate a fundamental understanding of warm dense matter (WDM) i.e. matter at high temperature and high density. The WDM regime, however, lacks any adequate highly developed class of simulation methods. Recent progress to address this deficit has been the development of orbital-free Density Functional Theory (ofDFT). However, scant benchmark information is available on temperature and pressure dependence of simple but realistic models in WDM regime. The present work aims to fill this critical gap using the restricted path-integral molecular dynamics (rPIMD) method. Within the discrete path integral representation, electrons are described as

  18. Bio-Inspired Molecular Catalysts for Hydrogen Oxidation and Hydrogen Production

    Energy Technology Data Exchange (ETDEWEB)

    Ho, Ming-Hsun; Chen, Shentan; Rousseau, Roger J.; Dupuis, Michel; Bullock, R. Morris; Raugei, Simone

    2013-06-03

    Recent advances in Ni-based bio-inspired catalysts obtained in the Center for Molecular Electrocatalysis, an Energy Frontier Research Center (EFRC) at the Pacific Northwest National Laboratory, demonstrated the possibility of cleaving H2 or generating H2 heterolytically with turnover frequencies comparable or superior to those of hydrogenase enzymes. In these catalysts the transformation between H2 and protons proceeds via an interplay between proton, hydride and electron transfer steps and involves the interaction of a dihydrogen molecule with both a Ni(II) center and with pendant amine bases incorporated in a six-membered ring, which act as proton relays. These catalytic platforms are well designed in that when protons are correctly positioned (endo) toward the Raugei-ACS-Books.docxPrinted 12/18/12 2 metal center, catalysis proceeds at very high rates. We will show that the proton removal (for H2 oxidation) and proton delivery (for H2 production) are often the rate determining steps. Furthermore, the presence of multiple protonation sites gives rise to reaction intermediates with protons not correctly positioned (exo relative to the metal center). These isomers are easily accessible kinetically and are detrimental to catalysis because of the slow isomerization processes necessary to convert them to the catalytically competent endo isomers. In this chapter we will review the major findings of our computational investigation on the role of proton relays for H2 chemistry and provide guidelines for the design of new catalysts. This research was carried out in the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science. Pacific Northwest National Laboratory is operated for the U.S. Department of Energy by Battelle. Computational resources were provided at W. R. Wiley Environmental Molecular Science Laboratory (EMSL), a Raugei-Bio-Inspired Molecular-Catalysts-for-Hydrogen- Oxidation-and-Hydrogen

  19. Molecular and Ionized Hydrogen in 30 Doradus. I. Imaging Observations

    CERN Document Server

    Yeh, Sherry C C; Matzner, Christopher D; Pellegrini, Eric W

    2015-01-01

    We present the first fully calibrated H$_2$, 1-0 S(1) image of the entire 30 Doradus nebula. The observations were conducted using the NOAO Extremely Wide-Field Infrared Imager on the CTIO 4-meter Blanco Telescope. Together with a NEWFIRM Br$\\gamma$ image of 30 Doradus, our data reveal the morphologies of the warm molecular gas and ionized gas in 30 Doradus. The brightest H$_2$-emitting area, which extends from the northeast to the southwest of R136, is a photodissociation region viewed face-on, while many clumps and pillar features located at the outer shells of 30 Doradus are photodissociation regions viewed edge-on. Based on the morphologies of H$_2$, Br$\\gamma$, $^{12}$CO, and 8$\\mu$m emission, the H$_2$ to Br$\\gamma$ line ratio and Cloudy models, we find that the H$_2$ emission is formed inside the photodissociation regions of 30 Doradus, 2 - 3 pc to the ionization front of the HII region, in a relatively low-density environment $<$ 10$^4$ cm$^{-3}$. Comparisons with Br$\\gamma$, 8$\\mu$m, and CO emissi...

  20. A giant cloud of hydrogen escaping the warm Neptune-mass planet GJ 436b

    Science.gov (United States)

    Ehrenreich, David

    2015-12-01

    Exoplanets in extreme irradiation environments, close to their parent stars, could lose some fraction of their atmospheres because of the extreme irradiation. Atmospheric mass loss has been observed during the past 12 years for hot gas giants, as large (~10%) ultraviolet absorption signals during transits. Meanwhile, no confident detection have been obtained for lower-mass planets, which are most likely to be significantly affected by atmospheric escape. In fact, hot rocky planets observed by Corot and Kepler might have lost all of their atmosphere, having begun as Neptune-like. The signature of this loss could be observed in the ultraviolet, when the planet and its escaping atmosphere transit the star, giving rise to deeper and longer transit signatures than in the optical. I will report on new Hubble observations of the Neptune-mass exoplanet GJ 436b, around which an extended atmosphere has been tentatively detected in 2014. The new data reveal that GJ 436b has huge transit depths of 56.3±3.5% in the hydrogen Lyman-alpha line, far beyond the 0.69% optical transit depth, and even far beyond mass loss signatures observed at the same wavelength from more irradiated gas giants. We infer from this repeated observations that the planet is surrounded and trailed by a large exospheric cloud of hydrogen, shaped as a giant comet, much bigger than the star. We estimate a mass-loss rate, which today is far too small to deplete the atmosphere of a Neptune-like planet in the lifetime of the parent star, but would have been much greater in the past. This 16-sigma detection opens exciting perspectives for the atmospheric characterization of low-mass and moderately-irradiated exoplanets, a large number of which will be detected by forthcoming transit surveys.

  1. Ionization of molecular hydrogen in ultrashort intense laser pulses

    Energy Technology Data Exchange (ETDEWEB)

    Vanne, Yulian V.

    2010-03-18

    A novel ab initio numerical approach is developed and applied that solves the time-dependent Schroedinger equation describing two-electron diatomic molecules (e.g. molecular hydrogen) exposed to an intense ultrashort laser pulse. The method is based on the fixed-nuclei and the non-relativistic dipole approximations and aims to accurately describe both correlated electrons in full dimensionality. The method is applicable for a wide range of the laser pulse parameters and is able to describe both few-photon and many-photon single ionization processes, also in a non-perturbative regime. A key advantage of the method is its ability to treat the strong-field response of the molecules with arbitrary orientation of the molecular axis with respect to the linear-polarized laser field. Thus, this work reports on the first successful orientation-dependent analysis of the multiphoton ionization of H{sub 2} performed by means of a full-dimensional numerical treatment. Besides the investigation of few-photon regime, an extensive numerical study of the ionization by ultrashort frequency-doubled Ti:sapphire laser pulses (400 nm) is presented. Performing a series of calculations for different internuclear separations, the total ionization yields of H{sub 2} and D{sub 2} in their ground vibrational states are obtained for both parallel and perpendicular orientations. A series of calculations for 800 nm laser pulses are used to test a popular simple interference model. Besides the discussion of the ab initio numerical method, this work considers different aspects related to the application of the strong-field approximation (SFA) for investigation of a strong-field response of an atomic and molecular system. Thus, a deep analysis of the gauge problem of SFA is performed and the quasistatic limit of the velocity-gauge SFA ionization rates is derived. The applications of the length-gauge SFA are examined and a recently proposed generalized Keldysh theory is criticized. (orig.)

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

    Science.gov (United States)

    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

  3. Molecular hydrogen emission as a density and temperature indicator

    Science.gov (United States)

    Wang, Xiang; Ferland, Gary J.; Baldwin, Jack A.; Loh, Edwin D.; Fabian, Andy C.; Williams, Robin

    2016-01-01

    Infrared observations have discovered a variety of objects, including filaments in the Crab Nebula and cool-core clusters of galaxies, where the 1-0 S(1) line is stronger than the infrared H I lines. A variety of processes could be responsible for this emission. Although many complete shock or PDR calculations of emission have been published, we know of no previous simple calculation that shows the emission spectrum and level populations of thermally excited low-density . We present a range of purely thermal collisional simulations, corresponding to constant gas kinetic temperature at different densities. We consider the cases where the collisions affecting H2 are predominantly with atomic or molecular hydrogen. The resulting level population (often called "excitation") diagrams show that excitation temperatures are sometimes lower than the gas kinetic temperature when the density is too low for the level populations to go to LTE. The atomic case goes to LTE at much lower densities than the molecular case due to larger collision rates. At low densities for the v=1 and 2 vibrational manifolds level populations are quasi-thermal, which could be misinterpreted as showing the gas is in LTE at high density. At low densities for the molecular case the level population diagrams are discontinuous between v=0 and 1 vibrational manifolds and between v=2, J=0, 1 and other higher J levels within the same vibrational manifold. These jumps could be used as density diagnostics. We show how much the H2 mass would be underestimated using the 1-0 S(1) line strength if the density is below that required for LTE. We give diagnostic diagrams showing level populations over a range of density and temperature. The density where the level populations are given by a Boltzmann distribution relative to the total molecular abundance (required to get the correct H2 mass), is shown for various cases. We discuss the implications of these results for the interpretation of H2 observations of the

  4. First Extragalactic Direct Detection of Large-Scale Molecular Hydrogen in the Disk of NGC 891

    Science.gov (United States)

    Valentijn, Edwin A.; van der Werf, Paul P.

    1999-09-01

    We present direct observations of molecular hydrogen in the disk of the nearby edge-on spiral galaxy NGC 891. With Infrared Space Observatory's Short-Wavelength Spectrometer (SWS) it has been possible, for the first time, to observe the lowest pure rotational lines of H2 [S(0) at 28.2 μm and S(1) at 17.0 μm] at eight positions throughout the stellar disk of NGC 891. Both lines have been detected at all the surveyed positions out to 11 kpc north of the center of the galaxy. An H2 rotation curve is derived, and we compare H2 radial profiles with CO and H I data. The observed line ratios indicate relatively warm (T=150-230 K) molecular clouds scattered throughout the disk in addition to a massive cooler (T=80-90 K) component which dominates the signal in the outer regions. For H2 ortho/para ratios of 2-3, the cool gas has typical edge-on column densities (1-3)×1023 cm-2 (or ~3000 Msolar pc-2), in which case it outweighs the H I by a factor of 5-15. This factor matches well the mass required to resolve the problem of the missing matter of spiral galaxies within at least the optical disk. The newly discovered cool H2 component would be less massive in the case in which its dominant ortho/para ratio is near unity. We address the thermal balance of this component by a comparison with [C II] 158 μm data. When combining the new coolish molecular gas results with recent SCUBA cold dust observations of NGC 891, the total gas-to-dust ratio at rISO, an ESA project with instruments funded by ESA member states (especially the PI countries: France, Germany, the Netherlands, and the United Kingdom) and with the participation of ISAS and NASA.

  5. Utilization of extremozymes for the bioconversion of renewable sugar to molecular hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Woodward, J. [Oak Ridge National Lab., TN (United States); Danson, M.; Hough, D.; Ward, N. [Univ. of Bath (United Kingdom)] [and others

    1997-12-31

    We have recently demonstrated the technical feasibility of the bioconversion of glucose and cellulose to molecular hydrogen using two extremozymes glucose dehydrogenase (GDH) and hydrogenase. The utilization of compatible extremozymes is important to obtain the fastest rates of hydrogen production possible. The rate limiting step in the conversion of hydrogen appears to be the rate at which insoluble cellulose is enzymatically hydrolyzed to glucose by cellulase since the rate of hydrogen production from soluble starch, hydrolyzed by glucoamylase, was similar to that obtained with glucose at the substrate. Xylose is also a substrate for the GDH used (from Thermoplasma acidophilum expressed in E coli) suggesting that the hemicellulose component of biomass can also be transformed to hydrogen. Current to hydrogen experimentation includes the use of cellulases from extremophiles for the bioconversion of cellulosic substrates to hydrogen and the utilization of enzymatic pathways for obtaining the maximum yield of hydrogen/mol of substrate.

  6. Molecular hydrogen regulated star formation in cosmological SPH simulations

    CERN Document Server

    Thompson, Robert; Jaacks, Jason; Choi, Jun-Hwan

    2013-01-01

    It has been shown observationally that star formation (SF) correlates tightly with the presence of molecular hydrogen (H2). Therefore it would be important to investigate its implication on galaxy formation in a cosmological context. In the present work, we track the H2 mass fraction within our cosmological smoothed particle hydrodynamics (SPH) code GADGET-3 using an equilibrium analytic model by Krumholz et al. This model allows us to regulate the star formation in our simulation by the local abundance of H2 rather than the total cold gas density, and naturally introduce the dependence of star formation on metallicity. We investigate implications of the equilibrium H2-based SF model on galaxy population properties, such as the stellar-to-halo mass ratio (SHMR), baryon fraction, cosmic star formation rate density (SFRD), galaxy specific SFR, galaxy stellar mass functions (GSMF), and Kennicutt-Schmidt (KS) relationship. The advantage of our work over the previous ones is having a large sample of simulated gala...

  7. Molecular Hydrogen in the Quiescent Disk of SW UMa

    Science.gov (United States)

    Raymond, John C.

    2004-01-01

    The FUSE observation has been reduced and a paper has been submitted to ApJ. The analysis has been slow because of the very noisy quality of the data, but we have derived line profile information for O VI and limits to the continuum brightness which place an interesting limit on the white dwarf temperature. The primary results are that a narrow O VI emission component seems to arise from the accretion flow onto the white dwarf itself, in agreement with cooling flow models for the X-ray spectra of low accretion rate dwarf novae. The broad component of the O VI lines is weaker than the observed C IV emission, suggesting that the UV line emission from the disk comes from photoionized plasma. A secondary result is that there is no H-2 fluorescent emission. The upper limits indicate that if molecular gas is present in the disk, it is shielded from Ly alpha photons by a layer of atomic hydrogen on the disk surface. We also derive an upper limit to the continuum level is below that observed by IUE. The limits are compatible with the lower end of the WD temperature range derived from IUE measurements, and they appear to agree with unpublished analysis of HST spectra. The grant has provided partial support for a data aide (Matt Povich) and a postdoc (Alex Lobel). It purchased a computer for M. Menou.

  8. Molecular hydrogen abundances of galaxies in the EAGLE simulations

    CERN Document Server

    Lagos, Claudia del P; Schaye, Joop; Furlong, Michelle; Frenk, Carlos S; Bower, Richard G; Schaller, Matthieu; Theuns, Tom; Trayford, James W; Bahe, Yannick M; Vecchia, Claudio Dalla

    2015-01-01

    We investigate the abundance of galactic molecular hydrogen (H$_2$) in the "Evolution and Assembly of GaLaxies and their Environments" (EAGLE) cosmological hydrodynamic simulations. We assign H$_2$ masses to gas particles in the simulations in post-processing using two different prescriptions that depend on the local dust-to-gas ratio and the interstellar radiation field. Both result in H$_2$ galaxy mass functions that agree well with observations in the local and high-redshift Universe. The simulations reproduce the observed scaling relations between the mass of H$_2$ and the stellar mass, star formation rate and stellar surface density. Towards high edshifts, galaxies in the simulations display larger H$_2$ mass fractions, and correspondingly lower H$_2$ depletion timescales, also in good agreement with observations. The comoving mass density of H$_2$ in units of the critical density, $\\Omega_{\\rm H_2}$, peaks at $z\\approx 1.2-1.5$, later than the predicted peak of the cosmic star formation rate activity, a...

  9. Molecular Statics Simulation of Hydrogen Defect Interaction in Tungsten

    Science.gov (United States)

    Li, Xiaochun; Liu, Yinan; Yu, Yi; Niu, Guojian; Luo, Guangnan; Shu, Xiaolin

    2015-06-01

    Hydrogen (H) defect interactions have been investigated by molecular statics simulations in tungsten (W), including H-H interactions and interactions between H and W self-interstitial atoms. The interactions between H and small H-vacancy clusters are also demonstrated; the binding energies of an H, a vacancy and a self-interstitial W to an H-vacancy cluster depend on the H-to-vacancy ratio. We conclude that H bubble formation needs a high concentration of H in W for the H bubble nucleation and growth, which are also governed by the H-to-vacancy ratio of the cluster. The vacancy first combines with H atoms and a cluster forms, then the H-vacancy cluster goes through the whole process of vacancy capture, H capture, and vacancy capture again, and as a result the H-vacancy cluster grows larger and larger. Finally, the H bubble forms. supported by National Natural Science Foundation of China (Nos. 51171008 and 11405201) and the National Magnetic Confinement Fusion Science Program of China (No. 2013GB1090)

  10. SUMER-Hinode observations of microflares: excitation of molecular hydrogen

    CERN Document Server

    Innes, D E

    2007-01-01

    Concentrations of molecular hydrogen (H2) have been detected by SUMER in active region plage. The H2 is excited by O VI line emission at 1031.94 A which, although not observed, must be brightening along with the observed transition region line, Si III 1113.24 A. We have made co-ordinated observations of active region plage with the spectrometer SUMER/SoHO in lines of H2 1119.10 A and Si III 1113.24 A and with XRT/Hinode X-ray and SOT/Hinode Ca II filters. In six hours of observation, six of the seven H2 events seen occurred near a footpoint of a brightening X-ray loop. The seventh is associated with an unusually strong Si III plasma outflow. We conclude that microflare energy dissipation heats the chromosphere, reducing its opacity, so that O VI microflare emission is able to reach the lower layers of the chromosphere and excite the H2.

  11. Molecular hydrogen emission in the interstellar medium of the Large Magellanic Cloud

    CERN Document Server

    Neelamkodan, Naslim; Madden, Suzanne; Hony, Sacha; Chu, You-Hua; Galliano, Frederic; Bot, Caroline; Yang, Yao-Lun; Seok, Ji Yeon; Oliveira, Joana M; van Loon, Jacco Th; Meixner, Margaret; Li, Aigen; Hughes, Annie; Gordon, Karl D; Otsuka, Masaaki; Hirashita, Hiroyuki; Morata, Oscar; Lebouteiller, Vianney; Indebetouw, Remy; Srinivasan, Sundar; Bernard, Jean-philippe; Reach, William T

    2014-01-01

    We present the detection and analysis of molecular hydrogen emission toward ten interstellar regions in the Large Magellanic Cloud. We examined low-resolution infrared spectral maps of twelve regions obtained with the Spitzer infrared spectrograph (IRS). The low-J rotational transitional lines of H2 at 28.2 and 17.1mu are detected in the IRS spectra for ten regions. The higher level transitions are mostly upper limit measurements except for three regions, where a 3sigma detection threshold is achieved for lines at 12.2 and 8.6mu. The excitation diagrams of the detected H2 transitions are used to determine the warm H2 gas column density and temperature. The single-temperature fits through the lower transition lines give temperatures in the range 80-130K. The bulk of the excited H2 gas is found at these temperatures and contributes a significant fraction of ~7-16% to the total gas mass. A tight correlation of the H2 surface brightness with PAH and total infrared emission has been found, which is a clear indicat...

  12. Role of hydrogen peroxide and hydroxyl radical in pyrite oxidation by molecular oxygen

    Science.gov (United States)

    Schoonen, Martin A. A.; Harrington, Andrea D.; Laffers, Richard; Strongin, Daniel R.

    2010-09-01

    Hydrogen peroxide and hydroxyl radical are readily formed during the oxidation of pyrite with molecular oxygen over a wide range of pH conditions. However, pretreatment of the pyrite surface influences how much of the intermediates are formed and their fate. Acid-washed pyrite produces significant amounts of hydrogen peroxide and hydroxyl radical when suspended in air-saturated water. However, the hydrogen peroxide concentration shows an exponential decrease with time. Suspensions made with partially oxidized pyrite yield significantly lower amounts of hydrogen peroxide product. The presence of Fe(III)-oxide or Fe(III)-hydroxide patches facilitates the conversion of hydrogen peroxide to oxygen and water. Hence, the degree to which a pyrite surface is covered with patches of Fe(III)-oxide or Fe(III)-hydroxide patches is an important control on the concentration of hydrogen peroxide in solution. Hydrogen peroxide appears to be an important intermediate in the four-electron transfer from pyrite to molecular oxygen. Addition of catalase, an enzyme that decomposes hydrogen peroxide to water and molecular oxygen, to a pyrite suspension reduces the oxidation rate by 40%. By contrast, hydroxyl radical does not appear to play a significant role in the oxidation mechanism. It is estimated on the basis of a molecular oxygen and sulfate mass balance that 5-6% of the molecular oxygen is consumed without forming sulfate.

  13. Molecular dynamics simulation of the deposition process of hydrogenated diamond-like carbon (DLC) films

    Institute of Scientific and Technical Information of China (English)

    ZHANG YuJun; DONG GuangNeng; MAO JunHong; XIE YouBai

    2008-01-01

    The deposition process of hydrogenated diamond-like carbon (DLC) film greatly affects its frictional properties. In this study, CH3 radicals are selected as source species to deposit hydrogenated DLC films for molecular dynamics simulation. The growth and structural properties of hydrogenated DLC films are investigated and elucidated in detail. By comparison and statistical analysis, the authors find that the ratio of carbon to hydrogen in the films generally shows a monotonously increasing trend with the increase of impact energy. Carbon atoms are more reactive during deposition and more liable to bond with substrate atoms than hydrogen atoms. In addition, there exists a peak value of the number of hydrogen atoms deposited in hydrogenated DLC films. The trends of the variation are opposite on the two sides of this peak point, and itbecomes stable when impact energy is greater than 80 eV. The average relative density also indicates a rising trend along with the increment of impact energy, while it does not reach the saturation value until impact energy comes to 50 eV. The hydrogen content in source species is a key factor to determine the hydrogen content in hydrogenated DLC films. When the hydrogen content in source species is high, the hydrogen content in hydrogenated DLC films is accordingly high.

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

    CERN Document Server

    Bakalov, Dimitar

    2013-01-01

    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 H2+, HD+, and D2+. The systematic shifts can be evaluated as simple expectation values of the perturbation hamiltonian. Results on radio-frequency (M1), one-photon electric dipole (E1) and two-photon E1 transitions between hyperfine states in HD+ are reported. For two-photon E1 transitions b...

  15. Quantum molecular dynamics study of expanded beryllium: evolution from warm dense matter to atomic fluid.

    Science.gov (United States)

    Li, Dafang; Liu, Haitao; Zeng, Siliang; Wang, Cong; Wu, Zeqing; Zhang, Ping; Yan, Jun

    2014-07-31

    By performing quantum molecular dynamics (QMD) simulations, we investigate the equation of states, electrical and optical properties of the expanded beryllium at densities two to one-hundred lower than the normal solid density, and temperatures ranging from 5000 to 30000 K. With decreasing the density of Be, the optical response evolves from the one characteristic of a simple metal to the one of an atomic fluid. By fitting the optical conductivity spectra with the Drude-Smith model, it is found that the conducting electrons become localized at lower densities. In addition, the negative derivative of the electrical resistivity on temperature at density about eight lower than the normal solid density demonstrates that the metal to nonmetal transition takes place in the expanded Be. To interpret this transition, the electronic density of states is analyzed systematically. Furthermore, a direct comparison of the Rosseland opacity obtained by using QMD and the standard opacity code demonstrates that QMD provides a powerful tool to validate plasma models used in atomic physics approaches in the warm dense matter regime.

  16. Toward efficient asymmetric hydrogenation: architectural and functional engineering of chiral molecular catalysts.

    Science.gov (United States)

    Noyori, Ryoji; Kitamura, Masato; Ohkuma, Takeshi

    2004-04-13

    Asymmetric hydrogenation uses inexpensive, clean hydrogen gas and a very small amount of a chiral molecular catalyst, providing the most powerful way to produce a wide array of enantio-enriched compounds in a large quantity without forming any waste. The recent revolutionary advances in this field have entirely changed the synthetic approach to producing performance chemicals that require a high degree of structural precision. The means of developing efficient asymmetric hydrogenations is discussed from a mechanistic point of view.

  17. H2 formation on PAHs in photodissociation regions: a high-temperature pathway to molecular hydrogen

    NARCIS (Netherlands)

    Boschman, L.; Cazaux, S.; Spaans, M.; Hoekstra, R.; Schlathölter, T.

    2015-01-01

    Aims: Molecular hydrogen is the most abundant molecule in the Universe. It is thought that a large portion of H2 forms by association of hydrogen atoms to polycyclic aromatic hydrocarbons (PAHs). We model the influence of PAHs on total H2 formation rates in photodissociation regions (PDRs) and asses

  18. H-2 formation on PAHs in photodissociation regions : a high-temperature pathway to molecular hydrogen

    NARCIS (Netherlands)

    Boschman, L.; Cazaux, S.; Spaans, M.; Hoekstra, R.; Schlatholter, T.

    2015-01-01

    Aims. Molecular hydrogen is the most abundant molecule in the Universe. It is thought that a large portion of H-2 forms by association of hydrogen atoms to polycyclic aromatic hydrocarbons (PAHs). We model the influence of PAHs on total H-2 formation rates in photodissociation regions (PDRs) and ass

  19. Linear hydrogen adsorbate structures on graphite induced by self-assembled molecular monolayers

    DEFF Research Database (Denmark)

    Nilsson, Louis; Sljivancanin, Zeljko; Balog, Richard

    2012-01-01

    Combined scanning tunnelling microscopy measurements and density functional theory calculations reveal a method to induce linear structures of hydrogen adsorbates on graphite by covering the surface with a self-assembled molecular monolayer of cyanuric acid and exposing it to atomic hydrogen...

  20. Molecular hydrogen alleviates motor deficits and muscle degeneration in mdx mice.

    Science.gov (United States)

    Hasegawa, Satoru; Ito, Mikako; Fukami, Mayu; Hashimoto, Miki; Hirayama, Masaaki; Ohno, Kinji

    2017-01-01

    Duchenne muscular dystrophy (DMD) is a devastating muscle disease caused by a mutation in DMD encoding dystrophin. Oxidative stress accounts for dystrophic muscle pathologies in DMD. We examined the effects of molecular hydrogen in mdx mice, a model animal for DMD. The pregnant mother started to take supersaturated hydrogen water (>5 ppm) ad libitum from E15.5 up to weaning of the offspring. The mdx mice took supersaturated hydrogen water from weaning until age 10 or 24 weeks when they were sacrificed. Hydrogen water prevented abnormal body mass gain that is commonly observed in mdx mice. Hydrogen improved the spontaneous running distance that was estimated by a counter-equipped running-wheel, and extended the duration on the rota-rod. Plasma creatine kinase activities were decreased by hydrogen at ages 10 and 24 weeks. Hydrogen also decreased the number of central nuclei of muscle fibers at ages 10 and 24 weeks, and immunostaining for nitrotyrosine in gastrocnemius muscle at age 24 weeks. Additionally, hydrogen tended to increase protein expressions of antioxidant glutathione peroxidase 1, as well as anti-apoptotic Bcl-2, in skeletal muscle at age 10 weeks. Although molecular mechanisms of the diverse effects of hydrogen remain to be elucidated, hydrogen potentially improves muscular dystrophy in DMD patients.

  1. Vibrational Distribution of Hydrogen Molecular Ions in High-Energy Ionization Processes

    Institute of Scientific and Technical Information of China (English)

    CHEN Shao-Hao; HE Chun-Long; CHEN Chao; LI Jia-Ming

    2005-01-01

    @@ A theoretical time-dependent wave-packet dynamics method is applied to calculate the distribution of vibrational states of hydrogen molecular ions produced in high-energy ionization processes of hydrogen molecules. The isotope effect is elucidated in agreement with the available experimental measurements. Our proposed method should be readily applied in other atomic and molecular processes considering great advances in electronic computation science and technology.

  2. Investigation of hydrogenase molecular marker to optimize hydrogen production from organic wastes and effluents of agro-food industries [abstract

    Directory of Open Access Journals (Sweden)

    Hamilton, C.

    2010-01-01

    Full Text Available In recent years policy makers have started looking for alternatives to fossil fuels, not only to counter the threat of global warming, but also to reduce the risk of overdependence on imported oil and gas supplies. By contrast with hydrocarbon fuels, hydrogen (H2, whether burned directly or used in fuel cells, is intrinsically a clean energy vector with near zero emission. However the main current method of producing hydrogen, steam reforming of methane, involves the release of large quantities of greenhouse gases. So although hydrogen already accounts for around 2% of world consumption of energy, its more widespread adoption is limited by several challenges. Therefore new processes are investigated, especially those using renewable raw material, e.g. woods and organic wastes, and/or involving microorganisms. Indeed, for some algae and bacteria, the generation of molecular hydrogen is an essential part of their energy metabolism. The approach with the greatest commercial potential is fermentative hydrogen generation (dark fermentation by bacteria from the Clostridium genus. This biological process, as a part of the methane-producing anaerobic digestion process, is very promising since it allows the production of hydrogen from a wide variety of renewable resources such as carbohydrate waste from the agricultural and agro-food industries or processed urban waste and sewage. To date most publications on hydrogen production by Clostridium strains have focused on the effects of operating parameters (such as temperature, pH, dilution rate, etc.. We now need to extend this knowledge by identifying and monitoring the various different metabolic agents involved in high H2 activity. Consequently the aim of this research at the CWBI in the University of Liege is to investigate the role of [Fe] hydrogenases, the key enzymes that remove excess electrons accumulating during fermentation. Clostridium butyricum CWBI1009, the strain used for these investigations

  3. Competition between Hydrogen Bonds and Coordination Bonds Steered by the Surface Molecular Coverage.

    Science.gov (United States)

    Cai, Liangliang; Sun, Qiang; Bao, Meiling; Ma, Honghong; Yuan, Chunxue; Xu, Wei

    2017-04-25

    In addition to the choices of metal atoms/molecular linkers and surfaces, several crucial parameters, including surface temperature, molecular stoichiometric ratio, electrical stimulation, concentration, and solvent effect for liquid/solid interfaces, have been demonstrated to play key roles in the formation of on-surface self-assembled supramolecular architectures. Moreover, self-assembled structural transformations frequently occur in response to a delicate control over those parameters, which, in most cases, involve either conversions from relatively weak interactions to stronger ones (e.g., hydrogen bonds to coordination bonds) or transformations between the comparable interactions (e.g., different coordination binding modes or hydrogen bonding configurations). However, intermolecular bond conversions from relatively strong coordination bonds to weak hydrogen bonds were rarely reported. Moreover, to our knowledge, a reversible conversion between hydrogen bonds and coordination bonds has not been demonstrated before. Herein, we have demonstrated a facile strategy for the regulation of stepwise intermolecular bond conversions from the metal-organic coordination bond (Cu-N) to the weak hydrogen bond (CH···N) by increasing the surface molecular coverage. From the DFT calculations we quantify that the loss in intermolecular interaction energy is compensated by the increased molecular adsorption energy at higher molecular coverage. Moreover, we achieved a reversible conversion from the weak hydrogen bond to the coordination bond by decreasing the surface molecular coverage.

  4. Catalytic Hydrogenation over Palladium Complex of Molecular Complex of Poly(4-vinylpyridine) with Acetic Acid

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    The palladium complex of the molecular complex of poly(4-vinylpyridine) with acetic acid(PVP/HAc-Pd) was prepared. Its catalytic activity for the hydrogenation of nitrobenzene was found much higher than that of the corresponding palladium complex of poly(4-vinylpyridine). In the presence of a strong inorganic alkali, especially potassium hydroxide, the catalytic activity is greatly improved. The suitable hydrogenation condition for PVP/HAc-Pd is to use 0.1 mol/L ethanol solution of potassium hydroxide as the hydrogenation medium and the hydrogenation is carried out at 45 ℃.

  5. Bioinspired molecular co-catalysts bonded to a silicon photocathode for solar hydrogen evolution

    DEFF Research Database (Denmark)

    Hou, Yidong; Abrams, Billie L.; Vesborg, Peter Christian Kjærgaard

    2011-01-01

    -abundant alternatives are needed for large-scale use. We show that bioinspired molecular clusters based on molybdenum and sulphur evolve hydrogen at rates comparable to that of platinum. The incomplete cubane-like clusters (Mo3S 4) efficiently catalyse the evolution of hydrogen when coupled to a p-type Si semiconductor......The production of fuels from sunlight represents one of the main challenges in the development of a sustainable energy system. Hydrogen is the simplest fuel to produce and although platinum and other noble metals are efficient catalysts for photoelectrochemical hydrogen evolution, earth...

  6. Ab initio molecular dynamics simulation study of successive hydrogenation reactions of carbon monoxide producing methanol

    Science.gov (United States)

    Pham, Thi Nu; Ono, Shota; Ohno, Kaoru

    2016-04-01

    Doing ab initio molecular dynamics simulations, we demonstrate a possibility of hydrogenation of carbon monoxide producing methanol step by step. At first, the hydrogen atom reacts with the carbon monoxide molecule at the excited state forming the formyl radical. Formaldehyde was formed after adding one more hydrogen atom to the system. Finally, absorption of two hydrogen atoms to formaldehyde produces methanol molecule. This study is performed by using the all-electron mixed basis approach based on the time dependent density functional theory within the adiabatic local density approximation for an electronic ground-state configuration and the one-shot GW approximation for an electronic excited state configuration.

  7. Molecular hydrogen (H2) emissions from gasoline and diesel vehicles.

    Science.gov (United States)

    Bond, S W; Alvarez, R; Vollmer, M K; Steinbacher, M; Weilenmann, M; Reimann, S

    2010-08-01

    This study assesses individual-vehicle molecular hydrogen (H2) emissions in exhaust gas from current gasoline and diesel vehicles measured on a chassis dynamometer. Absolute H2 emissions were found to be highest for motorcycles and scooters (141+/-38.6 mg km(-1)), approximately 5 times higher than for gasoline-powered automobiles (26.5+/-12.1 mg km(-1)). All diesel-powered vehicles emitted marginal amounts of H2 ( approximately 0.1 mg km(-1)). For automobiles, the highest emission factors were observed for sub-cycles subject to a cold-start (mean of 53.1+/-17.0 mg km(-1)). High speeds also caused elevated H2 emission factors for sub-cycles reaching at least 150 km h(-1) (mean of 40.4+/-7.1 mg km(-1)). We show that H2/CO ratios (mol mol(-1)) from gasoline-powered vehicles are variable (sub-cycle means of 0.44-5.69) and are typically higher (mean for automobiles 1.02, for 2-wheelers 0.59) than previous atmospheric ratios characteristic of traffic-influenced measurements. The lowest mean individual sub-cycle ratios, which correspond to high absolute emissions of both H2 and CO, were observed during cold starts (for automobiles 0.48, for 2-wheelers 0.44) and at high vehicle speeds (for automobiles 0.73, for 2-wheelers 0.45). This finding illustrates the importance of these conditions to observed H2/CO ratios in ambient air. Overall, 2-wheelers displayed lower H2/CO ratios (0.48-0.69) than those from gasoline-powered automobiles (0.75-3.18). This observation, along with the lower H2/CO ratios observed through studies without catalytic converters, suggests that less developed (e.g. 2-wheelers) and older vehicle technologies are largely responsible for the atmospheric H2/CO ratios reported in past literature. 2010 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

    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.

  9. NQR application to the study of hydrogen dynamics in hydrogen-bonded molecular dimers

    Science.gov (United States)

    Asaji, Tetsuo

    2016-12-01

    The temperature dependences of 1H NMR as well as 35Cl NQR spin-lattice relaxation times T 1 were investigated in order to study the hydrogen transfer dynamics in carboxylic acid dimers in 3,5-dichloro- and 2,6-dichlorobenzoic acids. The asymmetry energy A/ k B and the activation energy V/ k B for the hydrogen transfer were estimated to be 240 K and 900 K, and 840 K and 2500 K, respectively, for these compounds. In spite of a large asymmetric potential the quantum nature of hydrogen transfer is recognized in the slope of the temperature dependence of T 1 on the low-temperature side of the T 1 minimum. The NQR T 1 measurements was revealed to be a good probe for the hydrogen transfer dynamics.

  10. Resonant Scattering of Muonic Hydrogen Atoms and Dynamics of Muonic Molecular Complex

    CERN Document Server

    Fujiwara, M C; Bailey, J M; Beer, G A; Beveridge, J L; Faifman, M P; Huber, T M; Kammel, P; Kim, S K; Knowles, P E; Kunselman, A R; Maier, M; Markushin, V E; Marshall, G M; Martoff, C J; Mason, G R; Mulhauser, F; Olin, A; Petitjean, C; Porcelli, T A; Wozniak, J; Zmeskal, J

    2001-01-01

    Resonant scattering of muonic hydrogen atoms via back decay of molecular complex, a key process in the understanding of epithermal muonic molecular formation, is analyzed. The limitations of the effective rate approximation are discussed and the importance of the explicit treatment of the back decay is stressed. An expression of the energy distribution for the back-decayed atoms is given.

  11. Molecular hydrogen reduces LPS-induced neuroinflammation and promotes recovery from sickness behaviour in mice.

    Directory of Open Access Journals (Sweden)

    Stefan Spulber

    Full Text Available Molecular hydrogen has been shown to have neuroprotective effects in mouse models of acute neurodegeneration. The effect was suggested to be mediated by its free-radical scavenger properties. However, it has been shown recently that molecular hydrogen alters gene expression and protein phosphorylation. The aim of this study was to test whether chronic ad libitum consumption of molecular hydrogen-enriched electrochemically reduced water (H-ERW improves the outcome of lipopolysaccharide (LPS-induced neuroinflammation. Seven days after the initiation of H-ERW treatment, C57Bl/6 mice received a single injection of LPS (0.33 mg/kg i.p. or an equivalent volume of vehicle. The LPS-induced sickness behaviour was assessed 2 h after the injection, and recovery was assessed by monitoring the spontaneous locomotor activity in the homecage for 72 h after the administration of LPS. The mice were killed in the acute or recovery phase, and the expression of pro- and antiinflammatory cytokines in the hippocampus was assessed by real-time PCR. We found that molecular hydrogen reduces the LPS-induced sickness behaviour and promotes recovery. These effects are associated with a shift towards anti-inflammatory gene expression profile at baseline (downregulation of TNF- α and upregulation of IL-10. In addition, molecular hydrogen increases the amplitude, but shortens the duration and promotes the extinction of neuroinflammation. Consistently, molecular hydrogen modulates the activation and gene expression in a similar fashion in immortalized murine microglia (BV-2 cell line, suggesting that the effects observed in vivo may involve the modulation of microglial activation. Taken together, our data point to the regulation of cytokine expression being an additional critical mechanism underlying the beneficial effects of molecular hydrogen.

  12. Signatures of Hot Molecular Hydrogen Absorption from Protoplanetary Disks. I. Non-thermal Populations

    Science.gov (United States)

    Hoadley, Keri; France, Kevin; Arulanantham, Nicole; Parke Loyd, R. O.; Kruczek, Nicholas

    2017-09-01

    The environment around protoplanetary disks (PPDs) regulates processes that drive the chemical and structural evolution of circumstellar material. We perform a detailed empirical survey of warm molecular hydrogen (H2) absorption observed against H i-Lyα (Lyα: λ1215.67) emission profiles for 22 PPDs, using archival Hubble Space Telescope ultraviolet (UV) spectra to identify H2 absorption signatures and quantify the column densities of H2 ground states in each sightline. We compare thermal equilibrium models of H2 to the observed H2 rovibrational level distributions. We find that, for the majority of targets, there is a clear deviation in high-energy states (T exc ≳ 20,000 K) away from thermal equilibrium populations (T(H2) ≳ 3500 K). We create a metric to estimate the total column density of non-thermal H2 (N(H2)nLTE) and find that the total column densities of thermal (N(H2)) and N(H2)nLTE correlate for transition disks and targets with detectable C iv-pumped H2 fluorescence. We compare N(H2) and N(H2)nLTE to circumstellar observables and find that N(H2)nLTE correlates with X-ray and far-UV luminosities, but no correlations are observed with the luminosities of discrete emission features (e.g., Lyα, C iv). Additionally, N(H2) and N(H2)nLTE are too low to account for the H2 fluorescence observed in PPDs, so we speculate that this H2 may instead be associated with a diffuse, hot, atomic halo surrounding the planet-forming disk. We create a simple photon-pumping model for each target to test this hypothesis and find that Lyα efficiently pumps H2 levels with T exc ≥ 10,000 K out of thermal equilibrium.

  13. A General Catalogue of Molecular Hydrogen Emission-Line Objects (MHOs) in Outflows from Young Stars

    CERN Document Server

    Davis, Christopher J; Khanzadyan, Tigran; Smith, Michael D; Jenness, Tim

    2009-01-01

    We present a catalogue of Molecular Hydrogen emission-line Objects (MHOs) in outflows from embedded young stars. All objects are identified in the near-infrared lines of molecular hydrogen, all reside in the Milky Way, and all are associated with jets or molecular outflows from young stars. Objects in both low and high-mass star forming regions are included. This catalogue complements the existing database of Herbig-Haro objects; indeed, for completeness, HH objects that are detected in H2 emission are included in the MHO catalogue.

  14. Molecular cobalt pentapyridine catalysts for generating hydrogen from water

    Science.gov (United States)

    Long, Jeffrey R; Chang, Christopher J; Sun, Yujie

    2013-11-05

    A composition of matter suitable for the generation of hydrogen from water is described, the positively charged cation of the composition including the moiety of the general formula. [(PY5Me.sub.2)CoL].sup.2+, where L can be H.sub.2O, OH.sup.-, a halide, alcohol, ether, amine, and the like. In embodiments of the invention, water, such as tap water or sea water can be subject to low electric potentials, with the result being, among other things, the generation of hydrogen.

  15. VUV diagnostic of electron impact processes in low temperature molecular hydrogen plasma

    CERN Document Server

    Komppula, J

    2015-01-01

    Novel methods for diagnostics of molecular hydrogen plasma processes, such as ionization, production of high vibrational levels, dissociation of molecules via excitation to singlet and triplet states and production of metastable states, are presented for molecular hydrogen plasmas in corona equilibrium. The methods are based on comparison of rate coefficients of plasma processes and optical emission spectroscopy of lowest singlet and triplet transitions, i.e. Lyman-band ($B^1\\Sigma^+_u \\rightarrow X^1\\Sigma^+_g$) and molecular continuum ($a^3\\Sigma^+_g \\rightarrow b^3\\Sigma^+_u$), of the hydrogen molecule in VUV wavelength range. Comparison of rate coefficients of spin-allowed and/or spin-forbidden excitations reduces the uncertainty caused by the non-equilibrium distributions of electron energy and molecular vibrational level, which are typically known poorly in plasma sources. The described methods are applied to estimate the rates of various plasma processes in a filament arc discharge.

  16. Polycyclic aromatic hydrocarbons and molecular hydrogen in oxygen-rich planetary nebulae: the case of NGC6720

    CERN Document Server

    Cox, N L J; Berne, O; Cernicharo, J; Joblin, C

    2015-01-01

    Evolved stars are primary sources for the formation of polycyclic aromatic hydrocarbons (PAHs) and dust grains. Their circumstellar chemistry is usually designated as either oxygen-rich or carbon-rich, although dual-dust chemistry objects, whose infrared spectra reveal both silicate- and carbon-dust features, are also known. The exact origin and nature of this dual-dust chemistry is not yet understood. Spitzer-IRS mid-infrared spectroscopic imaging of the nearby, oxygen-rich planetary nebula NGC6720 reveals the presence of the 11.3 micron aromatic (PAH) emission band. It is attributed to emission from neutral PAHs, since no band is observed in the 7 to 8 micron range. The spatial distribution of PAHs is found to closely follow that of the warm clumpy molecular hydrogen emission. Emission from both neutral PAHs and warm H2 is likely to arise from photo-dissociation regions associated with dense knots that are located within the main ring. The presence of PAHs together with the previously derived high abundance...

  17. A Comprehensive Study of Hydrogen Adsorbing to Amorphous Water ice: Defining Adsorption in Classical Molecular Dynamics

    Science.gov (United States)

    Dupuy, John L.; Lewis, Steven P.; Stancil, P. C.

    2016-11-01

    Gas-grain and gas-phase reactions dominate the formation of molecules in the interstellar medium (ISM). Gas-grain reactions require a substrate (e.g., a dust or ice grain) on which the reaction is able to occur. The formation of molecular hydrogen (H2) in the ISM is the prototypical example of a gas-grain reaction. In these reactions, an atom of hydrogen will strike a surface, stick to it, and diffuse across it. When it encounters another adsorbed hydrogen atom, the two can react to form molecular hydrogen and then be ejected from the surface by the energy released in the reaction. We perform in-depth classical molecular dynamics simulations of hydrogen atoms interacting with an amorphous water-ice surface. This study focuses on the first step in the formation process; the sticking of the hydrogen atom to the substrate. We find that careful attention must be paid in dealing with the ambiguities in defining a sticking event. The technical definition of a sticking event will affect the computed sticking probabilities and coefficients. Here, using our new definition of a sticking event, we report sticking probabilities and sticking coefficients for nine different incident kinetic energies of hydrogen atoms [5-400 K] across seven different temperatures of dust grains [10-70 K]. We find that probabilities and coefficients vary both as a function of grain temperature and incident kinetic energy over the range of 0.99-0.22.

  18. Molecular Phylogeny Of Microbes In The Deep-Sea Sediments From Tropical West Pacific Warm Pool

    Science.gov (United States)

    Wang, F.; Xiao, X.; Wang, P.

    2005-12-01

    The presence and phylogeny of bacteria and archaea in five deep-sea sediment samples collected from west Pacific Warm Pool area (WP-0, WP-1, WP-2, WP-3, WP-4), and in five sediment layers (1cm-, 3cm-, 6cm-, 10cm-, 12cm- layer) of the 12-cm sediment core of WP-0 were checked and compared. The microbial diversity in the five deep-sea sediments were similar as revealed by denaturing gradient gel electrophoresis, and all of them contained members of non-thermophilic marine group I crenarchaeota as the predominant archaeal group. The composition of methylotrophs including methanotrophs, sulfate reducing bacteria in the WP-0 sediment core were further investigated by molecular marker based analysis of mxaF, pmoA, dsrAB, specific anoxic methane oxidation archaeal and sulfate reducing bacterial 16S rRNA genes. From MxaF amino acid sequence analysis, it was demonstrated that microbes belonging to α - Proteobacteria most related to Hyphomicrobium and Methylobacterium were dominant aerobic methylotrophs in this deep-sea sediment; and small percentage of type II methanotrophs affiliating closest to Methylocystis and Methylosinus were also detected in this environment. mxaF quantitative PCR results showed that in the west Pacific WP sediment there existed around 3× 10 4-5 methylotrophs per gram sediment, 10-100 times more than that in samples collected from several other deep-sea Pacific sediment sample, but about 10 times less than that present in samples collected from rice and flower garden soil. Diverse groups of novel archaea (named as WPA), not belonging to any known archaeal lineages were checked out. They could be placed in the euryarchaeota kingdom, separated into two distinct groups, the main group was peripherally related with methanogens, the other group related with Thermoplasma. Possible sulfate reducing bacterial related with Desulfotomaculum, Desulfacinum, Desulfomonile and Desulfanuticus were also detected in our study. The vertical distributions of WPA

  19. Warm molecular Hydrogen at high redshift with the James Webb Space Telescope

    CERN Document Server

    Guillard, P; Lehnert, M D; Appleton, P N; Forêts, G Pineau des

    2015-01-01

    The build-up of galaxies is regulated by a complex interplay between gravitational collapse, galaxy merging and feedback related to AGN and star formation. The energy released by these processes has to dissipate for gas to cool, condense, and form stars. How gas cools is thus a key to understand galaxy formation. \\textit{Spitzer Space Telescope} infrared spectroscopy revealed a population of galaxies with weak star formation and unusually powerful H$_2$ line emission. This is a signature of turbulent dissipation, sustained by large-scale mechanical energy injection. The cooling of the multiphase interstellar medium is associated with emission in the H$_2$ lines. These results have profound consequences on our understanding of regulation of star formation, feedback and energetics of galaxy formation in general. The fact that H$_2$ lines can be strongly enhanced in high-redshift turbulent galaxies will be of great importance for the \\textit{James Webb Space Telescope} observations which will unveil the role tha...

  20. Hydrogen Bonding and Related Properties in Liquid Water: A Car-Parrinello Molecular Dynamics Simulation Study.

    Science.gov (United States)

    Guardia, Elvira; Skarmoutsos, Ioannis; Masia, Marco

    2015-07-23

    The local hydrogen-bonding structure and dynamics of liquid water have been investigated using the Car-Parrinello molecular dynamics simulation technique. The radial distribution functions and coordination numbers around water molecules have been found to be strongly dependent on the number of hydrogen bonds formed by each molecule, revealing also the existence of local structural heterogeneities in the structure of the liquid. The results obtained have also revealed the strong effect of the local hydrogen-bonding network on the local tetrahedral structure and entropy. The investigation of the dynamics of the local hydrogen-bonding network in liquid water has shown that this network is very labile, and the hydrogen bonds break and reform very rapidly. Nevertheless, it has been found that the hydrogen-bonding states associated with the formation of four hydrogen bonds by a water molecule exhibit the largest survival probability and corresponding lifetime. The reorientational motions of water molecules have also been found to be strongly dependent on their initial hydrogen-bonding state. Finally, the dependence of the librational and vibrational modes of water molecules on the local hydrogen-bonding network has been carefully examined, revealing a significant effect upon the libration and bond-stretching peak frequencies. The calculated low frequency peaks come in agreement with previously reported interpretations of the experimental low-frequency Raman spectrum of liquid water.

  1. On the Intramolecular Hydrogen Bond in Solution: Car-Parrinello and Path Integral Molecular Dynamics Perspective.

    Science.gov (United States)

    Dopieralski, Przemyslaw; Perrin, Charles L; Latajka, Zdzislaw

    2011-11-08

    The issue of the symmetry of short, low-barrier hydrogen bonds in solution is addressed here with advanced ab initio simulations of a hydrogen maleate anion in different environments, starting with the isolated anion, going through two crystal structures (sodium and potassium salts), then to an aqueous solution, and finally in the presence of counterions. By Car-Parrinello and path integral molecular dynamics simulations, it is demonstrated that the position of the proton in the intramolecular hydrogen bond of an aqueous hydrogen maleate anion is entirely related to the solvation pattern around the oxygen atoms of the intramolecular hydrogen bond. In particular, this anion has an asymmetric hydrogen bond, with the proton always located on the oxygen atom that is less solvated, owing to the instantaneous solvation environment. Simulations of water solutions of hydrogen maleate ion with two different counterions, K(+) and Na(+), surprisingly show that the intramolecular hydrogen-bond potential in the case of the Na(+) salt is always asymmetric, regardless of the hydrogen bonds to water, whereas for the K(+) salt, the potential for H motion depends on the location of the K(+). It is proposed that repulsion by the larger and more hydrated K(+) is weaker than that by Na(+) and competitive with solvation by water.

  2. Molecular hydrogen suppresses FcepsilonRI-mediated signal transduction and prevents degranulation of mast cells.

    Science.gov (United States)

    Itoh, Tomohiro; Fujita, Yasunori; Ito, Mikako; Masuda, Akio; Ohno, Kinji; Ichihara, Masatoshi; Kojima, Toshio; Nozawa, Yoshinori; Ito, Masafumi

    2009-11-27

    Molecular hydrogen ameliorates oxidative stress-associated diseases in animal models. We found that oral intake of hydrogen-rich water abolishes an immediate-type allergic reaction in mice. Using rat RBL-2H3 mast cells, we demonstrated that hydrogen attenuates phosphorylation of the FcepsilonRI-associated Lyn and its downstream signal transduction, which subsequently inhibits the NADPH oxidase activity and reduces the generation of hydrogen peroxide. We also found that inhibition of NADPH oxidase attenuates phosphorylation of Lyn in mast cells, indicating the presence of a feed-forward loop that potentiates the allergic responses. Hydrogen accordingly inhibits all tested signaling molecule(s) in the loop. Hydrogen effects have been solely ascribed to exclusive removal of hydroxyl radical. In the immediate-type allergic reaction, hydrogen exerts its beneficial effect not by its radical scavenging activity but by modulating a specific signaling pathway. Effects of hydrogen in other diseases are possibly mediated by modulation of yet unidentified signaling pathways. Our studies also suggest that hydrogen is a gaseous signaling molecule like nitric oxide.

  3. Molecular nature of sulfhydryl modification by hydrogen peroxide on type 1 ryanodine receptor

    Institute of Scientific and Technical Information of China (English)

    Hong-mei HAN; Ri-sheng WEI; Anthony F LAI; Chang-cheng YIN

    2006-01-01

    Aim: To elucidate the molecular nature of sulfhydryl modification by hydrogen peroxide on type 1 ryanodine receptor (RyRl). Methods: Rabbit skeletal muscle sarcoplasmic reticulum was treated with hydrogen peroxide, then RyRl complex was isolated. The proteins in the complex were analysed by electrophoresis, Western blot and electron microscopy. Results: (1) Hydrogen peroxide induces inter-subunit cross-linking within the tetrameric RyR1 molecule; (2) in parallel to inter-subunit cross-linking, the RyR1 molecule changes morphology; (3) the chemical and morphological changes are reversible: upon reduction by reducing agents, the RyR1 molecule regains its original state. Conclusion: These findings suggest that the molecular mechanism of RyR1 channe1 activity in sarcoplasmic reticulum regulated by hydrogen peroxide is through inter-subunit cross-linking within the tetrameric RyR1 molecule, which in turn induces structural changes of RyR1.

  4. Cassini finds molecular hydrogen in the Enceladus plume: Evidence for hydrothermal processes

    Science.gov (United States)

    Waite, J. Hunter; Glein, Christopher R.; Perryman, Rebecca S.; Teolis, Ben D.; Magee, Brian A.; Miller, Greg; Grimes, Jacob; Perry, Mark E.; Miller, Kelly E.; Bouquet, Alexis; Lunine, Jonathan I.; Brockwell, Tim; Bolton, Scott J.

    2017-04-01

    Saturn’s moon Enceladus has an ice-covered ocean; a plume of material erupts from cracks in the ice. The plume contains chemical signatures of water-rock interaction between the ocean and a rocky core. We used the Ion Neutral Mass Spectrometer onboard the Cassini spacecraft to detect molecular hydrogen in the plume. By using the instrument’s open-source mode, background processes of hydrogen production in the instrument were minimized and quantified, enabling the identification of a statistically significant signal of hydrogen native to Enceladus. We find that the most plausible source of this hydrogen is ongoing hydrothermal reactions of rock containing reduced minerals and organic materials. The relatively high hydrogen abundance in the plume signals thermodynamic disequilibrium that favors the formation of methane from CO2 in Enceladus’ ocean.

  5. Hydrogen bonding and related properties in liquid water: a Car-Parrinello molecular dynamics simulation study

    OpenAIRE

    Guàrdia Manuel, Elvira; Skarmoutsos, Ioannis; Masia, Marco

    2015-01-01

    The local hydrogen-bonding structure and dynamics of liquid water have been investigated using the Car-Parrinello molecular dynamics simulation technique. The radial distribution functions and coordination numbers around water molecules have been found to be strongly dependent on the number of hydrogen bonds formed by each molecule, revealing also the existence of local structural heterogeneities in the structure of the liquid. The results obtained have also revealed the strong effect of the ...

  6. Ab initio molecular dynamics simulation of hydrogen fluoride at several thermodynamic states

    DEFF Research Database (Denmark)

    Kreitmeir, M.; Bertagnolli, H.; Mortensen, Jens Jørgen;

    2003-01-01

    Liquid hydrogen fluoride is a simple but interesting system for studies of the influence of hydrogen bonds on physical properties. We have performed ab initio molecular dynamics simulations of HF at several thermodynamic states, where we examine the microscopic structure of the liquid as well...... as its static and dynamic properties. The results obtained show good agreement with well established data, and, moreover, we were able to show significant changes within the structure depending on the system's temperature and density....

  7. Molecular metal-Oxo catalysts for generating hydrogen from water

    Science.gov (United States)

    Long, Jeffrey R; Chang, Christopher J; Karunadasa, Hemamala I

    2015-02-24

    A composition of matter suitable for the generation of hydrogen from water is described, the positively charged cation of the composition having the general formula [(PY5W.sub.2)MO].sup.2+, wherein PY5W.sub.2 is (NC.sub.5XYZ)(NC.sub.5H.sub.4).sub.4C.sub.2W.sub.2, M is a transition metal, and W, X, Y, and Z can be H, R, a halide, CF.sub.3, or SiR.sub.3, where R can be an alkyl or aryl group. The two accompanying counter anions, in one embodiment, can be selected from the following Cl.sup.-, I.sup.-, PF.sub.6.sup.-, and CF.sub.3SO.sub.3.sup.-. In embodiments of the invention, water, such as tap water containing electrolyte or straight sea water can be subject to an electric potential of between 1.0 V and 1.4 V relative to the standard hydrogen electrode, which at pH 7 corresponds to an overpotential of 0.6 to 1.0 V, with the result being, among other things, the generation of hydrogen with an optimal turnover frequency of ca. 1.5 million mol H.sub.2/mol catalyst per h.

  8. Covalent features in the hydrogen bond of a water dimer: molecular orbital analysis

    CERN Document Server

    Wang, Bo; Dai, Xing; Gao, Yang; Wang, Zhigang; Zhang, Rui-Qin

    2015-01-01

    The covalent-like characteristics of hydrogen bonds offer a new perspective on intermolecular interactions. Here, using density functional theory and post-Hartree-Fock methods, we reveal that there are two bonding molecular orbitals (MOs) crossing the O and H atoms of the hydrogen-bond in water dimer. Energy decomposition analysis also shows a non-negligible contribution of the induction term. These results illustrate the covalent-like character of the hydrogen bond between water molecules, which contributes to the essential understanding of ice, liquid water, related materials, and life sciences.

  9. Evidence of molecular hydrogen trapped in two-dimensional layered titanium carbide-based MXene

    Science.gov (United States)

    Osti, Naresh C.; Naguib, Michael; Tyagi, Madhusudan; Gogotsi, Yury; Kolesnikov, Alexander I.; Mamontov, Eugene

    2017-07-01

    Two-dimensional transition metal carbides and nitrides (MXenes) are one of the largest and fastest growing families of materials. The presence of molecular hydrogen at ambient conditions in a MXene (T i3C2Tx , where Tx represents a surface terminating species, including O, OH, and F) material is revealed here by inelastic and elastic neutron scatterings. The inelastic neutron-scattering spectrum measured at 5 K shows a peak at 14.6 meV, presenting a clear indication of the presence of parahydrogen in the MXene synthesized using 48 % hydrofluoric acid and annealed at 110 ∘C in vacuum prior to the measurement. An increase in the measurement temperature gradually reduces the peak intensity and increases the peak width due to the mobility of the molecular hydrogen in confinement. The presence of molecular hydrogen is confirmed further from the observed elastic intensity drop in a fixed energy-window scan of elastic intensity measurements in the temperature range of 10-35 K. Using milder etching conditions, ion intercalation, or an increase in the annealing temperature all result in the absence of the trapped hydrogen molecules in MXene. The results of this paper can guide the development of MXene materials with desired properties and improve our understanding of the behavior of MXenes in applications ranging from supercapacitors to hydrogen evolution reaction catalysis and hydrogen storage.

  10. Molecular Hydrogen as an Emerging Therapeutic Medical Gas for Neurodegenerative and Other Diseases

    Directory of Open Access Journals (Sweden)

    Kinji Ohno

    2012-01-01

    Full Text Available Effects of molecular hydrogen on various diseases have been documented for 63 disease models and human diseases in the past four and a half years. Most studies have been performed on rodents including two models of Parkinson's disease and three models of Alzheimer's disease. Prominent effects are observed especially in oxidative stress-mediated diseases including neonatal cerebral hypoxia; Parkinson's disease; ischemia/reperfusion of spinal cord, heart, lung, liver, kidney, and intestine; transplantation of lung, heart, kidney, and intestine. Six human diseases have been studied to date: diabetes mellitus type 2, metabolic syndrome, hemodialysis, inflammatory and mitochondrial myopathies, brain stem infarction, and radiation-induced adverse effects. Two enigmas, however, remain to be solved. First, no dose-response effect is observed. Rodents and humans are able to take a small amount of hydrogen by drinking hydrogen-rich water, but marked effects are observed. Second, intestinal bacteria in humans and rodents produce a large amount of hydrogen, but an addition of a small amount of hydrogen exhibits marked effects. Further studies are required to elucidate molecular bases of prominent hydrogen effects and to determine the optimal frequency, amount, and method of hydrogen administration for each human disease.

  11. Molecular Hydrogen as an Emerging Therapeutic Medical Gas for Neurodegenerative and Other Diseases

    Science.gov (United States)

    Ohno, Kinji; Ito, Mikako; Ichihara, Masatoshi; Ito, Masafumi

    2012-01-01

    Effects of molecular hydrogen on various diseases have been documented for 63 disease models and human diseases in the past four and a half years. Most studies have been performed on rodents including two models of Parkinson's disease and three models of Alzheimer's disease. Prominent effects are observed especially in oxidative stress-mediated diseases including neonatal cerebral hypoxia; Parkinson's disease; ischemia/reperfusion of spinal cord, heart, lung, liver, kidney, and intestine; transplantation of lung, heart, kidney, and intestine. Six human diseases have been studied to date: diabetes mellitus type 2, metabolic syndrome, hemodialysis, inflammatory and mitochondrial myopathies, brain stem infarction, and radiation-induced adverse effects. Two enigmas, however, remain to be solved. First, no dose-response effect is observed. Rodents and humans are able to take a small amount of hydrogen by drinking hydrogen-rich water, but marked effects are observed. Second, intestinal bacteria in humans and rodents produce a large amount of hydrogen, but an addition of a small amount of hydrogen exhibits marked effects. Further studies are required to elucidate molecular bases of prominent hydrogen effects and to determine the optimal frequency, amount, and method of hydrogen administration for each human disease. PMID:22720117

  12. Formation of molecular hydrogen on analogues of interstellar dust grains: experiments and modelling

    CERN Document Server

    Vidali, G; Manico, G; Pirronello, V; Perets, H B; Biham, O; Vidali, Gianfranco; Roser, Joe; Manico, Giulio; Pirronello, Valerio; Perets, Hagai B.; Biham, Ofer

    2005-01-01

    Molecular hydrogen has an important role in the early stages of star formation as well as in the production of many other molecules that have been detected in the interstellar medium. In this review we show that it is now possible to study the formation of molecular hydrogen in simulated astrophysical environments. Since the formation of molecular hydrogen is believed to take place on dust grains, we show that surface science techniques such as thermal desorption and time-of-flight can be used to measure the recombination efficiency, the kinetics of reaction and the dynamics of desorption. The analysis of the experimental results using rate equations gives useful insight on the mechanisms of reaction and yields values of parameters that are used in theoretical models of interstellar cloud chemistry.

  13. Tunable Molecular MoS2 Edge-Site Mimics for Catalytic Hydrogen Production.

    Science.gov (United States)

    Garrett, Benjamin R; Polen, Shane M; Click, Kevin A; He, Mingfu; Huang, Zhongjie; Hadad, Christopher M; Wu, Yiying

    2016-04-18

    Molybdenum sulfides represent state-of-the-art, non-platinum electrocatalysts for the hydrogen evolution reaction (HER). According to the Sabatier principle, the hydrogen binding strength to the edge active sites should be neither too strong nor too weak. Therefore, it is of interest to develop a molecular motif that mimics the catalytic sites structurally and possesses tunable electronic properties that influence the hydrogen binding strength. Furthermore, molecular mimics will be important for providing mechanistic insight toward the HER with molybdenum sulfide catalysts. In this work, a modular method to tune the catalytic properties of the S-S bond in MoO(S2)2L2 complexes is described. We studied the homogeneous electrocatalytic hydrogen production performance metrics of three catalysts with different bipyridine substitutions. By varying the electron-donating abilities, we present the first demonstration of using the ligand to tune the catalytic properties of the S-S bond in molecular MoS2 edge-site mimics. This work can shed light on the relationship between the structure and electrocatalytic activity of molecular MoS2 catalysts and thus is of broad importance from catalytic hydrogen production to biological enzyme functions.

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

    CERN Document Server

    Aznabayev, D T; Zhaugasheva, S A; Korobov, V I

    2016-01-01

    The static dipole polarizability for the hydrogen molecular ions H$_2^+$, HD$^+$, and D$_2^+$ are calculated. These new data for polarizability takes into account the leading order relativistic corrections to the wave function of the three-body system resulted from the Breit-Pauli Hamiltonian of $m\\alpha^4$ order. Our study covers a wide range of rotational ($L=0-5$) and vibrational ($v=0-10$) states, which are of practical interest for precision spectroscopy of the hydrogen molecular ions.

  15. Sum frequency generation spectroscopy study of hydrogenated stepped Si(111) surfaces made by molecular hydrogen exposure

    Science.gov (United States)

    Hien, K. T. T.; Sattar, M. A.; Miyauchi, Y.; Mizutani, G.; Rutt, H. N.

    2017-09-01

    Hydrogen adsorption on stepped Si(111) surfaces 9.5° miscut in the [ 1 ̅ 1 ̅ 2 ] direction has been investigated in situ in a UHV chamber with a base pressure of 10-8 Pa. The H-Si(111)1×1 surface was prepared by exposing the wafer to ultra-pure hydrogen gas at a pressure of 470 Pa. Termination of hydrogen on terraces and steps was observed by sum frequency generation (SFG) with several polarization combinations such as ppp, ssp, pps, spp, psp, sps, pss and sss. Here the 1st, 2nd and 3rd symbols indicate SFG, visible and IR polarizations, respectively. ppp and ssp-SFG clearly showed only two modes: the Si-H stretching vibration terrace mode at 2082 cm-1 (A) and the vertical step dihydride vibration mode at 2094 cm-1 (C1). Interesting points are the appearance of the C1 mode in contrast to the previous SFG spectrum of the H-Si(111)1×1 surface with the same miscut surface angle prepared by wet chemical etching. We suggest that the formation of step dihydride and its orientation on the Si(111) stepped surfaces depend strongly on the preparation method.

  16. Direct molecular hydrogen sulphide scrubbing with hollowfibre membranes.

    Science.gov (United States)

    Boucif, N; Jefferson, B; Parsons-, S A; Judd, S J; Stuetz, R M

    2001-01-01

    The emission of hydrogen sulphide is a major problem associated with anaerobic treatment of sulphate and sulphite containing wastewaters. Conventional absorbing processes, such as packed towers, spray towers or bubble columns, are all constrained by factors such as flooding and foaming. Membrane systems, on the other hand, enable independent control of the liquid and gas flow rate and a step change order of magnitude increase in the specific surface area of the contact process. The membrane acts as a gas absorber with a design similar to a shell and tube heat exchanger. On the other hand, they are limited by facets of the membrane such as its resistance to mass transfer and permselectivity, as well as its cost. The work presented in this paper refers to an absorption process based on a non-wetted hollow fibre membrane for the scrubbing of hydrogen sulphide from air, with water as the contact solvent. Results presented describe the performance of the unit in terms of overall transfer and outlet liquid concentration as a function of circulation regime, gas flow rate, liquid flow rate and specific surface area. In particular, results are presented using traditional plots of Sherwood number (Sh) against Graetz (Gr) number for the liquid flowing in the lumens, such that experimental and available empirical descriptions of the process performance are directly compared. Results suggest that, as expected, very efficient mass transfer is obtained. However, the mass transfer was found to reach a maximum value against Gr, contrary to available empirical models.

  17. Molecular Hydrogen in the Ionized Region of Planetary Nebulae

    CERN Document Server

    Aleman, I

    2004-01-01

    This paper presents an analysis of the concentration of the hydrogen molecule inside the ionized region of planetary nebulae. The equations corresponding to the ionization and chemical equilibria of H, H+, H-, H2, H2+, and H3+ are coupled with the equations of ionization and thermal balance for a photoionized atomic gas. Forty different reactions related to the formation or the destruction of these species are included. The presence of dust is taken into account, since grains act as catalysts for the production of H2, as well as shield the molecules against the stellar ionizing radiation. We analyze the effect of the stellar ionizing continuum, as well as of the gas and grain properties on the calculated H2 mass. It is shown that a significant concentration of H2 can survive inside the ionized region of planetary nebulae, mostly in the inner region of the recombination zone. The total H2 to total hydrogen mass ratio inside the ionized region increases with the central star temperature, and, depending on the P...

  18. The Link Between Warm Molecular Disks in Maser Nuclei and Star Formation Near the Black Hole at the Galactic Center

    CERN Document Server

    Milosavljevic, M; Milosavljevic, Milos; Loeb, Abraham

    2004-01-01

    The discovery of hundreds of young, bright stars within a parsec from the massive black hole at the center of the Galaxy presents a challenge to star formation theories. The requisite Roche densities for gravitational collapse of gas clouds are most naturally achieved in accretion disks. The water maser sources in Keplerian rotation in the nuclei of NGC4258, NGC1068, and the Circinus Galaxy indicate the presence of warm, extended, molecular accretion disks around black holes similar in mass to the Galactic black hole. We here argue that the current conditions in the maser nuclei, and those near the Galactic center, represent two consecutive, recurrent phases in the life cycle of the nucleus of a typical gas-rich spiral bulge. The warm molecular disks that give rise to the observed maser emission fragment into stellar-size objects. The stellar masses, their orbital geometry, and the total number of stars thus formed are consistent with the values identified at the Galactic Center. The stars tend to form in com...

  19. The JCMT Nearby Galaxies Legacy Survey II: Warm Molecular Gas and Star Formation in Three Field Spiral Galaxies

    CERN Document Server

    Warren, B E; Israel, F P; Serjeant, S; Bendo, G J; Brinks, E; Clements, D L; Irwin, J A; Knapen, J H; Leech, J; Matthews, H E; Mühle, S; Mortimer, A M J; Petitpas, G; Sinukoff, E; Spekkens, K; Tan, B K; Tilanus, R P J; Usero, A; van der Werf, P P; Vlahakis, C; Wiegert, T; Zhu, M

    2010-01-01

    We present the results of large-area CO J=3-2 emission mapping of three nearby field galaxies, NGC 628, NGC 3521, and NGC 3627, completed at the James Clerk Maxwell Telescope as part of the Nearby Galaxies Legacy Survey. These galaxies all have moderate to strong CO J=3-2 detections over large areas of the fields observed by the survey, showing resolved structure and dynamics in their warm/dense molecular gas disks. All three galaxies were part of the Spitzer Infrared Nearby Galaxies Survey sample, and as such have excellent published multi-wavelength ancillary data. These data sets allow us to examine the star formation properties, gas content, and dynamics of these galaxies on sub-kiloparsec scales. We find that the global gas depletion times for dense/warm molecular gas in these galaxies is consistent with other results for nearby spiral galaxies, indicating this may be independent of galaxy properties such as structures, gas compositions, and environments. Similar to the results from the THINGS HI survey,...

  20. PHENANTHROLINE-STABILIZED PALLADIUM NANOPARTICLES IN POLYETHYLENE GLYCOL—AN ACTIVE AND RECYCLABLE CATALYST SYSTEM FOR THE SELECTIVE HYDROGENATION OF OLEFINS USING MOLECULAR HYDROGEN

    Science.gov (United States)

    1,10-Phenanthroline-stabilized palladium nanoparticles dispersed in a polyethylene glycol (PEG) matrix is synthesized which is found to be a stable and active catalyst for the selective hydrogenation of olefins using molecular hydrogen under mild reaction conditions. A variety of...

  1. Chiral Hydrogen Bond Environment Providing Unidirectional Rotation in Photoactive Molecular Motors.

    Science.gov (United States)

    García-Iriepa, Cristina; Marazzi, Marco; Zapata, Felipe; Valentini, Alessio; Sampedro, Diego; Frutos, Luis Manuel

    2013-05-02

    Generation of a chiral hydrogen bond environment in efficient molecular photoswitches is proposed as a novel strategy for the design of photoactive molecular motors. Here, the following strategy is used to design a retinal-based motor presenting singular properties: (i) a single excitation wavelength is needed to complete the unidirectional rotation process (360°); (ii) the absence of any thermal step permits the process to take place at low temperatures; and (iii) the ultrafast process permits high rotational frequencies.

  2. Observing molecular hydrogen clouds and dark massive objects in galactic halos

    OpenAIRE

    F. De Paolis(University of Lecce and INFN, Lecce, Italy); Ingrosso, G.; Jetzer, Ph.; Quadir, A.; Roncadelli, M.

    1995-01-01

    Molecular hydrogen clouds can contribute substantially to the galactic halo< dark matter and may lead to the birth of massive halo objects (MHOs) observed indirectly by microlensing. We present a method to detect these molecular clouds in the halo of M31 using the Doppler shift effect. We also consider the possibility to directly observe MHOs in the halo of M31 via their infrared emission.

  3. Hydrogen in diffuse molecular clouds in the Milky Way. Atomic column densities and molecular fraction along prominent lines of sight

    Science.gov (United States)

    Winkel, B.; Wiesemeyer, H.; Menten, K. M.; Sato, M.; Brunthaler, A.; Wyrowski, F.; Neufeld, D.; Gerin, M.; Indriolo, N.

    2017-03-01

    Context. Recent submillimeter and far-infrared wavelength observations of absorption in the rotational ground-state lines of various simple molecules against distant Galactic continuum sources have opened the possibility of studying the chemistry of diffuse molecular clouds throughout the Milky Way. In order to calculate abundances, the column densities of molecular and atomic hydrogen, H i, must be known. Aims: We aim at determining the atomic hydrogen column densities for diffuse clouds located on the sight lines toward a sample of prominent high-mass star-forming regions that were intensely studied with the HIFI instrument onboard Herschel. Methods: Based on Jansky Very Large Array data, we employ the 21 cm H i absorption-line technique to construct profiles of the H i opacity versus radial velocity toward our target sources. These profiles are combined with lower resolution archival data of extended H i emission to calculate the H i column densities of the individual clouds along the sight lines. We employ Bayesian inference to estimate the uncertainties of the derived quantities. Results: Our study delivers reliable estimates of the atomic hydrogen column density for a large number of diffuse molecular clouds at various Galactocentric distances. Together with column densities of molecular hydrogen derived from its surrogates observed with HIFI, the measurements can be used to characterize the clouds and investigate the dependence of their chemistry on the molecular fraction, for example. The data sets are available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/600/A2

  4. Path integral centroid molecular dynamics simulation of para-hydrogen sandwiched by graphene sheets

    Science.gov (United States)

    Minamino, Yuki; Kinugawa, Kenichi

    2016-11-01

    The carbon-hydrogen composite systems of para-hydrogen (p-H2) sandwiched by a couple of graphene sheets have been investigated by means of path integral centroid molecular dynamics simulations at 17 K. It has been shown that sandwiched hydrogen is liquid-like but p-H2 molecules are preferably adsorbed onto the graphene sheets because of attractive graphene-hydrogen interaction. The diffusion coefficient of p-H2 molecules in the direction parallel to the graphene sheets is comparable to that in pure liquid p-H2. There exists a characteristic mode of 140 cm-1 of the p-H2 molecules, attributed to adsorption-binding motion perpendicular to the graphene sheets.

  5. Ab initio study of adsorption of molecular hydrogen on microporous metal-organic frameworks.

    Science.gov (United States)

    Hamel, Sébastien; Côté, Michel

    2004-03-01

    In the ongoing search for promising compounds for hydrogen storage, novel porous metal-organic frameworks (MOF) have been discovered recently [1]. Well defined binding sites were deduced from inelastic neutron scattering (INS) spectroscopy of the rotational transitions of the adsorbed molecular hydrogen. In light of this discovery we performed ab initio density functional theory (DFT) calculations of the adsorption of molecular hydrogen on this class of microporous MOF to compare different adsorption sites. Different approximations for the exchange-correlation potentials were accessed for a set of relevant properties such as binding energy, energetically favored configuration and distance between the adsorbents and adsorbates. In particular, theoretical rotational spectra of the adsorbed H2 were obtained that could be compared to the experimental INS spectra. [1] Rosi et al., Science Vol. 300, 1127 (2003)

  6. Molecular catalytic hydrogenation of aromatic hydrocarbons and hydrotreating of coal liquids.

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Shiyong; Stock, L.M.

    1996-05-01

    This report presents the results of research on the development of new catalytic pathways for the hydrogenation of multiring aromatic hydrocarbons and the hydrotreating of coal liquids at The University of Chicago under DOE Contract No. DE-AC22-91PC91056. The work, which is described in three parts, is primarily concerned with the research on the development of new catalytic systems for the hydrogenation of aromatic hydrocarbons and for the improvement of the quality of coal liquids by the addition of dihydrogen. Part A discusses the activation of dihydrogen by very basic molecular reagents to form adducts that can facilitate the reduction of multiring aromatic hydrocarbons. Part B examines the hydrotreating of coal liquids catalyzed by the same base-activated dihydrogen complexes. Part C concerns studies of molecular organometallic catalysts for the hydrogenation of monocyclic aromatic hydrocarbons under mild conditions.

  7. Molecular Simulation of Hydrogen Storage in Ion-Exchanged X Zeolites

    Directory of Open Access Journals (Sweden)

    Xiaoming Du

    2014-01-01

    Full Text Available Grand Canonical Monte Carlo (GCMC method was employed to simulate the adsorption properties of molecular hydrogen on ion-exchanged X zeolites at 100–293 K and pressures up to 10 MPa in this paper. The effect of cation type, temperature, and pressure on hydrogen adsorption capacity, heat of adsorption, adsorption sites, and adsorption potential energy of ion-exchanged X zeolites was analyzed. The results indicate that the hydrogen adsorption capacity increases with the decrease in temperatures and the increase in pressures and decreases in the order of KXhydrogen adsorption capacity. The hydrogen adsorption sites in the three zeolites were determined by the simulated distribution of hydrogen adsorption energy and the factors that influence their variations were discussed. Adsorption temperature has an important effect on the distribution of hydrogen molecules in zeolite pores.

  8. Synthesis, structural investigations, hydrogen-deuterium exchange studies, and molecular modeling of conformationally stablilized aromatic oligoamides.

    Science.gov (United States)

    Yan, Yan; Qin, Bo; Ren, Changliang; Chen, Xiuying; Yip, Yeow Kwan; Ye, Ruijuan; Zhang, Dawei; Su, Haibin; Zeng, Huaqiang

    2010-04-28

    Biasing the conformational preferences of aromatic oligoamides by internally placing intramolecular hydrogen bonds has led to a series of stably folded molecular strands. This article presents the results from extensive solid-state, solution, and computational studies on these folding oligomers. Depending on its backbone length, an oligoamide adopts a crescent or helical conformation. Surprisingly, despite the highly repetitive nature of the backbone, the internally placed, otherwise very similar intramolecular hydrogen bonds showed significantly different stabilities as demonstrated by hydrogen-deuterium exchange data. It was also observed that the hydrogen-bonding strength can be tuned by adjusting the substituents attached to the exterior of the aromatic backbones. Examining the amide hydrogen-deuterium exchange rates of trimers revealed that a six-membered hydrogen bond nearing the ester end is the weakest among all the four intramolecular hydrogen bonds of a molecule. This observation was verified by ab initio quantum mechanical calculations at the level of B3LYP/6-31G*. Such a "weak point" creates the "battle of the bulge" where backbone twisting is centered, which is consistently observed in the solid-state structures of the four trimer molecules studied. In the solid state, the oligomers assemble into interesting one-dimensional structures. A pronounced columnar packing of short oligomers (i.e., dimers, trimers, and tetramer) and channel-like, potentially ion-conducting stacks of longer oligomers (i.e., tetramer, pentamer, and hexamer) were observed.

  9. External-field shifts in precision spectroscopy of hydrogen molecular ions

    Energy Technology Data Exchange (ETDEWEB)

    Bakalov, Dimitar, E-mail: dbakalov@inrne.bas.bg [INRNE, Bulgarian Academy of Sciences (Bulgaria); Korobov, Vladimir [Joint Institute for Nuclear Research (Russian Federation); Schiller, Stephan [Heinrich-Heine-Universitat Dusseldorf, Institut fur Experimentalphysik (Germany)

    2015-08-15

    The Effective Hamiltonian of the hydrogen molecular ions is a convenient tool for the evaluation of the shift of the energy levels of the ro-vibrational states and the frequencies of the transitions between them, due to external electric and magnetic fields. Using the Effective Hamiltonian, composite frequencies of suppressed susceptibility to external fields are constructed.

  10. Self-assembled biomimetic [2Fe2S]-hydrogenase-based photocatalyst for molecular hydrogen evolution

    NARCIS (Netherlands)

    Kluwer, A.M.; Kapre, R.; Hartl, F.; Lutz, M.; Spek, A.L.; Brouwer, A.M.; van Leeuwen, P.W.N.M.; Reek, J.N.H.

    2009-01-01

    The large-scale production of clean energy is one of the major challenges society is currently facing. Molecular hydrogen is envisaged as a key green fuel for the future, but it becomes a sustainable alternative for classical fuels only if it is also produced in a clean fashion. Here, we report a su

  11. Collisions of low-energy antiprotons with molecular hydrogen: ionization, excitation and stopping power

    DEFF Research Database (Denmark)

    Lühr, Armin Christian; Saenz, Alejandro

    2009-01-01

    A time-dependent coupled-channel approach was used to calculate ionization, excitation, and energy-loss cross sections as well as energy spectra for antiproton and proton collisions with molecular hydrogen for impact energies 8 < E < 4000 keV....

  12. Full two-electron calculations of antiproton collisions with molecular hydrogen

    DEFF Research Database (Denmark)

    Lühr, Armin Christian; Saenz, Alejandro

    2010-01-01

    Total cross sections for single ionization and excitation of molecular hydrogen by antiproton impact are presented over a wide range of impact energies from 1 keV to 6.5 MeV. A nonperturbative time-dependent close-coupling method is applied to fully treat the correlated dynamics of the electrons....

  13. Solution of the Wang Chang-Uhlenbeck equation for molecular hydrogen

    Science.gov (United States)

    Anikin, Yu. A.

    2017-06-01

    Molecular hydrogen is modeled by numerically solving the Wang Chang-Uhlenbeck equation. The differential scattering cross sections of molecules are calculated using the quantum mechanical scattering theory of rigid rotors. The collision integral is computed by applying a fully conservative projection method. Numerical results for relaxation, heat conduction, and a one-dimensional shock wave are presented.

  14. A consistent molecular hydrogen isotope chemistry scheme based on an independent bond approximation

    NARCIS (Netherlands)

    Pieterse, G.; Krol, M.C.; Röckmann, T.

    2009-01-01

    The isotopic composition of molecular hydrogen (H2) produced by photochemical oxidation of methane (CH4) and Volatile Organic Compounds (VOCs) is a key quantity in the global isotope budget of (H2). The many individual reaction steps involved complicate its investigation. Here we present a simplifie

  15. Isotopic evidence for biogenic molecular hydrogen production in the Atlantic Ocean

    NARCIS (Netherlands)

    Walter, S.; Kock, A.; Steinhoff, T.; Fiedler, B.; Fietzek, P.; Kaiser, J.; Krol, M.; Popa, M. E.; Chen, Q.; Tanhua, T.; Röckmann, T.

    2016-01-01

    Oceans are a net source of molecular hydrogen (H2) to the atmosphere. The production of marine H2 is assumed to be mainly biological by N2 fixation, but photochemical pathways are also discussed. We present measurements of mole fraction and isotopic composition of dissolved and atmospheric H2 from t

  16. Molecular hydrogen formation on dust grains in the high-redshift universe

    NARCIS (Netherlands)

    Cazaux, S; Spaans, M

    2004-01-01

    We study the formation of molecular hydrogen on dust grain surfaces and apply our results to the high-redshift universe. We find that a range of physical parameters-in particular dust temperature and gas temperature, but not so much dust surface composition-influences the formation rate of H-2. The

  17. Molecular hydrogen isotope analysis of living and fossil plants——Metasequoia as an example

    Institute of Scientific and Technical Information of China (English)

    Hong Yang; Qin Leng

    2009-01-01

    Molecular hydrogen isotope analysis preformed on modern and fossil plants has made a significant impact on diverse research fields in biology and geology. Using living and fossil Metasequoia as an example, we review the technology of online GC-IRMS that made the molecular analysis of hydrogen isotope possible and discuss critical issues concerning with the studies of molecular δD and its applica-tions. The apparent hydrogen fractionation factors between lipid molecules and source water (δwater lipid) vary across plant taxonomy and differ among biomolecules and are affected by multiple environmental factors in which precipitation δD values exercise the first order of control. Eco-physiological factors and environmental parameters are also known to influence δD in plants. Molecular hydrogen isotope analysis of chemically stable lipid molecules, such as n-alkanes, finds a wide range of applications in detecting source sediments, recon-struction of paleoclimatic parameters, inference of air-mass trajectory, as well as in petroleum industry and environmental studies.2009 National Natural Science Foundation of China and Chinese Academy of Sciences. Published by Elsevier Limited and Science in China Press. All rights reserved.

  18. Global scale observations of atmospheric molecular hydrogen and its stable isotopic composition

    NARCIS (Netherlands)

    Batenburg, A.M.

    2012-01-01

    With average mixing ratios (χ) around 550 ppb (nmole/mole), molecular hydrogen (H2) is the most abundant reduced gas in our atmosphere after methane (CH4), but considerably less studied. H2 is also a promising energy carrier that might replace fossil fuels in vehicles with great sustainability

  19. The stable isotopic signature of biologically produced molecular hydrogen (H2)

    NARCIS (Netherlands)

    Walter, S.; Laukenmann, S.; Stams, A.J.M.; Vollmer, M.K.; Gleixner, G.; Roeckmann, T.

    2012-01-01

    Biologically produced molecular hydrogen (H2) is characterised by a very strong depletion in deuterium. Although the biological source to the atmosphere is small compared to photochemical or combustion sources, it makes an important contribution to the global isotope budget of H2. Large

  20. Molecular hydrogen formation on dust grains in the high-redshift universe

    NARCIS (Netherlands)

    Cazaux, S; Spaans, M

    2004-01-01

    We study the formation of molecular hydrogen on dust grain surfaces and apply our results to the high-redshift universe. We find that a range of physical parameters-in particular dust temperature and gas temperature, but not so much dust surface composition-influences the formation rate of H-2. The

  1. Studies of Diffuse Interstellar Bands. V. Pairwise Correlations of Eight Strong DIBs and Neutral Hydrogen, Molecular Hydrogen, and Color Excess

    CERN Document Server

    Friedman, Scott D; McCall, Benjamin J; Dahlstrom, Julie; Sonnentrucker, Paule; Welty, Daniel E; Drosback, Meredith M; Hobbs, L M; Rachford, Brian L; Snow, Theodore P

    2010-01-01

    We establish correlations between equivalent widths of eight diffuse interstellar bands (DIBs), and examine their correlations with atomic hydrogen, molecular hydrogen, and EB-V . The DIBs are centered at \\lambda\\lambda 5780.5, 6204.5, 6283.8, 6196.0, 6613.6, 5705.1, 5797.1, and 5487.7, in decreasing order of Pearson’s correlation coefficient with N(H) (here defined as the column density of neutral hydrogen), ranging from 0.96 to 0.82. We find the equivalent width of \\lambda 5780.5 is better correlated with column densities of H than with E(B-V) or H2, confirming earlier results based on smaller datasets. We show the same is true for six of the seven other DIBs presented here. Despite this similarity, the eight strong DIBs chosen are not well enough correlated with each other to suggest they come from the same carrier. We further conclude that these eight DIBs are more likely to be associated with H than with H2 , and hence are not preferentially located in the densest, most UV shielded parts of interste...

  2. Pandemics, pathogenicity and changing molecular epidemiology of cholera in the era of global warming.

    Science.gov (United States)

    Chowdhury, Fazle Rabbi; Nur, Zannatun; Hassan, Nazia; von Seidlein, Lorenz; Dunachie, Susanna

    2017-03-07

    Vibrio cholerae, a Gram-negative, non-spore forming curved rod is found in diverse aquatic ecosystems around the planet. It is classified according to its major surface antigen into around 206 serogroups, of which O1 and O139 cause epidemic cholera. A recent spatial modelling technique estimated that around 2.86 million cholera cases occur globally every year, and of them approximately 95,000 die. About 1.3 billion people are currently at risk of infection from cholera. Meta-analysis and mathematical modelling have demonstrated that due to global warming the burden of vector-borne diseases like malaria, leishmaniasis, meningococcal meningitis, viral encephalitis, dengue and chikungunya will increase in the coming years in the tropics and beyond. This review offers an overview of the interplay between global warming and the pathogenicity and epidemiology of V. cholerae. Several distinctive features of cholera survival (optimal thriving at 15% salinity, 30 °C water temperature, and pH 8.5) indicate a possible role of climate change in triggering the epidemic process. Genetic exchange (ctxAB, zot, ace, cep, and orfU) between strains and transduction process allows potential emergence of new toxigenic clones. These processes are probably controlled by precise environmental signals such as optimum temperature, sunlight and osmotic conditions. Environmental influences on phytoplankton growth and chitin remineralization will be discussed alongside the interplay of poor sanitary conditions, overcrowding, improper sewage disposal and global warming in promoting the growth and transmission of this deadly disease. The development of an effective early warning system based on climate data could help to prevent and control future outbreaks. It may become possible to integrate real-time monitoring of oceanic regions, climate variability and epidemiological and demographic population dynamics to predict cholera outbreaks and support the design of cost-effective public health

  3. Photoswitching a molecular catalyst to regulate CO2 hydrogenation.

    Science.gov (United States)

    Priyadarshani, Nilusha; Ginovska, Bojana; Bays, J Timothy; Linehan, John C; Shaw, Wendy J

    2015-09-07

    Inspired by nature's ability to regulate catalysis using physiological stimuli, azobenzene was incorporated into Rh(bis)diphosphine CO2 hydrogenation catalysts to photoinitiate structural changes to modulate the resulting catalytic activity. The rhodium bound diphosphine ligands (P(Ph2)-CH2-N(R)-CH2-P(Ph2)) contain the terminal amine of a non-natural amino acid, with the R-group being either β-alanine (β-Ala) or γ-aminobutyric acid (GABA). For both β-Ala and GABA containing complexes, the carboxylic acids of the amino acids were coupled to the amines of diaminoazobenzene, creating a complex consisting of a rhodium bound to a photo-responsive tetradentate ligand. The photo-induced cis-trans isomerization of the azobenzene-containing complexes imposes structural changes on these complexes, as evidenced by NMR studies. We found that the CO2 hydrogenation activity for the β-Ala bound rhodium complex is 40% faster at 27 °C with the light on, i.e. azobenzene in the cis-conformation (TOF = 16 s(-1)) than when the complex was in the dark and the azobenzene in the trans-conformation (TOF = 11 s(-1)). In contrast the γ-aminobutyric acid containing rhodium complex has the same rate (TOF ∼17 s(-1)) with the azobenzene in either the cis or the trans-conformation at 27 °C. The corresponding (bis)diphosphine complexes without the attached azobenzene were also prepared, characterized, and catalytically tested for comparison, and have TOF's of 30 s(-1). Computational studies were undertaken to evaluate if the difference in rate between the cis- and trans-azobenzene isomers for the β-Ala bound rhodium complex were due to structural differences. These computational investigations revealed major structural changes between all cis- and trans-azobenzene structures, but only minor structural changes that would be unique to the β-Ala bound rhodium complex. We postulate that the different rates between the cis- and trans-azobenzene β-Ala bound containing rhodium complexes are

  4. Altering intra- to inter-molecular hydrogen bonding by dimethylsulfoxide: A TDDFT study of charge transfer for coumarin 343

    Science.gov (United States)

    Liu, Xiaochun; Yin, Hang; Li, Hui; Shi, Ying

    2017-04-01

    DFT and TDDFT methods were carried out to investigate the influences of intramolecular and intermolecular hydrogen bonding on excited state charge transfer for coumarin 343 (C343). Intramolecular hydrogen bonding is formed between carboxylic acid group and carbonyl group in C343 monomer. However, in dimethylsulfoxide (DMSO) solution, DMSO 'opens up' the intramolecular hydrogen bonding and forms solute-solvent intermolecular hydrogen bonded C343-DMSO complex. Analysis of frontier molecular orbitals reveals that intramolecular charge transfer (ICT) occurs in the first excited state both for C343 monomer and complex. The results of optimized geometric structures indicate that the intramolecular hydrogen bonding interaction is strengthened while the intermolecular hydrogen bonding is weakened in excited state, which is confirmed again by monitoring the shifts of characteristic peaks of infrared spectra. We demonstrated that DMSO solvent can not only break the intramolecular hydrogen bonding to form intermolecular hydrogen bonding with C343 but also alter the mechanism of excited state hydrogen bonding strengthening.

  5. The influence of warm ischemia elimination on kidney injury during transplantation – clinical and molecular study

    Science.gov (United States)

    Kamińska, Dorota; Kościelska-Kasprzak, Katarzyna; Chudoba, Paweł; Hałoń, Agnieszka; Mazanowska, Oktawia; Gomółkiewicz, Agnieszka; Dzięgiel, Piotr; Drulis-Fajdasz, Dominika; Myszka, Marta; Lepiesza, Agnieszka; Polak, Wojciech; Boratyńska, Maria; Klinger, Marian

    2016-01-01

    Kidney surface cooling was used during implantation to assess the effect of warm ischemia elimination on allograft function, histological changes and immune-related gene expression. 23 recipients were randomly assigned to a group operated on with kidney surface cooling during implantation (ice bag technique, IBT group), and the other 23 recipients receiving the contralateral kidney from the same donor were operated on with a standard technique. Three consecutive kidney core biopsies were obtained during the transplantation procedure: after organ recovery, after cold ischemia and after reperfusion. Gene expression levels were determined using low-density arrays (Format 32, TaqMan). The IBT group showed a significantly lower rate of detrimental events (delayed graft function and/or acute rejection, p = 0.015) as well as higher glomerular filtration rate on day 14 (p = 0.026). A greater decrease of MMP9 and LCN2 gene expression was seen in the IBT group during total ischemia (p = 0.003 and p = 0.018). Elimination of second warm ischemia reduced the number of detrimental events after kidney transplantation, and thus had influence on the short-term but not long-term allograft function. Surface cooling of the kidney during vascular anastomosis may reduce some detrimental effects of immune activation resulting from both brain death and ischemia-reperfusion injury. PMID:27808277

  6. Modelling the interaction of molecular hydrogen with lithium-doped hydrogen storage materials

    Science.gov (United States)

    Kolmann, Stephen J.; Chan, Bun; Jordan, Meredith J. T.

    2008-12-01

    Density functional theory (DFT) and ab initio methods are used to investigate the interaction of one, two and three hydrogen molecules with Li +-doped benzene, a model for lithium-doped carbon-based and metal organic framework materials. M05-2X is found to be the best DFT method considered, reproducing MP2 and CCSD(T) H 2 binding energies to Li +-doped benzene. The M05-2X results also agree with H 2 binding energies previously obtained in an extended model of Li atom-doped MOF-5. These calculations suggest H 2 binding in Li-doped materials is, primarily, a local interaction, implying that model compounds can be used to describe these systems.

  7. Collective effects in physisorbed molecular hydrogen on Ni /Au (111 )

    Science.gov (United States)

    Therrien, A. J.; Pronschinske, A.; Murphy, C. J.; Lewis, E. A.; Liriano, M. L.; Marcinkowski, M. D.; Sykes, E. C. H.

    2015-10-01

    We report a system in which the rotational, vibrational, electronic, and structural properties of condensed molecular H2 can be measured with subnanometer precision using scanning tunneling microscopy. H2 physisorbs around Ni nanoparticles on Au (111 ) and displays many nonclassical characteristics, including unique disappearance upon heating that is due to changes in the time-averaged phonon ground state population. This collective phenomenon also gives rise to the appearance of submolecular features and constructive overlap at points where neighboring H2 ensembles meet. A model based on the spatial distribution of collective excitations is proposed to explain these properties.

  8. Microscopic Observation of Kinetic Molecular Sieving of Hydrogen Isotopes in a Nanoporous Material

    Science.gov (United States)

    Nguyen, T. X.; Jobic, H.; Bhatia, S. K.

    2010-08-01

    We report quasielastic neutron scattering studies of H2-D2 diffusion in a carbon molecular sieve, demonstrating remarkable quantum effects, with the heavier isotope diffusing faster below 100 K, confirming our recent predictions. Our transition state theory and molecular dynamics calculations show that while it is critical for this effect to have narrow windows of size comparable to the de Broglie wavelength, high flux requires that the energy barrier be reduced through small cages. Such materials will enable novel processes for kinetic molecular sieving of hydrogen isotopes.

  9. Line Overlap and Self-Shielding of Molecular Hydrogen in Galaxies

    Science.gov (United States)

    Gnedin, Nickolay Y.; Draine, Bruce T.

    2014-11-01

    The effect of line overlap in the Lyman and Werner bands, often ignored in galactic studies of the atomic-to-molecular transition, greatly enhances molecular hydrogen self-shielding in low metallicity environments and dominates over dust shielding for metallicities below about 10% solar. We implement that effect in cosmological hydrodynamics simulations with an empirical model, calibrated against the observational data, and provide fitting formulae for the molecular hydrogen fraction as a function of gas density on various spatial scales and in environments with varied dust abundance and interstellar radiation field. We find that line overlap, while important for detailed radiative transfer in the Lyman and Werner bands, has only a minor effect on star formation on galactic scales, which, to a much larger degree, is regulated by stellar feedback.

  10. Line Overlap and Self-Shielding of Molecular Hydrogen in Galaxies

    CERN Document Server

    Gnedin, Nickolay Y

    2014-01-01

    The effect of line overlap in the Lyman and Werner bands, often ignored in galactic studies of the atomic-to-molecular transition, greatly enhances molecular hydrogen self-shielding in low metallicity environments, and dominates over dust shielding for metallicities below about 10% solar. We implement that effect in cosmological hydrodynamics simulations with an empirical model, calibrated against the observational data, and provide fitting formulae for the molecular hydrogen fraction as a function of gas density on various spatial scales and in environments with varied dust abundance and interstellar radiation field. We find that line overlap, while important for detailed radiative transfer in the Lyman and Werner bands, has only a minor effect on star formation on galactic scales, which, to a much larger degree, is regulated by stellar feedback.

  11. A general catalogue of molecular hydrogen emission-line objects (MHOs) in outflows from young stars

    Science.gov (United States)

    Davis, C. J.; Gell, R.; Khanzadyan, T.; Smith, M. D.; Jenness, T.

    2010-02-01

    We present a catalogue of Molecular Hydrogen emission-line Objects (MHOs) in outflows from young stars, most of which are deeply embedded. All objects are identified in the near-infrared lines of molecular hydrogen, all reside in the Milky Way, and all are associated with jets or molecular outflows. Objects in both low and high-mass star forming regions are included. This catalogue complements the existing database of Herbig-Haro objects; indeed, for completeness, HH objects that are detected in H2 emission are included in the MHO catalogue. http://www.jach.hawaii.edu/UKIRT/MHCat/ Tables A.1 to A.15 are also available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb.u-strasbg.fr/cgi-bin/qcat?J/A+A/511/A24

  12. Nanostructured Boron Nitride: From Molecular Design to Hydrogen Storage Application

    Directory of Open Access Journals (Sweden)

    Georges Moussa

    2014-07-01

    Full Text Available The spray-pyrolysis of borazine at 1400 °C under nitrogen generates boron nitride (BN nanoparticles (NPs. The as-prepared samples form elementary blocks containing slightly agglomerated NPs with sizes ranging from 55 to 120 nm, a Brunauer-Emmett-Teller (BET-specific surface area of 34.6 m2 g−1 and a helium density of 1.95 g cm−3. They are relatively stable in air below 850 °C in which only oxidation of the NP surface proceeds, whereas under nitrogen, their lower size affects their high temperature thermal behavior in the temperature range of 1450–2000 °C. Nitrogen heat-treated nanostructures have been carefully analyzed using X-ray diffraction, electron microscopy and energy-dispersive X-ray spectroscopy. The high temperature treatment (2000 °C gives hollow-cored BN-NPs that are strongly facetted, and after ball-milling, hollow core-mesoporous shell NPs displaying a BET-specific surface area of 200.5 m2·g−1 and a total pore volume of 0.287 cm3·g−1 were produced. They have been used as host material to confine, then destabilize ammonia borane (AB, thus improving its dehydrogenation properties. The as-formed AB@BN nanocomposites liberated H2 at 40 °C, and H2 is pure in the temperature range 40–80 °C, leading to a safe and practical hydrogen storage composite material.

  13. Far-ultraviolet florescent molecular hydrogen emission map of the Milky Way Galaxy

    Science.gov (United States)

    Jo, Young-soo; Seon, Kwang-il; Min, Kyoung-wook; Edelstein, Jerry; Han, Wonyong

    2017-01-01

    We present the far-ultraviolet fluorescent molecular hydrogen (H2) emission map observed with FIMS/SPEAR for ~76% of the sky. The fluorescent H2 emission is found to be saturated by strong dust extinction at the optically thick, Galactic plane region. Nevertheless, the extinction-corrected intensity of the fluorescent H2 emission is found to have strong linear correlations with the well-known tracers of the cold interstellar medium, such as the E(B-V) color excess, neutral hydrogen column density N(HI), Hα emission, and CO J=1→0 emission. The all-sky molecular hydrogen column density map is also obtained using a simple photodissociation region model with interstellar radiation fields derived from UV star catalogs. We also estimate the hydrogen molecular fraction (fH2), CO-to-H2 conversion factor (XCO), and the gas-to-dust ratio of the diffuse interstellar medium. fH2 gradually increases from less than 1% at optically thin regions with E(B-V)converges to the Galactic mean value of 1.8×1020 cm-2 K-1 km-1 s at optically thick regions where E(B-V) is larger than 2.0. The estimated gas-to-dust ratio is consistent with the standard value of 5.8×1021 atoms cm-2 mag-1.

  14. Quantum Electrodynamics Effects in Rovibrational Spectra of Molecular Hydrogen.

    Science.gov (United States)

    Komasa, Jacek; Piszczatowski, Konrad; Łach, Grzegorz; Przybytek, Michał; Jeziorski, Bogumił; Pachucki, Krzysztof

    2011-10-11

    The dissociation energies from all rovibrational levels of H2 and D2 in the ground electronic state are calculated with high accuracy by including relativistic and quantum electrodynamics (QED) effects in the nonadiabatic treatment of the nuclear motion. For D2, the obtained energies have theoretical uncertainties of 0.001 cm(-1). For H2, similar uncertainties are for the lowest levels, while for the higher ones the uncertainty increases to 0.005 cm(-1). Very good agreement with recent high-resolution measurements of the rotational v = 0 levels of H2, including states with large angular momentum J, is achieved. This agreement would not have been possible without accurate evaluation of the relativistic and QED contributions and may be viewed as the first observation of the QED effects, mainly the electron self-energy, in a molecular spectrum. For several electric quadrupole transitions, we still observe certain disagreement with experimental results, which remains to be explained.

  15. Effective grain surface area in the formation of molecular hydrogen in interstellar clouds

    CERN Document Server

    Chakrabarti, Sandip Kumar; Acharyya, Kinsuk; Chakrabarti, Sonali

    2008-01-01

    In the interstellar clouds, molecular hydrogens are formed from atomic hydrogen on grain surfaces. An atomic hydrogen hops around till it finds another one with which it combines. This necessarily implies that the average recombination time, or equivalently, the effective grain surface area depends on the relative numbers of atomic hydrogen influx rate and the number of sites on the grain. Our aim is to discover this dependency. We perform a numerical simulation to study the recombination of hydrogen on grain surfaces in a variety of cloud conditions. We use a square lattice (with a periodic boundary condition) of various sizes on two types of grains, namely, amorphous carbon and olivine. We find that the steady state results of our simulation match very well with those obtained from a simpler analytical consideration provided the `effective' grain surface area is written as $\\sim S^{\\alpha}$, where, $S$ is the actual physical grain area and $\\alpha$ is a function of the flux of atomic hydrogen which is deter...

  16. Morphology and Kinematics of Warm Molecular Gas in the Nuclear Region of Arp 220 as Revealed by ALMA

    CERN Document Server

    Rangwala, Naseem; Wilson, Christine; Glenn, Jason; Kamenetzky, Julia; Spinoglio, Luigi

    2015-01-01

    We present Atacama Large Millimeter Array (ALMA) Cycle-0 observations of the CO J = 6-5 line in the advanced galaxy merger Arp 220. This line traces warm molecular gas, which dominates the total CO luminosity. The CO emission from the two nuclei is well resolved by the 0.39" x 0.22" beam and the exceptional sensitivity and spatial/spectral resolution reveal new complex features in the morphology and kinematics of the warm gas. The line profiles are asymmetric between the red and blue sides of the nuclear disks and the peak of the line emission is offset from the peak of the continuum emission in both nuclei by about 100 pc in the same direction. CO self-absorption is detected at the centers of both nuclei but it is much deeper in the eastern nucleus. We also clearly detect strong, highly redshifted CO absorption located near the southwest side of each nucleus. For the eastern nucleus, we reproduce the major line profile features with a simple kinematic model of a highly turbulent, rotating disk with a substan...

  17. On the relation between hydrogen bonds, tetrahedral order and molecular mobility in model water

    CERN Document Server

    Pereyra, R G; Malaspina, D C; Carignano, M A

    2013-01-01

    We studied by molecular dynamics simulations the relation existing between the lifetime of hydrogen bonds, the tetrahedral order and the diffusion coefficient of model water. We tested four different models: SPC/E, TIP4P-Ew, TIP5P-Ew and Six-site, these last two having sites explicitly resembling the water lone pairs. While all the models perform reasonably well at ambient conditions, their behavior is significantly different for temperatures below 270 K. The models with explicit lone-pairs have a longer hydrogen bond lifetime, a better tetrahedral order and a smaller diffusion coefficient than the models without them.

  18. QUANTUM-MECHANICAL PROPERTIES OF PROTON TRANSPORT IN THE HYDROGEN-BONDED MOLECULAR SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    PANG XIAO-FENG; LI PING

    2000-01-01

    The dynamic equations of the proton transport along the hydrogen bonded molecular systems have been obtainedby using completely quantum-mechanical method to be based on new Hamiltonian and model we proposed. Somequantum-mechanical features of the proton-solitons have also been given in such a case. The alternate motion of twodefects resulting from proton transfer occurred in the systems can be explained by the results. The results obtainedshow that the proton-soliton has corpuscle feature and obey classical equations of motion, while the free soliton movesin uniform velocity along the hydrogen bonded chains.

  19. Wave packet evolution approach to ionization of hydrogen molecular ion by fast electrons

    CERN Document Server

    Serov, V V; Joulakian, B B; Vinitsky, S I; Serov, Vladislav V.; Derbov, Vladimir L.; Joulakian, Boghos B.; Vinitsky, Sergue I.

    2000-01-01

    The multiply differential cross section of the ionization of hydrogen molecular ion by fast electron impact is calculated by a direct approach, which involves the reduction of the initial 6D Schr\\"{o}dinger equation to a 3D evolution problem followed by the modeling of the wave packet dynamics. This approach avoids the use of stationary Coulomb two-centre functions of the continuous spectrum of the ejected electron which demands cumbersome calculations. The results obtained, after verification of the procedure in the case atomic hydrogen, reveal interesting mechanisms in the case of small scattering angles.

  20. Crystal Properties and Radiation Effects in Solid Molecular Hydrogens

    Energy Technology Data Exchange (ETDEWEB)

    Kozioiziemski, B

    2000-09-01

    The crystal lattice structure, growth shapes and helium generated by beta-decay of solid deuterium-tritium (D-T) mixtures have been studied. Understanding of these D-T properties is important for predicting and optimizing the target design of the National Ignition Facility (NIF). Raman spectroscopy showed the D-T crystal structure is hexagonal close packed, common to the non-tritiated isotopes. The isotopic mixtures of both tritiated and non-tritiated species broadens the rotational transitions, especially of the lighter species in the mixture. The vibrational frequencies of each isotope is shifted to higher energy in the mixture than the pure components. The J = 1-0 population decreases exponentially with a 1/e time constant which rapidly increases above 10.5 K for both D{sub 2} and T{sub 2} in D-T. The conversion rate is nearly constant from 5 K to 10 K for both D{sub 2} and T{sub 2} at 7.1 hours and 2.1 hours, respectively. The smoothing of D-T layers by beta decay heating is limited by the crystal surface energy. Deuterium and hydrogen-deuteride crystals were grown at a number of temperatures below the triple point to determine the surface energy and roughening transition. Several distinct crystal shapes were observed on a number of different substrates. The a facet roughens between 0.9 T{sub TP} and T{sub TP}, while the c facet persists up to the melting temperature. This is very different from the behavior of the other rare gas crystals which grow completely rounded above 0.8 T{sub TP}. Helium bubbles formed as a product of the beta decay were observed using optical microscopy and the diffusion of smaller bubbles measured with dynamic light scattering. Bubble diffusion coefficients as high as 2.0 x 10{sup -16} m{sup 2}/s were measured for 10-50 nm bubbles. The bubbles move in response to a thermal gradient, with speeds between 1 {micro}m/hour and 100 {micro}m/hour for thermal gradients and temperatures appropriate to NIF targets.

  1. Investigation of hydrogen bonded molecular solids by diffraction, spectroscopy, and computational chemistry

    Science.gov (United States)

    Hudson, Matthew R.

    The nature of hydrogen-bonding interactions in the solid state is examined through the investigation of molecular crystals by incoherent inelastic neutron scattering (INS) spectroscopy, Raman spectroscopy, X-ray and neutron diffraction, and computational chemistry. The molecular solids studied range from small organic molecules to larger inorganic acid salts. Hydrogen bonding is the primary mode of interaction in the solid state for each of the systems studied. INS spectra were collected at 25 K for each molecular solid and the motions of the hydrogen atoms assigned. Raman spectra were collected at 78 and 298 K to aid in the molecular mode assignments of the INS spectra and to examine possible phase changes as a function of temperature. Neutron diffraction was employed, when possible, to accurately locate the hydrogen atom positions, and X-ray diffraction was performed to obtain accurate unit cell dimensions and to obtain initial characterizations of the samples. The diffraction structures served as the basis for solid-state density functional theory (DFT) calculations. DFT simulations were used to aid in the vibrational normal mode assignments, to investigate possible solid-phase transitions, and as a test of the limits of basis sets and the available DFT theory. Of the six molecular solids studied, several important observations were made: (1) the determination of a structural phase transition in L-alanine alaninium nitrate by both spectroscopic and theoretical methods, (2) the structure of picolinic acid was elucidated at 25 K and room-temperature by the combination of INS and theory, (3) glycine lithium sulfate was found to be a useful test of DFT to accurately optimize the structure and calculate the normal modes of a complex 3D network of hydrogen-bonding interactions, (4) nicotinic acid was found to be a useful test of one dimensional hydrogen-bonding interactions with pi-stacking interactions dominating the orthogonal directions, and (5) parabanic acid

  2. Raman spectroscopic determination of the molecular constants of the hydrogen isotopologues with high accuracy

    Energy Technology Data Exchange (ETDEWEB)

    Krasch, Bennet; Mirz, Sebastian; Groessle, Robin [Karlsruhe Institute of Technology KIT (Germany). Institute for Technical Physics (ITEP), Tritium Laboratory Karlsruhe (TLK); Collaboration: KATRIN-Collaboration

    2016-07-01

    The interest in the thermodynamic properties of gases as the chemical equilibrium is faced by the challenge of time-consuming and technical extensive experimental setups. One possible solution is the derivation of these properties from the molecular constants. The rotational and vibrational movement of diatomic molecules, as the hydrogen isotopologues, is described by the concept of the rotational anharmonic oscillator. The molecular constants are the free parameters of this concept. Molecular constants themselves can be determined by measuring the line position of rotational and/or rotational transitions e.g. with Raman spectroscopy for hydrogen as it has been done since several years. In this contribution a Raman method was development to measure the molecular constant of the hydrogen isotopologues with high accuracy to obtain reliable results. But not only the method was development but also a complete measurement uncertainty budget was set up. The uncertainty budget contains all possible sources for uncertainties from the measurement period or the analysis process as well the contribution of each single uncertainty. The method and the uncertainty budget were exemplary tested on Deuterium.

  3. Molecular Hydrogen in the FUSE Translucent Lines of Sight: The Full Sample

    CERN Document Server

    Rachford, Brian L; Destree, Joshua D; Ross, Teresa L; Ferlet, Roger; Friedman, Scott D; Gry, Cecile; Jenkins, Edward B; Morton, Donald C; Savage, Blair D; Shull, J Michael; Sonnentrucker, Paule; Tumlinson, Jason; Vidal-Madjar, Alfred; Welty, Daniel E; York, Donald G

    2008-01-01

    We report total abundances and related parameters for the full sample of the FUSE survey of molecular hydrogen in 38 translucent lines of sight. New results are presented for the "second half" of the survey involving 15 lines of sight to supplement data for the first 23 lines of sight already published. We assess the correlations between molecular hydrogen and various extinction parameters in the full sample, which covers a broader range of conditions than the initial sample. In particular, we are now able to confirm that many, but not all, lines of sight with shallow far-UV extinction curves and large values of the total-to-selective extinction ratio, $R_V$ = $A_V$ / $E(B-V)$ -- characteristic of larger than average dust grains -- are associated with particularly low hydrogen molecular fractions ($f_{\\rm H2}$). In the lines of sight with large $R_V$, there is in fact a wide range in molecular fractions, despite the expectation that the larger grains should lead to less H$_2$ formation. However, we see specif...

  4. The warm, the excited, and the molecular gas: GRB 121024A shining through its star-forming galaxy

    CERN Document Server

    Friis, M; Krühler, T; Fynbo, J P U; Ledoux, C; Vreeswijk, P M; Malesani, D; Gorosabel, J; Starling, R L C; Jakobsson, P; Varela, K; Watson, D J; Wiersema, K; Drachmann, A P; Trotter, A; Thöne, C C; Postigo, A de Ugarte; D'Elia, V; Elliott, J; Maturi, M; Goldoni, P; Greiner, J; Haislip, J; Kaper, L; Knust, F; LaCluyze, A; Milvang-Jensen, B; Reichart, D; Schulze, S; Sudilovsky, V; Vergani, S D

    2014-01-01

    We present the first reported case of the simultaneous metallicity determination of a gamma-ray burst (GRB) host galaxy, from both afterglow absorption lines as well as strong emission-line diagnostics. Using spectroscopic and imaging observations of the afterglow and host of the long-duration GRB121024A at z = 2.30, we give one of the most complete views of a GRB host/environment to date. We observe a strong damped Ly-alpha absorber (DLA) with a hydrogen column density of log N(HI) = 21.80+/-0.15, H_2 absorption in the Lyman-Werner bands (molecular fraction of log(f) ~ -1.4; fourth solid detection of molecular hydrogen in a GRB-DLA), the nebular emission lines H-alpha, H-beta, [OII], [OIII] and [NII], as well as a large variety of metal absorption lines. We find a GRB host galaxy that is highly star-forming (SFR ~ 40 Msolar/yr), with a dust-corrected metallicity along the line of sight of [Zn/H]corr = -0.5+/-0.2 ([O/H] ~ -0.3 from emission lines), and a depletion factor of refractory elements of [Zn/Fe] = 0....

  5. Three-dimensional molecular dynamics simulation of hydrogen-enhanced dislocation emission and crack propagation

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A three-dimensional molecular dynamics simulation using the embedded atom method (EAM) potentials shows that for both pure Ni and Ni+H, dislocations are firstly emitted during loading and the crack propagates after enough disloca tions are emitted. In the case of hydrogen embrittlement, local plastic deformat ion is a precondition for crack propagation. For the crack along the (1 11) slip pla ne, one atom fraction in percent of hydrogen can decrease the critical stress in tensity for dislocation emission KIe from 0.42 to 0.36 MPam 1/2, and that for crack propagation KIp from 0.80 to 0.76 MPam1/2. Therefore, hydrogen enhances dislocation emission and crack pro pagation.

  6. Ab Initio Path Integral Molecular Dynamics Simulation of Hydrogen in Silicon

    Science.gov (United States)

    Probert, M. I. J.; Glover, M. J.

    2006-05-01

    We report results of a first-principles theoretical study of an isolated neutral hydrogen atom in crystalline silicon. Spin-polarised density functional theory is used to treat the electrons, and the path-integral molecular dynamics method is used to describe the quantum properties of the nucleus at finite temperature. This is necessary as the hydrogen atom has sufficiently low mass that it exhibits significant nuclear quantum delocalisation and zero-point motion even at room temperature. Unlike post-hoc treatments, such as calculating a static potential energy surface, the path-integral treatment enables such effects to be included "on-the-fly". This is found to be significant, as a coupling is found between the structure of the host silicon lattice and the quantum delocalisation of the hydrogen defect.

  7. Hydrogen and muonium in diamond: A path-integral molecular dynamics simulation

    Science.gov (United States)

    Herrero, Carlos P.; Ramírez, Rafael; Hernández, Eduardo R.

    2006-06-01

    Isolated hydrogen, deuterium, and muonium in diamond have been studied by path-integral molecular dynamics simulations in the canonical ensemble. Finite-temperature properties of these point defects were analyzed in the range from 100 to 800K . Interatomic interactions were modeled by a tight-binding potential fitted to density-functional calculations. The most stable position for these hydrogenic impurities is found at the C-C bond center. Vibrational frequencies have been obtained from a linear-response approach, based on correlations of atom displacements at finite temperatures. The results show a large anharmonic effect in impurity vibrations at the bond center site, which hardens the vibrational modes with respect to a harmonic approximation. Zero-point motion causes an appreciable shift of the defect level in the electronic gap, as a consequence of electron-phonon interaction. This defect level goes down by 70meV when replacing hydrogen by muonium.

  8. Water dynamics: relation between hydrogen bond bifurcations, molecular jumps, local density & hydrophobicity.

    Science.gov (United States)

    Titantah, John Tatini; Karttunen, Mikko

    2013-10-21

    Structure and dynamics of water remain a challenge. Resolving the properties of hydrogen bonding lies at the heart of this puzzle. We employ ab initio Molecular Dynamics (AIMD) simulations over a wide temperature range. The total simulation time was ≈ 2 ns. Both bulk water and water in the presence of a small hydrophobic molecule were simulated. We show that large-angle jumps and bond bifurcations are fundamental properties of water dynamics and that they are intimately coupled to both local density and hydrogen bond strength oscillations in scales from about 60 to a few hundred femtoseconds: Local density differences are the driving force for bond bifurcations and the consequent large-angle jumps. The jumps are intimately connected to the recently predicted hydrogen bond energy asymmetry. Our analysis also appears to confirm the existence of the so-called negativity track provided by the lone pairs of electrons on the oxygen atom to enable water rotation.

  9. Anoxic photochemical oxidation of siderite generates molecular hydrogen and iron oxides.

    Science.gov (United States)

    Kim, J Dongun; Yee, Nathan; Nanda, Vikas; Falkowski, Paul G

    2013-06-18

    Photochemical reactions of minerals are underappreciated processes that can make or break chemical bonds. We report the photooxidation of siderite (FeCO3) by UV radiation to produce hydrogen gas and iron oxides via a two-photon reaction. The calculated quantum yield for the reaction suggests photooxidation of siderite would have been a significant source of molecular hydrogen for the first half of Earth's history. Further, experimental results indicate this abiotic, photochemical process may have led to the formation of iron oxides under anoxic conditions. The reaction would have continued through the Archean to at least the early phases of the Great Oxidation Event, and provided a mechanism for oxidizing the atmosphere through the loss of hydrogen to space, while simultaneously providing a key reductant for microbial metabolism. We propose that the photochemistry of Earth-abundant minerals with wide band gaps would have potentially played a critical role in shaping the biogeochemical evolution of early Earth.

  10. Effects of hydrogen bonding on current-voltage characteristics of molecular junctions

    Science.gov (United States)

    Kula, Mathias; Jiang, Jun; Lu, Wei; Luo, Yi

    2006-11-01

    We present a first-principles study of hydrogen bonding effect on current-voltage characteristics of molecular junctions. Three model charge-transfer molecules, 2'-amino-4,4'-di(ethynylphenyl)-1-benzenethiolate (DEPBT-D), 4,4'-di(ethynylphenyl)-2'-nitro-1-benzenethiolate (DEPBT-A), and 2'-amino-4,4'-di(ethynylphenyl)-5'-nitro-1-benzenethiolate (DEPBT-DA), have been examined and compared with the corresponding hydrogen bonded complexes formed with different water molecules. Large differences in current-voltage characteristics are observed for DEPBT-D and DEPBT-A molecules with or without hydrogen bonded waters, while relatively small differences are found for DEPBT-DA. It is predicted that the presence of water clusters can drastically reduce the conductivities of the charge-transfer molecules. The underlying microscopic mechanism has been discussed.

  11. Molecular dynamics simulation of temperature profile in partially hydrogenated graphene and graphene with grain boundary.

    Science.gov (United States)

    Lotfi, Erfan; Neek-Amal, M; Elahi, M

    2015-11-01

    Temperature profile in graphene, graphene with grain boundary and vacancy defects and hydrogenated graphene with different percentage of H-atoms are determined using molecular dynamics simulation. We also obtained the temperature profile in a graphene nanoribbon containing two types of grain boundaries with different misorientation angles, θ=21.8° and θ=32.2°. We found that a temperature gap appears in the temperature profile of a graphene nanoribbon with a grain boundary at the middle. Moreover, we found that the temperature profile in the partially hydrogenated graphene varies with the percentage of hydrogens, i.e. the C:H ratio. Our results show that a grain boundary line in the graphene sheet can change the thermal transport through the system which might be useful for controlling thermal flow in nanostructured graphene.

  12. "Zwitterionic Proton Sponge" Hydrogen Bonding Investigations on the Basis of Car-Parrinello Molecular Dynamics.

    Science.gov (United States)

    Jezierska, Aneta; Panek, Jarosław J

    2015-06-22

    1,8-Bis(dimethylamino)-4,5-dihydroxynaphthalene has been investigated on the basis of static DFT computations and Car-Parrinello molecular dynamics. The simulations were performed in the gas phase and in the solid state. The studied "zwitterionic proton sponge" possesses two, short intramolecular hydrogen bonds (O-H···O and N-H···N) classified as Low Barrier Hydrogen Bonds (LBHBs); therefore, the system studied is strongly anharmonic. In addition, the compound exists as a "zwitterion" in solution and in the solid state, thus the intramolecular hydrogen bonds belong to the class of charge-assisted interactions. The applied quantum-chemical methods enabled investigations of metric and spectroscopic parameters of the molecule. The time-evolution investigations of the H-bonding showed a strong delocalization of the bridge protons and their high mobility, reflected in the low barriers on the free energy surfaces. Frequent proton transfer phenomena were noticed. The power spectra of atomic velocity were computed to analyze the vibrational features associated with O-H and N-H stretching. A broad absorption was indicated for both hydrogen bridges. For the first time, Car-Parrinello molecular dynamics results are reported for the compound, and they indicate a broad, shallow but not barrierless, potential well for each of the bridge protons.

  13. Atomic and molecular hydrogen in the circumstellar envelopes of late-type stars

    Science.gov (United States)

    Glassgold, A. E.; Huggins, P. J.

    1983-01-01

    The distribution of atomic and molecular hydrogen in the expanding circumstellar envelopes of cool evolved stars is discussed. The main concern is to evaluate the effects of photodestruction of H2 by galactic UV radiation, including shielding of the radiation by H2 itself and by dust in the envelope. One of the most important parameters is the H/H2 ratio which is frozen out in the upper atmosphere of the star. For stars with photospheric temperatures greater than about 2500 K, atmospheric models suggest that the outflowing hydrogen is mainly atomic, whereas cooler stars should be substantially molecular. In the latter case, photodissociation of H2 and heavy molecules contribute to the atomic hydrogen content of the outer envelope. The presented estimates indicate that atomic hydrogen is almost at the limit of detection in the C-rich star IRC + 10216, and may be detectable in warmer stars. Failure to detect it would have important implications for the general understanding of circumstellar envelopes.

  14. Phase equilibria in molecular hydrogen-helium mixtures at high pressures

    Science.gov (United States)

    Streett, W. B.

    1973-01-01

    Experiments on phase behavior in hydrogen-helium mixtures have been carried out at pressures up to 9.3 kilobars, at temperatures from 26 to 100 K. Two distinct fluid phases are shown to exist at supercritical temperatures and high pressures. Both the trend of the experimental results and an analysis based on the van der Waals theory of mixtures suggest that this fluid-fluid phase separation persists at temperatures and pressures beyond the range of these experiments, perhaps even to the limits of stability of the molecular phases. The results confirm earlier predictions concerning the form of the hydrogen-helium phase diagram in the region of pressure-induced solidification of the molecular phases at supercritical temperatures. The implications of this phase diagram for planetary interiors are discussed.

  15. Solar-powered electrochemical oxidation of organic compounds coupled with the cathodic production of molecular hydrogen.

    Science.gov (United States)

    Park, Hyunwoong; Vecitis, Chad D; Hoffmann, Michael R

    2008-08-21

    A Bi-doped TiO2 anode, which is prepared from a mixed metal oxide coating deposited on Ti metal, is shown to be efficient for conventional water splitting. In this hybrid photovoltaic-electrochemical system, a photovoltaic (PV) cell is used to convert solar light to electricity, which is then used to oxidize a series of phenolic compounds at the semiconductor anode to carbon dioxide with the simultaneous production of molecular hydrogen from water/proton reduction at the stainless steel cathode. Degradation of phenol in the presence of a background NaCl electrolyte produces chlorinated phenols as reaction intermediates, which are subsequently oxidized completely to carbon dioxide and low-molecular weight carboxylic acids. The anodic current efficiency for the complete oxidation of phenolic compounds ranges from 3% to 17%, while the cathodic current efficiency and the energy efficiency for hydrogen gas generation range from 68% to 95% and 30% to 70%, respectively.

  16. Low-temperature metallic liquid hydrogen: an ab-initio path-integral molecular dynamics perspective

    Science.gov (United States)

    Chen, Ji; Li, Xin-Zheng; Zhang, Qianfan; Probert, Matthew; Pickard, Chris; Needs, Richard; Michaelides, Angelos; Wang, Enge

    2013-03-01

    Experiments and computer simulations have shown that the melting temperature of solid hydrogen drops with pressure above about 65 GPa, suggesting that a low temperature liquid state might exist. It has also been suggested that this liquid state might be non-molecular and metallic, although evidence for such behaviour is lacking. Using a combination of ab initio path-integral molecular dynamics and the two-phase methods, we have simulated the melting of solid hydrogen under finite temperatures. We found an atomic solid phase from 500 to 800 GPa which melts at < 200 K. Beyond this and up to pressures of 1,200 GPa a metallic atomic liquid is stable at temperatures as low as 50 K. The quantum motion of the protons is critical to the low melting temperature in this system as ab initio simulations with classical nuclei lead to a considerably higher melting temperature of ~300 K across the entire pressure range considered.

  17. Evaluation of RTV as a Moldable Matrix When Combined With Molecular Sieve and Organic Hydrogen Getter

    Energy Technology Data Exchange (ETDEWEB)

    Knight, J. A.

    2011-12-01

    This work was undertaken in an effort to develop a combined RTV 615/3Å molecular sieve/DEB molded component. A molded RTV 615/3Å molecular sieve component is currently in production, and an RTV 615/DEB component was produced in the past. However, all three materials have never before been combined in a single production part, and this is an opportunity to create a new component capable of being molded to shape, performing desiccation, and hydrogen gettering. This analysis looked at weapons system parameters and how they might influence part design. It also looked at material processing and how it related to mixing, activating a dessicant, and hydrogen uptake testing.

  18. N-doped carbon networks: alternative materials tracing new routes for activating molecular hydrogen.

    Science.gov (United States)

    Cortese, Remedios; Ferrante, Francesco; Roggan, Stefan; Duca, Dario

    2015-02-23

    The fragmentation of molecular hydrogen on N-doped carbon networks was investigated by using molecular (polyaromatic macrocycles) as well as truncated and periodic (carbon nanotubes) models. The computational study was focused on the ergonicity analysis of the reaction and on the properties of the transition states involved when constellations of three or four pyridinic nitrogen atom defects are present in the carbon network. Calculations show that whenever N-defects are embedded in species characterized by large conjugated π-systems, either in polyaromatic macrocycles or carbon nanotubes, the corresponding H2 bond cleavage is largely exergonic. The fragmentation Gibbs free energy is affected by the final arrangement of the hydrogen atoms on the defect and by the extension of the π-electron cloud, but it is not influenced by the curvature of the system.

  19. Laser shocks on helium, hydrogen and diamond: an experimental study of the warm dense matter zone; Chocs laser sur l'helium, l'hydrogene et le diamant: une etude experimentale de la 'Warm Dense Matter'

    Energy Technology Data Exchange (ETDEWEB)

    Brygoo, St

    2006-11-15

    The purpose of this work was to develop a new approach of laser shocks on pre-compressed targets in order to collect data concerning the equation of state in the warm dense matter zone of the phase diagram. The accuracy of the measurement has been increased by the use of a new metrology based on quartz. Quartz is considered as a standard for the measurement of both the pressure and the density, a model of an isentropic relaxation based on a Grueneisen type approximation has been developed. By combining laser shocks with diamond anvil cells and by using this new metrology, we have investigated the following systems: diamond, helium, hydrogen, deuterium and hydrogen-helium mixtures. The results for helium agree very well with the predictions of the Saumon-Chabrier model. The results for deuterium are consistent with the latest results found in literature. As for the results concerning hydrogen, they have showed the limits of the quartz-based metrology. In fact, by being so little dense we are at the limit of the application range of the quartz relaxation. A mixture of helium-hydrogen (50 %) has been investigated, no sign of phase separation has been found.

  20. Rate coefficients for low-energy electron dissociative attachment to molecular hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Horacek, J.; Houfek, K.; Cizek, M. [Charles University, Faculty of Mathematics and Physics, Prague (Czech Republic); Murakami, I.; Kato, T. [National Inst. for Fusion Science, Toki, Gifu (Japan)

    2003-02-01

    Calculation of rate constants for dissociative electron attachment to molecular hydrogen is reported. The calculation is based on an improved nonlocal resonance model of Cizek, Horacek and Domcke which takes fully into account the nonlocality of the resonance dynamics and uses potentials with correct asymptotic forms. The rate constants are calculated for all quantum numbers v and J of the target molecules and for electron temperature in the range 0-30000 K. (author)

  1. Rate coefficients for low-energy electron dissociative attachment to molecular hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Horacek, J.; Houfek, K.; Cizek, M. [Charles University, Faculty of Mathematics and Physics, Prague (Czech Republic); Murakami, I.; Kato, T. [National Inst. for Fusion Science, Toki, Gifu (Japan)

    2003-02-01

    Calculation of rate constants for dissociative electron attachment to molecular hydrogen is reported. The calculation is based on an improved nonlocal resonance model of Cizek, Horacek and Domcke which takes fully into account the nonlocality of the resonance dynamics and uses potentials with correct asymptotic forms. The rate constants are calculated for all quantum numbers v and J of the target molecules and for electron temperature in the range 0-30000 K. (author)

  2. Spectroscopy and Dynamics of Molecular and Ionic Impurities Embedded in Solid Hydrogen

    Science.gov (United States)

    1993-09-01

    hexagonal close packed (hcp) or face centered cubic ( fcc ) structure . Fundamental properties of solid hydrogen are sum- marized in a review by Silvera... fcc structure in which each molecular site is a center of symmetry. This is because each neighbor molecule has its counterpart at the position diamet...and found no other spectral features. This indicates that our crystal has a purely hcp structure. A crystal with mixed hcp and fcc structure would give

  3. Molecular deformation mechanisms in cellulose allomorphs and the role of hydrogen bonds.

    Science.gov (United States)

    Djahedi, Cyrus; Berglund, Lars A; Wohlert, Jakob

    2015-10-05

    Differences in tensile properties between cellulose crystal allomorphs cannot be rationalized by simply counting hydrogen bonds. From molecular dynamics computer simulations the cooperative nature of energy contributions to axial cellulose crystal modulus becomes apparent. Using a decomposition of inter and intramolecular forces as a function of tensile strain, the three allomorphs show dramatic differences in terms of how the contributions to elastic energy are distributed between covalent bonds, angles, dihedrals, electrostatic forces, dispersion and steric forces.

  4. Discovery of radiatively excited molecular hydrogen in the giant extragalactic HII region complex NGC 604

    NARCIS (Netherlands)

    Israel, F.P.; Hawarden, T.G.; Wade, R.S.; Geballe, T.R.; Dishoeck, van E.F.

    1989-01-01

    The 1-0S(1), 2-1S(1), 1-0S(0) and 1-0Q branch transitions of molecular hydrogen (H2) towards the giant emission nebula (HII region) NGC 604 in M33 have been detected. The line ratios are incompatible with shock-excited H2, but indicate the widespread presence of fluorescent H2 at a mean temperature

  5. Global scale observations of atmospheric molecular hydrogen and its stable isotopic composition

    OpenAIRE

    A. M. Batenburg

    2012-01-01

    With average mixing ratios (χ) around 550 ppb (nmole/mole), molecular hydrogen (H2) is the most abundant reduced gas in our atmosphere after methane (CH4), but considerably less studied. H2 is also a promising energy carrier that might replace fossil fuels in vehicles with great sustainability advantages, but there may be environmental side effects. Large-scale leakage of H2 into the atmosphere might affect the atmosphere’s oxidative capacity and stratospheric ozone chemistry. To assess these...

  6. Emergence of hydrogen bonds from molecular dynamics simulation of substituted N-phenylthiourea-catechol oxidase complex.

    Science.gov (United States)

    Park, Kyung-Lae

    2017-01-01

    A series of N-phenylthiourea derivatives was built starting from the X-ray structure in the molecular mechanics framework and the interaction profile in the complex with the catechol oxidase was traced using molecular dynamics simulation. The results showed that the geometry and interactions between ligand and receptor were highly related to the position of the substituted side chains of phenyl moiety. At the end of molecular dynamics run, a concentrated multicenter hydrogen bond was created between the substituted ligand and receptor. The conformation of the ligand itself were also restricted in the receptor pocket. Furthermore, the simulation time of 50 ns were found to be long enough to explore the relevant conformational space and the stationary behavior of the molecular dynamic could be observed.

  7. Ion channel stability and hydrogen bonding. Molecular modelling of channels formed by synthetic alamethicin analogues.

    Science.gov (United States)

    Breed, J; Kerr, I D; Molle, G; Duclohier, H; Sansom, M S

    1997-12-04

    Several analogues of the channel-forming peptaibol alamethicin have been demonstrated to exhibit faster switching between channel substates than does unmodified alamethicin. Molecular modelling studies are used to explore the possible molecular basis of these differences. Models of channels formed by alamethicin analogues were generated by restrained molecular dynamics in vacuo and refined by short molecular dynamics simulations with water molecules within and at either mouth of the channel. A decrease in backbone solvation was found to correlate with a decrease in open channel stability between alamethicin and an analogue in which all alpha-amino-isobutyric acid residues of alamethicin were replaced by leucine. A decrease in the extent of hydrogen-bonding at residue 7 correlates with lower open channel stabilities of analogues in which the glutamine at position 7 was replaced by smaller polar sidechains. These two observations indicate the importance of alamethicin/water H-bonds in stabilizing the open channel.

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

    Science.gov (United States)

    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.

  9. Simulation of the Correlated Electron Plasma in the Warm Dense Matter Regime by Restricted Path-Integral Molecular Dynamics

    Science.gov (United States)

    Kapila, Vivek; Deymier, Pierre; Runge, Keith

    2012-02-01

    Warm dense matter (WDM) can be characterized by electron temperatures of a few eV and densities an order of magnitude or more beyond ambient. This regime currently lacks any adequate highly developed class of simulation methods. Recent developments in orbital-free Density Functional Theory (ofDFT) aim to provide such a simulation method, however, little benchmark information is available on temperature and pressure dependence of simple but realistic models in WDM regime. The present work aims to fill this critical gap using the restricted path-integral molecular dynamics (rPIMD) method. Within the discrete path integral representation, electrons are described as harmonic necklaces, while, quantum exchange takes the form of cross linking between electron necklaces. The fermion sign problem is addressed by restricting the density matrix to positive values and a molecular dynamics algorithm is employed to sample phase space. Here, we focus on the behavior of strongly correlated electron plasmas under WDM conditions. We compute the kinetic and potential energies and compare them to those obtained with the ofDFT method.

  10. Molecular phylogenetic analysis of sulfate-reducing bacteria from deep sediment layers of the tropical West Pacific warm pool

    Institute of Scientific and Technical Information of China (English)

    LUO Zhuhua; YE Dezan; HUANG Xiangling

    2006-01-01

    The diversity of sulfate-reducing bacteria (SRB) from deep layers of deep-sea sediments [ more than 2 m bsf ( below seafloor) ] of two sites (W01 -3 and WP01 -4) in a tropical West Pacific warm pool region was characterized by using molecular phylogenetic analysis. The results of culture-independent samples demonstrated that the dominant clones from both sites were related to Grampositive spore forming genus, Desulfotomaculum, which accounted for 36.8% of all the sequencing clones from Site WP01 -3 and62.8% from Site WP01 -4. However, the other SRB group which was generally reported to be predominant in the deep-sea sediments of other regions, δ- subclass of the proteobacteria was found to be in very low percentages. Therefore, it could be speculated that there existed a unique chemical environment in the deep-sea sediment of this warm pool region. When comparing the Desulfotomaculum sp. related sequences from both sites, it was revealed that though the Desulfotomaculum-like sequences from Site WP01 -3 were more diverse than those from Site WP01 -4, all these sequences from both sites showed high similarity and formed a new phylogenetically homogeneous cluster in the Desulfotomaculum genus which had never been reported before. Successful enrichment of SRB was only achieved from samples of Site WP01 - 4 and the sequence analysis of culture-dependent samples further confirmed the dominance of Desulfotomaculum genus. But Desulfotomaculum-related sequences from culture-dependent and culture-independent samples belonged to two different clusters respectively. This difference showed the choice of cultivation to the microorganisms.

  11. Equation of state of warm dense deuterium and its isotopes from density-functional theory molecular dynamics.

    Science.gov (United States)

    Danel, J-F; Kazandjian, L; Piron, R

    2016-04-01

    Of the two approaches of density-functional theory molecular dynamics, quantum molecular dynamics is limited at high temperature by computational cost whereas orbital-free molecular dynamics, based on an approximation of the kinetic electronic free energy, can be implemented in this domain. In the case of deuterium, it is shown how orbital-free molecular dynamics can be regarded as the limit of quantum molecular dynamics at high temperature for the calculation of the equation of state. To this end, accurate quantum molecular dynamics calculations are performed up to 20 eV at mass densities as low as 0.5g/cm^{3} and up to 10 eV at mass densities as low as 0.2g/cm^{3}. As a result, the limitation in temperature so far attributed to quantum molecular dynamics is overcome and an approach combining quantum and orbital-free molecular dynamics is used to construct an equation of state of deuterium. The thermodynamic domain addressed is that of the fluid phase above 1 eV and 0.2g/cm^{3}. Both pressure and internal energy are calculated as functions of temperature and mass density, and various exchange-correlation contributions are compared. The generalized gradient approximation of the exchange-correlation functional, corrected to approximately include the influence of temperature, is retained and the results obtained are compared to other approaches and to experimental shock data; in parts of the thermodynamic domain addressed, these results significantly differ from those obtained in other first-principles investigations which themselves disagree. The equations of state of hydrogen and tritium above 1 eV and above, respectively, 0.1g/cm^{3} and 0.3g/cm^{3}, can be simply obtained by mass density scaling from the results found for deuterium. This ab initio approach allows one to consistently cover a very large domain of temperature on the domain of mass density outlined above.

  12. Warm gas in the rotating disk of the Red Rectangle: accurate models of molecular line emission

    CERN Document Server

    Bujarrabal, V

    2013-01-01

    We aim to study the excitation conditions of the molecular gas in the rotating disk of the Red Rectangle, the only post-Asymptotic-Giant-Branch object in which the existence of an equatorial rotating disk has been demonstrated. For this purpose, we developed a complex numerical code that accurately treats radiative transfer in 2-D, adapted to the study of molecular lines from rotating disks. We present far-infrared Herschel/HIFI observations of the 12CO and 13CO J=6-5, J=10-9, and J=16-15 transitions in the Red Rectangle. We also present our code in detail and discuss the accuracy of its predictions, from comparison with well-tested codes. Theoretical line profiles are compared with the empirical data to deduce the physical conditions in the disk by means of model fitting. We conclude that our code is very efficient and produces reliable results. The comparison of the theoretical predictions with our observations reveals that the temperature of the Red Rectangle disk is typically ~ 100-150 K, about twice as h...

  13. Dense gas in the Galactic central molecular zone is warm and heated by turbulence

    CERN Document Server

    Ginsburg, Adam; Ao, Yiping; Riquelme, Denise; Kauffmann, Jens; Pillai, Thushara; Mills, Elisabeth A C; Requena-Torres, Miguel A; Immer, Katharina; Testi, Leonardo; Ott, Juergen; Bally, John; Battersby, Cara; Darling, Jeremy; Aalto, Susanne; Stanke, Thomas; Kendrew, Sarah; Kruijssen, J M Diederik; Longmore, Steven; Dale, James; Guesten, Rolf; Menten, Karl M

    2016-01-01

    The Galactic center is the closest region in which we can study star formation under extreme physical conditions like those in high-redshift galaxies. We measure the temperature of the dense gas in the central molecular zone (CMZ) and examine what drives it. We mapped the inner 300 pc of the CMZ in the temperature-sensitive J = 3-2 para-formaldehyde (p-H$_2$CO) transitions. We used the $3_{2,1} - 2_{2,0} / 3_{0,3} - 2_{0,2}$ line ratio to determine the gas temperature in $n \\sim 10^4 - 10^5 $cm$^{-3}$ gas. We have produced temperature maps and cubes with 30" and 1 km/s resolution and published all data in FITS form. Dense gas temperatures in the Galactic center range from ~60 K to > 100 K in selected regions. The highest gas temperatures T_G > 100 K are observed around the Sgr B2 cores, in the extended Sgr B2 cloud, the 20 km/s and 50 km/s clouds, and in "The Brick" (G0.253+0.016). We infer an upper limit on the cosmic ray ionization rate ${\\zeta}_{CR} < 10^{-14}$ 1/s. The dense molecular gas temperature o...

  14. FIR Spectroscopy of the Galactic Center: Hot and Warm Molecular Gas

    Science.gov (United States)

    Goicoechea, Javier R.; Etxaluze, Mireya; Cernicharo, José; Gerin, Maryvonne; Pety, Jerome

    2017-01-01

    The angular resolution (~10'') achieved by the Herschel Space Observatory ~3.5 m telescope at FIR wavelengths allowed us to roughly separate the emission toward the inner parsec of the galaxy (the central cavity) from that of the surrounding circumnuclear disk (the CND). The FIR spectrum toward Sgr A* is dominated by intense [O III], [O I], [C II], [N III], [N II], and [C I] fine-structure lines (in decreasing order of luminosity) arising in gas irradiated by the strong UV field from the central stellar cluster. The high-J CO rotational line intensities observed at the interface between the inner CND and the central cavity are consistent with a hot isothermal component at T k ~ 103.1 K and n(H2)~ 104 cm-3. They are also consistent with a distribution of lower temperatures at higher gas density, with most CO at T k~300 K. The hot CO component (either the bulk of the CO column density or just a small fraction depending on the above scenario) likely results from a combination of UV and shock-driven heating. If UV-irradiated and heated dense clumps do not exist, shocks likely dominate the heating of the hot molecular gas component. Although this component is beam diluted in our FIR observations, it may be resolved at much higher angular resolution. An ALMA project using different molecular tracers to characterize UV-irradiated shocks in the innermost layers of the CND is ongoing.

  15. Contrasting impacts of ocean acidification and warming on the molecular responses of CO2-resilient oysters.

    Science.gov (United States)

    Goncalves, Priscila; Thompson, Emma L; Raftos, David A

    2017-06-02

    This study characterises the molecular processes altered by both elevated CO2 and increasing temperature in oysters. Differences in resilience of marine organisms against the environmental stressors associated with climate change will have significant implications for the sustainability of coastal ecosystems worldwide. Some evidence suggests that climate change resilience can differ between populations within a species. B2 oysters represent a unique genetic resource because of their capacity to better withstand the impacts of elevated CO2 at the physiological level, compared to non-selected oysters from the same species (Saccostrea glomerata). Here, we used proteomic and transcriptomic analysis of gill tissue to evaluate whether the differential response of B2 oysters to elevated CO2 also extends to increased temperature. Substantial and distinctive effects on protein concentrations and gene expression were evident among B2 oysters responding to elevated CO2 or elevated temperature. The combination of both stressors also altered oyster gill proteomes and gene expression. However, the impacts of elevated CO2 and temperature were not additive or synergistic, and may be antagonistic. The data suggest that the simultaneous exposure of CO2-resilient oysters to near-future projected ocean pH and temperature results in complex changes in molecular processes in order to prevent stress-induced cellular damage. The differential response of B2 oysters to the combined stressors also indicates that the addition of thermal stress may impair the resilience of these oysters to decreased pH. Overall, this study reveals the intracellular mechanisms that might enable marine calcifiers to endure the emergent, adverse seawater conditions resulting from climate change.

  16. Hydrogen.

    Science.gov (United States)

    Bockris, John O'M

    2011-11-30

    The idea of a "Hydrogen Economy" is that carbon containing fuels should be replaced by hydrogen, thus eliminating air pollution and growth of CO₂ in the atmosphere. However, storage of a gas, its transport and reconversion to electricity doubles the cost of H₂ from the electrolyzer. Methanol made with CO₂ from the atmosphere is a zero carbon fuel created from inexhaustible components from the atmosphere. Extensive work on the splitting of water by bacteria shows that if wastes are used as the origin of feed for certain bacteria, the cost for hydrogen becomes lower than any yet known. The first creation of hydrogen and electricity from light was carried out in 1976 by Ohashi et al. at Flinders University in Australia. Improvements in knowledge of the structure of the semiconductor-solution system used in a solar breakdown of water has led to the discovery of surface states which take part in giving rise to hydrogen (Khan). Photoelectrocatalysis made a ten times increase in the efficiency of the photo production of hydrogen from water. The use of two electrode cells; p and n semiconductors respectively, was first introduced by Uosaki in 1978. Most photoanodes decompose during the photoelectrolysis. To avoid this, it has been necessary to create a transparent shield between the semiconductor and its electronic properties and the solution. In this way, 8.5% at 25 °C and 9.5% at 50 °C has been reached in the photo dissociation of water (GaP and InAs) by Kainthla and Barbara Zeleney in 1989. A large consortium has been funded by the US government at the California Institute of Technology under the direction of Nathan Lewis. The decomposition of water by light is the main aim of this group. Whether light will be the origin of the post fossil fuel supply of energy may be questionable, but the maximum program in this direction is likely to come from Cal. Tech.

  17. Effects of glycerol on the molecular mobility and hydrogen bond network in starch matrix.

    Science.gov (United States)

    Liang, Jun; Ludescher, Richard D

    2015-01-22

    The effects of glycerol on molecular mobility and hydrogen bonding network in an amorphous glassy starch matrix were studied using phosphorescence and IR spectroscopy. Amorphous potato starch films containing varying amounts of glycerol (0, 5, 10, 20 and 30 wt.%) were formulated by rapidly dehydrating aqueous potato starch gel (5%, w/v) with a corresponding content of glycerol; X-ray diffraction data confirm that the films contained negligible content of crystalline starch. Erythrosin B (Ery B) phosphorescence was used to monitor the molecular mobility of these matrices over the temperature range from 0 to 100°C. Analysis of Ery B emission peak frequency, band width and intensity decay provided information about thermally-activated modes of molecular mobility in the matrix. Dipolar relaxation around the triplet state of Ery B was enhanced by addition of glycerol and the extent of relaxation increased at low and intermediate but decreased at higher temperature. The glycerol content-dependent onset temperature for this transition was 70°C for pure starch and decreased to 40°C for a matrix with 30% glycerol. Measurements of the rate of non-radiative decay from the Ery B triplet state indicated that glycerol plasticized the starch matrix above ∼10 wt.% while acting as an antiplastizer to increase the matrix molecular mobility at lower content. These matrix properties were related to glycerol-dependent increases in hydrogen bond strength as measured by IR.

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

    Science.gov (United States)

    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.

  19. Intermolecular hydrogen bonds: From temperature-driven proton transfer in molecular crystals to denaturation of DNA

    Indian Academy of Sciences (India)

    Mark Johnson

    2008-11-01

    We have combined neutron scattering and a range of numerical simulations to study hydrogen bonds in condensed matter. Two examples from a recent thesis will be presented. The first concerns proton transfer with increasing temperature in short inter-molecular hydrogen bonds [1,2]. These bonds have unique physical and chemical properties and are thought to play a fundamental role in processes like enzymatic catalysis. By combining elastic and inelastic neutron scattering results with ab initio, lattice dynamics and molecular dynamics simulations, low frequency lattice modes are identified which modulate the potential energy surface of the hydrogen bond proton and drive proton transfer. The second example concerns base-pair opening in DNA which is the fundamental physical process underlying biological processes like denaturation and transcription. We have used an emprical force field and a large scale, all-atom phonon calculation to gain insight into the base-pair opening modes and the apparent `energy gap' between the accepted frequencies for these modes (∼ 100 cm-1 or ∼ 140 K) and the temperature of the biological processes (room temperature to 100° C) [3]. Inelastic neutron scattering spectra on aligned, highly crystalline DNA samples, produced at the ILL, provide the reference data for evaluating the precision of these simulation results.

  20. Simulation of the Cosmic Evolution of Atomic and Molecular Hydrogen in Galaxies

    CERN Document Server

    Obreschkow, D; De Lucia, G; Khochfar, S; Rawlings, S

    2009-01-01

    We present a simulation of the cosmic evolution of the atomic and molecular phases of the cold hydrogen gas in about 3e7 galaxies, obtained by post-processing the virtual galaxy catalog produced by (De Lucia et al. 2007) on the Millennium Simulation of cosmic structure (Springel et al. 2005). Our method uses a set of physical prescriptions to assign neutral atomic hydrogen (HI) and molecular hydrogen (H2) to galaxies, based on their total cold gas masses and a few additional galaxy properties. These prescriptions are specially designed for large cosmological simulations, where, given current computational limitations, individual galaxies can only be represented by simplistic model-objects with a few global properties. Our recipes allow us to (i) split total cold gas masses between HI, H2, and Helium, (ii) assign realistic sizes to both the HI- and H2-disks, and (iii) evaluate the corresponding velocity profiles and shapes of the characteristic radio emission lines. The results presented in this paper include ...

  1. Hydrogen bonding-assisted interaction between amitriptyline hydrochloride and hemoglobin: spectroscopic and molecular dynamics studies.

    Science.gov (United States)

    Maurya, Neha; Maurya, Jitendra Kumar; Kumari, Meena; Khan, Abbul Bashar; Dohare, Ravins; Patel, Rajan

    2017-05-01

    Herein, we have explored the interaction between amitriptyline hydrochloride (AMT) and hemoglobin (Hb), using steady-state and time-resolved fluorescence spectroscopy, UV-visible spectroscopy, and circular dichroism spectroscopy, in combination with molecular docking and molecular dynamic (MD) simulation methods. The steady-state fluorescence reveals the static quenching mechanism in the interaction system, which was further confirmed by UV-visible and time-resolved fluorescence spectroscopy. The binding constant, number of binding sites, and thermodynamic parameters viz. ΔG, ΔH, ΔS are also considered; result confirms that the binding of the AMT with Hb is a spontaneous process, involving hydrogen bonding and van der Waals interactions with a single binding site, as also confirmed by molecular docking study. Synchronous fluorescence, CD data, and MD simulation results contribute toward understanding the effect of AMT on Hb to interpret the conformational change in Hb upon binding in aqueous solution.

  2. Detection of hydrogen fluoride absorption in diffuse molecular clouds with Herschel/HIFI: a ubiquitous tracer of molecular gas

    CERN Document Server

    Sonnentrucker, P; Phillips, T G; Gerin, M; Lis, D C; De Luca, M; Goicoechea, J R; Black, J H; Bell, T A; Boulanger, F; Cernicharo, J; Coutens, A; Dartois, E; Kazmierczak, M; Encrenaz, P; Falgarone, E; Geballe, T R; Giesen, T; Godard, B; Goldsmith, P F; Gry, C; Gupta, H; Hennebelle, P; Herbst, E; Hily-Blant, P; Joblin, C; Kolos, R; Krelowski, J; Mart\\in-Pintado, J; Menten, K M; Monje, R; Mookerjea, B; Pearson, J; Perault, M; Persson, C M; Plume, R; Salez, M; Schlemmer, S; Schmidt, M; Stutzki, J; Teyssier, D; Vastel, C; Yu, S; Caux, E; Gusten, R; Hatch, W A; Klein, T; Mehdi, I; Morris, P; Ward, J S

    2010-01-01

    We discuss the detection of absorption by interstellar hydrogen fluoride (HF) along the sight line to the submillimeter continuum sources W49N and W51. We have used Herschel's HIFI instrument in dual beam switch mode to observe the 1232.4762 GHz J = 1 - 0 HF transition in the upper sideband of the band 5a receiver. We detected foreground absorption by HF toward both sources over a wide range of velocities. Optically thin absorption components were detected on both sight lines, allowing us to measure - as opposed to obtain a lower limit on - the column density of HF for the first time. As in previous observations of HF toward the source G10.6-0.4, the derived HF column density is typically comparable to that of water vapor, even though the elemental abundance of oxygen is greater than that of fluorine by four orders of magnitude. We used the rather uncertain N(CH)-N(H2) relationship derived previously toward diffuse molecular clouds to infer the molecular hydrogen column density in the clouds exhibiting HF abs...

  3. A giant comet-like cloud of hydrogen escaping the warm Neptune-mass exoplanet GJ 436b.

    Science.gov (United States)

    Ehrenreich, David; Bourrier, Vincent; Wheatley, Peter J; des Etangs, Alain Lecavelier; Hébrard, Guillaume; Udry, Stéphane; Bonfils, Xavier; Delfosse, Xavier; Désert, Jean-Michel; Sing, David K; Vidal-Madjar, Alfred

    2015-06-25

    Exoplanets orbiting close to their parent stars may lose some fraction of their atmospheres because of the extreme irradiation. Atmospheric mass loss primarily affects low-mass exoplanets, leading to the suggestion that hot rocky planets might have begun as Neptune-like, but subsequently lost all of their atmospheres; however, no confident measurements have hitherto been available. The signature of this loss could be observed in the ultraviolet spectrum, when the planet and its escaping atmosphere transit the star, giving rise to deeper and longer transit signatures than in the optical spectrum. Here we report that in the ultraviolet the Neptune-mass exoplanet GJ 436b (also known as Gliese 436b) has transit depths of 56.3 ± 3.5% (1σ), far beyond the 0.69% optical transit depth. The ultraviolet transits repeatedly start about two hours before, and end more than three hours after the approximately one hour optical transit, which is substantially different from one previous claim (based on an inaccurate ephemeris). We infer from this that the planet is surrounded and trailed by a large exospheric cloud composed mainly of hydrogen atoms. We estimate a mass-loss rate in the range of about 10(8)-10(9) grams per second, which is far too small to deplete the atmosphere of a Neptune-like planet in the lifetime of the parent star, but would have been much greater in the past.

  4. A comparative study of cold- and warm-adapted Endonucleases A using sequence analyses and molecular dynamics simulations

    Science.gov (United States)

    Michetti, Davide; Brandsdal, Bjørn Olav; Bon, Davide; Isaksen, Geir Villy; Tiberti, Matteo; Papaleo, Elena

    2017-01-01

    The psychrophilic and mesophilic endonucleases A (EndA) from Aliivibrio salmonicida (VsEndA) and Vibrio cholera (VcEndA) have been studied experimentally in terms of the biophysical properties related to thermal adaptation. The analyses of their static X-ray structures was no sufficient to rationalize the determinants of their adaptive traits at the molecular level. Thus, we used Molecular Dynamics (MD) simulations to compare the two proteins and unveil their structural and dynamical differences. Our simulations did not show a substantial increase in flexibility in the cold-adapted variant on the nanosecond time scale. The only exception is a more rigid C-terminal region in VcEndA, which is ascribable to a cluster of electrostatic interactions and hydrogen bonds, as also supported by MD simulations of the VsEndA mutant variant where the cluster of interactions was introduced. Moreover, we identified three additional amino acidic substitutions through multiple sequence alignment and the analyses of MD-based protein structure networks. In particular, T120V occurs in the proximity of the catalytic residue H80 and alters the interaction with the residue Y43, which belongs to the second coordination sphere of the Mg2+ ion. This makes T120V an amenable candidate for future experimental mutagenesis. PMID:28192428

  5. Effects of hydrogen during molecular beam epitaxy of GaN

    Energy Technology Data Exchange (ETDEWEB)

    Dong, Y.; Feenstra, R.M. [Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States)

    2005-05-01

    We study the effect of introducing hydrogen gas through the RF plasma source during plasma-assisted molecular beam epitaxy of GaN(0001). The well-known smooth-to-rough transition that occurs for this surface as a function of decreasing Ga flux in the absence of H is found to persist even with H present. But, the critical Ga flux for this transition is increased by the presence of H, and for sufficiently high H pressure a new 2 x 2 surface structure that is believed to be H-terminated is observed. Under Ga-rich conditions, the presence of hydrogen is found to induce step bunching on the surface, from which we argue that H selectively bonds to surface step and/or kink sites. (copyright 2005 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  6. Molecular molybdenum persulfide and related catalysts for generating hydrogen from water

    Energy Technology Data Exchange (ETDEWEB)

    Long, Jeffrey R.; Chang, Christopher J.; Karunadasa, Hemamala I.; Majda, Marcin

    2016-11-22

    New metal persulfido compositions of matter are described. In one embodiment the metal is molybdenum and the metal persulfido complex mimics the structure and function of the triangular active edge site fragments of MoS.sub.2, a material that is the current industry standard for petroleum hydro desulfurization, as well as a promising low-cost alternative to platinum for electrocatalytic hydrogen production. This molecular [(PY5W.sub.2)MoS.sub.2].sup.x+ containing catalyst is capable of generating hydrogen from acidic-buffered water or even seawater at very low overpotentials at a turnover frequency rate in excess of 500 moles H.sub.2 per mole catalyst per second, with a turnover number (over a 20 hour period) of at least 19,000,000 moles H.sub.2 per mole of catalyst.

  7. Absolute measurements of electron capture cross sections of C3+ from atomic and molecular hydrogen

    Science.gov (United States)

    Sant'Anna, M. M.; Melo, W. S.; Santos, A. C. F.; Shah, M. B.; Sigaud, G. M.; Montenegro, E. C.

    2000-02-01

    Absolute measurements of single- and double-electron-capture cross sections by C3+ projectiles on atomic and molecular hydrogen targets were performed for projectile energies between 1.0 and 3.5 MeV for the single- and 1.0 and 2.0 MeV for the double-capture processes. The icons/Journals/Common/sigma" ALT="sigma" ALIGN="TOP"/> H /icons/Journals/Common/sigma" ALT="sigma" ALIGN="TOP"/> H2 cross section ratios were measured using an absolutely calibrated tungsten-tube furnace for the production of atomic hydrogen. The single-capture data are compared with calculations based on the boundary-corrected first Born approximation, the eikonal approximation and a semiclassical model, presenting a good overall agreement. Calculations for the double capture using an analytical expression, obtained within the independent electron approximation and based on the same semiclassical model, give a reasonable qualitative description of the data.

  8. Molecular molybdenum persulfide and related catalysts for generating hydrogen from water

    Energy Technology Data Exchange (ETDEWEB)

    Long, Jeffrey R.; Chang, Christopher J.; Karunadasa, Hemamala I.; Majda, Marcin

    2016-04-19

    New metal persulfido compositions of matter are described. In one embodiment the metal is molybdenum and the metal persulfido complex mimics the structure and function of the triangular active edge site fragments of MoS.sub.2, a material that is the current industry standard for petroleum hydro desulfurization, as well as a promising low-cost alternative to platinum for electrocatalytic hydrogen production. This molecular [(PY5W.sub.2)MoS.sub.2].sup.x+ containing catalyst is capable of generating hydrogen from acidic-buffered water or even seawater at very low overpotentials at a turnover frequency rate in excess of 500 moles H.sub.2 per mole catalyst per second, with a turnover number (over a 20 hour period) of at least 19,000,000 moles H.sub.2 per mole of catalyst.

  9. Pressure dependent deuterium fractionation in the formation of molecular hydrogen in formaldehyde photolysis

    DEFF Research Database (Denmark)

    Nilsson, Elna Johanna Kristina; Andersen, Vibeke Friis; Skov, Henrik;

    2009-01-01

    the channels has been estimated using available values for the absorption 10 cross section and quantum yield. As a result of the change in pressure with altitude the isotope effect for production of molecular hydrogen is found to change from a value of kH/kD=1.8±0.2 at the surface to unity at 50 km....... The relative importance of the two product channels changes with altitude as a result of changes in both pressure and actinic flux. The study concludes that the D of photochemical hydrogen produced in 15 situ will increase substantially with altitude.......The pressure dependence of the relative photolysis rates of HCHO and HCDO has been investigated using a new photochemical reactor at the University of Copenhagen. The relative photolysis rate of HCHO vs. HCDO under UVA lamp irradiation was mea- 5 sured at total pressures of 50, 200, 400, 600...

  10. Molecular Survey of Sulphate-Reducing Bacteria in the Deep-Sea Sediments of the West Pacific Warm Pool

    Institute of Scientific and Technical Information of China (English)

    WANG Peng; XIAO Xiang; ZHANG Haiyan; WANG Fengping

    2008-01-01

    The sulfate-reducing bacteria (SRB) community in the deep-sea sediments of the west Pacific Warm Pool (WP) was surveyed by molecular phylogenetic analyses using primers targeting the 16S rRNA gene fragments of SRB. Specific 16S rRNA gene libraries from five sediment layers (1-cm, 3-cm, 6-cm, 10-cm and 12-cm layer) of the 12-cm core of WP-0 were constructed. The clones in the five libraries were differentiated by restriction fragment length polymorphism (RFLP) and representative clones were selected to sequence. It was found that the clones fell into four groups, which were closest related to Desulfotomaculum, Desul- facinum, Desulfomonile and Desulfanuticus. Desulfacinum-like clones were only detected in the upper layers of the sediment core, whereas Desulfomonile-like clones were only present in the deeper layers. Fluorescence in situ hybridization (FISH) was further carried out to visualize and count the SRB and bacteria in the five sediment layers. It was found that SRB constituted only a small proportion of the bacteria community (0.34%-1.95%), it had the highest content in the 3-cm layer (1.95%) and had a depth- related decreasing tendency along the 12- cm core.

  11. Hydrogen

    Directory of Open Access Journals (Sweden)

    John O’M. Bockris

    2011-11-01

    Full Text Available The idea of a “Hydrogen Economy” is that carbon containing fuels should be replaced by hydrogen, thus eliminating air pollution and growth of CO2 in the atmosphere. However, storage of a gas, its transport and reconversion to electricity doubles the cost of H2 from the electrolyzer. Methanol made with CO2 from the atmosphere is a zero carbon fuel created from inexhaustible components from the atmosphere. Extensive work on the splitting of water by bacteria shows that if wastes are used as the origin of feed for certain bacteria, the cost for hydrogen becomes lower than any yet known. The first creation of hydrogen and electricity from light was carried out in 1976 by Ohashi et al. at Flinders University in Australia. Improvements in knowledge of the structure of the semiconductor-solution system used in a solar breakdown of water has led to the discovery of surface states which take part in giving rise to hydrogen (Khan. Photoelectrocatalysis made a ten times increase in the efficiency of the photo production of hydrogen from water. The use of two electrode cells; p and n semiconductors respectively, was first introduced by Uosaki in 1978. Most photoanodes decompose during the photoelectrolysis. To avoid this, it has been necessary to create a transparent shield between the semiconductor and its electronic properties and the solution. In this way, 8.5% at 25 °C and 9.5% at 50 °C has been reached in the photo dissociation of water (GaP and InAs by Kainthla and Barbara Zeleney in 1989. A large consortium has been funded by the US government at the California Institute of Technology under the direction of Nathan Lewis. The decomposition of water by light is the main aim of this group. Whether light will be the origin of the post fossil fuel supply of energy may be questionable, but the maximum program in this direction is likely to come from Cal. Tech.

  12. Effects of vitamin C, vitamin E, and molecular hydrogen on the placental function in trophoblast cells.

    Science.gov (United States)

    Guan, Zhong; Li, Huai-Fang; Guo, Li-Li; Yang, Xiang

    2015-08-01

    This study aimed to investigate the effects of three different antioxidants, namely vitamin C, vitamin E, and molecular hydrogen, on cytotrophoblasts in vitro. Two trophoblast cell lines, JAR and JEG-3, were exposed to different concentrations of vitamin C (0, 25, 50, 100, 500, 1,000, 5,000 μmol/L), vitamin E (0, 25, 50, 100, 500, 1,000, 5,000 μmol/L), and molecular hydrogen (0, 25, 50, 100, 500 μmol/L) for 48 h. The cell viability was detected using the MTS assay. The secretion of human chorionic gonadotropin (hCG) and the tumor necrosis factor-α (TNF-α) were assessed and the expression of TNF-α mRNA was observed by real-time RT-PCR. Cell viability was significantly suppressed by 500 μmol/L vitamins C and E (P 0.05). The expression of TNF-α was increased by 100 μmol/L vitamin C and 50 μmol/L vitamins E, separately or combined (P vitamin C and E, separately or combined. High levels of antioxidant vitamins C and E may have significant detrimental effects on placental function, as reflected by decreased cell viability and secretion of hCG; and placental immunity, as reflected by increased production of TNF-a. Meanwhile hydrogen showed no such effects on cell proliferation and TNF-α expression, but it could affect the level of hCG, indicating hydrogen as a potential candidate of antioxidant in the management of preeclampsia (PE) should be further studied.

  13. Hydrogen bonded charge transfer molecular salt (4-chloro anilinium-3-nitrophthalate) for photophysical and pharmacological applications

    Science.gov (United States)

    Singaravelan, K.; Chandramohan, A.; Saravanabhavan, M.; Muthu Vijayan Enoch, I. V.; Suganthi, V. S.

    2017-09-01

    Radical scavenging activity against DPPH radical and binding properties of a hydrogen bonded charge transfer molecular salt 4-chloro anilinium-3-nitrophthalate(CANP) with calf thymus DNA has been studied by electronic absorption and emission spectroscopy. The molecular structure and crystallinity of the CANP salt have been established by carried out powder and single crystal X-ray diffraction analysis which indicated that cation and anion are linked through strong N+sbnd H…O- type of hydrogen bond. FTIR spectroscopic study was carried out to know the various functional groups present in the crystal. 1H and 13C NMR spectra were recorded to further confirm the molecular structure of the salt crystal. The thermal stability of the title salt was established by TG/DTA analyses simultaneously on the powdered sample of the title crystal. Further, the CANP salt was examined against various bacteria and fungi strains which showed a remarkable antimicrobial activity compared to that of the standards Ciproflaxin and Clotrimazole. The results showed that the CANP salt could interact with CT-DNA through intercalation. Antioxidant studies of the substrates alone and synthesized CANP salt showed that the latter has been better radical scavenging activity than that of the former against DPPH radical. The third order nonlinear susceptibility of the CANP salt was established by the Z-scan study.

  14. Hydrogen Bonding and Dielectric Spectra of Ethylene Glycol–Water Mixtures from Molecular Dynamics Simulations

    Science.gov (United States)

    2016-01-01

    Mixtures of ethylene glycol with water are a prominent example of media with variable viscosity. Classical molecular dynamics simulations at room temperature were performed for mixtures of ethylene glycol (EG) and water with EG mole fractions of xE = 0.0, 0.1, 0.2, 0.4, 0.6, 0.9, 1.0. The calculated dielectric loss spectra were in qualitative agreement with experiment. We found a slightly overestimated slowdown of the dynamics with increasing EG concentration compared to experimental data. Statistics of the hydrogen bond network and hydrogen bond lifetimes were derived from suitable time correlation functions and also show a slowdown in the dynamics with increasing xE. A similar picture is predicted for the time scales of EG conformer changes and for molecular reorientation. A slight blue shift was obtained for the power spectra of the molecular center of mass motion. The results were used to give a qualitative interpretation of the origin of three different relaxation times that appear in experimental complex dielectric spectra and of their change with xE. PMID:27649083

  15. Molecular dynamics simulation of the formation of sp3 hybridized bonds in hydrogenated diamondlike carbon deposition processes.

    Science.gov (United States)

    Murakami, Yasuo; Horiguchi, Seishi; Hamaguchi, Satoshi

    2010-04-01

    The formation process of sp3 hybridized carbon networks (i.e., diamondlike structures) in hydrogenated diamondlike carbon (DLC) films has been studied with the use of molecular-dynamics simulations. The processes simulated in this study are injections of hydrocarbon (CH3 and CH) beams into amorphous carbon (a-C) substrates. It has been shown that diamondlike sp3 structures are formed predominantly at a subsurface level when the beam energy is relatively high, as in the "subplantation" process for hydrogen-free DLC deposition. However, for hydrogenated DLC deposition, the presence of abundant hydrogen at subsurface levels, together with thermal spikes caused by energetic ion injections, substantially enhances the formation of carbon-to-carbon sp3 bonds. Therefore, the sp3 bond formation process for hydrogenated DLC films essentially differs from that for hydrogen-free DLC films.

  16. Ab initio molecular dynamics simulations for the role of hydrogen in catalytic reactions of furfural on Pd(111)

    Science.gov (United States)

    Xue, Wenhua; Dang, Hongli; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu

    2014-03-01

    In the study of catalytic reactions of biomass, furfural conversion over metal catalysts with the presence of hydrogen has attracted wide attention. We report ab initio molecular dynamics simulations for furfural and hydrogen on the Pd(111) surface at finite temperatures. The simulations demonstrate that the presence of hydrogen is important in promoting furfural conversion. In particular, hydrogen molecules dissociate rapidly on the Pd(111) surface. As a result of such dissociation, atomic hydrogen participates in the reactions with furfural. The simulations also provide detailed information about the possible reactions of hydrogen with furfural. Supported by DOE (DE-SC0004600). This research used the supercomputer resources of the XSEDE, the NERSC Center, and the Tandy Supercomputing Center.

  17. A molecular superfluid: non-classical rotations in doped para-hydrogen clusters

    CERN Document Server

    Li, Hui; Roy, Pierre-Nicholas; McKellar, A R W; 10.1103/PhysRevLett.105.133401

    2010-01-01

    Clusters of para-hydrogen (pH2) have been predicted to exhibit superfluid behavior, but direct observation of this phenomenon has been elusive. Combining experiments and theoretical simulations, we have determined the size evolution of the superfluid response of pH2 clusters doped with carbon dioxide (CO2). Reduction of the effective inertia is observed when the dopant is surrounded by the pH2 solvent. This marks the onset of molecular superfluidity in pH2. The fractional occupation of solvation rings around CO2 correlates with enhanced superfluid response for certain cluster sizes.

  18. The ab initio equation of state of hydrogen in the warm dense matter and its application to the implosion of targets for the inertial confinement fusion; Equation d'etat ab initio de l'hydrogene dans la matiere dense et tiede et application a l'implosion de cibles pour la fusion par confinement inertiel

    Energy Technology Data Exchange (ETDEWEB)

    Caillabet, L.

    2011-03-25

    In the field of the inertial confinement fusion (ICF), the equation of state (EoS) of the hydrogen and its isotopes is one of the most important properties to know. The EoS based on chemical models have difficulty in giving an unambiguous description of the hydrogen in the strong coupled and partial degenerate regime, called Warm Dense Matter (WDM). Indeed, these models use potential with adjustable parameters to describe the many body interactions which are important in the WDM. On the other hand, the ab initio methods resolve almost exactly the quantum many body problem and are thus particularly relevant in this domain. In the first part of this thesis, we describe how we built a table of a multi-phase EoS of the hydrogen, using ab initio methods in the field of the WDM. We show in particular that this EoS is in very good agreement with most of the available experimental data (principal Hugoniot, sound velocity in the molecular fluid, melting curve at low pressure, measurements of multiple shocks). In the second part, we present a direct application of our EoS by showing its influence on the criteria of ignition and combustion of two target designs for ICF: a self-ignited target which will be used on the Laser MegaJoule (LMJ), and a shock-ignited target. We show in particular that the optimization of the laser pulse allowing maximizing the thermonuclear energy is strongly dependent on the precision of the EoS in the strong coupled and degenerate domain. (author) [French] Dans le domaine de la fusion par confinement inertiel (FCI), l'equation d'etat (EoS) de l'hydrogene et de ses isotopes est tres certainement une des proprietes les plus importantes a connaitre. Les EoS basees sur des modeles chimiques peinent a donner une description univoque de l'hydrogene dans le domaine de couplage et de degenerescence partiels, appele matiere dense et tiede, ou Warm Dense Matter (WDM). En effets, ces modeles utilisent des potentiels ad hoc pour decrire les

  19. Path integral centroid molecular dynamics simulations of semiinfinite slab and bulk liquid of para-hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Kinugawa, Kenichi [Nara Women`s Univ., Nara (Japan). Dept. of Chemistry

    1998-10-01

    It has been unsuccessful to solve a set of time-dependent Schroedinger equations numerically for many-body quantum systems which involve, e.g., a number of hydrogen molecules, protons, and excess electrons at a low temperature, where quantum effect evidently appears. This undesirable situation is fatal for the investigation of real low-temperature chemical systems because they are essentially composed of many quantum degrees of freedom. However, if we use a new technique called `path integral centroid molecular dynamics (CMD) simulation` proposed by Cao and Voth in 1994, the real-time semi-classical dynamics of many degrees of freedom can be computed by utilizing the techniques already developed in the traditional classical molecular dynamics (MD) simulations. Therefore, the CMD simulation is expected to be very powerful tool for the quantum dynamics studies or real substances. (J.P.N.)

  20. Characteristics of the molecular electron density, delocalization effect and hydrogen bonding interaction of nitroxoline

    Science.gov (United States)

    Arun Sasi, B. S.; Twinkle, A. R.; James, C.

    2017-08-01

    The density functional theoretical (DFT) calculations have been carried out at the B3LYP/6-311G(d,p) level of theory for nitroxoline monomer and dimer molecule. The dimer molecule formed between two nitroxoline subunits has the largest stability, and is held together by two Osbnd H⋯N hydrogen bonds. Stability of the molecule arising from hyperconjugative interaction and intra/inter molecular charge transfer has been analyzed using natural bond orbital (NBO) analysis. The topological analysis of electron localization function (ELF) provides effect of delocalization. Quantum theory of atoms in molecule (QTAIM) has been applied to gain deep understanding to the existence of intra- and inter-molecular interaction.

  1. Rotational quenching of H 2CO by molecular hydrogen - Suggestion on the work of Wiesenfeld & Faure

    Science.gov (United States)

    Sharma, Mohit Kumar; Sharma, Monika; Chandra, Suresh

    2017-01-01

    Wiesenfeld and Faure investigated rotational quenching of H 2CO by molecular hydrogen where they considered 40 rotational levels of o-H 2CO and 41 rotational levels of p-H 2CO. Data on energies of rotational levels of the molecule are fundamental in the investigation. We have found that the sequence of levels reported by Wiesenfeld and Faure is not as per convention of molecular physics. Their results are also available on the website: http://www.home.strw.leidenuniv.nl/ moldata/datafiles/ph2co-h2.dat, where the collisional transitions are shown even between the levels having equal energies. Data for such transitions should not be there.

  2. From ab initio quantum chemistry to molecular dynamics: The delicate case of hydrogen bonding in ammonia

    CERN Document Server

    Boese, A D; Martin, J M L; Marx, D; Chandra, Amalendu; Martin, Jan M.L.; Marx, Dominik

    2003-01-01

    The ammonia dimer (NH3)2 has been investigated using high--level ab initio quantum chemistry methods and density functional theory (DFT). The structure and energetics of important isomers is obtained to unprecedented accuracy without resorting to experiment. The global minimum of eclipsed C_s symmetry is characterized by a significantly bent hydrogen bond which deviates from linearity by about 20 degrees. In addition, the so-called cyclic C_{2h} structure is extremely close in energy on an overall flat potential energy surface. It is demonstrated that none of the currently available (GGA, meta--GGA, and hybrid) density functionals satisfactorily describe the structure and relative energies of this nonlinear hydrogen bond. We present a novel density functional, HCTH/407+, designed to describe this sort of hydrogen bond quantitatively on the level of the dimer, contrary to e.g. the widely used BLYP functional. This improved functional is employed in Car-Parrinello ab initio molecular dynamics simulations of liq...

  3. Molecular structure of hydrazoic acid with hydrogen-bonded tetramers in nearly planar layers.

    Science.gov (United States)

    Evers, Jürgen; Göbel, Michael; Krumm, Burkhard; Martin, Franz; Medvedyev, Sergey; Oehlinger, Gilbert; Steemann, Franz Xaver; Troyan, Ivan; Klapötke, Thomas M; Eremets, Mikhail I

    2011-08-10

    Hydrazoic acid (HN(3))--potentially explosive, highly toxic, and very hygroscopic--is the simplest covalent azide and contains 97.7 wt % nitrogen. Although its molecular structure was established decades ago, its crystal structure has now been solved by X-ray diffraction for the first time. Molecules of HN(3) are connected to each other by hydrogen bonds in nearly planar layers parallel to (001) with stacking sequence A, B, ... The layer distance, at 2.950(1) Å, is shorter than that in 2H-graphite [3.355(2) Å]. The hydrogen bonds N-H···N are of great interest, since the azido group consists of three homonuclear atoms with identical electronegativity, but different formal charges. These hydrogen bonds are bifurcated into moderate ones with ≈2.0 Å and into weak ones with ≈2.6 Å. The moderate ones build up tetramers (HN(3))(4) in a nearly planar net of eight-membered rings. To the best of our knowledge, such a network of tetramers of a simple molecule is unique.

  4. Ab initio path-integral molecular dynamics and the quantum nature of hydrogen bonds

    Science.gov (United States)

    Yexin, Feng; Ji, Chen; Xin-Zheng, Li; Enge, Wang

    2016-01-01

    The hydrogen bond (HB) is an important type of intermolecular interaction, which is generally weak, ubiquitous, and essential to life on earth. The small mass of hydrogen means that many properties of HBs are quantum mechanical in nature. In recent years, because of the development of computer simulation methods and computational power, the influence of nuclear quantum effects (NQEs) on the structural and energetic properties of some hydrogen bonded systems has been intensively studied. Here, we present a review of these studies by focussing on the explanation of the principles underlying the simulation methods, i.e., the ab initio path-integral molecular dynamics. Its extension in combination with the thermodynamic integration method for the calculation of free energies will also be introduced. We use two examples to show how this influence of NQEs in realistic systems is simulated in practice. Project supported by the National Natural Science Foundation of China (Grant Nos. 11275008, 91021007, and 10974012) and the China Postdoctoral Science Foundation (Grant No. 2014M550005).

  5. Evaluation of molecular assembly, spectroscopic interpretation, intra-/inter molecular hydrogen bonding and chemical reactivity of two pyrrole precursors

    Science.gov (United States)

    Rawat, Poonam; Singh, R. N.

    2014-10-01

    This paper describes the evaluation of conformational, spectroscopic, hydrogen bonding and chemical reactivity of pyrrole precursor: ethyl 3,5 dimethyl-1H-pyrrole-2-carboxylate (EDPC) and ethyl 3,4-dimethyl-4-acetyl-1H-pyrrole-2-carboxylate (EDAPC) for the convenient characterization, synthetic usefulness and comparative evaluations. All experimental spectral values of 1H NMR, UV-Vis and FT-IR spectra coincide well with calculated values by DFT. The orbital interactions in EDPC and EDAPC are found to lengthen their Nsbnd H and Cdbnd O bonds and lowers their vibrational frequencies (red shift) resulting to dimer formation. The QTAIM and NBO analyses provide the strength of interactions and charge transfer in the hydrogen bonding unit and stability of dimers. The binding energy of EDPC and EDPAC dimer are found to be 9.92, 10.22 kcal/mol, respectively. In EDPAC and EDPC dimer, hyperconjugative interactions between monomer units is due to n1(O) → σ*(Nsbnd H) that stabilize the molecule up to 9.7 and 9.3 kcal/mol, respectively. On evaluation of molecular electrostatic potential (MEP) and electronic descriptors for EDPC it has been found that it is a good precursor for synthesis of formyl and acetyl derivatives whereas EDAPC has been found to be a good precursor for synthesis of schiff base, hydrazones, hydrazide-hydrazones and chalcones.

  6. Enhanced Photochemical Hydrogen Production by a Molecular Diiron Catalyst Incorporated into a Metal-Organic Framework

    Energy Technology Data Exchange (ETDEWEB)

    Pullen, Sonja; Fei, Honghan; Orthaber, Andreas; Cohen, Seth M.; Ott, Sascha [Uppsala; (UCSD)

    2013-12-04

    A molecular proton reduction catalyst [FeFe](dcbdt)(CO)6 (1, dcbdt = 1,4-dicarboxylbenzene-2,3-dithiolate) with structural similarities to [FeFe]-hydrogenase active sites has been incorporated into a highly robust Zr(IV)-based metal–organic framework (MOF) by postsynthetic exchange (PSE). The PSE protocol is crucial as direct solvothermal synthesis fails to produce the functionalized MOF. The molecular integrity of the organometallic site within the MOF is demonstrated by a variety of techniques, including X-ray absorption spectroscopy. In conjunction with [Ru(bpy)3]2+ as a photosensitizer and ascorbate as an electron donor, MOF-[FeFe](dcbdt)(CO)6 catalyzes photochemical hydrogen evolution in water at pH 5. The immobilized catalyst shows substantially improved initial rates and overall hydrogen production when compared to a reference system of complex 1 in solution. Improved catalytic performance is ascribed to structural stabilization of the complex when incorporated in the MOF as well as the protection of reduced catalysts 1 and 12– from undesirable charge recombination with oxidized ascorbate.

  7. Molecular Hydrogen in Diffuse Interstellar Clouds of Arbitrary Three-Dimensional Geometry

    CERN Document Server

    Spaans, M; Spaans, Marco; Neufeld, David A.

    1997-01-01

    We have constructed three-dimensional models for the equilibrium abundance of molecular hydrogen within diffuse interstellar clouds of arbitrary geometry that are illuminated by ultraviolet radiation. The position-dependent photo- dissociation rate of H$_2$ within such clouds was computed using a 26-ray approximation to model the attenuation of the incident ultraviolet radiation field by dust and by H$_2$ line absorption. We have applied our modeling technique to the isolated diffuse cloud G236+39, assuming that the cloud has a constant density and that the thickness of the cloud along the line of sight is at every point proportional to the 100 um continuum intensity measured by IRAS. We find that our model can successfully account for observed variations in the ratio of 100 umu continuum intensity to HI column density, with larger values of that ratio occurring along lines of sight in which the molecular hydrogen fraction is expected to be largest. Using a standard chi^2 analysis to assess the goodness of fi...

  8. The relation between mid-plane pressure and molecular hydrogen in galaxies: Environmental dependence

    CERN Document Server

    Feldmann, Robert; Gnedin, Nickolay Y

    2012-01-01

    Molecular hydrogen (H2) is the primary component of the reservoirs of cold, dense gas that fuel star formation in our galaxy. While the H2 abundance is ultimately regulated by physical processes operating on small scales in the interstellar medium (ISM), observations have revealed a tight correlation between the ratio of molecular to atomic hydrogen in nearby spiral galaxies and the pressure in the mid-plane of their disks. This empirical relation has been used to predict H2 abundances in galaxies with potentially very different ISM conditions, such as metal-deficient galaxies at high redshifts. Here, we test the validity of this approach by studying the dependence of the pressure -- H2 relation on environmental parameters of the ISM. To this end, we follow the formation and destruction of H2 explicitly in a suite of hydrodynamical simulations of galaxies with different ISM parameters. We find that a pressure -- H2 relation arises naturally in our simulations for a variety of dust-to-gas ratios or strengths o...

  9. Enhanced photochemical hydrogen production by a molecular diiron catalyst incorporated into a metal-organic framework.

    Science.gov (United States)

    Pullen, Sonja; Fei, Honghan; Orthaber, Andreas; Cohen, Seth M; Ott, Sascha

    2013-11-13

    A molecular proton reduction catalyst [FeFe](dcbdt)(CO)6 (1, dcbdt = 1,4-dicarboxylbenzene-2,3-dithiolate) with structural similarities to [FeFe]-hydrogenase active sites has been incorporated into a highly robust Zr(IV)-based metal-organic framework (MOF) by postsynthetic exchange (PSE). The PSE protocol is crucial as direct solvothermal synthesis fails to produce the functionalized MOF. The molecular integrity of the organometallic site within the MOF is demonstrated by a variety of techniques, including X-ray absorption spectroscopy. In conjunction with [Ru(bpy)3](2+) as a photosensitizer and ascorbate as an electron donor, MOF-[FeFe](dcbdt)(CO)6 catalyzes photochemical hydrogen evolution in water at pH 5. The immobilized catalyst shows substantially improved initial rates and overall hydrogen production when compared to a reference system of complex 1 in solution. Improved catalytic performance is ascribed to structural stabilization of the complex when incorporated in the MOF as well as the protection of reduced catalysts 1(-) and 1(2-) from undesirable charge recombination with oxidized ascorbate.

  10. Preventive and therapeutic application of molecular hydrogen in situations with excessive production of free radicals.

    Science.gov (United States)

    Slezák, J; Kura, B; Frimmel, K; Zálešák, M; Ravingerová, T; Viczenczová, C; Okruhlicová, Ľ; Tribulová, N

    2016-09-19

    Excessive production of oxygen free radicals has been regarded as a causative common denominator of many pathological processes in the animal kingdom. Hydroxyl and nitrosyl radicals represent the major cause of the destruction of biomolecules either by a direct reaction or by triggering a chain reaction of free radicals. Scavenging of free radicals may act preventively or therapeutically. A number of substances that preferentially react with free radicals can serve as scavengers, thus increasing the internal capacity/activity of endogenous antioxidants and protecting cells and tissues against oxidative damage. Molecular hydrogen (H(2)) reacts with strong oxidants, such as hydroxyl and nitrosyl radicals, in the cells, that enables utilization of its potential for preventive and therapeutic applications. H(2) rapidly diffuses into tissues and cells without affecting metabolic redox reactions and signaling reactive species. H(2) reduces oxidative stress also by regulating gene expression, and functions as an anti-inflammatory and anti-apoptotic agent. There is a growing body of evidence based on the results of animal experiments and clinical observations that H(2) may represent an effective antioxidant for the prevention of oxidative stress-related diseases. Application of molecular hydrogen in situations with excessive production of free radicals, in particular, hydroxyl and nitrosyl radicals is relatively simple and effective, therefore, it deserves special attention.

  11. A molecular dynamics study of guest-host hydrogen bonding in alcohol clathrate hydrates.

    Science.gov (United States)

    Hiratsuka, Masaki; Ohmura, Ryo; Sum, Amadeu K; Alavi, Saman; Yasuoka, Kenji

    2015-05-21

    Clathrate hydrates are typically stabilized by suitably sized hydrophobic guest molecules. However, it has been experimentally reported that isomers of amyl-alcohol C5H11OH can be enclosed into the 5(12)6(4) cages in structure II (sII) clathrate hydrates, even though the effective radii of the molecules are larger than the van der Waals radii of the cages. To reveal the mechanism of the anomalous enclathration of hydrophilic molecules, we performed ab initio and classical molecular dynamics simulations (MD) and analyzed the structure and dynamics of a guest-host hydrogen bond for sII 3-methyl-1-butanol and structure H (sH) 2-methyl-2-butanol clathrate hydrates. The simulations clearly showed the formation of guest-host hydrogen bonds and the incorporation of the O-H group of 3-methyl-1-butanol guest molecules into the framework of the sII 5(12)6(4) cages, with the remaining hydrophobic part of the amyl-alcohol molecule well accommodated into the cages. The calculated vibrational spectra of alcohol O-H bonds showed large frequency shifts due to the strong guest-host hydrogen bonding. The 2-methyl-2-butanol guests form strong hydrogen bonds with the cage water molecules in the sH clathrate, but are not incorporated into the water framework. By comparing the structures of the alcohols in the hydrate phases, the effect of the location of O-H groups in the butyl chain of the guest molecules on the crystalline structure of the clathrate hydrates is indicated.

  12. Intramolecular hydrogen bond, molecular structure and vibrational assignment of tetra-acetylethane. A density functional study.

    Science.gov (United States)

    Raissi, Heidar; Nowroozi, Alireza; Mohammdi, Reza; Hakimi, Mohammad

    2006-11-01

    The intramolecular hydrogen bond, molecular structure and vibrational frequencies of tetra-acetylethane have been investigated by means of high-level density functional theory (DFT) methods with most popular basis sets. Fourier transform infrared and Fourier transform Raman spectra of this compound and its deuterated analogue were recorded in the regions 400-4000 cm(-1) and 40-4000 cm(-1), respectively. The calculated geometrical parameters of tetra-acetylethane were compared to the experimental results of this compound and its parent molecule (acetylacetone), obtained from X-ray diffraction. The O...O distance in tetra-acetylethane, about 2.424A, suggests that the hydrogen bond in this compound is stronger than acetylacetone. This conclusion is well supported by the NMR proton chemical shifts and O-H stretching mode at 2626 cm(-1). Furthermore, the calculated hydrogen bond energy in the title compound is 17.22 kcal/mol, which is greater than the acetylacetone value. On the other hand, the results of theoretical calculations show that the bulky substitution in alpha-position of acetylacetone results in an increase of the conjugation of pi electrons in the chelate ring. Finally, we applied the atoms in molecules (AIM) theory and natural bond orbital method (NBO) for detail analyzing the hydrogen bond in tetra-acetylethane and acetylacetone. These results are in agreement with the vibrational spectra interpretation and quantum chemical calculation results. Also, the conformations of methyl groups with respect to the plane of the molecule and with respect to each other were investigated.

  13. On the Relationship Between Molecular Hydrogen and Carbon Monoxide Abundances in Molecular Clouds

    CERN Document Server

    Glover, S C O

    2010-01-01

    The most usual tracer of molecular gas is line emission from CO. However, the reliability of that tracer has long been questioned in environments different from the Milky Way. We study the relationship between H2 and CO abundances using a fully dynamical model of magnetized turbulence coupled to a chemical network simplified to follow only the dominant pathways for H2 and CO formation and destruction, and including photodissociation using a six-ray approximation. We find that the abundance of H2 is primarily determined by the amount of time available for its formation, which is proportional to the product of the density and the metallicity, but insensitive to photodissociation. Photodissociation only becomes important at extinctions under a few tenths of a visual magnitude, in agreement with both observational and prior theoretical work. On the other hand, CO forms quickly, within a dynamical time, but its abundance depends primarily on photodissociation, with only a weak secondary dependence on H2 abundance....

  14. Measurement of atomic and molecular hydrogen in a tandem magnetic multicusp H sup minus ion source by VUV spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Young, A.T.; Stutzin, G.C.; Chen, P.; Kunkel, W.B.; Leung, K.N. (Lawrence Berkeley Laboratory, University of California, Berkeley, California 94720 (United States))

    1992-04-01

    The populations of ground electronic state atomic hydrogen and ground electronic state, vibrationally--rotationally excited hydrogen molecule in a negative hydrogen ion source discharge have been measured using vacuum ultraviolet (VUV) laser absorption spectroscopy. These populations have been measured under a variety of discharge conditions in two different regions of a tandem chamber ion source. Preliminary results of the measurements in the driver region and filter region are given. It is observed that the atomic hydrogen density decreases as one goes from the driver to the filter region. This indicates that the surfaces directly adjacent to the filter region are net sinks for hydrogen atoms. In contrast, the molecular vibrational population distribution shows only a small difference between the two regions, indicating that these surfaces are not net sinks for the excited molecules.

  15. An integral equation and simulation study of hydrogen inclusions in a molecular crystal of short-capped nanotubes

    Science.gov (United States)

    Lomba, Enrique; Bores, Cecilia; Notario, Rafael; Sánchez-Gil, V.

    2016-09-01

    In this work we have assessed the ability of a recently proposed three-dimensional integral equation approach to describe the explicit spatial distribution of molecular hydrogen confined in a crystal formed by short-capped nanotubes of C50 H10. To that aim we have resorted to extensive molecular simulation calculations whose results have been compared with our three-dimensional integral equation approximation. We have first tested the ability of a single C50 H10 nanocage for the encapsulation of H2 by means of molecular dynamics simulations, in particular using targeted molecular dynamics to estimate the binding Gibbs energy of a host hydrogen molecule inside the nanocage. Then, we have investigated the adsorption isotherm of the nanocage crystal using grand canonical Monte Carlo simulations in order to evaluate the maximum load of molecular hydrogen. For a packing close to the maximum load explicit hydrogen density maps and density profiles have been determined using molecular dynamics simulations and the three-dimensional Ornstein-Zernike equation with a hypernetted chain closure. In these conditions of extremely tight confinement the theoretical approach has shown to be able to reproduce the three-dimensional structure of the adsorbed fluid with accuracy down to the finest details.

  16. A Comprehensive Study of Hydrogen Adsorbing to Amorphous Water-Ice: Defining Adsorption in Classical Molecular Dynamics

    CERN Document Server

    Dupuy, John L; Stancil, P C

    2016-01-01

    Gas-grain and gas-phase reactions dominate the formation of molecules in the interstellar medium (ISM). Gas-grain reactions require a substrate (e.g. a dust or ice grain) on which the reaction is able to occur. The formation of molecular hydrogen (H$_2$) in the ISM is the prototypical example of a gas-grain reaction. In these reactions, an atom of hydrogen will strike a surface, stick to it, and diffuse across it. When it encounters another adsorbed hydrogen atom, the two can react to form molecular hydrogen and then be ejected from the surface by the energy released in the reaction. We perform in-depth classical molecular dynamics (MD) simulations of hydrogen atoms interacting with an amorphous water-ice surface. This study focuses on the first step in the formation process; the sticking of the hydrogen atom to the substrate. We find that careful attention must be paid in dealing with the ambiguities in defining a sticking event. The technical definition of a sticking event will affect the computed sticking ...

  17. VizieR Online Data Catalog: Hydrogen in diffuse molecular clouds (Winkel+, 2017)

    Science.gov (United States)

    Winkel, B.; Wiesemeyer, H.; Menten, K. M.; Sato, M.; Brunthaler, A.; Wyrowski, F.; Neufeld, D.; Gerin, M.; Indriolo, N.

    2017-01-01

    To study the Hydrogen in diffuse molecular clouds in the Milky Way, eight sources were observed with the Jansky Very Large Array in spectral line mode at 21-cm. The targets have bright continuum emission and were used as background sources for HI absorption spectroscopy. The brightest positions in the background continuum images were used to define several sight lines per source and to extract associated HI absorption spectra. To obtain spin temperatures and corrected HI column densities, suitable Off-position spectra were acquired, making use of the three Galactic plane surveys: Canadian Galactic Plane Survey (CGPS, Taylor et al., 2003AJ....125.3145T), Southern Galactic Plane Survey (SGPS, McClure-Griffiths et al., 2005ApJS..158..178M), and VLA Galactic Plane Survey (VGPS, Stil et al., 2006AJ....132.1158S). Furthermore, for some of the sight lines 550-GHz HF spectra are available, observed with the Herschel space telescope. With these, the molecular hydrogen column density can be estimated, and in combination with the HI column densities, the molecular fraction is determined. The calculation of all result spectra was done with Bayesian Markov-Chain Monte Carlo using the Python PyMC3 framework (Patil, Huard, and Fonnesbeck, DOI: 10.18637/jss.v035.i04). In the FITS binary tables, provided here, the results of our Bayes sampling are contained. For each sight line, we provide seven spectra per quantity (i.e, the -3, -2, -1, 0, 1, 2, and 3 confidence levels) plus the full Bayes chains (1000 steps) for the following variables: Tcsou, Tcbg, tau, Tspin, NHI, NH2, and F{H2/H}, because the latter are not Normal distributed. (3 data files).

  18. Herschel SPIRE-FTS Observations of Excited CO and [CI] in the Antennae (NGC 4038/39): Warm and Cold Molecular Gas

    CERN Document Server

    Schirm, Maximilien R P; Parkin, Tara J; Kamenetzky, Julia; Glenn, Jason; Rangwala, Naseem; Spinoglio, Luigi; Pereira-Santaella, Miguel; Baes, Maarten; Barlow, Michael J; Clements, Dave L; Cooray, Asantha; De Looze, Ilse; Karczewski, Oskar Ł; Madden, Suzanne C; Rémy-Ruyer, Aurélie; Wu, Ronin

    2013-01-01

    We present Herschel SPIRE-FTS observations of the Antennae (NGC 4038/39), a well studied, nearby ($22$ Mpc) ongoing merger between two gas rich spiral galaxies. We detect 5 CO transitions ($J=4-3$ to $J=8-7$), both [CI] transitions and the [NII]$205\\mu m$ transition across the entire system, which we supplement with ground based observations of the CO $J=1-0$, $J=2-1$ and $J=3-2$ transitions, and Herschel PACS observations of [CII] and [OI]$63\\mu m$. Using the CO and [CI] transitions, we perform both a LTE analysis of [CI], and a non-LTE radiative transfer analysis of CO and [CI] using the radiative transfer code RADEX along with a Bayesian likelihood analysis. We find that there are two components to the molecular gas: a cold ($T_{kin}\\sim 10-30$ K) and a warm ($T_{kin} \\gtrsim 100$ K) component. By comparing the warm gas mass to previously observed values, we determine a CO abundance in the warm gas of $x_{CO} \\sim 5\\times 10^{-5}$. If the CO abundance is the same in the warm and cold gas phases, this abund...

  19. Rovibrationally Resolved Time-Dependent Collisional-Radiative Model of Molecular Hydrogen and Its Application to a Fusion Detached Plasma

    Directory of Open Access Journals (Sweden)

    Keiji Sawada

    2016-12-01

    Full Text Available A novel rovibrationally resolved collisional-radiative model of molecular hydrogen that includes 4,133 rovibrational levels for electronic states whose united atom principal quantum number is below six is developed. The rovibrational X 1 Σ g + population distribution in a SlimCS fusion demo detached divertor plasma is investigated by solving the model time dependently with an initial 300 K Boltzmann distribution. The effective reaction rate coefficients of molecular assisted recombination and of other processes in which atomic hydrogen is produced are calculated using the obtained time-dependent population distribution.

  20. Discovery of Novel Complex Metal Hydrides for Hydrogen Storage through Molecular Modeling and Combinatorial Methods

    Energy Technology Data Exchange (ETDEWEB)

    Lesch, David A; Adriaan Sachtler, J.W. J.; Low, John J; Jensen, Craig M; Ozolins, Vidvuds; Siegel, Don; Harmon, Laurel

    2011-02-14

    UOP LLC, a Honeywell Company, Ford Motor Company, and Striatus, Inc., collaborated with Professor Craig Jensen of the University of Hawaii and Professor Vidvuds Ozolins of University of California, Los Angeles on a multi-year cost-shared program to discover novel complex metal hydrides for hydrogen storage. This innovative program combined sophisticated molecular modeling with high throughput combinatorial experiments to maximize the probability of identifying commercially relevant, economical hydrogen storage materials with broad application. A set of tools was developed to pursue the medium throughput (MT) and high throughput (HT) combinatorial exploratory investigation of novel complex metal hydrides for hydrogen storage. The assay programs consisted of monitoring hydrogen evolution as a function of temperature. This project also incorporated theoretical methods to help select candidate materials families for testing. The Virtual High Throughput Screening served as a virtual laboratory, calculating structures and their properties. First Principles calculations were applied to various systems to examine hydrogen storage reaction pathways and the associated thermodynamics. The experimental program began with the validation of the MT assay tool with NaAlH4/0.02 mole Ti, the state of the art hydrogen storage system given by decomposition of sodium alanate to sodium hydride, aluminum metal, and hydrogen. Once certified, a combinatorial 21-point study of the NaAlH4 LiAlH4Mg(AlH4)2 phase diagram was investigated with the MT assay. Stability proved to be a problem as many of the materials decomposed during synthesis, altering the expected assay results. This resulted in repeating the entire experiment with a mild milling approach, which only temporarily increased capacity. NaAlH4 was the best performer in both studies and no new mixed alanates were observed, a result consistent with the VHTS. Powder XRD suggested that the reverse reaction, the regeneration of the

  1. Discovery of Novel Complex Metal Hydrides for Hydrogen Storage through Molecular Modeling and Combinatorial Methods

    Energy Technology Data Exchange (ETDEWEB)

    Lesch, David A; Adriaan Sachtler, J.W. J.; Low, John J; Jensen, Craig M; Ozolins, Vidvuds; Siegel, Don; Harmon, Laurel

    2011-02-14

    UOP LLC, a Honeywell Company, Ford Motor Company, and Striatus, Inc., collaborated with Professor Craig Jensen of the University of Hawaii and Professor Vidvuds Ozolins of University of California, Los Angeles on a multi-year cost-shared program to discover novel complex metal hydrides for hydrogen storage. This innovative program combined sophisticated molecular modeling with high throughput combinatorial experiments to maximize the probability of identifying commercially relevant, economical hydrogen storage materials with broad application. A set of tools was developed to pursue the medium throughput (MT) and high throughput (HT) combinatorial exploratory investigation of novel complex metal hydrides for hydrogen storage. The assay programs consisted of monitoring hydrogen evolution as a function of temperature. This project also incorporated theoretical methods to help select candidate materials families for testing. The Virtual High Throughput Screening served as a virtual laboratory, calculating structures and their properties. First Principles calculations were applied to various systems to examine hydrogen storage reaction pathways and the associated thermodynamics. The experimental program began with the validation of the MT assay tool with NaAlH4/0.02 mole Ti, the state of the art hydrogen storage system given by decomposition of sodium alanate to sodium hydride, aluminum metal, and hydrogen. Once certified, a combinatorial 21-point study of the NaAlH4 LiAlH4Mg(AlH4)2 phase diagram was investigated with the MT assay. Stability proved to be a problem as many of the materials decomposed during synthesis, altering the expected assay results. This resulted in repeating the entire experiment with a mild milling approach, which only temporarily increased capacity. NaAlH4 was the best performer in both studies and no new mixed alanates were observed, a result consistent with the VHTS. Powder XRD suggested that the reverse reaction, the regeneration of the

  2. Structural and dynamical properties of hydrogen fluoride in aqueous solution: an ab initio quantum mechanical charge field molecular dynamics simulation.

    Science.gov (United States)

    Kritayakornupong, Chinapong; Vchirawongkwin, Viwat; Hofer, Thomas S; Rode, Bernd M

    2008-09-25

    The novel ab initio quantum mechanical charge field (QMCF) molecular dynamics simulation at the Hartree-Fock level has been employed to investigate hydration structure and dynamics of hydrogen fluoride in aqueous solution. The average H-F bond length of 0.93 A obtained from the QMCF MD simulation is in good agreement with the experimental data. The HHF...Ow distance of 1.62 A was evaluated for the first hydration shell, and 2.00 A was observed for the FHF...Hw distance. The stability of hydrogen bonding is more pronounced in the hydrogen site of hydrogen fluoride, with a single water molecule in this part of the first hydration shell. A wide range of coordination numbers between 3 and 9 with an average value of 5.6 was obtained for the fluorine site. The force constants of 819.1 and 5.9 N/m were obtained for the HHF-FHF and HHF...Ow interactions, respectively, proving the stability of the nondissociated form of hydrogen fluoride in aqueous solution. The mean residence times of 2.1 and 2.5 ps were determined for ligand exchange processes in the neighborhood of fluorine and hydrogen atoms of hydrogen fluoride, respectively, indicating a weak structure-making effect of hydrogen fluoride in water. The corresponding H-bond lifetimes attribute this effect to the H atom site of HF.

  3. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

    Science.gov (United States)

    Pyzer-Knapp, Edward O.; Thompson, Hugh P. G.; Day, Graeme M.

    2016-01-01

    We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%. PMID:27484370

  4. Fabrication variables affecting the structure and properties of supported carbon molecular sieve membranes for hydrogen separation

    KAUST Repository

    Briceño, Kelly

    2012-10-01

    A high molecular weight polyimide (Matrimid) was used as a precursor for fabricating supported carbon molecular sieve membranes without crack formation at 550-700°C pyrolysis temperature. A one-step polymer (polyimide) coating method as precursor of carbon layer was used without needing a prior modification of a TiO 2 macroporous support. The following fabrication variables were optimized and studied to determine their effect on the carbon structure: polymeric solution concentration, solvent extraction, heating rate and pyrolysis temperature. Two techniques (Thermogravimetric analysis and Raman spectroscopy) were used to determine these effects on final carbon structure. Likewise, the effect of the support was also reported as an additional and important variable in the design of supported carbon membranes. Atomic force microscopy and differential scanning calorimetry quantified the degree of influence. Pure gas permeation tests were performed using CH 4, CO, CO 2 and H 2. The presence of a molecular sieving mechanism was confirmed after defects were plugged with PDMS solution at 12wt%. Gas selectivities higher than Knudsen theoretical values were reached with membranes obtained over 650°C, showing as best values 4.46, 4.70 and 10.62 for H 2/N 2, H 2/CO and H 2/CH 4 ratio, respectively. Permeance values were over 9.82×10 -9mol/(m 2Pas)during pure hydrogen permeation tests. © 2012 Elsevier B.V.

  5. Detection of molecular hydrogen at z=1.15 toward HE 0515-4414

    CERN Document Server

    Reimers, D; Quast, R; Levshakov, S A

    2003-01-01

    A new molecular hydrogen cloud is found in the sub-damped Ly-alpha absorber [log N(HI)=19.88+/-0.05] at the redshift z=1.15 toward the bright quasar HE0515-4414 (zem = 1.71). More than 30 absorption features in the Lyman band system of H2 are identified in the UV spectrum of this quasar obtained with the Space Telescope Imaging Spectrograph (STIS) aboard the Hubble Space Telescope. The H2-bearing cloud shows a total H2 column density N(H2)=(8.7^{+8.7}_-{4.0}) 10^16 cm^-2, and a fractional molecular abundance f(H2)=(2.3^{+2.3}_{-1.1}) 10^-3 derived from the H2 lines arising from the J=0-5 rotational levels of the ground electronic vibrational state. The estimated rate of photodissociation at the cloud edge I_0<=1.8 10^{-8} s^-1 is much higher than the mean Galactic disk value, I_MW~=5.5 10^{-11} s^-1. This may indicate an enhanced star-formation activity in the z=1.15 system as compared with molecular clouds at z~=3 where I~=I_MW. We also find a tentative evidence that the formation rate coefficient of H2 u...

  6. Maternal molecular hydrogen administration ameliorates rat fetal hippocampal damage caused by in utero ischemia-reperfusion.

    Science.gov (United States)

    Mano, Yukio; Kotani, Tomomi; Ito, Mikako; Nagai, Taku; Ichinohashi, Yuko; Yamada, Kiyofumi; Ohno, Kinji; Kikkawa, Fumitaka; Toyokuni, Shinya

    2014-04-01

    Molecular hydrogen (H2) scavenges hydroxyl radicals. Recently, H2 has been reported to prevent a variety of diseases associated with oxidative stress in model systems and in humans. Here, we studied the effects of H2 on rat fetal hippocampal damage caused by ischemia and reperfusion (IR) on day 16 of pregnancy with the transient occlusion of the bilateral utero-ovarian arteries. Starting 2 days before the operation, we provided the mothers with hydrogen-saturated water ad libitum until vaginal delivery. We observed a significant increase in the concentration of H2 in the placenta after the oral administration of hydrogen-saturated water to the mothers, with less placental oxidative damage after IR in the presence of H2. Neonatal growth retardation was observed in the IR group, which was alleviated by the H2 administration. We analyzed the neuronal cell damage in the CA1 and CA3 areas of the hippocampus at day 7 after birth by immunohistochemical analysis of the 8-oxo-7,8-dihydro-2׳-deoxyguanosine- and 4-hydroxy-2-nonenal-modified proteins. Both oxidative stress markers were significantly increased in the IR group, which was again ameliorated by the H2 intake. Last, 8-week-old rats were subjected to a Morris water maze test. Maternal H2 administration improved the reference memory of the offspring to the sham level after IR injury during pregnancy. Overall, the present results support the idea that maternal H2 intake helps prevent the hippocampal impairment of offspring induced by IR during pregnancy. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. A Far-ultraviolet Fluorescent Molecular Hydrogen Emission Map of the Milky Way Galaxy

    Science.gov (United States)

    Jo, Young-Soo; Seon, Kwang-Il; Min, Kyoung-Wook; Edelstein, Jerry; Han, Wonyong

    2017-08-01

    We present the far-ultraviolet (FUV) fluorescent molecular hydrogen (H2) emission map of the Milky Way Galaxy obtained with FIMS/SPEAR covering ˜76% of the sky. The extinction-corrected intensity of the fluorescent H2 emission has a strong linear correlation with the well-known tracers of the cold interstellar medium (ISM), including color excess E(B-V), neutral hydrogen column density N(H i), and Hα emission. The all-sky H2 column density map was also obtained using a simple photodissociation region model and interstellar radiation fields derived from UV star catalogs. We estimated the fraction of H2 (f H2) and the gas-to-dust ratio (GDR) of the diffuse ISM. The f H2 gradually increases from <1% at optically thin regions where E(B-V) < 0.1 to ˜50% for E(B-V) = 3. The estimated GDR is ˜5.1 × 1021 atoms cm-2 mag-1, in agreement with the standard value of 5.8 × 1021 atoms cm-2 mag-1.

  8. H2 formation on PAHs in photodissociation regions: a high-temperature pathway to molecular hydrogen

    CERN Document Server

    Boschman, Leon; Spaans, Marco; Hoekstra, Ronnie; Schlathölter, Thomas

    2015-01-01

    Molecular hydrogen is the most abundant molecule in the Universe. It is thought that a large portion of H2 forms by association of hydrogen atoms to polycyclic aromatic hydrocarbons (PAHs). We model the influence of PAHs on total H2 formation rates in photodissociation regions (PDRs) and assess the effect of these formation rates on the total cloud structure. We set up a chemical kinetic model at steady state in a PDR environment and included adiative transfer to calculate the chemistry at different depths in the PDR. This model includes known dust grain chemistry for the formation of H2 and a H2 formation mechanism on PAHs. Since H2 formation on PAHs is impeded by thermal barriers, this pathway is only efficient at higher temperatures (T > 200 K). At these temperatures the conventional route of H2 formation via H atoms physisorbed on dust grains is no longer feasible, so the PAH mechanism enlarges the region where H2 formation is possible. We find that PAHs have a significant influence on the structure of PD...

  9. Molecular metal-Nx centres in porous carbon for electrocatalytic hydrogen evolution.

    Science.gov (United States)

    Liang, Hai-Wei; Brüller, Sebastian; Dong, Renhao; Zhang, Jian; Feng, Xinliang; Müllen, Klaus

    2015-08-07

    Replacement of precious platinum with efficient and low-cost catalysts for electrocatalytic hydrogen evolution at low overpotentials holds tremendous promise for clean energy devices. Here we report a novel type of robust cobalt-nitrogen/carbon catalyst for the hydrogen evolution reaction (HER) that is prepared by the pyrolysis of cobalt-N4 macrocycles or cobalt/o-phenylenediamine composites and using silica colloids as a hard template. We identify the well-dispersed molecular CoNx sites on the carbon support as the active sites responsible for the HER. The CoNx/C catalyst exhibits extremely high turnover frequencies per cobalt site in acids, for example, 0.39 and 6.5 s(-1) at an overpotential of 100 and 200 mV, respectively, which are higher than those reported for other scalable non-precious metal HER catalysts. Our results suggest the great promise of developing new families of non-precious metal HER catalysts based on the controlled conversion of homogeneous metal complexes into solid-state carbon catalysts via economically scalable protocols.

  10. Molecular hydrogen attenuates hypoxia/reoxygenation injury of intrahepatic cholangiocytes by activating Nrf2 expression.

    Science.gov (United States)

    Yu, Jianhua; Zhang, Weiguang; Zhang, Rongguo; Jiang, Guixing; Tang, Haijun; Ruan, Xinxian; Ren, Peitu; Lu, Baochun

    2015-11-01

    Hypoxia/reoxygenation (H/R) injury of cholangiocytes causes serious biliary complications during hepatobiliary surgeries. Molecular hydrogen (H2) has been shown to be effective in protecting various cells and organs against oxidative stress injury. Human liver cholangiocytes were used to determine the potential protective effects of hydrogen against cholangiocyte H/R injury and explore the underlying mechanisms. We found that H2 ameliorated H/R-induced cholangiocytes apoptosis. Our study revealed that H2 activated NF-E2-related factor 2 (Nrf2) and downstream cytoprotective protein expression. However, the protective function of H2 was abolished when Nrf2 was silenced. Apoptosis in cholangiocytes isolated from a rat model of liver ischemia/reperfusion injury indicated that H2 significantly attenuates ischemia/reperfusion cholangiocyte injury in vivo. In conclusion, our study shows that H2 protects intrahepatic cholangiocytes from hypoxia/reoxygenation-induced apoptosis in vitro or in vivo, and this phenomenon may depend on activating Nrf2 expression.

  11. On the dissociative electron attachment as a potential source of molecular hydrogen in irradiated liquid water

    Energy Technology Data Exchange (ETDEWEB)

    Cobut, V.; Jay-Gerin, J.-P.; Frongillo, Y. [Sherbrooke Univ., PQ (Canada). Faculte de Medecine; Patau, J.P. [Toulouse-3 Univ., 31 (France)

    1996-02-01

    In the radiolysis of liquid water, different mechanisms for the formation of molecular hydrogen (H{sub 2}) are involved at different times after the initial energy disposition. It has been suggested that the contributions of the e{sub aq}{sup -} + e{sub aq}{sup -}, H + e{sub aq}{sup -} and H + H reactions between hydrated electrons (e{sub aq}{sup -}) and hydrogen atoms in the spurs are not sufficient to account for all of the observed H{sub 2} yield (0.45 molecules/100 eV) on the microsecond time scale. Addressing the question of the origin of an unscavengeable H{sub 2} yield of 0.15 molecules/100 eV produced before spur expansion, we suggest that the dissociative capture of the so-called vibrationally-relaxing electrons by H{sub 2}O molecules is a possible pathway for the formation of part of the initial H{sub 2} yield. Comparison of recent dissociative-electron-attachment H{sup -}-anion yield-distribution measurements from amorphous H{sub 2}O films with the energy spectrum of vibrationally-relaxing electrons in irradiated liquid water, calculated by Monte Carlo simulations, plays in favor of this hypothesis. (author).

  12. Molecular dynamics simulation of hydrogen dissolution and diffusion in a tungsten grain boundary

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Yi; Shu, Xiaolin; Liu, Yi-Nan; Lu, Guang-Hong, E-mail: lgh@buaa.edu.cn

    2014-12-15

    We employ a classic molecular dynamics method to investigate the dissolution and diffusion properties of hydrogen (H) in a Σ5(3 1 0) tilt grain boundary (GB). A maximum binding energy of 2.5 eV and a diffusion barrier of 1.65 eV indicate that GB plays an important role in H trapping. Dynamic simulations with temperature ranging from 600 K to 1200 K verify the diffusion and the aggregation of H in the GB are closely associated with the temperature. Pair radius distribution function analysis suggests a high local GB concentration of H such as 30% at 900 K can lead to a disordered GB structure.

  13. Hydrogen bond dynamics in liquid water: Ab initio molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Cheolhee; Kim, Eunae [College of Pharmacy, Chosun University, Gwangju (Korea, Republic of); Yeom, Min Sun [Korea Institute of Science and Technology Information, Daejeon (Korea, Republic of)

    2016-01-15

    The effect of intermolecular interaction on the distribution of the harmonic vibrational frequencies of water molecules was investigated through ab initio molecular dynamics simulations based on the Born-Oppenheimer approach. For single water, the effect of the dynamics of the oxygen atom in single water and the simulation time step on the frequency distribution were examined. The distributions of the OH stretching and HOH bending vibrational frequencies of liquid water were compared to those of single water. The probability distributions of the change in OH bond length and the lifetime of the dangling OH bond were also obtained. The distribution of the frequencies was strongly affected by the long lifetime of the dangling OH bond, resulting in the formation of hydrogen bonds between water molecules.

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

    KAUST Repository

    Yu, Weili

    2014-08-19

    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. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Quadrupole transitions in the bound rotational-vibrational spectrum of the hydrogen molecular ion

    CERN Document Server

    Pilón, Horacio Olivares

    2013-01-01

    The three-body Schr\\"odinger equation of the H$_2^+$ hydrogen molecular ion with Coulomb potentials is solved in perimetric coordinates using the Lagrange-mesh method. The Lagrange-mesh method is an approximate variational calculation with variational accuracy and the simplicity of a calculation on a mesh. Energies and wave functions of up to four of the lowest vibrational bound or quasibound states for total orbital momenta from 0 to 40 are calculated. The obtained energies have an accuracy varying from about 13 digits for the lowest vibrational state to at least 9 digits for the third vibrational excited state. With the corresponding wave functions, a simple calculation using the associated Gauss quadrature provides accurate quadrupole transition probabilities per time unit between those states over the whole rotational bands. Extensive results are presented with six significant figures.

  16. Classical Dynamics of Harmonic Generation of the Hydrogen Molecular Ion Interacting with Ultrashort Intense Laser Pulses

    Institute of Scientific and Technical Information of China (English)

    LI Chao-Hong; DUAN Yi-Wu; Wing-Ki Liu; Jian-Min Yuan

    2001-01-01

    Within Born-Oppenheimer approximation, by using the classical trajectory theory, a description for the high order harmonic generation of the hydrogen molecular ion interacting with ultrashort laser pulses has been pre sented. The Coulomb singularities have been remedied by the regularization. The action-angle variables have been used to generate the initial inversion symmetry microcanonical distribution. Within a proper intensity range, a harmonic plateau with only odd harmonics appears. For a larger intensity, because of the existence of chaos, the harmonic spectra become noisier. For a large enough intensity, the ionization takes place and the harmonics disappear. So the chaos causes the noises, the ionization suppresses the harmonic generation, and the onset of the ionization follows the onset of chaos.

  17. The oxidation of tyrosine and tryptophan studied by a molecular dynamics normal hydrogen electrode.

    Science.gov (United States)

    Costanzo, Francesca; Sulpizi, Marialore; Della Valle, Raffaele Guido; Sprik, Michiel

    2011-06-28

    The thermochemical constants for the oxidation of tyrosine and tryptophan through proton coupled electron transfer in aqueous solution have been computed applying a recently developed density functional theory (DFT) based molecular dynamics method for reversible elimination of protons and electrons. This method enables us to estimate the solvation free energy of a proton (H(+)) in a periodic model system from the free energy for the deprotonation of an aqueous hydronium ion (H(3)O(+)). Using the computed solvation free energy of H(+) as reference, the deprotonation and oxidation free energies of an aqueous species can be converted to pK(a) and normal hydrogen electrode (NHE) potentials. This conversion requires certain thermochemical corrections which were first presented in a similar study of the oxidation of hydrobenzoquinone [J. Cheng, M. Sulpizi, and M. Sprik, J. Chem. Phys. 131, 154504 (2009)]. Taking a different view of the thermodynamic status of the hydronium ion, these thermochemical corrections are revised in the present work. The key difference with the previous scheme is that the hydronium is now treated as an intermediate in the transfer of the proton from solution to the gas-phase. The accuracy of the method is assessed by a detailed comparison of the computed pK(a), NHE potentials and dehydrogenation free energies to experiment. As a further application of the technique, we have analyzed the role of the solvent in the oxidation of tyrosine by the tryptophan radical. The free energy change computed for this hydrogen atom transfer reaction is very similar to the gas-phase value, in agreement with experiment. The molecular dynamics results however, show that the minimal solvent effect on the reaction free energy is accompanied by a significant reorganization of the solvent.

  18. Molecular dynamics simulation of amorphous indomethacin-poly(vinylpyrrolidone) glasses: solubility and hydrogen bonding interactions.

    Science.gov (United States)

    Xiang, Tian-Xiang; Anderson, Bradley D

    2013-03-01

    Amorphous drug dispersions are frequently employed to enhance solubility and dissolution of poorly water-soluble drugs and thereby increase their oral bioavailability. Because these systems are metastable, phase separation of the amorphous components and subsequent drug crystallization may occur during storage. Computational methods to determine the likelihood of these events would be very valuable, if their reliability could be validated. This study investigates amorphous systems of indomethacin (IMC) in poly(vinylpyrrolidone) (PVP) and their molecular interactions by means of molecular dynamics (MD) simulations. IMC and PVP molecules were constructed using X-ray diffraction data, and force-field parameters were assigned by analogy with similar groups in Amber-ff03. Five assemblies varying in PVP and IMC composition were equilibrated in their molten states then cooled at a rate of 0.03 K/ps to generate amorphous glasses. Prolonged aging dynamic runs (100 ns) at 298 K and 1 bar were then carried out, from which solubility parameters, the Flory-Huggins interaction parameter, and associated hydrogen bonding properties were obtained. Calculated glass transition temperature (T(g)) values were higher than experimental results because of the faster cooling rates in MD simulations. Molecular mobility as characterized by atomic fluctuations was substantially reduced below the T(g) with IMC-PVP systems exhibiting lower mobilities than that found in amorphous IMC, consistent with the antiplasticizing effect of PVP. The number of IMC-IMC hydrogen bonds (HBs) formed per IMC molecule was substantially lower in IMC-PVP mixtures, particularly the fractions of IMC molecules involved in two or three HBs with other IMC molecules that may be potential precursors for crystal growth. The loss of HBs between IMC molecules in the presence of PVP was largely compensated for by the formation of IMC-PVP HBs. The difference (6.5 MPa(1/2)) between the solubility parameters in amorphous IMC

  19. Design and Synthesis of a Highly Stable Six-hydrogen-bonded Self-assembly Yellowish Green Electroluminescent Molecular Duplex

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    This paper describes the design, synthesis and characterization of a hydrogen-bonded molecular duplex with 1,8-naphthalimide fluorescent pendants. The two oligoamide molecular strands, with complementary hydrogen bond sequences of DDADAA and AADADD, caa form an ultra stable self-assembly duplex. Its molecular structure was confirmed by 1H NMR and ESI-MS, and its photoluminescence properties were determined. The resulting duplex exhibited a dramatically enhanced photoluminescence (PL) quantum efficiency of 63.7% compared to the corresponding 1,8-naphthalimide segment (32.4%), suggesting that the formation of the duplex with larger molecular weight could successfully inhibit the quenching of the fluorescent pendant.This novel duplex is a prospective candidate for new electroluminescent emitter.

  20. Spectroscopy and energy transfer of molecular transients: Hydrogen isocyanide and the ketenyl radical

    Science.gov (United States)

    Wilhelm, Michael J.

    Energy transfer from molecular species has been a long standing topic of profound interest to the chemical physics community. It is worth noting however, that to date, most studies have preferentially focused on chemically stable molecular species. While the literature does contain numerous examples of energy transfer of small radical or chemically unstable species, there have been extremely few studies which have actually probed highly vibrationally excited species. This apparent lack of attention should not be confused with a lack of interest. On the contrary, given the prevalence of vibrationally excited radicals in complex chemical systems such as planetary atmospheres and combustion, it is highly desirable to gain a complete understanding of the energetic deactivation processes of these delicate species. More often than not, the limiting factor which prevents examination of such species is a lack of spectroscopic information which is necessary for the identification as well as modeling of the corresponding species. In this thesis, we explore the use of time-resolved Fourier transform infrared emission spectroscopy, coupled with ab initio quantum chemical calculations, as a means of characterizing the vibrationally excited energy transfer dynamics from hydrogen isocyanide (HNC) as well as the ketenyl (HCCO) radical. It has been determined that each of these radical species can be generated in appreciable relative concentrations and with excess internal energy, following the 193 nm photolysis of specific stable molecular precursors. Through variation of the associated inert atomic collider species, and repeated spectral fitting analysis, it becomes feasible to obtain a measure the time-resolved average internal energy (as a function of the collider species), and hence a measure of the vibrational energy transfer efficiency of each radical species. It is observed that both HNC and HCCO exhibit enhanced vibrational energy transfer, for all average internal

  1. Metallization of solid molecular hydrogen in two dimensions: Mott-Hubbard-type transition

    Science.gov (United States)

    Biborski, Andrzej; Kådzielawa, Andrzej P.; Spałek, Józef

    2017-08-01

    We analyze the pressure-induced metal-insulator transition in a two-dimensional vertical stack of H2 molecules in (x-y) plane, and show that it represents a striking example of the Mott-Hubbard-type transition. Our combined exact diagonalization approach, formulated and solved in the second quantization formalism, includes also simultaneous ab initio readjustment of the single-particle wave functions, contained in the model microscopic parameters. The system is studied as a function of applied side force (generalized pressure), both in the H2-molecular and H-quasiatomic states. Extended Hubbard model is taken at the start, together with longer-range electron-electron interactions incorporated into the scheme. The stacked molecular plane transforms discontinuously into a (quasi)atomic state under the applied force via a two-step transition: the first between molecular insulating phases and the second from the molecular to the quasiatomic metallic phase. No quasiatomic insulating phase occurs. All the transitions are accompanied by abrupt changes of the bond length and the intermolecular distance (lattice parameter), as well as by discontinuous changes of the principal electronic properties, which are characteristic of the Mott-Hubbard transition here associated with the jumps of the predetermined equilibrium lattice parameter and the effective bond length. The phase transition can be interpreted in terms of the solid hydrogen metallization under pressure exerted by, e.g., the substrate covered with a monomolecular H2 film of the vertically stacked molecules. Both the Mott and Hubbard criteria at the insulator to metal transition are discussed.

  2. Hydrogen bond dynamics and vibrational spectral diffusion in aqueous solution of acetone: A first principles molecular dynamics study

    Indian Academy of Sciences (India)

    Bhabani S Mallik; Amalendu Chandra

    2012-01-01

    We present an ab initio molecular dynamics study of vibrational spectral diffusion and hydrogen bond dynamics in aqueous solution of acetone at room temperature. It is found that the frequencies of OD bonds in the acetone hydration shell have a higher stretch frequency than those in the bulk water. Also, on average, the frequencies of hydration shell OD modes are found to increase with increase in the acetone-water hydrogen bond distance. The vibrational spectral diffusion of the hydration shell water molecules reveals three time scales: A short-time relaxation (∼80 fs) corresponding to the dynamics of intact acetone-water hydrogen bonds, a slower relaxation (∼1.3 ps) corresponding to the lifetime of acetone-water hydrogen bonds and another longer time constant (∼12 ps) corresponding to the escape dynamics of water from the solute hydration shell. The present first principles results are compared with those of available experiments and classical simulations.

  3. Implications of the complete basis set limit in valence bond theory : a case study of molecular hydrogen

    NARCIS (Netherlands)

    Duke, Brian J.; Havenith, Remco W. A.

    2016-01-01

    The use of larger basis sets to approach the complete basis limit, now common in quantum chemistry, is applied for the first time to a range of valence bond functions for the simplest case of molecular hydrogen. Good convergence of the energy is slow due to difficulty in getting a correct cusp near

  4. High-resolution measurements of atmospheric molecular hydrogen and its isotopic composition at the West African coast of Mauritania

    NARCIS (Netherlands)

    Walter, S.; Kock, A; Röckmann, T.

    2013-01-01

    Oceans are a net source of molecular hydrogen (H2) to the atmosphere, where nitrogen (N2) fixation is assumed to be the main biological production pathway followed by photochemical production from organic material. The sources can be distinguished using isotope measurements because of clearly

  5. Molecular hydrogen in the damped Lyman α system towards GRB 120815A at z = 2.36

    NARCIS (Netherlands)

    Krühler, T.; Ledoux, C.; Fynbo, J.P.U.; Vreeswijk, P.M.; Schmidl, S.; Malesani, D.; Christensen, L.; De Cia, A.; Hjorth, J.; Jakobsson, P.; Kann, D.A.; Kaper, L.; Vergani, S.D.; Afonso, P.M.J.; Covino, S.; de Ugarta Postigo, A.; D'Elia, V.; Filgas, R.; Goldoni, P.; Greiner, J.; Hartoog, O.E.; Milvang-Jensen, B.; Nardini, M.; Piranomonte, S.; Rossi, A.; Sánchez-Ramírez, R.; Schady, P.; Schulze, S.; Sudilovsky, V.; Tanvir, N.R.; Tagliaferri, G.; Watson, D.J.; Wiersema, K.; Wijers, R.A.M.J.; Xu, D.

    2013-01-01

    We present the discovery of molecular hydrogen (H2), including the presence of vibrationally-excited H2* in the optical spectrum of the afterglow of GRB 120815A at z = 2.36 obtained with X-shooter at the VLT. Simultaneous photometric broad-band data from GROND and X-ray observations by Swift/XRT pla

  6. Nuclear quantum effect on hydrogen adsorption site of zeolite-templated carbon model using path integral molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Suzuki, Kimichi, E-mail: ki-suzuki@aist.go.jp [Research Institute for Nanosystem, National Institute of Advanced Industrial Science and Technology, Chuo-2, 1-1-1, Umezono, Tsukuba, Ibaraki 305-8568 (Japan); Kayanuma, Megumi [Institut de Chimie, UMR 7177 CNRS/Universite de Strasbourg, 4 rue Blaise Pascal 67000, Strasbourg (France); Tachikawa, Masanori [Quantum Chemistry Division, Graduate School of Science, Yokohama-city University, Seto 22-2, Kanazawa-ku, Yokohama 236-0027 (Japan); Ogawa, Hiroshi [Research Institute for Nanosystem, National Institute of Advanced Industrial Science and Technology, Chuo-2, 1-1-1, Umezono, Tsukuba, Ibaraki 305-8568 (Japan); Nishihara, Hirotomo; Kyotani, Takashi [Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Nagashima, Umpei [Research Institute for Nanosystem, National Institute of Advanced Industrial Science and Technology, Chuo-2, 1-1-1, Umezono, Tsukuba, Ibaraki 305-8568 (Japan)

    2011-09-15

    Research highlights: > The stable hydrogen adsorption sites on C{sub 36}H{sub 12} were evaluated at 300 K using path integral molecular dynamics. > In the static MO calculation and conventional MD simulation, five stable adsorption sites of hydrogen atom were found. > In path integral simulation, only four stable adsorption sites were obtained. > The thermal and nuclear quantum effects are key role to settle the hydrogen adsorption sites on carbon materials. - Abstract: To settle the hydrogen adsorption sites on buckybowl C{sub 36}H{sub 12}, which is picked up from zeolite-templated carbon (ZTC), we have performed path integral molecular dynamics (PIMD) simulation including thermal and nuclear quantum fluctuations under semi-empirical PM3 method. In the static PM3 calculation and classical simulation the five stable adsorption sites of hydrogen atom are optimized inside a buckybowl C{sub 36}H{sub 12}, which are labeled as {alpha}-, {beta}{sub 1}-, {beta}{sub 2}-, {gamma}-, and {delta}-carbons from edge to innermost carbon. In PIMD simulation, meanwhile, stable adsorption site is not appeared on {delta}-carbon, but on only {alpha}-, {beta}{sub 1}-, {beta}{sub 2}-, and {gamma}-carbons. This result is due to the fact that the adsorbed hydrogen atom can easily go over the barrier for hydrogen transferring from {delta}- to {beta}{sub 1}-carbons by thermal and nuclear quantum fluctuations. The thermal and nuclear quantum effects are key role to settle the hydrogen adsorption sites on carbon materials.

  7. Carbon Molecular Sieve Membrane as a True One Box Unit for Large Scale Hydrogen Production

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Paul

    2012-05-01

    IGCC coal-fired power plants show promise for environmentally-benign power generation. In these plants coal is gasified to syngas then processed in a water gas-shift (WGS) reactor to maximize the hydrogen/CO{sub 2} content. The gas stream can then be separated into a hydrogen rich stream for power generation and/or further purified for sale as a chemical and a CO{sub 2} rich stream for the purpose of carbon capture and storage (CCS). Today, the separation is accomplished using conventional absorption/desorption processes with post CO{sub 2} compression. However, significant process complexity and energy penalties accrue with this approach, accounting for ~20% of the capital cost and ~27% parasitic energy consumption. Ideally, a one-box process is preferred in which the syngas is fed directly to the WGS reactor without gas pre-treatment, converting the CO to hydrogen in the presence of H{sub 2}S and other impurities and delivering a clean hydrogen product for power generation or other uses. The development of such a process is the primary goal of this project. Our proposed "one-box" process includes a catalytic membrane reactor (MR) that makes use of a hydrogen-selective, carbon molecular sieve (CMS) membrane, and a sulfur-tolerant Co/Mo/Al{sub 2}O{sub 3} catalyst. The membrane reactor's behavior has been investigated with a bench top unit for different experimental conditions and compared with the modeling results. The model is used to further investigate the design features of the proposed process. CO conversion >99% and hydrogen recovery >90% are feasible under the operating pressures available from IGCC. More importantly, the CMS membrane has demonstrated excellent selectivity for hydrogen over H{sub 2}S (>100), and shown no flux loss in the presence of a synthetic "tar"-like material, i.e., naphthalene. In summary, the proposed "one-box" process has been successfully demonstrated with the bench-top reactor. In parallel we have successfully designed and

  8. Molecular Hydrogen Absorption from the Halo of a z~0.4 Galaxy

    CERN Document Server

    Muzahid, Sowgat; Charlton, Jane C; Churchill, Christopher W

    2016-01-01

    Lyman- and Werner-band absorption of molecular hydrogen (H2) is detected in ~50% of low redshift (z10^14.4 cm^-2. However the true origin(s) of the H2 bearing gas remain elusive. Here we report a new detection of an H2 absorber at z = 0.4298 in the HST/COS spectra of quasar PKS~2128--123. The total N(HI) of 10^{19.50\\pm0.15} cm^-2 classifies the absorber as a sub-DLA. H2 absorption is detected up to the J=3 rotational level with a total log N(H2)=16.36\\pm0.08 corresponding to a molecular fraction of log f(H2)=-2.84\\pm0.17. The excitation temperature of T_ex = 206\\pm6K indicates the presence of cold gas. Using detailed ionization modelling we obtain a near-solar metallicity (i.e., [O/H]= -0.26\\pm0.19) and a dust-to-gas ratio of log \\kappa ~ -0.45 for the H2 absorbing gas. The host-galaxy of the sub-DLA is detected at an impact parameter of \\rho ~ 48 kpc with an inclination angle of i~48 degree and an azimuthal angle of \\Phi ~ 15 degree with respect to the QSO sightline. We show that co-rotating gas in an exten...

  9. Structural and thermotropic peculiarities of hydrogen-bonded liquid crystals confined in mesoporous molecular sieves

    Science.gov (United States)

    Gnatyuk, I.; Gavrilko, T.; Yaroshchuk, O.; Holovina, N.; Shcherban, N.; Baran, J.; Drozd, M.

    2016-12-01

    The phase behaviour and structural organization of hydrogen-bonded liquid crystals were investigated under confinement to mesoporous molecular sieves. As such liquid crystalline compounds, 4-hexylbenzoic and 4-butylcyclohexanecarboxylic acids with different head group structure and alkyl chain length where selected and filled in the AlMCM-41 sieves. With FTIR spectroscopy it was found that some part of incorporated acid molecules, presumably located in the inner space of the AlMCM-41 pores, is in undissociated form of open dimers or chain associates and thus shows spectroscopic features characteristic to the bulk-like species. The other FTIR spectra components indicate strong interaction of the incorporated monomeric molecules with the pore surface. Two specific mechanisms are shown to be involved in molecular interactions at the interface: (1) deprotonation of monomeric acid molecules on the pore surface with formation of COO- carboxylate ions and (2) bonding of these ions to the pore surface by a coordinated bond R-COO-…Al+ with Lewis acid sites. Differential scanning calorimetry revealed that these near-surface processes lead to complete suppression of mesomorphic properties of the studied acids under confinement to nanopores.

  10. Transport properties of liquid para-hydrogen: The path integral centroid molecular dynamics approach

    Science.gov (United States)

    Yonetani, Yoshiteru; Kinugawa, Kenichi

    2003-11-01

    Several fundamental transport properties of a quantum liquid para-hydrogen (p-H2) at 17 K have been numerically evaluated by means of the quantum dynamics simulation called the path integral centroid molecular dynamics (CMD). For comparison, classical molecular dynamics (MD) simulations have also been performed under the same condition. In accordance with the previous path integral simulations, the calculated static properties of the liquid agree well with the experimental results. For the diffusion coefficient, thermal conductivity, and shear viscosity, the CMD predicts the values closer to the experimental ones though the classical MD results are far from the reality. The agreement of the CMD result with the experimental one is especially good for the shear viscosity with the difference less than 5%. The calculated diffusion coefficient and the thermal conductivity agree with the experimental values at least in the same order. We predict that the ratio of bulk viscosity to shear viscosity for liquid p-H2 is much larger than classical van der Waals simple liquids such as rare gas liquids.

  11. The Cardioprotective Effects of Hydrogen Sulfide in Heart Diseases: From Molecular Mechanisms to Therapeutic Potential

    Directory of Open Access Journals (Sweden)

    Yaqi Shen

    2015-01-01

    Full Text Available Hydrogen sulfide (H2S is now recognized as a third gaseous mediator along with nitric oxide (NO and carbon monoxide (CO, though it was originally considered as a malodorous and toxic gas. H2S is produced endogenously from cysteine by three enzymes in mammalian tissues. An increasing body of evidence suggests the involvement of H2S in different physiological and pathological processes. Recent studies have shown that H2S has the potential to protect the heart against myocardial infarction, arrhythmia, hypertrophy, fibrosis, ischemia-reperfusion injury, and heart failure. Some mechanisms, such as antioxidative action, preservation of mitochondrial function, reduction of apoptosis, anti-inflammatory responses, angiogenic actions, regulation of ion channel, and interaction with NO, could be responsible for the cardioprotective effect of H2S. Although several mechanisms have been identified, there is a need for further research to identify the specific molecular mechanism of cardioprotection in different cardiac diseases. Therefore, insight into the molecular mechanisms underlying H2S action in the heart may promote the understanding of pathophysiology of cardiac diseases and lead to new therapeutic targets based on modulation of H2S production.

  12. Neuroprotective potential of molecular hydrogen against perinatal brain injury via suppression of activated microglia.

    Science.gov (United States)

    Imai, Kenji; Kotani, Tomomi; Tsuda, Hiroyuki; Mano, Yukio; Nakano, Tomoko; Ushida, Takafumi; Li, Hua; Miki, Rika; Sumigama, Seiji; Iwase, Akira; Hirakawa, Akihiro; Ohno, Kinji; Toyokuni, Shinya; Takeuchi, Hideyuki; Mizuno, Tetsuya; Suzumura, Akio; Kikkawa, Fumitaka

    2016-02-01

    Exposure to inflammation in utero is related to perinatal brain injury, which is itself associated with high rates of long-term morbidity and mortality in children. Novel therapeutic interventions during the perinatal period are required to prevent inflammation, but its pathogenesis is incompletely understood. Activated microglia are known to play a central role in brain injury by producing a variety of pro-inflammatory cytokines and releasing oxidative products. The study is aimed to investigate the preventative potential of molecular hydrogen (H2), which is an antioxidant and anti-inflammatory agent without mutagenicity. Pregnant ICR mice were injected with lipopolysaccharide (LPS) intraperitoneally on embryonic day 17 to create a model of perinatal brain injury caused by prenatal inflammation. In this model, the effect of maternal administration of hydrogen water (HW) on pups was also evaluated. The levels of pro-inflammatory cytokines, oxidative damage and activation of microglia were determined in the fetal brains. H2 reduced the LPS-induced expression of pro-inflammatory cytokines, oxidative damage and microglial activation in the fetal brains. Next, we investigated how H2 contributes to neuroprotection, focusing on microglia, using primary cultured microglia and neurons. H2 prevented LPS- or cytokine-induced generation of reactive oxidative species by microglia and reduced LPS-induced microglial neurotoxicity. Finally, we identified several molecules influenced by H2, involved in the process of activating microglia. These results suggested that H2 holds promise for the prevention of inflammation related to perinatal brain injury. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Molecular understanding of the interaction of methyl hydrogen sulfate with ammonia/dimethylamine/water.

    Science.gov (United States)

    Sheng, Xia; Zhao, Hailiang; Du, Lin

    2017-11-01

    Theoretical calculations at the B3LYP-D3/aug-cc-pVTZ (aug-cc-pV(T+d)Z for sulfur) level were used to investigate the contribution of methyl hydrogen sulfate (MHS) to new particle formation with the common atmospheric aerosol nucleation precursors including water (H2O), ammonia (NH3), and dimethylamine (DMA). A typical characteristic feature of the MHS-containing complexes is the formation of six- or eight-membered ring structures via SOH⋯O (MHS donor), OH⋯O/N (H2O donor) and NH⋯O/N (NH3/DMA donor). The stability of the complexes was evaluated based on the calculated binding energies. The molecular interactions between three molecules are found to be more thermodynamically favorable than the complexes consisting two molecules. The red shifts of the SOH-stretching (MHS donor) vibrational transitions with respect to the isolated monomers are much larger than the red shifts of the OH (H2O donor) and NH-stretching (NH3/DMA donor) vibrational transitions. Topological analysis shows that the electron density and Laplacian at the bond critical points beyond the range of hydrogen bonding criteria for most of the complexes. This is due to the strong acid-base interaction between MHS and DMA or NH3, thus leads to a proton transfer from MHS to DMA or NH3. Remarkably, the atmospheric relevance of the MHS-containing complexes is much higher than H2SO4, which is evaluated by combining the calculated thermodynamic data and the concentrations of the reactant species. This study reveals the environmental fate of MHS could serve as nucleation centers in new particle formation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Post pyrolysis trapping of molecular hydrogen improves precision for δD(CH4) analysis

    Science.gov (United States)

    Bock, M.; Schmitt, J.; Schneider, R.; Fischer, H.

    2012-04-01

    Methane (CH4) is the third most important greenhouse gas after water vapour and carbon dioxide (CO2). Since the industrial revolution the mixing ratio of CH4 in the atmosphere rose to ~1800 ppb, a value never reached within the last 800 000 years. This CH4 increase can only be assessed compared to its natural changes in the past. Firn air and air enclosures in polar ice cores represent the only direct paleoatmospheric archive. The latter show that atmospheric CH4 concentrations changed in concert with northern hemisphere temperature during both glacial/interglacial transitions as well as rapid climate changes (Dansgaard-Oeschger events). Since the different sources of atmospheric methane exhibit distinct carbon and hydrogen isotopic composition (δ13CH4 and δD(CH4)) reconstructions of these parameters on ice cores allow to constrain individual CH4 source/sink changes. δD(CH4) also reflects water cycle changes as hydrogen of precipitation is traced into methane produced from wetland/thermokarst/permafrost systems (Bock et al. 2010, Science). Here we present an updated high precision on line gas chromatography pyrolysis isotope ratio monitoring mass spectrometry technique (GC/P/irmMS) for analysis of δD(CH4) extracted from ice cores. It is based on earlier developments (Bock et al. 2010, RCM) and is improved concerning sample size and precision. The main achievement is post pyrolysis trapping (PPT) of molecular hydrogen after the high temperature conversion of methane leading to a better signal to noise ratio. Air from only 350 g of ice with CH4 concentrations as low as 350 ppb can now be measured with a precision of ~2‰. Such ice samples contain only approximately 30 mL of air and less than 1 nmol CH4. The new method was applied on ice samples from the EDML and EDC ice cores (European Project for Ice Coring in Antarctica, Dronning Maud Land, Dome Concordia). We present the first δD(CH4) records covering the penultimate termination and interglacial from EDML

  15. Molecular Hydrogen Emission from Protoplanetary Disks II. Effects of X-ray Irradiation and Dust Evolution

    CERN Document Server

    Nomura, H; Tsujimoto, M; Nakagawa, Y; Millar, T J

    2007-01-01

    Detailed models for the density and temperature profiles of gas and dust in protoplanetary disks are constructed by taking into account X-ray and ultraviolet (UV) irradiation from a central T Tauri star, as well as dust size growth and settling toward the disk midplane. The spatial and size distributions of dust grains in the disks are numerically computed by solving the coagulation equation for settling dust particles. The level populations and line emission of molecular hydrogen are calculated using the derived physical structure of the disks. X-ray irradiation is the dominant heating source of the gas in the inner disk region and in the surface layer, while the far UV heating dominates otherwise. If the central star has strong X-ray and weak UV radiation, the H2 level populations are controlled by X-ray pumping, and the X-ray induced transition lines could be observable. If the UV irradiation is strong, the level populations are controlled by thermal collisions or UV pumping, depending on the properties of...

  16. ORFEUS echelle spectra Molecular hydrogen in disk, IVC, and HVC gas in front of the LMC

    CERN Document Server

    Bluhm, H J; Marggraf, O; Richter, P; Bluhm, Hartmut; Boer, Klaas. S. de; Marggraf, Ole; Richter, Philipp

    2001-01-01

    In front of the LMC molecular hydrogen is found in absorption near 0 km/s, being local disk gas, near +60 km/s in an intermediate velocity cloud, and near +120 km/s, in a high velocity halo cloud. The nature of the gas is discussed based on four ORFEUS far UV spectra of LMC stars and including data from the ground and from the IUE satellite. The local gas is cool and, given a span of sight lines of only 2.5 deg, rather fluffy. The fractional abundance of H_2 varies from log(f)=-5.4 to -3.3. Metal depletions (up to -1.7 dex for Fe) are typical for galactic disk gas. In the IV and HV gas an apparent underabundance of neutral oxygen points to an ionization level of the gas of about 90%. H_2 is detected in IV and HV gas toward HD 269546. In the IV gas we find an H_2 column density of log(N)\\simeq15.6. The H_2 excitation indicates that the line of sight samples a cloud at a temperature below 150 K. Column densities are too small to detect the higher UV pumped excitation levels. The high velocity H_2 (log(N)\\simeq1...

  17. A FUSE Survey of Interstellar Molecular Hydrogen toward High-Latitude AGN

    CERN Document Server

    Gillmon, K; Tumlinson, J; Danforth, C; Gillmon, Kristen; Tumlinson, Jason; Danforth, Charles

    2006-01-01

    We report results from a FUSE survey of interstellar molecular hydrogen (H2) along 45 sight lines to AGN at high Galactic latitudes (|b| > 20 degrees). Most (39 of 45) of the sight lines show detectable Galactic H2 absorption from Lyman and Werner bands between 1000 and 1126 A, with column densities ranging from N(H2) = 10^(14.17-19.82) cm^-2. In the northern Galactic hemisphere, we identify many regions of low column, N(H2) 54 degrees. These `"H2 holes" provide valuable, uncontaminated sight lines for extragalactic UV spectroscopy, and a few may be related to the "Northern Chimney" (low Na I absorption) and "Lockman Hole" with low N(HI). A comparison of high-latitude H2 with 139 OB-star sight lines surveyed in the Galactic disk suggests that high-latitude and disk H2 clouds may have different rates of heating, cooling, and UV excitation. For rotational states J = 0 and 1, the mean excitation temperature at high latitude, = 124 +/- 8 K, is somewhat above that in the Galactic disk, = 86 +/- 20 K. For J = 2-...

  18. Star formation and molecular hydrogen in dwarf galaxies: a non-equilibrium view

    Science.gov (United States)

    Hu, Chia-Yu; Naab, Thorsten; Walch, Stefanie; Glover, Simon C. O.; Clark, Paul C.

    2016-06-01

    We study the connection of star formation to atomic (H I) and molecular hydrogen (H2) in isolated, low-metallicity dwarf galaxies with high-resolution (mgas = 4 M⊙, Nngb = 100) smoothed particle hydrodynamics simulations. The model includes self-gravity, non-equilibrium cooling, shielding from a uniform and constant interstellar radiation field, the chemistry of H2 formation, H2-independent star formation, supernova feedback and metal enrichment. We find that the H2 mass fraction is sensitive to the adopted dust-to-gas ratio and the strength of the interstellar radiation field, while the star formation rate is not. Star formation is regulated by stellar feedback, keeping the gas out of thermal equilibrium for densities n feedback at small radii and by the assumed radiation field at large radii. The decreasing cold gas fractions result in a rapid increase in depletion time (up to 100 Gyr) for total gas surface densities Σ _{H I+H_2} ≲ 10 M⊙ pc-2, in agreement with observations of dwarf galaxies in the Kennicutt-Schmidt plane.

  19. Molecular hydrogen and excitation in the HH 1-2 system

    Science.gov (United States)

    Noriega-Crespo, A.; Garnavich, P. M.

    1994-01-01

    We present a series of molecular hydrogen images of the Herbig-Haro 1-2 system in the 1-0 S(1) transition at 2.121 microns, with a spatial resolution of approximately 2 sec. The distribution of H2 is then compared with that of the excitation, given by the (S II) 6717+6731 to H-alpha line ratio. We find that most optical condensations in the HH 1-2 system, including the VLA 1 jet, have H2 counterparts. H2 emission is detected in most low excitation knots, as expected for low velocity shocks (50 km/s less than), but also in high excitation regions, like in HH 1F and HH 2A min. For these latter objects, the H2 emission could be due to the interaction of the preionizing flux, produced by 150-200 km/s shocks, with the surrounding interstellar matter, i.e., fluorescence. The lack fluorescent lines in the ultraviolet (UV), however, suggest a different mechanism. H2 is detected at the tip of the VLA 1 jet, where the knot morphology suggests the presence of a second bow shock. H2 is detected also SE of HH 2E and SW of HH 1F, in regions with known NH3 emission.

  20. Influence of Molecular Hydrogen Diffusion on Concentration and Distribution of Hydroxyl Groups in Silica Fibers

    Science.gov (United States)

    Plotnichenko, Victor G.; Ivanov, Gennadii A.; Kryukova, Elena B.; Aksenov, Vyacheslav A.; Sokolov, Vyacheslav O.; Isaev, Victor A.

    2005-01-01

    To study the hydroxyl (OH)-group contamination mechanisms in silica-based optical fibers, the transmission spectra of substrate tubes and fiber preforms made from various types of silica glasses ("Suprasil F-300," KS-4V, and KUVI) are measured by the method of infrared Fourier spectroscopy in a wavelength region of 2-5 μm. Due to the intensity of the fundamental OH stretching vibration band, the absorption coefficient, concentration, and a distribution profile of OH groups across the aforesaid samples are calculated. It is found that using an oxyhydrogen burner in the modified chemical vapor deposition (MCVD) process of manufacturing preforms and fiber drawing, the main source of impurity OH groups can be the molecular hydrogen H2 penetrating into glass much deeper than the OH groups diffusing from the substrate tube surface. A simple model explaining the formation and diffusion of OH groups into a fiber core and cladding is proposed. It is shown that heating tubes and preforms in a flame of oxyhydrogen burner during fiber fabrication causes a significant OH-group content growth (almost by two orders of magnitude) near to the outer preform surface. Using substrate tubes made from Suprasil F-300 glass, optical fibers are fabricated having a silica core and fluorosilicate reflecting cladding with optical losses of 0.3 dB/km at 1.55 μm and a refractive-index difference between core and cladding ~ 1 . 10^-2.

  1. Rotationally inelastic scattering of OH by molecular hydrogen: Theory and experiment

    Energy Technology Data Exchange (ETDEWEB)

    Schewe, H. Christian, E-mail: schewe@fhi-berlin.mpg.de; Meijer, Gerard [Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin (Germany); Ma, Qianli; Dagdigian, Paul J., E-mail: pjdagdigian@jhu.edu [Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218-2685 (United States); Vanhaecke, Nicolas [Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin (Germany); Laboratoire Aimé Cotton-UMR 9188 CNRS, Université Paris-Sud 11 and Ecole Normale Supérieure Cachan, 91405 Orsay (France); Wang, Xingan [Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin (Germany); Department of Chemical Physics, University of Science and Technology of China, Hefei 230026 (China); Kłos, Jacek [Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742-2021 (United States); Alexander, Millard H. [Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742-2021 (United States); Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742-2021 (United States); Meerakker, Sebastiaan Y. T. van de [Molecular and Laser Physics, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6265 AJ Nijmegen (Netherlands); Avoird, Ad van der, E-mail: A.vanderAvoird@theochem.ru.nl [Theoretical Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6265 AJ Nijmegen (Netherlands)

    2015-05-28

    We present an experimental and theoretical investigation of rotationally inelastic transitions of OH, prepared in the X{sup 2}Π, v = 0, j = 3/2 F{sub 1}f level, in collisions with molecular hydrogen (H{sub 2} and D{sub 2}). In a crossed beam experiment, the OH radicals were state selected and velocity tuned over the collision energy range 75–155 cm{sup −1} using a Stark decelerator. Relative parity-resolved state-to-state integral cross sections were determined for collisions with normal and para converted H{sub 2}. These cross sections, as well as previous OH–H{sub 2} measurements at 595 cm{sup −1} collision energy by Schreel and ter Meulen [J. Chem. Phys. 105, 4522 (1996)], and OH–D{sub 2} measurements for collision energies 100–500 cm{sup −1} by Kirste et al. [Phys. Rev. A 82, 042717 (2010)], were compared with the results of quantum scattering calculations using recently determined ab initio potential energy surfaces [Ma et al., J. Chem. Phys. 141, 174309 (2014)]. Good agreement between the experimental and computed relative cross sections was found, although some structure seen in the OH(j = 3/2 F{sub 1}f → j = 5/2 F{sub 1}e) + H{sub 2}(j = 0) cross section is not understood.

  2. Star formation and molecular hydrogen in dwarf galaxies: a non-equilibrium view

    CERN Document Server

    Hu, Chia-Yu; Walch, Stefanie; Glover, Simon C O; Clark, Paul C

    2015-01-01

    We study the connection of star formation to atomic (HI) and molecular hydrogen (H$_2$) in isolated, low metallicity dwarf galaxies with high-resolution ($m_{\\rm gas}$ = 4 M$_\\odot$, $N_{\\rm ngb}$ = 100) SPH simulations. The model includes self-gravity, non-equilibrium cooling, shielding from an interstellar radiation field, the chemistry of H$_2$ formation, H$_2$-independent star formation, supernova feedback and metal enrichment. We find that the H$_2$ mass fraction is sensitive to the adopted dust-to-gas ratio and the strength of the interstellar radiation field, while the star formation rate is not. Star formation is regulated by stellar feedback, keeping the gas out of thermal equilibrium for densities $n <$ 1 cm$^{-3}$. Because of the long chemical timescales, the H$_2$ mass remains out of chemical equilibrium throughout the simulation. Star formation is well-correlated with cold ( T $\\leqslant$ 100 K ) gas, but this dense and cold gas - the reservoir for star formation - is dominated by HI, not H$_2...

  3. The quantum nature of the hydrogen bond: insight from path-integral molecular dynamics

    Science.gov (United States)

    Walker, Brent; Li, Xin-Zheng; Michaelides, Angelos

    2011-03-01

    Hydrogen (H) bonds are weak, generally intermolecular bonds, that hold together much of soft matter, the condensed phases of water, network liquids, and many ferroelectric crystals. The small mass of H means H-bonds are inherently quantum mechanical; effects such as zero point motion and tunneling should be considered, although often are not. In particular, a consistent picture of quantum nuclear effects on the strength of H-bonds and consequently the structure of H-bonded systems is still absent. Here, we report ab initio path-integral molecular dynamics studies on the quantum nature of the H-bond. Systematic examination of a range of H-bonded systems shows that quantum nuclei weaken weak H-bonds but strengthen relatively strong ones. This correlation arises from a competition between anharmonic intermolecular bond bending and intramolecular bond stretching. A simple rule of thumb enables predictions to be made for H-bonded bonded materials in general with merely classical knowledge (e.g. H-bond strength or H-bond length). Our work rationalizes the contrasting influence of quantum nuclear dynamics on a wide variety of materials, including liquid water and HF, and highlights the need for flexible molecules in force-field based studies of quantum nuclear dynamics.

  4. Circumbinary Gas Accretion onto a Central Binary: Infrared Molecular Hydrogen Emission from GG Tau A

    CERN Document Server

    Beck, Tracy L; Dutrey, Anne; Piétu, Vincent; Guilloteau, Stephane; Lubow, S H; Simon, M

    2012-01-01

    We present high spatial resolution maps of ro-vibrational molecular hydrogen emission from the environment of the GG Tau A binary component in the GG Tau quadruple system. The H2 v= 1-0 S(1) emission is spatially resolved and encompasses the inner binary, with emission detected at locations that should be dynamically cleared on several hundred-year timescales. Extensions of H2 gas emission are seen to ~100 AU distances from the central stars. The v = 2-1 S(1) emission at 2.24 microns is also detected at ~30 AU from the central stars, with a line ratio of 0.05 +/- 0.01 with respect to the v = 1-0 S(1) emission. Assuming gas in LTE, this ratio corresponds to an emission environment at ~1700 K. We estimate that this temperature is too high for quiescent gas heated by X-ray or UV emission from the central stars. Surprisingly, we find that the brightest region of H2 emission arises from a spatial location that is exactly coincident with a recently revealed dust "streamer" which seems to be transferring material fr...

  5. Hydrogen bonding and vibrational energy relaxation of interfacial water: A full DFT molecular dynamics simulation.

    Science.gov (United States)

    Jeon, Jonggu; Hsieh, Cho-Shuen; Nagata, Yuki; Bonn, Mischa; Cho, Minhaeng

    2017-07-28

    The air-water interface has been a subject of extensive theoretical and experimental studies due to its ubiquity in nature and its importance as a model system for aqueous hydrophobic interfaces. We report on the structure and vibrational energy transfer dynamics of this interfacial water system studied with equilibrium and non-equilibrium molecular dynamics simulations employing a density functional theory -based description of the system and the kinetic energy spectral density analysis. The interfacial water molecules are found to make fewer and weaker hydrogen (H)-bonds on average compared to those in the bulk. We also find that (i) the H-bonded OH groups conjugate to the free OH exhibit rather low vibrational frequencies (3000-3500 cm(-1)); (ii) the presence of a significant fraction (>10%) of free and randomly oriented water molecules at the interface ("labile water"), neither of whose OH groups are strong H-bond donors; (iii) the inertial rotation of free OH groups, especially from the labile water, contribute to the population decay of excited free OH groups with comparable rate and magnitude as intramolecular energy transfer between the OH groups. These results suggest that the labile water, which might not be easily detectable by the conventional vibrational sum frequency generation method, plays an important role in the surface water dynamics.

  6. Hydrogen bonding and vibrational energy relaxation of interfacial water: A full DFT molecular dynamics simulation

    Science.gov (United States)

    Jeon, Jonggu; Hsieh, Cho-Shuen; Nagata, Yuki; Bonn, Mischa; Cho, Minhaeng

    2017-07-01

    The air-water interface has been a subject of extensive theoretical and experimental studies due to its ubiquity in nature and its importance as a model system for aqueous hydrophobic interfaces. We report on the structure and vibrational energy transfer dynamics of this interfacial water system studied with equilibrium and non-equilibrium molecular dynamics simulations employing a density functional theory -based description of the system and the kinetic energy spectral density analysis. The interfacial water molecules are found to make fewer and weaker hydrogen (H)-bonds on average compared to those in the bulk. We also find that (i) the H-bonded OH groups conjugate to the free OH exhibit rather low vibrational frequencies (3000-3500 cm-1); (ii) the presence of a significant fraction (>10%) of free and randomly oriented water molecules at the interface ("labile water"), neither of whose OH groups are strong H-bond donors; (iii) the inertial rotation of free OH groups, especially from the labile water, contribute to the population decay of excited free OH groups with comparable rate and magnitude as intramolecular energy transfer between the OH groups. These results suggest that the labile water, which might not be easily detectable by the conventional vibrational sum frequency generation method, plays an important role in the surface water dynamics.

  7. Formation and evolution of molecular hydrogen in disk galaxies with different masses and Hubble types

    CERN Document Server

    Bekki, Kenji

    2014-01-01

    We investigate the physical properties of molecular hydrogen (H2) in isolated and interacting disk galaxies with different masses and Hubble types by using chemodynamical simulations with H2 formation on dust grains and dust growth and destruction in interstellar medium (ISM). We particularly focus on the dependences of H2 gas mass fractions (f_H2), spatial distributions of HI and H2, and local H2-scaling relations on initial halo masses (M_h), baryonic fractions (f_bary), gas mass fractions (f_g), and Hubble types. The principal results are as follows. The final f_H2 can be larger in disk galaxies with higher M_h, f_bary, and f_g. Some low-mass disk models with M_h smaller than 10^10 M_sun show extremely low f_H2 and thus no/little star formation, even if initial f_g is quite large (>0.9). Big galactic bulges can severely suppress the formation of H2 from HI on dust grains whereas strong stellar bars can not only enhance f_H2 but also be responsible for the formation of H2-dominated central rings. The projec...

  8. Molecular hydrogen formation from photocatalysis of methanol on TiO2(110).

    Science.gov (United States)

    Xu, Chenbiao; Yang, Wenshao; Guo, Qing; Dai, Dongxu; Chen, Maodu; Yang, Xueming

    2013-07-17

    It is well established that adding methanol to water could significantly enhance H2 production by TiO2. Recently, we have found that methanol can be photocatalytically dissociated on TiO2(110) at 400 nm via a stepwise mechanism. However, how molecular hydrogen can be formed from the photocatalyzed methanol/TiO2(110) surface is still not clear. In this work, we have investigated deuterium formation from photocatalysis of the fully deuterated methanol (CD3OD) on TiO2(110) at 400 nm using a temperature programmed desorption (TPD) technique. Photocatalytic dissociation products formaldehyde (CD2O) and D-atoms on BBO sites (via D2O TPD product) have been detected. In addition to D2O formation by heating the photocatalyzed methanol/TiO2(110) surface, we have also observed D2 product formation. D2 is clearly formed via thermal recombination of the D-atoms on the BBO sites from photocatalysis of methanol. Experimental results indicate that D2O formation is more important than D2 formation and that D2 formation is clearly affected by the D2O formation process.

  9. Herschel-spire Fourier transform spectrometer observations of excited CO and [C I] in the antennae (NGC 4038/39): Warm and cold molecular gas

    Energy Technology Data Exchange (ETDEWEB)

    Schirm, Maximilien R. P.; Wilson, Christine D.; Parkin, Tara J. [Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1 (Canada); Kamenetzky, Julia; Glenn, Jason; Rangwala, Naseem [Center for Astrophysics and Space Astronomy, 389-UCB, University of Colorado, Boulder, CO 80303 (United States); Spinoglio, Luigi; Pereira-Santaella, Miguel [Istituto di Astrofisica e Planetologia Spaziali, INAF-IAPS, Via Fosso del Cavaliere 100, I-00133 Roma (Italy); Baes, Maarten; De Looze, Ilse [Sterrenkundig Observatorium, Universiteit Gent, Krijgslaan 281 S9, B-9000 Gent (Belgium); Barlow, Michael J. [Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT (United Kingdom); Clements, Dave L. [Astrophysics Group, Imperial College, Blackett Laboratory, Prince Consort Road, London SW7 2AZ (United Kingdom); Cooray, Asantha [Department of Physics and Astronomy, University of California, Irvine, CA 92697 (United States); Karczewski, Oskar Ł. [Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH (United Kingdom); Madden, Suzanne C.; Rémy-Ruyer, Aurélie; Wu, Ronin, E-mail: schirmmr@mcmaster.ca, E-mail: wilson@physics.mcmaster.ca [CEA, Laboratoire AIM, Irfu/SAp, Orme des Merisiers, F-91191 Gif-sur-Yvette (France)

    2014-02-01

    We present Herschel Spectral and Photometric Imaging Receiver (SPIRE) Fourier Transform Spectrometer (FTS) observations of the Antennae (NGC 4038/39), a well-studied, nearby (22 Mpc), ongoing merger between two gas-rich spiral galaxies. The SPIRE-FTS is a low spatial ( FWHM ∼ 19''-43'') and spectral (∼1.2 GHz) resolution mapping spectrometer covering a large spectral range (194-671 μm, 450-1545 GHz). We detect five CO transitions (J = 4-3 to J = 8-7), both [C I] transitions, and the [N II] 205 μm transition across the entire system, which we supplement with ground-based observations of the CO J = 1-0, J = 2-1, and J = 3-2 transitions and Herschel Photodetecting Array Camera and Spectrometer (PACS) observations of [C II] and [O I] 63 μm. Using the CO and [C I] transitions, we perform both a local thermodynamic equilibrium (LTE) analysis of [C I] and a non-LTE radiative transfer analysis of CO and [C I] using the radiative transfer code RADEX along with a Bayesian likelihood analysis. We find that there are two components to the molecular gas: a cold (T {sub kin} ∼ 10-30 K) and a warm (T {sub kin} ≳ 100 K) component. By comparing the warm gas mass to previously observed values, we determine a CO abundance in the warm gas of x {sub CO} ∼ 5 × 10{sup –5}. If the CO abundance is the same in the warm and cold gas phases, this abundance corresponds to a CO J = 1-0 luminosity-to-mass conversion factor of α{sub CO} ∼ 7 M {sub ☉} pc{sup –2} (K km s{sup –1}){sup –1} in the cold component, similar to the value for normal spiral galaxies. We estimate the cooling from H{sub 2}, [C II], CO, and [O I] 63 μm to be ∼0.01 L {sub ☉}/M {sub ☉}. We compare photon-dominated region models to the ratio of the flux of various CO transitions, along with the ratio of the CO flux to the far-infrared flux in NGC 4038, NGC 4039, and the overlap region. We find that the densities recovered from our non-LTE analysis are consistent with a

  10. Effects of traces of molecular gases (hydrogen, nitrogen) in glow discharges in noble gases

    Science.gov (United States)

    Steers, E. B. M.; Smid, P.; Hoffmann, V.

    2008-07-01

    The "Grimm" type of low pressure glow discharge source, introduced some forty years ago, has proved to be a versatile analytical source. A flat sample is used as the cathode and placed about 0.2mm away from the end of a hollow tubular anode leading to an obstructed discharge. When the source was first developed, it was used for the direct analysis of solid metallic samples by optical emission spectroscopy (OES), normally with argon as the plasma gas; it was soon found that, using suitable electrical parameters, the cathode material was sputtered uniformly from a circular crater of diameter equal to that of the tubular anode, so that the technique could be used for compositional depth profile analysis (CDPA). Over the years the capability and applications of the technique have steadily increased. The use of rf powered discharges now permits the analysis of non-conducting layers and samples; improved instrumental design now allows CDPA of ever thinner layers (e.g. resolution of layers 5 nm thick in multilayer stacks is possible). For the original bulk material application, pre-sputtering could be used to remove any surface contamination but for CDPA, analysis must start immediately the discharge is ignited, so that any surface contamination can introduce molecular gases into the plasma gas and have significant analytical consequences, especially for very thin layers; in addition, many types of samples now analysed contain molecular gases as components (either as occluded gas, or e.g. as a nitride or oxide), and this gas enters the discharge when the sample is sputtered. It is therefore important to investigate the effect of such foreign gases on the discharge, in particular on the spectral intensities and hence the analytical results. The presentation will concentrate mainly on the effect of hydrogen in argon discharges, in the concentration range 0-2 % v/v but other gas mixtures (e.g. Ar/N_2, Ne/H_2) will be considered for comparison. In general, the introduction of

  11. Quantum molecular dynamics and molecular interactions studied by NMR and INS Nuclear magnetic resonance; Proton tunnelling; Hydrogen bond

    CERN Document Server

    Jones, N

    2002-01-01

    The wavefunction of a particle extends into the classically forbidden barrier region of the potential energy surface. The consequence of this partial delocalisation is the phenomenon of quantum tunnelling, an effect which enables a particle to penetrate a potential barrier of magnitude greater than the energy of the particle. The tunnelling probability is an exponential function of the particle mass. The effect is therefore an important contribution to the behaviour of light atoms, in particular the proton. The hydrogen bond has long been appreciated to be an essential component of many biological and chemical systems, and the proton transfer reaction in the hydrogen bond is fundamental to many of these processes. The proton behaviour in the hydrogen bonds of benzoic acid, acetylacetone and calix-4-arene has been studied. A variety of techniques, both experimental and computational, were adopted for the study of the three hydrogen bonded systems. The complementary spectroscopic techniques of inelastic neutron...

  12. Formation of Water in the Warm Atmospheres of Protoplanetary Disks

    CERN Document Server

    Glassgold, A E; Najita, J R

    2009-01-01

    The gas-phase chemistry of water in protoplanetary disks is analyzed with a model based on X-ray heating and ionization of the disk atmosphere. Several uncertain processes appear to play critical roles in generating the column densities of warm water that are detected from disks at infrared wavelengths. The dominant factors are the reactions that form molecular hydrogen, including formation on warm grains, and the ionization and heating of the atmosphere. All of these can work together to produce a region of high water abundances in the molecular transition layer of the inner disk atmosphere, where atoms are transformed into molecules, the temperature drops from thousands to hundreds of Kelvins, and the ionization begins to be dominated by the heavy elements. Grain formation of molecular hydrogen and mechanical heating of the atmosphere can play important roles in this region and directly affect the amount of warm water in protoplanetary disk atmospheres. Thus it may be possible to account for the existing me...

  13. Spectroscopic and thermodynamic properties of molecular hydrogen dissolved in water at pressures up to 200 MPa

    Energy Technology Data Exchange (ETDEWEB)

    Borysow, Jacek, E-mail: jborysow@mtu.edu; Rosso, Leonardo del; Celli, Milva; Ulivi, Lorenzo, E-mail: lorenzo.ulivi@isc.cnr.it [Consiglio Nazionale delle Ricerche, Istituto dei Sistemi Complessi, Via Madonna del piano 10, I-50019 Sesto Fiorentino (Italy); Moraldi, Massimo [Dipartimento di Fisica e Astronomia, Università degli Studi di Firenze, Via Sansone 1, I-50019 Sesto Fiorentino (Italy)

    2014-04-28

    We have measured the Raman Q-branch of hydrogen in a solution with water at a temperature of about 280 K and at pressures from 20 to 200 MPa. From a least-mean-square fitting analysis of the broad Raman Q-branch, we isolated the contributions from the four lowest individual roto-vibrational lines. The vibrational lines were narrower than the pure rotational Raman lines of hydrogen dissolved in water measured previously, but significantly larger than in the gas. The separations between these lines were found to be significantly smaller than in gaseous hydrogen and their widths were slightly increasing with pressure. The lines were narrowing with increasing rotational quantum number. The Raman frequencies of all roto-vibrational lines were approaching the values of gas phase hydrogen with increasing pressure. Additionally, from the comparison of the integrated intensity signal of Q-branch of hydrogen to the integrated Raman signal of the water bending mode, we have obtained the concentration of hydrogen in a solution with water along the 280 K isotherm. Hydrogen solubility increases slowly with pressure, and no deviation from a smooth behaviour was observed, even reaching thermodynamic conditions very close to the transition to the stable hydrogen hydrate. The analysis of the relative hydrogen concentration in solution on the basis of a simple thermodynamic model has allowed us to obtain the molar volume for the hydrogen gas/water solution. Interestingly, the volume relative to one hydrogen molecule in solution does not decrease with pressure and, at high pressure, is larger than the volume pertinent to one molecule of water. This is in favour of the theory of hydrophobic solvation, for which a larger and more stable structure of the water molecules is expected around a solute molecule.

  14. Spectroscopic and thermodynamic properties of molecular hydrogen dissolved in water at pressures up to 200 MPa.

    Science.gov (United States)

    Borysow, Jacek; del Rosso, Leonardo; Celli, Milva; Moraldi, Massimo; Ulivi, Lorenzo

    2014-04-28

    We have measured the Raman Q-branch of hydrogen in a solution with water at a temperature of about 280 K and at pressures from 20 to 200 MPa. From a least-mean-square fitting analysis of the broad Raman Q-branch, we isolated the contributions from the four lowest individual roto-vibrational lines. The vibrational lines were narrower than the pure rotational Raman lines of hydrogen dissolved in water measured previously, but significantly larger than in the gas. The separations between these lines were found to be significantly smaller than in gaseous hydrogen and their widths were slightly increasing with pressure. The lines were narrowing with increasing rotational quantum number. The Raman frequencies of all roto-vibrational lines were approaching the values of gas phase hydrogen with increasing pressure. Additionally, from the comparison of the integrated intensity signal of Q-branch of hydrogen to the integrated Raman signal of the water bending mode, we have obtained the concentration of hydrogen in a solution with water along the 280 K isotherm. Hydrogen solubility increases slowly with pressure, and no deviation from a smooth behaviour was observed, even reaching thermodynamic conditions very close to the transition to the stable hydrogen hydrate. The analysis of the relative hydrogen concentration in solution on the basis of a simple thermodynamic model has allowed us to obtain the molar volume for the hydrogen gas/water solution. Interestingly, the volume relative to one hydrogen molecule in solution does not decrease with pressure and, at high pressure, is larger than the volume pertinent to one molecule of water. This is in favour of the theory of hydrophobic solvation, for which a larger and more stable structure of the water molecules is expected around a solute molecule.

  15. Molecular phylogeny of bark and ambrosia beetles reveals multiple origins of fungus farming during periods of global warming

    Directory of Open Access Journals (Sweden)

    Jordal Bjarte H

    2012-08-01

    Full Text Available Abstract Background Fungus farming is an unusual life style in insects that has evolved many times in the wood boring weevils named ‘ambrosia beetles’. Multiple occurrences of this behaviour allow for a detailed comparison of the different origins of fungus farming through time, its directionality, and possible ancestral states. We tested these hypotheses with a phylogeny representing the largest data set to date, nearly 4 kb of nucleotides from COI, EF-1α, CAD, ArgK, 28S, and 200 scolytine taxa. Results Phylogenetic analyses using Bayesian or parsimony approaches placed the root of Scolytinae close to the tribe Scolytini and Microborus, but otherwise indicated low resolution at older nodes. More recent clades were well resolved, including ten origins of fungus farming. There were no subsequent reversals to bark or phloem feeding in the fungus farming clades. The oldest origin of fungus farming was estimated near 50 Ma, long after the origin of Scolytinae (100-120 Ma. Younger origins included the species rich Xyleborini, dated to 21 Ma. Sister group comparisons and test of independence between traits indicated that neither gregarious larval feeding nor regular inbreeding by sibling mating was strongly correlated with the origin of fungus farming. Conclusion Origins of fungus farming corresponded mainly with two periods of global warming in the Cenozoic era, which were characterised by broadly distributed tropical forests. Hence, it seems likely that warm climates and expanding tropical angiosperm forests played critical roles in the successful radiation of diverse fungus farming groups. However, further investigation will likely reveal additional biological factors that promote fungus farming.

  16. Molecular diversity and high virulence of Legionella pneumophila strains isolated from biofilms developed within a warm spring of a thermal spa

    Directory of Open Access Journals (Sweden)

    Chaabna Zineddine

    2013-01-01

    Full Text Available Abstract Background Several cases of legionellosis have been diagnosed in the same French thermal spa in 1986, 1994 and 1997. L. pneumophila serogroup 1 (Lp1 strains have been isolated from several patients, but the source of contamination was not identified despite the presence of different Lp1 in water samples of the three natural springs feeding the spa at this period. Results Our strategy was to investigate L. pneumophila (Lp strains from natural biofilms developed in a sulphur-rich warm spring of this contaminated site. Biofilm analysis revealed the presence of three Lp serogroups (Lp1, Lp10 and Lp12. Surprisingly, Lp10 and Lp12 were not reported in the previous described studies from water samples. Besides, the new seven Lp1 we isolated exhibit a high molecular diversity and have been differentiated in five classes according to their DNA genome patterns obtained by PFGE and mip sequences. It must be noted that these DNA patterns are original and unknown in databases. Interestingly, the 27 Lp environmental strains we isolated display a higher cytotoxicity and virulence towards the amoeba Acanthamoeba castellanii than those of known Lp1 epidemic strains. Conclusion The characteristics of Legionella pneumophila Lp1 strains isolated from the warm spring are in agreement with their presence in biofilms and their probable long-term persistence in this ecosystem.

  17. Atmospheric molecular hydrogen (H2) at the Shangdianzi regional background station in China

    Science.gov (United States)

    Luan, Tian; Fang, Shuangxi; Yao, Bo; Wang, Hongyang; Dong, Fan; Shi, Qingfeng; Zhou, Liyan; Zhou, Huaigang

    2016-11-01

    Atmospheric molecular hydrogen (H2) mole fractions have been continuously measured at the Shangdianzi regional station in China. In this study, we present the atmospheric H2 time series from January 2015 to April 2016, and investigate the diurnal and seasonal cycles, and the impact of meteorological factors on the observed values. Atmospheric H2 mole fractions at Shangdianzi vary from a minimum of 381 ppb (parts per billion, 10-9 dry air mole fraction) to a maximum of 1535 ppb, with a median of 510 ppb and a mean (± standard deviation) of 555 ± 113 ppb during the observation period. The results indicate that H2 mole fractions at Shangdianzi are frequently influenced by local sources and sinks. Regionally representative conditions account for 44.7% of the total records with a mean mole fraction of 488 ± 20 ppb. The highest regionally representative H2 mole fraction is observed in July, while the lowest is observed in October. Peak-to-trough amplitude in the seasonal cycle is 63 ± 3 ppb. H2 mole fractions show nighttime depletion in all seasons, with the lowest values in the morning (7:00-10:00 local time). The H2 mole fractions are also influenced by local surface wind direction at Shangdianzi. Winds from NW-NNW-N-NNE-NE-ENE-E directions are always associated with negative contribution to atmospheric H2 loading, whereas winds from SSW-SW-WSW-W directions generally enhance the H2 values. The results of trajectory clustering analysis demonstrate that air masses from a southerly direction induce high H2 mole fractions. Conversely, mean H2 mole fractions are low when air masses are from the north, northwest, and east directions.

  18. Learning probabilistic models of hydrogen bond stability from molecular dynamics simulation trajectories

    KAUST Repository

    Chikalov, Igor

    2011-02-15

    Background: Hydrogen bonds (H-bonds) play a key role in both the formation and stabilization of protein structures. They form and break while a protein deforms, for instance during the transition from a non-functional to a functional state. The intrinsic strength of an individual H-bond has been studied from an energetic viewpoint, but energy alone may not be a very good predictor.Methods: This paper describes inductive learning methods to train protein-independent probabilistic models of H-bond stability from molecular dynamics (MD) simulation trajectories of various proteins. The training data contains 32 input attributes (predictors) that describe an H-bond and its local environment in a conformation c and the output attribute is the probability that the H-bond will be present in an arbitrary conformation of this protein achievable from c within a time duration ?. We model dependence of the output variable on the predictors by a regression tree.Results: Several models are built using 6 MD simulation trajectories containing over 4000 distinct H-bonds (millions of occurrences). Experimental results demonstrate that such models can predict H-bond stability quite well. They perform roughly 20% better than models based on H-bond energy alone. In addition, they can accurately identify a large fraction of the least stable H-bonds in a conformation. In most tests, about 80% of the 10% H-bonds predicted as the least stable are actually among the 10% truly least stable. The important attributes identified during the tree construction are consistent with previous findings.Conclusions: We use inductive learning methods to build protein-independent probabilistic models to study H-bond stability, and demonstrate that the models perform better than H-bond energy alone. 2011 Chikalov et al; licensee BioMed Central Ltd.

  19. Learning Probabilistic Models of Hydrogen Bond Stability from Molecular Dynamics Simulation Trajectories

    KAUST Repository

    Chikalov, Igor

    2011-04-02

    Hydrogen bonds (H-bonds) play a key role in both the formation and stabilization of protein structures. H-bonds involving atoms from residues that are close to each other in the main-chain sequence stabilize secondary structure elements. H-bonds between atoms from distant residues stabilize a protein’s tertiary structure. However, H-bonds greatly vary in stability. They form and break while a protein deforms. For instance, the transition of a protein from a nonfunctional to a functional state may require some H-bonds to break and others to form. The intrinsic strength of an individual H-bond has been studied from an energetic viewpoint, but energy alone may not be a very good predictor. Other local interactions may reinforce (or weaken) an H-bond. This paper describes inductive learning methods to train a protein-independent probabilistic model of H-bond stability from molecular dynamics (MD) simulation trajectories. The training data describes H-bond occurrences at successive times along these trajectories by the values of attributes called predictors. A trained model is constructed in the form of a regression tree in which each non-leaf node is a Boolean test (split) on a predictor. Each occurrence of an H-bond maps to a path in this tree from the root to a leaf node. Its predicted stability is associated with the leaf node. Experimental results demonstrate that such models can predict H-bond stability quite well. In particular, their performance is roughly 20% better than that of models based on H-bond energy alone. In addition, they can accurately identify a large fraction of the least stable H-bonds in a given conformation. The paper discusses several extensions that may yield further improvements.

  20. Intramolecular hydrogen bonding and cooperative interactions in carbohydrates via the molecular tailoring approach.

    Science.gov (United States)

    Deshmukh, Milind M; Bartolotti, Libero J; Gadre, Shridhar R

    2008-01-17

    In spite of many theoretical and experimental attempts for understanding intramolecular hydrogen bonding (H-bonding) in carbohydrates, a direct quantification of individual intramolecular H-bond energies and the cooperativity among the H-bonded networks has not been reported in the literature. The present work attempts, for the first time, a direct estimation of individual intramolecular O-H...O interaction energies in sugar molecules using the recently developed molecular tailoring approach (MTA). The estimated H-bond energies are in the range of 1.2-4.1 kcal mol(-1). It is seen that the OH...O equatorial-equatorial interaction energies lie between 1.8 and 2.5 kcal mol(-1), with axial-equatorial ones being stronger (2.0-3.5 kcal mol(-1)). The strongest bonds are nonvicinal axial-axial H-bonds (3.0-4.1 kcal mol(-1)). This trend in H-bond energies is in agreement with the earlier reports based on the water-water H-bond angle, solvent-accessible surface area (SASA), and (1)H NMR analysis. The contribution to the H-bond energy from the cooperativity is also estimated using MTA. This contribution is seen to be typically between 0.1 and 0.6 kcal mol(-1) when H-bonds are a part of a relatively weak equatorial-equatorial H-bond network and is much higher (0.5-1.1 kcal mol(-1)) when H-bonds participate in an axial-axial H-bond network.

  1. CIRCUMBINARY GAS ACCRETION ONTO A CENTRAL BINARY: INFRARED MOLECULAR HYDROGEN EMISSION FROM GG Tau A

    Energy Technology Data Exchange (ETDEWEB)

    Beck, Tracy L.; Lubow, S. H. [Space Telescope Science Institute, 3700 San Martin Dr. Baltimore, MD 21218 (United States); Bary, Jeffrey S. [Department of Physics and Astronomy, Colgate University, 13 Oak Drive, Hamilton, NY 13346 (United States); Dutrey, Anne; Guilloteau, Stephane [Observatoire Aquitain des Sciences de l' Univers (OASU), Universite de Bordeaux, 2 rue de l' Observatoire, BP89, F-33271 Floirac Cedex (France); Pietu, Vincent [IRAM, 300 Rue de la Piscine, 38406 Saint Martin d' Heres (France); Simon, M., E-mail: tbeck@stsci.edu, E-mail: lubow@stsci.edu, E-mail: jbary@colgate.edu, E-mail: Anne.Dutrey@obs.u-bordeaux1.fr, E-mail: Stephane.Guilloteau@obs.u-bordeaux1.fr, E-mail: pietu@iram.fr, E-mail: michal.simon@sunysb.edu [Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794 (United States)

    2012-07-20

    We present high spatial resolution maps of ro-vibrational molecular hydrogen emission from the environment of the GG Tau A binary component in the GG Tau quadruple system. The H{sub 2} v = 1-0 S(1) emission is spatially resolved and encompasses the inner binary, with emission detected at locations that should be dynamically cleared on several hundred year timescales. Extensions of H{sub 2} gas emission are seen to {approx}100 AU distances from the central stars. The v = 2-1 S(1) emission at 2.24 {mu}m is also detected at {approx}30 AU from the central stars, with a line ratio of 0.05 {+-} 0.01 with respect to the v = 1-0 S(1) emission. Assuming gas in LTE, this ratio corresponds to an emission environment at {approx}1700 K. We estimate that this temperature is too high for quiescent gas heated by X-ray or UV emission from the central stars. Surprisingly, we find that the brightest region of H{sub 2} emission arises from a spatial location that is exactly coincident with a recently revealed dust 'streamer' which seems to be transferring material from the outer circumbinary ring around GG Tau A into the inner region. As a result, we identify a new excitation mechanism for ro-vibrational H{sub 2} stimulation in the environment of young stars. The H{sub 2} in the GG Tau A system appears to be stimulated by mass accretion infall as material in the circumbinary ring accretes onto the system to replenish the inner circumstellar disks. We postulate that H{sub 2} stimulated by accretion infall could be present in other systems, particularly binaries and 'transition disk' systems which have dust-cleared gaps in their circumstellar environments.

  2. High-frequency urban measurements of molecular hydrogen and carbon monoxide in the United Kingdom

    Directory of Open Access Journals (Sweden)

    A. Grant

    2010-05-01

    Full Text Available High-frequency measurements of atmospheric molecular hydrogen (H2 and carbon monoxide (CO were made at an urban site in the United Kingdom (UK from mid-December, 2008 until early March, 2009. Very few measurements of H2 exist in the urban environment, particularly within the UK, but are an essential component in the assessment of anthropogenic emissions of H2 and to a certain extent CO. These data provide detailed information on urban time-series, diurnal cycles as well as sources and sinks of both H2 and CO at urban locations. High-frequency data were found to be strongly influenced by local meteorological conditions of wind speed and temperature. Diurnal cycles were found to follow transport frequency very closely due to the sites proximity to major carriageways, consequently a strong correlation was found between H2 and CO mole fractions. Background subtracted mean and rush hour molar H2/CO emission ratios of 0.53±0.08 and 0.57±0.06 respectively, were calculated from linear fitting of data. The scatter plot of all H2 and CO data displayed an unusual two population pattern, thought to be associated with a large industrial area 85 km to the west of the site. However, the definitive source of this two branch pattern could not be fully elucidated. H2 emissions from transport in the UK were estimated to be 188±39 Gg H2/yr, with 8.1±2.3 Tg/yr of H2 produced from vehicle emissions globally. H2 and CO deposition velocities were calculated during stable night-time inversion events when a clear decay of both species was observed. CO was found to have a much higher deposition velocity than H2, 1.3±0.8×10−3 and 2.2±1.5×10−4 m s−1 (1σ respectively, going against the law of molecular diffusivity. The source of this unusual result was investigated, however no conclusive

  3. Molecular Hydrogen Absorption from the Halo of a z ˜ 0.4 Galaxy

    Science.gov (United States)

    Muzahid, Sowgat; Kacprzak, Glenn G.; Charlton, Jane C.; Churchill, Christopher W.

    2016-05-01

    Lyman- and Werner-band absorption of molecular hydrogen ({{{H}}}2) is detected in ˜50% of low-redshift (z\\lt 1) DLAs/sub-DLAs with N({{{H}}}2) \\gt {10}14.4 cm-2. However, the true origin(s) of the {{{H}}}2-bearing gas remain elusive. Here we report a new detection of an {{{H}}}2 absorber at {z}{{abs}} = 0.4298 in the Hubble Space Telescope (HST)/Cosmic Origins Spectrograph spectra of quasar PKS 2128-123. The total N({{H}} {{i}}) of {10}19.50+/- 0.15 cm-2 classifies the absorber as a sub-DLA. {{{H}}}2 absorption is detected up to the J = 3 rotational level with a total {log}N({{{H}}}2) = 16.36 ± 0.08, corresponding to a molecular fraction of {log}{f}{{{H}}2} = -2.84 ± 0.17. The excitation temperature of {T}{{ex}} = 206 ± 6 K indicates the presence of cold gas. Using detailed ionization modeling, we obtain a near-solar metallicity (i.e., [O/H] = -0.26 ± 0.19) and a dust-to-gas ratio of {log}κ ˜ -0.45 for the {{{H}}}2-absorbing gas. The host galaxy of the sub-DLA is detected at an impact parameter of ρ ˜ 48 kpc with an inclination angle of i ˜ 48° and an azimuthal angle of Φ ˜ 15° with respect to the QSO sightline. We show that corotating gas in an extended disk cannot explain the observed kinematics of Mg ii absorption. Moreover, the inferred high metallicity is not consistent with the scenario of gas accretion. An outflow from the central region of the host galaxy, on the other hand, would require a large opening angle (i.e., 2θ \\gt 150^\\circ ), much larger than the observed outflow opening angles in Seyfert galaxies, in order to intercept the QSO sightline. We thus favor a scenario in which the {{{H}}}2-bearing gas is stemming from a dwarf-satellite galaxy, presumably via tidal and/or ram pressure stripping. Detection of a dwarf galaxy candidate in the HST/WFPC2 image at an impact parameter of ˜12 kpc reinforces such an idea.

  4. Intermolecula transfer and elimination of molecular hydrogen in thermal reactions of unsaturated organic compounds

    Energy Technology Data Exchange (ETDEWEB)

    Suria, Sabartanty [Iowa State Univ., Ames, IA (United States)

    1995-02-10

    Two reactions which are important to coal liquefaction include intermolecular transfer and the elimination of two hydrogen atoms. We have designed several model reactions to probe the viability of several hydrogen transfer and elimination pathways. This report described studies on these reactions using organic model compounds.

  5. Adsorption of molecular hydrogen on an ultrathin layer of Ni(111) hydride

    NARCIS (Netherlands)

    Shan, J. J.; Kleyn, A. W.; Juurlink, L. B. F.

    2009-01-01

    We have used high resolution electron energy loss spectroscopy and temperature-programmed desorption to study the interaction of atomic hydrogen with Ni(1 1 1). Our results agree mostly with previous reports. We find that exposing Ni(1 1 1) to atomic hydrogen below 90 K leads to a 125 K TPD feature

  6. Car-Parrinello Molecular Dynamics Simulations of Infrared Spectra of Crystalline Vitamin C with Analysis of Double Minimum Proton Potentials for Medium-Strong Hydrogen Bonds.

    Science.gov (United States)

    Brela, Mateusz Z; Wójcik, Marek J; Boczar, Marek; Witek, Łukasz; Yasuda, Mitsuru; Ozaki, Yukihiro

    2015-06-25

    We studied proton dynamics of a hydrogen bonds of the crystalline l-ascorbic acid. Our approach was based on the Car-Parrinello molecular dynamics. The focal point of our study was simulation of the infrared spectra of l-ascorbic acid associated with the O-H stretching modes that are very sensitive to the strength of hydrogen bonding. In the l-ascorbic acid there are four kinds of hydrogen bonds. We calculated their spectra by using anharmonic approximation and the time course of the dipole moment function as obtained from the Car-Parrinello simulation. The quantization of the nuclear motion of the protons was made to perform detailed analysis of strength and properties of hydrogen bonds. We presented double minimum proton potentials with small value of barriers for medium-strong hydrogen bonds. We have also shown the difference character of medium-strong hydrogen bonds compared to weaker hydrogen bonds in the l-ascorbic acid.

  7. Molecular hydrogen (H2) emissions and their isotopic signatures (H/D) from a motor vehicle : implications on atmospheric H2

    NARCIS (Netherlands)

    Vollmer, M.K.; Walter, S.; Bond, S.W.; Soltic, P.; Röckmann, T.

    2010-01-01

    Molecular hydrogen (H2), its isotopic signature (deuterium/hydrogen, δD), carbon monoxide (CO) and other compounds were studied in the exhaust of a passenger car engine fuelled with gasoline or methane and run under variable air-fuel ratios and operating modes. H2 and CO concentrations were largely

  8. Molecular hydrogen (H2) emissions and their isotopic signatures (H/D) from a motor vehicle : implications on atmospheric H2

    NARCIS (Netherlands)

    Vollmer, M.K.; Walter, S.; Bond, S.W.; Soltic, P.; Röckmann, T.

    2010-01-01

    Molecular hydrogen (H2), its isotopic signature (deuterium/hydrogen, δD), carbon monoxide (CO) and other compounds were studied in the exhaust of a passenger car engine fuelled with gasoline or methane and run under variable air-fuel ratios and operating modes. H2 and CO concentrations were largely

  9. INFLUENCE OF SOLVENT ON INTRAMOLECULAR PROTON-TRANSFER IN HYDROGEN MALONATE - MOLECULAR-DYNAMICS SIMULATION STUDY OF TUNNELING BY DENSITY-MATRIX EVOLUTION AND NONEQUILIBRIUM SOLVATION

    NARCIS (Netherlands)

    MAVRI, J; BERENDSEN, HJC; VANGUNSTEREN, WF

    1993-01-01

    A density matrix evolution (DME) method (Berendsen, H. J. C.; Mavri, J. J. Phys. Chem. the preceding paper in this issue) in combination with classical molecular dynamics simulation was applied to calculate the rate of proton tunneling in the intramolecular double-well hydrogen bond of hydrogen malo

  10. Warm Inflation

    Directory of Open Access Journals (Sweden)

    Øyvind Grøn

    2016-09-01

    Full Text Available I show here that there are some interesting differences between the predictions of warm and cold inflation models focusing in particular upon the scalar spectral index n s and the tensor-to-scalar ratio r. The first thing to be noted is that the warm inflation models in general predict a vanishingly small value of r. Cold inflationary models with the potential V = M 4 ( ϕ / M P p and a number of e-folds N = 60 predict δ n s C ≡ 1 − n s ≈ ( p + 2 / 120 , where n s is the scalar spectral index, while the corresponding warm inflation models with constant value of the dissipation parameter Γ predict δ n s W = [ ( 20 + p / ( 4 + p ] / 120 . For example, for p = 2 this gives δ n s W = 1.1 δ n s C . The warm polynomial model with Γ = V seems to be in conflict with the Planck data. However, the warm natural inflation model can be adjusted to be in agreement with the Planck data. It has, however, more adjustable parameters in the expressions for the spectral parameters than the corresponding cold inflation model, and is hence a weaker model with less predictive force. However, it should be noted that the warm inflation models take into account physical processes such as dissipation of inflaton energy to radiation energy, which is neglected in the cold inflationary models.

  11. Molecularly Tuning the Radicaloid N-H···O═C Hydrogen Bond.

    Science.gov (United States)

    Lu, Norman; Chung, Wei-Cheng; Ley, Rebecca M; Lin, Kwan-Yu; Francisco, Joseph S; Negishi, Ei-Ichi

    2016-03-01

    Substituent effects on the open shell N-H···O═C hydrogen-bond has never been reported. This study examines how 12 functional groups composed of electron donating groups (EDG), halogen atoms and electron withdrawing groups (EWG) affect the N-H···O═C hydrogen-bond properties in a six-membered cyclic model system of O═C(Y)-CH═C(X)N-H. It is found that group effects on this open shell H-bonding system are significant and have predictive trends when X = H and Y is varied. When Y is an EDG, the N-H···O═C hydrogen-bond is strengthened; and when Y is an EWG, the bond is weakened; whereas the variation in electronic properties of X group do not exhibit a significant impact upon the hydrogen bond strength. The structural impact of the stronger N-H···O═C hydrogen-bond are (1) shorter H and O distance, r(H···O) and (2) a longer N-H bond length, r(NH). The stronger N-H···O═C hydrogen-bond also acts to pull the H and O in toward one another which has an effect on the bond angles. Our findings show that there is a linear relationship between hydrogen-bond angle and N-H···O═C hydrogen-bond energy in this unusual H-bonding system. In addition, there is a linear correlation of the r(H···O) and the hydrogen bond energy. A short r(H···O) distance corresponds to a large hydrogen bond energy when Y is varied. The observed trends and findings have been validated using three different methods (UB3LYP, M06-2X, and UMP2) with two different basis sets.

  12. A path integral molecular dynamics study of the hyperfine coupling constants of the muoniated and hydrogenated acetone radicals

    Science.gov (United States)

    Oba, Yuki; Kawatsu, Tsutomu; Tachikawa, Masanori

    2016-08-01

    The on-the-fly ab initio density functional path integral molecular dynamics (PIMD) simulations, which can account for both the nuclear quantum effect and thermal effect, were carried out to evaluate the structures and "reduced" isotropic hyperfine coupling constants (HFCCs) for muoniated and hydrogenated acetone radicals (2-muoxy-2-propyl and 2-hydoxy-2-propyl) in vacuo. The reduced HFCC value from a simple geometry optimization calculation without both the nuclear quantum effect and thermal effect is -8.18 MHz, and that by standard ab initio molecular dynamics simulation with only the thermal effect and without the nuclear quantum effect is 0.33 MHz at 300 K, where these two methods cannot distinguish the difference between muoniated and hydrogenated acetone radicals. In contrast, the reduced HFCC value of the muoniated acetone radical by our PIMD simulation is 32.1 MHz, which is about 8 times larger than that for the hydrogenated radical of 3.97 MHz with the same level of calculation. We have found that the HFCC values are highly correlated with the local molecular structures; especially, the Mu—O bond length in the muoniated acetone radical is elongated due to the large nuclear quantum effect of the muon, which makes the expectation value of the HFCC larger. Although our PIMD result calculated in vacuo is about 4 times larger than the measured experimental value in aqueous solvent, the ratio of these HFCC values between muoniated and hydrogenated acetone radicals in vacuo is in reasonable agreement with the ratio of the experimental values in aqueous solvent (8.56 MHz and 0.9 MHz); the explicit presence of solvent molecules has a major effect on decreasing the reduced muon HFCC of in vacuo calculations for the quantitative reproduction.

  13. The characterization of low energy molecular hydrogen ion—induced defects in synthetic diamond by optical absorption

    Institute of Scientific and Technical Information of China (English)

    MaZhong-Quan; AokiY; 等

    1998-01-01

    The results of optical absorption analysis of the synthetic diamonds(type Ib) which were implanted with 40 keV molecular hydrogen ions at doses of 1015-1017H/cm2(at 100K),showed that the increase of optical density(OD) of modified layer(-140nm) in UV-VIS region was dependent upon the damage level caused by ion implantation process.The range of relative optical band gap(Er.opt) around 2.0eV suggested that an amorphous carbon network structure like a-C film,which probably contains some localized subtetrabedral-coordinated clusters embedded in the fourflod(sp3) sites.was tentatively found in this layer,basing on the optical gap of carbon materials.The evolution of Er,opt with ion fluence indicated that no more hydrogenated carbon compositions were produced in as -implanted samples,while the increase of Er,opt with annealing temperature was very similar to that of hydrogen content dependence of Eopt in hydrogenately amorphous carbon(a-C:H):In addition the optical inhomogeneity of type Ib diamond has been revealed by a 2-dimension topograph in transmission mode at λ=430nm。

  14. Nano-design of quantum dot-based photocatalysts for hydrogen generation using advanced surface molecular chemistry

    KAUST Repository

    Yu, Weili

    2015-01-01

    Efficient photocatalytic hydrogen generation in a suspension system requires a sophisticated nano-device that combines a photon absorber with effective redox catalysts. This study demonstrates an innovative molecular linking strategy for fabricating photocatalytic materials that allow effective charge separation of excited carriers, followed by efficient hydrogen evolution. The method for the sequential replacement of ligands with appropriate molecules developed in this study tethers both quantum dots (QDs), as photosensitizers, and metal nanoparticles, as hydrogen evolution catalysts, to TiO2 surfaces in a controlled manner at the nano-level. Combining hydrophobic and hydrophilic interactions on the surface, CdSe-ZnS core-shell QDs and an Au-Pt alloy were attached to TiO2 without overlapping during the synthesis. The resultant nano-photocatalysts achieved substantially high-performance visible-light-driven photocatalysis for hydrogen evolution. All syntheses were conducted at room temperature and in ambient air, providing a promising route for fabricating visible-light-responsive photocatalysts.

  15. Potential of hydrogen bond in water. Comparison of the theory with vibrational spectra and results of molecular dynamics simulations.

    Science.gov (United States)

    Efimov, Yuri Ya; Naberukhin, Yuri I

    2011-02-01

    Potential of hydrogen bond is the function which relates its energy to geometrical parameters of hydrogen bridge: its length R(O…O) and angles between direction O…O and OH group [φ (H-O…O)] and/or lone pair of proton accepting oxygen atom [χ(-O…O)]. Previously we have suggested an approach to design such potentials based on the approximate numerical solution of a reverse problem of the spectrum band shape in the frames of the fluctuation theory of hydrogen bonding. In the given work this method is applied to construction of the two-parameter potentials that depend on parameters {R(O…O), φ (H-O…O} or {φ (H-O…O), χ (-O…O)}. Using them, the spectra of OH vibrations of HOD molecules in a liquid phase are calculated theoretically in good agreement with experiment in the temperature range up to 200 °C. Distributions of angles P(φ, T), P(χ, T), and energies P(E) are calculated also. The same distributions and spectra are independently calculated on the basis of the geometrical parameters of the hydrogen bridges obtained from molecular dynamics models of water. The shapes of the spectral contours and their temperature evolution calculated for computer models turned out to be similar to experimental ones only for the potential that includes the length of H-bond R(O…O).

  16. Molecular interactions with CO2 for controlling the regioselectivity of liquid phase hydrogenation of 2,4-dinitroaniline.

    Science.gov (United States)

    Yoshida, Hiroshi; Tomizawa, Akitoshi; Tachikawa, Hiroto; Fujita, Shin-Ichiro; Arai, Masahiko

    2014-09-21

    The catalytic hydrogenation of 2,4-dinitroaniline using a 0.5 wt% Pt/TiO2 catalyst was investigated in a multiphase medium of tetrahydrofuran (THF) pressurized by CO2 at different pressures and at 323 K. When CO2 pressure was increased, the overall rate of hydrogenation simply decreased but the selectivity to the desired product of 4-nitro-1,2-phenylenediamine increased. The noticeable enhancement of the selectivity to 4-nitro-1,2-phenylenediamine can be explained by chemical reactivities of CO2 molecules. In situ high-pressure FTIR and molecular simulations demonstrate that the dissolved CO2 molecules may interact with amino groups of the substrate and weaken the intra-hydrogen bonding between the amino and 2-nitro groups, which results in the change in the relative reactivity of the two nitro groups, yielding the desired product in a higher selectivity. The change in the intra- and inter-molecular interactions between the substrate and CO2 molecules was theoretically examined by DFT calculations.

  17. Exploring adsorption and desorption characteristics of molecular hydrogen on neutral and charged Mg nanoclusters: A first principles study

    Science.gov (United States)

    Banerjee, Paramita; Chandrakumar, K. R. S.; Das, G. P.

    2016-05-01

    To surmount the limitations of bulk MgH2 for the purpose of hydrogen storage, we report here, a detailed first principles density functional theory (DFT) based study on the structure and stability of neutral (Mgm) and positively charged (Mgm+) Mg nanoclusters of different sizes (m = 2, 4, 8 and 12) and their interaction with molecular hydrogen (H2). Our results demonstrate that H2 is weakly bound to the Mg nanoclusters through van der Waals interactions. Incorporation of Grimme's dispersion correction (D3) in the DFT based exchange-correlation functionals leads to improved accuracy of H2 interaction energy (IE) values that fall within an energy window (between physisorption and chemisorption) desirable for hydrogen storage. Energy decomposition analysis reveals the significance of polarization energy for these Mg-H2 binding. Ab-initio molecular dynamics simulation shows that complete dehydrogenation from these Mg nanoclusters occur at ∼100 °C which is a significant improvement over bulk MgH2 (∼300 °C).

  18. Enhancement of the efficiency of photocatalytic reduction of protons to hydrogen via molecular assembly.

    Science.gov (United States)

    Wu, Li-Zhu; Chen, Bin; Li, Zhi-Jun; Tung, Chen-Ho

    2014-07-15

    Conspectus One of the best solutions for meeting future energy demands is the conversion of water into hydrogen fuel using solar energy. The splitting of water into molecular hydrogen (H2) and oxygen (O2) using light involves two half-reactions: the oxidation of water to O2 and the reduction of protons to H2. To take advantage of the full range of the solar spectrum, researchers have extensively investigated artificial photosynthesis systems consisting of two photosensitizers and two catalysts with a Z-configuration: one photosensitizer-catalyst pair for H2 evolution and the other for O2 evolution. This type of complete artificial photosynthesis system is difficult to build and optimize; therefore, researchers typically study the reductive half-reaction and the oxidative half-reaction separately. To study the two half-reactions, researchers use a sacrificial electron donor to provide electrons for the reductive half-reaction, and a sacrificial electron acceptor to capture electrons for the oxidative half-reaction. After optimization, they can eliminate the added donors and acceptors as the two half reactions are coupled to a complete photocatalytic water spitting system. Most photocatalytic systems for the H2 evolution half-reaction consist of a photosensitizer, a catalyst, and a sacrificial electron donor. To promote photoinduced electron transfer and photocatalytic H2 production, these three components should be assembled together in a controlled manner. Researchers have struggled to design a photocatalytic system for H2 evolution that uses earth-abundant materials and is both efficient and durable. This Account reviews advances our laboratory has made in the development of new systems for photocatalytic H evolution that uses earth-abundant materials and is both efficient and durable. We used organometallic complexes and quantum-confined semiconductor nanocrystals (QDs) as photosensitizers, and [FeFe]-H2ase mimics and inorganic transition metal salts as catalysts

  19. The stable isotopic signature of biologically produced molecular hydrogen (H2

    Directory of Open Access Journals (Sweden)

    T. Röckmann

    2012-10-01

    Full Text Available Biologically produced molecular hydrogen (H2 is characterised by a very strong depletion in deuterium. Although the biological source to the atmosphere is small compared to photochemical or combustion sources, it makes an important contribution to the global isotope budget of H2. Large uncertainties exist in the quantification of the individual production and degradation processes that contribute to the atmospheric budget, and isotope measurements are a tool to distinguish the contributions from the different sources. Measurements of δ D from the various H2 sources are scarce and for biologically produced H2 only very few measurements exist. Here the first systematic study of the isotopic composition of biologically produced H2 is presented. In a first set of experiments, we investigated δ D of H2 produced in a biogas plant, covering different treatments of biogas production. In a second set of experiments, we investigated pure cultures of several H2 producing microorganisms such as bacteria or green algae. A Keeling plot analysis provides a robust overall source signature of δ D = −712‰ (±13‰ for the samples from the biogas reactor (at 38 °C, δ DH2O= +73.4‰, with a fractionation constant ϵH2-H2O of −689‰ (±20‰ between H2 and the water. The five experiments using pure culture samples from different microorganisms give a mean source signature of δ D = −728‰ (±28‰, and a fractionation constant ϵH2-H2O of −711‰ (±34‰ between H2 and the water. The results confirm the massive deuterium depletion of biologically produced H2 as was predicted by the calculation of the thermodynamic fractionation factors for hydrogen exchange between H2 and water vapour. Systematic errors in the isotope scale are difficult to assess in the absence of international standards for δ D of H2. As expected for a thermodynamic equilibrium, the fractionation factor is temperature dependent, but largely independent of the

  20. π-Hydrogen Bonding of Aromatics on the Surface of Aerosols: Insights from Ab Initio and Molecular Dynamics Simulation.

    Science.gov (United States)

    Feng, Ya-Juan; Huang, Teng; Wang, Chao; Liu, Yi-Rong; Jiang, Shuai; Miao, Shou-Kui; Chen, Jiao; Huang, Wei

    2016-07-14

    Molecular level insight into the interaction between volatile organic compounds (VOCs) and aerosols is crucial for improvement of atmospheric chemistry models. In this paper, the interaction between adsorbed toluene, one of the most significant VOCs in the urban atmosphere, and the aqueous surface of aerosols was studied by means of combined molecular dynamics simulations and ab initio quantum chemistry calculations. It is revealed that toluene can be stably adsorbed on the surface of aqueous droplets via hydroxyl-π hydrogen bonding between the H atoms of the water molecules and the C atoms in the aromatic ring. Further, significant modifications on the electrostatic potential map and frontier molecular orbital are induced by the solvation effect of surface water molecules, which would affect the reactivity and pathway of the atmospheric photooxidation of toluene. This study demonstrates that the surface interactions should be taken into consideration in the atmospheric chemical models on oxidation of aromatics.

  1. Cobalt and Nickel Diimine-Dioxime Complexes as Molecular Electrocatalysts for Hydrogen Evolution with Low Overvoltages

    National Research Council Canada - National Science Library

    Pierre-André Jacques; Vincent Artero; Jacques Pécaut; Marc Fontecave; Jean-Marie P. Lehn

    2009-01-01

    ...) Proc Natl Acad Sei USA 103:1209-1214]. Here, we report on a new family of cobalt and nickel diimine-dioxime complexes as efficient and stable electrocatalysts for hydrogen evolution from acidic nonaqueous solutions with slightly lower...

  2. Hydrogen bonding in the crystal structure of the molecular salt of pyrazole-pyrazolium picrate.

    Science.gov (United States)

    Su, Ping; Song, Xue-Gang; Sun, Ren-Qiang; Xu, Xing-Man

    2016-06-01

    The asymmetric unit of the title organic salt [systematic name: 1H-pyrazol-2-ium 2,4,6-tri-nitro-phenolate-1H-pyrazole (1/1)], H(C3H4N2)2 (+)·C6H2N3O7 (-), consists of one picrate anion and one hydrogen-bonded dimer of a pyrazolium monocation. The H atom involved in the dimer N-H⋯N hydrogen bond is disordered over both symmetry-unique pyrazole mol-ecules with occupancies of 0.52 (5) and 0.48 (5). In the crystal, the component ions are linked into chains along [100] by two different bifurcated N-H⋯(O,O) hydrogen bonds. In addition, weak C-H⋯O hydrogen bonds link inversion-related chains, forming columns along [100].

  3. Molecular simulation studies of metal organic frameworks focusing on hydrogen purification

    OpenAIRE

    Banu, Ana Maria

    2014-01-01

    The process of purifying hydrogen gas using pressure swing adsorption columns heavily relies on highly efficient adsorbents. Such materials must be able to selectively adsorb a large amount of impurities, and must also be regenerated with ease. The work presented in this thesis focuses on a novel class of porous solids, metal-organic frameworks (MOFs), and their potential for use as adsorbents in hydrogen purification processes. MOFs are tuneable structures, a property that can...

  4. The stable isotopic composition of molecular hydrogen in the tropopause region probed by the CARIBIC aircraft

    Science.gov (United States)

    Batenburg, A. M.; Schuck, T. J.; Baker, A. K.; Zahn, A.; Brenninkmeijer, C. A. M.; Röckmann, T.

    2012-05-01

    More than 450 air samples that were collected in the upper troposphere - lower stratosphere (UTLS) region by the CARIBIC aircraft (Civil Aircraft for the Regular Investigation of the atmosphere Based on an Instrument Container) have been analyzed for molecular hydrogen (H2) mixing ratios (χ(H2)) and H2 isotopic composition (deuterium content, δD). More than 120 of the analyzed samples contained air from the lowermost stratosphere (LMS). These show that χ(H2) does not vary appreciably with O3-derived height above the thermal tropopause (TP), whereas δD does increase with height. The isotope enrichment is caused by H2 production and destruction processes that enrich the stratospheric H2 reservoir in deuterium (D); the exact shapes of the profiles are mainly determined by mixing of stratospheric with tropospheric air. Tight negative correlations are found between δD and the mixing ratios of methane (χ(CH4)) and nitrous oxide (χ(N2O)), as a result of the relatively long lifetimes of these three species. The correlations are described by δD[‰]=-0.35 · χ(CH4)[ppb]+768 and δD[‰]=-1.90· χ(N2O)[ppb]+745. These correlations are similar to previously published results and likely hold globally for the LMS. Samples that were collected from the Indian subcontinent up to 40° N before, during and after the summer monsoon season show no significant seasonal change in χ(H2), but δD is up to 12.3‰ lower in the July, August and September monsoon samples. This δD decrease is correlated with the χ(CH4) increase in these samples. The significant correlation with χ(CH4) and the absence of a perceptible χ(H2) increase that accompanies the δD decrease indicates that microbial production of very D-depleted H2 in the wet season may contribute to this phenomenon. Some of the samples have very high χ(H2) and very low δD values, which indicates a pollution effect. Aircraft engine exhaust plumes are a suspected cause, since the effect mostly occurs in samples

  5. High precision quantum-chemical treatment of adsorption: Benchmarking physisorption of molecular hydrogen on graphane

    Science.gov (United States)

    Usvyat, Denis

    2015-09-01

    A multilevel hierarchical ab initio protocol for calculating adsorption on non-conducting surfaces is presented. It employs fully periodic treatment, which reaches local Møller-Plesset perturbation theory of second order (MP2) with correction for the basis set incompleteness via the local F12 technique. Post-MP2 corrections are calculated using finite clusters. That includes the coupled cluster treatment in the local and canonical frameworks (up to perturbative quadruples) and correlated core (with MP2). Using this protocol, the potential surface of hydrogen molecules adsorbed on graphane was computed. According to the calculations, hydrogen molecules are adsorbed on graphane in a perpendicular to the surface orientation with the minimum of the potential surface of around -3.6 kJ/mol located at the distance of 3.85 Å between the bond center of the hydrogen molecule and the mid-plane of graphane. The adsorption sites along the path from the downward-pointing carbon to the ring center of the graphane are energetically virtually equally preferable, which can enable nearly free translations of hydrogen molecules along these paths. Consequently, the hydrogen molecules on graphane most likely form a non-commensurate monolayer. The analysis of the remaining errors reveals a very high accuracy of the computed potential surface with an error bar of a few tenths of a kJ/mol. The obtained results are a high-precision benchmark for further theoretical and experimental studies of hydrogen molecules interacting with graphane.

  6. High precision quantum-chemical treatment of adsorption: Benchmarking physisorption of molecular hydrogen on graphane

    Energy Technology Data Exchange (ETDEWEB)

    Usvyat, Denis, E-mail: denis.usvyat@chemie.uni-regensburg.de [Institute for Physical and Theoretical Chemistry, Universität Regensburg, Universitätsstrasse 31, D-93040 Regensburg (Germany)

    2015-09-14

    A multilevel hierarchical ab initio protocol for calculating adsorption on non-conducting surfaces is presented. It employs fully periodic treatment, which reaches local Møller-Plesset perturbation theory of second order (MP2) with correction for the basis set incompleteness via the local F12 technique. Post-MP2 corrections are calculated using finite clusters. That includes the coupled cluster treatment in the local and canonical frameworks (up to perturbative quadruples) and correlated core (with MP2). Using this protocol, the potential surface of hydrogen molecules adsorbed on graphane was computed. According to the calculations, hydrogen molecules are adsorbed on graphane in a perpendicular to the surface orientation with the minimum of the potential surface of around −3.6 kJ/mol located at the distance of 3.85 Å between the bond center of the hydrogen molecule and the mid-plane of graphane. The adsorption sites along the path from the downward-pointing carbon to the ring center of the graphane are energetically virtually equally preferable, which can enable nearly free translations of hydrogen molecules along these paths. Consequently, the hydrogen molecules on graphane most likely form a non-commensurate monolayer. The analysis of the remaining errors reveals a very high accuracy of the computed potential surface with an error bar of a few tenths of a kJ/mol. The obtained results are a high-precision benchmark for further theoretical and experimental studies of hydrogen molecules interacting with graphane.

  7. Rototranslational collision-induced absorption and collision-induced light scattering spectra of molecular hydrogen using isotropic intermolecular potentials

    Science.gov (United States)

    El-Kader, M. S. A.; Maroulis, G.; Bich, E.

    2012-07-01

    Quantum mechanical lineshapes of collision-induced absorption (CIA) at different temperatures and of collision-induced light scattering (CILS) at room temperature are computed for gaseous molecular hydrogen using theoretical values for induced dipole moments and pair-polarizability trace and anisotropy as input. Comparison with measured spectra of absorption, isotropic and anisotropic light scattering shows satisfactory agreement, for which the uncertainty in measurement of its spectral moments is seen to be large. Empirical models of the dipole moment and pair-polarizability trace and anisotropy which reproduce the experimental spectra and the first three spectral moments more closely than the fundamental theory are also given. Good agreement between computed and experimental lineshapes of both absorption and scattering is obtained when potential models which are constructed from the thermophysical, transport, total scattering cross-section and spectroscopic properties are used. Also, the use of the new potential in lattice dynamic calculations yields good results for several properties of solid hydrogen.

  8. Molecular hydrogen as a mesospheric hydrogen reservoir; evidence from tracer-tracer interrelationships in descended air measured within the northern polar stratospheric vortex

    Science.gov (United States)

    Meredith, L. K.; Ray, E. A.; Moore, F. L.; Plumb, R. A.

    2010-12-01

    The distribution and partitioning of all hydrogen-carrying species in and above the mesosphere inform our understanding of upper atmospheric chemistry and transport; however, many species are not easily measured. Molecular hydrogen (H2) is described as a mesospheric reservoir of hydrogen atoms released from methane (CH4) oxidation and water vapor (H2O) photolysis. Only limited indirect measurements and modeling studies have provided evidence for this reservoir until now. Measuring air that descends from upper levels within polar stratospheric vortices provides a unique opportunity to sample the chemical composition of the mesosphere at more accessible stratospheric altitudes. Such measurements were made of atmospheric H2 by the balloonborne, in situ Lightweight Airborne Chromatograph Experiment (LACE) instrument during the 1999-2000 SAGE III Ozone Loss and Validation Experiment (SOLVE). Vertical profiles of a number of tracers were made in November 1999 after the vortex formation and again in March 2000 just before vortex breakup. The tropospheric-stratospheric H2 profile shifted dramatically from being vertically uniform (~0.5 ppm) in the young vortex to exhibiting distinct minimum (~0.4 ppm) and maximum (~1 ppm) peak features after a winter of mixing and descent in the late polar vortex. Both observational and model results show that a significant fraction of mesospheric air was present in the late vortex, suggesting that the late vortex H2 features were of mesospheric origin. The goal of this study is to determine whether the chemical measurements made with LACE confirm the anticipated H2 mixing ratio peak in the mesosphere. Tracer-tracer interrelationships of H2 with concurrently measured tracers, such as SF6, CO, N2O, and CFCs, are used to determine the original altitude and mixing ratio of the H2 peak. A simple model of mixing and descent within the vortex will be used to infer the altitude distribution of H2 in the mesosphere by forcing its consistency with

  9. Neutron Scattering of Residual Hydrogen in 1,4-Dioxane-D8 Liquid. Understanding Measurements with Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    de Almeida, Valmor F. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Liu, Hongjun [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Herwig, Kenneth W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Kidder, Michelle [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2016-01-25

    That incoherent scattering from protiated molecular liquids adds a constant background to the measured scattering intensity is well known, but less appreciated is the fact that coherent scattering is also induced by the presence of hydrogen in a deuterated liquid. In fact, the scattering intensity can be very sensitive, in the small-q region, with respect to the amounts and distribution of residual H in the system. We used 1,4-dioxane liquid to demonstrate that the partial structure factors of the HD and DD atom pairs contribute significantly to inter-molecular scattering and that uncertainty in the extent of deuteration account for discrepancies between simulations and measurements. Both contributions to uncertainty have similar magnitudes: scattering interference of the hydrogen-deuterium pair, and complementary interference from the deuterium-deuterium pair by virtue of chemical inhomogeneity. This situation arises in practice since deuteration of liquids is often 99% or less. A combined experimental and extensive computational study of static thermal neutron scattering of 1,4-dioxane demonstrates the foregoing. We show, through simulations, that the reason for the differences is the content of protiated dioxane (vendors quote 1%). We estimate that up to 5% (at 298K and at 343K) protiated mole fraction may be involved in generating the scattering differences. Finally, we find that the particular distribution of hydrogen in the protiated molecules affects the results significantly; here we considered molecules to be either fully protiated or fully deuterated. This scenario best reconciles the computational and experimental results, and leads us to speculate that the deuteration synthesis process tends to leave a molecule either fully deuterated or fully protiated. Although we have used 1,4-dioxane as a model liquid, the effects described in this study extend to similar liquids and similar systematic experimental/computational studies can be performed to either

  10. The Transition from Atomic to Molecular Hydrogen in Interstellar Clouds: 21cm Signature of the Evolution of Cold Atomic Hydrogen in Dense Clouds

    CERN Document Server

    Goldsmith, P F; Krco, M; Goldsmith, Paul F.; Li, Di; Krco, Marko

    2006-01-01

    We have investigated the time scale for formation of molecular clouds by examining the conversion of HI to H2 using a time-dependent model. H2 formation on dust grains and cosmic ray and photo destruction are included in one-dimensional model slab clouds which incorporate time-independent density and temperature distributions. We calculate 21cm spectral line profiles seen in absorption against a background provided by general Galactic HI emission, and compare the model spectra with HI Narrow Self-Absorption, or HINSA, profiles absorbed in a number of nearby molecular clouds. The time evolution of the HI and H2 densities is dramatic, with the atomic hydrogen disappearing in a wave propagating from the central, denser regions which have a shorter H2 formation time scale, to the edges, where the density is lower and the time scale for H2 formation longer. The model 21cm spectra are characterized by very strong absorption at early times, when the HI column density through the model clouds is extremely large. The ...

  11. Infrared spectral evidence and DFT calculations of hydrogen-bonding and molecular structures of acetogenins

    Science.gov (United States)

    Afonso, Sabrina; Silva, Fabiano B.; Silva, Arnaldo F.; Scarminio, Ieda S.; Bruns, Roy E.

    2017-02-01

    FTIR spectra have been measured for 31 different five component - simplex centroid design solvent mixture extracts of shaded and sun-exposed Annonaceous leaves harvested in all four seasons. The spectral frequencies are characteristic of anonnaceous acetogenins known to be a major component of these leaves. Osbnd H stretching spectral bands in the 3100-3600 cm-1 region provide evidence of notable intensity changes for the shaded and sun-exposed leaves. Chemometric principal component analysis involving 264 spectra show that shaded samples tend to have more intense Osbnd H stretching bands than those grown in the sun. B3LYP density functional calculations indicate significant Osbnd H stretching band changes in this region owing to hydrogen bond formation. Weak Osbnd H intensity enhancements, around 40 km mol-1, occur when an Osbnd H group forms a hydrogen bond with the oxygen atom of an adjacent tetrahydrofuran ring oxygen atom. Much more intense enhancements, 400-500 km mol-1, are predicted to occur for acetogenins with two tetrahydrofuran rings for which the Osbnd H group hydrogen bonds with its fartherest removed tetrahydrofuran ring oxygen. Whereas weak or moderate H-bond stretching intensities are obtained for acetogenins with slightly bent carbon chain structures the strongest hydrogen bond intensities are calculated for molecules with a 45° V-type backbone structure. These important structural modifications as well as significant changes in bond lengths and angles owing to hydrogen bonding are detailed.

  12. Molecular Seesaw: How Increased Hydrogen Bonding Can Hinder Excited-State Proton Transfer.

    Science.gov (United States)

    Welsch, Ralph; Driscoll, Eric; Dawlaty, Jahan M; Miller, Thomas F

    2016-09-15

    A previously unexplained effect in the relative rate of excited-state intramolecular proton transfer (ESIPT) in related indole derivatives is investigated using both theory and experiment. Ultrafast spectroscopy [ J. Phys. Chem. A, 2015, 119, 5618-5625 ] found that although the diol 1,3-bis(2-pyridylimino)-4,7-dihydroxyisoindole exhibits two equivalent intramolecular hydrogen bonds, the ESIPT rate associated with tautomerization of either hydrogen bond is a factor of 2 slower than that of the single intramolecular hydrogen bond in the ethoxy-ol 1,3-bis(2-pyridylimino)-4-ethoxy-7-hydroxyisoindole. Excited-state electronic structure calculations suggest a resolution to this puzzle by revealing a seesaw effect in which the two hydrogen bonds of the diol are both longer than the single hydrogen bond in the ethoxy-ol. Semiclassical rate theory recovers the previously unexplained trends and leads to clear predictions regarding the relative H/D kinetic isotope effect (KIE) for ESIPT in the two systems. The theoretical KIE predictions are tested using ultrafast spectroscopy, confirming the seesaw effect.

  13. The role of the molecular-metallic transition of hydrogen in the evolution of Jupiter, Saturn, and brown dwarfs

    Science.gov (United States)

    Saumon, Didier; Hubbard, William B.; Chabrier, Gilles; Van Horn, Hugh M.

    1992-01-01

    An equation of state for hydrogen which predicts a molecular-metallic phase transition at finite temperatures has become available recently. The effect of this phase transition on the cooling histories of these two giant planets and of substellar brown dwarfs is studied. The phase transition alters the present age of Jupiter and of Saturn by a few percent. Interestingly, the cooling of brown dwarfs is most strongly affected at the time when the interior adiabat crosses the critical point of the phase transition.

  14. Molecular dynamics studies of electron-ion temperature equilibration in hydrogen plasmas within the coupled-mode regime

    Science.gov (United States)

    Benedict, Lorin X.; Surh, Michael P.; Stanton, Liam G.; Scullard, Christian R.; Correa, Alfredo A.; Castor, John I.; Graziani, Frank R.; Collins, Lee A.; Čertík, Ondřej; Kress, Joel D.; Murillo, Michael S.

    2017-04-01

    We use classical molecular dynamics (MD) to study electron-ion temperature equilibration in two-component plasmas in regimes for which the presence of coupled collective modes has been predicted to substantively reduce the equilibration rate. Guided by previous kinetic theory work, we examine hydrogen plasmas at a density of n =1026cm-3 , Ti=105K , and 107K theory including the QSPs. In particular, it is shown that the energy equilibration rates from MD are more similar to those of the theory when coupled modes are neglected. We suggest possible reasons for this surprising result and propose directions of further research along these lines.

  15. The role of the molecular-metallic transition of hydrogen in the evolution of Jupiter, Saturn, and brown dwarfs

    Science.gov (United States)

    Saumon, Didier; Hubbard, William B.; Chabrier, Gilles; Van Horn, Hugh M.

    1992-01-01

    An equation of state for hydrogen which predicts a molecular-metallic phase transition at finite temperatures has become available recently. The effect of this phase transition on the cooling histories of these two giant planets and of substellar brown dwarfs is studied. The phase transition alters the present age of Jupiter and of Saturn by a few percent. Interestingly, the cooling of brown dwarfs is most strongly affected at the time when the interior adiabat crosses the critical point of the phase transition.

  16. A Molecular Copper Catalyst for Hydrogenation of CO­2 to Formate

    Energy Technology Data Exchange (ETDEWEB)

    Zall, Christopher M.; Linehan, John C.; Appel, Aaron M.

    2015-09-04

    There is widespread interest in the hydrogenation of CO2 to energy-rich products such as formate. However, first-row transition metal complexes that catalyze the hydrogenation of CO2 to formate remain rare. Copper phosphine complexes are widely used in the reduction of organic substrates but have not previously been used as catalysts for the conversion of H2 and CO2 to formate. Here we demonstrate that the triphosphine-ligated copper(I) complex LCu(MeCN)PF6 is an active catalyst for CO2 hydrogenation in the presence of a suitable base. Screening of bases and studies of catalytic reactions by in operando spectroscopy revealed important and unusual roles for the base in promoting H2 activation and turnover.

  17. High-energy, stable and recycled molecular solar thermal storage materials using AZO/graphene hybrids by optimizing hydrogen bonds

    Science.gov (United States)

    Luo, Wen; Feng, Yiyu; Qin, Chengqun; Li, Man; Li, Shipei; Cao, Chen; Long, Peng; Liu, Enzuo; Hu, Wenping; Yoshino, Katsumi; Feng, Wei

    2015-10-01

    An important method for establishing a high-energy, stable and recycled molecular solar heat system is by designing and preparing novel photo-isomerizable molecules with a high enthalpy and a long thermal life by controlling molecular interactions. A meta- and ortho-bis-substituted azobenzene chromophore (AZO) is covalently grafted onto reduced graphene oxide (RGO) for solar thermal storage materials. High grafting degree and close-packed molecules enable intermolecular hydrogen bonds (H-bonds) for both trans-(E) and cis-(Z) isomers of AZO on the surface of nanosheets, resulting in a dramatic increase in enthalpy and lifetime. The metastable Z-form of AZO on RGO is thermally stabilized with a half-life of 52 days by steric hindrance and intermolecular H-bonds calculated using density functional theory (DFT). The AZO-RGO fuel shows a high storage capacity of 138 Wh kg-1 by optimizing intermolecular H-bonds with a good cycling stability for 50 cycles induced by visible light at 520 nm. Our work opens up a new method for making advanced molecular solar thermal storage materials by tuning molecular interactions on a nano-template.An important method for establishing a high-energy, stable and recycled molecular solar heat system is by designing and preparing novel photo-isomerizable molecules with a high enthalpy and a long thermal life by controlling molecular interactions. A meta- and ortho-bis-substituted azobenzene chromophore (AZO) is covalently grafted onto reduced graphene oxide (RGO) for solar thermal storage materials. High grafting degree and close-packed molecules enable intermolecular hydrogen bonds (H-bonds) for both trans-(E) and cis-(Z) isomers of AZO on the surface of nanosheets, resulting in a dramatic increase in enthalpy and lifetime. The metastable Z-form of AZO on RGO is thermally stabilized with a half-life of 52 days by steric hindrance and intermolecular H-bonds calculated using density functional theory (DFT). The AZO-RGO fuel shows a high

  18. Molecular recognition and self-assembly special feature: Self-assembled biomimetic [2Fe2S]-hydrogenase-based photocatalyst for molecular hydrogen evolution.

    Science.gov (United States)

    Kluwer, A M; Kapre, R; Hartl, F; Lutz, M; Spek, A L; Brouwer, A M; van Leeuwen, P W N M; Reek, J N H

    2009-06-30

    The large-scale production of clean energy is one of the major challenges society is currently facing. Molecular hydrogen is envisaged as a key green fuel for the future, but it becomes a sustainable alternative for classical fuels only if it is also produced in a clean fashion. Here, we report a supramolecular biomimetic approach to form a catalyst that produces molecular hydrogen using light as the energy source. It is composed of an assembly of chromophores to a bis(thiolate)-bridged diiron ([2Fe2S]) based hydrogenase catalyst. The supramolecular building block approach introduced in this article enabled the easy formation of a series of complexes, which are all thoroughly characterized, revealing that the photoactivity of the catalyst assembly strongly depends on its nature. The active species, formed from different complexes, appears to be the [Fe(2)(micro-pdt)(CO)(4){PPh(2)(4-py)}(2)] (3) with 2 different types of porphyrins (5a and 5b) coordinated to it. The modular supramolecular approach was important in this study as with a limited number of building blocks several different complexes were generated.

  19. Variation of molecular hydrogen tropospheric concentration over Southern Poland - results of the continuous chromatographic measurements.

    Science.gov (United States)

    Necki, J.; Chmura, L.

    2012-04-01

    Although hydrogen is one of the fundamental constituents of the earth's atmosphere its global balance is still poorly clarified. A few developed inventories diverging values for efficiency of sources and sinks of this gas. The European network for the hydrogen concentrations measurement is based on several unevenly spaced measurement points. While in 2009 MPI Jena has delivered accurate scale for hydrogen measurements and the techniques of analyses are well described, still large areas of Central Europe is uncovered by representative stations. The first measurement point, established under the EUROHYDROS EU program, on the territory of Poland was Kraków city. Different laboratory setups was tested there and compared to each other. The Kraków area has significant car traffic and its geographical location implies frequent temperature inversions in lower troposphere leading to the accumulation of trace gases in atmosphere of the city. Observations launched in 2007 revealed that the concentration of hydrogen fluctuates strongly within diurnal and seasonal timescales. Its average concentration is three times larger than this, observed at the other stations. The European "background" concentrations of hydrogen are not reflected in the Krakow record. An ideal place to carry out observation of the regional air composition for Central Europe is a research station located in the meteorological observatory at Kasprowy Wierch. Measurement point at the top of mountain peak with elevation of 2000m a.s.l. gives an access to the well mixed troposphere. The station delivers also the necessary facilities and logistics. Since year 1996 greenhouse gas measurement program has been operating at this point. The first measurements of atmospheric concentrations of hydrogen at Kasprowy Wierch were performed in year 2010, based on dedicated gas chromatograph using RGD detector installed at the station. Analysis of hydrogen content in the outside air is performed without any enrichment

  20. Car-Parrinello and path integral molecular dynamics study of the hydrogen bond in the chloroacetic acid dimer system.

    Science.gov (United States)

    Durlak, Piotr; Morrison, Carole A; Middlemiss, Derek S; Latajka, Zdzislaw

    2007-08-14

    We have studied the double proton transfer (DPT) reaction in the cyclic dimer of chloroacetic acid using both classical and path integral Car-Parrinello molecular dynamics. We also attempt to quantify the errors in the potential energy surface that arise from the use of a pure density functional. In the classical dynamics a clear reaction mechanism can be identified, where asynchronized DPT arises due to coupling between the O-H stretching oscillator and several low energy intermolecular vibrational modes. This mechanism is considerably altered when quantum tunneling is permitted in the simulation. The introduction of path integrals leads to considerable changes in the thermally averaged molecular geometry, leading to shorter and more centered hydrogen bond linkages.

  1. Car-Parrinello and path integral molecular dynamics study of the hydrogen bond in the chloroacetic acid dimer system

    Science.gov (United States)

    Durlak, Piotr; Morrison, Carole A.; Middlemiss, Derek S.; Latajka, Zdzislaw

    2007-08-01

    We have studied the double proton transfer (DPT) reaction in the cyclic dimer of chloroacetic acid using both classical and path integral Car-Parrinello molecular dynamics. We also attempt to quantify the errors in the potential energy surface that arise from the use of a pure density functional. In the classical dynamics a clear reaction mechanism can be identified, where asynchronized DPT arises due to coupling between the O-H stretching oscillator and several low energy intermolecular vibrational modes. This mechanism is considerably altered when quantum tunneling is permitted in the simulation. The introduction of path integrals leads to considerable changes in the thermally averaged molecular geometry, leading to shorter and more centered hydrogen bond linkages.

  2. Rotational quenching of H$_2$CO by molecular hydrogen – Suggestion on the work ofWiesenfeld & Faure

    Indian Academy of Sciences (India)

    MOHIT KUMAR SHARMA; MONIKA SHARMA; SURESH CHANDRA

    2017-01-01

    Wiesenfeld and Faure investigated rotational quenching of H$_2$CO by molecular hydrogen where they considered 40 rotational levels of $o$-H$_2$CO and 41 rotational levels of $p$-H$_2$CO. Data on energies of rotationallevels of the molecule are fundamental in the investigation. We have found that the sequence of levels reported by Wiesenfeld and Faure is not as per convention of molecular physics. Their results are also available on the website: http://home.strw.leidenuniv.nl/∼moldata/datafiles/ph2co-h2.dat, where the collisional transitions are shown even between the levels having equal energies. Data for such transitions should not be there.

  3. The stable isotopic composition of molecular hydrogen in the tropopause region probed by the CARIBIC aircraft

    Directory of Open Access Journals (Sweden)

    A. M. Batenburg

    2012-05-01

    Full Text Available More than 450 air samples that were collected in the upper troposphere – lower stratosphere (UTLS region by the CARIBIC aircraft (Civil Aircraft for the Regular Investigation of the atmosphere Based on an Instrument Container have been analyzed for molecular hydrogen (H2 mixing ratios (χ(H2 and H2 isotopic composition (deuterium content, δD.

    More than 120 of the analyzed samples contained air from the lowermost stratosphere (LMS. These show that χ(H2 does not vary appreciably with O3-derived height above the thermal tropopause (TP, whereas δD does increase with height. The isotope enrichment is caused by H2 production and destruction processes that enrich the stratospheric H2 reservoir in deuterium (D; the exact shapes of the profiles are mainly determined by mixing of stratospheric with tropospheric air. Tight negative correlations are found between δD and the mixing ratios of methane (χ(CH4 and nitrous oxide (χ(N2O, as a result of the relatively long lifetimes of these three species. The correlations are described by δD[‰]=−0.35 · χ(CH4[ppb]+768 and δD[‰]=−1.90· χ(N2O[ppb]+745. These correlations are similar to previously published results and likely hold globally for the LMS.

    Samples that were collected from the Indian subcontinent up to 40° N before, during and after the summer monsoon season show no significant seasonal change in χ(H2, but δD is up to 12.3‰ lower in the July, August and September monsoon samples. This δD decrease is correlated with the χ(CH4 increase in these samples. The significant correlation with χ(CH4 and the absence of a perceptible χ(H2 increase that accompanies the δD decrease indicates that microbial production of

  4. Rototranslational collision-induced absorption and collision-induced light scattering spectra of molecular hydrogen using isotropic intermolecular potentials

    Energy Technology Data Exchange (ETDEWEB)

    El-Kader, M.S.A., E-mail: Mohamedsay68@hotmail.com [Department of Engineering Mathematics and Physics, Faculty of Engineering, Cairo University, Giza 12211 (Egypt); Maroulis, G. [Department of Chemistry, University of Patras, GR-26500 Patras (Greece); Bich, E. [Institut fuer Chemie, Universitaet Rostock Albert-Einstein-Strasse 3a, D-18059 Rostock (Germany)

    2012-07-25

    Highlights: Black-Right-Pointing-Pointer We have determined an isotropic intermolecular potential for the interaction of hydrogen. Black-Right-Pointing-Pointer The thermophysical and transport properties are calculated for this system. Black-Right-Pointing-Pointer The rovibrational energy levels and scattering cross-sections are determined. Black-Right-Pointing-Pointer We have adopted a model for the induced dipole moment {mu}(r) with adjustable parameters. Black-Right-Pointing-Pointer The quantum lineshapes of absorption and scattering are calculated. -- Abstract: Quantum mechanical lineshapes of collision-induced absorption (CIA) at different temperatures and of collision-induced light scattering (CILS) at room temperature are computed for gaseous molecular hydrogen using theoretical values for induced dipole moments and pair-polarizability trace and anisotropy as input. Comparison with measured spectra of absorption, isotropic and anisotropic light scattering shows satisfactory agreement, for which the uncertainty in measurement of its spectral moments is seen to be large. Empirical models of the dipole moment and pair-polarizability trace and anisotropy which reproduce the experimental spectra and the first three spectral moments more closely than the fundamental theory are also given. Good agreement between computed and experimental lineshapes of both absorption and scattering is obtained when potential models which are constructed from the thermophysical, transport, total scattering cross-section and spectroscopic properties are used. Also, the use of the new potential in lattice dynamic calculations yields good results for several properties of solid hydrogen.

  5. Investigations of an O-H...S hydrogen bond via Car-Parrinello and path integral molecular dynamics.

    Science.gov (United States)

    Jezierska, Aneta; Panek, Jarosław J

    2009-06-01

    The presence of intramolecular hydrogen bonds influences the binding energy, tautomeric equilibrium, and spectroscopic properties of various classes of organic molecules. This article discusses the O-H...S bridge, one of the less commonly investigated types of intramolecular interactions. 3-mercapto-1,3-diphenylprop-2-en-1-one was considered as the model structure. This compound exhibits photochromic properties. Car-Parrinello molecular dynamics (CPMD) was applied to investigate the spectroscopic and molecular properties of this compound in the gas phase and in the solid state. The second part of the study is devoted to the effects of the quantization of nuclear motions, with special attention to the O-H...S moiety. Path integral molecular dynamics (PIMD) of the molecular crystal of 3-mercapto-1,3-diphenylprop-2-en-1-one was carried out for this purpose. The employment of this fully quantum mechanical technique enables one to study, in a time-averaged sense, the zero-point motion important for flat potential energy surfaces. Finally, the potentials of mean force (Pmfs) were calculated from the CPMD and PIMD data obtained for the solid-state calculations. The effect of including quantum nuclear motion was investigated. In the studied compound, quantum effects shortened the H-bridge and provided a better description of the free energy minimum. The computational results place this uncommon intramolecular H-bonding among the class of strong hydrogen bonds with large red shifts of O-H stretching modes, which correspond well with previously presented experimental data in the literature concerning this structure. 2008 Wiley Periodicals, Inc.

  6. Determination of the Relative Atomic Masses of Metals by Liberation of Molecular Hydrogen

    Science.gov (United States)

    Waghorne, W. Earle; Rous, Andrew J.

    2009-01-01

    Students determine the relative atomic masses of calcium, magnesium, and aluminum by reaction with hydrochloric acid and measurement of the volume of hydrogen gas liberated. The experiment demonstrates stoichiometry and illustrates clearly that mass of the reagent is not the determinant of the amounts in chemical reactions. The experiment is…

  7. Determination of the Relative Atomic Masses of Metals by Liberation of Molecular Hydrogen

    Science.gov (United States)

    Waghorne, W. Earle; Rous, Andrew J.

    2009-01-01

    Students determine the relative atomic masses of calcium, magnesium, and aluminum by reaction with hydrochloric acid and measurement of the volume of hydrogen gas liberated. The experiment demonstrates stoichiometry and illustrates clearly that mass of the reagent is not the determinant of the amounts in chemical reactions. The experiment is…

  8. Molecular hydrogen: An abundant energy source for bacterial activity in nuclear waste repositories

    Science.gov (United States)

    Libert, M.; Bildstein, O.; Esnault, L.; Jullien, M.; Sellier, R.

    A thorough understanding of the energy sources used by microbial systems in the deep terrestrial subsurface is essential since the extreme conditions for life in deep biospheres may serve as a model for possible life in a nuclear waste repository. In this respect, H 2 is known as one of the most energetic substrates for deep terrestrial subsurface environments. This hydrogen is produced from abiotic and biotic processes but its concentration in natural systems is usually maintained at very low levels due to hydrogen-consuming bacteria. A significant amount of H 2 gas will be produced within deep nuclear waste repositories, essentially from the corrosion of metallic components. This will consequently improve the conditions for microbial activity in this specific environment. This paper discusses different study cases with experimental results to illustrate the fact that microorganisms are able to use hydrogen for redox processes (reduction of O 2, NO3-, Fe III) in several waste disposal conditions. Consequences of microbial activity include: alteration of groundwater chemistry and shift in geochemical equilibria, gas production or consumption, biocorrosion, and potential modifications of confinement properties. In order to quantify the impact of hydrogen bacteria, the next step will be to determine the kinetic rate of the reactions in realistic conditions.

  9. Inelastic Tunneling Spectroscopy of Gold-Thiol and Gold-Thiolate Interfaces in Molecular Junctions: The Role of Hydrogen

    CERN Document Server

    Demir, Firuz

    2012-01-01

    It is widely believed that when a molecule with thiol (S-H) end groups bridges a pair of gold electrodes, the S atoms bond to the gold and the thiol H atoms detach from the molecule. However, little is known regarding the details of this process, its time scale, and whether molecules with and without thiol hydrogen atoms can coexist in molecular junctions. Here we explore theoretically how inelastic tunneling spectroscopy (IETS) can shed light on these issues. We present calculations of the geometries, low bias conductances and IETS of propanedithiol and propanedithiolate molecular junctions with gold electrodes. We show that IETS can distinguish between junctions with molecules having no, one or two thiol hydrogen atoms. We find that in most cases the single-molecule junctions in the IETS experiment of Hihath et al. [Nano Lett. 8, 1673 (2008)] had no thiol H atoms, but that a molecule with a single thiol H atom may have bridged their junction occasionally. We also consider the evolution of the IETS spectrum ...

  10. Molecular dynamics study of nanoscale organization and hydrogen bonding in binary mixtures of butylammonium nitrate ionic liquid and primary alcohols

    Science.gov (United States)

    Shrivastav, Gourav; Gupta, Aditya; Rastogi, Aman; Dhabal, Debdas; Kashyap, Hemant K.

    2017-02-01

    Molecular dynamics simulations are utilized here to explore the nanoscale morphology and the nature of hydrogen bonding in the equimolar mixtures of butylammonium nitrate protic ionic liquid with ethanol, propanol, and butanol. The X-ray scattering experimental study of Greaves et al. [Phys. Chem. Chem. Phys. 13, 13 501 (2011)] has evidenced that alkylammonium nitrate plus alcohol mixtures possess nanoscale structural order which becomes more pronounced as the chain length of the alcohol increases. Our analysis carried out using simulated total and partial X-ray scattering structure functions quantifies the basis of these observations. The partial structure functions highlight the off-phase density correlations of alcohol with both cation and anion in the low-q region. We demonstrate that the chain lengthening of alcohols offers significant variation in the structuring of the polar and apolar moieties in the mixtures. The inspection based on radial distribution functions manifests the non-linear hydrogen bonds of cations with nitrate anions as well as alcohol molecules. The alcohol's hydroxyl group prefers to form linear hydrogen bonds with anions and with other alcohol molecules. Incremented chain length of alcohol improves the extent of hydrogen bonding but does not alter their geometry. Spatial distribution functions delineate similar preferences. It shows stronger directional preferences of the hydroxyl group of alcohols than cation in the vicinity of an anion. Enhanced pair correlations associated with the terminal methyl carbons suggest aggregation of butanol chains in apolar domains. Triplet correlation functions (TCFs) are also used to evaluate the orientational preferences of the present polar moieties in the mixtures. Information based on TCFs for distribution of polar head group of cations and anions unveils the dominance of equilateral configurations over the less frequent isosceles configurations in all the three mixtures.

  11. Global warming

    Science.gov (United States)

    Houghton, John

    2005-06-01

    'Global warming' is a phrase that refers to the effect on the climate of human activities, in particular the burning of fossil fuels (coal, oil and gas) and large-scale deforestation, which cause emissions to the atmosphere of large amounts of 'greenhouse gases', of which the most important is carbon dioxide. Such gases absorb infrared radiation emitted by the Earth's surface and act as blankets over the surface keeping it warmer than it would otherwise be. Associated with this warming are changes of climate. The basic science of the 'greenhouse effect' that leads to the warming is well understood. More detailed understanding relies on numerical models of the climate that integrate the basic dynamical and physical equations describing the complete climate system. Many of the likely characteristics of the resulting changes in climate (such as more frequent heat waves, increases in rainfall, increase in frequency and intensity of many extreme climate events) can be identified. Substantial uncertainties remain in knowledge of some of the feedbacks within the climate system (that affect the overall magnitude of change) and in much of the detail of likely regional change. Because of its negative impacts on human communities (including for instance substantial sea-level rise) and on ecosystems, global warming is the most important environmental problem the world faces. Adaptation to the inevitable impacts and mitigation to reduce their magnitude are both necessary. International action is being taken by the world's scientific and political communities. Because of the need for urgent action, the greatest challenge is to move rapidly to much increased energy efficiency and to non-fossil-fuel energy sources.

  12. Car-Parrinello and path integral molecular dynamics study of the hydrogen bonds in 2-acetyl-1,8-dihydroxy-3,6-dimethylnaphthalene

    Science.gov (United States)

    Durlak, Piotr; Latajka, Zdzisław

    2010-10-01

    Theoretical studies of the structure and proton motion in the intramolecular O-H…O hydrogen bonds in 2-acetyl-1,8-dihydroxy-3,6-dimethylnapthlane were carried out at the DFT and molecular dynamics levels. Geometry optimization at the PBE1PBE/6-311++G(2d,2p) level demonstrate the existence of two tautomers on the potential energy surface. Dynamics of proton motion in intramolecular hydrogen bonds was investigated in vacuo at 100 K using Car-Parrinello and path integral molecular dynamics. For the strong intramolecular hydrogen bond very large delocalization of bridging proton is noted, especially in the path integral simulation where quantum effects are taken into account. No tautomerism was found for this intramolecular hydrogen bond.

  13. High-energy, stable and recycled molecular solar thermal storage materials using AZO/graphene hybrids by optimizing hydrogen bonds.

    Science.gov (United States)

    Luo, Wen; Feng, Yiyu; Qin, Chengqun; Li, Man; Li, Shipei; Cao, Chen; Long, Peng; Liu, Enzuo; Hu, Wenping; Yoshino, Katsumi; Feng, Wei

    2015-10-21

    An important method for establishing a high-energy, stable and recycled molecular solar heat system is by designing and preparing novel photo-isomerizable molecules with a high enthalpy and a long thermal life by controlling molecular interactions. A meta- and ortho-bis-substituted azobenzene chromophore (AZO) is covalently grafted onto reduced graphene oxide (RGO) for solar thermal storage materials. High grafting degree and close-packed molecules enable intermolecular hydrogen bonds (H-bonds) for both trans-(E) and cis-(Z) isomers of AZO on the surface of nanosheets, resulting in a dramatic increase in enthalpy and lifetime. The metastable Z-form of AZO on RGO is thermally stabilized with a half-life of 52 days by steric hindrance and intermolecular H-bonds calculated using density functional theory (DFT). The AZO-RGO fuel shows a high storage capacity of 138 Wh kg(-1) by optimizing intermolecular H-bonds with a good cycling stability for 50 cycles induced by visible light at 520 nm. Our work opens up a new method for making advanced molecular solar thermal storage materials by tuning molecular interactions on a nano-template.

  14. Molecular Ro-vibrational Collision Rates for Infrared Modeling of Warm Interstellar Gas from Full-dimensional Quantum Calculations

    Science.gov (United States)

    Stancil, Phillip

    We propose to compute accurate collisional excitation rate coefficients for rovibrational transitions of CS, SiO, SO, NO, H_2O, and HCN due to H_2, He, or H impact. This extends our previous grant which focused on 3- and 4-atom systems to 4- and 5-atom collision complexes, with dynamics to be performed on 6-9 dimensional potential energy surfaces (PESs). This work, which uses fully quantum mechanical methods for inelastic scattering and incorporates full-dimensional PESs, pushes beyond the state-of-the-art for such calculations, as recently established by our group for rovibrational transitions in CO-H_2 in 6D. Many of the required PESs will be computed as part of this project using ab initio theory and basis sets of the highest level feasible and particular attention will be given to the long range form of the PESs. The completion of the project will result in 6 new global PESs and state-to-state rate coefficients for a large range of initial rovibrational levels for temperatures between 1 and 3000 K. The chosen collision systems correspond to cases where data are limited or lacking, are important coolants or diagnostics, and result in observable emission features in the infrared (IR). The final project results will be important for the analysis of a variety of interstellar and extragalactic environments in which the local conditions of gas density, radiation field, and/or shocks drive the level populations out of equilibrium. In such cases, collisional excitation data are critical to the accurate prediction and interpretation of observed molecular IR emission lines in protoplanetary disks, star-forming regions, planetary nebulae, embedded protostars, photodissociation regions, etc. The use of the proposed collisional excitation data will lead to deeper examination and understanding of the properties of many astrophysical environments, hence elevating the scientific return from the upcoming JWST, as well as from current (SOFIA, Herschel, HST) and past IR missions

  15. Born-Oppenheimer Molecular Dynamics Study on Proton Dynamics of Strong Hydrogen Bonds in Aspirin Crystals, with Emphasis on Differences between Two Crystal Forms.

    Science.gov (United States)

    Brela, Mateusz Z; Wójcik, Marek J; Witek, Łukasz J; Boczar, Marek; Wrona, Ewa; Hashim, Rauzah; Ozaki, Yukihiro

    2016-04-28

    In this study, the proton dynamics of hydrogen bonds for two forms of crystalline aspirin was investigated by the Born-Oppenheimer molecular dynamics (BOMD) method. Analysis of the geometrical parameters of hydrogen bonds using BOMD reveals significant differences in hydrogen bonding between the two crystalline forms of aspirin, Form I and Form II. Analysis of the trajectory for Form I shows spontaneous proton transfer in cyclic dimers, which is absent in Form II. Quantization of the O-H stretching modes allows a detailed discussion on the strength of hydrogen-bonding interactions. The focal point of our study is examination of the hydrogen bond characteristics in the crystal structure and clarification of the influence of hydrogen bonding on the presence of the two crystalline forms of aspirin. In the BOMD method, thermal motions were taken into account. Solving the Schrödinger equation for the snapshots of 2D proton potentials, extracted from MD, gives the best agreement with IR spectra. The character of medium-strong hydrogen bonds in Form I of aspirin was compared with that of weaker hydrogen bonds in aspirin Form II. Two proton minima are present in the potential function for the hydrogen bonds in Form I. The band contours, calculated by using one- and two-dimensional O-H quantization, reflect the differences in the hydrogen bond strengths between the two crystalline forms of aspirin, as well as the strong hydrogen bonding in the cyclic dimers of Form I and the medium-strong hydrogen bonding in Form II.

  16. Influences of Temperature on Proton Conductivity in the Hydrogen-Bond Molecular Systems with Damping

    Institute of Scientific and Technical Information of China (English)

    PANG Xiao-Feng; YU Jia-Feng

    2007-01-01

    Influences of temperature of medium on proton conductivity in hydrogen-bonded systems exposed in an electric-field are numerically studied by the fourth-order Runge-Kutta method with our model. The results obtained show that the proton soliton is very robust against thermal perturbation and damping of medium, and is thermally stable in the temperature range T ≤273 K. From the simulation we find out that the mobility (or velocity) of proton conduction in ice crystal is a nonmonotonic function of temperature in the temperature range 170-273 K: i.e., it increases initially, reaches a maximum at about 191 K, subsequently decreases to a minimum at about 211 K, and then increases again. This changed rule of mobility is qualitatively consistent with its experimental data in ice in the same temperature range. This result provides an evidence for existence of solitons in the hydrogen-bonded systems.

  17. Hot hydrogen atoms reactions of interest in molecular evolution and interstellar chemistry

    Science.gov (United States)

    Becker, R. S.; Hong, K.; Hong, J. H.

    1974-01-01

    Hot hydrogen atoms which are photochemically generated initiate reactions among mixtures of methane, ethane, water and ammonia, to produce ethanol, organic amines, organic acids, and amino acids. Both ethanol and ethyl amine can also act as substrates for formation of amino acids. The one carbon substrate methane is sufficient as a carbon source to produce amino acids. Typical quantum yields for formation of amino acids are approximately 0.00002 to 0.00004. In one experiment, 6 protein amino acids were identified and 8 nonprotein amino acids verified utilizing gas chromatography-mass spectroscopy. We propose that hot atoms, especially hydrogen, initiate reactions in the thermodynamic nonequilibrium environment of interstellar space as well as in the atmospheres of planets.

  18. Recognizing molecular patterns by machine learning: an agnostic structural definition of the hydrogen bond

    CERN Document Server

    Gasparotto, Piero

    2014-01-01

    The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding -- a central concept to our understanding of the physical chemistry of water, biological systems and many technologically important materials. Since the hydrogen bond is a somewhat fuzzy entity that covers a broad range of energies and distances, many different criteria have been proposed and used over the years, based either on sophisticate electronic structure calculations followed by an energy decomposition analysis, or on somewhat arbitrary choices of a range of structural parameters that is deemed to correspond to a ...

  19. Molecularly Defined Nanostructures Based on a Novel AAA-DDD Triple Hydrogen-Bonding Motif.

    Science.gov (United States)

    Papmeyer, Marcus; Vuilleumier, Clément A; Pavan, Giovanni M; Zhurov, Konstantin O; Severin, Kay

    2016-01-26

    A facile and flexible method for the synthesis of a new AAA-DDD triple hydrogen-bonding motif is described. Polytopic supramolecular building blocks with precisely oriented AAA and DDD groups are thus accessible in few steps. These building blocks were used for the assembly of large macrocycles featuring four AAA-DDD interactions and a macrobicyclic complex with a total of six AAA-DDD interactions.

  20. The role of molecular vibration in nanosecond repetitively pulsed discharges and in DBDs in hydrogen plasmas

    Science.gov (United States)

    Colonna, G.; D'Ammando, G.; Pietanza, L. D.

    2016-10-01

    A self-consistent state-to-state model of pure hydrogen has been used to investigate the development of nanosecond repetitively pulsed discharges and dielectric barrier discharges, the latter coupling the kinetic model with an equation for the circuit, thus mimicking an insulated electrode with an external capacitance. Vibrationally excited states play a fundamental role, affecting the degrees of dissociation and ionization, as well as internal and free-electron distributions.

  1. Si-decorated graphene: A promising media for molecular hydrogen storage

    Energy Technology Data Exchange (ETDEWEB)

    Ganji, M. Darvish, E-mail: ganji_md@yahoo.com; Emami, S.N.; Khosravi, A.; Abbasi, M.

    2015-03-30

    Highlights: • The adsorption of H{sub 2} on Si-decorated graphene was studied by DFT-LDA method. • Chemisorbed Si atom exhibits as a potential positive center for H{sub 2} adsorption. • BSSE correction and spin polarization affect slightly on the binding energies estimation. • Si atom can absorb up to eight H{sub 2}molecules with the gravimetric density of 15 wt%. • The binding properties for the adsorbed H{sub 2}molecules are typical for the physisorption. - Abstract: The adsorption of hydrogen molecules (H{sub 2}) on Si-decorated graphene was studied by using density functional theory calculations based on local density approximation (LDA). The accuracy of our method was validated by high level quantum chemical calculation result at MP2 level of theory for similar system. Our calculations show that Si-decorated graphene has high adsorption energy, high net charge transfer values and small connecting distances to graphene surface due to chemisorption. This makes adsorbed Si on the surface as a positive center which can adsorb considerably H{sub 2} molecules. We find that up to 16 H{sub 2} molecules can stably bind to two Si atoms on both side of the graphene sheet with slightly desirable adsorption energy which indicates that the resultant system facilitates the hydrogen desorption at near ambient conditions for practical applications. This newly developed Si decorated graphene with its hydrogen storage capacity of about 15 wt% would be an excellent candidate for hydrogen storage mediums.

  2. Charged particle dynamics and molecular kinetics in the hydrogen postdischarge plasma

    Science.gov (United States)

    Diomede, P.; Longo, S.; Capitelli, M.

    2006-11-01

    The afterglow of a parallel plate radio frequency discharge in hydrogen is studied by numerical modelling to compare ion dynamics and chemical effects on the behavior of negative ions. While the ion dynamics requires a kinetic description of space dependent plasma relaxation (at least 1D), chemical effects require a vibrational kinetics of hydrogen molecules. Since previous models did not include both features it has not been possible until now to realize both effects in a single simulation. We apply an updated version of the 1D Bari model which includes a 1.5D (1Dr2Dv) Particle in Cell/Monte Carlo (PIC/MC) multispecies module coupled to the space and time dependent master equation for H2(X1Σg+,v=0,…,14) vibrational level population. Negative ion fronts are described in hydrogen for the first time and their impact on the plasma limiting surfaces produces a negative ion current evolution compatible with experimental findings. In the same conditions, the attachment rate overshoot is found to contribute about 7% to the average ion density in the plasma.

  3. Molecular hydrogen messengers can lead to structural infidelity: A cautionary tale of protonated glycine

    Science.gov (United States)

    Masson, Antoine; Williams, Evan R.; Rizzo, Thomas R.

    2015-09-01

    The effects of tagging protonated glycine with either He or between 1 and 14 H2 molecules on the infrared photodissociation spectra and the ion structure were investigated. Differences in the IR spectra with either a single He atom or H2 molecule attached indicate that even a single H2 molecule can affect the frequencies of some vibrational bands of this simple ion. The protonation site is the preferred location of the tag with He and with up to two H2 molecules, but evidence for H2 attachment to the hydrogen atom of the uncharged carboxylic acid is observed for ions tagged with three or more H2 molecules. This results in a 55 cm-1 red shift in the carboxylic acid OH stretch, and evidence for some structural isomers where the hydrogen bond between the protonated nitrogen and the carbonyl oxygen is partially broken; as a result H2 molecules attached to this site are observed. These results are supported by theory, which indicates that H2 molecules can effectively break this weak hydrogen bond with three or more H2 molecules. These results indicate that large spectral shifts as a result of H2 molecules attaching to sites remote from the charge can occur and affect stretching frequencies as a result of charge transfer, and that tagging with multiple H2 molecules can change the structure of the ion itself.

  4. Recognizing molecular patterns by machine learning: An agnostic structural definition of the hydrogen bond

    Energy Technology Data Exchange (ETDEWEB)

    Gasparotto, Piero; Ceriotti, Michele, E-mail: michele.ceriotti@epfl.ch [Laboratory of Computational Science and Modeling, and National Center for Computational Design and Discovery of Novel Materials MARVEL, IMX, École Polytechnique Fédérale de Lausanne, 1015 Lausanne (Switzerland)

    2014-11-07

    The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here, we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding – a central concept to our understanding of the physical chemistry of water, biological systems, and many technologically important materials. Since the hydrogen bond is a somewhat fuzzy entity that covers a broad range of energies and distances, many different criteria have been proposed and used over the years, based either on sophisticate electronic structure calculations followed by an energy decomposition analysis, or on somewhat arbitrary choices of a range of structural parameters that is deemed to correspond to a hydrogen-bonded configuration. We introduce here a definition that is univocal, unbiased, and adaptive, based on our machine-learning analysis of an atomistic simulation. The strategy we propose could be easily adapted to similar scenarios, where one has to recognize or classify structural patterns in a material or chemical compound.

  5. Detection of rovibrationally excited molecular hydrogen in the electronic ground state via synchrotron radiation

    Science.gov (United States)

    Béchu, S.; Aleiferis, S.; Bentounes, J.; Gavilan, L.; Shakhatov, V. A.; Bès, A.; Svarnas, P.; Mazouffre, S.; de Oliviera, N.; Engeln, R.; Lemaire, J. L.

    2017-08-01

    We describe an original setup named SCHEME (Source of exCited HydrogEn MolEcules) designed to study the recombinative desorption mechanisms of H atoms on a surface by means of high-brilliance monochromatic synchrotron radiation (SR). H atoms are produced on electrically heated filaments under vacuum (in the absence of any discharge) and subsequently recombine on a surface to produce excited hydrogen molecules, namely, H2 ( v″, J″ ). Once these levels are produced, they are probed in the vacuum chamber with 5-40 eV (248-31 nm) SR-photons. A preliminary test with Krypton has demonstrated the feasibility of SCHEME to obtain simultaneously VUV-synchrotron radiation induced fluorescence and VUV-absorption signals with room-temperature gas. In order to evaluate the hydrogen molecule dissociation induced by the heated filaments, the absolute density of H atoms has been measured by VUV-absorption. At 1800 K and 100 mTorr, we estimated a dissociation degree of 10-4 , which corresponds to an absolute density of 1.8 ×1017 m-3. VUV-absorption spectroscopy is shown to be a valuable tool to detect H2 ( v″, J″ ) molecules up to v″ = 3. Possible improvements of the experimental setup, to detect higher v″ levels, are suggested in the end of this paper.

  6. Formation of negative hydrogen ions in 7-keV OH+ + Ar and OH+ + acetone collisions: a general process for H-bearing molecular species

    CERN Document Server

    Juhász, Zoltán; Rangama, Jimmy; Bene, Erika; Sorgunlu-Frankland, Burcu; Frémont, François; Chesnel, Jean-Yves

    2015-01-01

    We demonstrate that the formation of negative hydrogen ions (H-) occurs in a wide class of atomic and molecular collisions. In our experiments, H- emission from hydroxyl cations and acetone molecules was observed in keV-energy collisions. We show that hydride (H-) anions are formed via direct collisional fragmentation of molecules, followed by electron grabbing by fast hydrogen fragments. Such general mechanism in hydrogen-containing molecules may significantly influence reaction networks in planetary atmospheres and astrophysical media and new reaction pathways may have to be added in radiolysis studies.

  7. Semiquantal molecular dynamics simulations of hydrogen-bond dynamics in liquid water using multi-dimensional Gaussian wave packets.

    Science.gov (United States)

    Ono, Junichi; Ando, Koji

    2012-11-01

    A semiquantal (SQ) molecular dynamics (MD) simulation method based on an extended Hamiltonian formulation has been developed using multi-dimensional thawed gaussian wave packets (WPs), and applied to an analysis of hydrogen-bond (H-bond) dynamics in liquid water. A set of Hamilton's equations of motion in an extended phase space, which includes variance-covariance matrix elements as auxiliary coordinates representing anisotropic delocalization of the WPs, is derived from the time-dependent variational principle. The present theory allows us to perform real-time and real-space SQMD simulations and analyze nuclear quantum effects on dynamics in large molecular systems in terms of anisotropic fluctuations of the WPs. Introducing the Liouville operator formalism in the extended phase space, we have also developed an explicit symplectic algorithm for the numerical integration, which can provide greater stability in the long-time SQMD simulations. The application of the present theory to H-bond dynamics in liquid water is carried out under a single-particle approximation in which the variance-covariance matrix and the corresponding canonically conjugate matrix are reduced to block-diagonal structures by neglecting the interparticle correlations. As a result, it is found that the anisotropy of the WPs is indispensable for reproducing the disordered H-bond network compared to the classical counterpart with the use of the potential model providing competing quantum effects between intra- and intermolecular zero-point fluctuations. In addition, the significant WP delocalization along the out-of-plane direction of the jumping hydrogen atom associated with the concerted breaking and forming of H-bonds has been detected in the H-bond exchange mechanism. The relevance of the dynamical WP broadening to the relaxation of H-bond number fluctuations has also been discussed. The present SQ method provides the novel framework for investigating nuclear quantum dynamics in the many

  8. Molecular hydrogen inhibits lipopolysaccharide-triggered NLRP3 inflammasome activation in macrophages by targeting the mitochondrial reactive oxygen species.

    Science.gov (United States)

    Ren, Jian-Dong; Wu, Xiao-Bo; Jiang, Rui; Hao, Da-Peng; Liu, Yi

    2016-01-01

    The NLRP3 inflammasome, an intracellular multi-protein complex controlling the maturation of cytokine interleukin-1β, plays an important role in lipopolysaccharide (LPS)-induced inflammatory cascades. Recently, the production of mitochondrial reactive oxygen species (mtROS) in macrophages stimulated with LPS has been suggested to act as a trigger during the process of NLRP3 inflammasome activation that can be blocked by some mitochondria-targeted antioxidants. Known as a ROS scavenger, molecular hydrogen (H2) has been shown to possess therapeutic benefit on LPS-induced inflammatory damage in many animal experiments. Due to the unique molecular structure, H2 can easily target the mitochondria, suggesting that H2 is a potential antagonist of mtROS-dependent NLRP3 inflammasome activation. Here we have showed that, in mouse macrophages, H2 exhibited substantial inhibitory activity against LPS-initiated NLRP3 inflammasome activation by scavenging mtROS. Moreover, the elimination of mtROS by H2 resultantly inhibited mtROS-mediated NLRP3 deubiquitination, a non-transcriptional priming signal of NLRP3 in response to the stimulation of LPS. Additionally, the removal of mtROS by H2 reduced the generation of oxidized mitochondrial DNA and consequently decreased its binding to NLRP3, thereby inhibiting the NLRP3 inflammasome activation. Our findings have, for the first time, revealed the novel mechanism underlying the inhibitory effect of molecular hydrogen on LPS-caused NLRP3 inflammasome activation, highlighting the promising application of this new antioxidant in the treatment of LPS-associated inflammatory pathological damage.

  9. Partition functions. I. Improved partition functions and thermodynamic quantities for normal, equilibrium, and ortho and para molecular hydrogen

    Science.gov (United States)

    Popovas, A.; Jørgensen, U. G.

    2016-11-01

    Context. Hydrogen is the most abundant molecule in the Universe. Its thermodynamic quantities dominate the physical conditions in molecular clouds, protoplanetary disks, etc. It is also of high interest in plasma physics. Therefore thermodynamic data for molecular hydrogen have to be as accurate as possible in a wide temperature range. Aims: We here rigorously show the shortcomings of various simplifications that are used to calculate the total internal partition function. These shortcomings can lead to errors of up to 40 percent or more in the estimated partition function. These errors carry on to calculations of thermodynamic quantities. Therefore a more complicated approach has to be taken. Methods: Seven possible simplifications of various complexity are described, together with advantages and disadvantages of direct summation of experimental values. These were compared to what we consider the most accurate and most complete treatment (case 8). Dunham coefficients were determined from experimental and theoretical energy levels of a number of electronically excited states of H2. Both equilibrium and normal hydrogen was taken into consideration. Results: Various shortcomings in existing calculations are demonstrated, and the reasons for them are explained. New partition functions for equilibrium, normal, and ortho and para hydrogen are calculated and thermodynamic quantities are reported for the temperature range 1-20 000 K. Our results are compared to previous estimates in the literature. The calculations are not limited to the ground electronic state, but include all bound and quasi-bound levels of excited electronic states. Dunham coefficients of these states of H2 are also reported. Conclusions: For most of the relevant astrophysical cases it is strongly advised to avoid using simplifications, such as a harmonic oscillator and rigid rotor or ad hoc summation limits of the eigenstates to estimate accurate partition functions and to be particularly careful when

  10. Molecular collective dynamics in solid para-hydrogen and ortho-deuterium: The Parrinello-Rahman-type path integral centroid molecular dynamics approach

    Science.gov (United States)

    Saito, Hiroaki; Nagao, Hidemi; Nishikawa, Kiyoshi; Kinugawa, Kenichi

    2003-07-01

    The single-particle and collective dynamics of hydrogen/deuterium molecules in solid hcp para-hydrogen (p-H2) and ortho-deuterium (o-D2) has been investigated by using the path integral centroid molecular dynamics (CMD) simulations at zero-pressure and 5.4 and 5.0 K, respectively. For this purpose, we have newly unified the standard CMD method with the Parrinello-Rahman-Nosé-Hoover-chain-type isothermal-isobaric technique. The phonon density of states have been obtained and the dynamic structure factors have been calculated to observe the phonon dispersion relations of both crystals. For solid p-H2, the high energy edge of the phonon energies of solid p-H2 is >13 meV, and the calculated phonon energies are significantly higher than those observed in Nielsen's previous neutron scattering experiments in the energy region >9 meV. The relationship between the present results and the data reported so far is discussed to resolve the outstanding controversy regarding the phonon energies in solid p-H2. On the other hand, the excitation energies for solid o-D2 are in fairly good agreement with those of the neutron experiments. The calculated isothermal compressibility of solid p-H2 is found to be very close to the experimental result.

  11. Molecular hydrogen messengers can lead to structural infidelity: A cautionary tale of protonated glycine

    Energy Technology Data Exchange (ETDEWEB)

    Masson, Antoine, E-mail: amasson@lbl.gov; Rizzo, Thomas R., E-mail: erw@berkeley.edu, E-mail: thomas.rizzo@epfl.ch [Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne (Switzerland); Williams, Evan R., E-mail: erw@berkeley.edu, E-mail: thomas.rizzo@epfl.ch [Department of Chemistry, University of California, Berkeley, California 94720-1460 (United States)

    2015-09-14

    The effects of tagging protonated glycine with either He or between 1 and 14 H{sub 2} molecules on the infrared photodissociation spectra and the ion structure were investigated. Differences in the IR spectra with either a single He atom or H{sub 2} molecule attached indicate that even a single H{sub 2} molecule can affect the frequencies of some vibrational bands of this simple ion. The protonation site is the preferred location of the tag with He and with up to two H{sub 2} molecules, but evidence for H{sub 2} attachment to the hydrogen atom of the uncharged carboxylic acid is observed for ions tagged with three or more H{sub 2} molecules. This results in a 55 cm{sup −1} red shift in the carboxylic acid OH stretch, and evidence for some structural isomers where the hydrogen bond between the protonated nitrogen and the carbonyl oxygen is partially broken; as a result H{sub 2} molecules attached to this site are observed. These results are supported by theory, which indicates that H{sub 2} molecules can effectively break this weak hydrogen bond with three or more H{sub 2} molecules. These results indicate that large spectral shifts as a result of H{sub 2} molecules attaching to sites remote from the charge can occur and affect stretching frequencies as a result of charge transfer, and that tagging with multiple H{sub 2} molecules can change the structure of the ion itself.

  12. Metabolic depression during warm torpor in the Golden spiny mouse (Acomys russatus) does not affect mitochondrial respiration and hydrogen peroxide release.

    Science.gov (United States)

    Grimpo, Kirsten; Kutschke, Maria; Kastl, Anja; Meyer, Carola W; Heldmaier, Gerhard; Exner, Cornelia; Jastroch, Martin

    2014-01-01

    Small mammals actively decrease metabolism during daily torpor and hibernation to save energy. Recently, depression of mitochondrial substrate oxidation in isolated liver mitochondria was observed and associated to hypothermic/hypometabolic states in Djungarian hamsters, mice and hibernators. We aimed to clarify whether hypothermia or hypometabolism causes mitochondrial depression during torpor by studying the Golden spiny mouse (Acomys russatus), a desert rodent which performs daily torpor at high ambient temperatures of 32°C. Notably, metabolic rate but not body temperature is significantly decreased under these conditions. In isolated liver, heart, skeletal muscle or kidney mitochondria we found no depression of respiration. Moderate cold exposure lowered torpor body temperature but had minor effects on minimal metabolic rate in torpor. Neither decreased body temperature nor metabolic rate impacted mitochondrial respiration. Measurements of mitochondrial proton leak kinetics and determination of P/O ratio revealed no differences in mitochondrial efficiency. Hydrogen peroxide release from mitochondria was not affected. We conclude that interspecies differences of mitochondrial depression during torpor do not support a general relationship between mitochondrial respiration, body temperature and metabolic rate. In Golden spiny mice, reduction of metabolic rate at mild temperatures is not triggered by depression of substrate oxidation as found in liver mitochondria from other cold-exposed rodents.

  13. Visualization and Interpretation of Attosecond Electron Dynamics in Laser-Driven Hydrogen Molecular Ion using Bohmian Trajectories

    CERN Document Server

    Takemoto, Norio

    2010-01-01

    We analyze the attosecond electron dynamics in hydrogen molecular ion driven by an external intense laser field using ab-initio numerical simulations of the corresponding time-dependent Schr{\\"{o}}dinger equation and Bohmian trajectories. To this end, we employ a one-dimensional model of the molecular ion in which the motion of the protons is frozen. The results of the Bohmian trajectory calculations do agree well with those of the ab-initio simulations and clearly visualize the electron transfer between the two protons in the field. In particular, the Bohmian trajectory calculations confirm the recently predicted attosecond transient localization of the electron at one of the protons and the related multiple bunches of the ionization current within a half cycle of the laser field. Further analysis based on the quantum trajectories shows that the electron dynamics in the molecular ion can be understood via the phase difference accumulated between the Coulomb wells at the two protons. Modeling of the dynamics ...

  14. Enhanced electron attachment to Rydberg states in molecular hydrogen volume discharges

    Science.gov (United States)

    Pinnaduwage, L. A.; Ding, W. X.; McCorkle, D. L.; Lin, S. H.; Mebel, A. M.; Garscadden, A.

    1999-05-01

    We review recent studies on negative ion formation and studies in other areas that are relevant to the role of high-Rydberg states of H2 and H3 in hydrogen negative ion sources. Possible mechanisms for the formation of these excited states are discussed, including the formation of long-lived superexcited (core-excited) Rydberg states. Experimental evidence for negative ion formation via electron attachment to core-excited Rydberg states in a glow discharge apparatus is presented. An expression for the dissociative electron attachment rate constant for Rydberg molecules is derived based on electron capture by a Rydberg molecule due to polarization interaction.

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

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, L Ph H; Schoessler, S; Schoeffler, M; Stiebing, K E; Schmidt-Boecking, H; Doerner, R [Institut fuer Kernphysik, Goethe-Universitaet, Max-von-Laue-Str. 1, 60438 Frankfurt am Main (Germany); Afaneh, F, E-mail: Lothar.Schmidt@atom.uni-frankfurt.d, E-mail: Doerner@atom.uni-frankfurt.d [Physics Department, The Hashemite University, PO Box 150459, Zarqa 13115 (Jordan)

    2009-11-01

    The dissociative electron transfer from He into 10 keV H''+{sub 2} was measured in a kinematically complete experiment. For electron transfer into the dissociative b''3{Sigma}''+{sub u} state of H{sub 2} we find a striking double slit interference pattern in the transverse momentum transfer which we can modify by selecting different internuclear distances of the hydrogen molecule. Compared to an optical double slit, interference minima and maxima are interchanged.

  16. Path integral molecular dynamics simulation of solid para-hydrogen with an aluminum impurity

    Science.gov (United States)

    Mirijanian, Dina T.; Alexander, Millard H.; Voth, Gregory A.

    2002-11-01

    The equilibrium properties of an aluminum impurity trapped in solid para-hydrogen have been studied. The results were compared to those of a previous study by Krumrine et al. [J. Chem. Phys. 113 (2000) 9079] with an atomic boron. In the presence of vacancy defect, when the orientation-dependent Al- pH 2 potential is used, the Al atom is displaced to a position half way between its original substituted site and the vacancy site. Thermodynamic results also indicate that the presence of a neighboring vacancy helps to stabilize the Al impurity to a far greater extent than in the case of the B impurity.

  17. Atomic hydrogen and diatomic titanium-monoxide molecular spectroscopy in laser-induced plasma

    Science.gov (United States)

    Parigger, Christian G.; Woods, Alexander C.

    2017-03-01

    This article gives a brief review of experimental studies of hydrogen Balmer series emission spectra. Ongoing research aims to evaluate early plasma evolution following optical breakdown in laboratory air. Of interest is as well laser ablation of metallic titanium and characterization of plasma evolution. Emission of titanium monoxide is discussed together with modeling of diatomic spectra to infer temperature. The behavior of titanium particles in plasma draws research interests ranging from the modeling of stellar atmospheres to the enhancement of thin film production via pulsed laser deposition.

  18. Small-molecule recognition for controlling molecular motion in hydrogen-bond-assembled rotaxanes.

    Science.gov (United States)

    Martinez-Cuezva, Alberto; Berna, Jose; Orenes, Raul-Angel; Pastor, Aurelia; Alajarin, Mateo

    2014-06-23

    Di(acylamino)pyridines successfully template the formation of hydrogen-bonded rotaxanes through five-component clipping reactions. A solid-state study showed the participation of the pyridine nitrogen atom in the stabilization of the mechanical bond between the thread and the benzylic amide macrocycle. The addition of external complementary binders to a series of interlocked bis(2,6-di(acylamino)pyridines) promoted restraint of the back and forward ring motion. The original translation can be restored through a competitive recognition event by the addition of a preorganized bis(di(acylamino)pyridine) that forms stronger ADA-DAD complexes with the external binders.

  19. Global warming

    CERN Document Server

    Hulme, M

    1998-01-01

    Global warming-like deforestation, the ozone hole and the loss of species- has become one of the late 20the century icons of global environmental damage. The threat, is not the reality, of such a global climate change has motivated governments. businesses and environmental organisations, to take serious action ot try and achieve serious control of the future climate. This culminated last December in Kyoto in the agreement for legally-binding climate protocol. In this series of three lectures I will provide a perspective on the phenomenon of global warming that accepts the scientific basis for our concern, but one that also recognises the dynamic interaction between climate and society that has always exited The future will be no different. The challenge of global warning is not to pretend it is not happening (as with some pressure groups), nor to pretend it threatens global civilisation (as with other pressure groups), and it is not even a challenge to try and stop it from happening-we are too far down the ro...

  20. A molecular dynamics simulation of hydrogen atoms collisions on an H-preadsorbed silica surface

    Science.gov (United States)

    Rutigliano, M.; Gamallo, P.; Sayós, R.; Orlandini, S.; Cacciatore, M.

    2014-08-01

    The interaction of hydrogen atoms and molecules with a silica surface is relevant for many research and technological areas. Here, the dynamics of hydrogen atoms colliding with an H-preadsorbed β-cristobalite (0 0 1) surface has been studied using a semiclassical collisional method in conjunction with a recently developed analytical potential energy surface based on density functional theory (DFT) calculations. The atomic recombination probability via an Eley-Rideal (E-R) mechanism, as well as the probabilities for other competitive surface processes, have been determined in a broad range of collision energies (0.04-3.0 eV) for off-normal (θv = 45°) and normal (θv = 0°) incidence and for two different surface temperatures (TS = 300 and 1000 K). H2,gas molecules form in roto-vibrational excited levels while the energy transferred to the solid surface is below 10% for all simulated conditions. Finally, the global atomic recombination coefficient (γE-R) and vibrational state resolved recombination coefficients (γ(v)) were calculated and compared with the available experimental values. The calculated collisional data are of interest in chemical kinetics studies and fluid dynamics simulations of silica surface processes in H-based low-temperature, low-pressure plasmas.

  1. Molecular and Cellular Effects of Hydrogen Peroxide on Human Lung Cancer Cells: Potential Therapeutic Implications

    Directory of Open Access Journals (Sweden)

    Gabriela Vilema-Enríquez

    2016-01-01

    Full Text Available Lung cancer has a very high mortality-to-incidence ratio, representing one of the main causes of cancer mortality worldwide. Therefore, new treatment strategies are urgently needed. Several diseases including lung cancer have been associated with the action of reactive oxygen species (ROS from which hydrogen peroxide (H2O2 is one of the most studied. Despite the fact that H2O2 may have opposite effects on cell proliferation depending on the concentration and cell type, it triggers several antiproliferative responses. H2O2 produces both nuclear and mitochondrial DNA lesions, increases the expression of cell adhesion molecules, and increases p53 activity and other transcription factors orchestrating cancer cell death. In addition, H2O2 facilitates the endocytosis of oligonucleotides, affects membrane proteins, induces calcium release, and decreases cancer cell migration and invasion. Furthermore, the MAPK pathway and the expression of genes related to inflammation including interleukins, TNF-α, and NF-κB are also affected by H2O2. Herein, we will summarize the main effects of hydrogen peroxide on human lung cancer leading to suggesting it as a potential therapeutic tool to fight this disease. Because of the multimechanistic nature of this molecule, novel therapeutic approaches for lung cancer based on the use of H2O2 may help to decrease the mortality from this malignancy.

  2. Hydrogen sulfide generation in mammals: the molecular biology of cystathionine-β- synthase (CBS) and cystathionine-γ-lyase (CSE).

    Science.gov (United States)

    Renga, Barbara

    2011-04-01

    Cystathionine-β-synthase (CBS) and cystathionine-γ-lyase (CSE) are two key enzymes involved in the synthesis of hydrogen sulphide (H(2)S). CBS catalyzes the pyridoxal 5'-phosphate (PLP)-dependent conversion of homocysteine in Cystathionine whilst CSE the pyridoxal 5'-phosphate (PLP)-dependent synthesis of L-cysteine from Cystathionine. In mammals, CBS gene transcription is poorly investigated and the activity of the enzyme is highly regulated. In fact, the CBS enzyme contains a heme cofactor that functions as a redox sensor and utilizes S-adenosylmethionine (SAM) as an allosteric activator. Impaired CBS activity causes hyperhomocystinuria and hyperhomocysteinemia, both risk factors for cardiovascular diseases. Murine CSE gene regulation is well characterized but little is known about the human counterpart and there is no information regarding the enzyme activity regulation. Recently it has been demonstrated that CSE transcription is regulated by the nuclear receptor Farnesoid X Receptor (FXR). Mutations that decrease the activity of CSE cause cystathioninuria, hypercystathioninemia and increase the risk of developing atherosclerosis and bladder cancer. This review focuses on the recent aspects of the molecular regulation of both CBS and CSE and highlights the possibility that members of the nuclear receptors superfamily might be involved in the regulation of hydrogen sulphide metabolism.

  3. Vibrational lifetimes of hydrogen on lead films: An ab initio molecular dynamics with electronic friction (AIMDEF) study

    Energy Technology Data Exchange (ETDEWEB)

    Saalfrank, Peter [Institut für Chemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, D-14476 Potsdam (Germany); Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián (Spain); Juaristi, J. I. [Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián (Spain); Centro de Física de Materiales CFM/MPC (CSIC-UPV/EHU), Paseo Manuel de Lardizabal 5, 20018 Donostia-San Sebastián (Spain); Departamento de Física de Materiales, Facultad de Químicas UPV/EHU, Apartado 1072, 20018 Donostia-San Sebastián (Spain); Alducin, M.; Muiño, R. Díez [Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián (Spain); Centro de Física de Materiales CFM/MPC (CSIC-UPV/EHU), Paseo Manuel de Lardizabal 5, 20018 Donostia-San Sebastián (Spain); Blanco-Rey, M. [Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián (Spain); Departamento de Física de Materiales, Facultad de Químicas UPV/EHU, Apartado 1072, 20018 Donostia-San Sebastián (Spain)

    2014-12-21

    Using density functional theory and Ab Initio Molecular Dynamics with Electronic Friction (AIMDEF), we study the adsorption and dissipative vibrational dynamics of hydrogen atoms chemisorbed on free-standing lead films of increasing thickness. Lead films are known for their oscillatory behaviour of certain properties with increasing thickness, e.g., energy and electron spillout change in discontinuous manner, due to quantum size effects [G. Materzanini, P. Saalfrank, and P. J. D. Lindan, Phys. Rev. B 63, 235405 (2001)]. Here, we demonstrate that oscillatory features arise also for hydrogen when chemisorbed on lead films. Besides stationary properties of the adsorbate, we concentrate on finite vibrational lifetimes of H-surface vibrations. As shown by AIMDEF, the damping via vibration-electron hole pair coupling dominates clearly over the vibration-phonon channel, in particular for high-frequency modes. Vibrational relaxation times are a characteristic function of layer thickness due to the oscillating behaviour of the embedding surface electronic density. Implications derived from AIMDEF for frictional many-atom dynamics, and physisorbed species will also be given.

  4. Modelling (1 0 0) hydrogen-induced platelets in silicon with a multi-scale molecular dynamics approach

    Energy Technology Data Exchange (ETDEWEB)

    Moras, G. [Department of Physics, King' s College London, Strand, London WC2R 2LS (United Kingdom)], E-mail: gianpietro.moras@kcl.ac.uk; Colombi Ciacchi, L. [Fraunhofer Institut fuer Werkstoffmechanik, Woehlerstrasse 11, 79108 Freiburg (Germany); Institut fuer Zuverlaessigkeit von Bauteilen und Systemen, University of Karlsruhe, Kaiserstrasse 12, 76131 Karlsruhe (Germany); Csanyi, G. [Department of Engineering, Centre for Micromechanics, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ (United Kingdom); De Vita, A. [Department of Physics, King' s College London, Strand, London WC2R 2LS (United Kingdom); INFM-DEMOCRITOS National Simulation Centre and Centre of Excellence for Nanostructured Materials (CENMAT), University of Trieste (Italy)

    2007-12-15

    We introduce a multiscale molecular dynamics (MD) approach to study the thermal evolution of (1 0 0) hydrogen-induced platelets (HIPs) in silicon. The HIPs are modeled by {approx}10 nm long planar defects in a periodically repeated crystalline model system containing {approx}25,000 silicon atoms. The initial defect models are created either by cleavage of atomic planes or by planar assemblies of vacancies, and are stabilized by saturating the resulting surface dangling bonds with hydrogen atoms. The time evolution of the defects is studied by finite-temperature MD using the 'Learn On The Fly' (LOTF) technique. This hybrid scheme allows us to perform accurate density-functional-tight-binding (DFTB) force calculations only on the chemically reactive platelet zone, while the surrounding silicon crystal is described by the Stillinger-Weber (SW) classical potential. Reliable dynamical trajectories are obtained by choosing the DFTB zone in a way which minimizes the errors on the atomic forces.

  5. Low-temperature phases of dense hydrogen and deuterium by first-principles path-integral molecular dynamics

    Science.gov (United States)

    Torrent, Marc; Geneste, Gregory

    2012-02-01

    The low-temperature phases of dense hydrogen and deuterium have been investigated using first-principles path-integral molecular dynamics, a technique that we have recently implemented in the ABINIT code and that allows to account for the quantum fluctuations of atomic nuclei. A massively parallelized scheme is applied to produce trajectories of several tens of thousands steps using a 64-atom supercell and a Trotter number of 64. The so-called phases I, II and III are studied and compared to the structures proposed in the literature. The quantum fluctuations produce configurational disorder and are shown to systematically enhance the symmetry of the system: a continuous gain of symmetry in the angular density of probability of the molecules is found from classical particles to quantum D2 and finally to quantum H2. Particular emphasis is made on the ``broken-symmetry'' phase (phase II).

  6. Cyclotetrabenzoin: Facile Synthesis of a Shape-Persistent Molecular Square and Its Assembly into Hydrogen-Bonded Nanotubes.

    Science.gov (United States)

    Ji, Qing; Le, Ha T M; Wang, Xiqu; Chen, Yu-Sheng; Makarenko, Tatyana; Jacobson, Allan J; Miljanić, Ognjen Š

    2015-11-23

    Cyanide-catalyzed benzoin condensation of terephthaldehyde produces a cyclic tetramer, which we propose to name cyclotetrabenzoin. Cyclotetrabenzoin is a square-shaped macrocycle ornamented with four α-hydroxyketone functionalities pointing away from the central cavity, the dimensions of which are 6.9×6.9 Å. In the solid state, these functional groups extensively hydrogen bond, resulting in a microporous three-dimensional organic framework with one-dimensional nanotube channels. This material exhibits permanent-albeit low-porosity, with a Langmuir surface area of 52 m(2)  g(-1) . Cyclotetrabenzoin's easy and inexpensive synthesis and purification may inspire the creation of other shape-persistent macrocycles and porous molecular crystals by benzoin condensation.

  7. 14N NQR study of polymorphism and hydrogen bonding in molecular complex isonicotinamide-oxalic acid (2:1).

    Science.gov (United States)

    Seliger, J; Žagar, V

    2010-11-18

    The complete (14)N nuclear quadrupole resonance (NQR) spectra have been measured in the two polymorphic crystalline phases of the molecular complex isonicotinamide-oxalic acid (2:1) by nuclear quadrupole double resonance. The observed NQR frequencies, quadrupole coupling constants, and asymmetry parameters (η) have been assigned to the two nitrogen positions (ring and amide) in a molecule on the basis of the intensity and multiplicity of the double resonance signals. The NQR data for the ring nitrogen in both polymorphic phases deviate from the correlation relations observed in substituted pyridines. This deviation is analyzed in a model, where it is assumed that an additional electric charge on the nitrogen atom changes the NQR parameters. The model suggests that this additional electric charge is negative so that the N···H-O hydrogen bond seem to be partially ionic, of the type N(-)···H-O.

  8. Ab initio design of Ca-decorated organic frameworks for high capacity molecular hydrogen storage with enhanced binding

    Science.gov (United States)

    Sun, Y. Y.; Lee, Kyuho; Kim, Yong-Hyun; Zhang, S. B.

    2009-07-01

    Ab initio calculations show that Ca can decorate organic linkers of metal-organic framework, MOF-5, with a binding energy of 1.25 eV. The Ca-decorated MOF-5 can store molecular hydrogen (H2) in both high gravimetric (4.6 wt %) and high volumetric (36 g/l) capacities. Even higher capacities (5.7 wt % and 45 g/l) can be obtained in a rationally designed covalent organic framework system, COF-α, with decorated Ca. Both density functional theory and second-order Møller-Plesset perturbation calculations show that the H2 binding in these systems is significantly stronger than the van der Waals interactions, which is required for H2 storage at near ambient conditions.

  9. On the Formation of Interstellar Water Ice: Constraints from a Search for Hydrogen Peroxide Ice in Molecular Clouds

    Science.gov (United States)

    Smith, R. G.; Charnely, S. B.; Pendleton, Y. J.; Wright, C. M.; Maldoni, M. M.; Robinson, G.

    2011-01-01

    Recent surface chemistry experiments have shown that the hydrogenation of molecular oxygen on interstellar dust grains is a plausible formation mechanism, via hydrogen peroxide (H2O2), for the production of water (H2O) ice mantles in the dense interstellar medium. Theoretical chemistry models also predict the formation of a significant abundance of H2O2 ice in grain mantles by this route. At their upper limits, the predicted and experimental abundances are sufficiently high that H2O2 should be detectable in molecular cloud ice spectra. To investigate this further, laboratory spectra have been obtained for H2O2/H2O ice films between 2.5 and 200 micron, from 10 to 180 K, containing 3%, 30%, and 97% H2O2 ice. Integrated absorbances for all the absorption features in low-temperature H2O2 ice have been derived from these spectra. For identifying H2O2 ice, the key results are the presence of unique features near 3.5, 7.0, and 11.3 micron. Comparing the laboratory spectra with the spectra of a group of 24 protostars and field stars, all of which have strong H2O ice absorption bands, no absorption features are found that can definitely be identified with H2O2 ice. In the absence of definite H2O2 features, the H2O2 abundance is constrained by its possible contribution to the weak absorption feature near 3.47 micron found on the long-wavelength wing of the 3 micron H2O ice band. This gives an average upper limit for H2O2, as a percentage of H2O, of 9% +/- 4%. This is a strong constraint on parameters for surface chemistry experiments and dense cloud chemistry models.

  10. Inelastic tunneling spectroscopy of gold-thiol and gold-thiolate interfaces in molecular junctions: the role of hydrogen.

    Science.gov (United States)

    Demir, Firuz; Kirczenow, George

    2012-09-07

    It is widely believed that when a molecule with thiol (S-H) end groups bridges a pair of gold electrodes, the S atoms bond to the gold and the thiol H atoms detach from the molecule. However, little is known regarding the details of this process, its time scale, and whether molecules with and without thiol hydrogen atoms can coexist in molecular junctions. Here, we explore theoretically how inelastic tunneling spectroscopy (IETS) can shed light on these issues. We present calculations of the geometries, low bias conductances, and IETS of propanedithiol and propanedithiolate molecular junctions with gold electrodes. We show that IETS can distinguish between junctions with molecules having no, one, or two thiol hydrogen atoms. We find that in most cases, the single-molecule junctions in the IETS experiment of Hihath et al. [Nano Lett. 8, 1673 (2008)] had no thiol H atoms, but that a molecule with a single thiol H atom may have bridged their junction occasionally. We also consider the evolution of the IETS spectrum as a gold STM tip approaches the intact S-H group at the end of a molecule bound at its other end to a second electrode. We predict the frequency of a vibrational mode of the thiol H atom to increase by a factor ~2 as the gap between the tip and molecule narrows. Therefore, IETS should be able to track the approach of the tip towards the thiol group of the molecule and detect the detachment of the thiol H atom from the molecule when it occurs.

  11. Probing molecular interaction in ionic liquids by low frequency spectroscopy: Coulomb energy, hydrogen bonding and dispersion forces.

    Science.gov (United States)

    Fumino, Koichi; Reimann, Sebastian; Ludwig, Ralf

    2014-10-28

    Ionic liquids are defined as salts composed solely of ions with melting points below 100 °C. These remarkable liquids have unique and fascinating properties and offer new opportunities for science and technology. New combinations of ions provide changing physical properties and thus novel potential applications for this class of liquid materials. To a large extent, the structure and properties of ionic liquids are determined by the intermolecular interaction between anions and cations. In this perspective we show that far infrared and terahertz spectroscopy are suitable methods for studying the cation-anion interaction in these Coulomb fluids. The interpretation of the measured low frequency spectra is supported by density functional theory calculations and molecular dynamics simulations. We present results for selected aprotic and protic ionic liquids and their mixtures with molecular solvents. In particular, we focus on the strength and type of intermolecular interaction and how both parameters are influenced by the character of the ions and their combinations. We show that the total interaction between cations and anions is a result of a subtle balance between Coulomb forces, hydrogen bonds and dispersion forces. For protic ionic liquids we could measure distinct vibrational modes in the low frequency spectra indicating clearly the cation-anion interaction characterized by linear and medium to strong hydrogen bonds. Using isotopic substitution we have been able to dissect frequency shifts related to pure interaction strength between cations and anions and to different reduced masses only. In this context we also show how these different types of interaction may influence the physical properties of ionic liquids such as the melting point, viscosity or enthalpy of vaporization. Furthermore we demonstrate that low frequency spectroscopy can also be used for studying ion speciation. Low vibrational features can be assigned to contact ion pairs and solvent separated

  12. Molecular structure and vibrational spectroscopic analysis of an antiplatelet drug; clopidogrel hydrogen sulphate (form 2) - A combined experimental and quantum chemical approach

    Science.gov (United States)

    Srivastava, Anubha; Mishra, Soni; Tandon, Poonam; Patel, Sarasvatkumar; Ayala, A. P.; Bansal, A. K.; Siesler, H. W.

    2010-02-01

    Clopidogrel hydrogen sulphate which belongs to a class of medicine called antiplatelet drugs. Chemically it is methyl (+)-(S)-α-(2-chlorophenyl)-4,5,6,7-tetrahydrothieno [3,2- c] pyridine-5-acetate hydrogen sulphate having the empirical formula C 16H 17ClNO 2S.HSO 4 and molecular mass 321.82 g/mol. The present study is confined to vibrational spectroscopy of the polymorph identified as form 2 of the clopidogrel hydrogen sulphate. The vibrational analysis of clopidogrel hydrogen sulphate salt (form 2) considering separately the two counterions has been performed. We also report a theoretical and experimental study of the molecular conformation and vibrational dynamics of the independent moieties of the clopidogrel hydrogen sulphate salt. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and activities of Raman scattering were calculated by ab initio Hartree-Fock and density functional theory employing B3LYP with complete relaxation in the potential energy surface using 6-311++G(d,p) basis set. The calculated wavenumbers after a proper scaling show a very good agreement with the observed values. A complete vibrational assignment is provided for the observed Raman and infrared spectra of clopidogrel hydrogen sulphate form 2.

  13. Warm Breeze

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    Middle-aged female painter Wang Yingchun is a first-grade artist at the Research Instituteof Chinese Painting. With a solid foundation in: Chinese painting, oil painting andsculpture she began to experiment in the early 1980s with stone carving, murals, folkart, landscapes, flowers and birds, cubism, expressionism and abstractionism. Living ina time of social transformation, she felt pressed to create her own artistic style. Aftervisiting South America, she produced a batch of works which drew the essence of theBeast Group and used a new technique, without sketching the contours of flowers, sothat the paintings look wild, romantic and exuberant. This painting Warm Breeze displaysWang’s style: While extensively studying the paintings of various schools, she makes hertraditional Chinese ink paintings tinted with modern color.

  14. High Spectral and Spatial Resolution Observations of Shocked Molecular Hydrogen at the Galactic Center

    CERN Document Server

    Yusef-Zadeh, F; Burton, M; Wardle, M; Ashley, M C B

    2001-01-01

    The presence of OH (1720 MHz) masers, and the absence of counterparts at 1665/1667 MHz has proved to be a clear diagnostic of shocked molecular gas associated with Galactic supernova remnants. This suggests that shocked molecular gas should be associated with the OH (1720 MHz) masers that have been detected in the circumnuclear disk (CND) and Sgr A East at the Galactic center. In order to test this hypothesis, we observed the H$_2$ 1--0 S(1) and Br $\\gamma$ lines using NICMOS on the HST and UNSWIRF on the AAT, near the regions where OH (1720 MHz) masers are detected in the CND and Sgr A East. We present the distribution of H$_2$ in the North and South lobes of the CND and in Sgr A East. H$_2$ emission accompanies almost all of the maser spots detected at the Galactic center. In particular, we find a striking filamentary structure near the Northwest of the CND and evidence that shocked molecular gas is associated with the 70 \\kms molecular cloud at the Galactic center. We argue that the emission from the CND c...

  15. Temporal and spatial variability of the stable isotopic composition of atmospheric molecular hydrogen: observations at six EUROHYDROS stations

    Directory of Open Access Journals (Sweden)

    A. M. Batenburg

    2011-03-01

    Full Text Available Despite the potential of isotope measurements to improve our understanding of the global atmospheric molecular hydrogen (H2 cycle, few H2 isotope data have been published so far. Now, within the EUROpean network for atmospheric HYDRogen Observations and Studies project (EUROHYDROS, weekly to monthly air samples from six locations in a global sampling network have been analysed for hydrogen mixing ratio (m(H2 and the stable hydrogen isotopic composition of H2 (δ(D,H2, hereafter referred to as δ(D. The time series thus obtained now cover one to five years for all stations. This is the largest set of ground station observations of δ(D so far. Annual average δ(D values are higher at the Southern Hemisphere (SH than at the Northern Hemisphere (NH stations; the maximum is observed at Neumayer (Antarctica, and the minimum at the NH midlatitude or subtropical stations. The maximum seasonal differences in δ(D range from ≈18‰ at Neumayer to ≈45‰ at Schauinsland (Southern Germany; in general, seasonal variability is largest at the NH stations. The timing of minima and maxima differs per station as well. In Alert (Arctic Canada, the variations in δ(D and m(H2 can be approximated as simple harmonic functions with a ≈5-month phase shift. This out-of-phase seasonal behaviour of δ(D and m(H2 can also be detected, but with a ≈6-month phase shift, at Mace Head and Cape Verde. However, no seasonal δ(D cycle could be observed at Schauinsland, which likely reflects the larger influence of local sources and sinks at this continental station. At the two SH stations, no seasonal cycle could be detected in the δ(D data. Assuming that the sink processes are the main drivers of the observed seasonality in m(H2 and δ(D on the NH, the relative seasonal variations can be used to estimate the relative sink strength of the two major sinks

  16. Test of the theoretical hyperfine structure of the molecular hydrogen ion at the 1-ppm level

    CERN Document Server

    Korobov, Vladimir I; Hilico, Laurent; Karr, Jean-Philippe

    2015-01-01

    We revisit the $m \\alpha^6 (m/M)$ order corrections to the hyperfine splitting in the H$_2^+$ ion, and find a hitherto unrecognized second-order relativistic contribution associated with the vibrational motion of the nuclei. Inclusion of this correction term produces theoretical predictions which are in excellent agreement with experimental data [K. B. Jefferts, Phys.\\ Rev.\\ Lett.\\ \\textbf{23}, 1476 (1969)], thereby concluding a nearly fifty years long theoretical quest to explain the experimental results within their 1-ppm error. The agreement between theory and experiment corroborates the proton structural properties as derived from the hyperfine structure of atomic hydrogen. Our work furthermore indicates that for future improvements, a full three-body evaluation of the $m \\alpha^6 (m/M)$ correction term will be mandatory.

  17. Molecular structure and intramolecular hydrogen bonding in 2-hydroxybenzophenones: A theoretical study

    Indian Academy of Sciences (India)

    Mansoureh Zahedi-Tabrizi; Sayyed Faramarz Tayyari; Farideh Badalkhani-Khamseh; Reihaneh Ghomi; Fatemeh Afshar-Qahremani

    2014-07-01

    The intramolecular hydrogen bonding (IHB) in a series of 3-, 4- and 5-substituted 2-hydroxybenzophenone (HBP) is studied using density functional theory calculations. All calculations are performed at the B3LYP level, using 6-311++G∗∗ basis set. To understand the substitution effects on the nature of IHB and the electronic structure of the chelated ring system, the vibrational frequencies, 1H chemical shift, topological parameters, natural bond orders and natural charges over atoms involved in the chelated ring of HBP and its derivatives were calculated. TheWiberg bond indices and the natural charges over atoms involved in the chelated ring have been computed using the natural bond orbital (NBO) analysis. The computations were further complemented with an atoms-in-molecules (AIM) topological analysis to characterize the nature of the IHB in the considered molecules. Several correlations between geometrical parameters, 1H NMR chemical shift and topological parameters with the IHB strength are obtained.

  18. Hydrogen-terminated silicon substrates for low-temperature molecular beam epitaxy

    Science.gov (United States)

    Grunthaner, P. J.; Grunthaner, F. J.; Fathauer, R. W.; Lin, T. L.; Hecht, M. H.; Bell, L. D.; Kaiser, W. J.

    1989-01-01

    The preparation of hydrogen-terminated silicon surfaces for use as starting substrates for low-temperature MBE growth is examined in detail. The procedure involves the ex situ removal under nitrogen of residual oxide from a silicon substrate using a spin-clean with HF in ethanol, followed by the in situ low-temperature desorption (150 C) of physisorbed etch residues. The critical steps and the chemical basis for these steps are examined using X-ray photoelectron spectroscopy. Impurity residues at the epilayer-substrate interface following subsequent homoepitaxial growth are studied using AES, SIMS and TEM. Finally, scanning tunneling microscopy is used to examine the effect of cleaning methods on substrate morphology.

  19. Ab initio molecular dynamics study of hydrogen removal by ion-surface interactions

    Energy Technology Data Exchange (ETDEWEB)

    Rosen, Johanna [Materials Chemistry, RWTH-Aachen, D-52056 Aachen (Germany); Larsson, Karin [Department of Materials Chemistry, Angstroem Laboratory, Uppsala University, Box 538, 751 21 Uppsala (Sweden); Schneider, Jochen M [Materials Chemistry, RWTH-Aachen, D-52056 Aachen (Germany)

    2005-04-20

    The energy dependence of surface reactions has been investigated through ab initio MD simulations for collisions between Al{sup 1+} and a gibbsite surface. No change in surface composition was observed for 0 eV initial kinetic energy of Al{sup 1+}. An increase in energy to 3.5 eV resulted in extended surface migration of hydrogen, subsequent H{sub 2} formation and desorption from the surface. These results may be understood based on thermodynamics and an increase in entropy upon H{sub 2} formation. They are of fundamental importance for an increased understanding of thin film growth through the correlation between ion energy and film composition. They may also indicate a pathway to affect impurity incorporation during film growth. (letter to the editor)

  20. Monte Carlo simulation to investigate the formation of molecular hydrogen and its deuterated forms

    CERN Document Server

    Sahu, DIpen; Majumdar, Liton; Chakrabarti, Sandip K

    2015-01-01

    $H_2$ is the most abundant interstellar species. Its deuterated forms ($HD$ and $D_2$) are also significantly abundant. Huge abundances of these molecules could be explained by considering the chemistry occurring on the interstellar dust. Because of its simplicity, Rate equation method is widely used to study the formation of grain-surface species. However, since recombination efficiency of formation of any surface species are heavily dependent on various physical and chemical parameters, Monte Carlo method would be best method suited to take care of randomness of the processes. We perform Monte Carlo simulation to study the formation of $H_2$, $HD$ and $D_2$ on interstellar ices. Adsorption energies of surface species are the key inputs for the formation of any species on interstellar dusts but binding energies of deuterated species are yet to known with certainty. A zero point energy correction exists between hydrogenated and deuterated species which should be considered while modeling the chemistry on the ...

  1. 3.2.1. Synthesis, crystal and molecular structure of catena-(bis(µ1-oxalic acid-µ3-hydrogen oxalate-di-aqua-sodium(I.

    Directory of Open Access Journals (Sweden)

    Olga Kovalchukova*, Sergey Aldoshin, Andrey Utenyshev, Konstantin Bogenko, Valeriy Tkachev

    2015-07-01

    Full Text Available The crystal and molecular structure of catena-(bis(µ- oxalic acid-µ-hydrogen oxalate-di-aqua-sodium(I was detected by X-Ray analysis. The compound crystallizes in the triclinic space group P-1, with a(Å 6.2378(12; b(Å 7,1115(14; c(Å 10.489(2; α(° 94.65(3; β(° 100.12(3; γ(° 97.78(3. The sodium cation in the title compound is eight coordinated and forms a square antiprism. It is surrounded by two molecules of oxalic acid, one hydrogen oxalate anion and one water molecule. Both oxalic acid and hydrogen oxalate anion act as polydentate bridging ligands. Centrosymmetric sodium cations are bounded by hydrogen oxalate anions through a system of H bonds involving the molecules of oxalic acid. In the lattice, the 3D structure stabilized by H bonds is formed.

  2. Dimeric [Mo2 S12 ](2-) Cluster: A Molecular Analogue of MoS2 Edges for Superior Hydrogen-Evolution Electrocatalysis.

    Science.gov (United States)

    Huang, Zhongjie; Luo, Wenjia; Ma, Lu; Yu, Mingzhe; Ren, Xiaodi; He, Mingfu; Polen, Shane; Click, Kevin; Garrett, Benjamin; Lu, Jun; Amine, Khalil; Hadad, Christopher; Chen, Weilin; Asthagiri, Aravind; Wu, Yiying

    2015-12-07

    Proton reduction is one of the most fundamental and important reactions in nature. MoS2 edges have been identified as the active sites for hydrogen evolution reaction (HER) electrocatalysis. Designing molecular mimics of MoS2 edge sites is an attractive strategy to understand the underlying catalytic mechanism of different edge sites and improve their activities. Herein we report a dimeric molecular analogue [Mo2 S12 ](2-) , as the smallest unit possessing both the terminal and bridging disulfide ligands. Our electrochemical tests show that [Mo2 S12 ](2-) is a superior heterogeneous HER catalyst under acidic conditions. Computations suggest that the bridging disulfide ligand of [Mo2 S12 ](2-) exhibits a hydrogen adsorption free energy near zero (-0.05 eV). This work helps shed light on the rational design of HER catalysts and biomimetics of hydrogen-evolving enzymes.

  3. Dimeric [Mo₂S₁₂]²⁻ Cluster: A Molecular Analogue of MoS₂ Edges for Superior Hydrogen-Evolution Electrocatalysis

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Zhongjie; Luo, Wenjia; Ma, Lu; Yu, Mingzhe; Ren, Xiaodi; He, Mingfu; Polen, Shan; Click, Kevin; Garrett, Benjamin R.; Lu, Jun; Amine, Khalil

    2015-12-07

    Proton reduction is one of the most fundamental and important reactions in nature. MoS2 edges have been identified as the active sites for hydrogen evolution reaction (HER) electrocatalysis. Designing molecular mimics of MoS2 edge sites is an attractive strategy to understand the underlying catalytic mechanism of different edge sites and improve their activities. Herein we report a dimeric molecular analogue [Mo₂S₁₂]²⁻, as the smallest unit possessing both the terminal and bridging disulfide ligands. Our electrochemical tests show that [Mo₂S₁₂]²⁻ is a superior heterogeneous HER catalyst under acidic conditions. Computations suggest that the bridging disulfide ligand of [Mo₂S₁₂]²⁻ exhibits a hydrogen adsorption free energy near zero (-0.05eV). This work helps shed light on the rational design of HER catalysts and biomimetics of hydrogen-evolving enzymes.

  4. The increased susceptibility to hydrogen peroxide of the (post)-ischemic rat heart is associated with the magnitude of the low molecular weight iron pool

    NARCIS (Netherlands)

    A. Voogd (Arthur); W.J. Sluiter (Wim); J.F. Koster (Johan)

    1994-01-01

    textabstractRecently we have shown that intracellular low molecular weight (LMW) iron increases during ischemia. It is hypothesized that this increase in LMW iron during ischemia underlies the reported hydrogen peroxide toxicity toward ischemic hearts. To investigate this hypothesis, rat hearts were

  5. Hydrothermal synthesis and characterization of a novel supramolecular network compound of Co(NIA) 2(H 2O) 4 with molecular ladder hydrogen bond chains (NIA=nicotinate)

    Science.gov (United States)

    Jia, Hong-Bin; Yu, Jie-Hui; Xu, Ji-Qing; Ye, Ling; Ding, Hong; Jing, Wei-Jie; Wang, Tie-Gang; Xu, Jia-Ning; Li, Zeng-Chun

    2002-10-01

    By hydrothermal method, a novel supramolecular compound, Co(NIA) 2(H 2O) 4 was synthesized and its structure was characterized with elemental analysis, FT-IR spectrum, TGA and X-ray diffractometer, indicating that it is a novel polyporous supramolecule with molecular ladder hydrogen-bonded chains. TGA curve shows its thermal stability up to 520 °C.

  6. Molecular hydrogen (H2) combustion emissions and their isotope (D/H) signatures from domestic heaters, diesel vehicle engines, waste incinerator plants, and biomass burning

    NARCIS (Netherlands)

    Vollmer, M.K.; Walter, S.; Mohn, J.; Steinbacher, M.; Bond, S.W.; Röckmann, T.; Reimann, S.

    2012-01-01

    Molecular hydrogen (H2), its stable isotope signature ( D), and the key combustion parameters carbon monoxide (CO), carbon dioxide (CO2), and methane (CH4) were measured from various combustion processes. H2 in the exhaust of gas and oil-fired heaters and of waste incinerator plants was generally de

  7. Molecular hydrogen (H2) combustion emissions and their isotope (D/H) signatures from domestic heaters, diesel vehicle engines, waste incinerator plants, and biomass burning

    NARCIS (Netherlands)

    Vollmer, M.K.; Walter, S.; Mohn, J.; Steinbacher, M.; Bond, S.W.; Röckmann, T.; Reimann, S.

    2012-01-01

    Molecular hydrogen (H2), its stable isotope signature ( D), and the key combustion parameters carbon monoxide (CO), carbon dioxide (CO2), and methane (CH4) were measured from various combustion processes. H2 in the exhaust of gas and oil-fired heaters and of waste incinerator plants was generally

  8. Constraints on short-range spin-dependent interactions from scalar spin-spin coupling in deuterated molecular hydrogen

    CERN Document Server

    Ledbetter, Micah; Jackson-Kimball, Derek

    2012-01-01

    A comparison between existing measurements and calculations of the scalar spin-spin interaction (J-coupling) in deuterated molecular hydrogen (HD) yields stringent constraints on anomalous spin-dependent potentials between nucleons at the atomic scale (${\\rm \\sim 1 \\AA}$). The dimensionless coupling constant $g_P^pg_P^{N}/4\\pi$ associated with exchange of pseudoscalar (axion-like) bosons between nucleons is constrained to be less than $5\\times 10^{-7}$ for boson masses in the range of $5 {\\rm keV}$. This represents improvement by a factor of about 100 over constraints placed by measurements of the dipole-dipole interaction in molecular ${\\rm H_2}$. The dimensionless coupling constant $g_A^pg_A^N/4 \\pi$ associated with exchange of a heretofore undiscovered axial-vector boson between nucleons is constrained to be $g_A^pg_A^N/4 \\pi < 2 \\times 10^{-19}$ for bosons of mass $\\lesssim 1000 {\\rm eV}$, improving constraints at this distance scale by a factor of 100 for proton-proton couplings and more than 8 orders...

  9. Direct assessment of quantum nuclear effects on hydrogen bond strength by constrained-centroid ab initio path integral molecular dynamics

    Science.gov (United States)

    Walker, Brent; Michaelides, Angelos

    2010-11-01

    The impact of quantum nuclear effects on hydrogen (H-) bond strength has been inferred in earlier work from bond lengths obtained from path integral molecular dynamics (PIMD) simulations. To obtain a direct quantitative assessment of such effects, we use constrained-centroid PIMD simulations to calculate the free energy changes upon breaking the H-bonds in dimers of HF and water. Comparing ab initio simulations performed using PIMD and classical nucleus molecular dynamics (MD), we find smaller dissociation free energies with the PIMD method. Specifically, at 50 K, the H-bond in (HF)2 is about 30% weaker when quantum nuclear effects are included, while that in (H2O)2 is about 15% weaker. In a complementary set of simulations, we compare unconstrained PIMD and classical nucleus MD simulations to assess the influence of quantum nuclei on the structures of these systems. We find increased heavy atom distances, indicating weakening of the H-bond consistent with that observed by direct calculation of the free energies of dissociation.

  10. Atomic structure of unligated laccase from Cerrena maxima at 1.76 A with molecular oxygen and hydrogen peroxide

    Energy Technology Data Exchange (ETDEWEB)

    Zhukova, Yu. N., E-mail: amm@ns.crys.ras.ru; Lyashenko, A. V.; Lashkov, A. A.; Gur' yanov, V. A.; Kobyl' skaya, Yu. V.; Zhukhlistova, N. E.; Mikhailov, A. M. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2010-05-15

    The three-dimensional structure of unligated laccase from Cerrena maxima was established by X-ray diffraction at 1.76-A resolution; R{sub work} = 18.07%, R{sub free} = 21.71%, rmsd of bond lengths, bond angles, and chiral angles are 0.008 A, 1.19{sup o}, and 0.077{sup o}, respectively. The coordinate error for the refined structure estimated from the Luzzati plot is 0.195 A. The maximum average error in the atomic coordinates is 0.047 A. A total of 99.4% of amino-acid residues of the polypeptide chain are in the most favorable, allowable, and accessible regions of the Ramachandran plot. The three-dimensional structures of the complexes of laccase from C. maxima with molecular oxygen and hydrogen peroxide were determined by the molecular simulation. These data provide insight into the structural aspect of the mechanism of the enzymatic cycle. The structure factors and the refined atomic coordinates were deposited in the Protein Data Bank (PDB-ID code is 3DIV).

  11. Molecular Hydrogen in the Damped Lyman-alpha System towards GRB 120815A at z=2.36

    CERN Document Server

    Krühler, T; Fynbo, J P U; Vreeswijk, P M; Schmidl, S; Malesani, D; Christensen, L; De Cia, A; Hjorth, J; Jakobsson, P; Kann, D A; Kaper, L; Vergani, S D; Afonso, P M J; Covino, S; Postigo, A de Ugarte; D'Elia, V; Filgas, R; Goldoni, P; Greiner, J; Hartoog, O E; Milvang-Jensen, B; Nardini, M; Piranomonte, S; Rossi, A; Sánchez-Ramírez, R; Schady, P; Schulze, S; Sudilovsky, V; Tanvir, N R; Tagliaferri, G; Watson, D J; Wiersema, K; Wijers, R A M J; Xu, D

    2013-01-01

    [Abridged] Molecular hydrogen H_2 is a key requirement for star-formation, frequently observed along sightlines in the Galaxy and to the Magellanic Clouds, but notoriously hard to detect directly beyond z ~ 0. In the DLAs associated with long gamma-ray bursts (GRBs), which are tightly linked to vigorous star-formation, H_2 has remained largely elusive, and has been unequivocally detected only towards GRB 080607 and possibly towards GRB 060206. Here, we present the discovery of H_2-rich gas, including the presence of vibrationally-excited H_2^* in the optical spectrum of the afterglow of GRB 120815A at z=2.36 obtained with X-shooter at the VLT. The galactic environment of GRB 120815A is characterized by a strong DLA with log(N(H)/cm^-2) = 21.95 +/- 0.10, prominent H_2 absorption in the Lyman-Werner bands (log(N(H_2)/cm^-2) = 20.53 +/- 0.04) and thus a molecular gas fraction log f(H_2)=-1.14 +/- 0.10. The distance d between the absorbing neutral gas and GRB 120815A is constrained via photo-excitation modeling o...

  12. Photoswitching a Molecular Catalyst to Regulate CO2 Hydrogenation

    Energy Technology Data Exchange (ETDEWEB)

    Priyadarshani, Nilusha [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Ginovska-Pangovska, Bojana [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Bays, J. Timothy [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Linehan, John C. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Shaw, Wendy J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2015-07-24

    Inspired by nature’s ability to regulate catalysis using physiological stimuli, azobenzene was incorporated into Rh(bis)diphosphine CO2 hydrogenation catalysts to photoinitiate structural changes to modulate the resulting catalytic activity. The rhodium bound diphosphine ligands (P(Ph2)-CH2-N(R) CH2-P(Ph2)) contain the terminal amine of a non-natural amino acid, either β-alanine (β-Ala) or γ-aminobutyric acid (GABA). For both β-ala and GABA containing complexes, the carboxylic acids of the amino acids were coupled to the amines of diaminoazobenzene, creating a rhodium bound trans-spanning tetraphosphine complex. The photo-induced cis-trans isomerization of the azobenzene-containing complexes imposes structural changes on these complexes, as evidenced by 1H NMR. We found that the CO2 hydrogenation activity for the β-ala bound Rh complex is 40% faster with azobenzene in the cis configuration (16 s-1) than in the trans conformation (11 s-1), while the γ-aminobutyric acid containing Rh complex has the same rate (~17 s-1) in either the cis or the trans configuration at 27 °C. The corresponding complexes without the attached azobenzene were also prepared, characterized, and catalytically tested for comparison, and have rates of 30 s-1. Computational studies were undertaken to evaluate the difference in rate between the cis and trans isomers for the β-Ala bound Rh complex, and revealed major structural changes between all cis and trans structures, but only minor structural changes that would be unique to the β-Ala bound Rh complex. We postulate that the slower rate of the azobenzene-containing β-Ala bound Rh complex is due to subtle changes in the bite angle arising from steric strain due to the trans-spanning azobenzene, altering hydricity and consequently rate. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy

  13. Hydrogen bonding discotic liquid crystals: Synthesis, self-assembly, and molecular recognition

    Science.gov (United States)

    Bushey, Mark Lawrence

    The triamides shown below form discotic liquid crystalline phases with intermolecular hydrogen bonding stabilizing the columnar structure, A and B. The mesomorphic orientations of the columns are dependent on the amide side chain. Three mesophasic orientations are described: columns aligned perpendicular to the surface, columns aligned parallel to the surface in a radial pattern, and columns aligned parallel to the surface in a parallel or aligned pattern. The aggregation of the tridodecyloxy-triamides show N-H shifting in the IR at elevated temperatures, an indication that hydrogen bonding is important in the association of liquid crystalline mesophases. Powder X-ray diffraction studies indicate packing of the columns into a hexagonal lattice.* Studies on triamides with chiral side chains result in molecules stacking into columns displaying a helical pitch. In concentrated solutions of dodecane, molecules with chiral side chains display behavior consistent with chiral nematic liquid crystals; a super helical packing of the chiral columns. These superhelical packed systems show temperature dependent selective reflection of visible light and fingerprint textures. Atomic force microscopy (AFM) confirms in sub-monolayer films, that molecules preferring an edge-on orientation form long columns on highly ordered pyrolytic graphite (HOPG), those that prefer a face-on orientation form large amorphous domains. Electrostatic force microscopy (EFM) images of the domains of molecules in the edge-on orientation provides no discernible polarity, imaging of the domains of molecules in the face-on orientation indicates a negative polar orientation. Scanning probe measurements (SPM) of the tridodecynyl-triamide have shown similar edge-on orientations of other tridodecyloxy-triamides. Powder X-ray diffraction of these liquid crystalline phases shows a hexagonal packing of the columnar assembly. Electro-optic switching studies indicate a piezoelectric switching mechanism, possibly

  14. Collision-Induced Infrared Absorption by Molecular Hydrogen Pairs at Thousands of Kelvin

    Directory of Open Access Journals (Sweden)

    Xiaoping Li

    2010-01-01

    Full Text Available Collision-induced absorption by hydrogen and helium in the stellar atmospheres of cool white dwarfs causes the emission spectra to differ significantly from the expected blackbody spectra of the cores. For detailed modeling of radiative processes at temperatures up to 7000 K, the existing H2–H2 induced dipole and potential energy surfaces of high quality must be supplemented by calculations with the H2 bonds stretched or compressed far from the equilibrium length. In this work, we describe new dipole and energy surfaces, based on more than 20 000 ab initio calculations for H2–H2. Our results agree well with previous ab initio work (where those data exist; the calculated rototranslational absorption spectrum at 297.5 K matches experiment similarly well. We further report the calculated absorption spectra of H2–H2 for frequencies from the far infrared to 20 000 cm−1, at temperatures of 600 K, 1000 K, and 2000 K, for which there are no experimental data.

  15. Detection and isolation of plant-associated bacteria scavenging atmospheric molecular hydrogen.

    Science.gov (United States)

    Kanno, Manabu; Constant, Philippe; Tamaki, Hideyuki; Kamagata, Yoichi

    2016-09-01

    High-affinity hydrogen (H2 )-oxidizing bacteria possessing group 5 [NiFe]-hydrogenase genes are important contributors to atmospheric H2 uptake in soil environments. Although previous studies reported the occurrence of a significant H2 uptake activity in vegetation, there has been no report on the identification and diversity of the responsible microorganisms. Here, we show the existence of plant-associated bacteria with the ability to consume atmospheric H2 that may be a potential energy source required for their persistence in plants. Detection of the gene hhyL - encoding the large subunit of group 5 [NiFe]-hydrogenase - in plant tissues showed that plant-associated high-affinity H2 -oxidizing bacteria are widely distributed in herbaceous plants. Among a collection of 145 endophytic isolates, seven Streptomyces strains were shown to possess hhyL gene and exhibit high- or intermediate-affinity H2 uptake activity. Inoculation of Arabidopsis thaliana (thale cress) and Oryza sativa (rice) seedlings with selected isolates resulted in an internalization of the bacteria in plant tissues. H2 uptake activity per bacterial cells was comparable between plant and soil, demonstrating that both environments are favourable for the H2 uptake activity of streptomycetes. This study first demonstrated the occurrence of plant-associated high-affinity H2 -oxidizing bacteria and proposed their potential contribution as atmospheric H2 sink.

  16. P-hydrogen-substituted 1,3,2-diazaphospholenes: molecular hydrides.

    Science.gov (United States)

    Burck, Sebastian; Gudat, Dietrich; Nieger, Martin; Du Mont, Wolf-Walther

    2006-03-29

    P-Hydrogen-substituted 1,3,2-diazaphospholenes 1 were prepared by an improved procedure from diazadienes and were characterized by spectroscopy and in one case by X-ray diffraction. A unique hydride-type reactivity of the P-H bonds was documented by extensive reactivity studies. Aldehydes and ketones were readily reduced to diazaphospholene derivatives of the corresponding alcohols, with alkyl-substituted ketones being converted at much lower rates than aldehydes or diaryl ketones. Reactions with the tetrachlorides of group 14 elements proceeded via hydride/chloride metathesis to give either partially chlorinated derivatives EH(n)Cl(4-n) (n = 0-3 for E = C, Si) or HCl and phosphenium salts 16c[ECl3] (for E = Ge, Sn) which were characterized by spectroscopic and X-ray diffraction studies. Tin dichloride was readily reduced to the element. Reactions of 1c with the P-chloro-diazaphospholene 3c and the salt 16c[OTf] allowed the first experimental detection of intermolecular exchange of a hydride, rather than a proton, between phosphine derivatives. Computational studies indicated that the hydride transfer between 1c and the cation 16c involves a transient H-bridged species with bonding properties similar to those of B2H7-. The preference for the formation of these bridged intermediates over P-P bonded phosphenium-phosphine adducts is attributed to the low electrophilicity of the diazaphospholenium cations and characterizes a novel reaction mode for phosphenium ions.

  17. Genetics and Molecular Biology of Hydrogen Metabolism in Sulfate-Reducing Bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Wall, Judy D. [Univ. of Missouri, Columbia, MO (United States)

    2014-12-23

    The degradation of our environment and the depletion of fossil fuels make the exploration of alternative fuels evermore imperative. Among the alternatives is biohydrogen which has high energy content by weight and produces only water when combusted. Considerable effort is being expended to develop photosynthetic systems -- algae, cyanobacteria, and anaerobic phototrophs -- for sustainable H2 production. While promising, this approach also has hurdles such as the harvesting of light in densely pigmented cultures that requires costly constant mixing and large areas for exposure to sunlight. Little attention is given to fermentative H2 generation. Thus understanding the microbial pathways to H2 evolution and metabolic processes competing for electrons is an essential foundation that may expand the variety of fuels that can be generated or provide alternative substrates for fine chemical production. We studied a widely found soil anaerobe of the class Deltaproteobacteria, a sulfate-reducing bacterium to determine the electron pathways used during the oxidation of substrates and the potential for hydrogen production.

  18. Genetics and Molecular Biology of Hydrogen Metabolism in Sulfate-Reducing Bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Wall, Judy D. [University of Missouri-Columbia

    2014-12-23

    The degradation of our environment and the depletion of fossil fuels make the exploration of alternative fuels evermore imperative. Among the alternatives is biohydrogen which has high energy content by weight and produces only water when combusted. Considerable effort is being expended to develop photosynthetic systems -- algae, cyanobacteria, and anaerobic phototrophs -- for sustainable H2 production. While promising, this approach also has hurdles such as the harvesting of light in densely pigmented cultures that requires costly constant mixing and large areas for exposure to sunlight. Little attention is given to fermentative H2 generation. Thus understanding the microbial pathways to H2 evolution and metabolic processes competing for electrons is an essential foundation that may expand the variety of fuels that can be generated or provide alternative substrates for fine chemical production. We studied a widely found soil anaerobe of the class Deltaproteobacteria, a sulfate-reducing bacterium to determine the electron pathways used during the oxidation of substrates and the potential for hydrogen production.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2008-10-24

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

  1. Development of simulation approach for two-dimensional chiral molecular self-assembly driven by hydrogen bond at the liquid/solid interface

    Science.gov (United States)

    Qin, Yuan; Yao, Man; Hao, Ce; Wan, Lijun; Wang, Yunhe; Chen, Ting; Wang, Dong; Wang, Xudong; Chen, Yonggang

    2017-09-01

    Two-dimensional (2D) chiral self-assembly system of 5-(benzyloxy)-isophthalic acid derivative/(S)-(+)-2-octanol/highly oriented pyrolytic graphite was studied. A combined density functional theory/molecular mechanics/molecular dynamics (DFT/MM/MD) approach for system of 2D chiral molecular self-assembly driven by hydrogen bond at the liquid/solid interface was thus proposed. Structural models of the chiral assembly were built on the basis of scanning tunneling microscopy (STM) images and simplified for DFT geometry optimization. Merck Molecular Force Field (MMFF) was singled out as the suitable force field by comparing the optimized configurations of MM and DFT. MM and MD simulations for hexagonal unit model which better represented the 2D assemble network were then preformed with MMFF. The adhesion energy, evolution of self-assembly process and characteristic parameters of hydrogen bond were obtained and analyzed. According to the above simulation, the stabilities of the clockwise and counterclockwise enantiomorphous networks were evaluated. The calculational results were supported by STM observations and the feasibility of the simulation method was confirmed by two other systems in the presence of chiral co-absorbers (R)-(-)-2-octanol and achiral co-absorbers 1-octanol. This theoretical simulation method assesses the stability trend of 2D enantiomorphous assemblies with atomic scale and can be applied to the similar hydrogen bond driven 2D chirality of molecular self-assembly system.

  2. Experimental and Computational Mechanistic Studies Guiding the Rational Design of Molecular Electrocatalysts for Production and Oxidation of Hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Raugei, Simone; Helm, Monte L.; Hammes-Schiffer, Sharon; Appel, Aaron M.; O' Hagan, Molly J.; Wiedner, Eric S.; Bullock, R. Morris

    2016-01-19

    Understanding how to control the movement of protons and electrons is crucial to the design of fast, efficient electrocatalysts for hydrogen production and oxidation based on earth-abundant metals. Our work seeks to elucidate fundamental questions about proton movement. We have demonstrated that incorporating a pendant amine functioning as a proton relay in the second coordination sphere of a metal complex helps proton mobility, resulting in faster and more energy efficient catalysts. Proton transfer reactions are often rate limiting, and are influenced by several factors, such as pKa values, steric effects, hydrogen bonding, and solvation/desolvation of the exogenous base and acid employed. The presence of multiple protonation sites introduces branching points along the catalytic cycle, making less productive pathways accessible, or leading to the formation of stable off-cycle species. Using ligands with only one pendant amine mitigates this problem and results in catalysts with high rates for production of H2. For H2 oxidation catalysts, iron complexes with a high H2 binding affinity were developed. However, the improvement of H2 binding enthalpy resulted in a pKa mismatch between the protonated metal center and the protonated pendant amine, and consequently to rate-limiting intramolecular proton movement. Taken altogether, our results demonstrate the necessity of optimizing the entire catalytic cycle, as the optimization of a specific catalytic step can negatively influence another step, and not necessarily lead to better catalytic performance. We discuss a general procedure, based on thermodynamic arguments, which allows the simultaneous minimization of the free energy change of each catalytic step, yielding a nearly flat free energy surface, with no large barriers due to energy mismatches from either high- or low-energy intermediates. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by

  3. Density dependence of hydrogen bonding and the translational-orientational structural order in supercritical water: a molecular dynamics study.

    Science.gov (United States)

    Ma, Haibo; Ma, Jing

    2011-08-07

    Molecular dynamics simulation have been performed with a wide range of densities along a near critical isotherm of supercritical water (SCW) in order to study the density dependence of the structure order and hydrogen bonding (HB). It is revealed that the translational structure order is nearly invariant while the orientational tetrahedral structure order is very sensitive to the bulk density under supercritical conditions. Meanwhile, some energetically unfavorable intermediate water dimer structures are found to appear under supercritical conditions due to the reduced energy difference and the enhanced energy fluctuation. As a consequence, a general geometrical criterion or the inclusion of a energy-based criterion instead of currently widely adopted pure r(OH)-based geometric criterion is suggested to be used in the HB statistics under supercritical conditions. It is found that the average HB number per H(2)O molecule (n(HB)) reduces with the decreasing SCW bulk density although a given pair of H(2)O molecules are shown to have a stronger ability to form a hydrogen bond under lower SCW bulk densities. Accordingly, the orientational tetrahedral structure order q decreases with the reducing bulk density under supercritical conditions. However, when the fluid is dilute with ρ ≤ 0.19ρ(c) (ρ(c) = 0.322 g/cm(3)), the energy fluctuation increases sharply and the short-range order is destroyed, signifying the supercritical fluid (SCF)-gas state transition. Accordingly, the orientational tetrahedral structure order q gets reversal around ρ = 0.19ρ(c) and approaches zero under very dilute conditions. The sensitivity of the orientational order to the density implies the microscopic origin of the significant dependence of SCF's physicochemical properties on the pressure.

  4. Molecular basis of the mechanism of thiol oxidation by hydrogen peroxide in aqueous solution: challenging the SN2 paradigm.

    Science.gov (United States)

    Zeida, Ari; Babbush, Ryan; Lebrero, Mariano C González; Trujillo, Madia; Radi, Rafael; Estrin, Darío A

    2012-03-19

    The oxidation of cellular thiol-containing compounds, such as glutathione and protein Cys residues, is considered to play an important role in many biological processes. Among possible oxidants, hydrogen peroxide (H(2)O(2)) is known to be produced in many cell types as a response to a variety of extracellular stimuli and could work as an intracellular messenger. This reaction has been reported to proceed through a S(N)2 mechanism, but despite its importance, the reaction is not completely understood at the atomic level. In this work, we elucidate the reaction mechanism of thiol oxidation by H(2)O(2) for a model methanethiolate system using state of the art hybrid quantum-classical (QM-MM) molecular dynamics simulations. Our results show that the solvent plays a key role in positioning the reactants, that there is a significant charge redistribution in the first stages of the reaction, and that there is a hydrogen transfer process between H(2)O(2) oxygen atoms that occurs after reaching the transition state. These observations challenge the S(N)2 mechanism hypothesis for this reaction. Specifically, our results indicate that the reaction is driven by a tendency of the slightly charged peroxidatic oxygen to become even more negative in the product via an electrophilic attack on the negative sulfur atom. This is inconsistent with the S(N)2 mechanism, which predicts a protonated sulfenic acid and hydroxyl anion as stable intermediates. These intermediates are not found. Instead, the reaction proceeds directly to unprotonated sulfenic acid and water.

  5. Car-Parrinello and path integral molecular dynamics study of the intramolecular hydrogen bonds in the crystals of benzoylacetone and dideuterobenzoylacetone.

    Science.gov (United States)

    Durlak, Piotr; Latajka, Zdzisław

    2014-11-14

    The dynamics of the intramolecular short hydrogen bond in the molecular crystal of benzoylacetone and its deuterated analogue are investigated using ab initio molecular dynamics simulations. A study on intramolecular hydrogen bonding in 1-phenyl-1,3-butadione (I) and 1-deuteroxy-2-deutero-1-phenylbut-1-en-3-one (II) crystals has been carried out at 160 K and 300 K on the CPMD method level and at 300 K on the PIMD method level. The analysis of the two-dimensional free-energy landscape of reaction coordinate δ-parameter and ROO distances shows that the hydrogen (deuter) between the two oxygen atoms adopts a slightly asymmetrical position in the single potential well. When the nuclear quantum effects are taken into account, very large delocalization of the bridging proton is observed. These studies indicate that hydrogen bonds in the crystal of benzoylacetone have characteristic properties for the type of bonding model resonance-assisted hydrogen bonds (RAHB) without existing the equilibrium of the two tautomers. The infrared spectrum has been calculated, and a comparative vibrational analysis has been performed. The CPMD vibrational results appear to qualitatively agree with the experimental ones.

  6. Anharmonic enhancement of superconductivity in metallic molecular Cmca  -  4 hydrogen at high pressure: a first-principles study.

    Science.gov (United States)

    Borinaga, Miguel; Riego, P; Leonardo, A; Calandra, Matteo; Mauri, Francesco; Bergara, Aitor; Errea, Ion

    2016-12-14

    First-principles calculations based on density-functional theory including anharmonicity within the variational stochastic self-consistent harmonic approximation are applied to understand how the quantum character of the proton affects the candidate metallic molecular Cmca  -  4 structure of hydrogen in the 400-450 GPa pressure range, where metallization of hydrogen is expected to occur. Anharmonic effects, which become crucial due to the zero-point motion, have a large impact on the hydrogen molecules by increasing the intramolecular distance by approximately a 6%. This induces two new electron pockets at the Fermi surface opening new scattering channels for the electron-phonon interaction. Consequently, the electron-phonon coupling constant and the superconducting critical temperature are approximately doubled by anharmonicity and Cmca  -  4 hydrogen becomes a superconductor above 200 K in all the studied pressure range. Contrary to many superconducting hydrides, where anharmoncity tends to lower the superconducting critical temperature, our results show that it can enhance superconductivity in molecular hydrogen.

  7. 3D Results in VTK with data for gravitational collapse of a molecular hydrogen cloud; Resultados 3D en VTK con datos para colapso gravitacional de una nube de hidrogeno molecular

    Energy Technology Data Exchange (ETDEWEB)

    Duarte P, R.; Klapp E, J. [ININ, Carretera Mexico-Toluca, s/n, La Marquesa, Ocoyoacac, Mexico, C.P. 52750 (Mexico)

    2007-07-01

    With the objective of using free software for visualization, we experience with VTK (Visualization Toolkit) system guided to objects, using a VTK classes library, Tcl languages and PV-WAVE, to create an application and to produce some images in 3D with data of 3D coordinated points, in this case of a gravitational collapse of a cloud of molecular hydrogen. (Author)

  8. An exceptional kinetic quantum sieving separation effect of hydrogen isotopes on commercially available carbon molecular sieves.

    Science.gov (United States)

    Xing, Yanlong; Cai, Jinjun; Li, Liangjun; Yang, Menglong; Zhao, Xuebo

    2014-08-14

    The quantum sieving effect of H2/D2 at 77 K on commercially available carbon molecular sieves (1.5GN-H and 3KT-172) was studied. An exceptional reverse kinetic quantum effect is observed on 1.5GN-H where D2 diffuses much faster than H2 with a ratio of up to 5.83 at low pressure, and the difference is still very evident even as the pressure increases up to 1 bar. D2 also diffuses faster than H2 on 3KT-172 with a ratio of up to 1.86. However, the reverse kinetic sieving disappears in a polymer-based carbon (PC). The present kinetic quantum sieving effect of H2 and D2 at 77 K on 1.5GN-H is the highest to date.

  9. Hydrogen-bond vibrational and energetic dynamical properties in sI and sII clathrate hydrates and in ice Ih: Molecular dynamics insights.

    Science.gov (United States)

    Chakraborty, Somendra Nath; English, Niall J

    2015-10-21

    Equilibrium molecular dynamics (MD) simulations have been performed on cubic (sI and sII) polymorphs of methane hydrate, and hexagonal ice (ice Ih), to study the dynamical properties of hydrogen-bond vibrations and hydrogen-bond self-energy. It was found that hydrogen-bond energies are greatest in magnitude in sI hydrates, followed by sII, and their energies are least in magnitude in ice Ih. This is consistent with recent MD-based findings on thermal conductivities for these various materials [N. J. English and J. S. Tse, Phys. Rev. Lett. 103, 015901 (2009)], in which the lower thermal conductivity of sI methane hydrate was rationalised in terms of more strained hydrogen-bond arrangements. Further, modes for vibration and energy-transfer via hydrogen bonds in sI hydrate were found to occur at higher frequencies vis-à-vis ice Ih and sII hydrate in both the water-librational and OH⋯H regions because of the more strained nature of hydrogen bonds therein.

  10. High-resolution measurements of atmospheric molecular hydrogen and its isotopic composition at the West African coast of Mauritania

    Directory of Open Access Journals (Sweden)

    S. Walter

    2013-05-01

    Full Text Available Oceans are a net source of molecular hydrogen (H2 to the atmosphere, where nitrogen (N2 fixation is assumed to be the main biological production pathway followed by photochemical production from organic material. The sources can be distinguished using isotope measurements because of clearly differing isotopic signatures of the produced hydrogen. Here we present the first ship-borne measurements of atmospheric molecular H2 mixing ratio and isotopic composition at the West African coast of Mauritania (16–25° W, 17–24° N. This area is one of the biologically most active regions of the world's oceans with seasonal upwelling events and characterized by strongly differing hydrographical/biological properties and phytoplankton community structures. The aim of this study was to identify areas of H2 production and distinguish H2 sources by isotopic signatures of atmospheric H2. For this more than 100 air samples were taken during two cruises in February 2007 and 2008. During both cruises a transect from the Cape Verde Islands towards the Mauritanian Coast was sampled to cover differing oceanic regions such as upwelling and oligotrophic regimes. In 2007, additionally, four days were sampled at high resolution of one sample per hour to investigate a possible diurnal cycle of atmospheric H2. Our results indicate the influence of local sources and suggest the Banc d'Arguin as a pool for precursors for photochemical H2 production, whereas oceanic N2 fixation could not be identified as a source for atmospheric H2 during these two cruises. The variability in diurnal cycles is probably influenced by released precursors for photochemical H2 production and also affected by a varying origin of air masses. This means for future investigations that only measuring the mixing ratio of H2 is insufficient to explain the variability of an atmospheric diurnal cycle and support is needed, e.g. by isotopic measurements. Nevertheless, measurements of atmospheric H2

  11. The molecular transport and intercalation of guest molecules into hydrogen-bonded metal-organic frameworks (HMOFs)

    Science.gov (United States)

    Hogan, Greg Anthony

    The process of molecular transport and intercalation has been widely studied for many years, resulting in the discovery of molecular frameworks that are capable of hosting guest molecules or ions. Layered and porous metal-organic frameworks (MOFs) have been found to have applications in the field of catalysis, storage, separations, and ion-exchange. More recently, molecular components with peripheral hydrogen-bonding moieties have been used to affect the synthesis of hydrogen-bonded metal-organic frameworks (HMOFs) as an alternative to MOFs, which are interconnected via coordinate-covalent bonds. While MOFs are perhaps stronger materials, HMOFs have the advantage of being easily modifiable and more flexible. Because HMOFs have not been extensively studied for their ability to host molecules, and because their ability to withstand guest loss and guest exchange is essentially unknown, here we report the synthesis and molecular transport properties of both close-packed and porous HMOFs. Layered materials can mimic the behavior of naturally occurring clays, where guest molecules are absorbed and the layer will expand to accommodate the entering guest molecule. We have created a clay mimic composed of a metal pyridine-dicarboxylates and ammonium counterions (a layered HMOF), which is suitable for studying the ability of such materials to absorb guest molecules. We can control the distance of the interlayer region, as well as the chemical nature (hydrophobic or hydrophilic) by varying the organic amine. The metal complex contains axial water ligands that are replaceable, and such ligand exchange has precedence in coordination polymer (MOF) systems, and has been termed "coordinative intercalation". Using the synthesized layered material we examined the process of intercalation, having chosen a variety of guest molecules ranging from alkyl to aryl molecules, each of which have substituents varying in size, shape and electronics. The first set of guest molecules are non

  12. Kinematics and Excitation of the Molecular Hydrogen Accretion Disc in NGC 1275

    CERN Document Server

    Scharwaechter, J; Dopita, M A; Beck, T L

    2012-01-01

    We report the results of high spatial and spectral resolution integral-field spectroscopy of the central ~3 x 3 arcsec^2 of the active galaxy NGC 1275 (Perseus A), based on observations with the Near-infrared Integral Field Spectrograph (NIFS) and the ALTAIR adaptive-optics system on the Gemini North telescope. The circum-nuclear disc in the inner R~50 pc of NGC 1275 is seen in both the H2 and [FeII] lines. The disc is interpreted as the outer part of a collisionally-excited turbulent accretion disc. The kinematic major axis of the disc at a position angle of 68 deg is oriented perpendicular to the radio jet. A streamer-like feature to the south-west of the disc, detected in H2 but not in [FeII], is discussed as one of possibly several molecular streamers, presumably falling into the nuclear region. Indications of an ionization structure within the disc are deduced from the HeI and Br gamma emission lines, which may partially originate from the inner portions of the accretion disc. The kinematics of these two...

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

    Science.gov (United States)

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

    2017-01-01

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

  14. Molecular hydrogen from z = 0.0963 DLA towards the QSO J1619+3342

    CERN Document Server

    Srianand, Raghunathan; Muzahid, Sowgat; Mohan, Vijay

    2014-01-01

    We report the detection of H2 in a zabs= 0.0963 Damped Lyman-{\\alpha} (DLA) system towards zem = 0.4716 QSO J1619+3342. This DLA has log N(H I) = 20.55 (0.10), 18.13 < log N(H2) < 18.40, [S/H] = -0.62 (0.13), [Fe/S] = -1.00 (0.17) and the molecular fraction -2.11 < log f(H2) < -1.85. The inferred gas kinetic temperature using the rotational level population is in the range 95 - 132 K. We do not detect C I or C II* absorption from this system. Using R- and V-band deep images we identify a sub-L* galaxy at an impact parameter of 14 kpc from the line of sight, having consistent photometric redshift, as a possible host for the absorber. We use the photoionization code CLOUDY to get the physical conditions in the H2 component using the observational constrains from H2, C I, C II* and Mg I. All the observations can be consistently explained if one or more of the following is true: (i) Carbon is underabundant by more than 0.6 dex as seen in halo stars with Z ~ 0.1 Z_sun, (ii) H I associated with H2 compo...

  15. Solvation of triplet Rydberg states of molecular hydrogen in superfluid helium

    Science.gov (United States)

    Kiljunen, Toni; Lehtovaara, Lauri; Kunttu, Henrik; Eloranta, Jussi

    2004-01-01

    We report ab initio interaction potentials, transition dipole moments, and radiative lifetimes for the four lowest triplet states of H2: b 3Σ+u, c 3Πu, a 3Σ+g, and e 3Σ+u, and their response to the perturbation due to approaching ground state He atom. Hybrid density functional quantum Monte Carlo calculations employing the ab initio interaction potentials are then used for calculating the liquid structure around the molecular excimers in bulk superfluid 4He. Calculations demonstrate a wide variety of possible solvation structures, both spherical and highly anisotropic in geometry, depending on the electronic state of H2. The experimentally observed H2 (3e3a) emission bands [Trottier et al., Phys. Rev. A 61, 052504 (2000)] are simulated and the origins of the line shifts discussed. Absorption spectra of the same system are predicted to be broader and more blue shifted compared to the gas phase. Feasibility of the metastable 3c state for absorption experiments in liquid helium is proposed.

  16. A FUSE Survey of Interstellar Molecular Hydrogen in the Small and Large Magellanic Clouds

    CERN Document Server

    Tumlinson, J; Rachford, B L; Browning, M K; Snow, T P; Fullerton, A W; Jenkins, E B; Savage, B D; Crowther, P A; Moos, H W; Sembach, K R; Sonneborn, G; York, D G; Tumlinson, Jason; Rachford, Brian L.; Browning, Matthew K.; Snow, Theodore P.; Fullerton, Alex W.; Jenkins, Edward B.; Savage, Blair D.; Crowther, Paul A.; Sembach, Kenneth R.; Sonneborn, George; York, Donald G.

    2001-01-01

    We describe a moderate-resolution FUSE survey of H2 along 70 sight lines to the Small and Large Magellanic Clouds, using hot stars as background sources. FUSE spectra of 67% of observed Magellanic Cloud sources (52% of LMC and 92% of SMC) exhibit absorption lines from the H2 Lyman and Werner bands between 912 and 1120 A. Our survey is sensitive to N(H2) >= 10^14 cm^-2; the highest column densities are log N(H2) = 19.9 in the LMC and 20.6 in the SMC. We find reduced H2 abundances in the Magellanic Clouds relative to the Milky Way, with average molecular fractions = 0.010 (+0.005, -0.002) for the SMC and = 0.012 (+0.006, -0.003) for the LMC, compared with = 0.095 for the Galactic disk over a similar range of reddening. The dominant uncertainty in this measurement results from the systematic differences between 21 cm radio emission and Lya in pencil-beam sight lines as measures of N(HI). These results imply that the diffuse H2 masses of the LMC and SMC are 8 x 10^6 Msun and 2 x 10^6 Msun, respectively, 2% and...

  17. Molecular simulation and macroscopic modeling of the diffusion of hydrogen, carbon monoxide and water in heavy n-alkane mixtures.

    Science.gov (United States)

    Makrodimitri, Zoi A; Unruh, Dominik J M; Economou, Ioannis G

    2012-03-28

    The self-diffusion coefficient of hydrogen (H(2)), carbon monoxide (CO) and water (H(2)O) in n-alkanes was studied by molecular dynamics simulation. Diffusion in a few pure n-alkanes (namely n-C(8), n-C(20), n-C(64) and n-C(96)) was examined. In addition, binary n-C(12)-n-C(96) mixtures with various compositions as well as more realistic five- and six-n-alkane component mixtures were simulated. In all cases, the TraPPE united atom force field was used for the n-alkane molecules. The force field for the mixture of n-alkanes was initially validated against experimental density values and was shown to be accurate. Moreover, macroscopic correlations for predicting diffusion coefficient of H(2), CO and H(2)O in n-alkanes and mixtures of n-alkanes were developed. The functional form of the correlation was based on the rough hard sphere theory (RHS). The correlation was applied to simulation data and an absolute average deviation (AAD) of 5.8% for pure n-alkanes and 3.4% for n-alkane mixtures was obtained. Correlation parameters vary in a systematic way with carbon number and so they can be used to provide predictions in the absence of any experimental or molecular simulation data. Finally, in order to reduce the number of adjustable parameters, for the n-alkane mixtures the "pseudo-carbon number" approach was used. This approach resulted in relatively higher deviation from MD simulation data (AAD of 18.2%); however, it provides a convenient and fast method to predict diffusion coefficients. The correlations developed here are expected to be useful for engineering calculations related to the design of the Gas-to-Liquid process.

  18. MHOs toward HMOs: A Search for Molecular Hydrogen Emission-Line Objects toward High-mass Outflows

    Science.gov (United States)

    Wolf-Chase, Grace; Arvidsson, Kim; Smutko, Michael

    2017-07-01

    We present the results of a narrow-band near-infrared imaging survey for Molecular Hydrogen emission-line Objects (MHOs) toward 26 regions containing high-mass protostellar candidates and massive molecular outflows. We have detected a total of 236 MHOs, 156 of which are new detections, in 22 out of the 26 regions. We use H2 2.12 μm/H2 2.25 μm flux ratios, together with morphology, to separate the signatures of fluorescence associated with photo-dissociation regions (PDRs) from shocks associated with outflows in order to identify the MHOs. PDRs have typical low flux ratios of ˜1.5-3, while the vast majority of MHOs display flux ratios typical of C-type shocks (˜6-20). A few MHOs exhibit flux ratios consistent with expected values for J-type shocks (˜3-4), but these are located in regions that may be contaminated with fluorescent emission. Some previously reported MHOs have low flux ratios, and are likely parts of PDRs rather than shocks indicative of outflows. We identify a total of 36 outflows across the 22 target regions where MHOs were detected. In over half these regions, MHO arrangements and fluorescent structures trace features present in CO outflow maps, suggesting that the CO emission traces a combination of dynamical effects, which may include gas entrained in expanding PDRs as well as bipolar outflows. Where possible, we link MHO complexes to distinct outflows and identify candidate driving sources.

  19. Molecular hydrogen and catalytic combustion in the production of hyperpolarized 83Kr and 129Xe MRI contrast agents

    Science.gov (United States)

    Rogers, Nicola J.; Hill-Casey, Fraser; Stupic, Karl F.; Six, Joseph S.; Lesbats, Clémentine; Rigby, Sean P.; Fraissard, Jacques; Pavlovskaya, Galina E.; Meersmann, Thomas

    2016-03-01

    Hyperpolarized (hp) 83Kr is a promising MRI contrast agent for the diagnosis of pulmonary diseases affecting the surface of the respiratory zone. However, the distinct physical properties of 83Kr that enable unique MRI contrast also complicate the production of hp 83Kr. This work presents a previously unexplored approach in the generation of hp 83Kr that can likewise be used for the production of hp 129Xe. Molecular nitrogen, typically used as buffer gas in spin-exchange optical pumping (SEOP), was replaced by molecular hydrogen without penalty for the achievable hyperpolarization. In this particular study, the highest obtained nuclear spin polarizations were P = 29% for 83Kr and P = 63% for 129Xe. The results were reproduced over many SEOP cycles despite the laser-induced on-resonance formation of rubidium hydride (RbH). Following SEOP, the H2 was reactively removed via catalytic combustion without measurable losses in hyperpolarized spin state of either 83Kr or 129Xe. Highly spin-polarized 83Kr can now be purified for the first time, to our knowledge, to provide high signal intensity for the advancement of in vivo hp 83Kr MRI. More generally, a chemical reaction appears as a viable alternative to the cryogenic separation process, the primary purification method of hp 129Xe for the past 2 1/2 decades. The inherent simplicity of the combustion process will facilitate hp 129Xe production and should allow for on-demand continuous flow of purified and highly spin-polarized 129Xe.

  20. Influences of Structure Disorder and Temperature on Properties of Proton Conductivity in Hydrogen-Bond Molecular Systems

    Institute of Scientific and Technical Information of China (English)

    PANG Xiao-Feng; YU Jia-Feng

    2007-01-01

    The dynamic properties of proton conductivity along hydrogen-bonded molecular systems,for example,ice crystal,with structure disorder or damping and finite temperatures exposed in an externally applied electric-field have been numerically studied by Runge-Kutta way in our Soliton model.The results obtained show that the proton-soliton is very robust against the structure disorder including the fluctuation of the force constant and disorder in the sequence of masses and thermal perturbation and damping of medium,the velocity of its conductivity increases with increasing of the externally applied electric-field and decreasing of the damping coefficient of medium,but the proton-soliton disperses for quite great fluctuation of the force constant and damping coefficient.In the numerical simulation we find that the proton-soliton in our model is thermally stable in a large region of temperature of T ≤ 273 K under influences of damping and externally applied electric-field in ice crystal.This shows that our model is available and appropriate to ice.

  1. Interaction of molecular hydrogen with open transition metal centers for enhanced binding in metal-organic frameworks: a computational study.

    Science.gov (United States)

    Lochan, Rohini C; Khaliullin, Rustam Z; Head-Gordon, Martin

    2008-05-19

    Molecular hydrogen is known to form stable, "nonclassical" sigma complexes with transition metal centers that are stabilized by donor-acceptor interactions and electrostatics. In this computational study, we establish that strong H2 sorption sites can be obtained in metal-organic frameworks by incorporating open transition metal sites on the organic linkers. Using density functional theory and energy decomposition analysis, we investigate the nature and characteristics of the H2 interaction with models of exposed open metal binding sites {half-sandwich piano-stool shaped complexes of the form (Arene)ML(3- n)(H2)n [M=Cr, Mo, V(-), Mn(+); Arene = C6H5X (X=H, F, Cl, OCH3, NH2, CH3, CF3) or C6H3Y2X (Y=COOH, X=CF3, Cl; L=CO; n=1-3]}. The metal-H2 bond dissociation energy of the studied complexes is calculated to be between 48 and 84 kJ/mol, based on the introduction of arene substituents, changes to the metal core, and of charge-balancing ligands. Thus, design of the binding site controls the H2 binding affinity and could be potentially used to control the magnitude of the H2 interaction energy to achieve reversible sorption characteristics at ambient conditions. Energy decomposition analysis illuminates both the possibilities and present challenges associated with rational materials design.

  2. Surface Functionalization of g-C 3 N 4 : Molecular-Level Design of Noble-Metal-Free Hydrogen Evolution Photocatalysts

    KAUST Repository

    Chen, Yin

    2015-06-12

    A stable noble-metal-free hydrogen evolution photocatalyst based on graphite carbon nitride (g-C3N4) was developed by a molecular-level design strategy. Surface functionalization was successfully conducted to introduce a single nickel active site onto the surface of the semiconducting g-C3N4. This catalyst family (with less than 0.1 wt% of Ni) has been found to produce hydrogen with a rate near to the value obtained by using 3 wt% platinum as co-catalyst. This new catalyst also exhibits very good stability under hydrogen evolution conditions, without any evidence of deactivation after 24h. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Characterization of the hydrogen bond in molecular systems of biological interest by neutron scattering; Caracterisation de la liaison hydrogene dans des systemes moleculaires d'interet biologique par diffusion de neutrons

    Energy Technology Data Exchange (ETDEWEB)

    Cavillon, F

    2004-10-15

    This work presents a methodology for the analysis of the scattering spectra of neutrons on molecular liquids. This method is based on the adjustment of the molecular form factor concerning great momentum transfer. The subtraction of the intra-molecular contributions gives access to information on inter-molecular interactions such as the hydrogen bond. 3 systems with increasing levels of difficulty have been studied: the ammonia molecule, the N-methyl-formamide (NMF) and the N-methyl-acetamide (NMA). The value we get for the N-D intermolecular distance of the liquid ammonia molecule is 1.7 angstrom, this value is different from the value generally admitted (2.3 angstrom) but we have validated it by studying the isotopic substitution N{sup 14}/N{sup 15}. The adjustment to the NMF is obtained with a good accuracy but the characterization of the hydrogen bound is more delicate to infer. A preliminary study of the NMA molecule shows that this method can give relevant results on complex molecules.

  4. Herschel Survey of Galactic OH+, H2O+, and H3O+: Probing the Molecular Hydrogen Fraction and Cosmic-Ray Ionization Rate

    CERN Document Server

    Indriolo, Nick; Gerin, M; Schilke, P; Benz, A O; Winkel, B; Menten, K M; Chambers, E T; Black, John H; Bruderer, S; Falgarone, E; Godard, B; Goicoechea, J R; Gupta, H; Lis, D C; Ossenkopf, V; Persson, C M; Sonnentrucker, P; van der Tak, F F S; van Dishoeck, E F; Wolfire, Mark G; Wyrowski, F

    2014-01-01

    In diffuse interstellar clouds the chemistry that leads to the formation of the oxygen bearing ions OH+, H2O+, and H3O+ begins with the ionization of atomic hydrogen by cosmic rays, and continues through subsequent hydrogen abstraction reactions involving H2. Given these reaction pathways, the observed abundances of these molecules are useful in constraining both the total cosmic-ray ionization rate of atomic hydrogen (zeta_H) and molecular hydrogen fraction, f(H2). We present observations targeting transitions of OH+, H2O+, and H3O+ made with the Herschel Space Observatory along 20 Galactic sight lines toward bright submillimeter continuum sources. Both OH+ and H2O+ are detected in absorption in multiple velocity components along every sight line, but H3O+ is only detected along 7 sight lines. From the molecular abundances we compute f(H2) in multiple distinct components along each line of sight, and find a Gaussian distribution with mean and standard deviation 0.042+-0.018. This confirms previous findings t...

  5. The description of dense hydrogen with Wave Packet Molecular Dynamics (WPMD) simulations; Die Beschreibung von dichtem Wasserstoff mit der Methode der Wellenpaket-Molekulardynamik (WPMD)

    Energy Technology Data Exchange (ETDEWEB)

    Jakob, B.

    2006-10-10

    In this work the wave packet molecular dynamics (WPMD) is presented and applied to dense hydrogen. In the WPMD method the electrons are described by a slater determinant of periodic Gaussian wave packets. Each single particle wave function can parametrised through 8 coordinates which can be interpreted as the position and momentum, the width and its conjugate momentum. The equation of motion for these coordinates can be derived from a time depended variational principle. Properties of the equilibrium can be ascertained by a Monte Carlo simulation. With the now completely implemented antisymmetrisation the simulation yields a fundamental different behavior for dense hydrogen compare to earlier simplified models. The results show a phase transition to metallic hydrogen with a higher density than in the molecular phase. This behavior has e.g. a large implication to the physics of giant planets. This work describes the used model and explains in particular the calculation of the energy and forces. The periodicity of the wave function leads to a description in the Fourier space. The antisymmetrisation is done by Matrix operations. Moreover the numerical implementation is described in detail to allow the further development of the code. The results provided in this work show the equation of state in the temperature range 300K - 50000K an density 10{sup 23}-10{sup 24} cm{sup -3}, according a pressure 1 GPa-1000 GPa. In a phase diagram the phase transition to metallic hydrogen can be red off. The electrical conductivity of both phases is destined. (orig.)

  6. Successive hydrogen-elimination reactions with low activation energies in the a-Si:H formation process: An ab initio molecular-orbital study

    Science.gov (United States)

    Sato, Kota; Sugiyama, Yoko; Uchiyama, Akihiko; Iwabuchi, Susumu; Hirano, Tsuneo; Koinuma, Hideomi

    1992-07-01

    Successive hydrogen elimination reactions with low activation energies during the formation of a-Si:H by silane plasma chemical vapor deposition are proposed on the basis of an ab initio molecular-orbital method. The activation energy of the first step, the reaction of a dangling-bond site with an adjacent tetrahedrally coordinated silicon atom, was found to be 25.2 kcal/mol at 0 K when the zero-point vibrational energy was taken into account. The subsequent step was an exothermic process with a lower activation energy. The total process was thermodynamically much more favorable than the molecular processes by which a hydrogen atom or molecule is eliminated.

  7. Temporal and spatial variability of the stable isotopic composition of atmospheric molecular hydrogen: observations at six EUROHYDROS stations

    Directory of Open Access Journals (Sweden)

    A. M. Batenburg

    2011-07-01

    Full Text Available Despite the potential of isotope measurements to improve our understanding of the global atmospheric molecular hydrogen (H2 cycle, few H2 isotope data have been published so far. Now, within the EUROpean network for atmospheric HYDRogen Observations and Studies project (EUROHYDROS, weekly to monthly air samples from six locations in a global sampling network have been analysed for H2 mixing ratio (m(H2 and the stable isotopic composition of the H2 (δ(D,H2, hereafter referred to as δD. The time series thus obtained now cover one to five years for all stations. This is the largest set of ground station observations of δD so far. Annual average δD values are higher at the Southern Hemisphere (SH than at the Northern Hemisphere (NH stations; the maximum is observed at Neumayer (Antarctica, and the minimum at the non-arctic NH stations. The maximum seasonal differences in δD range from ≈18 ‰ at Neumayer to ≈45 ‰ at Schauinsland (Southern Germany; in general, seasonal variability is largest at the NH stations. The timing of minima and maxima differs per station as well. In Alert (Arctic Canada, the variations in δD and m(H2 can be approximated as simple harmonic functions with a ≈5-month relative phase shift. This out-of-phase seasonal behaviour of δD and m(H2 can also be detected, but delayed and with a ≈6-month relative phase shift, at Mace Head and Cape Verde. However, no seasonal δD cycle could be observed at Schauinsland, which likely reflects the larger influence of local sources and sinks at this continental station. At the two SH stations, no seasonal cycle could be detected in the δD data. If it is assumed that the sink processes are the main drivers of the observed seasonality in m(H2 and δD on the NH, the relative seasonal variations can be used to estimate the relative sink strength of the two

  8. Investigations of the very short hydrogen bond in the crystal of nitromalonamide via Car-Parrinello and path integral molecular dynamics.

    Science.gov (United States)

    Durlak, Piotr; Mierzwicki, Krzysztof; Latajka, Zdzisław

    2013-05-09

    In this paper are presented the results of theoretical studies of the structure in proton motion in a very short O···O and two weak N-H···O intramolecular hydrogen bonds in the nitromalonamide crystal. The dynamics of proton motion in hydrogen bonds were investigated in the NVT ensemble at 298 K using the Car-Parrinello and the path integral molecular dynamics. A very large delocalization of proton in the slightly asymmetrical single well of free energy potential of O-H···O intramolecular hydrogen bond was noted especially in the path integral simulation where quantum effects are taken into account. This hydrogen bond is very strong with the estimated energy of hydrogen bond ca. -27 kcal/mol. The nature of intra- and intermolecular interactions was studied by means of quantum theory of atoms in molecules. The infrared spectra were calculated and compared with available experimental data. CPMD vibrational results appear to be in good agreement with the experimental ones.

  9. Molecular dynamics study of effects of temperature and concentration on hydrogen-bond abilities of ethylene glycol and glycerol: implications for cryopreservation.

    Science.gov (United States)

    Weng, Lindong; Chen, Cong; Zuo, Jianguo; Li, Weizhong

    2011-05-12

    The state of intracellular water is important in all phases of cryopreservation. Intracellular water can be transported out of the cell, transferred into its solid phase, or blocked by cryoprotectants and proteins in the cytoplasm. The purpose of the present study is to determine the amount of hydrogen-bonded water in aqueous ethylene glycol and glycerol solutions. The effects of temperature and concentration on the density and the hydrogen bonding characteristics of the solution are evaluated quantitatively in this study. To achieve these aims, a series of molecular dynamics simulations of ethylene glycol/water and glycerol/water mixtures of molalities ranging from 1 to 5 m are conducted at 1 atm and at 273, 285, and 298 K, respectively. The simulation results show that temperature and concentration have variable effects on solution density. The proportion of the hydrogen-bonded water by solute molecules increases with rising molality. The ability of the solute molecules to hydrogen bond with water molecules weakens as the solution becomes more concentrated. Moreover, it turns out that the solution concentration can influence the hydrogen bonding characteristics more greatly than the temperature. The glycerol molecule should be a stronger "water blocker" than the ethylene glycol molecule corresponding to the same conditions. These findings provide insight into the cryoprotective mechanisms of ethylene glycol and glycerol in aqueous solutions, which will confer benefits on the cryopreservation.

  10. Use of the hydrogen bond potential function in a comparative molecular field analysis (CoMFA) on a set of benzodiazepines

    Science.gov (United States)

    Kim, Ki Hwan; Greco, Giovanni; Novellino, Ettore; Silipo, Carlo; Vittoria, Antonio

    1993-06-01

    The results of the GRID-Comparative Molecular Field Analysis (CoMFA) were compared with those of the SYBYL-CoMFA in a study of benzodiazepines. The results demonstrate that the hydrogen bonding function using the GRID H2O probe in a CoMFA can successfully describe the hydrophobic effects of substituents without any bias or preconcept of their effects in the development.

  11. Path-integral molecular dynamics simulations of hydrated hydrogen chloride cluster HCl(H{sub 2}O){sub 4} on a semiempirical potential energy surface

    Energy Technology Data Exchange (ETDEWEB)

    Takayanagi, Toshiyuki, E-mail: tako@mail.saitama-u.ac.jp [Department of Chemistry, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570 (Japan); Takahashi, Kenta; Kakizaki, Akira [Department of Chemistry, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570 (Japan); Shiga, Motoyuki [Center for Computational Science and E-systems, Japan Atomic Energy Agency, Higashi-Ueno 6-9-3, Taito-ku, Tokyo 110-0015 (Japan); Tachikawa, Masanori [Quantum Chemistry Division, International Graduate School of Arts and Sciences, Yokohama-City University, Seto 22-2, Kanazawa-ku, Yokohama 236-0027 (Japan)

    2009-04-22

    Path-integral molecular dynamics simulations for the HCl(H{sub 2}O){sub 4} cluster have been performed on the ground-state potential energy surface directly obtained on-the-fly from semiempirical PM3-MAIS molecular orbital calculations. It is found that the HCl(H{sub 2}O){sub 4} cluster has structural rearrangement above the temperature of 300 K showing a liquid-like behavior. Quantum mechanical fluctuation of hydrogen nuclei plays a significant role in structural arrangement processes in this cluster.

  12. Path-integral molecular dynamics simulations of hydrated hydrogen chloride cluster HCl(H 2O) 4 on a semiempirical potential energy surface

    Science.gov (United States)

    Takayanagi, Toshiyuki; Takahashi, Kenta; Kakizaki, Akira; Shiga, Motoyuki; Tachikawa, Masanori

    2009-04-01

    Path-integral molecular dynamics simulations for the HCl(H 2O) 4 cluster have been performed on the ground-state potential energy surface directly obtained on-the-fly from semiempirical PM3-MAIS molecular orbital calculations. It is found that the HCl(H 2O) 4 cluster has structural rearrangement above the temperature of 300 K showing a liquid-like behavior. Quantum mechanical fluctuation of hydrogen nuclei plays a significant role in structural arrangement processes in this cluster.

  13. Enhanced half-metallicity in the zigzag graphene nanoribbons by adsorption of the zigzag hydrogen fluoride molecular chains

    Directory of Open Access Journals (Sweden)

    Xue Gong

    2014-06-01

    Full Text Available A comprehensive theoretical study of the half-metallicity in the zigzag graphene nanoribbons (ZGNRs by adsorption of the zigzag hydrogen fluoride chains was presented. The ZGNR by adsorption of the hydrogen fluoride chains could be half-metallic when a critical length of the hydrogen fluoride chain is achieved on the ZGNR at low temperature. It was found that the strong dipole moments of the hydrogen fluoride chains act as the constant electric field. Our results suggest a huge possibility in spintronics device applications for achieving half-metallicity in the ZGNRs without the excessively high external electric fields.

  14. Binding characteristics of homogeneous molecularly imprinted polymers for acyclovir using an (acceptor-donor-donor)-(donor-acceptor-acceptor) hydrogen-bond strategy, and analytical applications for serum samples.

    Science.gov (United States)

    Wu, Suqin; Tan, Lei; Wang, Ganquan; Peng, Guiming; Kang, Chengcheng; Tang, Youwen

    2013-04-12

    This paper demonstrates a novel approach to assembling homogeneous molecularly imprinted polymers (MIPs) based on mimicking multiple hydrogen bonds between nucleotide bases by preparing acyclovir (ACV) as a template and using coatings grafted on silica supports. (1)H NMR studies confirmed the AAD-DDA (A for acceptor, D for donor) hydrogen-bond array between template and functional monomer, while the resultant monodisperse molecularly imprinted microspheres (MIMs) were evaluated using a binding experiment, high performance liquid chromatography (HPLC), and solid phase extraction. The Langmuir isothermal model and the Langmuir-Freundlich isothermal model suggest that ACV-MIMs have more homogeneous binding sites than MIPs prepared through normal imprinting. In contrast to previous MIP-HPLC columns, there were no apparent tailings for the ACV peaks, and ACV-MIMs had excellent specific binding properties with a Ka peak of 3.44 × 10(5)M(-1). A complete baseline separation is obtained for ACV and structurally similar compounds. This work also successfully used MIMs as a specific sorbent for capturing ACV from serum samples. The detection limit and mean recovery of ACV was 1.8 ng/mL(-1) and 95.6%, respectively, for molecularly imprinted solid phase extraction coupled with HPLC. To our knowledge, this was the first example of MIPs using AAD-DDA hydrogen bonds.

  15. Hydrogen-bonding structure and dynamics of aqueous carbonate species from car-parrinello molecular dynamics simulations.

    Science.gov (United States)

    Kumar, P Padma; Kalinichev, Andrey G; Kirkpatrick, R James

    2009-01-22

    A comprehensive Car-Parrinello molecular dynamics (CP-MD) study of aqueous solutions of carbonic acid (H(2)CO(3)), bicarbonate (HCO(3)(-)), carbonate (CO(3)(2-)), and carbon dioxide (CO(2)) provides new quantitative insight into the structural and dynamic aspects of the hydrogen-bonding environments for these important aqueous species and their effects on the structure, H-bonding, and dynamical behavior of the surrounding water molecules. The hydration structures of the different carbonate species depend on their ability to accept and donate H-bonds with H(2)O. The H-bonds donated by the C-O-H sites of the carbonate species to water molecules are generally stronger and longer-lived than those accepted by these sites from water molecules. The structural relaxation among the water molecules is dominated by diffusional (translational) motion of H(2)O, whereas the H-bond reorganization is dominated by the librational motion of the water molecules and the carbonate species. The rates of structural relaxation of the H(2)O molecules and the rates of H-bond reorganization among them are slower in systems containing carbonate species, consistent with previous studies of simple salt solutions. The strengths and lifetimes of H-bonds involving the carbonate species positively correlate with the total negative charge on the species. H-bond donation from H(2)O to CO(2) is weak, but the presence of CO(2) noticeably affects the structure and structural relaxation of the surrounding H-bonding network leading to generally stronger H-bonds and slower relaxation rates, the behavior typical of a hydrophobic solute.

  16. The reaction enthalpy of hydrogen dissociation calculated with the Small System Method from simulation of molecular fluctuations.

    Science.gov (United States)

    Skorpa, Ragnhild; Simon, Jean-Marc; Bedeaux, Dick; Kjelstrup, Signe

    2014-09-28

    We show how we can find the enthalpy of a chemical reaction under non-ideal conditions using the Small System Method to sample molecular dynamics simulation data for fluctuating variables. This method, created with Hill's thermodynamic analysis, is used to find properties in the thermodynamic limit, such as thermodynamic correction factors, partial enthalpies, volumes, heat capacities and compressibility. The values in the thermodynamic limit at (T,V, μj) are then easily transformed into other ensembles, (T,V,Nj) and (T,P,Nj), where the last ensemble gives the partial molar properties which are of interest to chemists. The dissociation of hydrogen from molecules to atoms was used as a convenient model system. Molecular dynamics simulations were performed with three densities; ρ = 0.0052 g cm(-3) (gas), ρ = 0.0191 g cm(-3) (compressed gas) and ρ = 0.0695 g cm(-3) (liquid), and temperatures in the range; T = 3640-20,800 K. The enthalpy of reaction was observed to follow a quadratic trend as a function of temperature for all densities. The enthalpy of reaction was observed to only have a small pressure dependence. With a reference point close to an ideal state (T = 3640 K and ρ = 0.0052 g cm(-3)), we were able to calculate the thermodynamic equilibrium constant, and thus the deviation from ideal conditions for the lowest density. We found the thermodynamic equilibrium constant to increase with increasing temperature, and to have a negligible pressure dependence. Taking the enthalpy variation into account in the calculation of the thermodynamic equilibrium constant, we found the ratio of activity coefficients to be in the order of 0.7-1.0 for the lowest density, indicating repulsive forces between H and H2. This study shows that the compressed gas- and liquid density values at higher temperatures are far from those calculated under ideal conditions. It is important to have a method that can give access to partial molar properties, independent of the ideality of

  17. Molecular recognition of naphthalene diimide ligands by telomeric quadruplex-DNA: the importance of the protonation state and mediated hydrogen bonds.

    Science.gov (United States)

    Spinello, A; Barone, G; Grunenberg, J

    2016-01-28

    In depth Monte Carlo conformational scans in combination with molecular dynamics (MD) simulations and electronic structure calculations were applied in order to study the molecular recognition process between tetrasubstituted naphthalene diimide (ND) guests and G-quadruplex (G4) DNA receptors. ND guests are a promising class of telomere stabilizers due to which they are used in novel anticancer therapeutics. Though several ND guests have been studied experimentally in the past, the protonation state under physiological conditions is still unclear. Based on chemical intuition, in the case of N-methyl-piperazine substitution, different protonation states are possible and might play a crucial role in the molecular recognition process by G4-DNA. Depending on the proton concentration, different nitrogen atoms of the N-methyl-piperazine might (or might not) be protonated. This fact was considered in our simulation in terms of a case by case analysis, since the process of molecular recognition is determined by possible donor or acceptor positions. The results of our simulations show that the electrostatic interactions between the ND ligands and the G4 receptor are maximized in the case of the protonation of the terminal nitrogen atoms, forming compact ND G4 complexes inside the grooves. The influence of different protonation states in terms of the ability to form hydrogen bonds with the sugar-phosphate backbone, as well as the importance of mediated vs. direct hydrogen bonding, was analyzed in detail by MD and relaxed force constant (compliance constant) simulations.

  18. An integral equation model for warm and hot dense mixtures

    CERN Document Server

    Starrett, C E; Daligault, J; Hamel, S

    2014-01-01

    In Starrett and Saumon [Phys. Rev. E 87, 013104 (2013)] a model for the calculation of electronic and ionic structures of warm and hot dense matter was described and validated. In that model the electronic structure of one "atom" in a plasma is determined using a density functional theory based average-atom (AA) model, and the ionic structure is determined by coupling the AA model to integral equations governing the fluid structure. That model was for plasmas with one nuclear species only. Here we extend it to treat plasmas with many nuclear species, i.e. mixtures, and apply it to a carbon-hydrogen mixture relevant to inertial confinement fusion experiments. Comparison of the predicted electronic and ionic structures with orbital-free and Kohn-Sham molecular dynamics simulations reveals excellent agreement wherever chemical bonding is not significant.

  19. Sudden Stratospheric Warming Compendium

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Sudden Stratospheric Warming Compendium (SSWC) data set documents the stratospheric, tropospheric, and surface climate impacts of sudden stratospheric warmings. This...

  20. Investigation of the structure of ethanol-water mixtures by molecular dynamics simulation I: analyses concerning the hydrogen-bonded pairs.

    Science.gov (United States)

    Gereben, Orsolya; Pusztai, László

    2015-02-19

    Series of molecular dynamics simulations for ethanol-water mixtures with 20-80 mol % ethanol content, pure ethanol, and water were performed. In each mixture, for ethanol the OPLS force field was used, combined with three different water force fields, the SPC/E, the TIP4P-2005, and the SWM4-DP. Water potential models were distinguished on the basis of deviations between calculated and measured total scattering X-ray structure factors aided by ethanol-water pair binding energy comparison. No single water force field could provide the best agreement with experimental data at all concentrations: at the ethanol content of 80% the SWM-DP, for 60 mol % the SWM4-DP and the TIP4P-2005, whereas for the 40 and 20 mol % mixtures TIP4P-2005 water force field provided the closest match. Coordination numbers and hydrogen bonds/molecule values were calculated, revealing that the oxygen-oxygen first coordination numbers strongly overestimate the average number of hydrogen bonds/molecule. The center-of-molecule distributions indicate that the ethanol-ethanol first coordination sphere expands with increasing water concentration while the size of the first water-water coordination sphere does not change. Various two and three-dimensional distributions were calculated that reveal the differences between simulations with different water force fields. Detailed conformational analyses of the hydrogen-bonded pairs were performed; drawings of the characteristic molecular arrangements are provided.